IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/catabolism.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/biosynthesis.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis
Seed:    956250 (Using SPRNG - Scalable Parallel Random Number Generator)
Seed:    956160 (Using SPRNG - Scalable Parallel Random Number Generator)
IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/cdhit_phobius_tm_RECEPTORS.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS
Seed:    957372 (Using SPRNG - Scalable Parallel Random Number Generator)
IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport
Seed:    958747 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Mon Jul  7 13:13:13 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/catabolism.fasta ... Fasta format detected
Reading fasta file: done in 0.000612974 secs using 9.462% CPU
Time:    Mon Jul  7 13:13:13 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Time:    Mon Jul  7 13:13:13 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/biosynthesis.fasta ... Fasta format detected
Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/cdhit_phobius_tm_RECEPTORS.fasta ... Fasta format detected
Reading fasta file: done in 0.00190187 secs using 99.59% CPU
Time:    Mon Jul  7 13:13:13 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Reading fasta file: done in 0.00295997 secs using 67.94% CPU
Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta ... Fasta format detected
Alignment most likely contains protein sequences
Reading fasta file: done in 0.00654602 secs using 82.55% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.00588894 secs using 3063% CPU
Alignment has 57 sequences with 758 columns, 756 distinct patterns
696 parsimony-informative, 34 singleton sites, 28 constant sites
            Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.000427008 secs using 2622% CPU
   1  v2gkNHbKhv    0.40%    passed     64.34%
   2  zYkG3lENQo    0.40%    passed     61.23%
   3  L5pA3FW0hp    0.40%    passed     50.56%
   4  9O6NDaxhQm    0.79%    passed     81.52%
   5  iub43BeWKd    0.66%    passed     67.84%
Alignment most likely contains protein sequences
   6  vLTsWmisrg    0.79%    passed     95.80%
   7  rCRxmoNtvj   23.88%    passed     51.94%
   8  b8tOgrxOlI    0.92%    passed      9.49%
   9  p8FtEb61Lq   12.40%    failed      0.12%
  10  ENyocd0l5S   62.66%    failed      0.23%
  11  sum3sAivE6    1.58%    passed     54.73%
  12  8QYmfOoydQ    5.01%    passed     20.88%
  13  xrK6W6u9hg   38.52%    passed     15.02%
  14  aCPQPDeHY3    4.75%    failed      0.04%
  15  O0OCj8CgTw    0.66%    failed      1.61%
  16  njHlLxE4FP    1.19%    failed      0.02%
  17  1Nh6TGG1wy    7.65%    passed     58.90%
  18  irMPUi2N9N   70.58%    passed     67.37%
  19  TEyZk1vXSt    3.30%    passed     51.22%
  20  GLeZP3AfXS    0.92%    passed     50.80%
  21  I1RNArB9g4    1.58%    passed     79.46%
  22  wjklmZwKVI   68.73%    passed     46.39%
  23  qFpyRJS1oM   12.53%    failed      0.15%
  24  lI5p7wzpEY    1.06%    failed      0.07%
  25  sESbPuzy4g    3.96%    passed      6.26%
  26  s7zi5AqPph    1.19%    failed      0.00%
  27  r6zdJbyb9Q   20.18%    failed      0.31%
  28  H2VEqEbI9w    0.92%    failed      4.75%
  29  rsp0gZpwHI    0.66%    failed      3.38%
  30  YQ4IkrKyLP    0.66%    failed      2.08%
  31  ezV6cuyMeO    3.69%    failed      0.00%
  32  FWYborJRi1   39.97%    failed      3.97%
  33  kVXEhvM49L   79.55%    passed     69.48%
  34  B1xll48Pfj   25.20%    failed      0.01%
  35  eItYISUevo    8.44%    passed     13.04%
  36  W0yIByNcsa    9.50%    passed     92.82%
  37  ArbvcV63kt   31.66%    passed     57.12%
  38  rmwYdfMIbt    0.79%    failed      0.26%
  39  MfVDqCcbR4   56.99%    failed      0.04%
  40  SohXi7Gsv6   58.84%    failed      0.01%
  41  QdZdCjrqci   62.80%    passed      5.28%
  42  6Tr8KmZrh7   58.84%    failed      0.57%
  43  gELpB8Eq61   62.80%    passed      7.93%
  44  K6mavzvKju   62.80%    passed      8.16%
  45  ZM0yXjcxWZ   59.63%    passed     31.57%
  46  iYpKYVVqlE   61.87%    passed     51.51%
  47  uHRWKmWr2I   61.74%    passed     25.11%
  48  ji6GLY55xr   65.17%    passed     24.69%
  49  Nr7qdx4uPs   62.80%    failed      0.54%
  50  i62QK9QQH4   61.35%    passed     61.50%
  51  EOP93ezGdP   81.00%    failed      0.52%
  52  tNeEHQY7H5   80.47%    failed      0.24%
  53  NrXU0J6m0C   62.66%    failed      0.07%
  54  bxaToy37B1   62.80%    failed      0.00%
  55  2nsMhLefaD   58.44%    failed      0.04%
  56  J9NzCDUHYE   58.84%    passed     21.65%
  57  yRuVLBrAlC   58.71%    passed     26.12%
WARNING: 23 sequences contain more than 50% gaps/ambiguity
****  TOTAL        30.64%  25 sequences failed composition chi2 test (p-value<5%; df=19)

Constructing alignment: done in 0.00451708 secs using 1063% CPU

Alignment has 269 sequences with 414 columns, 410 distinct patterns
397 parsimony-informative, 5 singleton sites, 12 constant sites
            Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.00069809 secs using 1197% CPU
   1  c2nvJkfrfN   14.49%    passed     16.79%
   2  6v71cA4wPA   17.39%    passed     61.71%
   3  KoMzCAq4js   18.60%    passed     93.43%
   4  lxlM6A3JbT   10.87%    failed      0.28%
   5  E4wkUUcW9k   14.25%    passed     88.60%
   6  zNKTwqlwI7   17.15%    passed     64.10%
   7  xJCaoYe6x7   20.77%    passed     61.31%
   8  hRN1Wy69Ah   19.08%    passed     92.85%
   9  ZvBC32nrED   19.08%    failed      0.12%
  10  RaObTYvjqb    8.45%    passed     89.43%
  11  lHRXTHlK1w   16.43%    failed      0.00%
  12  XEbJPCtGac   15.22%    passed     25.66%
  13  5cKSP1mz8P   14.73%    failed      1.15%
  14  XEMbna5PTc   16.91%    passed     42.05%
  15  7nQDPMneN2   14.01%    passed     27.59%
  16  e40qziD7i7   17.15%    passed     95.87%
  17  ZG3Jmo6e7V   19.57%    passed     40.97%
  18  wHZy5Q8IJI    8.45%    passed     71.01%
  19  b74PatoLe4    8.21%    passed     39.31%
  20  XGas1ggnUa   11.11%    passed     19.19%
  21  IVTbt8Udzq   11.84%    passed     95.94%
  22  Pfn5zv9XX5    9.18%    passed     30.82%
  23  YCsFSoRXqE    8.21%    failed      2.84%
  24  ot7OqrLzX5   22.22%    passed     18.48%
  25  PWjd4lRbiM   16.18%    passed     62.94%
  26  AICC2u7c3U   12.08%    failed      0.00%
  27  IZ5hNTt2vT   17.39%    failed      0.00%
  28  Z51fe4z5fd   14.01%    passed     85.03%
  29  Tkqfc0SeOG   20.77%    passed     20.69%
  30  iiIa5izPqm   22.22%    passed     12.87%
  31  v4fUVbAyCP   16.43%    passed     87.63%
  32  6Uoim418Lz   22.71%    passed     86.96%
  33  fm80Plhz7F   12.08%    failed      4.29%
  34  onW0cY5h5o   10.39%    passed     81.72%
  35  N9pESfrjq2   14.25%    passed     33.04%
  36  5rjVc8vWLK   12.32%    passed     90.02%
  37  ipy3Nr1Y7C   14.01%    passed     34.00%
  38  Yrr4ZSKKC9   20.29%    passed     68.26%
  39  AuJ54E1C8c   21.01%    passed     53.09%
  40  jva1qkj7r3    9.42%    passed      7.23%
  41  tPS4ZlQpLO   20.53%    passed     93.70%
  42  ZuL1ZJlBoc   14.25%    passed     98.78%
  43  6smEYSMtgB   13.77%    passed     50.25%
  44  OmEFZmh9Xk   19.32%    passed     59.86%
  45  HPGR8QqxLN   14.49%    passed     89.86%
  46  BhNqusWZNJ   19.08%    passed     58.02%
  47  UW8C8HS7IW   14.49%    passed     23.66%
  48  IXVYbhEiFa    8.21%    failed      0.01%
  49  AjttkrIBDE   16.91%    passed     76.47%
  50  o4DTptAEa7   16.67%    passed     92.22%
  51  3569NNqeHr   10.63%    passed     16.11%
  52  VbeUA5Lmv1   11.35%    passed     10.81%
  53  s438BUrIld   12.08%    passed     97.72%
  54  kZxa6ms4fT   12.32%    passed     35.70%
  55  yKB0rmTTAd   13.53%    passed     99.88%
  56  R3rYagRgkA   21.74%    passed      9.58%
  57  LbAfNvLG0L   15.22%    passed     85.99%
  58  VyRxiwg9OH   16.91%    passed     55.88%
  59  Ih0FYSZPuQ   11.84%    passed     98.11%
  60  lhDnsli570   13.04%    passed     96.03%
  61  oxTFCHgUrH   14.98%    passed     93.85%
  62  lxbMM8cWpP   16.43%    passed     36.26%
  63  Uw4WAsVs2V   12.80%    passed     55.06%
  64  lyrWZMVXT3   13.77%    passed     70.12%
  65  OyaeKE1frb   16.43%    passed     86.38%
  66  d1JUougmwO   13.29%    passed     88.72%
  67  n3cpwW2FHB   13.29%    passed     65.82%
  68  AlrwQSS6wg   14.25%    passed     17.97%
  69  UuXrZQLZFl   16.67%    passed     25.64%
  70  4erBqEBFMP   19.81%    passed     10.98%
  71  jxhNFGngrh   21.01%    passed     84.69%
  72  Wm098GODX1   22.95%    passed     22.93%
  73  9yBRcXGPW3    9.42%    passed     95.14%
  74  XdXJPD1B99   14.98%    passed     74.55%
  75  36Z3LxBjPl   17.63%    passed     63.50%
  76  kvpaBQTK2F   17.15%    passed     22.83%
  77  OPtLNHMxEK   13.77%    passed     38.90%
  78  FNavqnaurn   15.70%    passed     43.86%
  79  U9atOteYMr   18.84%    passed     76.67%
  80  jW1iHKeXfb   25.36%    passed     27.48%
  81  yQ6RZhmbOA   14.73%    passed     99.94%
  82  i0aI5XCRaQ   18.60%    passed     99.75%
  83  Emh5GVVBM7   11.59%    passed     59.87%
  84  seCpqYzobh   17.39%    failed      2.12%
  85  Yild6PEkHw   17.87%    passed     30.32%
  86  kbUXzYwyJT   18.12%    passed     64.46%
  87  BnaGpooeOd   11.84%    failed      2.60%
  88  ObxFZPrSW5   18.84%    passed     29.19%
  89  SuSbie4gj4   23.19%    passed     34.58%
  90  4bfvNf8AFQ   13.77%    passed     74.75%
  91  IDqCgXNOAR   21.74%    passed     72.57%
  92  ylLkHnrsg4   12.08%    passed     90.58%
  93  6CsniPjxAT   20.29%    passed     11.78%
  94  EbHYNkVDGh   15.22%    passed     10.10%
  95  ClUKTDfvJI   23.19%    passed     80.74%
  96  mHWkgELohz   17.15%    passed     97.96%
  97  YwLM4N6m6Z   19.81%    passed     17.28%
  98  YH2jvsJ8dY   24.40%    passed     86.48%
  99  G9b28gN5VH   13.77%    passed     80.92%
 100  3kndjxAPF9   23.43%    passed     60.78%
 101  fSOOhYALAC   10.63%    passed     18.24%
 102  MYEUikYcJB   22.22%    passed     59.06%
 103  ihdDnmX2iD   11.11%    passed     14.19%
 104  gYvledWOAb   19.08%    passed     44.03%
 105  Ez9ZtxssKH    9.66%    passed     56.14%
 106  Yu2cfILHmc   21.26%    passed     99.19%
 107  sXb4pc8vkJ   17.63%    passed     99.18%
 108  OPaiUWVYAg   19.32%    passed     16.86%
 109  0oe9qWxWgC   12.08%    passed     43.62%
 110  QQ58S3chME   20.53%    passed     53.70%
 111  GsNfFnNm9k   12.56%    passed     77.57%
 112  Nvc3tne6MO   18.60%    passed     66.88%
 113  9NFHCOJ3mt   15.94%    passed     96.43%
 114  7abZLMDRv5   11.84%    passed     90.56%
 115  A9MeIBAjV9   22.46%    passed     27.72%
 116  tFq6SZ4duR   13.29%    failed      3.67%
 117  hsGr8UQtI6   14.49%    passed     72.12%
 118  PsaQsrOOic   21.26%    passed     92.40%
 119  b3rYWyuQhm   25.12%    passed     21.71%
 120  D2Ut2I6kRR   16.43%    passed     99.88%
 121  oZNYuBDmJR   19.32%    passed     99.83%
 122  oHJYtIofr8   13.04%    passed     54.36%
 123  2VQ2kdTDs8   16.67%    passed     97.28%
 124  0BEqzqGTzo   13.29%    passed     37.44%
 125  V7UFl5t0og   12.56%    passed     82.75%
 126  yWWKXX0tOb   18.12%    passed     81.89%
 127  BEwYUowpIl   19.57%    passed     94.20%
 128  6RP65KbJuF   21.50%    failed      0.39%
 129  eCQKmw2pOP   15.22%    passed    100.00%
 130  SHrMCYIrqF   21.98%    passed     83.59%
 131  SuTPtZY9fG   13.04%    passed     34.72%
 132  ywcAduJMee   16.67%    failed      0.00%
 133  ZsVb4os2cb   12.80%    passed     45.91%
 134  UP6HfeKfau   15.22%    passed     95.40%
 135  98pkxfYHE6   20.53%    passed     69.80%
 136  dScYTJASy3   13.29%    passed     17.91%
 137  A83Zj7fGiH   21.74%    passed     98.02%
 138  aegE8u72ZI   14.01%    passed     52.74%
 139  Uj66wqobxX   21.50%    passed     86.94%
 140  ZKBdy0qp0c   21.74%    passed     67.74%
 141  setTvQyVfa   21.26%    passed     68.97%
 142  6YcyVMi9HU   19.08%    passed     72.90%
 143  bKXtRZnILM   18.84%    passed     93.87%
 144  9zCo3T9kHs   13.77%    passed     80.09%
 145  FM3U96ERbZ   12.32%    passed     28.38%
 146  vtxKriXTJb   14.01%    passed     16.96%
 147  mHAx5tEew1   11.11%    passed     27.92%
 148  tK9Y1h0vmG   19.32%    failed      0.83%
Alignment most likely contains protein sequences
 149  rddJIJqTyp   14.25%    passed     75.77%
 150  iLQ3EX95bZ   13.29%    passed     67.27%
 151  clTHPO2kTP   15.46%    passed     79.49%
 152  srLFcibeWN   10.63%    passed     54.55%
 153  HMsATDtoEZ   19.81%    passed     65.15%
 154  rTOE0myIj1   16.43%    failed      0.74%
 155  Kj5hAn4v6q   19.81%    passed     79.07%
 156  LsoOtPQfJ5   13.53%    passed     60.22%
 157  ECanJJ4ncI   12.08%    passed     93.08%
 158  COqJyjUzEG   19.57%    passed     98.63%
 159  Z6xloI3oDo   11.84%    passed     93.32%
 160  vpMwgz3vLP    9.66%    passed     88.22%
 161  BAxjMqLOrV   14.49%    passed      7.89%
 162  tWLDJkeSf6   12.80%    failed      0.40%
 163  Ogxj4OyvD7   13.04%    passed     94.62%
 164  bSuFG152uE   14.01%    passed     96.44%
 165  HdLYk2vd7J   22.22%    passed     44.48%
 166  ahsba9i3Ki   13.29%    passed      7.71%
 167  J9JRrc39aH   12.56%    passed     49.24%
 168  9X41ZUX7sk   14.01%    passed     76.04%
 169  2lLPbY3bIA   17.39%    passed     80.34%
 170  fsCKb933p1   15.46%    passed     61.43%
 171  HR9CNTg3nN   15.46%    passed    100.00%
 172  ej0NOsAKz0   14.49%    passed     20.03%
 173  3JBHsIlGYM   14.73%    passed     89.02%
 174  cIJDI1ElWX    9.90%    passed     71.92%
 175  rDwRatbDPi   13.04%    passed     64.87%
 176  eTS75PP6iB   22.46%    failed      1.84%
 177  aHVp2cBgGN   21.26%    passed     89.22%
 178  htw6R69tCN   15.94%    passed     82.97%
 179  Y6nMrUpOQy   20.05%    failed      1.71%
 180  gZEsHkbcuV   17.15%    passed     53.80%
 181  r36YE0G9qX   14.01%    passed     62.04%
 182  Nq94vUXx6J   12.56%    passed     52.75%
 183  UrVDM79A7d   19.81%    passed     94.40%
 184  RrHy6Wx7gZ   16.43%    passed     42.62%
 185  jr16YVdriy   17.63%    passed     84.57%
 186  LmkMEQF4DR   21.01%    failed      0.01%
 187  zJFuHTnbRq   19.57%    passed     87.77%
 188  YI1L8xHuuM   18.12%    failed      0.02%
 189  zlKlE9DMy9   17.87%    passed     63.67%
 190  XIKdpG1v5e   27.78%    failed      1.44%
 191  y26Opks9vx   16.67%    passed     61.80%
 192  HpehaSDGPK   14.73%    passed      9.89%
 193  RX5cDS5ygC   22.71%    passed     67.07%
 194  aJXccw9WVd   14.01%    passed     67.55%
 195  CFlZ3Yynoy   11.35%    passed      5.35%
 196  1PKgVKI1on   14.49%    passed     45.97%
 197  BfAlPFZr1B   19.81%    passed     97.14%
 198  HzW9kYfmiG   11.35%    passed     29.13%
 199  jf8HZslfsd   13.77%    passed     96.06%
 200  1gjVsly7ZT   29.71%    passed     81.90%
 201  yTN3HKtHgW   12.56%    passed     96.72%
 202  DzXQl3ixjn   24.15%    passed     45.97%
 203  H8w47ZcyKP   10.39%    passed     21.67%
 204  50AYMHqNK0   29.47%    passed     48.69%
 205  52ZDhjNETE   21.01%    passed     75.42%
 206  EG8X1IG6EU   18.12%    passed     27.36%
 207  hHDQviDuXc   17.39%    passed     99.16%
 208  lbOxXnN8b7   24.15%    passed     36.55%
 209  lSJwJYUL1Y   19.08%    passed     95.92%
 210  PMbKXaBN6F    9.90%    passed     84.87%
 211  bSHRAKMHsK   14.49%    passed     99.44%
 212  LGe5jQhMVY   21.50%    passed     78.65%
 213  xCao0DuYt0   14.73%    passed     64.52%
 214  xarXCvI4gY   14.73%    passed     83.15%
 215  GN9LlBOOkT   14.25%    passed     20.02%
 216  oEPBj45bmy   21.50%    failed      0.00%
 217  fP4fRY7tjS   14.98%    passed      8.93%
 218  a5QvoSesca   10.39%    passed     20.43%
 219  5DU1LU9aZ2   11.11%    passed     60.11%
 220  ioXzsSSnhq   21.01%    passed      7.39%
 221  VuLMFqp5mG   16.43%    passed     40.09%
 222  aPdY5V1uOS   13.04%    passed     21.85%
 223  iVLIgog8ZD   23.67%    passed     96.25%
 224  ZcjF0aDH2l   12.56%    passed     92.81%
 225  rBn0zuuQO5   10.63%    passed     86.81%
 226  WYxLjs2S65   21.50%    passed     50.01%
 227  1tOEEBFDV2   21.26%    passed     91.36%
 228  4AQGhYYqZd   22.95%    passed     95.25%
 229  fuPQWxprqQ   14.98%    passed     93.04%
 230  MQ9V4Zj61g   20.53%    passed     96.80%
 231  t6dNTk9ubs   25.85%    failed      3.36%
 232  79Py93EM0n   13.53%    passed     95.10%
 233  RVJDDAJe6D    9.90%    passed     85.58%
 234  yAtKAqFh3f   13.29%    passed     98.59%
 235  3qTi4z1Qys   11.35%    passed      9.95%
 236  AsEACEZyje   15.22%    passed     76.91%
 237  14Cv16S4pA   21.50%    passed     70.32%
 238  09y9SNapkT   25.85%    passed     65.76%
 239  uM6QBwh65Q   20.29%    passed     68.80%
 240  CKvs8jeInU   16.43%    passed     95.25%
 241  s1HvKHReky   15.46%    passed     89.91%
 242  AEVEctaMi5   13.77%    passed     41.83%
 243  fFkKaIm0M3   18.36%    passed     64.11%
 244  2WeFoqGNAI   24.64%    passed     99.23%
 245  DH1HoFGqtF   21.98%    failed      4.28%
 246  E01291uRl2   15.22%    passed     19.71%
 247  RMNeZ2LTKq   14.01%    passed     24.64%
 248  t5BNkjMP5g   14.98%    passed     97.68%
 249  wuqkcc1DBy   18.60%    passed     45.97%
 250  oBOfif9LBJ   13.29%    passed     57.86%
 251  lWYIhCDZyl   18.84%    passed     15.77%
 252  WH8Pi4c3UY   14.98%    passed     98.40%
 253  HWHIYqt9D2   21.74%    passed      6.30%
 254  o5Gb2AX50s   15.22%    passed     66.91%
 255  vyxoQRA4cI   14.49%    passed     87.89%
 256  cOF5xGJ8FX   15.94%    passed     77.56%
 257  BCOck7IwQD   15.22%    passed     45.92%
 258  VYWJtTRjIz   13.77%    passed     97.90%
 259  QP7Akm5rRv   14.73%    passed     95.10%
 260  p5bEB7zEbb   18.36%    passed     54.85%
 261  n1WIkGjHMl   18.36%    passed     87.38%
 262  WSkvfJAjT0   17.63%    passed     52.24%
 263  pNNoFuexDA   12.08%    failed      3.92%
 264  WQ1lDIUS8r   13.53%    passed     15.84%
 265  1R3SzgebA4   10.14%    failed      3.69%
 266  vZS2mZsiyg   15.46%    failed      2.93%
 267  TUCHbMHBCQ   16.67%    failed      0.94%
 268  5StJ1ELBQ5   14.01%    passed     95.29%
 269  W0kYhrEL8O   14.01%    passed     68.31%
****  TOTAL        16.37%  29 sequences failed composition chi2 test (p-value<5%; df=19)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.026 seconds

Measuring multi-threading efficiency up to 96 CPU cores
Constructing alignment: done in 0.0600891 secs using 1908% CPU
Constructing alignment: done in 0.037065 secs using 1583% CPU
Alignment has 153 sequences with 492 columns, 492 distinct patterns
459 parsimony-informative, 24 singleton sites, 9 constant sites
            Gap/Ambiguity  Composition  p-value
Alignment has 495 sequences with 575 columns, 575 distinct patterns
575 parsimony-informative, 0 singleton sites, 0 constant sites
            Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.0135441 secs using 1872% CPU

Analyzing sequences: done in 0.00423002 secs using 1878% CPU
   1  NsewqfDnSs    3.46%    passed     97.60%
   2  658EaRrivK    2.64%    passed     23.03%
   3  tKsE6g1a0S    4.07%    passed     54.20%
   4  aQNZilE2JJ    0.41%    passed     92.98%
   5  UwrRLjbq3B    3.86%    passed     74.56%
   6  TV90ozJidG    3.86%    passed     25.51%
   7  c3HM96fVqq    5.28%    passed     20.38%
   8  xxTGRlTa7K    4.67%    passed      9.52%
   9  Jvz3UnpNYR    4.88%    failed      3.89%
  10  mdN0ObKfmv    4.67%    failed      2.52%
  11  qum1IQqgRL    4.47%    passed     28.80%
  12  ucpMvNZqY4   50.61%    passed     58.99%
  13  Dwmf0ZcWVI    3.86%    passed     95.81%
  14  7ahTE2wEe5    5.49%    passed     89.63%
  15  tCzrpKtpcF    2.64%    passed     80.54%
  16  J0P8Xwv2Bh    6.10%    passed     96.97%
  17  vjnC2m0pnm   34.15%    passed     13.88%
  18  BhMleetcPb    0.61%    passed     88.14%
  19  83HNImqlFJ    4.27%    passed     97.08%
  20  9fh7iXeyTa    2.44%    passed     78.96%
  21  RCuQu9oGZY    2.85%    passed     96.58%
  22  W6nHCI2Wsy    0.81%    passed      5.62%
  23  S1A8zUjUKT    1.22%    passed     22.40%
  24  LcCM4OUpmU    4.47%    failed      0.40%
  25  Q2DajquNQZ    3.05%    passed     87.23%
  26  PmpEdiT477    4.88%    failed      3.14%
  27  F21or9tcNh    5.08%    failed      0.00%
  28  AsTKtmGBgC    1.42%    passed     74.54%
  29  bXEBREFYJ7    1.42%    passed     84.71%
  30  oyPE5XbvlM    7.32%    passed     98.65%
  31  rMwSb8FeWI    0.61%    passed     93.96%
  32  AveHckggo7    9.76%    passed     91.63%
  33  8Yqrasn3bU    0.61%    passed     97.00%
  34  3oJexyoj51    2.64%    passed     97.79%
  35  I8haDcxmGF   18.50%    passed     68.65%
  36  AqcNj4ozIg   10.37%    passed     87.07%
  37  RA52wdQzM0   21.54%    passed     84.92%
  38  INof63Zg1b   12.40%    passed     95.27%
  39  xIGuGjnQck    0.61%    passed     99.65%
  40  B9HWzepxl3    0.41%    passed     99.98%
  41  oWBZGcpKdf    2.44%    passed     97.48%
  42  jMq4G1hugD   18.29%    passed     76.03%
  43  CRHzNcE7hH   10.16%    passed     87.13%
  44  npLJ3gBI7w   21.34%    passed     94.19%
  45  CBxBTRkg8F   12.20%    passed     99.39%
  46  6AmSNES3Yt    0.41%    passed     98.49%
  47  W9sWvMxXl8    2.44%    passed     98.39%
  48  dPbJJzuHAw    0.61%    passed     97.60%
  49  NUP3Qg7UKZ    1.63%    passed     99.28%
  50  KSpoqshUGd    0.41%    passed     99.94%
  51  y6RinBeWkh   12.20%    passed     99.94%
  52  2aqY9Y5XOA   10.16%    passed     98.19%
  53  9uej6gprBY    2.44%    passed     99.12%
  54  kbAupxTeXc    2.44%    passed     92.38%
  55  jH3L6ZyOSg    2.44%    passed     88.23%
  56  o43in6b1l6    0.41%    passed     94.88%
  57  sSXbGZ4LtJ    9.96%    passed     93.06%
  58  pEm28yHrqJ    0.41%    passed     99.73%
  59  B8avP7St1b    1.63%    passed     99.42%
  60  MU8hXHYjfg    0.61%    passed     99.12%
  61  Q62u69DgSU    1.42%    passed     99.16%
  62  aA4U3jpPBM    2.44%    passed     99.66%
  63  SJOWQe9Pls   16.87%    failed      1.88%
  64  vJMp8Q8WIF    2.64%    failed      2.52%
  65  V4d7bLFWj5    0.20%    failed      0.46%
  66  AMAF22mqG6    0.61%    failed      2.30%
  67  wjzmloRyhK    0.61%    failed      4.77%
  68  91p63ULeyU    0.41%    failed      1.14%
  69  gud5XcZSky    2.85%    failed      0.78%
  70  p5Vp0bEK1M   19.92%    failed      0.64%
  71  oziMBoUfTw    0.61%    passed     14.68%
  72  9wLRCRFTWk    0.61%    passed     11.43%
  73  v7XgG9Q2Mu    0.61%    passed     14.68%
  74  YvUlv8Ajlj   28.25%    passed      9.64%
  75  hkFgAfCQMe   43.70%    failed      0.08%
  76  vFYRvvYw5q    1.83%    passed     67.23%
  77  MDZgl64OFf    2.24%    passed     99.18%
  78  dARK0kAImG    4.27%    passed     95.59%
  79  XTMxyDh5Jp   34.55%    passed     78.07%
  80  hGUbtT0sPx   27.03%    passed     67.25%
  81  4MEg44jcgn    4.27%    passed     95.59%
  82  xMQtzFnFjY    3.86%    passed     94.85%
  83  vSUoiw4nAv    3.86%    passed     94.85%
  84  zd4NP5bgCn    3.86%    passed     94.85%
  85  SrcTR9TVTe    4.88%    passed     78.14%
  86  LUOTpsMW9Z   10.37%    passed     73.84%
  87  lS9cRq1wDg    3.25%    passed     81.37%
  88  ibzyhlVeLd    1.02%    passed     99.99%
  89  PrzRBbweDr    0.41%    passed     88.33%
  90  UgrgpQ3Re3    3.05%    passed     11.72%
  91  uo1wFa9kTY    3.66%    passed     32.55%
  92  04evyV0x2J    1.02%    passed    100.00%
  93  VQOYTWEXRd    1.02%    passed     35.73%
  94  nGZxWJfnLq   10.57%    passed     99.36%
  95  VrFNoG8CSK    3.05%    passed     98.20%
  96  qAnI4od5wb    3.05%    passed     98.53%
  97  1Nf8MNh0qe    5.28%    passed     95.57%
  98  v1DX3Octxe    2.24%    passed     99.87%
  99  GBB9rjdLAe    3.46%    passed     65.29%
 100  xAnABV48FP   23.78%    passed      9.80%
 101  WBN81pJk9d   41.46%    passed     16.12%
 102  ukj88OiCCs    0.61%    passed     99.96%
 103  7HVBf2lN5X    3.86%    passed     85.96%
 104  fW6nXZ4jo9    0.61%    passed     99.35%
 105  gD9lJD4Soc    0.81%    passed     73.95%
 106  VSLI0QFCNE    0.81%    passed     37.23%
 107  NpXX0H6JOz    5.28%    passed     99.78%
 108  4Co497GPZv    0.81%    passed     99.21%
 109  d35px4TEeG    3.05%    passed     16.82%
 110  MarWtGvQwP    2.85%    passed     67.22%
 111  AGwsEagGat    3.05%    passed     69.04%
 112  Mfjn35Y7sd    3.86%    passed     90.71%
 113  zw0LKEkItm    3.86%    passed     90.71%
 114  LfDxwAh7Vj    4.67%    passed     94.69%
 115  2tKIrteaC9   29.07%    passed     96.69%
 116  7ek5ox6dTM    3.86%    passed     96.21%
 117  J9yhwttCKv    3.86%    passed     95.92%
 118  Ms0jxML186    3.05%    passed     92.93%
 119  2LhvyAjgLE    1.02%    passed     97.44%
 120  hcgITnpCwJ    0.81%    passed     97.28%
 121  Spa2PmhvTm    0.81%    passed     47.00%
 122  kxrQDICQMY    0.81%    passed     47.00%
 123  lHBAun0J0R   17.68%    passed     99.94%
 124  LR9r4dhR2l    2.24%    passed     56.33%
 125  p2YgBHtdE6    3.46%    passed     96.80%
 126  ZFU9VNJsz8    3.46%    passed     99.94%
 127  UY2QKYWPGB    1.22%    passed    100.00%
 128  bYmVEY2Ndb    0.41%    passed     99.08%
 129  JA7h40jhHP    0.61%    passed     89.33%
 130  R9Kzaow2zy    1.02%    passed     92.82%
 131  9sNaZtxabc    1.22%    passed     92.85%
 132  rJgjpUVrep    0.61%    passed     77.37%
 133  ilhlAyWtMf    1.22%    passed     97.90%
 134  JI55JkIpoJ    0.61%    passed     97.27%
 135  BwOn3B9Qlp    7.32%    passed     97.58%
 136  EqQL1uIwj2    1.22%    passed     99.72%
 137  QxgvHLRTMH    2.64%    passed     99.86%
 138  69uQAcSijv   12.40%    passed     99.88%
 139  fB3H4TdUAh   12.40%    passed     97.83%
 140  JEz9kz3nnP    4.27%    passed     99.85%
 141  AaUKTvI6pt   27.44%    passed     69.34%
 142  MiIKhPn35C    1.02%    passed     87.28%
 143  sqzWAXE12K    4.88%    passed     77.67%
 144  wKc1R5h9ZW    4.27%    passed     72.88%
 145  6bnym5iDFB    0.61%    passed     75.18%
 146  AmfA6Wj4Um    0.81%    passed     97.64%
 147  Lcs5teD2mW    0.41%    passed     74.06%
 148  jwiftTw4qK    7.11%    passed     10.75%
 149  jq2abWHxsF    3.86%    passed     85.06%
 150  F6xcUciw9j    0.41%    passed     97.31%
 151  0GIcC3M4B0    3.66%    passed     83.11%
 152  qCyccTtF6Y    3.66%    passed     86.68%
 153  3fRiMt57tm    2.24%    passed     32.43%
WARNING: 1 sequences contain more than 50% gaps/ambiguity
****  TOTAL         5.99%  14 sequences failed composition chi2 test (p-value<5%; df=19)

   1  8nJh6NUzJV   12.00%    passed     10.27%
   2  z0YCu0xtFo   11.30%    passed     15.88%
   3  1JN1q1h7Jh    8.35%    passed      9.02%
   4  E2n5Y5UQiG    8.52%    passed     43.28%
   5  cMoC1WsTO6    8.17%    failed      2.01%
   6  ys0DcEs0US    8.35%    passed     77.31%
   7  1s9qnaxMSp    9.04%    failed      2.14%
   8  FtHEpsU1vB    9.04%    failed      2.61%
   9  oeJuwbyE7Q    9.91%    passed      8.44%
  10  qCgVEYLhzI   17.39%    passed      9.43%
  11  zyhovbZkFP    9.91%    passed      8.44%
  12  jOk4aex96C   19.65%    passed      9.17%
  13  AR0npWZQ83    8.17%    passed     22.96%
  14  F5Si2gBtZe   21.91%    passed     13.69%
  15  FG021XCxMA   18.09%    passed     68.58%
  16  MCX7xygB2V    8.70%    passed     73.82%
  17  iVpOwiZzba    9.04%    passed     21.82%
  18  iPjBM3iYZR   80.35%    failed      2.62%
  19  qbFBJDOQUO    9.39%    passed     92.00%
  20  x5jv5lpB2O    9.22%    passed     43.94%
  21  y5M7y721WQ   11.30%    passed     52.45%
  22  MwDLYKIKBx   16.70%    passed     52.35%
  23  EsTTc2nPxQ    8.00%    passed     56.73%
  24  vnhywKRkFl   13.91%    passed     61.80%
  25  7JZdwvMv24   10.09%    passed     62.94%
  26  dQjyx7OIYV   27.30%    passed     66.63%
  27  irBovt5bLa    8.17%    passed     37.03%
  28  Ewm24Mlvnq    8.17%    failed      0.91%
  29  XDJ4JoLzyH   17.22%    passed     87.03%
  30  4kC0x0kjdn    7.65%    passed     35.61%
  31  RARcF60S6a    8.00%    passed     18.15%
  32  WlelCJO26H   12.17%    passed     15.31%
  33  mhk5OTojgz    7.83%    passed     22.72%
  34  pTM2DvE1xM    7.83%    passed     23.80%
  35  tlXXT5aWqu    8.35%    passed     25.18%
  36  TC8Xnd4iFa    8.35%    passed     68.65%
  37  02HhJs6pa3   11.13%    passed     51.90%
  38  NEeqpPtHg5    9.91%    passed     53.60%
  39  qbTDasygHV    8.00%    failed      4.34%
  40  7Yh1YhvFVC    9.04%    passed     82.42%
  41  VvE6sMyCv8    9.22%    passed     82.98%
  42  WjMMQYeUC2    9.74%    passed     28.42%
  43  W7Mh0FRDU6    9.57%    passed     47.24%
  44  2nrE64urGV    7.83%    failed      0.05%
  45  UzprTJ7K6d    7.83%    failed      0.07%
  46  UlwuxTyGoO    8.17%    passed     35.83%
  47  iaXjDyTif3    9.91%    passed     26.12%
  48  B6M0EvUDsT    8.17%    passed     57.64%
  49  1G5hXRghEG    7.83%    passed     46.06%
  50  gTvhxQmbWZ    7.83%    passed     59.90%
  51  8l37MLA1ms    7.83%    passed     66.42%
  52  vLizyHtRBL    6.96%    passed     45.67%
  53  S5ByYpGeqY    7.30%    passed     14.75%
  54  Fedl6T4xon    7.83%    passed     26.99%
  55  4BymctPkH6    9.22%    passed     90.46%
  56  s5wLZ9vWaO   22.96%    passed     14.42%
  57  awKrv6hUok    8.00%    failed      0.00%
  58  kWFqKgyYB3   18.61%    failed      0.35%
  59  DcYLS8gvW9    8.17%    passed     14.76%
  60  McRlo7Hy0B    8.35%    failed      1.15%
  61  tf71jZDs7S   14.78%    failed      0.00%
  62  vMqsZO8YaG   12.00%    passed     25.19%
  63  5AMYxNwgiK   14.26%    passed     72.77%
  64  wxoZBV0PHy    7.65%    passed     28.65%
  65  KeSH8I0Fea   10.96%    passed     34.97%
  66  KCrIGLQ7Q1    8.87%    passed     28.42%
  67  4LT0U0c0Do    8.17%    passed     45.98%
  68  CGeXrJPsGL    7.30%    passed     26.80%
  69  xxKiyIW1gr    8.35%    passed     42.35%
  70  xs9ieaVe53   24.17%    passed      5.89%
  71  NQWmJIpRFE    8.17%    passed     36.46%
  72  nkfchBpcgh    9.91%    passed     49.94%
  73  jdOhfl36g8    9.91%    passed     49.94%
  74  KVoy4GxdpT    8.70%    passed     30.77%
  75  WUIEff6ikU    9.74%    failed      3.44%
  76  coeQ6zHZ24    8.52%    passed     15.26%
  77  HWG7P94Eio    7.65%    passed     33.53%
  78  9Vw494DXPc    9.74%    passed     30.82%
  79  g6PJxKZvcf    8.17%    passed     67.92%
  80  AvvCKxHYp4    8.87%    passed     94.08%
  81  CemxIJafw8    8.87%    passed     94.94%
  82  dsBdLHptXN    7.30%    passed     26.31%
  83  4MVqW0qAIi    8.17%    passed      7.58%
  84  LcWgRv0iB6    8.17%    passed      6.57%
  85  fd8RtQX78T    8.35%    passed     67.99%
  86  D9LASQ998i    7.13%    passed     64.85%
  87  Uz7TnODNGf    8.17%    passed     61.10%
  88  Sp3Vq6QoAR   12.00%    passed     25.06%
  89  gtPloLimDb   14.61%    passed     16.69%
  90  GFnS6AyinZ   13.74%    passed     62.22%
  91  U9Eib0qR6X    9.39%    passed     80.44%
  92  dZ9ze414KZ    8.52%    passed     34.81%
  93  ydHAIeuwbW    9.04%    passed     24.32%
  94  e67HigPrjf    8.70%    passed     10.03%
  95  U5KrYXobqi    7.83%    passed     28.30%
  96  rqX0m8aZs1    8.52%    passed     74.68%
  97  JTOoSRn6ib    8.52%    passed     63.83%
  98  X4XbPR7Rfa    9.91%    passed     88.47%
  99  etCZH2Htco   11.30%    passed     96.50%
 100  7kS1ZU0pFM    9.74%    passed     63.62%
 101  rUnfYSLNJJ    8.35%    passed     25.59%
 102  YjqMqBCaiv    7.13%    passed     35.60%
 103  YXN7x6IbOx    8.35%    passed     52.18%
 104  bN8jt2Atwp   10.43%    passed     56.67%
 105  hgeyXdJgqq    9.22%    passed     56.85%
 106  1horVoEi3u    7.13%    failed      1.07%
 107  EDGqQf981n   10.09%    passed     86.16%
 108  3nDVNG9sKr   10.61%    passed     15.44%
 109  fFDoKaygf0    8.00%    passed     43.10%
 110  cRRsJgsBlZ    8.70%    passed     85.09%
 111  BI3jho3ECe    9.22%    passed     51.11%
 112  TIeppwLKSz    9.57%    passed     34.47%
 113  a8nt9ktZTC   24.35%    passed     70.98%
 114  GtfO72MtR2   22.26%    passed     65.46%
 115  xKzEmKT1dB   21.39%    passed     47.26%
 116  cTDPKciopP   11.83%    passed     67.98%
 117  xdNOUh7eMp    8.00%    passed     86.96%
 118  k3bzPFly41    8.17%    failed      0.00%
 119  ukUu00fP6L    9.39%    failed      0.29%
 120  up1UWJJzNf    9.22%    failed      3.36%
 121  GZASsy6wnT    8.17%    failed      0.00%
 122  PbkNCoK5ix   10.96%    passed     34.06%
 123  GfLEAInBd6   10.26%    passed     45.24%
 124  7OOuM97Qkr    8.70%    passed     42.00%
 125  d9kVhxwUcH    9.22%    passed     36.90%
 126  pn3nIof2qW    8.70%    passed     82.33%
 127  jYBcxGIen7   19.30%    passed     48.83%
 128  Y2YJcqt3IL   27.30%    passed     72.36%
 129  DQnwdMJsVl    9.39%    passed     17.77%
 130  Gvb4AsKEVi    8.35%    failed      0.00%
 131  d5E6EHDpwi    7.65%    passed     78.94%
 132  yA69Aemq0C    9.57%    passed     51.08%
 133  9f7AMvazZf    8.70%    passed     87.18%
 134  tD3ewCYOQG    9.22%    passed     39.14%
 135  yHwEtbE4JZ    8.87%    passed     51.50%
 136  HZpFQAW00k   12.87%    passed     16.94%
 137  FCPk6mdvI6    8.35%    passed     85.41%
 138  C50stY8CeY    9.22%    passed     15.26%
 139  WQOxpzhoLN    8.17%    passed     95.19%
 140  lU6fN5cAZQ   16.87%    passed     26.00%
 141  w34zJrGIvJ   13.04%    passed     46.23%
 142  R4SazYxajJ   13.22%    passed     24.74%
 143  oyLJTIsT1Z   12.00%    passed     35.61%
 144  95FTGjmRiw   16.87%    passed     10.92%
 145  MVSYHU9DCt   12.17%    passed     83.71%
 146  RhS1O12ekg    8.52%    passed     98.08%
 147  sthKhyT8fy    9.04%    passed     79.34%
 148  O2gQ2myCZn   11.30%    passed     66.29%
 149  B7PVgc3v8q    8.52%    passed     67.20%
 150  FlAHhYz62Q    6.96%    passed     92.12%
 151  PZqL2meUHi    8.35%    passed     89.55%
 152  XJTzBvD6pQ    8.70%    passed     73.32%
 153  FtEYGIUfBM   10.78%    passed     55.74%
 154  NUAWacASLt   10.26%    passed     81.70%
 155  3FdA2TKbHR   10.26%    passed     77.97%
 156  TCgaJethwm    9.74%    passed     51.49%
 157  V8Ort0OUIV    9.39%    passed     75.80%
 158  gKxOBa9lC3   80.35%    failed      4.37%
 159  ZJBcyycwk4   21.91%    passed     83.00%
 160  BXOEqGyzK2    9.04%    passed     82.96%
 161  5yy8DKtZ5c   12.35%    passed     70.92%
 162  cY7oeSnppq    9.74%    passed     78.00%
 163  vUEx5gqasN    9.74%    passed     22.71%
 164  2jCJDig3v9   17.39%    passed     45.79%
 165  lzBWRCtyx0   17.39%    passed     45.79%
 166  DBMxujRgHK   10.43%    passed     76.44%
 167  x3ZrH0XGfQ   13.04%    passed     40.57%
 168  SgWCfVzTG4    9.39%    passed     23.64%
 169  f62ksK5UEj   33.39%    passed     48.62%
 170  hkIztfSCD1   10.09%    passed     60.28%
 171  iRnB4M1GLD   11.30%    passed     35.88%
 172  CU0XuCnsFL   42.61%    failed      1.05%
 173  42tdKq8PSX   12.87%    passed     50.93%
 174  gXeZ52LCvM   12.87%    passed     50.93%
 175  u8cLLIfWEX   12.87%    passed     50.93%
 176  dmOh7r7eKT   12.52%    passed     43.59%
 177  3c6hZoOqvP   12.87%    passed     51.70%
 178  bu2UDzewiZ   16.35%    passed     97.52%
 179  SYc4eSftSt    7.30%    passed     55.76%
 180  zlSzVB3W0P    9.91%    passed     23.47%
 181  3C2pM8OlsA   16.00%    passed     44.07%
 182  Pxcz4xw4KG    8.52%    passed     89.90%
 183  UcghE30qVq   10.26%    passed     98.72%
 184  qIB6gS9bgA   10.26%    passed     99.50%
 185  UDehzYJL1w    9.91%    passed     84.08%
 186  BB4241mZBL    9.74%    passed     18.51%
 187  c6c8r06RzT   14.09%    passed     51.46%
 188  XQT9xr4ybf   14.09%    passed     51.46%
 189  SCnTy3bpY1   12.00%    passed     52.85%
 190  jev8yDUHvc   37.22%    passed     46.96%
 191  bK3G4lRT3G    9.74%    passed     18.84%
 192  Z5XH3L582l    9.39%    passed     64.30%
 193  dhUTnrRr7d    9.04%    passed     17.65%
 194  2ifGWJmasz   13.39%    passed     53.39%
 195  WB36HQui6V   13.22%    passed     13.09%
 196  QNNkPiHWnJ   13.57%    passed     15.99%
 197  WHGNQkrc10   16.70%    passed     15.42%
 198  h5LGHiiOXm   13.04%    passed      8.14%
 199  3zhlkwsAL6   11.65%    passed     68.02%
 200  i2Lb0rchl2   17.74%    passed     40.76%
 201  yMqx9t1LVd   11.83%    passed     95.23%
 202  2W3WY0vBww   18.09%    passed     31.19%
 203  wTTqfzkYo6   12.35%    passed     65.69%
 204  0vKBWD6wpY   19.83%    passed     72.14%
 205  SJgohIdqev   13.04%    passed     56.62%
 206  9DPLpYQWNv    8.35%    passed     79.37%
 207  8uUTsKFjlb    9.74%    passed     57.77%
 208  xVujdvY6Nr   15.65%    passed     86.08%
 209  NImtrhZGKE   18.61%    passed     29.08%
 210  YugOzGk8Ov    8.00%    passed     61.92%
 211  DeWEtikGbq    9.39%    passed     58.48%
 212  x0olbpog9B   10.78%    failed      3.15%
 213  pAhidh8xBZ    9.22%    passed     20.39%
 214  PlPvNaQDzl   78.26%    failed      2.70%
 215  NPvXCeLNmx    9.22%    passed     19.23%
 216  yVup7G0SEF    9.39%    passed      5.94%
 217  vPQhR8sENE    9.22%    passed     25.50%
 218  nU2WbHAcGl    8.00%    passed     38.25%
 219  5LDURAlPH2   18.96%    passed     93.03%
 220  BWFcvfZnO3   19.83%    passed     80.72%
 221  pygYFVFfpx   18.96%    passed     64.25%
 222  SHqN6p0dYV   11.65%    passed     77.47%
 223  qsVXrYaG9q   16.52%    passed     62.49%
 224  3cAaekWMpW   17.57%    passed     67.41%
 225  N40B32hpg1   12.00%    passed     79.79%
 226  JPT5lhIP82   16.17%    passed     61.51%
 227  ZLXDnoVm6b    8.87%    passed     65.21%
 228  X85YtZdfkf    9.04%    passed     76.50%
 229  8UiTG47Ec2    9.04%    passed     76.50%
 230  rIeH6RocN2   11.13%    passed     16.99%
 231  JEeirH12E1   31.48%    passed     21.21%
 232  UzAtwShlJN   15.48%    failed      0.00%
 233  2pVvPoBi2c   15.65%    failed      0.00%
 234  scQ10Wo461   39.13%    passed     23.66%
 235  Nb1rJKftmp   17.91%    failed      0.00%
 236  nhoqJOOPX2   17.04%    passed     88.57%
 237  39gkmZTScW   18.26%    passed     91.96%
 238  BGkr4JUYAf   13.39%    passed     93.93%
 239  DulbVCzsEt   24.35%    passed     66.60%
 240  cSruxLJuyQ   26.96%    passed     10.64%
 241  1XfSwqn4ef   25.04%    passed     39.48%
 242  96xj01KeXJ   68.17%    passed     84.97%
 243  eq1zGc6rtT   29.04%    passed     18.35%
 244  VfUM5i9jsn   41.91%    failed      4.66%
 245  20sicocoSo   23.83%    failed      0.74%
 246  RLpJhYeIPE   25.91%    passed     47.76%
 247  C8YPeCC1NI   28.87%    passed     14.80%
 248  xxnHHiKI8Z   28.52%    passed      5.76%
 249  3Je7M7o4rZ   33.39%    passed     11.10%
 250  47EKfQlPcw   28.35%    passed     38.14%
 251  9C0byE309K   34.43%    passed     22.05%
 252  TsIfWQzrph   28.35%    passed     38.14%
 253  hTPGiqrFV4   42.09%    passed     88.30%
 254  aFMglfB8eH   24.52%    passed     15.36%
 255  JQcRFbokY2   28.35%    passed     32.19%
 256  jFdaAxFg6n   23.13%    passed     47.94%
 257  KRYbednenZ   23.13%    passed     42.60%
 258  FyIDyqrLwr   23.13%    passed     47.94%
 259  8XGfcNsQ09   23.83%    passed     62.09%
 260  QyNf0mVNlz   23.83%    passed     10.54%
 261  f9oKgpE1wE   23.48%    passed     56.82%
 262  REBVZFiPEf   23.30%    passed     27.01%
 263  ItesG8T6sN   23.83%    passed     47.79%
 264  TSGS90hx1G   23.30%    passed     24.55%
 265  ZRAzqCtrNA   24.17%    passed     57.76%
 266  eeM5JHuVuf   24.35%    passed     50.06%
 267  oe9Vawfrxg   24.35%    passed     26.16%
 268  rgglFfiKnC   28.00%    passed     45.26%
 269  bCjdcpAF4v   24.00%    passed     70.09%
 270  OmcerY3zVm   64.35%    passed     66.28%
 271  zcG6I9U7zt   43.13%    passed     73.90%
 272  QKniumy84t   24.00%    passed     71.91%
 273  158IGk2w8A   24.00%    passed     40.59%
 274  kI8iG2U2gQ   23.30%    passed     85.81%
 275  fPZNEk39Af   26.78%    passed     15.99%
 276  hrBvV4AmlN   24.17%    passed     20.25%
 277  myGUzZ8LDH   24.00%    passed     24.24%
 278  sHkv5UU91e   23.65%    passed     10.45%
 279  GNzRUX9ddm   23.65%    passed     13.36%
 280  zsnvwGvGgv   24.00%    passed     30.90%
 281  9OoygEJxNJ   23.13%    passed     19.47%
 282  IjtzwwEpZt   24.70%    passed     32.04%
 283  nSDhHtKOaz   76.87%    passed     72.40%
 284  A0R7Dl6WnL   24.00%    passed     27.63%
 285  CvviaWP5QG   24.17%    passed     57.70%
 286  pPSEGFgq5j   79.13%    passed     12.51%
 287  UdG6KQNIp6   24.52%    passed      9.66%
 288  8EVSPtaAhX   24.35%    passed     42.22%
 289  uiafGbGfwA   27.30%    passed     85.86%
 290  XZFyxFJmTO   24.70%    passed     34.27%
 291  H6HkWi4jLJ   26.26%    passed     57.81%
 292  uALm9y36Bq   28.70%    passed     22.86%
 293  EUEmaNv0jU   23.30%    passed     16.64%
 294  miFIpMQUO8   25.04%    passed      5.34%
 295  qsWsb5TOjf   26.09%    passed     11.23%
 296  WLDkRifOr1   25.74%    passed     31.25%
 297  u7RGaLBmh5   25.74%    passed     85.68%
 298  n4n2Sa9hou   25.39%    passed     53.48%
 299  gZV6bt6UCn   24.17%    passed     46.31%
 300  PortTSlpTI   41.74%    passed     26.87%
 301  2Nn52BMVGD   28.00%    passed     32.50%
 302  sQl8vIYhWL   27.30%    passed     24.87%
 303  nlyynuwvAY   27.13%    passed     84.06%
 304  iM9z6TKAcr   41.39%    passed     18.69%
 305  pVpmbqWKfw   36.70%    failed      1.72%
 306  r4JpMWXYFJ   26.09%    passed     11.04%
 307  CcX8oiPHcg   27.83%    passed     27.83%
 308  G2BVFEVILA   25.04%    passed     61.18%
 309  BNYVmW4TYG   25.91%    passed     54.90%
 310  ExQ8uNPj7h   34.26%    passed     66.82%
 311  whmj06xoF5   28.17%    failed      0.02%
 312  VqFVtnHfVy   25.22%    passed     79.18%
 313  Mqy8imXZ6G   25.91%    failed      0.02%
 314  s0NXcs97L3   25.91%    failed      0.02%
 315  Iqt8ZiOu6k   25.74%    failed      0.00%
 316  XsWTxkH1p7   25.57%    passed     19.64%
 317  zoRaGfFB7U   24.52%    passed     48.77%
 318  qqN1dh1OOy   24.35%    passed     14.36%
 319  T1wQDvF98B   24.35%    passed      7.77%
 320  lkTsXyry76   26.43%    passed     26.11%
 321  hSqg5YYyOm   27.48%    failed      0.44%
 322  puRVWMvppN   28.35%    passed     22.55%
 323  1LbFAdgLuC   25.74%    passed     11.73%
 324  y5MmiioIHk   25.91%    failed      1.83%
 325  BnR8odZPBs   25.91%    passed     15.58%
 326  ajGvkpi5As   25.91%    passed      8.73%
 327  qbTJcwpdwP   26.61%    passed     13.99%
 328  vCxAIjCqNl   24.87%    passed     46.42%
 329  mPlwp1JlUK   27.30%    passed     36.54%
 330  rYWDHuLHvt   29.91%    failed      1.32%
 331  C0RnyRzFMX   71.65%    passed     45.95%
 332  7Aa2sW2uFn   28.00%    failed      3.36%
 333  0djEp2FhF9   28.00%    failed      3.36%
 334  l1pN6WjG1N   80.17%    passed     21.40%
 335  XLgmciWSgo   46.09%    passed     14.00%
 336  D8WaLv1pNN   30.78%    passed     27.06%
 337  12VY0qcAbu   29.39%    passed     74.33%
 338  JNoGNci0kO   28.87%    passed     95.56%
 339  VGEALS8WvR   40.70%    passed     16.49%
 340  D7iWRjKQ8X   25.74%    passed     47.65%
 341  upEmmPcbTB   27.48%    passed     22.48%
 342  UpKcpH8xp2   26.78%    passed      7.74%
 343  hreWbDAWDh   23.65%    passed      8.09%
 344  5oPFYbGk9x   24.52%    passed     66.68%
 345  bKMx8usLZf   35.83%    passed      9.39%
 346  9waTHuOjG2   43.48%    passed     27.73%
 347  y13PUGF6fd   29.39%    passed     50.29%
 348  MCxeCrj6og   25.22%    passed     77.92%
 349  JqQlZRu8jp   25.91%    passed     38.60%
 350  ZrMp8mhVn3   56.35%    passed      9.73%
 351  PVum0t8D9w   48.52%    failed      3.01%
 352  mA0FIy0SqW   24.70%    passed      5.42%
 353  EacivjsFt1   26.61%    passed     43.72%
 354  FKAuFXjrK2   29.57%    failed      2.12%
 355  eOn8Fw1qPv   27.48%    failed      3.53%
 356  D0XDiTOIfD   34.78%    passed      9.81%
 357  910hgdbBRd   28.00%    passed     51.49%
 358  ijUTPEstS6   33.39%    passed     28.87%
 359  bUU4czn7NG   27.83%    passed     60.40%
 360  INEhHLWnmb   37.04%    failed      1.97%
 361  LMA81zzKSe   37.04%    failed      0.01%
 362  TUCOIK4ZQn   33.91%    failed      0.52%
 363  yvso4goGdQ   34.96%    failed      4.00%
 364  YWPX00OZwF   36.00%    failed      3.54%
 365  qKqJ6yzKtT   34.61%    passed     10.13%
 366  49Qin0CHkb   34.61%    passed      9.62%
 367  63Q15egMZA   34.26%    passed      6.18%
 368  nWYlGrbPPc   34.61%    failed      4.67%
 369  JvcE4PBExA   33.74%    passed      7.73%
 370  LUlT7ehgwb   36.00%    passed     26.12%
 371  pVpykOHqYZ   39.48%    failed      0.85%
 372  v2K68153zf   38.26%    failed      0.55%
 373  qYhA4tEOW1   34.78%    failed      0.03%
 374  grGtjFUUTt   34.43%    failed      0.23%
 375  qWhSnx7aMf   44.87%    passed      5.50%
 376  v1oAyLSJtz   50.96%    passed     28.72%
 377  BadtzwpMMs   38.43%    passed      9.62%
 378  6DLNJCEk13   34.61%    passed      8.29%
 379  w2DOMr7ED6   41.39%    failed      3.23%
 380  JK0CadwxtV   33.74%    failed      1.62%
 381  thXzqzsTWd   33.04%    failed      4.58%
 382  cza9cyArKR   33.04%    failed      3.45%
 383  64i2bPRqyf   38.09%    failed      1.24%
 384  Tu05kR9iNy   35.30%    failed      2.13%
 385  ryyuwN9EeF   35.83%    failed      3.08%
 386  9i9iYEz14b   36.87%    passed     43.29%
 387  e5Z7VURlcd   56.00%    failed      0.95%
 388  ndIdlcACpn   34.61%    failed      0.11%
 389  miylOtOHke   36.00%    passed      5.91%
 390  jGxqmOPSFz   33.91%    failed      1.22%
 391  UpRnjomc4O   36.17%    passed     26.63%
 392  ebCUnMXr2f   38.43%    passed     15.56%
 393  21yjS1P784   34.43%    failed      0.27%
 394  XU8ct59Imq   34.26%    failed      0.70%
 395  mWu9nYUMB2   34.26%    passed      5.63%
 396  6N8VC2LDv6   34.26%    passed      5.63%
 397  Tp4oCldie4   38.09%    failed      4.42%
 398  LdahhT5atZ   34.26%    passed      5.63%
 399  ohdNT1wCFZ   34.26%    passed      7.14%
 400  QY3dkiwN48   41.57%    failed      3.72%
 401  Ip06mTdO2e   35.65%    failed      2.00%
 402  P5RXO2szhK   29.57%    passed     33.39%
 403  offjx75l6X   85.22%    passed     26.57%
 404  EdOuOhohBn   33.91%    passed     23.13%
 405  ZjYUAXvbUC   34.26%    passed      8.29%
 406  lpxtOw9xf3   36.52%    passed     12.71%
 407  4bSmqRgfRI   34.09%    passed     12.39%
 408  gminDyGtcG   34.78%    failed      2.44%
 409  lDQWwcBkMU   34.78%    passed     33.99%
 410  CUTMeJuwSv   33.74%    passed     78.03%
 411  OI80q3iM3F   33.74%    passed     81.17%
 412  xnKco929hT   37.57%    passed      8.65%
 413  RPfcmWXHCA   37.57%    passed     20.91%
 414  6mj1jZTKcU   36.17%    failed      4.67%
 415  Gr87dxYVyz   43.83%    failed      4.55%
 416  VGvhdii6IX   73.22%    passed     54.33%
 417  wJTuSg6Gc6   35.65%    passed     75.44%
 418  K3Flz6km5g   35.65%    passed     71.14%
 419  Tu0u89fzoU   35.48%    passed     16.33%
 420  IpceOBVrBQ   35.48%    passed     13.04%
 421  JAjUuwFnV7   36.35%    passed     34.52%
 422  wSnvqYXqTg   32.00%    passed     24.03%
 423  keWKiDv5J1   36.35%    passed     23.38%
 424  r5NSp8dbtM   37.39%    passed     32.60%
 425  wxLKLb6SMC   35.13%    passed     25.74%
 426  qw6gF6ZapY   35.13%    passed     25.74%
 427  ZGvDd4xvwy   37.91%    passed     30.11%
 428  8lXCZuvq8q   34.26%    passed     25.11%
 429  qvg1my8Wlp   48.70%    failed      3.30%
 430  ZdWaANa0Et   32.87%    passed      6.04%
 431  Onz2iyjxH3   42.96%    failed      0.02%
 432  AJImOJUang   66.09%    passed      8.67%
 433  rbo3OKIe4x   36.52%    failed      0.54%
 434  pGufZSTMNB   36.52%    passed     12.14%
 435  FLjy3W79tg   36.52%    passed     17.85%
 436  jYaSjXdhUR   34.78%    passed     22.31%
 437  HGW1EoyaVz   49.22%    passed     75.08%
 438  HQpmvbcKV0   36.35%    passed     71.28%
 439  Us22uQdloc   73.22%    passed     88.61%
 440  Nczi5Cos47   34.96%    passed     68.86%
 441  IV8TgD1mQj   36.52%    passed     65.05%
 442  QKsY8kV1rB   34.43%    passed     49.51%
 443  TrIc96BqkG   34.96%    passed      7.64%
 444  pnjqLcOivm   34.61%    passed      9.34%
 445  SY2alUymun   36.00%    passed     31.87%
 446  GXBps2FgSH   37.57%    failed      4.23%
 447  ZldeYJmzLx   39.48%    failed      0.13%
 448  8biR24Gazc   33.91%    passed     22.85%
 449  NBJ6cvHYoU   34.43%    passed     22.55%
 450  egq7pHRqeL   38.78%    passed     36.06%
 451  y0r2SVxwqI   35.30%    passed     55.80%
 452  evUBWmPjS2   35.30%    passed     23.87%
 453  ikh1qtxydC   36.00%    failed      2.62%
 454  BRdJ9RHZQj   35.65%    passed      8.09%
 455  l25CgIsmfn   35.65%    passed      8.09%
 456  XPdvjShyOo   37.57%    passed      7.82%
 457  M144qciIKM   34.96%    passed     30.15%
 458  BnE96TDyk8   35.48%    passed     26.42%
 459  jeohLZ0eYF   36.87%    failed      0.20%
 460  YvoxlQmxl7   36.87%    failed      0.20%
 461  R0wuUn8J0h   33.57%    passed     30.51%
 462  oeFPRaQBYZ   33.39%    passed     26.87%
 463  xqlhblg6dL   33.91%    passed     25.42%
 464  6Qs9p4Rx4f   34.09%    passed     25.71%
 465  QPlyWfEtzz   34.43%    passed     29.56%
 466  Yo6roMcRLy   35.30%    passed     25.15%
 467  PwuAxgsPD6   42.78%    passed     42.46%
 468  vaFUdeGB10   33.91%    failed      2.49%
 469  8GM1psnK6y   36.87%    failed      0.09%
 470  E6RVlyXu6C   33.74%    passed     45.21%
 471  SuF6hGymBQ   36.00%    failed      2.74%
 472  cgJCegWwAr   70.96%    passed     99.24%
 473  i10ONbBPRV   34.96%    passed     50.77%
 474  FaaaR0oHe4   35.13%    passed     47.29%
 475  RrNP3l8SS7   36.52%    failed      0.47%
 476  BuFyz2PMN4   34.43%    passed     49.11%
 477  Y10Qa1Da4V   38.78%    passed     65.87%
 478  8zkzdNvfM0   34.43%    passed     49.11%
 479  rA4KjQCVx3   32.00%    passed     90.85%
 480  au044S3YHW   35.30%    passed     43.12%
 481  cIR66o13VD   35.65%    passed     81.03%
 482  fkB1xaD3I7   35.83%    passed     66.46%
 483  CwGGcZADEn   35.30%    passed     25.37%
 484  fNHflelF6b   34.61%    passed     14.83%
 485  8zGWBmbKDs   83.65%    passed     77.32%
 486  LC2TsjjWfV   35.65%    passed     44.42%
 487  rsgxiUIZDl   41.74%    passed     41.79%
 488  Srvt2UziZu   34.43%    passed     97.83%
 489  zPT9rylEFV   34.43%    passed     97.83%
 490  rXls0PgjJv   35.48%    passed      5.47%
 491  TcLIjpisFo   51.83%    passed     29.28%
 492  RMfRwwtcqL   32.17%    passed      5.11%
 493  zzJMOnIGaE   34.09%    failed      0.02%
 494  bkj6PiDj99   34.78%    passed     36.79%
 495  QPtDeO8Fse   34.61%    passed     64.43%
WARNING: 19 sequences contain more than 50% gaps/ambiguity
****  TOTAL        23.94%  82 sequences failed composition chi2 test (p-value<5%; df=19)



Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.121 seconds
Measuring multi-threading efficiency up to 96 CPU cores
Increase to 10 rounds for branch lengths
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.303 seconds
Measuring multi-threading efficiency up to 96 CPU cores
Increase to 10 rounds for branch lengths
Increase to 10 rounds for branch lengths
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.417 seconds
Measuring multi-threading efficiency up to 96 CPU cores
Increase to 10 rounds for branch lengths
156 trees examined
Threads: 1 / Time: 96.394 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -54260
84 trees examined
Threads: 1 / Time: 96.112 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -102127
15 trees examined
Threads: 1 / Time: 96.564 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -473906
57 trees examined
Threads: 1 / Time: 97.103 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -176084
Threads: 2 / Time: 55.678 sec / Speedup: 1.734 / Efficiency: 87% / LogL: -473906
Threads: 2 / Time: 56.109 sec / Speedup: 1.731 / Efficiency: 87% / LogL: -176084
Threads: 2 / Time: 59.220 sec / Speedup: 1.628 / Efficiency: 81% / LogL: -54260
Threads: 2 / Time: 61.242 sec / Speedup: 1.569 / Efficiency: 78% / LogL: -102127
Threads: 3 / Time: 45.452 sec / Speedup: 2.136 / Efficiency: 71% / LogL: -176084
Threads: 3 / Time: 43.549 sec / Speedup: 2.207 / Efficiency: 74% / LogL: -102127
Threads: 3 / Time: 45.967 sec / Speedup: 2.097 / Efficiency: 70% / LogL: -54260
Threads: 3 / Time: 48.711 sec / Speedup: 1.982 / Efficiency: 66% / LogL: -473906
Threads: 4 / Time: 41.071 sec / Speedup: 2.351 / Efficiency: 59% / LogL: -473906
Threads: 4 / Time: 42.922 sec / Speedup: 2.246 / Efficiency: 56% / LogL: -54260
Threads: 4 / Time: 46.453 sec / Speedup: 2.090 / Efficiency: 52% / LogL: -176084
Threads: 4 / Time: 46.617 sec / Speedup: 2.062 / Efficiency: 52% / LogL: -102127
Threads: 5 / Time: 39.513 sec / Speedup: 2.444 / Efficiency: 49% / LogL: -473906
Determining AUTO threadcount: done in 281.613 secs using 252.7% CPU
BEST NUMBER OF THREADS: 4

Perform fast likelihood tree search using LG+G model...
Estimate model parameters (epsilon = 5.000)
Threads: 5 / Time: 39.362 sec / Speedup: 2.449 / Efficiency: 49% / LogL: -54260
Determining AUTO threadcount: done in 283.869 secs using 254.8% CPU
BEST NUMBER OF THREADS: 4

Perform fast likelihood tree search using LG+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.396707 secs using 398.3% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -36061.293
Optimal log-likelihood: -36061.101
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.095
Parameters optimization took 1 rounds (0.094 sec)
Time for fast ML tree search: 0.872 seconds

NOTE: ModelFinder requires 68 MB RAM!
ModelFinder will test up to 1232 protein models (sample size: 758) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  LG            36800.069    111 73822.138    73860.627    74336.144
  2  LG+I          36701.774    112 73627.548    73666.791    74146.184
  3  LG+G4         36069.615    112 72363.231    72402.474    72881.867
  4  LG+I+G4       36060.908    113 72347.817    72387.823    72871.084
Perform nearest neighbor interchange...
  5  LG+R2         36180.178    113 72586.356    72626.362    73109.623
  6  LG+R3         36068.747    115 72367.495    72409.052    72900.023
  7  LG+R4         36057.206    117 72348.412    72391.556    72890.202
Optimizing NNI: done in 4.65187 secs using 398.7% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -195470.534
Optimal log-likelihood: -195470.337
Gamma shape alpha: 2.185
Parameters optimization took 1 rounds (0.588 sec)
Time for fast ML tree search: 8.824 seconds

NOTE: ModelFinder requires 455 MB RAM!
ModelFinder will test up to 616 protein models (sample size: 575) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  LG            200322.611   987 402619.222   2352931.222  406916.985
Threads: 5 / Time: 43.988 sec / Speedup: 2.185 / Efficiency: 44% / LogL: -102127
Determining AUTO threadcount: done in 291.532 secs using 259% CPU
BEST NUMBER OF THREADS: 3

Perform fast likelihood tree search using LG+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.855267 secs using 299.3% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -59520.980
  8  LG+R5         36050.883    119 72339.766    72384.531    72890.817
Optimal log-likelihood: -59520.754
Proportion of invariable sites: 0.010
Gamma shape alpha: 1.046
Parameters optimization took 1 rounds (0.169 sec)
Time for fast ML tree search: 1.580 seconds

NOTE: ModelFinder requires 121 MB RAM!
ModelFinder will test up to 1232 protein models (sample size: 492) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  LG            62877.656    303 126361.312   127341.227   127633.451
  2  LG+I          62746.902    304 126101.805   127093.462   127378.142
 14  LG+I+R2       36151.833    114 72531.667    72572.445    73059.565
  3  LG+G4         59525.217    304 119658.433   120650.091   120934.771
Threads: 5 / Time: 48.966 sec / Speedup: 1.983 / Efficiency: 40% / LogL: -176084
Determining AUTO threadcount: done in 294.113 secs using 263% CPU
BEST NUMBER OF THREADS: 3

Perform fast likelihood tree search using LG+I+G model...
Estimate model parameters (epsilon = 5.000)
  2  LG+G4         195470.344   988 392916.688   2347180.688  397218.805
  4  LG+I+G4       59520.759    305 119651.519   120655.067   120932.055
 15  LG+I+R3       36059.148    116 72350.296    72392.642    72887.455
  5  LG+R2         60281.148    305 121172.296   122175.844   122452.832
 16  LG+I+R4       36054.090    118 72344.179    72388.129    72890.600
  6  LG+R3         59673.480    307 119960.960   120988.742   121249.893
 26  LG+F+I+G4     36008.321    132 72280.642    72336.821    72891.892
Perform nearest neighbor interchange...
 48  WAG+I+G4      36044.870    113 72315.741    72355.747    72839.008
 70  WAG+F+I+G4    35971.074    132 72206.148    72262.327    72817.398
 92  JTT+I+G4      36054.314    113 72334.629    72374.635    72857.896
  3  LG+R2         196589.598   989 395157.196   2353377.196  399463.668
114  JTT+F+I+G4    36021.830    132 72307.661    72363.840    72918.911
WARNING: Normalizing state frequencies so that sum of them equals to 1
136  Q.pfam+I+G4   36034.379    113 72294.757    72334.763    72818.024
WARNING: Normalizing state frequencies so that sum of them equals to 1
158  Q.pfam+F+I+G4 35995.688    132 72255.377    72311.556    72866.627
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 2.04783 secs using 299.5% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -105983.853
180  Q.bird+I+G4   36584.188    113 73394.375    73434.381    73917.642
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimal log-likelihood: -105983.357
Proportion of invariable sites: 0.029
Gamma shape alpha: 0.841
Parameters optimization took 1 rounds (0.281 sec)
Time for fast ML tree search: 3.913 seconds

NOTE: ModelFinder requires 179 MB RAM!
ModelFinder will test up to 1232 protein models (sample size: 414) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  7  LG+R4         59517.015    309 119652.030   120704.667   120949.360
  1  LG            114655.790   535 230381.579   803901.579   232535.418
202  Q.bird+F+I+G4 36550.761    132 73365.521    73421.700    73976.771
WARNING: Normalizing state frequencies so that sum of them equals to 1
  2  LG+I          113905.280   536 228882.559   804546.559   231040.423
224  Q.mammal+I+G4 36360.413    113 72946.827    72986.833    73470.094
WARNING: Normalizing state frequencies so that sum of them equals to 1
246  Q.mammal+F+I+G4 36338.579    132 72941.159    72997.338    73552.409
268  Q.insect+I+G4 36139.832    113 72505.663    72545.670    73028.931
290  Q.insect+F+I+G4 36140.966    132 72545.931    72602.111    73157.182
WARNING: Normalizing state frequencies so that sum of them equals to 1
312  Q.plant+I+G4  36183.351    113 72592.701    72632.707    73115.968
WARNING: Normalizing state frequencies so that sum of them equals to 1
334  Q.plant+F+I+G4 36158.219    132 72580.438    72636.617    73191.688
WARNING: Normalizing state frequencies so that sum of them equals to 1
  3  LG+G4         106067.111   536 213206.222   788870.222   215364.086
  8  LG+R5         59458.290    311 119538.580   120616.713   120844.306
356  Q.yeast+I+G4  36214.076    113 72654.152    72694.158    73177.419
WARNING: Normalizing state frequencies so that sum of them equals to 1
378  Q.yeast+F+I+G4 36096.959    132 72457.918    72514.097    73069.168
  4  LG+I+G4       105983.331   537 213040.662   790852.662   215202.552
400  JTTDCMut+I+G4 36056.354    113 72338.709    72378.715    72861.976
422  JTTDCMut+F+I+G4 36026.394    132 72316.788    72372.967    72928.038
444  DCMut+I+G4    36592.084    113 73410.168    73450.174    73933.435
  5  LG+R2         108144.740   537 217363.479   795175.479   219525.369
466  DCMut+F+I+G4  36424.371    132 73112.742    73168.921    73723.992
488  VT+I+G4       36117.345    113 72460.689    72500.695    72983.956
510  VT+F+I+G4     36084.443    132 72432.885    72489.064    73044.135
  4  LG+R3         195780.341   991 393542.681   2359686.681  397857.862
532  PMB+I+G4      36449.377    113 73124.755    73164.761    73648.022
554  PMB+F+I+G4    36409.191    132 73082.383    73138.562    73693.633
576  Blosum62+I+G4 36431.429    113 73088.859    73128.865    73612.126
598  Blosum62+F+I+G4 36356.603    132 72977.206    73033.386    73588.457
620  Dayhoff+I+G4  36591.479    113 73408.957    73448.963    73932.224
642  Dayhoff+F+I+G4 36423.691    132 73111.382    73167.562    73722.633
664  mtREV+I+G4    37843.694    113 75913.389    75953.395    76436.656
686  mtREV+F+I+G4  36628.735    132 73521.471    73577.650    74132.721
708  mtART+I+G4    38788.297    113 77802.594    77842.601    78325.862
730  mtART+F+I+G4  37431.520    132 75127.039    75183.219    75738.290
752  mtZOA+I+G4    37767.194    113 75760.388    75800.394    76283.655
774  mtZOA+F+I+G4  36779.606    132 73823.213    73879.392    74434.463
  6  LG+R3         106577.709   539 214233.419   796353.419   216403.361
796  mtMet+I+G4    37801.532    113 75829.065    75869.071    76352.332
818  mtMet+F+I+G4  36538.292    132 73340.584    73396.763    73951.834
840  mtVer+I+G4    38034.665    113 76295.330    76335.337    76818.598
  9  LG+R6         59413.228    313 119452.455   120556.748   120766.579
862  mtVer+F+I+G4  36927.671    132 74119.341    74175.520    74730.591
884  mtInv+I+G4    38092.554    113 76411.108    76451.114    76934.375
906  mtInv+F+I+G4  36434.606    132 73133.213    73189.392    73744.463
928  mtMAM+I+G4    38661.054    113 77548.107    77588.114    78071.375
950  mtMAM+F+I+G4  37383.694    132 75031.389    75087.568    75642.639
WARNING: Normalizing state frequencies so that sum of them equals to 1
972  FLAVI+I+G4    37381.078    113 74988.157    75028.163    75511.424
WARNING: Normalizing state frequencies so that sum of them equals to 1
994  FLAVI+F+I+G4  37276.588    132 74817.176    74873.355    75428.426
1016  HIVb+I+G4     36763.728    113 73753.456    73793.463    74276.724
1038  HIVb+F+I+G4   36620.638    132 73505.276    73561.455    74116.526
  5  LG+R4         195429.122   993 392844.244   2366928.244  397168.133
1060  HIVw+I+G4     37947.900    113 76121.799    76161.805    76645.066
1082  HIVw+F+I+G4   37348.858    132 74961.717    75017.896    75572.967
1104  FLU+I+G4      36559.262    113 73344.525    73384.531    73867.792
1126  FLU+F+I+G4    36304.591    132 72873.182    72929.361    73484.432
1148  rtREV+I+G4    36443.832    113 73113.664    73153.670    73636.931
1170  rtREV+F+I+G4  36282.477    132 72828.953    72885.132    73440.203
1192  cpREV+I+G4    36292.426    113 72810.851    72850.858    73334.119
1214  cpREV+F+I+G4  36199.404    132 72662.807    72718.986    73274.057
Akaike Information Criterion:           WAG+F+I+G4
Corrected Akaike Information Criterion: WAG+F+I+G4
Bayesian Information Criterion:         WAG+F+I+G4
Best-fit model: WAG+F+I+G4 chosen according to BIC

All model information printed to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.model.gz
CPU time for ModelFinder: 855.379 seconds (0h:14m:15s)
Wall-clock time for ModelFinder: 316.725 seconds (0h:5m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 1

Creating bootstrap alignment (seed: 956160)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Thoroughly optimizing +I+G parameters from 10 start values...
 10  LG+R7         59406.451    315 119442.902   120574.039   120765.423
Init pinv, alpha: 0.000, 2.469 / Estimate: 0.000, 2.038 / LogL: -36342.724
Init pinv, alpha: 0.004, 2.469 / Estimate: 0.027, 2.404 / LogL: -36325.581
Init pinv, alpha: 0.009, 2.469 / Estimate: 0.027, 2.403 / LogL: -36325.586
Init pinv, alpha: 0.013, 2.469 / Estimate: 0.027, 2.399 / LogL: -36325.596
Init pinv, alpha: 0.017, 2.469 / Estimate: 0.027, 2.402 / LogL: -36325.592
Init pinv, alpha: 0.021, 2.469 / Estimate: 0.027, 2.404 / LogL: -36325.591
Init pinv, alpha: 0.026, 2.469 / Estimate: 0.027, 2.406 / LogL: -36325.592
Init pinv, alpha: 0.030, 2.469 / Estimate: 0.028, 2.409 / LogL: -36325.592
Init pinv, alpha: 0.034, 2.469 / Estimate: 0.028, 2.408 / LogL: -36325.593
Init pinv, alpha: 0.038, 2.469 / Estimate: 0.028, 2.408 / LogL: -36325.594
Optimal pinv,alpha: 0.027, 2.404 / LogL: -36325.581

Parameters optimization took 2.533 sec
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.081301 secs using 397.5% CPU
Computing ML distances took 0.081456 sec (of wall-clock time) 0.323663 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00019598 secs using 453.6% CPU
Constructing RapidNJ tree: done in 0.0020659 secs using 382.7% CPU
Computing RapidNJ tree took 0.002322 sec (of wall-clock time) 0.010127 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36903.945
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees...   7  LG+R4         106043.319   541 213168.637   799612.637   215346.631
1.475 second
Computing log-likelihood of 98 initial trees ... 2.399 seconds
Current best score: -36325.581

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.309748 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36289.787
Optimizing NNI: done in 0.400109 secs using 397.3% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36289.750
Optimizing NNI: done in 0.409983 secs using 397.2% CPU
Optimizing NNI: done in 0.428051 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -36287.045
Optimizing NNI: done in 0.430781 secs using 397.2% CPU
Optimizing NNI: done in 0.387918 secs using 397.6% CPU
Optimizing NNI: done in 0.455831 secs using 398.7% CPU
Optimizing NNI: done in 0.492718 secs using 398.5% CPU
Optimizing NNI: done in 0.433018 secs using 398.3% CPU
Optimizing NNI: done in 0.366962 secs using 398.2% CPU
Iteration 10 / LogL: -36287.063 / Time: 0h:0m:11s
Optimizing NNI: done in 0.429281 secs using 398.3% CPU
Optimizing NNI: done in 0.374891 secs using 395.6% CPU
Optimizing NNI: done in 0.397632 secs using 399.5% CPU
Optimizing NNI: done in 0.391399 secs using 399.2% CPU
Optimizing NNI: done in 0.421506 secs using 398.1% CPU
Optimizing NNI: done in 0.43879 secs using 397.8% CPU
Optimizing NNI: done in 0.473572 secs using 398.1% CPU
Optimizing NNI: done in 0.46764 secs using 398.5% CPU
Optimizing NNI: done in 0.377811 secs using 399.5% CPU
Optimizing NNI: done in 0.437341 secs using 399.5% CPU
Iteration 20 / LogL: -36287.050 / Time: 0h:0m:15s
Finish initializing candidate tree set (2)
Current best tree score: -36287.045 / CPU time: 12.455
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.717374 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36286.155
  6  LG+R5         195312.276   995 392614.553   2374654.553  396947.151
Optimizing NNI: done in 0.717186 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -36283.161
Optimizing NNI: done in 0.793775 secs using 398.8% CPU
Optimizing NNI: done in 0.579126 secs using 399% CPU
Optimizing NNI: done in 0.870062 secs using 398.3% CPU
Optimizing NNI: done in 0.641797 secs using 398.5% CPU
 11  LG+R8         59398.958    317 119431.915   120590.605   120762.833
Optimizing NNI: done in 0.822881 secs using 398.2% CPU
Optimizing NNI: done in 0.643068 secs using 398.2% CPU
Optimizing NNI: done in 0.615155 secs using 399.2% CPU
Optimizing NNI: done in 0.65232 secs using 398.9% CPU
Iteration 30 / LogL: -36299.853 / Time: 0h:0m:22s (0h:1m:11s left)
Optimizing NNI: done in 0.613553 secs using 398.6% CPU
Optimizing NNI: done in 0.530643 secs using 398.5% CPU
Optimizing NNI: done in 0.687699 secs using 397.5% CPU
Optimizing NNI: done in 0.914712 secs using 397.7% CPU
Optimizing NNI: done in 0.602292 secs using 399% CPU
Optimizing NNI: done in 0.666665 secs using 398.4% CPU
Optimizing NNI: done in 0.906586 secs using 399.3% CPU
Optimizing NNI: done in 0.788961 secs using 399.1% CPU
Optimizing NNI: done in 0.728482 secs using 398.3% CPU
Optimizing NNI: done in 0.66995 secs using 397.8% CPU
Iteration 40 / LogL: -36283.167 / Time: 0h:0m:29s (0h:1m:2s left)
Optimizing NNI: done in 0.811771 secs using 399% CPU
Optimizing NNI: done in 0.597268 secs using 398.7% CPU
Optimizing NNI: done in 0.671845 secs using 397.4% CPU
Optimizing NNI: done in 0.668382 secs using 397.5% CPU
Optimizing NNI: done in 0.913324 secs using 399.2% CPU
Optimizing NNI: done in 0.54224 secs using 396.6% CPU
Optimizing NNI: done in 0.76981 secs using 398.4% CPU
Optimizing NNI: done in 0.603748 secs using 399.5% CPU
Optimizing NNI: done in 0.741908 secs using 398.2% CPU
Optimizing NNI: done in 0.859631 secs using 398% CPU
Iteration 50 / LogL: -36283.182 / Time: 0h:0m:36s (0h:0m:54s left)
Optimizing NNI: done in 0.609642 secs using 398.1% CPU
Optimizing NNI: done in 0.605772 secs using 399.1% CPU
Optimizing NNI: done in 0.618865 secs using 398.1% CPU
Optimizing NNI: done in 0.72801 secs using 398.4% CPU
Optimizing NNI: done in 0.691929 secs using 397.6% CPU
Optimizing NNI: done in 0.721942 secs using 398.2% CPU
Optimizing NNI: done in 0.595602 secs using 398.4% CPU
 12  LG+R9         59397.375    319 119432.749   120619.726   120772.064
Optimizing NNI: done in 0.601857 secs using 399% CPU
 14  LG+I+R2       60231.507    306 121075.014   122090.603   122359.748
Optimizing NNI: done in 0.668198 secs using 397.9% CPU
 15  LG+I+R3       59658.571    308 119933.141   120973.272   121226.273
Optimizing NNI: done in 0.76867 secs using 399% CPU
Iteration 60 / LogL: -36287.078 / Time: 0h:0m:43s (0h:0m:45s left)
Optimizing NNI: done in 0.696286 secs using 398.8% CPU
Optimizing NNI: done in 0.51674 secs using 398.8% CPU
  8  LG+R5         105748.991   543 212583.982   803367.982   214770.027
 16  LG+I+R4       59512.518    310 119645.036   120710.340   120946.564
Optimizing NNI: done in 0.704865 secs using 399.2% CPU
Optimizing NNI: done in 0.655226 secs using 398.7% CPU
Optimizing NNI: done in 0.763141 secs using 397.5% CPU
  7  LG+R6         195240.929   997 392475.859   2382487.859  396817.166
 17  LG+I+R5       59456.780    312 119537.561   120628.689   120847.486
Optimizing NNI: done in 0.761981 secs using 398.1% CPU
Optimizing NNI: done in 0.691236 secs using 397.7% CPU
Optimizing NNI: done in 0.599029 secs using 398.3% CPU
Optimizing NNI: done in 0.707957 secs using 398% CPU
Optimizing NNI: done in 0.600387 secs using 398.4% CPU
Iteration 70 / LogL: -36295.068 / Time: 0h:0m:50s (0h:0m:37s left)
Optimizing NNI: done in 0.634032 secs using 398.7% CPU
Optimizing NNI: done in 0.681012 secs using 396.9% CPU
Optimizing NNI: done in 0.575332 secs using 398.1% CPU
Optimizing NNI: done in 0.578524 secs using 399.3% CPU
Optimizing NNI: done in 0.576386 secs using 397.6% CPU
Optimizing NNI: done in 0.728135 secs using 398.8% CPU
 18  LG+I+R6       59412.217    314 119452.434   120570.062   120770.757
Optimizing NNI: done in 0.608209 secs using 398.4% CPU
Optimizing NNI: done in 0.54889 secs using 398.7% CPU
Optimizing NNI: done in 0.663759 secs using 398.8% CPU
Optimizing NNI: done in 0.611304 secs using 399% CPU
Iteration 80 / LogL: -36287.606 / Time: 0h:0m:56s (0h:0m:30s left)
Optimizing NNI: done in 0.810877 secs using 397.9% CPU
Optimizing NNI: done in 0.544172 secs using 393.2% CPU
Optimizing NNI: done in 0.558658 secs using 394.3% CPU
Optimizing NNI: done in 0.520055 secs using 394.5% CPU
Optimizing NNI: done in 0.616445 secs using 394.2% CPU
Optimizing NNI: done in 0.709738 secs using 393.3% CPU
Optimizing NNI: done in 0.715511 secs using 395% CPU
Optimizing NNI: done in 0.582729 secs using 395.5% CPU
 19  LG+I+R7       59406.446    316 119444.893   120589.716   120771.612
Optimizing NNI: done in 0.823423 secs using 394.9% CPU
Optimizing NNI: done in 0.776375 secs using 395.3% CPU
Iteration 90 / LogL: -36283.168 / Time: 0h:1m:3s (0h:0m:22s left)
 31  LG+F+R6       59437.121    332 119538.243   120928.884   120932.138
Optimizing NNI: done in 0.76277 secs using 395.8% CPU
Optimizing NNI: done in 0.759759 secs using 395.5% CPU
Optimizing NNI: done in 0.71648 secs using 396.1% CPU
Optimizing NNI: done in 0.679198 secs using 396.2% CPU
 32  LG+F+R7       59430.407    334 119528.813   120954.163   120931.105
Optimizing NNI: done in 0.677921 secs using 396.3% CPU
Optimizing NNI: done in 0.766802 secs using 396% CPU
Optimizing NNI: done in 0.586637 secs using 396.4% CPU
Optimizing NNI: done in 0.706716 secs using 396.6% CPU
Optimizing NNI: done in 0.717166 secs using 396.2% CPU
Optimizing NNI: done in 0.573025 secs using 396.2% CPU
Iteration 100 / LogL: -36283.161 / Time: 0h:1m:10s (0h:0m:15s left)
Optimizing NNI: done in 0.766198 secs using 396.6% CPU
Optimizing NNI: done in 0.863334 secs using 396.2% CPU
Optimizing NNI: done in 0.421624 secs using 397.1% CPU
Optimizing NNI: done in 0.482156 secs using 397% CPU
 33  LG+F+R8       59421.458    336 119514.916   120975.974   120925.605
Optimizing NNI: done in 0.821529 secs using 397.4% CPU
Optimizing NNI: done in 0.688739 secs using 396.8% CPU
Optimizing NNI: done in 0.627296 secs using 397.7% CPU
Optimizing NNI: done in 0.507933 secs using 397.1% CPU
Optimizing NNI: done in 0.488236 secs using 397.3% CPU
Optimizing NNI: done in 0.559286 secs using 397.2% CPU
Iteration 110 / LogL: -36289.962 / Time: 0h:1m:16s (0h:0m:8s left)
Optimizing NNI: done in 0.464301 secs using 397.8% CPU
  8  LG+R7         195209.395   999 392416.790   2390416.790  396766.806
Optimizing NNI: done in 0.612775 secs using 396.6% CPU
Optimizing NNI: done in 0.505421 secs using 397.1% CPU
Optimizing NNI: done in 0.424698 secs using 395.8% CPU
Optimizing NNI: done in 0.625689 secs using 395.7% CPU
Optimizing NNI: done in 0.749093 secs using 394.8% CPU
Optimizing NNI: done in 0.865226 secs using 396.8% CPU
Optimizing NNI: done in 0.567706 secs using 396.7% CPU
Optimizing NNI: done in 0.847028 secs using 397% CPU
Optimizing NNI: done in 0.683476 secs using 396.1% CPU
Iteration 120 / LogL: -36289.857 / Time: 0h:1m:22s (0h:0m:1s left)
Optimizing NNI: done in 0.40794 secs using 395.5% CPU
Optimizing NNI: done in 0.94924 secs using 397.5% CPU
Optimizing NNI: done in 0.538049 secs using 398% CPU
TREE SEARCH COMPLETED AFTER 123 ITERATIONS / Time: 0h:1m:24s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36283.161
Optimal log-likelihood: -36283.160
Proportion of invariable sites: 0.027
Gamma shape alpha: 2.378
Parameters optimization took 1 rounds (0.056 sec)
BEST SCORE FOUND : -36283.160
Total tree length: 19.569

Total number of iterations: 123
CPU time used for tree search: 322.052 sec (0h:5m:22s)
Wall-clock time used for tree search: 81.958 sec (0h:1m:21s)
Total CPU time used: 333.703 sec (0h:5m:33s)
Total wall-clock time used: 84.839 sec (0h:1m:24s)

===> START BOOTSTRAP REPLICATE NUMBER 2

Creating bootstrap alignment (seed: 956161)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.010 seconds

NOTE: 16 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37214.036
2. Current log-likelihood: -36329.109
3. Current log-likelihood: -36307.019
4. Current log-likelihood: -36306.044
Optimal log-likelihood: -36305.897
Proportion of invariable sites: 0.029
Gamma shape alpha: 2.717
Parameters optimization took 4 rounds (0.337 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0788589 secs using 398.1% CPU
Computing ML distances took 0.079026 sec (of wall-clock time) 0.314442 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000175953 secs using 414.3% CPU
Constructing RapidNJ tree: done in 0.00213194 secs using 424.2% CPU
Computing RapidNJ tree took 0.002366 sec (of wall-clock time) 0.010882 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36630.350
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.482 second
Computing log-likelihood of 98 initial trees ... 2.220 seconds
Current best score: -36258.970

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.433383 secs using 397.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36184.222
Optimizing NNI: done in 0.458848 secs using 395% CPU
Optimizing NNI: done in 0.446431 secs using 397.8% CPU
Optimizing NNI: done in 0.450527 secs using 397.8% CPU
Optimizing NNI: done in 0.357327 secs using 398.5% CPU
Optimizing NNI: done in 0.44348 secs using 398% CPU
Optimizing NNI: done in 0.348238 secs using 397.6% CPU
Optimizing NNI: done in 0.44753 secs using 398.4% CPU
Optimizing NNI: done in 0.451052 secs using 397.6% CPU
 34  LG+F+R9       59420.206    338 119516.412   121014.216   120935.498
Optimizing NNI: done in 0.359761 secs using 398.1% CPU
Iteration 10 / LogL: -36184.614 / Time: 0h:0m:8s
Optimizing NNI: done in 0.465861 secs using 397.8% CPU
Optimizing NNI: done in 0.463227 secs using 397.3% CPU
Optimizing NNI: done in 0.359947 secs using 397.8% CPU
  9  LG+R6         105619.462   545 212328.924   807468.924   214523.021
Optimizing NNI: done in 0.450199 secs using 398.1% CPU
Optimizing NNI: done in 0.437 secs using 397.7% CPU
Optimizing NNI: done in 0.465987 secs using 398.7% CPU
Optimizing NNI: done in 0.433107 secs using 397.9% CPU
Optimizing NNI: done in 0.455874 secs using 396.6% CPU
Optimizing NNI: done in 0.461238 secs using 397.7% CPU
Optimizing NNI: done in 0.363847 secs using 398.3% CPU
Iteration 20 / LogL: -36184.474 / Time: 0h:0m:13s
Finish initializing candidate tree set (2)
Current best tree score: -36184.222 / CPU time: 12.493
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.520069 secs using 398% CPU
Optimizing NNI: done in 0.540947 secs using 398% CPU
Optimizing NNI: done in 0.677368 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -36182.532
Optimizing NNI: done in 0.749928 secs using 398% CPU
Optimizing NNI: done in 0.725308 secs using 398.5% CPU
Optimizing NNI: done in 0.559885 secs using 398% CPU
 40  LG+F+I+R6     59436.464    333 119538.929   120946.802   120937.022
Optimizing NNI: done in 0.815727 secs using 398% CPU
Optimizing NNI: done in 0.471062 secs using 398.2% CPU
Optimizing NNI: done in 0.741775 secs using 398.4% CPU
Optimizing NNI: done in 0.99189 secs using 398.2% CPU
Iteration 30 / LogL: -36182.608 / Time: 0h:0m:20s (0h:1m:4s left)
Optimizing NNI: done in 0.742746 secs using 398.8% CPU
Optimizing NNI: done in 0.65356 secs using 398.3% CPU
Optimizing NNI: done in 0.742877 secs using 398% CPU
Optimizing NNI: done in 0.702256 secs using 398% CPU
Optimizing NNI: done in 0.658466 secs using 398.4% CPU
Optimizing NNI: done in 0.802177 secs using 398.1% CPU
Optimizing NNI: done in 0.778439 secs using 397.9% CPU
 41  LG+F+I+R7     59430.640    335 119531.280   120974.357   120937.770
Optimizing NNI: done in 0.627926 secs using 398.1% CPU
Optimizing NNI: done in 0.458561 secs using 398.3% CPU
Optimizing NNI: done in 0.921505 secs using 398.3% CPU
Iteration 40 / LogL: -36183.224 / Time: 0h:0m:27s (0h:0m:57s left)
Optimizing NNI: done in 0.779428 secs using 398% CPU
Optimizing NNI: done in 0.928514 secs using 398.4% CPU
Optimizing NNI: done in 0.542004 secs using 398.3% CPU
Optimizing NNI: done in 0.525832 secs using 398.2% CPU
Optimizing NNI: done in 0.782361 secs using 399.2% CPU
Optimizing NNI: done in 0.736493 secs using 398.9% CPU
Optimizing NNI: done in 0.578906 secs using 397.5% CPU
Optimizing NNI: done in 0.76488 secs using 398.7% CPU
Optimizing NNI: done in 0.716538 secs using 398.7% CPU
 53  WAG+R6        59804.889    313 120235.778   121340.071   121549.902
Optimizing NNI: done in 0.796266 secs using 397.8% CPU
Iteration 50 / LogL: -36221.778 / Time: 0h:0m:34s (0h:0m:51s left)
Optimizing NNI: done in 0.866026 secs using 398.7% CPU
Optimizing NNI: done in 0.86727 secs using 398.6% CPU
Optimizing NNI: done in 0.824199 secs using 398.6% CPU
Optimizing NNI: done in 0.891863 secs using 399.1% CPU
Optimizing NNI: done in 0.817394 secs using 399.1% CPU
 54  WAG+R7        59796.966    315 120223.932   121355.068   121546.453
Optimizing NNI: done in 0.935823 secs using 399% CPU
Optimizing NNI: done in 0.757567 secs using 399.6% CPU
Optimizing NNI: done in 0.683114 secs using 398.8% CPU
Optimizing NNI: done in 0.510542 secs using 399.8% CPU
Optimizing NNI: done in 0.453997 secs using 399.1% CPU
Iteration 60 / LogL: -36184.822 / Time: 0h:0m:41s (0h:0m:44s left)
Optimizing NNI: done in 0.519134 secs using 399% CPU
Optimizing NNI: done in 0.822783 secs using 399.2% CPU
 55  WAG+R8        59792.254    317 120218.509   121377.199   121549.427
Optimizing NNI: done in 0.51809 secs using 399.3% CPU
Optimizing NNI: done in 0.750212 secs using 398.6% CPU
Optimizing NNI: done in 0.773973 secs using 398.4% CPU
Optimizing NNI: done in 0.786132 secs using 398.8% CPU
Optimizing NNI: done in 0.714147 secs using 398.5% CPU
Optimizing NNI: done in 0.471877 secs using 398.2% CPU
Optimizing NNI: done in 0.57491 secs using 399.2% CPU
 62  WAG+I+R6      59804.263    314 120236.525   121354.152   121554.848
Optimizing NNI: done in 0.843984 secs using 399.1% CPU
Iteration 70 / LogL: -36182.535 / Time: 0h:0m:48s (0h:0m:37s left)
Optimizing NNI: done in 0.742778 secs using 398.7% CPU
Optimizing NNI: done in 0.985478 secs using 399.3% CPU
Optimizing NNI: done in 0.538363 secs using 399.5% CPU
Optimizing NNI: done in 0.833548 secs using 399.2% CPU
Optimizing NNI: done in 0.779479 secs using 399% CPU
Optimizing NNI: done in 0.607246 secs using 397.9% CPU
Optimizing NNI: done in 0.875413 secs using 398.2% CPU
Optimizing NNI: done in 0.568762 secs using 399.3% CPU
Optimizing NNI: done in 0.852372 secs using 399.6% CPU
 63  WAG+I+R7      59796.876    316 120225.753   121370.576   121552.472
Optimizing NNI: done in 0.714587 secs using 398.8% CPU
Iteration 80 / LogL: -36221.781 / Time: 0h:0m:56s (0h:0m:30s left)
Optimizing NNI: done in 0.812816 secs using 399.2% CPU
Optimizing NNI: done in 0.664551 secs using 399.1% CPU
Optimizing NNI: done in 0.670965 secs using 398.8% CPU
 75  WAG+F+R6      59751.895    332 120167.790   121558.431   121561.685
Optimizing NNI: done in 0.570133 secs using 398.9% CPU
Optimizing NNI: done in 0.660528 secs using 399% CPU
Optimizing NNI: done in 0.761959 secs using 398.6% CPU
Optimizing NNI: done in 0.78338 secs using 398.9% CPU
Optimizing NNI: done in 0.795451 secs using 399.2% CPU
Optimizing NNI: done in 0.787236 secs using 399.1% CPU
Optimizing NNI: done in 0.52818 secs using 399.7% CPU
Iteration 90 / LogL: -36184.351 / Time: 0h:1m:3s (0h:0m:23s left)
Optimizing NNI: done in 0.78862 secs using 398.8% CPU
Optimizing NNI: done in 0.677539 secs using 398.9% CPU
 76  WAG+F+R7      59743.193    334 120154.385   121579.736   121556.677
 10  LG+R7         105552.987   547 212199.974   811711.974   214402.123
Optimizing NNI: done in 0.6362 secs using 398.3% CPU
Optimizing NNI: done in 0.793995 secs using 399.4% CPU
Optimizing NNI: done in 0.817609 secs using 399% CPU
Optimizing NNI: done in 0.681543 secs using 399% CPU
Optimizing NNI: done in 0.756876 secs using 398.9% CPU
Optimizing NNI: done in 0.588207 secs using 398.5% CPU
Optimizing NNI: done in 0.666682 secs using 398.6% CPU
 77  WAG+F+R8      59737.298    336 120146.595   121607.653   121557.284
Optimizing NNI: done in 0.836369 secs using 398.4% CPU
Iteration 100 / LogL: -36182.538 / Time: 0h:1m:10s (0h:0m:16s left)
Optimizing NNI: done in 0.659493 secs using 398.6% CPU
Optimizing NNI: done in 0.733673 secs using 398.3% CPU
Optimizing NNI: done in 0.434193 secs using 398.3% CPU
Optimizing NNI: done in 0.60276 secs using 397.8% CPU
Optimizing NNI: done in 0.648836 secs using 399% CPU
Optimizing NNI: done in 0.670438 secs using 398% CPU
Optimizing NNI: done in 0.56353 secs using 398.8% CPU
Optimizing NNI: done in 0.607385 secs using 399.2% CPU
 84  WAG+F+I+R6    59750.194    333 120166.387   121574.261   121564.481
Optimizing NNI: done in 0.813311 secs using 399.2% CPU
Optimizing NNI: done in 0.445899 secs using 399.2% CPU
Iteration 110 / LogL: -36184.374 / Time: 0h:1m:16s (0h:0m:9s left)
Optimizing NNI: done in 0.855653 secs using 398.3% CPU
Optimizing NNI: done in 0.592017 secs using 398.1% CPU
Optimizing NNI: done in 0.919163 secs using 399.2% CPU
Optimizing NNI: done in 0.813086 secs using 398.7% CPU
Optimizing NNI: done in 0.85651 secs using 398.1% CPU
Optimizing NNI: done in 0.741247 secs using 398% CPU
Optimizing NNI: done in 0.649781 secs using 398.1% CPU
 85  WAG+F+I+R7    59743.566    335 120157.133   121600.209   121563.623
Optimizing NNI: done in 0.501759 secs using 399% CPU
Optimizing NNI: done in 0.737617 secs using 398.8% CPU
Optimizing NNI: done in 0.890168 secs using 398.2% CPU
Iteration 120 / LogL: -36182.533 / Time: 0h:1m:24s (0h:0m:2s left)
 97  JTT+R6        60074.266    313 120774.532   121878.824   122088.656
Optimizing NNI: done in 0.871298 secs using 397.5% CPU
  9  LG+R8         195184.144   1001 392370.288   2398374.288  396729.013
Optimizing NNI: done in 0.825658 secs using 398.5% CPU
Optimizing NNI: done in 0.60447 secs using 398.1% CPU
Optimizing NNI: done in 0.648481 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 124 ITERATIONS / Time: 0h:1m:27s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36182.532
Optimal log-likelihood: -36182.532
Proportion of invariable sites: 0.029
Gamma shape alpha: 2.674
Parameters optimization took 1 rounds (0.056 sec)
BEST SCORE FOUND : -36182.532
Total tree length: 19.567

Total number of iterations: 124
CPU time used for tree search: 342.327 sec (0h:5m:42s)
Wall-clock time used for tree search: 86.881 sec (0h:1m:26s)
Total CPU time used: 345.239 sec (0h:5m:45s)
Total wall-clock time used: 87.571 sec (0h:1m:27s)

===> START BOOTSTRAP REPLICATE NUMBER 3

Creating bootstrap alignment (seed: 956162)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36073.019
2. Current log-likelihood: -35246.285
3. Current log-likelihood: -35234.976
4. Current log-likelihood: -35234.801
Optimal log-likelihood: -35234.785
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.164
Parameters optimization took 4 rounds (0.355 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.084739 secs using 399.1% CPU
Computing ML distances took 0.084930 sec (of wall-clock time) 0.338346 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000179052 secs using 433.4% CPU
Constructing RapidNJ tree: done in 0.00243092 secs using 467.7% CPU
Computing RapidNJ tree took 0.002674 sec (of wall-clock time) 0.013519 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35758.842
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.436 second
Computing log-likelihood of 98 initial trees ... 2.349 seconds
Current best score: -35234.785

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.397797 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35200.852
Optimizing NNI: done in 0.394535 secs using 397.3% CPU
Optimizing NNI: done in 0.395497 secs using 396.5% CPU
Optimizing NNI: done in 0.373609 secs using 393.8% CPU
Optimizing NNI: done in 0.457801 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -35195.217
Optimizing NNI: done in 0.354609 secs using 399.7% CPU
 98  JTT+R7        60060.733    315 120751.466   121882.603   122073.987
Optimizing NNI: done in 0.362786 secs using 397% CPU
Optimizing NNI: done in 0.389649 secs using 397.6% CPU
Optimizing NNI: done in 0.341628 secs using 398.4% CPU
Optimizing NNI: done in 0.330456 secs using 397.6% CPU
Iteration 10 / LogL: -35204.625 / Time: 0h:0m:8s
Optimizing NNI: done in 0.334765 secs using 398.3% CPU
Optimizing NNI: done in 0.357135 secs using 399.2% CPU
Optimizing NNI: done in 0.333592 secs using 398.1% CPU
Optimizing NNI: done in 0.35853 secs using 398% CPU
Optimizing NNI: done in 0.379547 secs using 398.6% CPU
Optimizing NNI: done in 0.350156 secs using 398.6% CPU
Optimizing NNI: done in 0.339319 secs using 398.3% CPU
Optimizing NNI: done in 0.383277 secs using 398.1% CPU
Optimizing NNI: done in 0.368961 secs using 397.8% CPU
 99  JTT+R8        60055.294    317 120744.588   121903.277   122075.505
Optimizing NNI: done in 0.368977 secs using 398.2% CPU
Iteration 20 / LogL: -35204.539 / Time: 0h:0m:12s
Finish initializing candidate tree set (4)
Current best tree score: -35195.217 / CPU time: 11.406
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.674265 secs using 397.3% CPU
Optimizing NNI: done in 0.548029 secs using 395.8% CPU
Optimizing NNI: done in 0.584391 secs using 397.6% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35195.100
Optimizing NNI: done in 0.56775 secs using 398.3% CPU
Optimizing NNI: done in 0.530803 secs using 398.5% CPU
Optimizing NNI: done in 0.470591 secs using 399.1% CPU
Optimizing NNI: done in 0.733885 secs using 399.2% CPU
Optimizing NNI: done in 0.501259 secs using 398.8% CPU
Optimizing NNI: done in 0.55548 secs using 399.3% CPU
Optimizing NNI: done in 0.536762 secs using 398.9% CPU
Iteration 30 / LogL: -35198.986 / Time: 0h:0m:17s (0h:0m:46s left)
Optimizing NNI: done in 0.71361 secs using 399.7% CPU
Optimizing NNI: done in 0.595283 secs using 398.3% CPU
Optimizing NNI: done in 0.528585 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35195.075
Optimizing NNI: done in 0.517248 secs using 398% CPU
Optimizing NNI: done in 0.611993 secs using 399.3% CPU
Optimizing NNI: done in 0.522379 secs using 398.5% CPU
106  JTT+I+R6      60070.838    314 120769.676   121887.303   122087.998
Optimizing NNI: done in 0.600719 secs using 399.4% CPU
Optimizing NNI: done in 0.553598 secs using 398.5% CPU
Optimizing NNI: done in 0.588845 secs using 399.2% CPU
Optimizing NNI: done in 0.48377 secs using 399.2% CPU
Iteration 40 / LogL: -35195.441 / Time: 0h:0m:23s (0h:0m:39s left)
Optimizing NNI: done in 0.622803 secs using 398.7% CPU
Optimizing NNI: done in 0.385602 secs using 399.5% CPU
Optimizing NNI: done in 0.34868 secs using 399.5% CPU
Optimizing NNI: done in 0.500362 secs using 399.6% CPU
Optimizing NNI: done in 0.35773 secs using 399.4% CPU
Optimizing NNI: done in 0.391309 secs using 398.7% CPU
Optimizing NNI: done in 0.448323 secs using 398.6% CPU
Optimizing NNI: done in 0.351853 secs using 400.4% CPU
Optimizing NNI: done in 0.468077 secs using 399.6% CPU
Optimizing NNI: done in 0.310364 secs using 399.1% CPU
Iteration 50 / LogL: -35195.134 / Time: 0h:0m:28s (0h:0m:31s left)
Optimizing NNI: done in 0.544885 secs using 399.6% CPU
Optimizing NNI: done in 0.352623 secs using 398.7% CPU
Optimizing NNI: done in 0.401624 secs using 399.8% CPU
Optimizing NNI: done in 0.403757 secs using 399.6% CPU
Optimizing NNI: done in 0.478031 secs using 399.2% CPU
Optimizing NNI: done in 0.519146 secs using 399% CPU
Optimizing NNI: done in 0.49412 secs using 398.8% CPU
Optimizing NNI: done in 0.280044 secs using 400.7% CPU
Optimizing NNI: done in 0.455355 secs using 399.3% CPU
Optimizing NNI: done in 0.396487 secs using 399.4% CPU
Iteration 60 / LogL: -35198.838 / Time: 0h:0m:32s (0h:0m:24s left)
Optimizing NNI: done in 0.39866 secs using 399% CPU
Optimizing NNI: done in 0.378692 secs using 399.7% CPU
Optimizing NNI: done in 0.404158 secs using 398.9% CPU
107  JTT+I+R7      60059.283    316 120750.566   121895.389   122077.286
Optimizing NNI: done in 0.387707 secs using 399.5% CPU
Optimizing NNI: done in 0.332112 secs using 395.8% CPU
Optimizing NNI: done in 0.397938 secs using 399.7% CPU
Optimizing NNI: done in 0.296494 secs using 397.8% CPU
Optimizing NNI: done in 0.349303 secs using 399.2% CPU
Optimizing NNI: done in 0.402995 secs using 398.9% CPU
Optimizing NNI: done in 0.358406 secs using 400% CPU
Iteration 70 / LogL: -35195.447 / Time: 0h:0m:36s (0h:0m:18s left)
Optimizing NNI: done in 0.4594 secs using 399.4% CPU
119  JTT+F+R6      60066.585    332 120797.169   122187.811   122191.064
Optimizing NNI: done in 0.382753 secs using 399.5% CPU
Optimizing NNI: done in 0.387625 secs using 399.7% CPU
Optimizing NNI: done in 0.432545 secs using 399.3% CPU
Optimizing NNI: done in 0.47059 secs using 399.3% CPU
Optimizing NNI: done in 0.310293 secs using 398.7% CPU
Optimizing NNI: done in 0.381907 secs using 398.5% CPU
Optimizing NNI: done in 0.485755 secs using 399.6% CPU
Optimizing NNI: done in 0.443638 secs using 399.5% CPU
Optimizing NNI: done in 0.409178 secs using 399.5% CPU
Iteration 80 / LogL: -35197.367 / Time: 0h:0m:40s (0h:0m:12s left)
Optimizing NNI: done in 0.317135 secs using 399.1% CPU
Optimizing NNI: done in 0.435485 secs using 399.2% CPU
Optimizing NNI: done in 0.428624 secs using 399.5% CPU
Optimizing NNI: done in 0.306891 secs using 399.4% CPU
Optimizing NNI: done in 0.406793 secs using 399.7% CPU
Optimizing NNI: done in 0.441393 secs using 399.3% CPU
Optimizing NNI: done in 0.361722 secs using 397.9% CPU
Optimizing NNI: done in 0.363917 secs using 398.8% CPU
Optimizing NNI: done in 0.414526 secs using 398% CPU
Optimizing NNI: done in 0.589866 secs using 398.5% CPU
Iteration 90 / LogL: -35195.303 / Time: 0h:0m:44s (0h:0m:7s left)
Optimizing NNI: done in 0.465287 secs using 399% CPU
Optimizing NNI: done in 0.363564 secs using 399.4% CPU
Optimizing NNI: done in 0.434139 secs using 398.3% CPU
Optimizing NNI: done in 0.455765 secs using 398.5% CPU
120  JTT+F+R7      60056.320    334 120780.640   122205.990   122182.932
Optimizing NNI: done in 0.330984 secs using 399.3% CPU
Optimizing NNI: done in 0.344781 secs using 397.5% CPU
Optimizing NNI: done in 0.408503 secs using 400.1% CPU
Optimizing NNI: done in 0.432861 secs using 398.4% CPU
Optimizing NNI: done in 0.482959 secs using 398% CPU
Optimizing NNI: done in 0.385549 secs using 398.7% CPU
Iteration 100 / LogL: -35195.583 / Time: 0h:0m:48s (0h:0m:2s left)
Optimizing NNI: done in 0.347829 secs using 398.6% CPU
Optimizing NNI: done in 0.375743 secs using 398.9% CPU
Optimizing NNI: done in 0.378638 secs using 398.5% CPU
Optimizing NNI: done in 0.353088 secs using 398% CPU
Optimizing NNI: done in 0.41196 secs using 397.6% CPU
Optimizing NNI: done in 0.244156 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 106 ITERATIONS / Time: 0h:0m:50s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35195.075
Optimal log-likelihood: -35195.073
Proportion of invariable sites: 0.021
Gamma shape alpha: 2.206
Parameters optimization took 1 rounds (0.046 sec)
BEST SCORE FOUND : -35195.073
Total tree length: 19.432

Total number of iterations: 106
CPU time used for tree search: 195.468 sec (0h:3m:15s)
Wall-clock time used for tree search: 49.965 sec (0h:0m:49s)
Total CPU time used: 198.858 sec (0h:3m:18s)
Total wall-clock time used: 50.768 sec (0h:0m:50s)

===> START BOOTSTRAP REPLICATE NUMBER 4

Creating bootstrap alignment (seed: 956163)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37497.802
2. Current log-likelihood: -36629.628
3. Current log-likelihood: -36615.135
121  JTT+F+R8      60049.742    336 120771.484   122232.542   122182.173
4. Current log-likelihood: -36614.659
Optimal log-likelihood: -36614.571
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.496
Parameters optimization took 4 rounds (0.293 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0781901 secs using 395.6% CPU
Computing ML distances took 0.078331 sec (of wall-clock time) 0.309640 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000159979 secs using 426.9% CPU
Constructing RapidNJ tree: done in 0.00214195 secs using 435.8% CPU
Computing RapidNJ tree took 0.002364 sec (of wall-clock time) 0.010974 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36992.105
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.552 second
Computing log-likelihood of 98 initial trees ... 1.659 seconds
Current best score: -36610.479

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.227675 secs using 397.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36547.897
Optimizing NNI: done in 0.265092 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36547.643
Optimizing NNI: done in 0.272553 secs using 397.7% CPU
Optimizing NNI: done in 0.247079 secs using 397.6% CPU
Optimizing NNI: done in 0.297668 secs using 398.8% CPU
Optimizing NNI: done in 0.289391 secs using 396.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -36547.640
Optimizing NNI: done in 0.256223 secs using 399% CPU
Optimizing NNI: done in 0.329406 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
 11  LG+R8         105537.254   549 212172.509   816072.509   214382.709
BETTER TREE FOUND at iteration 8: -36546.740
Optimizing NNI: done in 0.265955 secs using 397.3% CPU
Optimizing NNI: done in 0.266986 secs using 397.8% CPU
Iteration 10 / LogL: -36551.997 / Time: 0h:0m:6s
Optimizing NNI: done in 0.278002 secs using 397.5% CPU
Optimizing NNI: done in 0.369124 secs using 398.8% CPU
Optimizing NNI: done in 0.27834 secs using 399.3% CPU
Optimizing NNI: done in 0.294059 secs using 398.5% CPU
Optimizing NNI: done in 0.306245 secs using 397.8% CPU
Optimizing NNI: done in 0.301172 secs using 397.7% CPU
Optimizing NNI: done in 0.275509 secs using 399.1% CPU
Optimizing NNI: done in 0.254748 secs using 398.6% CPU
Optimizing NNI: done in 0.238059 secs using 398.5% CPU
Optimizing NNI: done in 0.278068 secs using 398.9% CPU
Iteration 20 / LogL: -36576.175 / Time: 0h:0m:9s
Finish initializing candidate tree set (10)
Current best tree score: -36546.740 / CPU time: 9.059
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.345657 secs using 397.2% CPU
Optimizing NNI: done in 0.424381 secs using 397.2% CPU
Optimizing NNI: done in 0.828206 secs using 398.3% CPU
Optimizing NNI: done in 0.530697 secs using 397.7% CPU
Optimizing NNI: done in 0.626924 secs using 398.2% CPU
Optimizing NNI: done in 0.595809 secs using 398.4% CPU
BETTER TREE FOUND at iteration 26: -36546.740
Optimizing NNI: done in 0.812204 secs using 398.4% CPU
Optimizing NNI: done in 0.489835 secs using 398.9% CPU
Optimizing NNI: done in 0.371757 secs using 397.7% CPU
Optimizing NNI: done in 0.436572 secs using 398% CPU
Iteration 30 / LogL: -36627.298 / Time: 0h:0m:15s (0h:0m:49s left)
Optimizing NNI: done in 0.419736 secs using 398% CPU
122  JTT+F+R9      60048.136    338 120772.273   122270.077   122191.359
Optimizing NNI: done in 0.558625 secs using 396.6% CPU
Optimizing NNI: done in 0.891081 secs using 398.2% CPU
Optimizing NNI: done in 0.377785 secs using 398.8% CPU
Optimizing NNI: done in 0.394526 secs using 399% CPU
Optimizing NNI: done in 0.397296 secs using 399.8% CPU
Optimizing NNI: done in 0.389502 secs using 398.9% CPU
Optimizing NNI: done in 0.764727 secs using 399.1% CPU
Optimizing NNI: done in 0.379468 secs using 399.1% CPU
Optimizing NNI: done in 0.549971 secs using 398.4% CPU
Iteration 40 / LogL: -36569.511 / Time: 0h:0m:20s (0h:0m:44s left)
Optimizing NNI: done in 0.745696 secs using 399.1% CPU
Optimizing NNI: done in 0.60156 secs using 398.9% CPU
Optimizing NNI: done in 0.651176 secs using 396.9% CPU
Optimizing NNI: done in 0.529973 secs using 399% CPU
Optimizing NNI: done in 0.73124 secs using 398.9% CPU
128  JTT+F+I+R6    60063.360    333 120792.720   122200.594   122190.814
Optimizing NNI: done in 0.584242 secs using 398.4% CPU
Optimizing NNI: done in 0.813195 secs using 398.8% CPU
Optimizing NNI: done in 0.421798 secs using 397.6% CPU
Optimizing NNI: done in 0.374504 secs using 398.9% CPU
Optimizing NNI: done in 0.324639 secs using 399% CPU
Iteration 50 / LogL: -36551.515 / Time: 0h:0m:26s (0h:0m:40s left)
Optimizing NNI: done in 0.323658 secs using 398.1% CPU
Optimizing NNI: done in 0.779859 secs using 397.6% CPU
Optimizing NNI: done in 0.291794 secs using 399.2% CPU
Optimizing NNI: done in 0.681702 secs using 399.3% CPU
Optimizing NNI: done in 0.358459 secs using 399.8% CPU
Optimizing NNI: done in 0.387342 secs using 399.8% CPU
Optimizing NNI: done in 0.732995 secs using 399.2% CPU
Optimizing NNI: done in 0.471427 secs using 399.1% CPU
Optimizing NNI: done in 0.467059 secs using 399% CPU
Optimizing NNI: done in 0.741088 secs using 398% CPU
Iteration 60 / LogL: -36547.408 / Time: 0h:0m:31s (0h:0m:35s left)
Optimizing NNI: done in 0.37535 secs using 399.5% CPU
Optimizing NNI: done in 0.356431 secs using 399.8% CPU
Optimizing NNI: done in 0.345916 secs using 398.4% CPU
Optimizing NNI: done in 0.680632 secs using 398.8% CPU
 10  LG+R9         195175.348   1003 392356.697   2406380.697  396724.130
Optimizing NNI: done in 0.755801 secs using 399.2% CPU
Optimizing NNI: done in 0.410598 secs using 400.1% CPU
Optimizing NNI: done in 0.775601 secs using 399.5% CPU
Optimizing NNI: done in 0.321246 secs using 400.2% CPU
Optimizing NNI: done in 0.829943 secs using 398.9% CPU
Optimizing NNI: done in 0.740329 secs using 398% CPU
Iteration 70 / LogL: -36547.427 / Time: 0h:0m:36s (0h:0m:29s left)
129  JTT+F+I+R7    60054.636    335 120779.271   122222.348   122185.762
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.559894 secs using 399.5% CPU
Optimizing NNI: done in 0.558423 secs using 398.4% CPU
Optimizing NNI: done in 0.508484 secs using 399.1% CPU
141  Q.pfam+R6     59479.017    313 119584.035   120688.327   120898.159
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.705106 secs using 399.3% CPU
Optimizing NNI: done in 0.739246 secs using 398.9% CPU
Optimizing NNI: done in 0.377985 secs using 399.3% CPU
Optimizing NNI: done in 0.360017 secs using 399.9% CPU
142  Q.pfam+R7     59473.613    315 119577.227   120708.363   120899.747
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.616241 secs using 399.5% CPU
Optimizing NNI: done in 0.445539 secs using 399% CPU
Optimizing NNI: done in 0.361193 secs using 398.8% CPU
Iteration 80 / LogL: -36547.877 / Time: 0h:0m:42s (0h:0m:24s left)
Optimizing NNI: done in 0.473375 secs using 398.6% CPU
Optimizing NNI: done in 0.339532 secs using 399.4% CPU
Optimizing NNI: done in 0.378108 secs using 399.7% CPU
Optimizing NNI: done in 0.390396 secs using 398.8% CPU
Optimizing NNI: done in 0.380874 secs using 399.2% CPU
Optimizing NNI: done in 0.396458 secs using 398.2% CPU
Optimizing NNI: done in 0.595667 secs using 399.3% CPU
Optimizing NNI: done in 0.491473 secs using 398.8% CPU
Optimizing NNI: done in 0.560962 secs using 399.6% CPU
Optimizing NNI: done in 0.649951 secs using 399.6% CPU
Iteration 90 / LogL: -36547.407 / Time: 0h:0m:46s (0h:0m:18s left)
Optimizing NNI: done in 0.387271 secs using 399.6% CPU
Optimizing NNI: done in 0.328271 secs using 399.4% CPU
150  Q.pfam+I+R6   59478.275    314 119584.550   120702.177   120902.872
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.841315 secs using 399.7% CPU
Optimizing NNI: done in 0.466312 secs using 399.9% CPU
Optimizing NNI: done in 0.691051 secs using 399.7% CPU
Optimizing NNI: done in 0.644594 secs using 397.5% CPU
Optimizing NNI: done in 0.429794 secs using 399.5% CPU
Optimizing NNI: done in 0.734026 secs using 398.8% CPU
Optimizing NNI: done in 0.648461 secs using 399.2% CPU
Optimizing NNI: done in 0.77424 secs using 399.2% CPU
Iteration 100 / LogL: -36546.743 / Time: 0h:0m:52s (0h:0m:13s left)
Optimizing NNI: done in 0.333633 secs using 399.7% CPU
Optimizing NNI: done in 0.387079 secs using 399.7% CPU
Optimizing NNI: done in 0.739939 secs using 399.8% CPU
151  Q.pfam+I+R7   59473.897    316 119579.795   120724.617   120906.514
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.534052 secs using 399.7% CPU
Optimizing NNI: done in 0.369382 secs using 399.3% CPU
Optimizing NNI: done in 0.79299 secs using 398.8% CPU
Optimizing NNI: done in 0.393459 secs using 398.6% CPU
163  Q.pfam+F+R6   59490.640    332 119645.281   121035.922   121039.176
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.389136 secs using 397.7% CPU
Optimizing NNI: done in 0.514312 secs using 398.2% CPU
Optimizing NNI: done in 0.417392 secs using 397.7% CPU
Iteration 110 / LogL: -36546.978 / Time: 0h:0m:57s (0h:0m:8s left)
164  Q.pfam+F+R7   59486.230    334 119640.460   121065.810   121042.752
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.746874 secs using 398.1% CPU
Optimizing NNI: done in 0.483254 secs using 398.1% CPU
Optimizing NNI: done in 0.832448 secs using 399.6% CPU
Optimizing NNI: done in 0.449926 secs using 399.3% CPU
Optimizing NNI: done in 0.755209 secs using 399.7% CPU
Optimizing NNI: done in 0.681922 secs using 398.8% CPU
Optimizing NNI: done in 0.574306 secs using 399.3% CPU
Optimizing NNI: done in 0.633266 secs using 398.9% CPU
Optimizing NNI: done in 0.785236 secs using 399.4% CPU
Optimizing NNI: done in 0.461297 secs using 398.3% CPU
Iteration 120 / LogL: -36546.766 / Time: 0h:1m:4s (0h:0m:3s left)
Optimizing NNI: done in 0.33188 secs using 399.4% CPU
Optimizing NNI: done in 0.439946 secs using 399.5% CPU
Optimizing NNI: done in 0.340692 secs using 400% CPU
Optimizing NNI: done in 0.573837 secs using 398.8% CPU
Optimizing NNI: done in 0.520672 secs using 399.3% CPU
Optimizing NNI: done in 0.388133 secs using 399% CPU
172  Q.pfam+F+I+R6 59490.182    333 119646.364   121054.237   121044.457
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.579746 secs using 399.5% CPU
TREE SEARCH COMPLETED AFTER 127 ITERATIONS / Time: 0h:1m:7s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36546.740
Optimal log-likelihood: -36546.739
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.506
Parameters optimization took 1 rounds (0.054 sec)
BEST SCORE FOUND : -36546.739
Total tree length: 20.269

Total number of iterations: 127
CPU time used for tree search: 263.129 sec (0h:4m:23s)
Wall-clock time used for tree search: 66.978 sec (0h:1m:6s)
Total CPU time used: 265.480 sec (0h:4m:25s)
Total wall-clock time used: 67.545 sec (0h:1m:7s)

===> START BOOTSTRAP REPLICATE NUMBER 5

Creating bootstrap alignment (seed: 956164)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37349.563
2. Current log-likelihood: -36454.513
3. Current log-likelihood: -36433.467
4. Current log-likelihood: -36432.384
Optimal log-likelihood: -36432.242
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.534
Parameters optimization took 4 rounds (0.284 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0813899 secs using 400% CPU
Computing ML distances took 0.081535 sec (of wall-clock time) 0.326016 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000166178 secs using 430.3% CPU
Constructing RapidNJ tree: done in 0.00222492 secs using 510.4% CPU
Computing RapidNJ tree took 0.002447 sec (of wall-clock time) 0.012352 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36694.458
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.555 second
Computing log-likelihood of 98 initial trees ... 1.630 seconds
Current best score: -36401.381

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.228627 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36319.377
Optimizing NNI: done in 0.462597 secs using 400.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36319.294
Optimizing NNI: done in 0.266485 secs using 399.4% CPU
Optimizing NNI: done in 0.294176 secs using 398.7% CPU
Optimizing NNI: done in 0.303057 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -36316.234
Optimizing NNI: done in 0.246784 secs using 399.9% CPU
Optimizing NNI: done in 0.250413 secs using 398.3% CPU
Optimizing NNI: done in 0.281649 secs using 399% CPU
Optimizing NNI: done in 0.239629 secs using 399.5% CPU
Optimizing NNI: done in 0.294887 secs using 398.2% CPU
Iteration 10 / LogL: -36319.370 / Time: 0h:0m:6s
Optimizing NNI: done in 0.278964 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 11: -36315.407
Optimizing NNI: done in 0.238431 secs using 399.8% CPU
Optimizing NNI: done in 0.244915 secs using 397.3% CPU
Optimizing NNI: done in 0.287568 secs using 399.4% CPU
Optimizing NNI: done in 0.494559 secs using 397.6% CPU
 11  LG+R10        195171.997   1005 392353.994   2414413.994  396730.136
Optimizing NNI: done in 0.27941 secs using 399% CPU
173  Q.pfam+F+I+R7 59486.432    335 119642.864   121085.941   121049.354
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.487022 secs using 398.6% CPU
Optimizing NNI: done in 0.342952 secs using 399.2% CPU
Optimizing NNI: done in 0.265224 secs using 399.1% CPU
Optimizing NNI: done in 0.231475 secs using 398.8% CPU
Iteration 20 / LogL: -36315.530 / Time: 0h:0m:10s
Finish initializing candidate tree set (6)
Current best tree score: -36315.407 / CPU time: 9.549
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.375463 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36315.300
Optimizing NNI: done in 0.419771 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -36315.247
Optimizing NNI: done in 0.271777 secs using 399.1% CPU
Optimizing NNI: done in 0.389554 secs using 398.7% CPU
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Optimizing NNI: done in 0.393594 secs using 398.7% CPU
Iteration 30 / LogL: -36315.357 / Time: 0h:0m:13s (0h:0m:43s left)
Optimizing NNI: done in 0.437301 secs using 399% CPU
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Optimizing NNI: done in 0.340354 secs using 398.4% CPU
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Optimizing NNI: done in 0.356647 secs using 400.2% CPU
Iteration 40 / LogL: -36315.355 / Time: 0h:0m:17s (0h:0m:37s left)
Optimizing NNI: done in 0.3537 secs using 399.3% CPU
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Optimizing NNI: done in 0.370193 secs using 399% CPU
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Optimizing NNI: done in 0.752906 secs using 399.6% CPU
Optimizing NNI: done in 0.34665 secs using 399.1% CPU
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Optimizing NNI: done in 0.290272 secs using 399.5% CPU
Iteration 50 / LogL: -36315.446 / Time: 0h:0m:21s (0h:0m:32s left)
Optimizing NNI: done in 0.366379 secs using 400.2% CPU
Optimizing NNI: done in 0.339218 secs using 399.5% CPU
 20  LG+F+R8       194402.294   1020 390844.587   2473684.587  395286.045
Optimizing NNI: done in 0.368949 secs using 396.8% CPU
Optimizing NNI: done in 0.404904 secs using 399.3% CPU
Optimizing NNI: done in 0.363027 secs using 399% CPU
185  Q.bird+R6     61133.071    313 122892.142   123996.434   124206.266
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.432638 secs using 399.6% CPU
Optimizing NNI: done in 0.434993 secs using 399.5% CPU
Optimizing NNI: done in 0.432308 secs using 398.1% CPU
Optimizing NNI: done in 0.383706 secs using 398.7% CPU
Optimizing NNI: done in 0.664857 secs using 399.3% CPU
Iteration 60 / LogL: -36316.995 / Time: 0h:0m:26s (0h:0m:27s left)
Optimizing NNI: done in 0.436473 secs using 399.2% CPU
Optimizing NNI: done in 0.541931 secs using 399.3% CPU
Optimizing NNI: done in 0.839646 secs using 398.9% CPU
Optimizing NNI: done in 0.369008 secs using 398.7% CPU
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Optimizing NNI: done in 0.365881 secs using 399.8% CPU
Optimizing NNI: done in 0.38346 secs using 398.5% CPU
Iteration 70 / LogL: -36315.596 / Time: 0h:0m:30s (0h:0m:23s left)
Optimizing NNI: done in 0.456408 secs using 398.8% CPU
Optimizing NNI: done in 0.4181 secs using 399% CPU
Optimizing NNI: done in 0.565597 secs using 398.9% CPU
Optimizing NNI: done in 0.413482 secs using 399.4% CPU
Optimizing NNI: done in 0.435736 secs using 399.8% CPU
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Optimizing NNI: done in 0.366437 secs using 399.1% CPU
Optimizing NNI: done in 0.352166 secs using 398.9% CPU
Optimizing NNI: done in 0.442772 secs using 398% CPU
Optimizing NNI: done in 0.59512 secs using 398.3% CPU
Iteration 80 / LogL: -36316.301 / Time: 0h:0m:35s (0h:0m:18s left)
Optimizing NNI: done in 0.553293 secs using 399.6% CPU
Optimizing NNI: done in 0.540367 secs using 399.2% CPU
Optimizing NNI: done in 0.684572 secs using 397.8% CPU
Optimizing NNI: done in 0.393497 secs using 399% CPU
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Optimizing NNI: done in 0.428418 secs using 399.1% CPU
Optimizing NNI: done in 0.464842 secs using 399% CPU
Optimizing NNI: done in 0.377678 secs using 399.8% CPU
Optimizing NNI: done in 0.284038 secs using 399.2% CPU
186  Q.bird+R7     61117.291    315 122864.582   123995.719   124187.103
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.449095 secs using 399.1% CPU
Iteration 90 / LogL: -36318.361 / Time: 0h:0m:39s (0h:0m:14s left)
Optimizing NNI: done in 0.314151 secs using 399.5% CPU
Optimizing NNI: done in 0.269127 secs using 398% CPU
Optimizing NNI: done in 0.549638 secs using 399.2% CPU
Optimizing NNI: done in 0.380298 secs using 399.3% CPU
Optimizing NNI: done in 0.351529 secs using 397.4% CPU
Optimizing NNI: done in 0.381361 secs using 398.7% CPU
Optimizing NNI: done in 0.408796 secs using 399.8% CPU
Optimizing NNI: done in 0.45546 secs using 399.4% CPU
Optimizing NNI: done in 0.406046 secs using 398.2% CPU
Optimizing NNI: done in 0.400862 secs using 398.9% CPU
Iteration 100 / LogL: -36315.389 / Time: 0h:0m:43s (0h:0m:9s left)
Optimizing NNI: done in 0.370534 secs using 396.9% CPU
Optimizing NNI: done in 0.402854 secs using 399.3% CPU
Optimizing NNI: done in 0.419989 secs using 396.7% CPU
Optimizing NNI: done in 0.414226 secs using 398.7% CPU
Optimizing NNI: done in 0.321935 secs using 398.9% CPU
187  Q.bird+R8     61111.896    317 122857.793   124016.483   124188.711
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.329139 secs using 399.7% CPU
Optimizing NNI: done in 0.393873 secs using 399% CPU
Optimizing NNI: done in 0.282322 secs using 400.2% CPU
Optimizing NNI: done in 0.411031 secs using 399.1% CPU
Optimizing NNI: done in 0.387187 secs using 399.3% CPU
Iteration 110 / LogL: -36315.304 / Time: 0h:0m:47s (0h:0m:5s left)
Optimizing NNI: done in 0.284756 secs using 399.9% CPU
Optimizing NNI: done in 0.463295 secs using 399.3% CPU
Optimizing NNI: done in 0.479173 secs using 398.5% CPU
Optimizing NNI: done in 0.389016 secs using 398.6% CPU
Optimizing NNI: done in 0.349306 secs using 399.7% CPU
Optimizing NNI: done in 0.372223 secs using 399.7% CPU
Optimizing NNI: done in 0.345171 secs using 398.6% CPU
Optimizing NNI: done in 0.370741 secs using 399.7% CPU
Optimizing NNI: done in 0.47861 secs using 398.8% CPU
Optimizing NNI: done in 0.466008 secs using 398.8% CPU
Iteration 120 / LogL: -36315.323 / Time: 0h:0m:51s (0h:0m:0s left)
Optimizing NNI: done in 0.474345 secs using 398.5% CPU
Optimizing NNI: done in 0.405889 secs using 398.6% CPU
Optimizing NNI: done in 0.4418 secs using 398.6% CPU
TREE SEARCH COMPLETED AFTER 123 ITERATIONS / Time: 0h:0m:52s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36315.247
Optimal log-likelihood: -36315.247
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.527
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36315.247
Total tree length: 20.169

Total number of iterations: 123
CPU time used for tree search: 204.841 sec (0h:3m:24s)
Wall-clock time used for tree search: 52.346 sec (0h:0m:52s)
Total CPU time used: 207.184 sec (0h:3m:27s)
Total wall-clock time used: 52.906 sec (0h:0m:52s)

===> START BOOTSTRAP REPLICATE NUMBER 6

Creating bootstrap alignment (seed: 956165)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.021 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37180.924
2. Current log-likelihood: -36336.383
3. Current log-likelihood: -36321.215
4. Current log-likelihood: -36320.857
Optimal log-likelihood: -36320.785
Proportion of invariable sites: 0.022
Gamma shape alpha: 2.813
Parameters optimization took 4 rounds (0.276 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0798221 secs using 398.7% CPU
Computing ML distances took 0.079964 sec (of wall-clock time) 0.318570 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000163794 secs using 424.9% CPU
Constructing RapidNJ tree: done in 0.00216103 secs using 509% CPU
Computing RapidNJ tree took 0.002396 sec (of wall-clock time) 0.012141 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37033.983
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.451 second
Computing log-likelihood of 98 initial trees ... 1.673 seconds
Current best score: -36320.785

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.199309 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36292.182
Optimizing NNI: done in 0.250802 secs using 399.8% CPU
Optimizing NNI: done in 0.2724 secs using 397.9% CPU
Optimizing NNI: done in 0.270763 secs using 400% CPU
Optimizing NNI: done in 0.226369 secs using 398.5% CPU
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Optimizing NNI: done in 0.286982 secs using 398.7% CPU
Optimizing NNI: done in 0.278677 secs using 399.5% CPU
Optimizing NNI: done in 0.222311 secs using 398.6% CPU
Optimizing NNI: done in 0.239553 secs using 398.2% CPU
Iteration 10 / LogL: -36292.818 / Time: 0h:0m:6s
 21  LG+F+R9       194396.917   1022 390837.834   2481849.834  395288.000
Optimizing NNI: done in 0.245833 secs using 396.7% CPU
Optimizing NNI: done in 0.245449 secs using 399.4% CPU
Optimizing NNI: done in 0.222432 secs using 399.1% CPU
Optimizing NNI: done in 0.240687 secs using 399.1% CPU
194  Q.bird+I+R6   61131.985    314 122891.970   124009.597   124210.292
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.225231 secs using 399% CPU
Optimizing NNI: done in 0.274717 secs using 399.1% CPU
Optimizing NNI: done in 0.277303 secs using 397.7% CPU
Optimizing NNI: done in 0.273845 secs using 398.8% CPU
Optimizing NNI: done in 0.24686 secs using 399.1% CPU
Optimizing NNI: done in 0.262871 secs using 398% CPU
Iteration 20 / LogL: -36293.701 / Time: 0h:0m:8s
Finish initializing candidate tree set (5)
Current best tree score: -36292.182 / CPU time: 8.304
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.468577 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36291.108
Optimizing NNI: done in 0.332492 secs using 398.5% CPU
Optimizing NNI: done in 0.369209 secs using 399.2% CPU
Optimizing NNI: done in 0.391026 secs using 399.1% CPU
Optimizing NNI: done in 0.498697 secs using 398.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -36291.106
Optimizing NNI: done in 0.31099 secs using 399% CPU
Optimizing NNI: done in 0.406779 secs using 398.8% CPU
Optimizing NNI: done in 0.529312 secs using 399.1% CPU
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Optimizing NNI: done in 0.437103 secs using 399.1% CPU
Iteration 30 / LogL: -36294.518 / Time: 0h:0m:13s (0h:0m:41s left)
Optimizing NNI: done in 0.284946 secs using 399.3% CPU
Optimizing NNI: done in 0.540959 secs using 398.5% CPU
Optimizing NNI: done in 0.545407 secs using 398.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -36291.100
Optimizing NNI: done in 0.519531 secs using 398.7% CPU
Optimizing NNI: done in 0.471706 secs using 398.6% CPU
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Optimizing NNI: done in 0.331138 secs using 399.3% CPU
Optimizing NNI: done in 0.54198 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -36290.725
Optimizing NNI: done in 0.468243 secs using 399.1% CPU
Optimizing NNI: done in 0.445151 secs using 398.2% CPU
Iteration 40 / LogL: -36290.726 / Time: 0h:0m:17s (0h:0m:45s left)
Optimizing NNI: done in 0.365742 secs using 399% CPU
Optimizing NNI: done in 0.463814 secs using 398.6% CPU
Optimizing NNI: done in 0.522698 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 43: -36289.871
Optimizing NNI: done in 0.602545 secs using 399.1% CPU
Optimizing NNI: done in 0.405052 secs using 399.6% CPU
Optimizing NNI: done in 0.622138 secs using 399.5% CPU
Optimizing NNI: done in 0.531674 secs using 398.9% CPU
 31  WAG+R8        196252.507   1001 394507.014   2400511.014  398865.738
Optimizing NNI: done in 0.586483 secs using 398.9% CPU
195  Q.bird+I+R7   61116.198    316 122864.396   124009.219   124191.115
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.552148 secs using 398.3% CPU
Optimizing NNI: done in 0.518054 secs using 398.9% CPU
Iteration 50 / LogL: -36290.496 / Time: 0h:0m:23s (0h:0m:43s left)
Optimizing NNI: done in 0.354632 secs using 399.2% CPU
Optimizing NNI: done in 0.326706 secs using 399.4% CPU
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Optimizing NNI: done in 0.457015 secs using 397.9% CPU
Iteration 60 / LogL: -36296.125 / Time: 0h:0m:28s (0h:0m:39s left)
Optimizing NNI: done in 0.3109 secs using 398.1% CPU
 12  LG+R9         105459.436   551 212020.872   820324.872   214239.124
Optimizing NNI: done in 0.512227 secs using 398.3% CPU
Optimizing NNI: done in 0.497682 secs using 398.7% CPU
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Optimizing NNI: done in 0.437946 secs using 399.3% CPU
Optimizing NNI: done in 0.571823 secs using 399.4% CPU
Iteration 70 / LogL: -36324.453 / Time: 0h:0m:33s (0h:0m:35s left)
Optimizing NNI: done in 0.418917 secs using 399.5% CPU
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Optimizing NNI: done in 0.473271 secs using 399.3% CPU
207  Q.bird+F+R6   61244.582    332 123153.164   124543.806   124547.059
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.556507 secs using 399.5% CPU
Iteration 80 / LogL: -36289.996 / Time: 0h:0m:38s (0h:0m:30s left)
Optimizing NNI: done in 0.418522 secs using 398.4% CPU
Optimizing NNI: done in 0.503554 secs using 398.8% CPU
Optimizing NNI: done in 0.368586 secs using 399% CPU
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Optimizing NNI: done in 0.36318 secs using 399.4% CPU
Iteration 90 / LogL: -36290.742 / Time: 0h:0m:42s (0h:0m:25s left)
Optimizing NNI: done in 0.56685 secs using 399.3% CPU
Optimizing NNI: done in 0.41716 secs using 398.6% CPU
Optimizing NNI: done in 0.509872 secs using 398.1% CPU
Optimizing NNI: done in 0.406283 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36289.756
Optimizing NNI: done in 0.672338 secs using 397.3% CPU
Optimizing NNI: done in 0.376166 secs using 398.2% CPU
Optimizing NNI: done in 0.477909 secs using 398.7% CPU
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Optimizing NNI: done in 0.442542 secs using 399% CPU
Optimizing NNI: done in 0.49023 secs using 399.3% CPU
Iteration 100 / LogL: -36290.287 / Time: 0h:0m:47s (0h:0m:20s left)
Optimizing NNI: done in 0.531085 secs using 399% CPU
Optimizing NNI: done in 0.585889 secs using 398.1% CPU
Optimizing NNI: done in 0.615335 secs using 398.2% CPU
208  Q.bird+F+R7   61227.499    334 123122.999   124548.349   124525.291
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.407951 secs using 398.7% CPU
BETTER TREE FOUND at iteration 104: -36289.747
Optimizing NNI: done in 0.437256 secs using 397.5% CPU
Optimizing NNI: done in 0.405564 secs using 398.1% CPU
BETTER TREE FOUND at iteration 106: -36289.745
Optimizing NNI: done in 0.483107 secs using 399.3% CPU
Optimizing NNI: done in 0.490842 secs using 399.2% CPU
 32  WAG+R9        196242.300   1003 394490.599   2408514.599  398858.033
Optimizing NNI: done in 0.487702 secs using 397.8% CPU
Optimizing NNI: done in 0.478469 secs using 398.8% CPU
Iteration 110 / LogL: -36290.740 / Time: 0h:0m:52s (0h:0m:46s left)
Optimizing NNI: done in 0.383111 secs using 399.5% CPU
Optimizing NNI: done in 0.433797 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -36289.744
Optimizing NNI: done in 0.52099 secs using 398.1% CPU
Optimizing NNI: done in 0.585349 secs using 398.7% CPU
209  Q.bird+F+R8   61224.264    336 123120.529   124581.587   124531.218
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.352992 secs using 399.2% CPU
Optimizing NNI: done in 0.453923 secs using 398.5% CPU
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Iteration 120 / LogL: -36292.757 / Time: 0h:0m:57s (0h:0m:41s left)
Optimizing NNI: done in 0.504061 secs using 398.8% CPU
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Iteration 130 / LogL: -36290.733 / Time: 0h:1m:3s (0h:0m:37s left)
Optimizing NNI: done in 0.415315 secs using 397.5% CPU
Optimizing NNI: done in 0.474075 secs using 398.1% CPU
Optimizing NNI: done in 0.569053 secs using 399.2% CPU
Optimizing NNI: done in 0.437352 secs using 399.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -36289.743
Optimizing NNI: done in 0.387569 secs using 398.6% CPU
Optimizing NNI: done in 0.381473 secs using 397.8% CPU
Optimizing NNI: done in 0.506546 secs using 398.6% CPU
Optimizing NNI: done in 0.496164 secs using 399.1% CPU
Optimizing NNI: done in 0.322868 secs using 399.2% CPU
Optimizing NNI: done in 0.60108 secs using 399.4% CPU
Iteration 140 / LogL: -36290.740 / Time: 0h:1m:7s (0h:0m:32s left)
Optimizing NNI: done in 0.355828 secs using 397.3% CPU
Optimizing NNI: done in 0.403936 secs using 398.7% CPU
Optimizing NNI: done in 0.471865 secs using 399.3% CPU
Optimizing NNI: done in 0.495716 secs using 399.1% CPU
Optimizing NNI: done in 0.373899 secs using 399% CPU
Optimizing NNI: done in 0.488937 secs using 397.6% CPU
216  Q.bird+F+I+R6 61244.077    333 123154.154   124562.027   124552.247
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.490429 secs using 397.9% CPU
Optimizing NNI: done in 0.547202 secs using 398.9% CPU
Optimizing NNI: done in 0.552581 secs using 399.6% CPU
Optimizing NNI: done in 0.429267 secs using 399.3% CPU
Iteration 150 / LogL: -36290.016 / Time: 0h:1m:12s (0h:0m:27s left)
Optimizing NNI: done in 0.583721 secs using 399.7% CPU
Optimizing NNI: done in 0.560087 secs using 399.4% CPU
Optimizing NNI: done in 0.604835 secs using 398.9% CPU
Optimizing NNI: done in 0.328854 secs using 397.5% CPU
Optimizing NNI: done in 0.551098 secs using 399.5% CPU
Optimizing NNI: done in 0.498543 secs using 399.5% CPU
Optimizing NNI: done in 0.495709 secs using 399.3% CPU
Optimizing NNI: done in 0.361522 secs using 398.5% CPU
Optimizing NNI: done in 0.341404 secs using 397.5% CPU
Optimizing NNI: done in 0.385538 secs using 398.9% CPU
Iteration 160 / LogL: -36292.249 / Time: 0h:1m:17s (0h:0m:22s left)
Optimizing NNI: done in 0.368951 secs using 399.3% CPU
Optimizing NNI: done in 0.650545 secs using 398.1% CPU
Optimizing NNI: done in 0.458361 secs using 398.6% CPU
Optimizing NNI: done in 0.512963 secs using 398.9% CPU
Optimizing NNI: done in 0.356268 secs using 397.8% CPU
Optimizing NNI: done in 0.392394 secs using 396.6% CPU
Optimizing NNI: done in 0.330024 secs using 398.8% CPU
Optimizing NNI: done in 0.556795 secs using 397.2% CPU
Optimizing NNI: done in 0.403114 secs using 397.9% CPU
Optimizing NNI: done in 0.515612 secs using 399.4% CPU
Iteration 170 / LogL: -36290.098 / Time: 0h:1m:21s (0h:0m:17s left)
Optimizing NNI: done in 0.586571 secs using 397.8% CPU
Optimizing NNI: done in 0.273285 secs using 397.4% CPU
Optimizing NNI: done in 0.573154 secs using 399.1% CPU
Optimizing NNI: done in 0.572513 secs using 398% CPU
Optimizing NNI: done in 0.434343 secs using 399.3% CPU
217  Q.bird+F+I+R7 61226.730    335 123123.459   124566.536   124529.950
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.646943 secs using 399.1% CPU
Optimizing NNI: done in 0.413136 secs using 398.2% CPU
Optimizing NNI: done in 0.472452 secs using 399.4% CPU
Optimizing NNI: done in 0.564875 secs using 397.8% CPU
Optimizing NNI: done in 0.55466 secs using 398.2% CPU
Iteration 180 / LogL: -36291.104 / Time: 0h:1m:27s (0h:0m:12s left)
Optimizing NNI: done in 0.494445 secs using 398.3% CPU
Optimizing NNI: done in 0.267701 secs using 396.9% CPU
Optimizing NNI: done in 0.450776 secs using 398.9% CPU
Optimizing NNI: done in 0.468386 secs using 398.7% CPU
Optimizing NNI: done in 0.551286 secs using 399% CPU
Optimizing NNI: done in 0.607686 secs using 398.3% CPU
Optimizing NNI: done in 0.419148 secs using 397.7% CPU
Optimizing NNI: done in 0.515123 secs using 396.8% CPU
Optimizing NNI: done in 0.44058 secs using 399% CPU
Optimizing NNI: done in 0.487415 secs using 399.2% CPU
Iteration 190 / LogL: -36295.113 / Time: 0h:1m:31s (0h:0m:7s left)
Optimizing NNI: done in 0.429127 secs using 398.7% CPU
Optimizing NNI: done in 0.376064 secs using 398.9% CPU
Optimizing NNI: done in 0.414987 secs using 397.3% CPU
Optimizing NNI: done in 0.454698 secs using 398.9% CPU
Optimizing NNI: done in 0.561607 secs using 397.4% CPU
Optimizing NNI: done in 0.614767 secs using 398.3% CPU
Optimizing NNI: done in 0.416837 secs using 397.6% CPU
Optimizing NNI: done in 0.431975 secs using 398% CPU
Optimizing NNI: done in 0.559917 secs using 398.4% CPU
229  Q.mammal+R6   60679.748    313 121985.496   123089.788   123299.619
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.320261 secs using 398.8% CPU
Iteration 200 / LogL: -36296.684 / Time: 0h:1m:36s (0h:0m:2s left)
Optimizing NNI: done in 0.385373 secs using 398.9% CPU
Optimizing NNI: done in 0.527413 secs using 399% CPU
Optimizing NNI: done in 0.462724 secs using 399.3% CPU
Optimizing NNI: done in 0.501393 secs using 399.1% CPU
Optimizing NNI: done in 0.487307 secs using 398.3% CPU
Optimizing NNI: done in 0.50496 secs using 399.5% CPU
Optimizing NNI: done in 0.51436 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 207 ITERATIONS / Time: 0h:1m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36289.743
Optimal log-likelihood: -36289.742
Proportion of invariable sites: 0.022
Gamma shape alpha: 2.795
Parameters optimization took 1 rounds (0.046 sec)
BEST SCORE FOUND : -36289.742
Total tree length: 18.902

Total number of iterations: 207
CPU time used for tree search: 391.753 sec (0h:6m:31s)
Wall-clock time used for tree search: 99.203 sec (0h:1m:39s)
Total CPU time used: 394.782 sec (0h:6m:34s)
Total wall-clock time used: 99.911 sec (0h:1m:39s)

===> START BOOTSTRAP REPLICATE NUMBER 7

Creating bootstrap alignment (seed: 956166)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37253.222
2. Current log-likelihood: -36454.213
3. Current log-likelihood: -36431.874
4. Current log-likelihood: -36430.780
Optimal log-likelihood: -36430.758
Proportion of invariable sites: 0.027
Gamma shape alpha: 2.519
Parameters optimization took 4 rounds (0.264 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0744889 secs using 401.6% CPU
Computing ML distances took 0.074645 sec (of wall-clock time) 0.299215 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000150204 secs using 434.7% CPU
Constructing RapidNJ tree: done in 0.00215602 secs using 479.9% CPU
Computing RapidNJ tree took 0.002363 sec (of wall-clock time) 0.011924 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37117.422
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 230  Q.mammal+R7   60672.349    315 121974.698   123105.835   123297.219
WARNING: Normalizing state frequencies so that sum of them equals to 1
1.622 second
 33  WAG+R10       196241.628   1005 394493.256   2416553.256  398869.398
Computing log-likelihood of 98 initial trees ... 1.614 seconds
Current best score: -36430.758

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.221283 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36388.297
Optimizing NNI: done in 0.310464 secs using 397.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36387.361
Optimizing NNI: done in 0.203369 secs using 397.4% CPU
Optimizing NNI: done in 0.298296 secs using 398.5% CPU
Optimizing NNI: done in 0.301166 secs using 397.8% CPU
Optimizing NNI: done in 0.300551 secs using 398.2% CPU
Optimizing NNI: done in 0.298192 secs using 399.3% CPU
Optimizing NNI: done in 0.277953 secs using 398.8% CPU
Optimizing NNI: done in 0.285571 secs using 398.5% CPU
Optimizing NNI: done in 0.280383 secs using 398.6% CPU
Iteration 10 / LogL: -36388.694 / Time: 0h:0m:6s
Optimizing NNI: done in 0.28682 secs using 399.7% CPU
Optimizing NNI: done in 0.301252 secs using 398.4% CPU
Optimizing NNI: done in 0.251402 secs using 398.5% CPU
Optimizing NNI: done in 0.319275 secs using 397.6% CPU
Optimizing NNI: done in 0.312981 secs using 397.3% CPU
231  Q.mammal+R8   60660.688    317 121955.377   123114.066   123286.294
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.298747 secs using 397.5% CPU
Optimizing NNI: done in 0.28121 secs using 399.2% CPU
Optimizing NNI: done in 0.282809 secs using 398.4% CPU
Optimizing NNI: done in 0.241124 secs using 398.3% CPU
Optimizing NNI: done in 0.330081 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36387.240
Iteration 20 / LogL: -36387.240 / Time: 0h:0m:9s
Finish initializing candidate tree set (5)
Current best tree score: -36387.240 / CPU time: 9.122
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.416051 secs using 397.7% CPU
Optimizing NNI: done in 0.464575 secs using 398.1% CPU
Optimizing NNI: done in 0.378063 secs using 398.1% CPU
Optimizing NNI: done in 0.519542 secs using 397.7% CPU
Optimizing NNI: done in 0.455085 secs using 398.1% CPU
Optimizing NNI: done in 0.458924 secs using 399.5% CPU
Optimizing NNI: done in 0.461567 secs using 399.2% CPU
Optimizing NNI: done in 0.456391 secs using 398.6% CPU
Optimizing NNI: done in 0.505885 secs using 397.1% CPU
Optimizing NNI: done in 0.39565 secs using 399% CPU
Iteration 30 / LogL: -36387.250 / Time: 0h:0m:14s (0h:0m:35s left)
Optimizing NNI: done in 0.352682 secs using 399.2% CPU
Optimizing NNI: done in 0.348447 secs using 399.4% CPU
Optimizing NNI: done in 0.404423 secs using 398.7% CPU
Optimizing NNI: done in 0.487445 secs using 398.6% CPU
Optimizing NNI: done in 0.395976 secs using 398% CPU
Optimizing NNI: done in 0.345415 secs using 398.9% CPU
Optimizing NNI: done in 0.572985 secs using 398.3% CPU
Optimizing NNI: done in 0.381303 secs using 398.5% CPU
Optimizing NNI: done in 0.491879 secs using 398.9% CPU
Optimizing NNI: done in 0.642734 secs using 398.8% CPU
Iteration 40 / LogL: -36392.062 / Time: 0h:0m:18s (0h:0m:29s left)
Optimizing NNI: done in 0.488913 secs using 398.1% CPU
Optimizing NNI: done in 0.513969 secs using 398.2% CPU
Optimizing NNI: done in 0.378027 secs using 399% CPU
232  Q.mammal+R9   60658.391    319 121954.782   123141.759   123294.097
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.553373 secs using 399.1% CPU
Optimizing NNI: done in 0.521189 secs using 398.7% CPU
Optimizing NNI: done in 0.363762 secs using 398.4% CPU
Optimizing NNI: done in 0.435883 secs using 399.1% CPU
 42  WAG+F+R8      194842.645   1020 391725.291   2474565.291  396166.748
Optimizing NNI: done in 0.442694 secs using 399.3% CPU
Optimizing NNI: done in 0.409864 secs using 398.8% CPU
Optimizing NNI: done in 0.464342 secs using 397.1% CPU
Iteration 50 / LogL: -36388.457 / Time: 0h:0m:23s (0h:0m:24s left)
Optimizing NNI: done in 0.398848 secs using 398.3% CPU
Optimizing NNI: done in 0.453663 secs using 399% CPU
Optimizing NNI: done in 0.507512 secs using 398.5% CPU
Optimizing NNI: done in 0.344294 secs using 398.8% CPU
Optimizing NNI: done in 0.403103 secs using 399.8% CPU
Optimizing NNI: done in 0.580217 secs using 398.5% CPU
Optimizing NNI: done in 0.494838 secs using 398.6% CPU
Optimizing NNI: done in 0.443459 secs using 399.2% CPU
Optimizing NNI: done in 0.414278 secs using 398.8% CPU
Optimizing NNI: done in 0.394517 secs using 398.3% CPU
Iteration 60 / LogL: -36387.698 / Time: 0h:0m:27s (0h:0m:19s left)
Optimizing NNI: done in 0.534597 secs using 397.7% CPU
Optimizing NNI: done in 0.538281 secs using 399% CPU
Optimizing NNI: done in 0.410945 secs using 398.3% CPU
Optimizing NNI: done in 0.402069 secs using 397.3% CPU
238  Q.mammal+I+R6 60677.423    314 121982.846   123100.473   123301.168
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.449803 secs using 398.7% CPU
Optimizing NNI: done in 0.368057 secs using 398.9% CPU
Optimizing NNI: done in 0.409458 secs using 397.9% CPU
Optimizing NNI: done in 0.477471 secs using 398.1% CPU
Optimizing NNI: done in 0.526777 secs using 398.7% CPU
Optimizing NNI: done in 0.394245 secs using 398.7% CPU
Iteration 70 / LogL: -36389.044 / Time: 0h:0m:32s (0h:0m:15s left)
Optimizing NNI: done in 0.394871 secs using 398.6% CPU
Optimizing NNI: done in 0.537167 secs using 398.9% CPU
Optimizing NNI: done in 0.461232 secs using 398.4% CPU
Optimizing NNI: done in 0.536503 secs using 399% CPU
Optimizing NNI: done in 0.491875 secs using 398.7% CPU
Optimizing NNI: done in 0.536498 secs using 398.5% CPU
Optimizing NNI: done in 0.52039 secs using 398.1% CPU
Optimizing NNI: done in 0.355546 secs using 398% CPU
Optimizing NNI: done in 0.380786 secs using 397.5% CPU
Optimizing NNI: done in 0.500991 secs using 399.1% CPU
Iteration 80 / LogL: -36388.555 / Time: 0h:0m:37s (0h:0m:10s left)
Optimizing NNI: done in 0.409409 secs using 397.8% CPU
239  Q.mammal+I+R7 60670.841    316 121973.683   123118.505   123300.402
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.424974 secs using 397.5% CPU
Optimizing NNI: done in 0.384395 secs using 398.4% CPU
Optimizing NNI: done in 0.550567 secs using 398.6% CPU
Optimizing NNI: done in 0.454039 secs using 398.9% CPU
Optimizing NNI: done in 0.455901 secs using 398.4% CPU
Optimizing NNI: done in 0.370578 secs using 399.3% CPU
Optimizing NNI: done in 0.466233 secs using 399.4% CPU
Optimizing NNI: done in 0.416494 secs using 399.2% CPU
Optimizing NNI: done in 0.437533 secs using 398.6% CPU
Iteration 90 / LogL: -36388.286 / Time: 0h:0m:41s (0h:0m:5s left)
Optimizing NNI: done in 0.479626 secs using 397.4% CPU
Optimizing NNI: done in 0.481394 secs using 398.9% CPU
Optimizing NNI: done in 0.406965 secs using 397% CPU
Optimizing NNI: done in 0.446914 secs using 397.9% CPU
Optimizing NNI: done in 0.508553 secs using 399.2% CPU
Optimizing NNI: done in 0.397078 secs using 399.5% CPU
Optimizing NNI: done in 0.444875 secs using 398.8% CPU
Optimizing NNI: done in 0.315484 secs using 399.1% CPU
Optimizing NNI: done in 0.493337 secs using 399.5% CPU
Optimizing NNI: done in 0.562521 secs using 398.5% CPU
Iteration 100 / LogL: -36387.334 / Time: 0h:0m:46s (0h:0m:0s left)
Optimizing NNI: done in 0.486207 secs using 398.2% CPU
Optimizing NNI: done in 0.410813 secs using 397.9% CPU
Optimizing NNI: done in 0.425518 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36387.240
Optimal log-likelihood: -36387.239
Proportion of invariable sites: 0.027
Gamma shape alpha: 2.542
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36387.239
Total tree length: 19.757

Total number of iterations: 103
CPU time used for tree search: 182.460 sec (0h:3m:2s)
Wall-clock time used for tree search: 46.862 sec (0h:0m:46s)
Total CPU time used: 185.496 sec (0h:3m:5s)
Total wall-clock time used: 47.576 sec (0h:0m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 8

Creating bootstrap alignment (seed: 956167)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.010 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37020.322
2. Current log-likelihood: -36134.426
3. Current log-likelihood: -36118.193
4. Current log-likelihood: -36117.373
Optimal log-likelihood: -36117.365
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.429
Parameters optimization took 4 rounds (0.294 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0747671 secs using 399.2% CPU
Computing ML distances took 0.074906 sec (of wall-clock time) 0.298822 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000145912 secs using 424.9% CPU
Constructing RapidNJ tree: done in 0.00227284 secs using 417.6% CPU
Computing RapidNJ tree took 0.002476 sec (of wall-clock time) 0.011498 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36481.261
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.427 second
251  Q.mammal+F+R6 60769.205    332 122202.410   123593.051   123596.305
WARNING: Normalizing state frequencies so that sum of them equals to 1
Computing log-likelihood of 98 initial trees ... 1.627 seconds
Current best score: -36117.365

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.219969 secs using 400.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36075.850
Optimizing NNI: done in 0.279567 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36071.973
Optimizing NNI: done in 0.261244 secs using 399.7% CPU
Optimizing NNI: done in 0.270921 secs using 398.6% CPU
Optimizing NNI: done in 0.27809 secs using 396.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -36069.233
Optimizing NNI: done in 0.273062 secs using 399.7% CPU
Optimizing NNI: done in 0.290818 secs using 399.1% CPU
Optimizing NNI: done in 0.276568 secs using 398.3% CPU
Optimizing NNI: done in 0.29463 secs using 398.7% CPU
Optimizing NNI: done in 0.257025 secs using 398.2% CPU
Iteration 10 / LogL: -36069.339 / Time: 0h:0m:6s
Optimizing NNI: done in 0.265687 secs using 398.3% CPU
Optimizing NNI: done in 0.306103 secs using 397.8% CPU
Optimizing NNI: done in 0.278221 secs using 398.6% CPU
Optimizing NNI: done in 0.266666 secs using 399.8% CPU
Optimizing NNI: done in 0.265494 secs using 399.7% CPU
Optimizing NNI: done in 0.278036 secs using 398.6% CPU
Optimizing NNI: done in 0.276276 secs using 399.7% CPU
Optimizing NNI: done in 0.284278 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 18: -36068.895
Optimizing NNI: done in 0.265957 secs using 398.3% CPU
Optimizing NNI: done in 0.282156 secs using 398.6% CPU
Iteration 20 / LogL: -36072.128 / Time: 0h:0m:9s
Finish initializing candidate tree set (8)
Current best tree score: -36068.895 / CPU time: 8.822
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.447985 secs using 397.7% CPU
Optimizing NNI: done in 0.449889 secs using 398.2% CPU
 43  WAG+F+R9      194839.005   1022 391722.011   2482734.011  396172.177
Optimizing NNI: done in 0.440137 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -36064.726
Optimizing NNI: done in 0.415507 secs using 399.4% CPU
Optimizing NNI: done in 0.380516 secs using 398% CPU
Optimizing NNI: done in 0.40149 secs using 398.4% CPU
Optimizing NNI: done in 0.399104 secs using 399.4% CPU
Optimizing NNI: done in 0.433236 secs using 399.3% CPU
Optimizing NNI: done in 0.340004 secs using 399.4% CPU
Optimizing NNI: done in 0.36817 secs using 399.2% CPU
Iteration 30 / LogL: -36069.168 / Time: 0h:0m:13s (0h:0m:43s left)
Optimizing NNI: done in 0.393992 secs using 398.2% CPU
Optimizing NNI: done in 0.516907 secs using 398.7% CPU
Optimizing NNI: done in 0.343234 secs using 399.1% CPU
Optimizing NNI: done in 0.32763 secs using 400.1% CPU
Optimizing NNI: done in 0.402093 secs using 399.6% CPU
Optimizing NNI: done in 0.400209 secs using 399.4% CPU
Optimizing NNI: done in 0.451058 secs using 398.8% CPU
Optimizing NNI: done in 0.515144 secs using 397.7% CPU
Optimizing NNI: done in 0.440151 secs using 400.2% CPU
Optimizing NNI: done in 0.35201 secs using 398.8% CPU
Iteration 40 / LogL: -36071.191 / Time: 0h:0m:17s (0h:0m:37s left)
Optimizing NNI: done in 0.438551 secs using 399% CPU
Optimizing NNI: done in 0.370862 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -36063.842
Optimizing NNI: done in 0.487092 secs using 399% CPU
Optimizing NNI: done in 0.4071 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -36062.217
Optimizing NNI: done in 0.45092 secs using 398.1% CPU
Optimizing NNI: done in 0.308051 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 46: -36062.011
Optimizing NNI: done in 0.516715 secs using 398.6% CPU
252  Q.mammal+F+R7 60756.768    334 122181.537   123606.887   123583.829
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.393235 secs using 398.5% CPU
Optimizing NNI: done in 0.339399 secs using 400% CPU
Optimizing NNI: done in 0.188289 secs using 398.6% CPU
Iteration 50 / LogL: -36063.013 / Time: 0h:0m:22s (0h:0m:43s left)
Optimizing NNI: done in 0.362321 secs using 397.8% CPU
UPDATE BEST LOG-LIKELIHOOD: -36062.008
Optimizing NNI: done in 0.393387 secs using 398.4% CPU
Optimizing NNI: done in 0.348581 secs using 398.6% CPU
Optimizing NNI: done in 0.319329 secs using 398.3% CPU
Optimizing NNI: done in 0.339883 secs using 397.6% CPU
Optimizing NNI: done in 0.335146 secs using 399.3% CPU
Optimizing NNI: done in 0.397492 secs using 398.6% CPU
Optimizing NNI: done in 0.515386 secs using 398.1% CPU
Optimizing NNI: done in 0.350301 secs using 398.9% CPU
Optimizing NNI: done in 0.384194 secs using 399.6% CPU
Iteration 60 / LogL: -36062.353 / Time: 0h:0m:25s (0h:0m:37s left)
Optimizing NNI: done in 0.481939 secs using 399.4% CPU
Optimizing NNI: done in 0.423047 secs using 398.7% CPU
Optimizing NNI: done in 0.433226 secs using 398.7% CPU
Optimizing NNI: done in 0.377254 secs using 399% CPU
253  Q.mammal+F+R8 60753.074    336 122178.148   123639.207   123588.837
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.353179 secs using 398% CPU
Optimizing NNI: done in 0.392593 secs using 397.6% CPU
Optimizing NNI: done in 0.466835 secs using 398.2% CPU
Optimizing NNI: done in 0.55065 secs using 397.5% CPU
Optimizing NNI: done in 0.433362 secs using 398.3% CPU
 53  JTT+R8        195608.757   1001 393219.514   2399223.514  397578.238
Optimizing NNI: done in 0.443166 secs using 399.5% CPU
Iteration 70 / LogL: -36063.802 / Time: 0h:0m:30s (0h:0m:33s left)
Optimizing NNI: done in 0.311006 secs using 397.8% CPU
Optimizing NNI: done in 0.437058 secs using 399.4% CPU
Optimizing NNI: done in 0.3851 secs using 399.4% CPU
Optimizing NNI: done in 0.415114 secs using 398.7% CPU
Optimizing NNI: done in 0.430556 secs using 398.4% CPU
Optimizing NNI: done in 0.337142 secs using 398.4% CPU
Optimizing NNI: done in 0.443503 secs using 398.2% CPU
Optimizing NNI: done in 0.31208 secs using 399.1% CPU
Optimizing NNI: done in 0.2194 secs using 398% CPU
Optimizing NNI: done in 0.395568 secs using 399.4% CPU
Iteration 80 / LogL: -36068.960 / Time: 0h:0m:33s (0h:0m:28s left)
Optimizing NNI: done in 0.320706 secs using 398.3% CPU
Optimizing NNI: done in 0.347476 secs using 398.8% CPU
Optimizing NNI: done in 0.487535 secs using 399.5% CPU
Optimizing NNI: done in 0.407749 secs using 399.4% CPU
Optimizing NNI: done in 0.365617 secs using 399.3% CPU
Optimizing NNI: done in 0.387533 secs using 399% CPU
Optimizing NNI: done in 0.327938 secs using 399% CPU
Optimizing NNI: done in 0.456179 secs using 397.8% CPU
Optimizing NNI: done in 0.356093 secs using 399.5% CPU
Optimizing NNI: done in 0.40831 secs using 398.6% CPU
Iteration 90 / LogL: -36062.771 / Time: 0h:0m:37s (0h:0m:23s left)
Optimizing NNI: done in 0.386653 secs using 398.9% CPU
Optimizing NNI: done in 0.438572 secs using 397.6% CPU
260  Q.mammal+F+I+R6 60767.982    333 122201.963   123609.837   123600.057
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.398401 secs using 398.8% CPU
Optimizing NNI: done in 0.289123 secs using 397.6% CPU
Optimizing NNI: done in 0.314414 secs using 398.3% CPU
Optimizing NNI: done in 0.357314 secs using 398.9% CPU
Optimizing NNI: done in 0.371032 secs using 398.4% CPU
Optimizing NNI: done in 0.322725 secs using 398.7% CPU
Optimizing NNI: done in 0.360808 secs using 399.1% CPU
Optimizing NNI: done in 0.397719 secs using 399.5% CPU
Iteration 100 / LogL: -36062.799 / Time: 0h:0m:41s (0h:0m:19s left)
Optimizing NNI: done in 0.400573 secs using 399.8% CPU
Optimizing NNI: done in 0.345707 secs using 399.1% CPU
Optimizing NNI: done in 0.451775 secs using 397.9% CPU
Optimizing NNI: done in 0.401245 secs using 397.9% CPU
Optimizing NNI: done in 0.404641 secs using 399.1% CPU
Optimizing NNI: done in 0.314426 secs using 398% CPU
Optimizing NNI: done in 0.356346 secs using 399.1% CPU
Optimizing NNI: done in 0.408968 secs using 398% CPU
Optimizing NNI: done in 0.48714 secs using 399% CPU
Optimizing NNI: done in 0.332501 secs using 399% CPU
Iteration 110 / LogL: -36063.455 / Time: 0h:0m:45s (0h:0m:15s left)
Optimizing NNI: done in 0.397146 secs using 398.4% CPU
Optimizing NNI: done in 0.355021 secs using 398.9% CPU
Optimizing NNI: done in 0.276445 secs using 397.6% CPU
Optimizing NNI: done in 0.351046 secs using 398.6% CPU
Optimizing NNI: done in 0.378205 secs using 398.3% CPU
Optimizing NNI: done in 0.396224 secs using 398.3% CPU
Optimizing NNI: done in 0.318985 secs using 399.1% CPU
Optimizing NNI: done in 0.3074 secs using 398.8% CPU
 54  JTT+R9        195593.125   1003 393192.250   2407216.250  397559.683
Optimizing NNI: done in 0.380078 secs using 399.6% CPU
Optimizing NNI: done in 0.343469 secs using 398.5% CPU
Iteration 120 / LogL: -36067.417 / Time: 0h:0m:48s (0h:0m:10s left)
Optimizing NNI: done in 0.338064 secs using 399% CPU
Optimizing NNI: done in 0.388228 secs using 397.1% CPU
Optimizing NNI: done in 0.417216 secs using 399.6% CPU
Optimizing NNI: done in 0.234649 secs using 397.6% CPU
Optimizing NNI: done in 0.343894 secs using 399.6% CPU
Optimizing NNI: done in 0.301957 secs using 399.3% CPU
Optimizing NNI: done in 0.418413 secs using 399% CPU
Optimizing NNI: done in 0.30373 secs using 399.8% CPU
Optimizing NNI: done in 0.314843 secs using 399.6% CPU
Optimizing NNI: done in 0.343453 secs using 399.4% CPU
Iteration 130 / LogL: -36067.413 / Time: 0h:0m:52s (0h:0m:6s left)
Optimizing NNI: done in 0.296938 secs using 397.6% CPU
Optimizing NNI: done in 0.306225 secs using 398.2% CPU
Optimizing NNI: done in 0.37701 secs using 398.9% CPU
Optimizing NNI: done in 0.319757 secs using 399% CPU
Optimizing NNI: done in 0.387303 secs using 399% CPU
Optimizing NNI: done in 0.372372 secs using 399% CPU
Optimizing NNI: done in 0.393454 secs using 398.6% CPU
Optimizing NNI: done in 0.348289 secs using 398.9% CPU
Optimizing NNI: done in 0.346059 secs using 399% CPU
Optimizing NNI: done in 0.336148 secs using 399.1% CPU
Iteration 140 / LogL: -36068.322 / Time: 0h:0m:55s (0h:0m:2s left)
Optimizing NNI: done in 0.373438 secs using 398.7% CPU
Optimizing NNI: done in 0.345022 secs using 398% CPU
Optimizing NNI: done in 0.269459 secs using 398.5% CPU
261  Q.mammal+F+I+R7 60755.456    335 122180.913   123623.990   123587.403
Optimizing NNI: done in 0.242833 secs using 399.6% CPU
Optimizing NNI: done in 0.416614 secs using 399.2% CPU
Optimizing NNI: done in 0.326967 secs using 399.1% CPU
Optimizing NNI: done in 0.348354 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 147 ITERATIONS / Time: 0h:0m:58s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36062.008
Optimal log-likelihood: -36062.002
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.460
Parameters optimization took 1 rounds (0.046 sec)
BEST SCORE FOUND : -36062.002
Total tree length: 19.712

Total number of iterations: 147
CPU time used for tree search: 226.317 sec (0h:3m:46s)
Wall-clock time used for tree search: 57.687 sec (0h:0m:57s)
Total CPU time used: 229.203 sec (0h:3m:49s)
Total wall-clock time used: 58.365 sec (0h:0m:58s)

===> START BOOTSTRAP REPLICATE NUMBER 9

Creating bootstrap alignment (seed: 956168)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37199.789
2. Current log-likelihood: -36379.188
3. Current log-likelihood: -36364.079
4. Current log-likelihood: -36363.748
Optimal log-likelihood: -36363.717
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.446
Parameters optimization took 4 rounds (0.262 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.076256 secs using 399.3% CPU
Computing ML distances took 0.076382 sec (of wall-clock time) 0.304771 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000174046 secs using 248.2% CPU
Constructing RapidNJ tree: done in 0.00213099 secs using 379.1% CPU
Computing RapidNJ tree took 0.002362 sec (of wall-clock time) 0.009004 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36507.982
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.461 second
273  Q.insect+R6   59495.703    313 119617.406   120721.698   120931.530
Computing log-likelihood of 98 initial trees ... 1.599 seconds
Current best score: -36234.845

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.351858 secs using 397.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36167.158
Optimizing NNI: done in 0.454801 secs using 399.2% CPU
Optimizing NNI: done in 0.239626 secs using 399.8% CPU
Optimizing NNI: done in 0.32513 secs using 399% CPU
Optimizing NNI: done in 0.284553 secs using 398.7% CPU
Optimizing NNI: done in 0.427984 secs using 398.8% CPU
Optimizing NNI: done in 0.359177 secs using 398.1% CPU
Optimizing NNI: done in 0.45127 secs using 398.3% CPU
Optimizing NNI: done in 0.303949 secs using 397.8% CPU
Optimizing NNI: done in 0.317851 secs using 398.5% CPU
Iteration 10 / LogL: -36173.163 / Time: 0h:0m:7s
Optimizing NNI: done in 0.426277 secs using 397.9% CPU
Optimizing NNI: done in 0.338624 secs using 398.8% CPU
274  Q.insect+R7   59486.836    315 119603.673   120734.809   120926.194
Optimizing NNI: done in 0.553332 secs using 399.4% CPU
Optimizing NNI: done in 0.491815 secs using 398.8% CPU
Optimizing NNI: done in 0.416785 secs using 398.4% CPU
Optimizing NNI: done in 0.394951 secs using 398% CPU
Optimizing NNI: done in 0.3515 secs using 400% CPU
Optimizing NNI: done in 0.480073 secs using 398.1% CPU
Optimizing NNI: done in 0.277359 secs using 399.8% CPU
Optimizing NNI: done in 0.509131 secs using 398.5% CPU
Iteration 20 / LogL: -36174.709 / Time: 0h:0m:11s
Finish initializing candidate tree set (12)
Current best tree score: -36167.158 / CPU time: 10.930
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.570212 secs using 399.4% CPU
Optimizing NNI: done in 0.500213 secs using 399% CPU
Optimizing NNI: done in 0.507168 secs using 397.8% CPU
Optimizing NNI: done in 0.371562 secs using 399.2% CPU
Optimizing NNI: done in 0.462886 secs using 399% CPU
275  Q.insect+R8   59477.039    317 119588.079   120746.768   120918.996
Optimizing NNI: done in 0.665782 secs using 399.2% CPU
Optimizing NNI: done in 0.428526 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -36167.086
Optimizing NNI: done in 0.668005 secs using 398.3% CPU
Optimizing NNI: done in 0.522344 secs using 399% CPU
Optimizing NNI: done in 0.523223 secs using 398.8% CPU
Iteration 30 / LogL: -36172.946 / Time: 0h:0m:16s (0h:0m:55s left)
Optimizing NNI: done in 0.513434 secs using 398.8% CPU
Optimizing NNI: done in 0.588043 secs using 398.2% CPU
Optimizing NNI: done in 0.402296 secs using 396.8% CPU
Optimizing NNI: done in 0.404623 secs using 398.2% CPU
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Optimizing NNI: done in 0.428524 secs using 398.4% CPU
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Optimizing NNI: done in 0.378046 secs using 398.9% CPU
Optimizing NNI: done in 0.411825 secs using 398.9% CPU
Iteration 40 / LogL: -36170.148 / Time: 0h:0m:21s (0h:0m:46s left)
Optimizing NNI: done in 0.503124 secs using 398.3% CPU
Optimizing NNI: done in 0.685391 secs using 398.6% CPU
Optimizing NNI: done in 0.57804 secs using 398.6% CPU
Optimizing NNI: done in 0.544033 secs using 397.9% CPU
Optimizing NNI: done in 0.506908 secs using 399.6% CPU
Optimizing NNI: done in 0.520025 secs using 398.6% CPU
Optimizing NNI: done in 0.427314 secs using 398.2% CPU
Optimizing NNI: done in 0.370551 secs using 398.3% CPU
Optimizing NNI: done in 0.311228 secs using 398.7% CPU
Optimizing NNI: done in 0.40798 secs using 398.5% CPU
Iteration 50 / LogL: -36169.706 / Time: 0h:0m:25s (0h:0m:40s left)
Optimizing NNI: done in 0.499731 secs using 399.2% CPU
Optimizing NNI: done in 0.564055 secs using 399.1% CPU
Optimizing NNI: done in 0.437903 secs using 398.2% CPU
Optimizing NNI: done in 0.424237 secs using 399.5% CPU
Optimizing NNI: done in 0.560808 secs using 399.5% CPU
Optimizing NNI: done in 0.421472 secs using 399.3% CPU
Optimizing NNI: done in 0.337725 secs using 399.3% CPU
Optimizing NNI: done in 0.362044 secs using 398.7% CPU
Optimizing NNI: done in 0.439767 secs using 398.6% CPU
Optimizing NNI: done in 0.430627 secs using 398% CPU
Iteration 60 / LogL: -36170.124 / Time: 0h:0m:30s (0h:0m:34s left)
Optimizing NNI: done in 0.537125 secs using 399.3% CPU
Optimizing NNI: done in 0.411826 secs using 398.9% CPU
Optimizing NNI: done in 0.432075 secs using 399.7% CPU
 55  JTT+R10       195590.207   1005 393190.414   2415250.414  397566.556
Optimizing NNI: done in 0.549132 secs using 399% CPU
276  Q.insect+R9   59475.145    319 119588.290   120775.266   120927.604
Optimizing NNI: done in 0.307564 secs using 398.5% CPU
Optimizing NNI: done in 0.387509 secs using 399.7% CPU
Optimizing NNI: done in 0.431386 secs using 399.5% CPU
 13  LG+R10        105453.457   553 212012.914   824736.914   214239.218
Optimizing NNI: done in 0.307003 secs using 398.6% CPU
Optimizing NNI: done in 0.36513 secs using 398.5% CPU
 14  LG+I+R2       107868.169   538 216812.338   796776.338   218978.254
Optimizing NNI: done in 0.566472 secs using 399.3% CPU
Iteration 70 / LogL: -36170.164 / Time: 0h:0m:34s (0h:0m:28s left)
Optimizing NNI: done in 0.380144 secs using 398.3% CPU
Optimizing NNI: done in 0.771182 secs using 397.9% CPU
Optimizing NNI: done in 0.472826 secs using 398.3% CPU
Optimizing NNI: done in 0.448622 secs using 399.1% CPU
Optimizing NNI: done in 0.490409 secs using 399.2% CPU
Optimizing NNI: done in 0.580199 secs using 399.4% CPU
Optimizing NNI: done in 0.46304 secs using 399.1% CPU
Optimizing NNI: done in 0.489502 secs using 398.4% CPU
Optimizing NNI: done in 0.458545 secs using 398% CPU
Optimizing NNI: done in 0.535189 secs using 398.7% CPU
Iteration 80 / LogL: -36170.016 / Time: 0h:0m:39s (0h:0m:23s left)
Optimizing NNI: done in 0.44309 secs using 399.7% CPU
 15  LG+I+R3       106437.616   540 213955.233   798235.233   216129.200
Optimizing NNI: done in 0.379293 secs using 399.1% CPU
Optimizing NNI: done in 0.704645 secs using 398.5% CPU
Optimizing NNI: done in 0.397971 secs using 398.5% CPU
Optimizing NNI: done in 0.415819 secs using 398.9% CPU
Optimizing NNI: done in 0.438192 secs using 398.1% CPU
Optimizing NNI: done in 0.893876 secs using 398.3% CPU
Optimizing NNI: done in 0.508429 secs using 398.3% CPU
Optimizing NNI: done in 0.319063 secs using 399.1% CPU
282  Q.insect+I+R6 59492.203    314 119612.407   120730.034   120930.729
Optimizing NNI: done in 0.522825 secs using 397.8% CPU
Iteration 90 / LogL: -36172.617 / Time: 0h:0m:44s (0h:0m:18s left)
Optimizing NNI: done in 0.628959 secs using 398.6% CPU
 64  JTT+F+R8      194695.864   1020 391431.729   2474271.729  395873.186
Optimizing NNI: done in 0.756392 secs using 398.8% CPU
Optimizing NNI: done in 0.348345 secs using 399.7% CPU
Optimizing NNI: done in 0.51003 secs using 399.1% CPU
Optimizing NNI: done in 0.353977 secs using 398.1% CPU
Optimizing NNI: done in 0.536798 secs using 398.3% CPU
Optimizing NNI: done in 0.335251 secs using 398.4% CPU
Optimizing NNI: done in 0.47997 secs using 398.9% CPU
Optimizing NNI: done in 0.496419 secs using 399.5% CPU
Optimizing NNI: done in 0.780588 secs using 398.9% CPU
Iteration 100 / LogL: -36167.253 / Time: 0h:0m:50s (0h:0m:13s left)
Optimizing NNI: done in 0.335512 secs using 399.5% CPU
Optimizing NNI: done in 0.421722 secs using 399.4% CPU
Optimizing NNI: done in 0.414123 secs using 399.1% CPU
Optimizing NNI: done in 0.431689 secs using 398.8% CPU
Optimizing NNI: done in 0.456712 secs using 398.3% CPU
Optimizing NNI: done in 0.347885 secs using 399.2% CPU
Optimizing NNI: done in 0.414075 secs using 398.3% CPU
Optimizing NNI: done in 0.42691 secs using 398.1% CPU
Optimizing NNI: done in 0.590591 secs using 399.2% CPU
Optimizing NNI: done in 0.59116 secs using 398.2% CPU
Iteration 110 / LogL: -36167.262 / Time: 0h:0m:54s (0h:0m:8s left)
Optimizing NNI: done in 0.708165 secs using 398.4% CPU
Optimizing NNI: done in 0.435578 secs using 397.9% CPU
283  Q.insect+I+R7 59485.174    316 119602.348   120747.171   120929.067
Optimizing NNI: done in 0.537007 secs using 398.5% CPU
Optimizing NNI: done in 0.491282 secs using 398.5% CPU
Optimizing NNI: done in 0.390484 secs using 398.7% CPU
Optimizing NNI: done in 0.446619 secs using 399.6% CPU
Optimizing NNI: done in 0.434791 secs using 398.1% CPU
Optimizing NNI: done in 0.405696 secs using 398.4% CPU
 16  LG+I+R4       105964.348   542 213012.696   801624.696   215194.716
Optimizing NNI: done in 0.587848 secs using 398% CPU
Optimizing NNI: done in 0.394719 secs using 397.7% CPU
Iteration 120 / LogL: -36167.479 / Time: 0h:0m:59s (0h:0m:3s left)
295  Q.insect+F+R6 59769.062    332 120202.125   121592.766   121596.020
Optimizing NNI: done in 0.504549 secs using 398.8% CPU
Optimizing NNI: done in 0.437193 secs using 399.4% CPU
Optimizing NNI: done in 0.368703 secs using 398.8% CPU
Optimizing NNI: done in 0.597867 secs using 397.6% CPU
Optimizing NNI: done in 0.452956 secs using 398% CPU
Optimizing NNI: done in 0.443959 secs using 398.5% CPU
Optimizing NNI: done in 0.47503 secs using 397.9% CPU
Optimizing NNI: done in 0.316035 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 128 ITERATIONS / Time: 0h:1m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36167.086
Optimal log-likelihood: -36167.085
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.392
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36167.085
Total tree length: 20.924

Total number of iterations: 128
CPU time used for tree search: 246.550 sec (0h:4m:6s)
Wall-clock time used for tree search: 62.776 sec (0h:1m:2s)
Total CPU time used: 248.648 sec (0h:4m:8s)
Total wall-clock time used: 63.281 sec (0h:1m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 10

Creating bootstrap alignment (seed: 956169)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37480.986
2. Current log-likelihood: -36497.904
3. Current log-likelihood: -36480.293
4. Current log-likelihood: -36479.776
Optimal log-likelihood: -36479.694
Proportion of invariable sites: 0.031
Gamma shape alpha: 2.537
Parameters optimization took 4 rounds (0.273 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.07919 secs using 398.6% CPU
Computing ML distances took 0.079337 sec (of wall-clock time) 0.316051 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000164032 secs using 427.4% CPU
Constructing RapidNJ tree: done in 0.00216913 secs using 479.1% CPU
Computing RapidNJ tree took 0.002475 sec (of wall-clock time) 0.012558 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36741.977
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.451 second
 65  JTT+F+R9      194690.743   1022 391425.486   2482437.486  395875.652
WARNING: Normalizing state frequencies so that sum of them equals to 1
Computing log-likelihood of 98 initial trees ... 1.634 seconds
Current best score: -36479.694

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.206754 secs using 396.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36450.714
Optimizing NNI: done in 0.254801 secs using 396.7% CPU
Optimizing NNI: done in 0.2264 secs using 397.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -36449.028
Optimizing NNI: done in 0.244448 secs using 399% CPU
Optimizing NNI: done in 0.213742 secs using 398.4% CPU
Optimizing NNI: done in 0.226246 secs using 397.6% CPU
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Iteration 10 / LogL: -36452.644 / Time: 0h:0m:5s
Optimizing NNI: done in 0.233022 secs using 395.5% CPU
Optimizing NNI: done in 0.206788 secs using 397.2% CPU
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Optimizing NNI: done in 0.26982 secs using 399.1% CPU
Iteration 20 / LogL: -36452.636 / Time: 0h:0m:8s
Finish initializing candidate tree set (3)
Current best tree score: -36449.028 / CPU time: 7.816
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 0.335207 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36448.948
Optimizing NNI: done in 0.367776 secs using 399.8% CPU
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Iteration 30 / LogL: -36450.754 / Time: 0h:0m:12s (0h:0m:30s left)
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296  Q.insect+F+R7 59752.577    334 120173.154   121598.505   121575.446
Optimizing NNI: done in 0.38935 secs using 398.7% CPU
Iteration 40 / LogL: -36504.219 / Time: 0h:0m:15s (0h:0m:25s left)
Optimizing NNI: done in 0.40152 secs using 397.5% CPU
 75  Q.pfam+R8     194892.568   1001 391787.135   2397791.135  396145.860
WARNING: Normalizing state frequencies so that sum of them equals to 1
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 47: -36443.158
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Iteration 50 / LogL: -36450.206 / Time: 0h:0m:20s (0h:0m:39s left)
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297  Q.insect+F+R8 59745.192    336 120162.385   121623.443   121573.073
Optimizing NNI: done in 0.358497 secs using 398.4% CPU
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Iteration 60 / LogL: -36443.351 / Time: 0h:0m:23s (0h:0m:35s left)
Optimizing NNI: done in 0.427241 secs using 396.8% CPU
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 17  LG+I+R5       105690.494   544 212468.988   805428.988   214659.059
Optimizing NNI: done in 0.407742 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36442.926
Optimizing NNI: done in 0.496954 secs using 399.9% CPU
Optimizing NNI: done in 0.415687 secs using 399.9% CPU
Iteration 70 / LogL: -36443.636 / Time: 0h:0m:28s (0h:0m:31s left)
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Iteration 80 / LogL: -36443.025 / Time: 0h:0m:32s (0h:0m:27s left)
Optimizing NNI: done in 0.38017 secs using 399.9% CPU
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Iteration 90 / LogL: -36443.075 / Time: 0h:0m:36s (0h:0m:23s left)
Optimizing NNI: done in 0.612332 secs using 398.1% CPU
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298  Q.insect+F+R9 59743.208    338 120162.416   121660.220   121581.502
Optimizing NNI: done in 0.447887 secs using 399.6% CPU
Optimizing NNI: done in 0.326032 secs using 399.1% CPU
Iteration 100 / LogL: -36445.159 / Time: 0h:0m:40s (0h:0m:19s left)
Optimizing NNI: done in 0.475218 secs using 397.8% CPU
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Iteration 110 / LogL: -36443.320 / Time: 0h:0m:45s (0h:0m:15s left)
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304  Q.insect+F+I+R6 59768.715    333 120203.430   121611.303   121601.523
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Iteration 120 / LogL: -36495.061 / Time: 0h:0m:49s (0h:0m:11s left)
Optimizing NNI: done in 0.388936 secs using 397.4% CPU
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Optimizing NNI: done in 0.335065 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36442.885
Iteration 130 / LogL: -36442.885 / Time: 0h:0m:53s (0h:0m:6s left)
Optimizing NNI: done in 0.464614 secs using 399% CPU
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Optimizing NNI: done in 0.347468 secs using 398.3% CPU
Iteration 140 / LogL: -36443.214 / Time: 0h:0m:57s (0h:0m:2s left)
Optimizing NNI: done in 0.429094 secs using 399.2% CPU
Optimizing NNI: done in 0.335125 secs using 398.6% CPU
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Optimizing NNI: done in 0.381084 secs using 398.6% CPU
Optimizing NNI: done in 0.330474 secs using 397.9% CPU
TREE SEARCH COMPLETED AFTER 148 ITERATIONS / Time: 0h:1m:0s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36442.885
Optimal log-likelihood: -36442.874
Proportion of invariable sites: 0.031
Gamma shape alpha: 2.564
Parameters optimization took 1 rounds (0.046 sec)
BEST SCORE FOUND : -36442.874
Total tree length: 20.913

Total number of iterations: 148
CPU time used for tree search: 236.335 sec (0h:3m:56s)
Wall-clock time used for tree search: 60.215 sec (0h:1m:0s)
Total CPU time used: 238.501 sec (0h:3m:58s)
Total wall-clock time used: 60.735 sec (0h:1m:0s)

===> START BOOTSTRAP REPLICATE NUMBER 11

Creating bootstrap alignment (seed: 956170)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37756.113
2. Current log-likelihood: -36929.919
3. Current log-likelihood: -36916.761
4. Current log-likelihood: -36916.525
Optimal log-likelihood: -36916.470
Proportion of invariable sites: 0.022
Gamma shape alpha: 2.529
Parameters optimization took 4 rounds (0.273 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0783238 secs using 395.6% CPU
Computing ML distances took 0.078456 sec (of wall-clock time) 0.310183 sec (of CPU time)
 76  Q.pfam+R9     194887.665   1003 391781.330   2405805.330  396148.763
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000156164 secs using 422.6% CPU
WARNING: Normalizing state frequencies so that sum of them equals to 1
Constructing RapidNJ tree: done in 0.00216007 secs using 438.6% CPU
Computing RapidNJ tree took 0.002374 sec (of wall-clock time) 0.011009 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37297.054
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... 1.557 second
Computing log-likelihood of 98 initial trees ... 1.631 seconds
Current best score: -36815.457

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.234211 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36765.169
Optimizing NNI: done in 0.247579 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36758.373
Optimizing NNI: done in 0.221388 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -36756.463
 18  LG+I+R6       105562.433   546 212216.866   809540.866   214414.989
Optimizing NNI: done in 0.225867 secs using 397.9% CPU
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Iteration 10 / LogL: -36758.679 / Time: 0h:0m:6s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 16: -36755.468
Optimizing NNI: done in 0.228273 secs using 398.2% CPU
Optimizing NNI: done in 0.244353 secs using 398.6% CPU
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Optimizing NNI: done in 0.317688 secs using 398.7% CPU
Iteration 20 / LogL: -36757.931 / Time: 0h:0m:9s
Finish initializing candidate tree set (15)
Current best tree score: -36755.468 / CPU time: 8.792
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 0.438114 secs using 398.6% CPU
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Iteration 30 / LogL: -36757.370 / Time: 0h:0m:13s (0h:0m:40s left)
Optimizing NNI: done in 0.400911 secs using 399.8% CPU
 86  Q.pfam+F+R8   194521.401   1020 391082.801   2473922.801  395524.259
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.438521 secs using 399.6% CPU
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305  Q.insect+F+I+R7 59751.169    335 120172.337   121615.414   121578.828
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.449201 secs using 398% CPU
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Iteration 40 / LogL: -36756.723 / Time: 0h:0m:17s (0h:0m:34s left)
Optimizing NNI: done in 0.34288 secs using 399% CPU
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Iteration 50 / LogL: -36757.472 / Time: 0h:0m:21s (0h:0m:29s left)
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317  Q.plant+R6    60006.620    313 120639.241   121743.533   121953.364
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.37948 secs using 398.8% CPU
UPDATE BEST LOG-LIKELIHOOD: -36755.468
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UPDATE BEST LOG-LIKELIHOOD: -36755.465
Optimizing NNI: done in 0.336857 secs using 398.7% CPU
Iteration 60 / LogL: -36760.159 / Time: 0h:0m:25s (0h:0m:24s left)
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Iteration 70 / LogL: -36756.050 / Time: 0h:0m:30s (0h:0m:20s left)
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Iteration 80 / LogL: -36756.056 / Time: 0h:0m:34s (0h:0m:15s left)
Optimizing NNI: done in 0.302158 secs using 398.8% CPU
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Iteration 90 / LogL: -36756.185 / Time: 0h:0m:39s (0h:0m:11s left)
 19  LG+I+R7       105501.993   548 212099.985   813803.985   214306.160
Optimizing NNI: done in 0.475119 secs using 399% CPU
BETTER TREE FOUND at iteration 91: -36755.461
Optimizing NNI: done in 0.416888 secs using 398.2% CPU
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318  Q.plant+R7    59991.276    315 120612.551   121743.687   121935.072
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.438592 secs using 398.2% CPU
Iteration 100 / LogL: -36757.099 / Time: 0h:0m:43s (0h:0m:39s left)
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 87  Q.pfam+F+R9   194515.431   1022 391074.862   2482086.862  395525.029
WARNING: Normalizing state frequencies so that sum of them equals to 1
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Iteration 110 / LogL: -36756.403 / Time: 0h:0m:47s (0h:0m:35s left)
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Optimizing NNI: done in 0.546837 secs using 397.8% CPU
319  Q.plant+R8    59987.162    317 120608.323   121767.013   121939.241
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.521857 secs using 399% CPU
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Iteration 120 / LogL: -36755.942 / Time: 0h:0m:52s (0h:0m:31s left)
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Optimizing NNI: done in 0.466157 secs using 399.8% CPU
Iteration 130 / LogL: -36756.951 / Time: 0h:0m:57s (0h:0m:26s left)
Optimizing NNI: done in 0.404658 secs using 399.7% CPU
Optimizing NNI: done in 0.516446 secs using 398.5% CPU
326  Q.plant+I+R6  60005.328    314 120638.655   121756.282   121956.977
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.390227 secs using 399.5% CPU
Optimizing NNI: done in 0.40458 secs using 400% CPU
Optimizing NNI: done in 0.486828 secs using 399.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -36755.459
Optimizing NNI: done in 0.39341 secs using 400.4% CPU
Optimizing NNI: done in 0.450931 secs using 399.3% CPU
Optimizing NNI: done in 0.434413 secs using 399.6% CPU
 97  Q.bird+R8     197829.393   1001 397660.786   2403664.786  402019.511
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.407436 secs using 397.8% CPU
Optimizing NNI: done in 0.423585 secs using 398.9% CPU
Iteration 140 / LogL: -36762.600 / Time: 0h:1m:1s (0h:0m:22s left)
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Iteration 150 / LogL: -36755.549 / Time: 0h:1m:6s (0h:0m:18s left)
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Iteration 160 / LogL: -36755.898 / Time: 0h:1m:10s (0h:0m:13s left)
Optimizing NNI: done in 0.520349 secs using 398.3% CPU
BETTER TREE FOUND at iteration 161: -36755.458
Optimizing NNI: done in 0.363701 secs using 399.1% CPU
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Optimizing NNI: done in 0.503004 secs using 398.2% CPU
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Iteration 170 / LogL: -36756.331 / Time: 0h:1m:15s (0h:0m:40s left)
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Optimizing NNI: done in 0.482131 secs using 399.5% CPU
327  Q.plant+I+R7  59990.384    316 120612.768   121757.590   121939.487
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.456049 secs using 399.8% CPU
Optimizing NNI: done in 0.450799 secs using 398.7% CPU
Iteration 180 / LogL: -36755.571 / Time: 0h:1m:19s (0h:0m:36s left)
 20  LG+I+R8       105487.013   550 212074.026   818174.026   214288.252
Optimizing NNI: done in 0.420327 secs using 398.6% CPU
Optimizing NNI: done in 0.440678 secs using 400% CPU
 98  Q.bird+R9     197820.275   1003 397646.550   2411670.550  402013.983
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.447639 secs using 399% CPU
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Optimizing NNI: done in 0.4622 secs using 399.1% CPU
339  Q.plant+F+R6  60121.458    332 120906.916   122297.557   122300.811
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.471381 secs using 399.7% CPU
Iteration 190 / LogL: -36755.579 / Time: 0h:1m:24s (0h:0m:31s left)
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340  Q.plant+F+R7  60115.627    334 120899.253   122324.604   122301.545
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.554025 secs using 398.8% CPU
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Iteration 200 / LogL: -36755.459 / Time: 0h:1m:28s (0h:0m:27s left)
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Optimizing NNI: done in 0.420713 secs using 398.5% CPU
UPDATE BEST LOG-LIKELIHOOD: -36755.457
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Iteration 210 / LogL: -36756.712 / Time: 0h:1m:33s (0h:0m:22s left)
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348  Q.plant+F+I+R6 60120.118    333 120906.237   122314.110   122304.330
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.419771 secs using 398.9% CPU
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Iteration 220 / LogL: -36756.118 / Time: 0h:1m:37s (0h:0m:18s left)
Optimizing NNI: done in 0.396658 secs using 399% CPU
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Iteration 230 / LogL: -36757.465 / Time: 0h:1m:42s (0h:0m:13s left)
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Optimizing NNI: done in 0.501524 secs using 399.3% CPU
 99  Q.bird+R10    197814.318   1005 397638.636   2419698.636  402014.778
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.393365 secs using 398.7% CPU
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349  Q.plant+F+I+R7 60115.178    335 120900.356   122343.433   122306.846
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.41321 secs using 399.6% CPU
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Iteration 240 / LogL: -36755.459 / Time: 0h:1m:46s (0h:0m:9s left)
Optimizing NNI: done in 0.454471 secs using 397.3% CPU
Optimizing NNI: done in 0.51018 secs using 398.5% CPU
Optimizing NNI: done in 0.407637 secs using 399.1% CPU
361  Q.yeast+R6    59532.562    313 119691.124   120795.417   121005.248
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.379363 secs using 399.8% CPU
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Iteration 250 / LogL: -36755.572 / Time: 0h:1m:50s (0h:0m:4s left)
Optimizing NNI: done in 0.412225 secs using 398.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -36755.456
Optimizing NNI: done in 0.370294 secs using 398.8% CPU
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Optimizing NNI: done in 0.299141 secs using 398.8% CPU
362  Q.yeast+R7    59522.381    315 119674.763   120805.899   120997.283
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.601497 secs using 399.5% CPU
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Iteration 260 / LogL: -36767.369 / Time: 0h:1m:54s (0h:0m:0s left)
Optimizing NNI: done in 0.38449 secs using 399.3% CPU
Optimizing NNI: done in 0.534809 secs using 399.4% CPU
TREE SEARCH COMPLETED AFTER 262 ITERATIONS / Time: 0h:1m:55s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36755.456
Optimal log-likelihood: -36755.456
Proportion of invariable sites: 0.021
Gamma shape alpha: 2.498
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36755.456
Total tree length: 20.112

Total number of iterations: 262
CPU time used for tree search: 455.717 sec (0h:7m:35s)
Wall-clock time used for tree search: 115.295 sec (0h:1m:55s)
Total CPU time used: 458.421 sec (0h:7m:38s)
Total wall-clock time used: 115.927 sec (0h:1m:55s)

===> START BOOTSTRAP REPLICATE NUMBER 12

Creating bootstrap alignment (seed: 956171)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36473.814
2. Current log-likelihood: -35492.222
3. Current log-likelihood: -35470.146
4. Current log-likelihood: -35468.798
5. Current log-likelihood: -35468.617
Optimal log-likelihood: -35468.616
Proportion of invariable sites: 0.034
Gamma shape alpha: 2.796
Parameters optimization took 5 rounds (0.322 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0737369 secs using 397.3% CPU
Computing ML distances took 0.073872 sec (of wall-clock time) 0.293282 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000144005 secs using 418.7% CPU
Constructing RapidNJ tree: done in 0.00218916 secs using 487.6% CPU
Computing RapidNJ tree took 0.002394 sec (of wall-clock time) 0.012057 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35806.586
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 363  Q.yeast+R8    59515.869    317 119665.738   120824.428   120996.656
WARNING: Normalizing state frequencies so that sum of them equals to 1
1.678 second
Computing log-likelihood of 98 initial trees ... 1.615 seconds
Current best score: -35468.616

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.248976 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35430.490
Optimizing NNI: done in 0.198592 secs using 398.8% CPU
Optimizing NNI: done in 0.214287 secs using 396.7% CPU
Optimizing NNI: done in 0.218609 secs using 398% CPU
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Optimizing NNI: done in 0.23209 secs using 398.2% CPU
Iteration 10 / LogL: -35434.337 / Time: 0h:0m:6s
Optimizing NNI: done in 0.278155 secs using 397.2% CPU
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Optimizing NNI: done in 0.25619 secs using 398.2% CPU
108  Q.bird+F+R8   198079.035   1020 398198.069   2481038.069  402639.527
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.242806 secs using 397.1% CPU
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Iteration 20 / LogL: -35436.317 / Time: 0h:0m:8s
Finish initializing candidate tree set (5)
Current best tree score: -35430.490 / CPU time: 8.265
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.434526 secs using 397.8% CPU
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Iteration 30 / LogL: -35437.356 / Time: 0h:0m:13s (0h:0m:32s left)
Optimizing NNI: done in 0.392862 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -35430.127
Optimizing NNI: done in 0.524642 secs using 396.9% CPU
Optimizing NNI: done in 0.360269 secs using 397.8% CPU
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Optimizing NNI: done in 0.398979 secs using 399.1% CPU
Optimizing NNI: done in 0.389055 secs using 399.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -35430.126
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Optimizing NNI: done in 0.348223 secs using 399.4% CPU
Iteration 40 / LogL: -35432.537 / Time: 0h:0m:17s (0h:0m:40s left)
Optimizing NNI: done in 0.401697 secs using 398.4% CPU
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Iteration 50 / LogL: -35435.992 / Time: 0h:0m:21s (0h:0m:35s left)
Optimizing NNI: done in 0.309586 secs using 398.5% CPU
Optimizing NNI: done in 0.404473 secs using 397.7% CPU
364  Q.yeast+R9    59514.866    319 119667.732   120854.708   121007.046
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.377492 secs using 398.9% CPU
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Iteration 60 / LogL: -35433.218 / Time: 0h:0m:25s (0h:0m:30s left)
Optimizing NNI: done in 0.386187 secs using 400.2% CPU
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Iteration 70 / LogL: -35430.683 / Time: 0h:0m:29s (0h:0m:25s left)
Optimizing NNI: done in 0.420543 secs using 399% CPU
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370  Q.yeast+I+R6  59530.703    314 119689.406   120807.033   121007.728
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.398158 secs using 398.9% CPU
Iteration 80 / LogL: -35432.225 / Time: 0h:0m:32s (0h:0m:21s left)
Optimizing NNI: done in 0.309761 secs using 397.7% CPU
Optimizing NNI: done in 0.298883 secs using 397% CPU
Optimizing NNI: done in 0.351882 secs using 399.1% CPU
Optimizing NNI: done in 0.294388 secs using 399.8% CPU
Optimizing NNI: done in 0.341773 secs using 399.6% CPU
Optimizing NNI: done in 0.377236 secs using 399.3% CPU
Optimizing NNI: done in 0.517923 secs using 399.4% CPU
Optimizing NNI: done in 0.270002 secs using 399.6% CPU
Optimizing NNI: done in 0.449028 secs using 399.1% CPU
Optimizing NNI: done in 0.340761 secs using 399.7% CPU
Iteration 90 / LogL: -35432.987 / Time: 0h:0m:36s (0h:0m:16s left)
Optimizing NNI: done in 0.466157 secs using 398.2% CPU
Optimizing NNI: done in 0.36473 secs using 399% CPU
Optimizing NNI: done in 0.373394 secs using 398.8% CPU
Optimizing NNI: done in 0.369274 secs using 398% CPU
Optimizing NNI: done in 0.361341 secs using 398.3% CPU
Optimizing NNI: done in 0.378281 secs using 399.6% CPU
Optimizing NNI: done in 0.285215 secs using 399.5% CPU
Optimizing NNI: done in 0.370979 secs using 398.4% CPU
Optimizing NNI: done in 0.336571 secs using 397.6% CPU
Optimizing NNI: done in 0.445513 secs using 398.6% CPU
Iteration 100 / LogL: -35431.694 / Time: 0h:0m:40s (0h:0m:12s left)
Optimizing NNI: done in 0.499399 secs using 399.1% CPU
Optimizing NNI: done in 0.479084 secs using 398.7% CPU
Optimizing NNI: done in 0.319398 secs using 398.7% CPU
371  Q.yeast+I+R7  59521.895    316 119675.790   120820.613   121002.510
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.591733 secs using 397% CPU
Optimizing NNI: done in 0.425479 secs using 398.5% CPU
Optimizing NNI: done in 0.327783 secs using 398.6% CPU
Optimizing NNI: done in 0.346025 secs using 399.5% CPU
Optimizing NNI: done in 0.366139 secs using 397.4% CPU
Optimizing NNI: done in 0.482823 secs using 399% CPU
Optimizing NNI: done in 0.529202 secs using 397.7% CPU
Iteration 110 / LogL: -35431.694 / Time: 0h:0m:44s (0h:0m:8s left)
Optimizing NNI: done in 0.401731 secs using 398.6% CPU
Optimizing NNI: done in 0.298595 secs using 398.5% CPU
383  Q.yeast+F+R6  59600.416    332 119864.832   121255.474   121258.727
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.363347 secs using 398.1% CPU
Optimizing NNI: done in 0.356796 secs using 397.8% CPU
Optimizing NNI: done in 0.427607 secs using 397.8% CPU
Optimizing NNI: done in 0.627337 secs using 398.2% CPU
109  Q.bird+F+R9   198072.616   1022 398189.232   2489201.232  402639.398
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.354808 secs using 397.5% CPU
Optimizing NNI: done in 0.302607 secs using 398.5% CPU
Optimizing NNI: done in 0.34507 secs using 398.5% CPU
Optimizing NNI: done in 0.276319 secs using 398.8% CPU
Iteration 120 / LogL: -35432.912 / Time: 0h:0m:48s (0h:0m:4s left)
Optimizing NNI: done in 0.391512 secs using 398% CPU
Optimizing NNI: done in 0.383757 secs using 398.5% CPU
Optimizing NNI: done in 0.421196 secs using 399% CPU
Optimizing NNI: done in 0.353217 secs using 399.5% CPU
Optimizing NNI: done in 0.365452 secs using 397.9% CPU
Optimizing NNI: done in 0.460645 secs using 399.1% CPU
Optimizing NNI: done in 0.326311 secs using 398.3% CPU
Optimizing NNI: done in 0.435558 secs using 398.4% CPU
Optimizing NNI: done in 0.355184 secs using 398.2% CPU
Optimizing NNI: done in 0.430938 secs using 399.3% CPU
Iteration 130 / LogL: -35430.133 / Time: 0h:0m:52s (0h:0m:0s left)
Optimizing NNI: done in 0.415466 secs using 398.6% CPU
Optimizing NNI: done in 0.435863 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 132 ITERATIONS / Time: 0h:0m:53s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35430.126
Optimal log-likelihood: -35430.119
Proportion of invariable sites: 0.034
Gamma shape alpha: 2.770
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -35430.119
Total tree length: 19.348

Total number of iterations: 132
CPU time used for tree search: 205.591 sec (0h:3m:25s)
Wall-clock time used for tree search: 52.692 sec (0h:0m:52s)
Total CPU time used: 208.694 sec (0h:3m:28s)
Total wall-clock time used: 53.422 sec (0h:0m:53s)

===> START BOOTSTRAP REPLICATE NUMBER 13

Creating bootstrap alignment (seed: 956172)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.011 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36646.861
2. Current log-likelihood: -35818.801
3. Current log-likelihood: -35787.638
4. Current log-likelihood: -35786.262
5. Current log-likelihood: -35785.883
Optimal log-likelihood: -35785.732
Proportion of invariable sites: 0.044
Gamma shape alpha: 2.509
Parameters optimization took 5 rounds (0.335 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0773048 secs using 400% CPU
Computing ML distances took 0.077450 sec (of wall-clock time) 0.309560 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000137806 secs using 463.7% CPU
Constructing RapidNJ tree: done in 0.00124192 secs using 384.5% CPU
Computing RapidNJ tree took 0.001431 sec (of wall-clock time) 0.007315 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36361.762
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.584 second
Computing log-likelihood of 98 initial trees ... 1.533 seconds
Current best score: -35785.732

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.224455 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35729.774
Optimizing NNI: done in 0.250718 secs using 399.4% CPU
Optimizing NNI: done in 0.212608 secs using 399.4% CPU
Optimizing NNI: done in 0.224944 secs using 399.9% CPU
Optimizing NNI: done in 0.207922 secs using 399.3% CPU
Optimizing NNI: done in 0.237075 secs using 398.2% CPU
Optimizing NNI: done in 0.247861 secs using 398.5% CPU
Optimizing NNI: done in 0.18198 secs using 398.2% CPU
Optimizing NNI: done in 0.263232 secs using 398.2% CPU
Optimizing NNI: done in 0.262418 secs using 399.3% CPU
Iteration 10 / LogL: -35737.819 / Time: 0h:0m:6s
Optimizing NNI: done in 0.273842 secs using 399.1% CPU
Optimizing NNI: done in 0.276835 secs using 399.9% CPU
384  Q.yeast+F+R7  59583.663    334 119835.327   121260.677   121237.619
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.260547 secs using 399.4% CPU
Optimizing NNI: done in 0.26186 secs using 399.5% CPU
Optimizing NNI: done in 0.262453 secs using 398.1% CPU
Optimizing NNI: done in 0.273814 secs using 400.3% CPU
Optimizing NNI: done in 0.264534 secs using 398.5% CPU
Optimizing NNI: done in 0.270231 secs using 398.2% CPU
Optimizing NNI: done in 0.313604 secs using 398.2% CPU
Optimizing NNI: done in 0.313781 secs using 398.7% CPU
Iteration 20 / LogL: -35729.813 / Time: 0h:0m:8s
Finish initializing candidate tree set (5)
Current best tree score: -35729.774 / CPU time: 8.317
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.391702 secs using 398.4% CPU
Optimizing NNI: done in 0.376648 secs using 397.8% CPU
Optimizing NNI: done in 0.337019 secs using 399.4% CPU
Optimizing NNI: done in 0.333564 secs using 399% CPU
Optimizing NNI: done in 0.373981 secs using 399.6% CPU
Optimizing NNI: done in 0.433175 secs using 399.8% CPU
Optimizing NNI: done in 0.381539 secs using 399.3% CPU
Optimizing NNI: done in 0.283424 secs using 399% CPU
Optimizing NNI: done in 0.466081 secs using 399.6% CPU
Optimizing NNI: done in 0.392975 secs using 398.7% CPU
Iteration 30 / LogL: -35729.817 / Time: 0h:0m:12s (0h:0m:31s left)
385  Q.yeast+F+R8  59576.754    336 119825.507   121286.565   121236.196
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.430866 secs using 398.7% CPU
Optimizing NNI: done in 0.378441 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35729.744
Optimizing NNI: done in 0.289894 secs using 398.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -35729.743
Optimizing NNI: done in 0.377499 secs using 399.3% CPU
Optimizing NNI: done in 0.424732 secs using 399.7% CPU
Optimizing NNI: done in 0.407879 secs using 399.4% CPU
Optimizing NNI: done in 0.449001 secs using 398.7% CPU
Optimizing NNI: done in 0.344813 secs using 399.5% CPU
Optimizing NNI: done in 0.448515 secs using 398.7% CPU
Optimizing NNI: done in 0.420774 secs using 399.5% CPU
Iteration 40 / LogL: -35730.465 / Time: 0h:0m:16s (0h:0m:26s left)
Optimizing NNI: done in 0.435697 secs using 398.8% CPU
Optimizing NNI: done in 0.378414 secs using 399.2% CPU
Optimizing NNI: done in 0.346416 secs using 398.9% CPU
Optimizing NNI: done in 0.37822 secs using 397.9% CPU
Optimizing NNI: done in 0.387755 secs using 399.5% CPU
Optimizing NNI: done in 0.445473 secs using 399% CPU
Optimizing NNI: done in 0.390566 secs using 397.4% CPU
Optimizing NNI: done in 0.390905 secs using 398.8% CPU
Optimizing NNI: done in 0.429396 secs using 399.3% CPU
Optimizing NNI: done in 0.408605 secs using 399.4% CPU
Iteration 50 / LogL: -35729.908 / Time: 0h:0m:20s (0h:0m:21s left)
Optimizing NNI: done in 0.401022 secs using 400.3% CPU
Optimizing NNI: done in 0.296243 secs using 399.5% CPU
Optimizing NNI: done in 0.330444 secs using 399.2% CPU
Optimizing NNI: done in 0.299425 secs using 399.9% CPU
 21  LG+I+R9       105437.969   552 211979.939   822491.939   214202.217
Optimizing NNI: done in 0.44181 secs using 398.9% CPU
Optimizing NNI: done in 0.357345 secs using 399.3% CPU
Optimizing NNI: done in 0.381461 secs using 400.5% CPU
Optimizing NNI: done in 0.378071 secs using 399.6% CPU
Optimizing NNI: done in 0.431023 secs using 399.9% CPU
Optimizing NNI: done in 0.482418 secs using 399% CPU
Iteration 60 / LogL: -35735.857 / Time: 0h:0m:24s (0h:0m:17s left)
Optimizing NNI: done in 0.406531 secs using 399.6% CPU
Optimizing NNI: done in 0.253201 secs using 399.1% CPU
Optimizing NNI: done in 0.408431 secs using 400% CPU
Optimizing NNI: done in 0.373126 secs using 399.3% CPU
Optimizing NNI: done in 0.378945 secs using 398.8% CPU
Optimizing NNI: done in 0.368195 secs using 399.5% CPU
Optimizing NNI: done in 0.391574 secs using 399.1% CPU
Optimizing NNI: done in 0.310802 secs using 399.4% CPU
Optimizing NNI: done in 0.349763 secs using 399.5% CPU
Optimizing NNI: done in 0.407436 secs using 399.6% CPU
Iteration 70 / LogL: -35736.123 / Time: 0h:0m:28s (0h:0m:12s left)
Optimizing NNI: done in 0.315983 secs using 399.2% CPU
Optimizing NNI: done in 0.363959 secs using 399% CPU
Optimizing NNI: done in 0.394143 secs using 399.9% CPU
386  Q.yeast+F+R9  59576.014    338 119828.027   121325.831   121247.113
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.395963 secs using 398% CPU
Optimizing NNI: done in 0.347829 secs using 400.3% CPU
Optimizing NNI: done in 0.377557 secs using 399.3% CPU
Optimizing NNI: done in 0.322881 secs using 399.2% CPU
Optimizing NNI: done in 0.393395 secs using 399.5% CPU
Optimizing NNI: done in 0.390477 secs using 399.1% CPU
Optimizing NNI: done in 0.415785 secs using 399.3% CPU
Iteration 80 / LogL: -35730.862 / Time: 0h:0m:32s (0h:0m:8s left)
110  Q.bird+F+R10  198068.569   1024 398185.139   2497385.139  402644.013
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.402017 secs using 398.3% CPU
Optimizing NNI: done in 0.33722 secs using 399% CPU
Optimizing NNI: done in 0.413134 secs using 399.5% CPU
Optimizing NNI: done in 0.290704 secs using 399.6% CPU
Optimizing NNI: done in 0.383074 secs using 398.5% CPU
Optimizing NNI: done in 0.578584 secs using 399.1% CPU
Optimizing NNI: done in 0.326884 secs using 398.3% CPU
Optimizing NNI: done in 0.396732 secs using 399.5% CPU
Optimizing NNI: done in 0.431167 secs using 399.8% CPU
Optimizing NNI: done in 0.399669 secs using 399.5% CPU
Iteration 90 / LogL: -35735.262 / Time: 0h:0m:36s (0h:0m:4s left)
Optimizing NNI: done in 0.420855 secs using 399.8% CPU
Optimizing NNI: done in 0.452059 secs using 399.1% CPU
392  Q.yeast+F+I+R6 59601.742    333 119869.483   121277.357   121267.577
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.358593 secs using 399% CPU
Optimizing NNI: done in 0.437099 secs using 399.2% CPU
Optimizing NNI: done in 0.472494 secs using 399.2% CPU
Optimizing NNI: done in 0.345371 secs using 399.3% CPU
Optimizing NNI: done in 0.395239 secs using 400.1% CPU
Optimizing NNI: done in 0.371496 secs using 398.8% CPU
Optimizing NNI: done in 0.327809 secs using 399.3% CPU
Optimizing NNI: done in 0.324193 secs using 398.5% CPU
Iteration 100 / LogL: -35729.769 / Time: 0h:0m:40s (0h:0m:0s left)
Optimizing NNI: done in 0.314791 secs using 399% CPU
Optimizing NNI: done in 0.450628 secs using 399.7% CPU
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:40s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35729.743
Optimal log-likelihood: -35729.741
Proportion of invariable sites: 0.043
Gamma shape alpha: 2.474
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -35729.741
Total tree length: 19.433

Total number of iterations: 102
CPU time used for tree search: 156.341 sec (0h:2m:36s)
Wall-clock time used for tree search: 40.216 sec (0h:0m:40s)
Total CPU time used: 159.302 sec (0h:2m:39s)
Total wall-clock time used: 40.909 sec (0h:0m:40s)

===> START BOOTSTRAP REPLICATE NUMBER 14

Creating bootstrap alignment (seed: 956173)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37320.435
2. Current log-likelihood: -36442.868
3. Current log-likelihood: -36424.648
4. Current log-likelihood: -36424.232
Optimal log-likelihood: -36424.166
Proportion of invariable sites: 0.029
Gamma shape alpha: 2.722
Parameters optimization took 4 rounds (0.261 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0797901 secs using 400% CPU
Computing ML distances took 0.079926 sec (of wall-clock time) 0.319449 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000152826 secs using 415.5% CPU
Constructing RapidNJ tree: done in 0.00208306 secs using 437.9% CPU
Computing RapidNJ tree took 0.002288 sec (of wall-clock time) 0.011518 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37048.032
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.425 second
Computing log-likelihood of 98 initial trees ... 1.563 seconds
Current best score: -36424.166

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.216345 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36386.992
Optimizing NNI: done in 0.270688 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36371.897
Optimizing NNI: done in 0.277526 secs using 397.6% CPU
Optimizing NNI: done in 0.289617 secs using 400% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -36369.822
Optimizing NNI: done in 0.310809 secs using 397.8% CPU
119  Q.mammal+R8   196715.407   1001 395432.814   2401436.814  399791.538
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.261156 secs using 399.4% CPU
Optimizing NNI: done in 0.297691 secs using 398.5% CPU
Optimizing NNI: done in 0.261951 secs using 399% CPU
Optimizing NNI: done in 0.313405 secs using 399.5% CPU
Optimizing NNI: done in 0.300729 secs using 399.5% CPU
Iteration 10 / LogL: -36369.837 / Time: 0h:0m:6s
Optimizing NNI: done in 0.293661 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 11: -36369.014
Optimizing NNI: done in 0.283777 secs using 399.4% CPU
Optimizing NNI: done in 0.291886 secs using 399.4% CPU
Optimizing NNI: done in 0.271361 secs using 399.1% CPU
Optimizing NNI: done in 0.296714 secs using 399.2% CPU
Optimizing NNI: done in 0.272609 secs using 399.2% CPU
Optimizing NNI: done in 0.316842 secs using 398.7% CPU
Optimizing NNI: done in 0.250045 secs using 397.5% CPU
Optimizing NNI: done in 0.297801 secs using 399.8% CPU
Optimizing NNI: done in 0.296125 secs using 398.2% CPU
Iteration 20 / LogL: -36372.297 / Time: 0h:0m:9s
Finish initializing candidate tree set (7)
Current best tree score: -36369.014 / CPU time: 8.907
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.395941 secs using 399.2% CPU
Optimizing NNI: done in 0.378234 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -36368.968
Optimizing NNI: done in 0.406349 secs using 399.5% CPU
Optimizing NNI: done in 0.509525 secs using 398.9% CPU
Optimizing NNI: done in 0.353459 secs using 400.2% CPU
Optimizing NNI: done in 0.489066 secs using 399.1% CPU
Optimizing NNI: done in 0.40254 secs using 398.9% CPU
Optimizing NNI: done in 0.390649 secs using 398.7% CPU
Optimizing NNI: done in 0.460514 secs using 399% CPU
Optimizing NNI: done in 0.370184 secs using 400.4% CPU
Iteration 30 / LogL: -36370.047 / Time: 0h:0m:13s (0h:0m:43s left)
Optimizing NNI: done in 0.351911 secs using 399.2% CPU
Optimizing NNI: done in 0.397178 secs using 398.4% CPU
Optimizing NNI: done in 0.49929 secs using 399.6% CPU
Optimizing NNI: done in 0.289981 secs using 399.5% CPU
Optimizing NNI: done in 0.385075 secs using 398.5% CPU
Optimizing NNI: done in 0.472375 secs using 399.5% CPU
Optimizing NNI: done in 0.471174 secs using 399.7% CPU
Optimizing NNI: done in 0.506073 secs using 399.1% CPU
Optimizing NNI: done in 0.397213 secs using 399.4% CPU
Optimizing NNI: done in 0.424805 secs using 398.9% CPU
Iteration 40 / LogL: -36370.342 / Time: 0h:0m:17s (0h:0m:37s left)
Optimizing NNI: done in 0.397922 secs using 399.3% CPU
Optimizing NNI: done in 0.357359 secs using 399.3% CPU
Optimizing NNI: done in 0.426941 secs using 399.7% CPU
Optimizing NNI: done in 0.445347 secs using 398.8% CPU
Optimizing NNI: done in 0.353325 secs using 398.9% CPU
Optimizing NNI: done in 0.422822 secs using 399.6% CPU
Optimizing NNI: done in 0.338224 secs using 399.5% CPU
Optimizing NNI: done in 0.310797 secs using 398.3% CPU
Optimizing NNI: done in 0.411197 secs using 399.4% CPU
Optimizing NNI: done in 0.485438 secs using 399.2% CPU
Iteration 50 / LogL: -36381.917 / Time: 0h:0m:21s (0h:0m:32s left)
Optimizing NNI: done in 0.417646 secs using 398.8% CPU
393  Q.yeast+F+I+R7 59583.173    335 119836.346   121279.423   121242.836
Optimizing NNI: done in 0.401705 secs using 399.5% CPU
Optimizing NNI: done in 0.405419 secs using 399.3% CPU
Optimizing NNI: done in 0.359583 secs using 399.4% CPU
Optimizing NNI: done in 0.3802 secs using 399.3% CPU
Optimizing NNI: done in 0.347277 secs using 397.9% CPU
Optimizing NNI: done in 0.407462 secs using 398.8% CPU
405  JTTDCMut+R6   60065.179    313 120756.357   121860.649   122070.481
Optimizing NNI: done in 0.419738 secs using 399.3% CPU
Optimizing NNI: done in 0.422789 secs using 399% CPU
120  Q.mammal+R9   196707.402   1003 395420.804   2409444.804  399788.237
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.396642 secs using 399.4% CPU
Iteration 60 / LogL: -36407.841 / Time: 0h:0m:25s (0h:0m:27s left)
Optimizing NNI: done in 0.546471 secs using 399.6% CPU
Optimizing NNI: done in 0.402462 secs using 398.7% CPU
Optimizing NNI: done in 0.415062 secs using 399.3% CPU
Optimizing NNI: done in 0.476116 secs using 399.4% CPU
Optimizing NNI: done in 0.315769 secs using 398.6% CPU
Optimizing NNI: done in 0.378814 secs using 399.9% CPU
Optimizing NNI: done in 0.402129 secs using 398.9% CPU
Optimizing NNI: done in 0.370177 secs using 400.4% CPU
Optimizing NNI: done in 0.353918 secs using 399.1% CPU
Optimizing NNI: done in 0.330642 secs using 399.7% CPU
Iteration 70 / LogL: -36370.643 / Time: 0h:0m:29s (0h:0m:22s left)
Optimizing NNI: done in 0.4703 secs using 399.4% CPU
Optimizing NNI: done in 0.326497 secs using 399.5% CPU
Optimizing NNI: done in 0.311708 secs using 398.4% CPU
Optimizing NNI: done in 0.423284 secs using 400% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36368.939
Optimizing NNI: done in 0.300152 secs using 399.3% CPU
Optimizing NNI: done in 0.307313 secs using 399.6% CPU
Optimizing NNI: done in 0.361537 secs using 399.3% CPU
Optimizing NNI: done in 0.410449 secs using 398.9% CPU
Optimizing NNI: done in 0.441363 secs using 398.9% CPU
Optimizing NNI: done in 0.420234 secs using 399.5% CPU
Iteration 80 / LogL: -36368.994 / Time: 0h:0m:33s (0h:0m:17s left)
Optimizing NNI: done in 0.308028 secs using 399.9% CPU
Optimizing NNI: done in 0.45491 secs using 399.9% CPU
406  JTTDCMut+R7   60051.419    315 120732.838   121863.974   122055.359
Optimizing NNI: done in 0.325005 secs using 398.7% CPU
Optimizing NNI: done in 0.539742 secs using 398.6% CPU
Optimizing NNI: done in 0.301695 secs using 399.1% CPU
Optimizing NNI: done in 0.464596 secs using 398% CPU
Optimizing NNI: done in 0.384411 secs using 399.1% CPU
Optimizing NNI: done in 0.329844 secs using 399.5% CPU
Optimizing NNI: done in 0.414219 secs using 398.6% CPU
Optimizing NNI: done in 0.387446 secs using 398.8% CPU
Iteration 90 / LogL: -36368.979 / Time: 0h:0m:37s (0h:0m:13s left)
Optimizing NNI: done in 0.344612 secs using 399.5% CPU
Optimizing NNI: done in 0.478267 secs using 398.7% CPU
Optimizing NNI: done in 0.472993 secs using 398.4% CPU
407  JTTDCMut+R8   60045.997    317 120725.994   121884.683   122056.911
Optimizing NNI: done in 0.401805 secs using 398.5% CPU
Optimizing NNI: done in 0.427133 secs using 398.8% CPU
Optimizing NNI: done in 0.343331 secs using 399.1% CPU
Optimizing NNI: done in 0.441727 secs using 398.8% CPU
Optimizing NNI: done in 0.315098 secs using 398.9% CPU
Optimizing NNI: done in 0.405777 secs using 398.3% CPU
Optimizing NNI: done in 0.381227 secs using 397.7% CPU
Iteration 100 / LogL: -36373.122 / Time: 0h:0m:41s (0h:0m:9s left)
Optimizing NNI: done in 0.445715 secs using 399.1% CPU
Optimizing NNI: done in 0.422855 secs using 400% CPU
Optimizing NNI: done in 0.442403 secs using 398.6% CPU
Optimizing NNI: done in 0.387071 secs using 399% CPU
Optimizing NNI: done in 0.456278 secs using 399% CPU
Optimizing NNI: done in 0.346056 secs using 399.1% CPU
Optimizing NNI: done in 0.470707 secs using 399.2% CPU
Optimizing NNI: done in 0.35612 secs using 399.3% CPU
Optimizing NNI: done in 0.429729 secs using 399.7% CPU
Optimizing NNI: done in 0.626093 secs using 399.2% CPU
Iteration 110 / LogL: -36408.833 / Time: 0h:0m:46s (0h:0m:5s left)
Optimizing NNI: done in 0.456605 secs using 398.5% CPU
Optimizing NNI: done in 0.446449 secs using 399.4% CPU
Optimizing NNI: done in 0.548769 secs using 399.2% CPU
414  JTTDCMut+I+R6 60061.676    314 120751.351   121868.978   122069.673
Optimizing NNI: done in 0.587369 secs using 398.6% CPU
121  Q.mammal+R10  196703.479   1005 395416.958   2417476.958  399793.100
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.515005 secs using 399.3% CPU
Optimizing NNI: done in 0.425383 secs using 399.8% CPU
Optimizing NNI: done in 0.281314 secs using 399.8% CPU
Optimizing NNI: done in 0.375873 secs using 399.6% CPU
Optimizing NNI: done in 0.364837 secs using 399.5% CPU
Optimizing NNI: done in 0.382626 secs using 399.6% CPU
Iteration 120 / LogL: -36369.294 / Time: 0h:0m:50s (0h:0m:0s left)
Optimizing NNI: done in 0.281068 secs using 399.8% CPU
Optimizing NNI: done in 0.301186 secs using 398.8% CPU
Optimizing NNI: done in 0.42953 secs using 399.5% CPU
TREE SEARCH COMPLETED AFTER 123 ITERATIONS / Time: 0h:0m:51s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36368.939
Optimal log-likelihood: -36368.936
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.791
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -36368.936
Total tree length: 19.633

Total number of iterations: 123
CPU time used for tree search: 200.438 sec (0h:3m:20s)
Wall-clock time used for tree search: 51.134 sec (0h:0m:51s)
Total CPU time used: 202.722 sec (0h:3m:22s)
Total wall-clock time used: 51.675 sec (0h:0m:51s)

===> START BOOTSTRAP REPLICATE NUMBER 15

Creating bootstrap alignment (seed: 956174)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.018 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36436.672
2. Current log-likelihood: -35578.219
3. Current log-likelihood: -35564.373
4. Current log-likelihood: -35564.032
Optimal log-likelihood: -35563.968
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.511
Parameters optimization took 4 rounds (0.265 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0755949 secs using 398.7% CPU
Computing ML distances took 0.075726 sec (of wall-clock time) 0.301558 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000150919 secs using 426.7% CPU
Constructing RapidNJ tree: done in 0.00208998 secs using 473.3% CPU
Computing RapidNJ tree took 0.002299 sec (of wall-clock time) 0.011626 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35903.063
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.504 second
Computing log-likelihood of 98 initial trees ... 1.613 seconds
Current best score: -35563.968

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.186489 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35515.863
Optimizing NNI: done in 0.401544 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35513.888
Optimizing NNI: done in 0.361557 secs using 397.2% CPU
Optimizing NNI: done in 0.240037 secs using 399.4% CPU
Optimizing NNI: done in 0.441345 secs using 398.4% CPU
Optimizing NNI: done in 0.370527 secs using 399.2% CPU
BETTER TREE FOUND at iteration 6: -35513.880
Optimizing NNI: done in 0.25083 secs using 399.6% CPU
Optimizing NNI: done in 0.247691 secs using 400.4% CPU
Optimizing NNI: done in 0.410045 secs using 399.3% CPU
Optimizing NNI: done in 0.228891 secs using 399.4% CPU
Iteration 10 / LogL: -35514.550 / Time: 0h:0m:6s
Optimizing NNI: done in 0.260526 secs using 398.9% CPU
Optimizing NNI: done in 0.220095 secs using 398.5% CPU
Optimizing NNI: done in 0.219455 secs using 399.8% CPU
Optimizing NNI: done in 0.39635 secs using 399.1% CPU
Optimizing NNI: done in 0.42193 secs using 399.3% CPU
Optimizing NNI: done in 0.247669 secs using 399.3% CPU
Optimizing NNI: done in 0.260125 secs using 399.4% CPU
Optimizing NNI: done in 0.255417 secs using 399.9% CPU
Optimizing NNI: done in 0.245985 secs using 399.8% CPU
Optimizing NNI: done in 0.229216 secs using 398.6% CPU
Iteration 20 / LogL: -35518.184 / Time: 0h:0m:9s
Finish initializing candidate tree set (7)
Current best tree score: -35513.880 / CPU time: 9.216
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
415  JTTDCMut+I+R7 60049.755    316 120731.509   121876.332   122058.228
Optimizing NNI: done in 0.454993 secs using 398.9% CPU
Optimizing NNI: done in 0.441953 secs using 399.3% CPU
Optimizing NNI: done in 0.495686 secs using 399.8% CPU
Optimizing NNI: done in 0.40436 secs using 399.1% CPU
130  Q.mammal+F+R8 196877.834   1020 395795.669   2478635.669  400237.126
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.590689 secs using 398.7% CPU
Optimizing NNI: done in 0.489833 secs using 399.3% CPU
427  JTTDCMut+F+R6 60058.397    332 120780.793   122171.435   122174.688
Optimizing NNI: done in 0.54506 secs using 399.5% CPU
Optimizing NNI: done in 0.605223 secs using 398.9% CPU
Optimizing NNI: done in 0.485643 secs using 399.5% CPU
Optimizing NNI: done in 0.626395 secs using 399.7% CPU
Iteration 30 / LogL: -35514.030 / Time: 0h:0m:14s (0h:0m:38s left)
Optimizing NNI: done in 0.347714 secs using 399.3% CPU
Optimizing NNI: done in 0.304651 secs using 399.1% CPU
Optimizing NNI: done in 0.78564 secs using 399.4% CPU
Optimizing NNI: done in 0.31392 secs using 399.4% CPU
Optimizing NNI: done in 0.403428 secs using 399.3% CPU
Optimizing NNI: done in 0.448013 secs using 399.7% CPU
Optimizing NNI: done in 0.590177 secs using 399.2% CPU
Optimizing NNI: done in 0.534504 secs using 398.9% CPU
Optimizing NNI: done in 0.337567 secs using 398.2% CPU
Optimizing NNI: done in 0.419615 secs using 399.1% CPU
Iteration 40 / LogL: -35918.240 / Time: 0h:0m:19s (0h:0m:32s left)
Optimizing NNI: done in 0.367484 secs using 399.7% CPU
Optimizing NNI: done in 0.365864 secs using 399.6% CPU
Optimizing NNI: done in 0.343542 secs using 399.3% CPU
Optimizing NNI: done in 0.542399 secs using 399.2% CPU
Optimizing NNI: done in 0.348333 secs using 399.5% CPU
Optimizing NNI: done in 0.452571 secs using 399.9% CPU
428  JTTDCMut+F+R7 60047.984    334 120763.969   122189.319   122166.261
Optimizing NNI: done in 0.503617 secs using 399.2% CPU
Optimizing NNI: done in 0.454985 secs using 399.1% CPU
Optimizing NNI: done in 0.632757 secs using 398.7% CPU
Optimizing NNI: done in 0.335745 secs using 399.6% CPU
Iteration 50 / LogL: -35568.453 / Time: 0h:0m:23s (0h:0m:27s left)
Optimizing NNI: done in 0.558754 secs using 399.5% CPU
Optimizing NNI: done in 0.439655 secs using 399.6% CPU
Optimizing NNI: done in 0.428143 secs using 399.2% CPU
Optimizing NNI: done in 0.45872 secs using 399.5% CPU
Optimizing NNI: done in 0.474572 secs using 398.5% CPU
Optimizing NNI: done in 0.399575 secs using 399.5% CPU
Optimizing NNI: done in 0.351173 secs using 399.3% CPU
429  JTTDCMut+F+R8 60041.317    336 120754.634   122215.692   122165.323
Optimizing NNI: done in 0.367846 secs using 398.7% CPU
Optimizing NNI: done in 0.375357 secs using 399.5% CPU
Optimizing NNI: done in 0.396982 secs using 399.7% CPU
Iteration 60 / LogL: -35514.295 / Time: 0h:0m:28s (0h:0m:21s left)
Optimizing NNI: done in 0.408622 secs using 399.5% CPU
Optimizing NNI: done in 0.347242 secs using 399.4% CPU
Optimizing NNI: done in 0.492434 secs using 399.2% CPU
Optimizing NNI: done in 0.512544 secs using 398.7% CPU
Optimizing NNI: done in 0.407939 secs using 399.5% CPU
Optimizing NNI: done in 0.403379 secs using 398.8% CPU
Optimizing NNI: done in 0.50136 secs using 399.2% CPU
Optimizing NNI: done in 0.444564 secs using 398.4% CPU
Optimizing NNI: done in 0.296867 secs using 398.3% CPU
Optimizing NNI: done in 0.326406 secs using 399.1% CPU
Iteration 70 / LogL: -35514.114 / Time: 0h:0m:32s (0h:0m:16s left)
 22  LG+I+R10      105433.974   554 211975.948   826915.948   214206.278
Optimizing NNI: done in 0.995587 secs using 399.2% CPU
Optimizing NNI: done in 0.316304 secs using 399.6% CPU
Optimizing NNI: done in 0.472281 secs using 398.9% CPU
Optimizing NNI: done in 0.451013 secs using 398.5% CPU
Optimizing NNI: done in 0.450968 secs using 399.1% CPU
Optimizing NNI: done in 0.530983 secs using 400.3% CPU
Optimizing NNI: done in 0.521967 secs using 398.7% CPU
Optimizing NNI: done in 0.893833 secs using 398.4% CPU
Optimizing NNI: done in 0.381646 secs using 399% CPU
Optimizing NNI: done in 0.394825 secs using 399.5% CPU
Iteration 80 / LogL: -35514.084 / Time: 0h:0m:37s (0h:0m:12s left)
Optimizing NNI: done in 0.290728 secs using 398.9% CPU
Optimizing NNI: done in 0.346087 secs using 399.5% CPU
Optimizing NNI: done in 0.885604 secs using 398.5% CPU
Optimizing NNI: done in 0.440902 secs using 399.4% CPU
Optimizing NNI: done in 0.395411 secs using 399.4% CPU
Optimizing NNI: done in 0.570297 secs using 398.7% CPU
430  JTTDCMut+F+R9 60039.752    338 120755.505   122253.309   122174.590
Optimizing NNI: done in 0.397532 secs using 399% CPU
Optimizing NNI: done in 0.345564 secs using 399% CPU
Optimizing NNI: done in 0.311879 secs using 399.4% CPU
Optimizing NNI: done in 0.263986 secs using 400.2% CPU
Iteration 90 / LogL: -35514.148 / Time: 0h:0m:41s (0h:0m:7s left)
Optimizing NNI: done in 0.301008 secs using 399% CPU
Optimizing NNI: done in 0.521249 secs using 399% CPU
Optimizing NNI: done in 0.353367 secs using 398.7% CPU
Optimizing NNI: done in 0.355256 secs using 399.2% CPU
Optimizing NNI: done in 0.460183 secs using 399.7% CPU
Optimizing NNI: done in 0.574212 secs using 399% CPU
Optimizing NNI: done in 1.00594 secs using 399.4% CPU
Optimizing NNI: done in 0.585458 secs using 399.4% CPU
Optimizing NNI: done in 0.433339 secs using 399.7% CPU
Optimizing NNI: done in 0.384275 secs using 399.1% CPU
Iteration 100 / LogL: -35514.392 / Time: 0h:0m:46s (0h:0m:2s left)
Optimizing NNI: done in 0.600015 secs using 399.2% CPU
Optimizing NNI: done in 0.366387 secs using 399.6% CPU
Optimizing NNI: done in 0.393982 secs using 399.4% CPU
436  JTTDCMut+F+I+R6 60055.030    333 120776.060   122183.933   122174.153
Optimizing NNI: done in 0.518089 secs using 399.2% CPU
Optimizing NNI: done in 0.336255 secs using 399.8% CPU
Optimizing NNI: done in 0.515743 secs using 399.7% CPU
Optimizing NNI: done in 0.419934 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 107 ITERATIONS / Time: 0h:0m:50s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35513.880
Optimal log-likelihood: -35513.879
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.471
Parameters optimization took 1 rounds (0.047 sec)
BEST SCORE FOUND : -35513.879
Total tree length: 19.522

Total number of iterations: 107
CPU time used for tree search: 194.568 sec (0h:3m:14s)
Wall-clock time used for tree search: 49.709 sec (0h:0m:49s)
Total CPU time used: 196.694 sec (0h:3m:16s)
Total wall-clock time used: 50.223 sec (0h:0m:50s)

===> START BOOTSTRAP REPLICATE NUMBER 16

Creating bootstrap alignment (seed: 956175)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.010 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -38040.830
2. Current log-likelihood: -37030.452
3. Current log-likelihood: -37016.787
4. Current log-likelihood: -37015.636
5. Current log-likelihood: -37015.045
Optimal log-likelihood: -37015.038
Proportion of invariable sites: 0.013
Gamma shape alpha: 2.764
Parameters optimization took 5 rounds (0.335 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0818059 secs using 400.9% CPU
Computing ML distances took 0.081941 sec (of wall-clock time) 0.328129 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000156164 secs using 439.9% CPU
Constructing RapidNJ tree: done in 0.00220394 secs using 473.9% CPU
Computing RapidNJ tree took 0.002418 sec (of wall-clock time) 0.012239 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37523.220
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.432 second
131  Q.mammal+F+R9 196872.663   1022 395789.327   2486801.327  400239.493
Computing log-likelihood of 98 initial trees ... 1.602 seconds
Current best score: -37015.038

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.375594 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36979.235
Optimizing NNI: done in 0.295669 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36979.156
Optimizing NNI: done in 0.299325 secs using 399.4% CPU
Optimizing NNI: done in 0.411292 secs using 399.6% CPU
Optimizing NNI: done in 0.306477 secs using 399.1% CPU
Optimizing NNI: done in 0.39079 secs using 399.2% CPU
Optimizing NNI: done in 0.392337 secs using 399.4% CPU
Optimizing NNI: done in 0.377796 secs using 399.5% CPU
Optimizing NNI: done in 0.390974 secs using 399.1% CPU
Optimizing NNI: done in 0.350334 secs using 399.2% CPU
Iteration 10 / LogL: -36989.963 / Time: 0h:0m:7s
Optimizing NNI: done in 0.419879 secs using 398.9% CPU
Optimizing NNI: done in 0.253884 secs using 399.5% CPU
Optimizing NNI: done in 0.307351 secs using 399.9% CPU
Optimizing NNI: done in 0.319869 secs using 399.6% CPU
Optimizing NNI: done in 0.423916 secs using 399.5% CPU
Optimizing NNI: done in 0.506056 secs using 399.4% CPU
Optimizing NNI: done in 0.503707 secs using 399.1% CPU
 43  LG+F+I+R9     105583.661   571 212309.321   865533.321   214608.091
Optimizing NNI: done in 0.435373 secs using 399.2% CPU
Optimizing NNI: done in 0.440661 secs using 399.2% CPU
Optimizing NNI: done in 0.432521 secs using 399% CPU
Iteration 20 / LogL: -37008.830 / Time: 0h:0m:11s
Finish initializing candidate tree set (10)
Current best tree score: -36979.156 / CPU time: 10.826
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.475146 secs using 399.5% CPU
437  JTTDCMut+F+I+R7 60046.210    335 120762.419   122205.496   122168.910
Optimizing NNI: done in 0.43463 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -36977.922
Optimizing NNI: done in 0.466189 secs using 399.4% CPU
Optimizing NNI: done in 0.339098 secs using 399.7% CPU
Optimizing NNI: done in 0.342741 secs using 398.4% CPU
Optimizing NNI: done in 0.473202 secs using 399.8% CPU
Optimizing NNI: done in 0.257251 secs using 399.7% CPU
Optimizing NNI: done in 0.47005 secs using 399.5% CPU
Optimizing NNI: done in 0.554778 secs using 399.6% CPU
Optimizing NNI: done in 0.511215 secs using 398% CPU
Iteration 30 / LogL: -36977.957 / Time: 0h:0m:15s (0h:0m:50s left)
Optimizing NNI: done in 0.402335 secs using 399.9% CPU
Optimizing NNI: done in 0.506205 secs using 399.2% CPU
Optimizing NNI: done in 0.47001 secs using 399.1% CPU
Optimizing NNI: done in 0.543973 secs using 399% CPU
Optimizing NNI: done in 0.488058 secs using 399.9% CPU
Optimizing NNI: done in 0.360696 secs using 399.8% CPU
Optimizing NNI: done in 0.374174 secs using 399.5% CPU
Optimizing NNI: done in 0.424707 secs using 399.5% CPU
Optimizing NNI: done in 0.447922 secs using 399.4% CPU
Optimizing NNI: done in 0.552574 secs using 399.1% CPU
Iteration 40 / LogL: -36979.580 / Time: 0h:0m:20s (0h:0m:42s left)
Optimizing NNI: done in 0.452923 secs using 399.3% CPU
Optimizing NNI: done in 0.28752 secs using 398.2% CPU
Optimizing NNI: done in 0.371139 secs using 399.2% CPU
Optimizing NNI: done in 0.560932 secs using 399.1% CPU
141  Q.insect+R8   195081.318   1001 392164.635   2398168.635  396523.360
Optimizing NNI: done in 0.454561 secs using 399.1% CPU
Optimizing NNI: done in 0.430625 secs using 399.6% CPU
Optimizing NNI: done in 0.424279 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36977.877
Optimizing NNI: done in 0.296865 secs using 399.5% CPU
Optimizing NNI: done in 0.451928 secs using 399.1% CPU
Optimizing NNI: done in 0.509373 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -36977.875
Iteration 50 / LogL: -36977.875 / Time: 0h:0m:24s (0h:0m:36s left)
Optimizing NNI: done in 0.429843 secs using 399.9% CPU
Optimizing NNI: done in 0.290426 secs using 399.5% CPU
Optimizing NNI: done in 0.385859 secs using 399.7% CPU
Optimizing NNI: done in 0.460709 secs using 399.7% CPU
Optimizing NNI: done in 0.623227 secs using 398.9% CPU
Optimizing NNI: done in 0.265313 secs using 400.2% CPU
Optimizing NNI: done in 0.410631 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36977.831
Optimizing NNI: done in 0.377316 secs using 398.4% CPU
449  DCMut+R6      60668.488    313 121962.975   123067.268   123277.099
Optimizing NNI: done in 0.461904 secs using 399.4% CPU
Optimizing NNI: done in 0.346035 secs using 399.4% CPU
Iteration 60 / LogL: -36979.596 / Time: 0h:0m:28s (0h:0m:30s left)
Optimizing NNI: done in 0.367776 secs using 399.2% CPU
Optimizing NNI: done in 0.395978 secs using 400.3% CPU
Optimizing NNI: done in 0.389077 secs using 398.6% CPU
Optimizing NNI: done in 0.434178 secs using 399.5% CPU
Optimizing NNI: done in 0.400114 secs using 398.5% CPU
Optimizing NNI: done in 0.508028 secs using 398.3% CPU
Optimizing NNI: done in 0.360775 secs using 399.2% CPU
Optimizing NNI: done in 0.38499 secs using 399.8% CPU
Optimizing NNI: done in 0.372911 secs using 399.6% CPU
Optimizing NNI: done in 0.425245 secs using 399.4% CPU
Iteration 70 / LogL: -37017.163 / Time: 0h:0m:32s (0h:0m:24s left)
Optimizing NNI: done in 0.516932 secs using 399.2% CPU
Optimizing NNI: done in 0.302822 secs using 399.8% CPU
Optimizing NNI: done in 0.426238 secs using 399.6% CPU
Optimizing NNI: done in 0.45275 secs using 399.2% CPU
Optimizing NNI: done in 0.494133 secs using 399.2% CPU
Optimizing NNI: done in 0.41686 secs using 399.1% CPU
Optimizing NNI: done in 0.321716 secs using 398.5% CPU
Optimizing NNI: done in 0.397573 secs using 399.6% CPU
Optimizing NNI: done in 0.484802 secs using 398.7% CPU
Optimizing NNI: done in 0.408002 secs using 399.3% CPU
Iteration 80 / LogL: -37002.210 / Time: 0h:0m:37s (0h:0m:19s left)
Optimizing NNI: done in 0.397185 secs using 399% CPU
Optimizing NNI: done in 0.396823 secs using 399.4% CPU
Optimizing NNI: done in 0.380404 secs using 399.6% CPU
Optimizing NNI: done in 0.421626 secs using 399.3% CPU
Optimizing NNI: done in 0.477963 secs using 398.4% CPU
Optimizing NNI: done in 0.456843 secs using 399.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -36977.826
Optimizing NNI: done in 0.465691 secs using 399.2% CPU
Optimizing NNI: done in 0.356317 secs using 400.7% CPU
Optimizing NNI: done in 0.366821 secs using 399.8% CPU
Optimizing NNI: done in 0.422194 secs using 399.6% CPU
Iteration 90 / LogL: -36978.316 / Time: 0h:0m:41s (0h:0m:14s left)
Optimizing NNI: done in 0.382275 secs using 399.3% CPU
Optimizing NNI: done in 0.517543 secs using 399% CPU
Optimizing NNI: done in 0.446292 secs using 399% CPU
142  Q.insect+R9   195076.551   1003 392159.102   2406183.102  396526.535
Optimizing NNI: done in 0.420648 secs using 398.6% CPU
Optimizing NNI: done in 0.505342 secs using 399.8% CPU
Optimizing NNI: done in 0.523309 secs using 399.4% CPU
450  DCMut+R7      60652.813    315 121935.626   123066.762   123258.147
Optimizing NNI: done in 0.412474 secs using 398.6% CPU
Optimizing NNI: done in 0.440964 secs using 398.9% CPU
Optimizing NNI: done in 0.436957 secs using 398.8% CPU
Optimizing NNI: done in 0.452234 secs using 399.3% CPU
Iteration 100 / LogL: -36979.246 / Time: 0h:0m:45s (0h:0m:10s left)
Optimizing NNI: done in 0.487289 secs using 399.5% CPU
Optimizing NNI: done in 0.457479 secs using 399.1% CPU
Optimizing NNI: done in 0.399995 secs using 400.3% CPU
Optimizing NNI: done in 0.458305 secs using 399.6% CPU
Optimizing NNI: done in 0.48406 secs using 399.6% CPU
Optimizing NNI: done in 0.437122 secs using 399.3% CPU
Optimizing NNI: done in 0.501958 secs using 398.1% CPU
Optimizing NNI: done in 0.315886 secs using 400.6% CPU
Optimizing NNI: done in 0.502179 secs using 399% CPU
Optimizing NNI: done in 0.40673 secs using 399.8% CPU
Iteration 110 / LogL: -36978.019 / Time: 0h:0m:50s (0h:0m:5s left)
Optimizing NNI: done in 0.422623 secs using 399.6% CPU
Optimizing NNI: done in 0.3663 secs using 399.3% CPU
Optimizing NNI: done in 0.569613 secs using 399.4% CPU
Optimizing NNI: done in 0.486944 secs using 399.6% CPU
Optimizing NNI: done in 0.48213 secs using 399.6% CPU
Optimizing NNI: done in 0.371776 secs using 399.3% CPU
Optimizing NNI: done in 0.554974 secs using 399.1% CPU
451  DCMut+R8      60648.578    317 121931.156   123089.845   123262.074
152  Q.insect+F+R8 194860.269   1020 391760.539   2474600.539  396201.996
Optimizing NNI: done in 0.299095 secs using 399.5% CPU
Optimizing NNI: done in 0.370071 secs using 399% CPU
Optimizing NNI: done in 0.450717 secs using 399.5% CPU
Iteration 120 / LogL: -36979.661 / Time: 0h:0m:54s (0h:0m:0s left)
Optimizing NNI: done in 0.401273 secs using 399.8% CPU
Optimizing NNI: done in 0.45147 secs using 399.4% CPU
Optimizing NNI: done in 0.500156 secs using 399.6% CPU
TREE SEARCH COMPLETED AFTER 123 ITERATIONS / Time: 0h:0m:56s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36977.826
Optimal log-likelihood: -36977.814
Proportion of invariable sites: 0.013
Gamma shape alpha: 2.747
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36977.814
Total tree length: 22.754

Total number of iterations: 123
CPU time used for tree search: 218.629 sec (0h:3m:38s)
Wall-clock time used for tree search: 55.674 sec (0h:0m:55s)
Total CPU time used: 221.218 sec (0h:3m:41s)
Total wall-clock time used: 56.293 sec (0h:0m:56s)

===> START BOOTSTRAP REPLICATE NUMBER 17

Creating bootstrap alignment (seed: 956176)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36593.343
2. Current log-likelihood: -35682.562
3. Current log-likelihood: -35673.420
4. Current log-likelihood: -35672.904
Optimal log-likelihood: -35672.771
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.207
Parameters optimization took 4 rounds (0.279 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0770791 secs using 400% CPU
Computing ML distances took 0.077213 sec (of wall-clock time) 0.308647 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000149012 secs using 416.7% CPU
Constructing RapidNJ tree: done in 0.00210094 secs using 488.5% CPU
Computing RapidNJ tree took 0.002307 sec (of wall-clock time) 0.011599 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36117.096
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.567 second
Computing log-likelihood of 98 initial trees ... 1.632 seconds
Current best score: -35586.985

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.517527 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35532.862
Optimizing NNI: done in 0.496597 secs using 399.6% CPU
Optimizing NNI: done in 0.497439 secs using 399.1% CPU
Optimizing NNI: done in 0.451697 secs using 398.2% CPU
Optimizing NNI: done in 0.23286 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -35530.768
Optimizing NNI: done in 0.535142 secs using 398.4% CPU
458  DCMut+I+R6    60665.033    314 121958.067   123075.694   123276.389
Optimizing NNI: done in 0.500454 secs using 397.5% CPU
Optimizing NNI: done in 0.286541 secs using 399.4% CPU
Optimizing NNI: done in 0.271092 secs using 398.6% CPU
Optimizing NNI: done in 0.219598 secs using 399.4% CPU
Iteration 10 / LogL: -35530.811 / Time: 0h:0m:7s
Optimizing NNI: done in 0.218257 secs using 399.8% CPU
Optimizing NNI: done in 0.252318 secs using 399.4% CPU
Optimizing NNI: done in 0.219053 secs using 398.3% CPU
Optimizing NNI: done in 0.234573 secs using 399.7% CPU
Optimizing NNI: done in 0.234793 secs using 399.3% CPU
Optimizing NNI: done in 0.28731 secs using 399.5% CPU
UPDATE BEST LOG-LIKELIHOOD: -35530.768
Optimizing NNI: done in 0.237992 secs using 397.8% CPU
Optimizing NNI: done in 0.22563 secs using 399.7% CPU
Optimizing NNI: done in 0.259582 secs using 398.9% CPU
Optimizing NNI: done in 0.253696 secs using 398.2% CPU
Iteration 20 / LogL: -35531.212 / Time: 0h:0m:10s
Finish initializing candidate tree set (4)
Current best tree score: -35530.768 / CPU time: 9.789
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.380515 secs using 397.7% CPU
Optimizing NNI: done in 0.286047 secs using 399.6% CPU
Optimizing NNI: done in 0.335538 secs using 397.6% CPU
Optimizing NNI: done in 0.380861 secs using 397.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -35530.386
Optimizing NNI: done in 0.358657 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -35529.046
Optimizing NNI: done in 0.440753 secs using 399.2% CPU
Optimizing NNI: done in 0.349887 secs using 399.5% CPU
Optimizing NNI: done in 0.306564 secs using 399.9% CPU
Optimizing NNI: done in 0.284858 secs using 399.4% CPU
Optimizing NNI: done in 0.325844 secs using 398% CPU
Iteration 30 / LogL: -35529.306 / Time: 0h:0m:13s (0h:0m:45s left)
Optimizing NNI: done in 0.305907 secs using 399.9% CPU
Optimizing NNI: done in 0.228937 secs using 398.5% CPU
Optimizing NNI: done in 0.363436 secs using 399.2% CPU
Optimizing NNI: done in 0.290827 secs using 399.3% CPU
Optimizing NNI: done in 0.383866 secs using 399.6% CPU
Optimizing NNI: done in 0.406898 secs using 398% CPU
Optimizing NNI: done in 0.415451 secs using 398.1% CPU
Optimizing NNI: done in 0.368877 secs using 399.4% CPU
Optimizing NNI: done in 0.448952 secs using 399.4% CPU
Optimizing NNI: done in 0.299153 secs using 398.3% CPU
Iteration 40 / LogL: -35531.304 / Time: 0h:0m:17s (0h:0m:38s left)
Optimizing NNI: done in 0.336978 secs using 399.5% CPU
Optimizing NNI: done in 0.414259 secs using 399.4% CPU
Optimizing NNI: done in 0.321472 secs using 399.5% CPU
Optimizing NNI: done in 0.453785 secs using 399.6% CPU
Optimizing NNI: done in 0.289544 secs using 397.9% CPU
Optimizing NNI: done in 0.361021 secs using 399.2% CPU
Optimizing NNI: done in 0.445179 secs using 398.7% CPU
459  DCMut+I+R7    60649.047    316 121930.094   123074.917   123256.813
Optimizing NNI: done in 0.471319 secs using 398% CPU
Optimizing NNI: done in 0.323375 secs using 398.4% CPU
Optimizing NNI: done in 0.315506 secs using 398.2% CPU
Iteration 50 / LogL: -35529.832 / Time: 0h:0m:21s (0h:0m:32s left)
Optimizing NNI: done in 0.274302 secs using 399% CPU
Optimizing NNI: done in 0.338651 secs using 399.4% CPU
Optimizing NNI: done in 0.294795 secs using 399.3% CPU
Optimizing NNI: done in 0.325818 secs using 398.9% CPU
Optimizing NNI: done in 0.38288 secs using 398.2% CPU
Optimizing NNI: done in 0.434548 secs using 398.3% CPU
Optimizing NNI: done in 0.411771 secs using 399.2% CPU
Optimizing NNI: done in 0.500877 secs using 399.3% CPU
Optimizing NNI: done in 0.453505 secs using 398.6% CPU
Optimizing NNI: done in 0.377925 secs using 398.9% CPU
Iteration 60 / LogL: -35530.862 / Time: 0h:0m:25s (0h:0m:27s left)
471  DCMut+F+R6    60593.102    332 121850.204   123240.846   123244.099
Optimizing NNI: done in 0.416484 secs using 398.4% CPU
Optimizing NNI: done in 0.287975 secs using 398.5% CPU
Optimizing NNI: done in 0.335862 secs using 398.6% CPU
Optimizing NNI: done in 0.352889 secs using 398.3% CPU
Optimizing NNI: done in 0.313303 secs using 399.2% CPU
Optimizing NNI: done in 0.274493 secs using 399.2% CPU
Optimizing NNI: done in 0.277394 secs using 399.5% CPU
Optimizing NNI: done in 0.372235 secs using 398.9% CPU
Optimizing NNI: done in 0.412843 secs using 399.1% CPU
Optimizing NNI: done in 0.33326 secs using 398.8% CPU
Iteration 70 / LogL: -35529.086 / Time: 0h:0m:28s (0h:0m:22s left)
Optimizing NNI: done in 0.389658 secs using 399.2% CPU
Optimizing NNI: done in 0.357299 secs using 397.6% CPU
Optimizing NNI: done in 0.312859 secs using 398.2% CPU
Optimizing NNI: done in 0.36875 secs using 398.7% CPU
Optimizing NNI: done in 0.436613 secs using 397.6% CPU
Optimizing NNI: done in 0.368372 secs using 398.2% CPU
Optimizing NNI: done in 0.31735 secs using 399.2% CPU
Optimizing NNI: done in 0.41473 secs using 398.5% CPU
Optimizing NNI: done in 0.415722 secs using 397.9% CPU
Optimizing NNI: done in 0.302411 secs using 398% CPU
Iteration 80 / LogL: -35530.156 / Time: 0h:0m:32s (0h:0m:18s left)
Optimizing NNI: done in 0.327606 secs using 399.6% CPU
Optimizing NNI: done in 0.343416 secs using 399% CPU
Optimizing NNI: done in 0.355401 secs using 400.5% CPU
Optimizing NNI: done in 0.405169 secs using 399.4% CPU
Optimizing NNI: done in 0.400332 secs using 399.4% CPU
Optimizing NNI: done in 0.33843 secs using 397.2% CPU
Optimizing NNI: done in 0.357638 secs using 399.5% CPU
Optimizing NNI: done in 0.408183 secs using 399.1% CPU
Optimizing NNI: done in 0.423167 secs using 399.4% CPU
Optimizing NNI: done in 0.476259 secs using 399.7% CPU
Iteration 90 / LogL: -35529.870 / Time: 0h:0m:36s (0h:0m:14s left)
Optimizing NNI: done in 0.305408 secs using 399.8% CPU
Optimizing NNI: done in 0.276593 secs using 399.1% CPU
Optimizing NNI: done in 0.393262 secs using 399.9% CPU
Optimizing NNI: done in 0.400528 secs using 399.9% CPU
Optimizing NNI: done in 0.32345 secs using 399.4% CPU
Optimizing NNI: done in 0.368199 secs using 399% CPU
153  Q.insect+F+R9 194858.288   1022 391760.576   2482772.576  396210.742
WARNING: Normalizing state frequencies so that sum of them equals to 1
472  DCMut+F+R7    60580.254    334 121828.509   123253.859   123230.801
Optimizing NNI: done in 0.376702 secs using 399.7% CPU
Optimizing NNI: done in 0.392302 secs using 399.6% CPU
Optimizing NNI: done in 0.360604 secs using 399.5% CPU
Optimizing NNI: done in 0.467337 secs using 399.7% CPU
Iteration 100 / LogL: -35529.313 / Time: 0h:0m:39s (0h:0m:10s left)
Optimizing NNI: done in 0.342158 secs using 399.9% CPU
Optimizing NNI: done in 0.390878 secs using 399.3% CPU
Optimizing NNI: done in 0.323745 secs using 399.8% CPU
Optimizing NNI: done in 0.378349 secs using 399.8% CPU
Optimizing NNI: done in 0.354872 secs using 399.3% CPU
Optimizing NNI: done in 0.297065 secs using 399.9% CPU
Optimizing NNI: done in 0.44146 secs using 399.5% CPU
Optimizing NNI: done in 0.366286 secs using 399.3% CPU
Optimizing NNI: done in 0.29667 secs using 399.6% CPU
473  DCMut+F+R8    60574.694    336 121821.387   123282.445   123232.076
Optimizing NNI: done in 0.377975 secs using 398.5% CPU
Iteration 110 / LogL: -35529.607 / Time: 0h:0m:43s (0h:0m:5s left)
Optimizing NNI: done in 0.417549 secs using 399.7% CPU
Optimizing NNI: done in 0.415557 secs using 399.7% CPU
Optimizing NNI: done in 0.39851 secs using 399.6% CPU
Optimizing NNI: done in 0.372154 secs using 399.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -35529.041
Optimizing NNI: done in 0.450883 secs using 399.9% CPU
Optimizing NNI: done in 0.319932 secs using 399.6% CPU
Optimizing NNI: done in 0.31506 secs using 398.6% CPU
Optimizing NNI: done in 0.374662 secs using 400.1% CPU
Optimizing NNI: done in 0.323103 secs using 399% CPU
Optimizing NNI: done in 0.377679 secs using 398.6% CPU
Iteration 120 / LogL: -35533.650 / Time: 0h:0m:47s (0h:0m:1s left)
Optimizing NNI: done in 0.475228 secs using 398.7% CPU
Optimizing NNI: done in 0.37449 secs using 399.4% CPU
Optimizing NNI: done in 0.467914 secs using 399.7% CPU
Optimizing NNI: done in 0.334182 secs using 398.9% CPU
480  DCMut+F+I+R6  60586.513    333 121839.025   123246.899   123237.119
Optimizing NNI: done in 0.409077 secs using 399.5% CPU
Optimizing NNI: done in 0.38189 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 126 ITERATIONS / Time: 0h:0m:49s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35529.041
Optimal log-likelihood: -35529.041
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.235
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -35529.041
Total tree length: 19.388

Total number of iterations: 126
CPU time used for tree search: 192.338 sec (0h:3m:12s)
Wall-clock time used for tree search: 49.219 sec (0h:0m:49s)
Total CPU time used: 194.625 sec (0h:3m:14s)
Total wall-clock time used: 49.765 sec (0h:0m:49s)

===> START BOOTSTRAP REPLICATE NUMBER 18

Creating bootstrap alignment (seed: 956177)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37101.753
2. Current log-likelihood: -36173.785
3. Current log-likelihood: -36160.651
4. Current log-likelihood: -36160.150
Optimal log-likelihood: -36160.084
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.352
Parameters optimization took 4 rounds (0.286 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.077117 secs using 400% CPU
Computing ML distances took 0.077248 sec (of wall-clock time) 0.308748 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000150919 secs using 417.4% CPU
Constructing RapidNJ tree: done in 0.00218582 secs using 433.3% CPU
Computing RapidNJ tree took 0.002392 sec (of wall-clock time) 0.011042 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36822.606
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.549 second
163  Q.plant+R8    194919.373   1001 391840.745   2397844.745  396199.470
WARNING: Normalizing state frequencies so that sum of them equals to 1
Computing log-likelihood of 98 initial trees ... 1.835 seconds
Current best score: -36141.072

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.251543 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36070.742
Optimizing NNI: done in 0.21311 secs using 399.8% CPU
Optimizing NNI: done in 0.228888 secs using 399% CPU
Optimizing NNI: done in 0.247286 secs using 399.5% CPU
Optimizing NNI: done in 0.26034 secs using 399.1% CPU
Optimizing NNI: done in 0.266487 secs using 400.2% CPU
Optimizing NNI: done in 0.260752 secs using 399.5% CPU
Optimizing NNI: done in 0.234058 secs using 398.6% CPU
Optimizing NNI: done in 0.249774 secs using 398.8% CPU
Optimizing NNI: done in 0.299666 secs using 398.8% CPU
Iteration 10 / LogL: -36070.783 / Time: 0h:0m:6s
Optimizing NNI: done in 0.264486 secs using 399.9% CPU
Optimizing NNI: done in 0.275457 secs using 399% CPU
Optimizing NNI: done in 0.256368 secs using 398.9% CPU
Optimizing NNI: done in 0.25882 secs using 398.7% CPU
Optimizing NNI: done in 0.244535 secs using 399.7% CPU
Optimizing NNI: done in 0.240042 secs using 399.8% CPU
Optimizing NNI: done in 0.241553 secs using 398.7% CPU
Optimizing NNI: done in 0.264356 secs using 399.3% CPU
Optimizing NNI: done in 0.239873 secs using 399.3% CPU
481  DCMut+F+I+R7  60579.937    335 121829.875   123272.951   123236.365
Optimizing NNI: done in 0.245956 secs using 398.5% CPU
Iteration 20 / LogL: -36081.784 / Time: 0h:0m:9s
Finish initializing candidate tree set (3)
Current best tree score: -36070.742 / CPU time: 8.571
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.353154 secs using 399.5% CPU
Optimizing NNI: done in 0.37035 secs using 399.3% CPU
Optimizing NNI: done in 0.509783 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -36068.067
Optimizing NNI: done in 0.427551 secs using 398.2% CPU
Optimizing NNI: done in 0.405744 secs using 399.6% CPU
493  VT+R6         59991.693    313 120609.386   121713.678   121923.510
Optimizing NNI: done in 0.477863 secs using 398.6% CPU
Optimizing NNI: done in 0.367372 secs using 399.1% CPU
Optimizing NNI: done in 0.415555 secs using 399.8% CPU
Optimizing NNI: done in 0.524447 secs using 399.5% CPU
Optimizing NNI: done in 0.313896 secs using 399.8% CPU
Iteration 30 / LogL: -36071.355 / Time: 0h:0m:13s (0h:0m:43s left)
Optimizing NNI: done in 0.521322 secs using 398.8% CPU
Optimizing NNI: done in 0.387441 secs using 399.3% CPU
Optimizing NNI: done in 0.4191 secs using 399% CPU
Optimizing NNI: done in 0.300624 secs using 398.6% CPU
Optimizing NNI: done in 0.443616 secs using 398.9% CPU
 44  LG+F+I+R10    105575.798   573 212297.596   870101.596   214604.417
Optimizing NNI: done in 0.410215 secs using 398.7% CPU
Optimizing NNI: done in 0.344446 secs using 397.7% CPU
494  VT+R7         59983.961    315 120597.921   121729.058   121920.442
Optimizing NNI: done in 0.417572 secs using 398.5% CPU
Optimizing NNI: done in 0.248012 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36068.029
Optimizing NNI: done in 0.354454 secs using 399.5% CPU
Iteration 40 / LogL: -36069.921 / Time: 0h:0m:17s (0h:0m:37s left)
Optimizing NNI: done in 0.397322 secs using 399.4% CPU
Optimizing NNI: done in 0.349102 secs using 397.9% CPU
Optimizing NNI: done in 0.478042 secs using 399.2% CPU
Optimizing NNI: done in 0.467362 secs using 398.9% CPU
Optimizing NNI: done in 0.340837 secs using 398.7% CPU
Optimizing NNI: done in 0.36698 secs using 399.9% CPU
Optimizing NNI: done in 0.396396 secs using 398.8% CPU
Optimizing NNI: done in 0.260351 secs using 399.6% CPU
Optimizing NNI: done in 0.352204 secs using 399.6% CPU
495  VT+R8         59977.569    317 120589.139   121747.828   121920.057
Optimizing NNI: done in 0.506006 secs using 399.5% CPU
Iteration 50 / LogL: -36073.507 / Time: 0h:0m:21s (0h:0m:31s left)
Optimizing NNI: done in 0.3236 secs using 399.5% CPU
Optimizing NNI: done in 0.402055 secs using 398.3% CPU
Optimizing NNI: done in 0.541335 secs using 398.6% CPU
Optimizing NNI: done in 0.461175 secs using 398.2% CPU
Optimizing NNI: done in 0.50396 secs using 399.8% CPU
Optimizing NNI: done in 0.325053 secs using 399.8% CPU
Optimizing NNI: done in 0.403619 secs using 398.9% CPU
Optimizing NNI: done in 0.320452 secs using 398.5% CPU
Optimizing NNI: done in 0.267076 secs using 398.6% CPU
Optimizing NNI: done in 0.273697 secs using 399.4% CPU
Iteration 60 / LogL: -36072.266 / Time: 0h:0m:25s (0h:0m:26s left)
Optimizing NNI: done in 0.414878 secs using 399.1% CPU
 65  WAG+I+R9      105824.621   552 212753.242   823265.242   214975.521
Optimizing NNI: done in 0.32784 secs using 399.5% CPU
Optimizing NNI: done in 0.38048 secs using 398.4% CPU
Optimizing NNI: done in 0.246821 secs using 399% CPU
Optimizing NNI: done in 0.419482 secs using 399.6% CPU
Optimizing NNI: done in 0.488077 secs using 399.6% CPU
Optimizing NNI: done in 0.454889 secs using 399.7% CPU
Optimizing NNI: done in 0.352847 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 68: -36067.405
Optimizing NNI: done in 0.406026 secs using 399.5% CPU
Optimizing NNI: done in 0.332825 secs using 399.6% CPU
Iteration 70 / LogL: -36068.891 / Time: 0h:0m:29s (0h:0m:41s left)
Optimizing NNI: done in 0.401854 secs using 399.9% CPU
Optimizing NNI: done in 0.401567 secs using 399.1% CPU
Optimizing NNI: done in 0.360074 secs using 399.6% CPU
164  Q.plant+R9    194913.090   1003 391832.180   2405856.180  396199.613
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.287816 secs using 397.4% CPU
Optimizing NNI: done in 0.368564 secs using 398.5% CPU
Optimizing NNI: done in 0.519573 secs using 397.8% CPU
Optimizing NNI: done in 0.399121 secs using 398.6% CPU
Optimizing NNI: done in 0.301879 secs using 399% CPU
Optimizing NNI: done in 0.391135 secs using 398.3% CPU
Optimizing NNI: done in 0.365991 secs using 398.5% CPU
Iteration 80 / LogL: -36068.593 / Time: 0h:0m:33s (0h:0m:36s left)
Optimizing NNI: done in 0.314841 secs using 397.9% CPU
Optimizing NNI: done in 0.392927 secs using 399% CPU
Optimizing NNI: done in 0.353378 secs using 399.2% CPU
496  VT+R9         59976.356    319 120590.712   121777.689   121930.027
Optimizing NNI: done in 0.42635 secs using 398.6% CPU
Optimizing NNI: done in 0.377177 secs using 399.4% CPU
Optimizing NNI: done in 0.393131 secs using 399.1% CPU
Optimizing NNI: done in 0.482254 secs using 399.1% CPU
Optimizing NNI: done in 0.340549 secs using 398.5% CPU
Optimizing NNI: done in 0.333207 secs using 399.1% CPU
Optimizing NNI: done in 0.380161 secs using 398.8% CPU
Iteration 90 / LogL: -36069.457 / Time: 0h:0m:36s (0h:0m:32s left)
Optimizing NNI: done in 0.354918 secs using 399.1% CPU
Optimizing NNI: done in 0.497585 secs using 398.7% CPU
Optimizing NNI: done in 0.315144 secs using 398.7% CPU
Optimizing NNI: done in 0.347234 secs using 398.6% CPU
Optimizing NNI: done in 0.271345 secs using 397.3% CPU
Optimizing NNI: done in 0.311869 secs using 399.5% CPU
Optimizing NNI: done in 0.272274 secs using 398.9% CPU
Optimizing NNI: done in 0.343642 secs using 399.1% CPU
Optimizing NNI: done in 0.30018 secs using 398.4% CPU
Optimizing NNI: done in 0.353711 secs using 399.4% CPU
Iteration 100 / LogL: -36073.826 / Time: 0h:0m:40s (0h:0m:27s left)
Optimizing NNI: done in 0.389169 secs using 399.6% CPU
Optimizing NNI: done in 0.379804 secs using 399.3% CPU
Optimizing NNI: done in 0.352122 secs using 399.8% CPU
Optimizing NNI: done in 0.359255 secs using 399.6% CPU
Optimizing NNI: done in 0.254948 secs using 398.6% CPU
502  VT+I+R6       59989.999    314 120607.998   121725.625   121926.321
Optimizing NNI: done in 0.35478 secs using 399.7% CPU
Optimizing NNI: done in 0.340796 secs using 399.3% CPU
Optimizing NNI: done in 0.384198 secs using 398.5% CPU
Optimizing NNI: done in 0.357531 secs using 399.9% CPU
174  Q.plant+F+R8  194822.604   1020 391685.208   2474525.208  396126.665
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.371954 secs using 399.5% CPU
Iteration 110 / LogL: -36067.509 / Time: 0h:0m:43s (0h:0m:23s left)
Optimizing NNI: done in 0.276243 secs using 399.4% CPU
Optimizing NNI: done in 0.384144 secs using 399.1% CPU
Optimizing NNI: done in 0.32543 secs using 398.9% CPU
Optimizing NNI: done in 0.39898 secs using 396.7% CPU
Optimizing NNI: done in 0.424569 secs using 399.2% CPU
Optimizing NNI: done in 0.344878 secs using 399.5% CPU
Optimizing NNI: done in 0.423206 secs using 399.3% CPU
Optimizing NNI: done in 0.339057 secs using 399% CPU
Optimizing NNI: done in 0.300898 secs using 399.7% CPU
Optimizing NNI: done in 0.341059 secs using 398.7% CPU
Iteration 120 / LogL: -36076.233 / Time: 0h:0m:47s (0h:0m:19s left)
Optimizing NNI: done in 0.367342 secs using 399.2% CPU
Optimizing NNI: done in 0.317983 secs using 399.7% CPU
Optimizing NNI: done in 0.393527 secs using 399.1% CPU
Optimizing NNI: done in 0.306587 secs using 398.1% CPU
Optimizing NNI: done in 0.383238 secs using 397.7% CPU
Optimizing NNI: done in 0.497132 secs using 398.4% CPU
503  VT+I+R7       59983.952    316 120599.903   121744.726   121926.623
Optimizing NNI: done in 0.417411 secs using 397.7% CPU
Optimizing NNI: done in 0.289497 secs using 399.6% CPU
Optimizing NNI: done in 0.339345 secs using 399% CPU
Optimizing NNI: done in 0.327435 secs using 397.5% CPU
Iteration 130 / LogL: -36070.027 / Time: 0h:0m:51s (0h:0m:15s left)
Optimizing NNI: done in 0.386065 secs using 398.2% CPU
Optimizing NNI: done in 0.422135 secs using 396.2% CPU
Optimizing NNI: done in 0.496961 secs using 397.6% CPU
515  VT+F+R6       60006.991    332 120677.982   122068.623   122071.877
Optimizing NNI: done in 0.502419 secs using 398.7% CPU
Optimizing NNI: done in 0.350643 secs using 399.6% CPU
Optimizing NNI: done in 0.351381 secs using 398.9% CPU
Optimizing NNI: done in 0.292951 secs using 399% CPU
Optimizing NNI: done in 0.391894 secs using 399.4% CPU
Optimizing NNI: done in 0.338505 secs using 399.1% CPU
Optimizing NNI: done in 0.35173 secs using 398.6% CPU
Iteration 140 / LogL: -36077.303 / Time: 0h:0m:55s (0h:0m:11s left)
Optimizing NNI: done in 0.259641 secs using 399.2% CPU
Optimizing NNI: done in 0.355294 secs using 399% CPU
Optimizing NNI: done in 0.389334 secs using 398.1% CPU
Optimizing NNI: done in 0.361694 secs using 398.7% CPU
516  VT+F+R7       60000.049    334 120668.098   122093.448   122070.390
Optimizing NNI: done in 0.360539 secs using 400.3% CPU
Optimizing NNI: done in 0.285556 secs using 399.2% CPU
Optimizing NNI: done in 0.381893 secs using 399.6% CPU
Optimizing NNI: done in 0.30908 secs using 399.4% CPU
Optimizing NNI: done in 0.411005 secs using 398.8% CPU
Optimizing NNI: done in 0.372097 secs using 397.3% CPU
Iteration 150 / LogL: -36070.024 / Time: 0h:0m:58s (0h:0m:7s left)
Optimizing NNI: done in 0.372011 secs using 400.4% CPU
Optimizing NNI: done in 0.510734 secs using 398.8% CPU
Optimizing NNI: done in 0.394411 secs using 399% CPU
Optimizing NNI: done in 0.332446 secs using 398.3% CPU
Optimizing NNI: done in 0.362346 secs using 398.9% CPU
Optimizing NNI: done in 0.316811 secs using 397.2% CPU
Optimizing NNI: done in 0.315312 secs using 397.1% CPU
517  VT+F+R8       59993.844    336 120659.688   122120.746   122070.377
Optimizing NNI: done in 0.25692 secs using 398.9% CPU
Optimizing NNI: done in 0.423571 secs using 397.9% CPU
Optimizing NNI: done in 0.383464 secs using 399.1% CPU
Iteration 160 / LogL: -36081.133 / Time: 0h:1m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.339847 secs using 399.5% CPU
Optimizing NNI: done in 0.323381 secs using 398.9% CPU
Optimizing NNI: done in 0.451162 secs using 399.2% CPU
Optimizing NNI: done in 0.281219 secs using 399% CPU
Optimizing NNI: done in 0.497957 secs using 399.4% CPU
Optimizing NNI: done in 0.374977 secs using 398.3% CPU
Optimizing NNI: done in 0.389337 secs using 398.6% CPU
Optimizing NNI: done in 0.303583 secs using 397.4% CPU
Optimizing NNI: done in 0.381536 secs using 399.2% CPU
TREE SEARCH COMPLETED AFTER 169 ITERATIONS / Time: 0h:1m:5s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36067.405
2. Current log-likelihood: -36067.379
Optimal log-likelihood: -36067.366
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.295
Parameters optimization took 2 rounds (0.090 sec)
BEST SCORE FOUND : -36067.366
Total tree length: 20.646

Total number of iterations: 169
CPU time used for tree search: 255.421 sec (0h:4m:15s)
Wall-clock time used for tree search: 65.051 sec (0h:1m:5s)
Total CPU time used: 258.577 sec (0h:4m:18s)
Total wall-clock time used: 65.798 sec (0h:1m:5s)

===> START BOOTSTRAP REPLICATE NUMBER 19

Creating bootstrap alignment (seed: 956178)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.023 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36755.850
2. Current log-likelihood: -35861.716
3. Current log-likelihood: -35847.769
4. Current log-likelihood: -35846.963
5. Current log-likelihood: -35846.574
Optimal log-likelihood: -35846.461
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.223
Parameters optimization took 5 rounds (0.340 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0760989 secs using 400% CPU
Computing ML distances took 0.076231 sec (of wall-clock time) 0.304728 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000232935 secs using 432.7% CPU
Constructing RapidNJ tree: done in 0.00214005 secs using 464.6% CPU
Computing RapidNJ tree took 0.002429 sec (of wall-clock time) 0.011378 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36308.972
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.582 second
Computing log-likelihood of 98 initial trees ... 1.652 seconds
Current best score: -35846.461

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.183353 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35826.490
Optimizing NNI: done in 0.210269 secs using 400.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35810.724
Optimizing NNI: done in 0.210252 secs using 398.9% CPU
Optimizing NNI: done in 0.199778 secs using 399.8% CPU
Optimizing NNI: done in 0.214395 secs using 399.8% CPU
Optimizing NNI: done in 0.198727 secs using 399.7% CPU
Optimizing NNI: done in 0.218373 secs using 398.7% CPU
Optimizing NNI: done in 0.221155 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35810.520
Optimizing NNI: done in 0.211294 secs using 398.9% CPU
Optimizing NNI: done in 0.2029 secs using 399.8% CPU
Iteration 10 / LogL: -35811.147 / Time: 0h:0m:6s
Optimizing NNI: done in 0.208418 secs using 399.3% CPU
Optimizing NNI: done in 0.231523 secs using 400.8% CPU
Optimizing NNI: done in 0.241502 secs using 398.7% CPU
Optimizing NNI: done in 0.224353 secs using 398.5% CPU
Optimizing NNI: done in 0.225123 secs using 398.9% CPU
Optimizing NNI: done in 0.215428 secs using 397.8% CPU
Optimizing NNI: done in 0.230207 secs using 398.2% CPU
Optimizing NNI: done in 0.230928 secs using 399.1% CPU
Optimizing NNI: done in 0.229785 secs using 399.3% CPU
Optimizing NNI: done in 0.209639 secs using 398.6% CPU
Iteration 20 / LogL: -35813.787 / Time: 0h:0m:8s
Finish initializing candidate tree set (3)
Current best tree score: -35810.520 / CPU time: 7.801
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.362422 secs using 399.6% CPU
Optimizing NNI: done in 0.475037 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -35805.564
Optimizing NNI: done in 0.415232 secs using 399.2% CPU
Optimizing NNI: done in 0.363025 secs using 399.3% CPU
Optimizing NNI: done in 0.578987 secs using 398.9% CPU
Optimizing NNI: done in 0.327534 secs using 399.1% CPU
518  VT+F+R9       59992.313    338 120660.625   122158.429   122079.711
Optimizing NNI: done in 0.340469 secs using 399.8% CPU
Optimizing NNI: done in 0.441318 secs using 396.8% CPU
175  Q.plant+F+R9  194819.592   1022 391683.184   2482695.184  396133.350
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.403997 secs using 398.1% CPU
Optimizing NNI: done in 0.395015 secs using 397.9% CPU
Iteration 30 / LogL: -35808.916 / Time: 0h:0m:12s (0h:0m:39s left)
Optimizing NNI: done in 0.464903 secs using 398.5% CPU
Optimizing NNI: done in 0.385745 secs using 398.7% CPU
Optimizing NNI: done in 0.3716 secs using 399.2% CPU
Optimizing NNI: done in 0.288302 secs using 399.6% CPU
Optimizing NNI: done in 0.349603 secs using 398.6% CPU
Optimizing NNI: done in 0.369713 secs using 398.3% CPU
Optimizing NNI: done in 0.50128 secs using 397.8% CPU
Optimizing NNI: done in 0.420056 secs using 398.2% CPU
Optimizing NNI: done in 0.432591 secs using 398.4% CPU
Optimizing NNI: done in 0.345632 secs using 398.8% CPU
Iteration 40 / LogL: -35806.023 / Time: 0h:0m:16s (0h:0m:34s left)
Optimizing NNI: done in 0.32919 secs using 399.2% CPU
Optimizing NNI: done in 0.443656 secs using 397.6% CPU
Optimizing NNI: done in 0.345673 secs using 398.7% CPU
Optimizing NNI: done in 0.352865 secs using 399.1% CPU
524  VT+F+I+R6     60005.611    333 120677.222   122085.095   122075.315
Optimizing NNI: done in 0.265767 secs using 398.2% CPU
Optimizing NNI: done in 0.379048 secs using 399.7% CPU
Optimizing NNI: done in 0.425692 secs using 399.4% CPU
Optimizing NNI: done in 0.348016 secs using 399.4% CPU
Optimizing NNI: done in 0.40397 secs using 399.3% CPU
Optimizing NNI: done in 0.375645 secs using 399.3% CPU
Iteration 50 / LogL: -35805.669 / Time: 0h:0m:20s (0h:0m:29s left)
Optimizing NNI: done in 0.236049 secs using 399.7% CPU
Optimizing NNI: done in 0.357108 secs using 399.1% CPU
Optimizing NNI: done in 0.334641 secs using 399.6% CPU
Optimizing NNI: done in 0.438623 secs using 399.9% CPU
Optimizing NNI: done in 0.493554 secs using 399.6% CPU
Optimizing NNI: done in 0.439589 secs using 398.4% CPU
Optimizing NNI: done in 0.362924 secs using 398.5% CPU
Optimizing NNI: done in 0.350322 secs using 397.6% CPU
Optimizing NNI: done in 0.379245 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35805.439
Optimizing NNI: done in 0.384853 secs using 399.5% CPU
Iteration 60 / LogL: -35805.814 / Time: 0h:0m:24s (0h:0m:25s left)
Optimizing NNI: done in 0.371732 secs using 398.4% CPU
525  VT+F+I+R7     60000.235    335 120670.470   122113.547   122076.960
Optimizing NNI: done in 0.378137 secs using 398.3% CPU
Optimizing NNI: done in 0.382954 secs using 398.5% CPU
Optimizing NNI: done in 0.319327 secs using 398.3% CPU
Optimizing NNI: done in 0.457437 secs using 398.1% CPU
Optimizing NNI: done in 0.351889 secs using 399.3% CPU
Optimizing NNI: done in 0.379678 secs using 399.2% CPU
537  PMB+R6        60396.277    313 121418.554   122522.846   122732.678
Optimizing NNI: done in 0.419779 secs using 399.5% CPU
Optimizing NNI: done in 0.319712 secs using 398.5% CPU
Optimizing NNI: done in 0.439064 secs using 398.4% CPU
Iteration 70 / LogL: -35813.320 / Time: 0h:0m:27s (0h:0m:21s left)
Optimizing NNI: done in 0.400682 secs using 398.6% CPU
Optimizing NNI: done in 0.354018 secs using 399.3% CPU
Optimizing NNI: done in 0.306859 secs using 398.4% CPU
Optimizing NNI: done in 0.394713 secs using 398.5% CPU
Optimizing NNI: done in 0.416497 secs using 397.9% CPU
Optimizing NNI: done in 0.292686 secs using 399.1% CPU
538  PMB+R7        60390.118    315 121410.236   122541.372   122732.757
Optimizing NNI: done in 0.391479 secs using 399.4% CPU
Optimizing NNI: done in 0.30575 secs using 399.3% CPU
Optimizing NNI: done in 0.349829 secs using 399.6% CPU
Optimizing NNI: done in 0.323055 secs using 399.5% CPU
Iteration 80 / LogL: -35897.538 / Time: 0h:0m:31s (0h:0m:16s left)
Optimizing NNI: done in 0.355021 secs using 399.1% CPU
Optimizing NNI: done in 0.327751 secs using 399.4% CPU
Optimizing NNI: done in 0.485927 secs using 399.3% CPU
Optimizing NNI: done in 0.414952 secs using 398.8% CPU
Optimizing NNI: done in 0.450022 secs using 399.5% CPU
Optimizing NNI: done in 0.366037 secs using 398.9% CPU
185  Q.yeast+R8    195446.700   1001 392895.400   2398899.400  397254.125
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.366362 secs using 399.6% CPU
Optimizing NNI: done in 0.400047 secs using 399.4% CPU
Optimizing NNI: done in 0.50846 secs using 399.5% CPU
Optimizing NNI: done in 0.387822 secs using 398.8% CPU
Iteration 90 / LogL: -35805.927 / Time: 0h:0m:35s (0h:0m:12s left)
Optimizing NNI: done in 0.401545 secs using 399.9% CPU
546  PMB+I+R6      60395.163    314 121418.327   122535.954   122736.649
Optimizing NNI: done in 0.512132 secs using 397.8% CPU
Optimizing NNI: done in 0.324677 secs using 398.3% CPU
Optimizing NNI: done in 0.400686 secs using 399.2% CPU
Optimizing NNI: done in 0.403098 secs using 400.1% CPU
Optimizing NNI: done in 0.35204 secs using 399.2% CPU
Optimizing NNI: done in 0.50467 secs using 399% CPU
Optimizing NNI: done in 0.440975 secs using 398.3% CPU
Optimizing NNI: done in 0.393084 secs using 398.8% CPU
Optimizing NNI: done in 0.313711 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35805.283
Iteration 100 / LogL: -35805.283 / Time: 0h:0m:39s (0h:0m:8s left)
Optimizing NNI: done in 0.469412 secs using 399.4% CPU
Optimizing NNI: done in 0.395285 secs using 399.4% CPU
Optimizing NNI: done in 0.292622 secs using 399.2% CPU
Optimizing NNI: done in 0.403716 secs using 398.8% CPU
Optimizing NNI: done in 0.412822 secs using 397.9% CPU
Optimizing NNI: done in 0.43718 secs using 398.1% CPU
Optimizing NNI: done in 0.43058 secs using 398.8% CPU
547  PMB+I+R7      60390.809    316 121413.618   122558.441   122740.338
Optimizing NNI: done in 0.403624 secs using 399.4% CPU
Optimizing NNI: done in 0.32583 secs using 399% CPU
Optimizing NNI: done in 0.33285 secs using 399.3% CPU
Iteration 110 / LogL: -35805.300 / Time: 0h:0m:43s (0h:0m:4s left)
Optimizing NNI: done in 0.348879 secs using 399.5% CPU
Optimizing NNI: done in 0.562027 secs using 399.5% CPU
Optimizing NNI: done in 0.356991 secs using 398.6% CPU
Optimizing NNI: done in 0.308206 secs using 398.8% CPU
559  PMB+F+R6      60473.358    332 121610.716   123001.357   123004.611
Optimizing NNI: done in 0.350674 secs using 397.8% CPU
Optimizing NNI: done in 0.350167 secs using 398.4% CPU
Optimizing NNI: done in 0.290174 secs using 398.9% CPU
Optimizing NNI: done in 0.396393 secs using 399.3% CPU
Optimizing NNI: done in 0.375467 secs using 396.9% CPU
Optimizing NNI: done in 0.400117 secs using 398.3% CPU
Iteration 120 / LogL: -35808.652 / Time: 0h:0m:47s (0h:0m:0s left)
Optimizing NNI: done in 0.347721 secs using 399.3% CPU
Optimizing NNI: done in 0.347278 secs using 398.4% CPU
Optimizing NNI: done in 0.475029 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 123 ITERATIONS / Time: 0h:0m:48s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35805.283
Optimal log-likelihood: -35805.282
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.219
Parameters optimization took 1 rounds (0.046 sec)
BEST SCORE FOUND : -35805.282
Total tree length: 20.163

Total number of iterations: 123
CPU time used for tree search: 187.980 sec (0h:3m:7s)
Wall-clock time used for tree search: 48.149 sec (0h:0m:48s)
Total CPU time used: 190.518 sec (0h:3m:10s)
Total wall-clock time used: 48.760 sec (0h:0m:48s)

===> START BOOTSTRAP REPLICATE NUMBER 20

Creating bootstrap alignment (seed: 956179)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.020 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -35415.534
560  PMB+F+R7      60466.670    334 121601.340   123026.690   123003.632
2. Current log-likelihood: -34460.703
3. Current log-likelihood: -34441.694
4. Current log-likelihood: -34441.249
Optimal log-likelihood: -34441.171
Proportion of invariable sites: 0.039
Gamma shape alpha: 2.526
Parameters optimization took 4 rounds (0.273 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.077812 secs using 398.6% CPU
Computing ML distances took 0.077944 sec (of wall-clock time) 0.310467 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000148058 secs using 426.2% CPU
Constructing RapidNJ tree: done in 0.00222993 secs using 470.6% CPU
Computing RapidNJ tree took 0.002437 sec (of wall-clock time) 0.012309 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35048.716
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.511 second
Computing log-likelihood of 98 initial trees ... 1.632 seconds
Current best score: -34432.185

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.254196 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -34392.933
Optimizing NNI: done in 0.24755 secs using 399% CPU
Optimizing NNI: done in 0.231757 secs using 399.1% CPU
561  PMB+F+R8      60460.735    336 121593.470   123054.528   123004.159
Optimizing NNI: done in 0.213557 secs using 398.3% CPU
Optimizing NNI: done in 0.245252 secs using 398.3% CPU
Optimizing NNI: done in 0.249224 secs using 398.4% CPU
Optimizing NNI: done in 0.244063 secs using 399.6% CPU
Optimizing NNI: done in 0.224719 secs using 399.7% CPU
186  Q.yeast+R9    195439.881   1003 392885.762   2406909.762  397253.195
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.242165 secs using 398.1% CPU
Optimizing NNI: done in 0.260871 secs using 397.6% CPU
Iteration 10 / LogL: -34393.044 / Time: 0h:0m:6s
 66  WAG+I+R10     105818.585   554 212745.170   827685.170   214975.500
Optimizing NNI: done in 0.238403 secs using 398.7% CPU
Optimizing NNI: done in 0.211567 secs using 399% CPU
Optimizing NNI: done in 0.210266 secs using 399% CPU
Optimizing NNI: done in 0.224031 secs using 398.8% CPU
Optimizing NNI: done in 0.229374 secs using 398.8% CPU
Optimizing NNI: done in 0.242938 secs using 399.6% CPU
Optimizing NNI: done in 0.239163 secs using 399.6% CPU
Optimizing NNI: done in 0.259226 secs using 399.2% CPU
Optimizing NNI: done in 0.244703 secs using 398.8% CPU
Optimizing NNI: done in 0.246079 secs using 400.4% CPU
Iteration 20 / LogL: -34393.102 / Time: 0h:0m:8s
Finish initializing candidate tree set (1)
Current best tree score: -34392.933 / CPU time: 8.081
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.600253 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -34392.560
Optimizing NNI: done in 0.429545 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -34390.586
Optimizing NNI: done in 0.553133 secs using 399.2% CPU
Optimizing NNI: done in 0.48622 secs using 398.7% CPU
Optimizing NNI: done in 0.391701 secs using 398.2% CPU
568  PMB+F+I+R6    60471.900    333 121609.800   123017.674   123007.894
Optimizing NNI: done in 0.45811 secs using 398.1% CPU
Optimizing NNI: done in 0.364224 secs using 399.6% CPU
Optimizing NNI: done in 0.467133 secs using 399.4% CPU
Optimizing NNI: done in 0.446056 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -34390.319
Optimizing NNI: done in 0.327174 secs using 397.9% CPU
Iteration 30 / LogL: -34391.464 / Time: 0h:0m:13s (0h:0m:46s left)
Optimizing NNI: done in 0.425943 secs using 399.1% CPU
UPDATE BEST LOG-LIKELIHOOD: -34390.314
Optimizing NNI: done in 0.372404 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -34389.857
Optimizing NNI: done in 0.410213 secs using 397.7% CPU
 87  WAG+F+I+R9    105735.415   571 212612.830   865836.830   214911.600
Optimizing NNI: done in 0.539023 secs using 398.3% CPU
Optimizing NNI: done in 0.378792 secs using 399.6% CPU
Optimizing NNI: done in 0.476254 secs using 397.4% CPU
Optimizing NNI: done in 0.484066 secs using 398.8% CPU
Optimizing NNI: done in 0.43496 secs using 399% CPU
Optimizing NNI: done in 0.34839 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -34389.853
Optimizing NNI: done in 0.345676 secs using 398.2% CPU
Iteration 40 / LogL: -34390.212 / Time: 0h:0m:17s (0h:0m:41s left)
569  PMB+F+I+R7    60467.163    335 121604.326   123047.403   123010.817
Optimizing NNI: done in 0.414923 secs using 399.1% CPU
Optimizing NNI: done in 0.437094 secs using 398.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -34389.846
Optimizing NNI: done in 0.351987 secs using 399% CPU
Optimizing NNI: done in 0.450371 secs using 398.9% CPU
Optimizing NNI: done in 0.58181 secs using 399.4% CPU
Optimizing NNI: done in 0.506426 secs using 399.6% CPU
581  Blosum62+R6   60277.331    313 121180.661   122284.953   122494.785
Optimizing NNI: done in 0.390167 secs using 399.5% CPU
Optimizing NNI: done in 0.420922 secs using 399% CPU
Optimizing NNI: done in 0.424276 secs using 399.1% CPU
Optimizing NNI: done in 0.389797 secs using 399.3% CPU
Iteration 50 / LogL: -34392.348 / Time: 0h:0m:22s (0h:0m:37s left)
Optimizing NNI: done in 0.433467 secs using 399.6% CPU
Optimizing NNI: done in 0.357165 secs using 399.3% CPU
Optimizing NNI: done in 0.326001 secs using 397.7% CPU
Optimizing NNI: done in 0.557813 secs using 398.3% CPU
Optimizing NNI: done in 0.535508 secs using 399.8% CPU
582  Blosum62+R7   60270.511    315 121171.022   122302.159   122493.543
Optimizing NNI: done in 0.459376 secs using 399.4% CPU
Optimizing NNI: done in 0.332183 secs using 399.3% CPU
Optimizing NNI: done in 0.50279 secs using 398.2% CPU
Optimizing NNI: done in 0.328556 secs using 399.3% CPU
Optimizing NNI: done in 0.449573 secs using 398.2% CPU
Iteration 60 / LogL: -34390.289 / Time: 0h:0m:26s (0h:0m:32s left)
Optimizing NNI: done in 0.404409 secs using 398.4% CPU
Optimizing NNI: done in 0.449409 secs using 399.4% CPU
Optimizing NNI: done in 0.406943 secs using 397.9% CPU
Optimizing NNI: done in 0.558091 secs using 398.5% CPU
187  Q.yeast+R10   195435.549   1005 392881.097   2414941.097  397257.239
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.504606 secs using 399.4% CPU
Optimizing NNI: done in 0.291568 secs using 398.8% CPU
583  Blosum62+R8   60263.582    317 121161.163   122319.853   122492.081
Optimizing NNI: done in 0.398332 secs using 399.6% CPU
Optimizing NNI: done in 0.424903 secs using 399.3% CPU
Optimizing NNI: done in 0.444317 secs using 398.3% CPU
Optimizing NNI: done in 0.518091 secs using 399.7% CPU
Iteration 70 / LogL: -34389.950 / Time: 0h:0m:30s (0h:0m:27s left)
Optimizing NNI: done in 0.326245 secs using 399.6% CPU
Optimizing NNI: done in 0.697014 secs using 399.7% CPU
Optimizing NNI: done in 0.442905 secs using 399% CPU
Optimizing NNI: done in 0.394901 secs using 399.4% CPU
Optimizing NNI: done in 0.488577 secs using 398.7% CPU
Optimizing NNI: done in 0.476197 secs using 399.8% CPU
Optimizing NNI: done in 0.320171 secs using 399.9% CPU
Optimizing NNI: done in 0.401378 secs using 399.4% CPU
Optimizing NNI: done in 0.593466 secs using 398.5% CPU
Optimizing NNI: done in 0.482503 secs using 398.3% CPU
Iteration 80 / LogL: -34389.895 / Time: 0h:0m:35s (0h:0m:23s left)
Optimizing NNI: done in 0.498712 secs using 397.9% CPU
Optimizing NNI: done in 0.435074 secs using 397.7% CPU
Optimizing NNI: done in 0.435418 secs using 398.4% CPU
196  Q.yeast+F+R8  194579.068   1020 391198.136   2474038.136  395639.593
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.445108 secs using 398.6% CPU
Optimizing NNI: done in 0.446218 secs using 399.6% CPU
Optimizing NNI: done in 0.543617 secs using 399.9% CPU
Optimizing NNI: done in 0.513987 secs using 399.3% CPU
Optimizing NNI: done in 0.522514 secs using 399.3% CPU
Optimizing NNI: done in 0.385209 secs using 399.4% CPU
Optimizing NNI: done in 0.438271 secs using 399% CPU
Iteration 90 / LogL: -34390.586 / Time: 0h:0m:40s (0h:0m:19s left)
Optimizing NNI: done in 0.644015 secs using 398.8% CPU
Optimizing NNI: done in 0.453098 secs using 399.6% CPU
Optimizing NNI: done in 0.396611 secs using 397.8% CPU
Optimizing NNI: done in 0.4992 secs using 400% CPU
Optimizing NNI: done in 0.315247 secs using 398.7% CPU
Optimizing NNI: done in 0.649066 secs using 399.8% CPU
Optimizing NNI: done in 0.572898 secs using 399.4% CPU
Optimizing NNI: done in 0.336919 secs using 399.7% CPU
Optimizing NNI: done in 0.528878 secs using 399.4% CPU
584  Blosum62+R9   60262.225    319 121162.450   122349.427   122501.765
Optimizing NNI: done in 0.408355 secs using 399.5% CPU
Iteration 100 / LogL: -34391.476 / Time: 0h:0m:45s (0h:0m:14s left)
Optimizing NNI: done in 0.365502 secs using 398.1% CPU
Optimizing NNI: done in 0.385197 secs using 398% CPU
Optimizing NNI: done in 0.59348 secs using 399.5% CPU
Optimizing NNI: done in 0.517954 secs using 399.5% CPU
Optimizing NNI: done in 0.384783 secs using 398.4% CPU
Optimizing NNI: done in 0.432694 secs using 397.8% CPU
Optimizing NNI: done in 0.559457 secs using 397.7% CPU
Optimizing NNI: done in 0.42673 secs using 399.1% CPU
Optimizing NNI: done in 0.333683 secs using 398.6% CPU
Optimizing NNI: done in 0.537821 secs using 399.5% CPU
Iteration 110 / LogL: -34389.852 / Time: 0h:0m:49s (0h:0m:10s left)
Optimizing NNI: done in 0.403362 secs using 399.4% CPU
Optimizing NNI: done in 0.369289 secs using 399.5% CPU
Optimizing NNI: done in 0.390156 secs using 399.1% CPU
Optimizing NNI: done in 0.45779 secs using 397.9% CPU
Optimizing NNI: done in 0.486075 secs using 399.2% CPU
Optimizing NNI: done in 0.366753 secs using 399.1% CPU
590  Blosum62+I+R6 60277.217    314 121182.434   122300.061   122500.757
Optimizing NNI: done in 0.48207 secs using 397.9% CPU
Optimizing NNI: done in 0.295933 secs using 397.9% CPU
Optimizing NNI: done in 0.462965 secs using 396.9% CPU
Optimizing NNI: done in 0.421495 secs using 398.5% CPU
Iteration 120 / LogL: -34389.847 / Time: 0h:0m:53s (0h:0m:5s left)
Optimizing NNI: done in 0.506276 secs using 399.5% CPU
Optimizing NNI: done in 0.389627 secs using 399.9% CPU
Optimizing NNI: done in 0.536326 secs using 399.9% CPU
Optimizing NNI: done in 0.569344 secs using 399.5% CPU
Optimizing NNI: done in 0.414576 secs using 399.4% CPU
Optimizing NNI: done in 0.418279 secs using 399.5% CPU
Optimizing NNI: done in 0.386483 secs using 398.8% CPU
Optimizing NNI: done in 0.389684 secs using 399.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -34389.846
Optimizing NNI: done in 0.432201 secs using 399.6% CPU
Optimizing NNI: done in 0.453205 secs using 399.2% CPU
Iteration 130 / LogL: -34390.881 / Time: 0h:0m:58s (0h:0m:0s left)
Optimizing NNI: done in 0.405378 secs using 399.6% CPU
Optimizing NNI: done in 0.443618 secs using 398.2% CPU
Optimizing NNI: done in 0.366744 secs using 396.6% CPU
TREE SEARCH COMPLETED AFTER 133 ITERATIONS / Time: 0h:0m:59s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -34389.846
Optimal log-likelihood: -34389.846
Proportion of invariable sites: 0.040
Gamma shape alpha: 2.625
Parameters optimization took 1 rounds (0.048 sec)
BEST SCORE FOUND : -34389.846
Total tree length: 18.780

Total number of iterations: 133
CPU time used for tree search: 231.372 sec (0h:3m:51s)
Wall-clock time used for tree search: 58.989 sec (0h:0m:58s)
Total CPU time used: 234.654 sec (0h:3m:54s)
Total wall-clock time used: 59.765 sec (0h:0m:59s)

===> START BOOTSTRAP REPLICATE NUMBER 21

Creating bootstrap alignment (seed: 956180)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36882.012
2. Current log-likelihood: -36084.692
3. Current log-likelihood: -36071.771
4. Current log-likelihood: -36071.317
591  Blosum62+I+R7 60271.055    316 121174.111   122318.933   122500.830
Optimal log-likelihood: -36071.271
Proportion of invariable sites: 0.033
Gamma shape alpha: 2.236
Parameters optimization took 4 rounds (0.286 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0796621 secs using 398.6% CPU
Computing ML distances took 0.079793 sec (of wall-clock time) 0.317873 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000153065 secs using 422.7% CPU
Constructing RapidNJ tree: done in 0.00221896 secs using 475.9% CPU
Computing RapidNJ tree took 0.002426 sec (of wall-clock time) 0.012179 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36890.716
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.569 second
603  Blosum62+F+R6 60372.862    332 121409.723   122800.365   122803.618
Computing log-likelihood of 98 initial trees ... 1.666 seconds
Current best score: -36071.271

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.236678 secs using 397% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36046.712
Optimizing NNI: done in 0.252413 secs using 397.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36037.292
Optimizing NNI: done in 0.266704 secs using 399.6% CPU
Optimizing NNI: done in 0.27217 secs using 398.3% CPU
Optimizing NNI: done in 0.293698 secs using 399.1% CPU
Optimizing NNI: done in 0.307501 secs using 399.2% CPU
Optimizing NNI: done in 0.299822 secs using 399% CPU
Optimizing NNI: done in 0.262175 secs using 399.2% CPU
604  Blosum62+F+R7 60365.124    334 121398.248   122823.598   122800.540
Optimizing NNI: done in 0.281985 secs using 399.5% CPU
Optimizing NNI: done in 0.267482 secs using 399.5% CPU
Iteration 10 / LogL: -36038.858 / Time: 0h:0m:6s
Optimizing NNI: done in 0.271794 secs using 398.5% CPU
Optimizing NNI: done in 0.308447 secs using 399.5% CPU
Optimizing NNI: done in 0.270609 secs using 399.3% CPU
Optimizing NNI: done in 0.260896 secs using 397.5% CPU
Optimizing NNI: done in 0.284211 secs using 399.2% CPU
Optimizing NNI: done in 0.270133 secs using 399.2% CPU
197  Q.yeast+F+R9  194573.539   1022 391191.077   2482203.077  395641.243
Optimizing NNI: done in 0.265344 secs using 399.5% CPU
Optimizing NNI: done in 0.334439 secs using 397.5% CPU
Optimizing NNI: done in 0.274577 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 19: -36031.082
Optimizing NNI: done in 0.250139 secs using 398.8% CPU
Iteration 20 / LogL: -36041.801 / Time: 0h:0m:9s
Finish initializing candidate tree set (11)
Current best tree score: -36031.082 / CPU time: 9.133
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.393282 secs using 399% CPU
Optimizing NNI: done in 0.538505 secs using 398.4% CPU
Optimizing NNI: done in 0.355074 secs using 399.1% CPU
605  Blosum62+F+R8 60358.971    336 121389.941   122850.999   122800.630
Optimizing NNI: done in 0.362787 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -36030.349
Optimizing NNI: done in 0.389124 secs using 397.5% CPU
Optimizing NNI: done in 0.432233 secs using 399.2% CPU
Optimizing NNI: done in 0.322462 secs using 399.4% CPU
Optimizing NNI: done in 0.430824 secs using 399.5% CPU
Optimizing NNI: done in 0.44723 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -36030.347
Optimizing NNI: done in 0.361032 secs using 399.1% CPU
Iteration 30 / LogL: -36030.889 / Time: 0h:0m:13s (0h:0m:44s left)
Optimizing NNI: done in 0.302281 secs using 397.7% CPU
Optimizing NNI: done in 0.390726 secs using 398.9% CPU
Optimizing NNI: done in 0.366161 secs using 399.5% CPU
Optimizing NNI: done in 0.430862 secs using 398.1% CPU
Optimizing NNI: done in 0.344376 secs using 399% CPU
Optimizing NNI: done in 0.437083 secs using 398.8% CPU
Optimizing NNI: done in 0.328075 secs using 398.9% CPU
Optimizing NNI: done in 0.314524 secs using 398.3% CPU
Optimizing NNI: done in 0.339329 secs using 398.9% CPU
Optimizing NNI: done in 0.390951 secs using 397.6% CPU
Iteration 40 / LogL: -36030.366 / Time: 0h:0m:17s (0h:0m:37s left)
Optimizing NNI: done in 0.308174 secs using 397.9% CPU
Optimizing NNI: done in 0.398566 secs using 399.7% CPU
Optimizing NNI: done in 0.342965 secs using 399.4% CPU
Optimizing NNI: done in 0.377436 secs using 397.3% CPU
612  Blosum62+F+I+R6 60372.554    333 121411.108   122818.982   122809.202
Optimizing NNI: done in 0.412329 secs using 399% CPU
Optimizing NNI: done in 0.355317 secs using 399% CPU
Optimizing NNI: done in 0.424615 secs using 399.7% CPU
Optimizing NNI: done in 0.455151 secs using 399.3% CPU
Optimizing NNI: done in 0.417427 secs using 399.3% CPU
Optimizing NNI: done in 0.39086 secs using 399.3% CPU
Iteration 50 / LogL: -36030.918 / Time: 0h:0m:21s (0h:0m:32s left)
Optimizing NNI: done in 0.290828 secs using 398.7% CPU
Optimizing NNI: done in 0.441877 secs using 398.9% CPU
Optimizing NNI: done in 0.362815 secs using 399.6% CPU
Optimizing NNI: done in 0.369879 secs using 399.5% CPU
Optimizing NNI: done in 0.330389 secs using 399.5% CPU
Optimizing NNI: done in 0.43532 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 56: -36027.613
Optimizing NNI: done in 0.404988 secs using 398.6% CPU
Optimizing NNI: done in 0.409681 secs using 398.8% CPU
Optimizing NNI: done in 0.414311 secs using 399.6% CPU
Optimizing NNI: done in 0.334506 secs using 399% CPU
Iteration 60 / LogL: -36031.277 / Time: 0h:0m:25s (0h:0m:41s left)
Optimizing NNI: done in 0.23308 secs using 399.2% CPU
Optimizing NNI: done in 0.365649 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36027.326
Optimizing NNI: done in 0.390628 secs using 399.6% CPU
613  Blosum62+F+I+R7 60365.655    335 121401.310   122844.387   122807.800
Optimizing NNI: done in 0.283761 secs using 399.6% CPU
Optimizing NNI: done in 0.375064 secs using 398.7% CPU
Optimizing NNI: done in 0.362018 secs using 398.4% CPU
Optimizing NNI: done in 0.317143 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36027.182
Optimizing NNI: done in 0.483028 secs using 397.8% CPU
Optimizing NNI: done in 0.344357 secs using 398.7% CPU
Optimizing NNI: done in 0.327249 secs using 399.7% CPU
Iteration 70 / LogL: -36027.976 / Time: 0h:0m:29s (0h:0m:36s left)
Optimizing NNI: done in 0.354038 secs using 398.7% CPU
Optimizing NNI: done in 0.414831 secs using 399.3% CPU
Optimizing NNI: done in 0.386037 secs using 398.7% CPU
Optimizing NNI: done in 0.383272 secs using 398.8% CPU
Optimizing NNI: done in 0.437502 secs using 398.8% CPU
207  JTTDCMut+R8   195684.064   1001 393370.127   2399374.127  397728.852
Optimizing NNI: done in 0.380339 secs using 398.7% CPU
Optimizing NNI: done in 0.311499 secs using 399.5% CPU
Optimizing NNI: done in 0.332291 secs using 399.3% CPU
Optimizing NNI: done in 0.363358 secs using 399.5% CPU
Optimizing NNI: done in 0.359661 secs using 399.7% CPU
Iteration 80 / LogL: -36036.362 / Time: 0h:0m:32s (0h:0m:31s left)
Optimizing NNI: done in 0.322082 secs using 399.6% CPU
Optimizing NNI: done in 0.317393 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36027.108
Optimizing NNI: done in 0.335079 secs using 399.4% CPU
Optimizing NNI: done in 0.334106 secs using 399.2% CPU
Optimizing NNI: done in 0.278281 secs using 399% CPU
Optimizing NNI: done in 0.365577 secs using 398.8% CPU
Optimizing NNI: done in 0.395023 secs using 398.7% CPU
Optimizing NNI: done in 0.43733 secs using 399.3% CPU
Optimizing NNI: done in 0.377104 secs using 399% CPU
Optimizing NNI: done in 0.435306 secs using 398.6% CPU
Iteration 90 / LogL: -36028.639 / Time: 0h:0m:36s (0h:0m:27s left)
Optimizing NNI: done in 0.297978 secs using 399.4% CPU
Optimizing NNI: done in 0.50546 secs using 399.6% CPU
Optimizing NNI: done in 0.340314 secs using 399.4% CPU
Optimizing NNI: done in 0.36563 secs using 399.9% CPU
Optimizing NNI: done in 0.338188 secs using 399.1% CPU
Optimizing NNI: done in 0.32692 secs using 399.6% CPU
Optimizing NNI: done in 0.407859 secs using 399.9% CPU
Optimizing NNI: done in 0.331703 secs using 399.5% CPU
Optimizing NNI: done in 0.367461 secs using 399.2% CPU
Optimizing NNI: done in 0.306625 secs using 399.4% CPU
Iteration 100 / LogL: -36030.465 / Time: 0h:0m:40s (0h:0m:22s left)
Optimizing NNI: done in 0.506523 secs using 398.1% CPU
Optimizing NNI: done in 0.483091 secs using 398.7% CPU
Optimizing NNI: done in 0.389093 secs using 399.6% CPU
Optimizing NNI: done in 0.497443 secs using 398% CPU
Optimizing NNI: done in 0.430168 secs using 399% CPU
Optimizing NNI: done in 0.250414 secs using 397.7% CPU
Optimizing NNI: done in 0.408649 secs using 398.8% CPU
625  Dayhoff+R6    60665.533    313 121957.066   123061.358   123271.190
Optimizing NNI: done in 0.513506 secs using 399.3% CPU
Optimizing NNI: done in 0.41882 secs using 398.1% CPU
Optimizing NNI: done in 0.393322 secs using 399.4% CPU
Iteration 110 / LogL: -36030.551 / Time: 0h:0m:44s (0h:0m:18s left)
Optimizing NNI: done in 0.382521 secs using 399% CPU
Optimizing NNI: done in 0.434975 secs using 398.9% CPU
Optimizing NNI: done in 0.373994 secs using 397.9% CPU
Optimizing NNI: done in 0.331206 secs using 398.4% CPU
Optimizing NNI: done in 0.417048 secs using 398.5% CPU
Optimizing NNI: done in 0.449938 secs using 398.7% CPU
Optimizing NNI: done in 0.398727 secs using 398.8% CPU
Optimizing NNI: done in 0.362882 secs using 399.8% CPU
Optimizing NNI: done in 0.41557 secs using 399.3% CPU
Optimizing NNI: done in 0.396533 secs using 399.6% CPU
Iteration 120 / LogL: -36071.081 / Time: 0h:0m:48s (0h:0m:14s left)
Optimizing NNI: done in 0.371822 secs using 398.4% CPU
Optimizing NNI: done in 0.438125 secs using 399.9% CPU
Optimizing NNI: done in 0.404127 secs using 399.2% CPU
Optimizing NNI: done in 0.312134 secs using 398.9% CPU
208  JTTDCMut+R9   195667.689   1003 393341.377   2407365.377  397708.810
Optimizing NNI: done in 0.323724 secs using 399.2% CPU
Optimizing NNI: done in 0.448618 secs using 399.9% CPU
Optimizing NNI: done in 0.532702 secs using 399.2% CPU
Optimizing NNI: done in 0.418896 secs using 399.3% CPU
Optimizing NNI: done in 0.389136 secs using 399.9% CPU
Optimizing NNI: done in 0.345455 secs using 399.9% CPU
Iteration 130 / LogL: -36027.760 / Time: 0h:0m:52s (0h:0m:10s left)
Optimizing NNI: done in 0.319848 secs using 399.1% CPU
Optimizing NNI: done in 0.369569 secs using 399.2% CPU
Optimizing NNI: done in 0.327969 secs using 399.9% CPU
Optimizing NNI: done in 0.388557 secs using 399% CPU
Optimizing NNI: done in 0.328205 secs using 399.3% CPU
Optimizing NNI: done in 0.278659 secs using 399.5% CPU
Optimizing NNI: done in 0.327591 secs using 399.9% CPU
Optimizing NNI: done in 0.465389 secs using 399.5% CPU
Optimizing NNI: done in 0.328315 secs using 399.8% CPU
Optimizing NNI: done in 0.393344 secs using 399% CPU
Iteration 140 / LogL: -36027.643 / Time: 0h:0m:56s (0h:0m:6s left)
Optimizing NNI: done in 0.329637 secs using 399.5% CPU
Optimizing NNI: done in 0.435106 secs using 398.4% CPU
Optimizing NNI: done in 0.434348 secs using 399.1% CPU
Optimizing NNI: done in 0.361152 secs using 398.8% CPU
Optimizing NNI: done in 0.339238 secs using 399.9% CPU
Optimizing NNI: done in 0.383047 secs using 399.4% CPU
Optimizing NNI: done in 0.342792 secs using 398.5% CPU
Optimizing NNI: done in 0.450584 secs using 399.4% CPU
Optimizing NNI: done in 0.367477 secs using 399.9% CPU
Optimizing NNI: done in 0.364259 secs using 398.2% CPU
Iteration 150 / LogL: -36030.429 / Time: 0h:0m:59s (0h:0m:2s left)
626  Dayhoff+R7    60649.782    315 121929.564   123060.700   123252.085
Optimizing NNI: done in 0.377864 secs using 400.4% CPU
Optimizing NNI: done in 0.343369 secs using 399.5% CPU
Optimizing NNI: done in 0.339405 secs using 399.9% CPU
Optimizing NNI: done in 0.344433 secs using 399.9% CPU
 88  WAG+F+I+R10   105733.677   573 212613.354   870417.354   214920.175
Optimizing NNI: done in 0.340806 secs using 398.6% CPU
Optimizing NNI: done in 0.39385 secs using 399.5% CPU
Optimizing NNI: done in 0.297401 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 157 ITERATIONS / Time: 0h:1m:2s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36027.108
Optimal log-likelihood: -36027.095
Proportion of invariable sites: 0.033
Gamma shape alpha: 2.240
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -36027.095
Total tree length: 20.054

Total number of iterations: 157
CPU time used for tree search: 242.571 sec (0h:4m:2s)
Wall-clock time used for tree search: 61.818 sec (0h:1m:1s)
Total CPU time used: 245.085 sec (0h:4m:5s)
Total wall-clock time used: 62.416 sec (0h:1m:2s)

===> START BOOTSTRAP REPLICATE NUMBER 22

Creating bootstrap alignment (seed: 956181)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.010 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36540.461
2. Current log-likelihood: -35614.834
3. Current log-likelihood: -35603.313
4. Current log-likelihood: -35603.057
Optimal log-likelihood: -35603.041
Proportion of invariable sites: 0.011
Gamma shape alpha: 2.183
Parameters optimization took 4 rounds (0.233 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0776172 secs using 396.1% CPU
Computing ML distances took 0.077750 sec (of wall-clock time) 0.307753 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00016284 secs using 415.1% CPU
Constructing RapidNJ tree: done in 0.00210214 secs using 443.2% CPU
Computing RapidNJ tree took 0.002323 sec (of wall-clock time) 0.010681 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36138.766
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.485 second
Computing log-likelihood of 98 initial trees ... 1.604 seconds
Current best score: -35599.439

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.317574 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35539.973
Optimizing NNI: done in 0.206163 secs using 397.5% CPU
Optimizing NNI: done in 0.288639 secs using 399.7% CPU
Optimizing NNI: done in 0.307493 secs using 398.2% CPU
Optimizing NNI: done in 0.2951 secs using 399.2% CPU
Optimizing NNI: done in 0.263401 secs using 399.9% CPU
Optimizing NNI: done in 0.294007 secs using 399.6% CPU
Optimizing NNI: done in 0.297799 secs using 399.9% CPU
Optimizing NNI: done in 0.2923 secs using 399.5% CPU
Optimizing NNI: done in 0.301504 secs using 399.2% CPU
Iteration 10 / LogL: -35546.645 / Time: 0h:0m:6s
Optimizing NNI: done in 0.308589 secs using 398.6% CPU
627  Dayhoff+R8    60645.551    317 121925.102   123083.791   123256.019
Optimizing NNI: done in 0.295251 secs using 399.5% CPU
Optimizing NNI: done in 0.317332 secs using 399.3% CPU
Optimizing NNI: done in 0.278411 secs using 399.2% CPU
Optimizing NNI: done in 0.321868 secs using 399.1% CPU
Optimizing NNI: done in 0.310606 secs using 399.1% CPU
Optimizing NNI: done in 0.279071 secs using 399.7% CPU
Optimizing NNI: done in 0.29915 secs using 400.2% CPU
Optimizing NNI: done in 0.293401 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 19: -35539.392
Optimizing NNI: done in 0.315782 secs using 399.8% CPU
Iteration 20 / LogL: -35539.991 / Time: 0h:0m:9s
Finish initializing candidate tree set (11)
Current best tree score: -35539.392 / CPU time: 9.131
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.561831 secs using 399.2% CPU
Optimizing NNI: done in 0.374673 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -35539.329
Optimizing NNI: done in 0.532462 secs using 399.4% CPU
Optimizing NNI: done in 0.549311 secs using 399.4% CPU
Optimizing NNI: done in 0.517442 secs using 398.9% CPU
Optimizing NNI: done in 0.458937 secs using 399.2% CPU
Optimizing NNI: done in 0.350524 secs using 399% CPU
Optimizing NNI: done in 0.556996 secs using 400.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -35536.896
Optimizing NNI: done in 0.389281 secs using 399% CPU
Optimizing NNI: done in 0.551945 secs using 399.4% CPU
Iteration 30 / LogL: -35538.759 / Time: 0h:0m:14s (0h:0m:49s left)
Optimizing NNI: done in 0.501762 secs using 399.8% CPU
Optimizing NNI: done in 0.552295 secs using 398.9% CPU
634  Dayhoff+I+R6  60662.272    314 121952.544   123070.171   123270.866
Optimizing NNI: done in 0.443129 secs using 399.2% CPU
Optimizing NNI: done in 0.561857 secs using 399.7% CPU
Optimizing NNI: done in 0.394893 secs using 399.8% CPU
Optimizing NNI: done in 0.478208 secs using 399.5% CPU
Optimizing NNI: done in 0.398849 secs using 399% CPU
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Optimizing NNI: done in 0.483496 secs using 398.4% CPU
Optimizing NNI: done in 0.473346 secs using 399.4% CPU
Iteration 40 / LogL: -35538.883 / Time: 0h:0m:19s (0h:0m:43s left)
109  JTT+I+R9      105304.164   552 211712.327   822224.327   213934.605
Optimizing NNI: done in 0.441115 secs using 398.7% CPU
Optimizing NNI: done in 0.494057 secs using 399.8% CPU
Optimizing NNI: done in 0.605027 secs using 399.5% CPU
Optimizing NNI: done in 0.528963 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -35536.404
Optimizing NNI: done in 0.386383 secs using 398.7% CPU
Optimizing NNI: done in 0.412123 secs using 399.8% CPU
Optimizing NNI: done in 0.537445 secs using 399.2% CPU
Optimizing NNI: done in 0.541344 secs using 399.4% CPU
Optimizing NNI: done in 0.469226 secs using 399.6% CPU
Optimizing NNI: done in 0.495343 secs using 399.3% CPU
Iteration 50 / LogL: -35536.421 / Time: 0h:0m:24s (0h:0m:46s left)
209  JTTDCMut+R10  195664.727   1005 393339.454   2415399.454  397715.596
Optimizing NNI: done in 0.549679 secs using 399.8% CPU
Optimizing NNI: done in 0.547249 secs using 399.9% CPU
Optimizing NNI: done in 0.39258 secs using 399.1% CPU
Optimizing NNI: done in 0.56491 secs using 399.1% CPU
Optimizing NNI: done in 0.553158 secs using 399.7% CPU
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Optimizing NNI: done in 0.5852 secs using 399.4% CPU
Optimizing NNI: done in 0.458622 secs using 399.8% CPU
Optimizing NNI: done in 0.530558 secs using 399.1% CPU
635  Dayhoff+I+R7  60646.014    316 121924.028   123068.851   123250.747
Optimizing NNI: done in 0.553274 secs using 399.8% CPU
Iteration 60 / LogL: -35544.877 / Time: 0h:0m:29s (0h:0m:42s left)
Optimizing NNI: done in 0.538212 secs using 399.6% CPU
Optimizing NNI: done in 0.599847 secs using 399.4% CPU
Optimizing NNI: done in 0.351691 secs using 399.8% CPU
Optimizing NNI: done in 0.523082 secs using 399.3% CPU
Optimizing NNI: done in 0.515988 secs using 399.5% CPU
Optimizing NNI: done in 0.45771 secs using 399.6% CPU
Optimizing NNI: done in 0.471147 secs using 399.2% CPU
Optimizing NNI: done in 0.449071 secs using 400.3% CPU
Optimizing NNI: done in 0.44091 secs using 399.4% CPU
647  Dayhoff+F+R6  60590.639    332 121845.279   123235.920   123239.174
Optimizing NNI: done in 0.524572 secs using 399.4% CPU
Iteration 70 / LogL: -35545.791 / Time: 0h:0m:34s (0h:0m:36s left)
Optimizing NNI: done in 0.436452 secs using 398.6% CPU
Optimizing NNI: done in 0.396041 secs using 399.1% CPU
Optimizing NNI: done in 0.616738 secs using 399.7% CPU
Optimizing NNI: done in 0.499114 secs using 399.6% CPU
Optimizing NNI: done in 0.436114 secs using 399.6% CPU
Optimizing NNI: done in 0.577618 secs using 398.9% CPU
Optimizing NNI: done in 0.416328 secs using 400% CPU
Optimizing NNI: done in 0.537337 secs using 399.5% CPU
218  JTTDCMut+F+R8 194737.502   1020 391515.003   2474355.003  395956.461
Optimizing NNI: done in 0.54446 secs using 399.6% CPU
Optimizing NNI: done in 0.430665 secs using 399.1% CPU
Iteration 80 / LogL: -35538.472 / Time: 0h:0m:39s (0h:0m:31s left)
Optimizing NNI: done in 0.647405 secs using 399.8% CPU
Optimizing NNI: done in 0.553062 secs using 398.6% CPU
Optimizing NNI: done in 0.541962 secs using 399.1% CPU
Optimizing NNI: done in 0.384509 secs using 399.2% CPU
Optimizing NNI: done in 0.470829 secs using 399% CPU
Optimizing NNI: done in 0.479928 secs using 398.9% CPU
Optimizing NNI: done in 0.483599 secs using 399.9% CPU
Optimizing NNI: done in 0.484734 secs using 399.9% CPU
Optimizing NNI: done in 0.468371 secs using 398.9% CPU
Optimizing NNI: done in 0.503078 secs using 399.2% CPU
Iteration 90 / LogL: -35536.461 / Time: 0h:0m:44s (0h:0m:26s left)
Optimizing NNI: done in 0.454336 secs using 399.6% CPU
Optimizing NNI: done in 0.554171 secs using 399.5% CPU
Optimizing NNI: done in 0.52004 secs using 399.6% CPU
Optimizing NNI: done in 0.557765 secs using 399.4% CPU
Optimizing NNI: done in 0.514334 secs using 399.2% CPU
648  Dayhoff+F+R7  60577.726    334 121823.452   123248.802   123225.744
Optimizing NNI: done in 0.627688 secs using 399.8% CPU
Optimizing NNI: done in 0.546212 secs using 399.7% CPU
Optimizing NNI: done in 0.422642 secs using 398.6% CPU
Optimizing NNI: done in 0.469854 secs using 399.3% CPU
Optimizing NNI: done in 0.548625 secs using 399.3% CPU
Iteration 100 / LogL: -35536.409 / Time: 0h:0m:49s (0h:0m:22s left)
Optimizing NNI: done in 0.523184 secs using 399.3% CPU
Optimizing NNI: done in 0.431499 secs using 399.4% CPU
Optimizing NNI: done in 0.393087 secs using 399.3% CPU
Optimizing NNI: done in 0.428474 secs using 399.4% CPU
Optimizing NNI: done in 0.42386 secs using 399.1% CPU
649  Dayhoff+F+R8  60572.198    336 121816.396   123277.454   123227.085
Optimizing NNI: done in 0.498648 secs using 399.5% CPU
Optimizing NNI: done in 0.587255 secs using 398.4% CPU
Optimizing NNI: done in 0.537253 secs using 399.7% CPU
Optimizing NNI: done in 0.414777 secs using 398.3% CPU
Optimizing NNI: done in 0.420324 secs using 398.6% CPU
Iteration 110 / LogL: -35536.405 / Time: 0h:0m:54s (0h:0m:16s left)
Optimizing NNI: done in 0.311749 secs using 398.5% CPU
Optimizing NNI: done in 0.499262 secs using 399.3% CPU
Optimizing NNI: done in 0.605998 secs using 399.2% CPU
Optimizing NNI: done in 0.563771 secs using 399.2% CPU
Optimizing NNI: done in 0.304821 secs using 399.2% CPU
Optimizing NNI: done in 0.376459 secs using 398.2% CPU
Optimizing NNI: done in 0.503085 secs using 398.8% CPU
656  Dayhoff+F+I+R6 60584.026    333 121834.052   123241.926   123232.146
Optimizing NNI: done in 0.542393 secs using 399.3% CPU
Optimizing NNI: done in 0.550402 secs using 399.2% CPU
Optimizing NNI: done in 0.481811 secs using 399.5% CPU
Iteration 120 / LogL: -35536.987 / Time: 0h:0m:59s (0h:0m:11s left)
Optimizing NNI: done in 0.373037 secs using 399.3% CPU
Optimizing NNI: done in 0.579829 secs using 399.2% CPU
219  JTTDCMut+F+R9 194732.541   1022 391509.083   2482521.083  395959.249
Optimizing NNI: done in 0.597944 secs using 398.8% CPU
Optimizing NNI: done in 0.488584 secs using 399.5% CPU
Optimizing NNI: done in 0.492256 secs using 398.5% CPU
Optimizing NNI: done in 0.413209 secs using 399.2% CPU
Optimizing NNI: done in 0.500794 secs using 398.5% CPU
Optimizing NNI: done in 0.397726 secs using 398.2% CPU
Optimizing NNI: done in 0.48774 secs using 399.6% CPU
Optimizing NNI: done in 0.506742 secs using 399.6% CPU
Iteration 130 / LogL: -35538.953 / Time: 0h:1m:4s (0h:0m:6s left)
Optimizing NNI: done in 0.531835 secs using 399.3% CPU
Optimizing NNI: done in 0.42517 secs using 399.4% CPU
Optimizing NNI: done in 0.507676 secs using 399.1% CPU
Optimizing NNI: done in 0.548499 secs using 399.1% CPU
Optimizing NNI: done in 0.387001 secs using 398.6% CPU
Optimizing NNI: done in 0.595825 secs using 399.5% CPU
Optimizing NNI: done in 0.494077 secs using 398.9% CPU
Optimizing NNI: done in 0.577797 secs using 398.5% CPU
Optimizing NNI: done in 0.451278 secs using 398.5% CPU
Optimizing NNI: done in 0.578136 secs using 399.5% CPU
Iteration 140 / LogL: -35536.421 / Time: 0h:1m:9s (0h:0m:1s left)
Optimizing NNI: done in 0.418385 secs using 399.2% CPU
Optimizing NNI: done in 0.481524 secs using 398.4% CPU
Optimizing NNI: done in 0.383488 secs using 398.2% CPU
Optimizing NNI: done in 0.334978 secs using 399.3% CPU
Optimizing NNI: done in 0.457323 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 145 ITERATIONS / Time: 0h:1m:11s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35536.404
Optimal log-likelihood: -35536.404
Proportion of invariable sites: 0.011
Gamma shape alpha: 2.226
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -35536.404
Total tree length: 20.817

Total number of iterations: 145
CPU time used for tree search: 278.916 sec (0h:4m:38s)
Wall-clock time used for tree search: 70.821 sec (0h:1m:10s)
Total CPU time used: 281.133 sec (0h:4m:41s)
Total wall-clock time used: 71.343 sec (0h:1m:11s)

===> START BOOTSTRAP REPLICATE NUMBER 23

Creating bootstrap alignment (seed: 956182)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.018 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36731.953
2. Current log-likelihood: -35849.071
3. Current log-likelihood: -35838.970
4. Current log-likelihood: -35838.762
Optimal log-likelihood: -35838.688
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.149
Parameters optimization took 4 rounds (0.263 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.079077 secs using 398.6% CPU
Computing ML distances took 0.079217 sec (of wall-clock time) 0.315521 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000144005 secs using 423.6% CPU
Constructing RapidNJ tree: done in 0.00216389 secs using 426.7% CPU
Computing RapidNJ tree took 0.002360 sec (of wall-clock time) 0.010900 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36424.067
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... 1.485 second
Computing log-likelihood of 98 initial trees ... 1.625 seconds
Current best score: -35838.688

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.186174 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35802.696
Optimizing NNI: done in 0.221801 secs using 398.7% CPU
Optimizing NNI: done in 0.232217 secs using 399.2% CPU
Optimizing NNI: done in 0.23278 secs using 397.8% CPU
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Optimizing NNI: done in 0.231291 secs using 398.5% CPU
Iteration 10 / LogL: -35803.298 / Time: 0h:0m:6s
Optimizing NNI: done in 0.213272 secs using 400.1% CPU
Optimizing NNI: done in 0.194511 secs using 399.5% CPU
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Optimizing NNI: done in 0.271053 secs using 399.9% CPU
Optimizing NNI: done in 0.220663 secs using 399.9% CPU
657  Dayhoff+F+I+R7 60572.635    335 121815.269   123258.346   123221.760
Optimizing NNI: done in 0.249986 secs using 399.8% CPU
Optimizing NNI: done in 0.260854 secs using 399.7% CPU
Optimizing NNI: done in 0.211655 secs using 400.5% CPU
Iteration 20 / LogL: -35805.522 / Time: 0h:0m:8s
Finish initializing candidate tree set (11)
Current best tree score: -35802.696 / CPU time: 7.957
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 0.365062 secs using 399.6% CPU
Optimizing NNI: done in 0.405902 secs using 398.6% CPU
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Optimizing NNI: done in 0.40881 secs using 399.1% CPU
Optimizing NNI: done in 0.228579 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -35802.347
669  mtREV+R6      62499.837    313 125625.675   126729.967   126939.798
Optimizing NNI: done in 0.349338 secs using 400% CPU
Optimizing NNI: done in 0.393583 secs using 399.3% CPU
Optimizing NNI: done in 0.396676 secs using 399.6% CPU
Optimizing NNI: done in 0.394332 secs using 399.2% CPU
Iteration 30 / LogL: -35802.636 / Time: 0h:0m:12s (0h:0m:40s left)
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Iteration 40 / LogL: -35804.151 / Time: 0h:0m:15s (0h:0m:34s left)
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Iteration 50 / LogL: -35804.198 / Time: 0h:0m:19s (0h:0m:30s left)
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670  mtREV+R7      62487.330    315 125604.660   126735.796   126927.181
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Optimizing NNI: done in 0.335048 secs using 399.3% CPU
Iteration 60 / LogL: -35803.288 / Time: 0h:0m:22s (0h:0m:25s left)
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Optimizing NNI: done in 0.362369 secs using 399.1% CPU
Optimizing NNI: done in 0.356121 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35802.208
Optimizing NNI: done in 0.346034 secs using 399.8% CPU
Optimizing NNI: done in 0.306866 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 66: -35801.674
Optimizing NNI: done in 0.807162 secs using 398.6% CPU
Optimizing NNI: done in 0.395465 secs using 399.6% CPU
Optimizing NNI: done in 0.36904 secs using 398.9% CPU
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Iteration 70 / LogL: -35802.572 / Time: 0h:0m:27s (0h:0m:37s left)
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Optimizing NNI: done in 0.355841 secs using 399.6% CPU
671  mtREV+R8      62485.980    317 125605.961   126764.650   126936.878
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Iteration 80 / LogL: -35802.567 / Time: 0h:0m:30s (0h:0m:33s left)
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Optimizing NNI: done in 0.440583 secs using 399.2% CPU
Iteration 90 / LogL: -35802.022 / Time: 0h:0m:34s (0h:0m:29s left)
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Optimizing NNI: done in 0.244256 secs using 399.8% CPU
Iteration 100 / LogL: -35801.735 / Time: 0h:0m:37s (0h:0m:25s left)
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Optimizing NNI: done in 0.357367 secs using 399.1% CPU
Optimizing NNI: done in 0.412944 secs using 398.3% CPU
678  mtREV+I+R6    62500.369    314 125628.737   126746.364   126947.059
Optimizing NNI: done in 0.367095 secs using 398.7% CPU
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Optimizing NNI: done in 0.405479 secs using 399.6% CPU
Optimizing NNI: done in 0.335795 secs using 399.9% CPU
Iteration 110 / LogL: -35802.285 / Time: 0h:0m:41s (0h:0m:21s left)
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Optimizing NNI: done in 0.35782 secs using 399.7% CPU
Optimizing NNI: done in 0.379959 secs using 399.8% CPU
UPDATE BEST LOG-LIKELIHOOD: -35801.667
Optimizing NNI: done in 0.298989 secs using 399.5% CPU
Optimizing NNI: done in 0.409842 secs using 399.6% CPU
229  DCMut+R8      198858.399   1001 399718.798   2405722.798  404077.523
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Iteration 120 / LogL: -35815.602 / Time: 0h:0m:45s (0h:0m:17s left)
Optimizing NNI: done in 0.426521 secs using 399.1% CPU
Optimizing NNI: done in 0.280634 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35801.485
Optimizing NNI: done in 0.355982 secs using 399.8% CPU
Optimizing NNI: done in 0.27181 secs using 399.9% CPU
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Iteration 130 / LogL: -35802.471 / Time: 0h:0m:49s (0h:0m:13s left)
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679  mtREV+I+R7    62487.692    316 125607.385   126752.208   126934.104
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Iteration 140 / LogL: -35801.808 / Time: 0h:0m:52s (0h:0m:9s left)
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Optimizing NNI: done in 0.275877 secs using 399.5% CPU
691  mtREV+F+R6    60468.631    332 121601.263   122991.904   122995.158
Optimizing NNI: done in 0.322133 secs using 399.2% CPU
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Iteration 150 / LogL: -35809.217 / Time: 0h:0m:56s (0h:0m:6s left)
Optimizing NNI: done in 0.32541 secs using 399.6% CPU
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Iteration 160 / LogL: -35801.818 / Time: 0h:1m:0s (0h:0m:2s left)
Optimizing NNI: done in 0.368227 secs using 399.1% CPU
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Optimizing NNI: done in 0.376858 secs using 399.4% CPU
TREE SEARCH COMPLETED AFTER 167 ITERATIONS / Time: 0h:1m:2s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35801.485
Optimal log-likelihood: -35801.482
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.168
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -35801.482
Total tree length: 20.684

Total number of iterations: 167
CPU time used for tree search: 244.775 sec (0h:4m:4s)
Wall-clock time used for tree search: 62.257 sec (0h:1m:2s)
Total CPU time used: 247.539 sec (0h:4m:7s)
Total wall-clock time used: 62.903 sec (0h:1m:2s)

===> START BOOTSTRAP REPLICATE NUMBER 24

Creating bootstrap alignment (seed: 956183)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36496.345
2. Current log-likelihood: -35595.906
3. Current log-likelihood: -35582.946
4. Current log-likelihood: -35582.701
Optimal log-likelihood: -35582.645
Proportion of invariable sites: 0.027
Gamma shape alpha: 2.398
Parameters optimization took 4 rounds (0.277 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0770121 secs using 400% CPU
Computing ML distances took 0.077151 sec (of wall-clock time) 0.308405 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000151873 secs using 423.4% CPU
Constructing RapidNJ tree: done in 0.00231504 secs using 405.7% CPU
Computing RapidNJ tree took 0.002529 sec (of wall-clock time) 0.010696 sec (of CPU time)
692  mtREV+F+R7    60454.479    334 121576.958   123002.308   122979.250
Log-likelihood of RapidNJ tree: -36313.605
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|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.403 second
Computing log-likelihood of 98 initial trees ... 1.629 seconds
Current best score: -35582.645

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.253463 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35530.109
Optimizing NNI: done in 0.217002 secs using 399.9% CPU
Optimizing NNI: done in 0.248154 secs using 398.7% CPU
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Iteration 10 / LogL: -35534.060 / Time: 0h:0m:6s
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Optimizing NNI: done in 0.232444 secs using 400.1% CPU
Estimate model parameters (epsilon = 0.100)
230  DCMut+R9      198850.908   1003 399707.816   2413731.816  404075.249
BETTER TREE FOUND at iteration 16: -35527.500
Optimizing NNI: done in 0.252303 secs using 399.8% CPU
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Optimizing NNI: done in 0.254358 secs using 398.5% CPU
Optimizing NNI: done in 0.268648 secs using 398.8% CPU
Iteration 20 / LogL: -35534.416 / Time: 0h:0m:9s
Finish initializing candidate tree set (13)
Current best tree score: -35527.500 / CPU time: 8.638
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 0.430941 secs using 399% CPU
Optimizing NNI: done in 0.378615 secs using 399% CPU
Optimizing NNI: done in 0.362085 secs using 400.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -35526.633
Optimizing NNI: done in 0.367587 secs using 399.5% CPU
693  mtREV+F+R8    60448.613    336 121569.227   123030.285   122979.915
Optimizing NNI: done in 0.405991 secs using 399.6% CPU
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Iteration 30 / LogL: -35526.768 / Time: 0h:0m:13s (0h:0m:41s left)
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Iteration 40 / LogL: -35527.916 / Time: 0h:0m:16s (0h:0m:36s left)
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700  mtREV+F+I+R6  60467.056    333 121600.111   123007.985   122998.205
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Iteration 50 / LogL: -35527.486 / Time: 0h:0m:20s (0h:0m:31s left)
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Optimizing NNI: done in 0.448188 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35526.573
Optimizing NNI: done in 0.392214 secs using 398.9% CPU
Iteration 60 / LogL: -35526.678 / Time: 0h:0m:25s (0h:0m:26s left)
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Optimizing NNI: done in 0.513375 secs using 399.1% CPU
701  mtREV+F+I+R7  60454.408    335 121578.815   123021.892   122985.306
Optimizing NNI: done in 0.439888 secs using 400.4% CPU
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Optimizing NNI: done in 0.387379 secs using 399.9% CPU
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Iteration 70 / LogL: -35528.761 / Time: 0h:0m:29s (0h:0m:22s left)
Optimizing NNI: done in 0.412333 secs using 399.7% CPU
231  DCMut+R10     198848.803   1005 399707.606   2421767.606  404083.748
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Optimizing NNI: done in 0.417887 secs using 398.9% CPU
713  mtART+R6      62852.803    313 126331.607   127435.899   127645.731
Optimizing NNI: done in 0.425727 secs using 399% CPU
Iteration 80 / LogL: -35526.920 / Time: 0h:0m:33s (0h:0m:18s left)
Optimizing NNI: done in 0.359784 secs using 399.6% CPU
Optimizing NNI: done in 0.339425 secs using 399.9% CPU
Optimizing NNI: done in 0.337392 secs using 399.9% CPU
Optimizing NNI: done in 0.436813 secs using 399.4% CPU
Optimizing NNI: done in 0.312877 secs using 399.5% CPU
Optimizing NNI: done in 0.450024 secs using 397.3% CPU
Optimizing NNI: done in 0.486148 secs using 398.7% CPU
Optimizing NNI: done in 0.371386 secs using 399% CPU
Optimizing NNI: done in 0.460204 secs using 400% CPU
Optimizing NNI: done in 0.398083 secs using 399.5% CPU
Iteration 90 / LogL: -35527.409 / Time: 0h:0m:37s (0h:0m:13s left)
Optimizing NNI: done in 0.369869 secs using 399.2% CPU
Optimizing NNI: done in 0.496291 secs using 399.3% CPU
Optimizing NNI: done in 0.327566 secs using 399.3% CPU
Optimizing NNI: done in 0.38568 secs using 399.3% CPU
Optimizing NNI: done in 0.353086 secs using 399.9% CPU
Optimizing NNI: done in 0.312061 secs using 399.6% CPU
Optimizing NNI: done in 0.359136 secs using 399.9% CPU
Optimizing NNI: done in 0.347953 secs using 399.6% CPU
Optimizing NNI: done in 0.360957 secs using 399% CPU
Optimizing NNI: done in 0.43361 secs using 399.3% CPU
Iteration 100 / LogL: -35527.285 / Time: 0h:0m:41s (0h:0m:9s left)
Optimizing NNI: done in 0.36013 secs using 399.4% CPU
Optimizing NNI: done in 0.381504 secs using 398.8% CPU
Optimizing NNI: done in 0.375236 secs using 399.1% CPU
Optimizing NNI: done in 0.347382 secs using 399.2% CPU
Optimizing NNI: done in 0.404096 secs using 399.3% CPU
Optimizing NNI: done in 0.37771 secs using 399.6% CPU
Optimizing NNI: done in 0.3969 secs using 398.8% CPU
Optimizing NNI: done in 0.383685 secs using 399.4% CPU
714  mtART+R7      62831.608    315 126293.216   127424.352   127615.737
Optimizing NNI: done in 0.462792 secs using 399.1% CPU
Optimizing NNI: done in 0.417987 secs using 399.1% CPU
Iteration 110 / LogL: -35527.101 / Time: 0h:0m:45s (0h:0m:5s left)
Optimizing NNI: done in 0.386287 secs using 399.1% CPU
Optimizing NNI: done in 0.358414 secs using 399.3% CPU
Optimizing NNI: done in 0.357778 secs using 399.3% CPU
Optimizing NNI: done in 0.43525 secs using 399.6% CPU
Optimizing NNI: done in 0.352294 secs using 399.3% CPU
Optimizing NNI: done in 0.407369 secs using 398.9% CPU
Optimizing NNI: done in 0.422744 secs using 399.1% CPU
Optimizing NNI: done in 0.360884 secs using 398.2% CPU
Optimizing NNI: done in 0.441751 secs using 399.4% CPU
Optimizing NNI: done in 0.317363 secs using 399.9% CPU
Iteration 120 / LogL: -35526.760 / Time: 0h:0m:49s (0h:0m:1s left)
Optimizing NNI: done in 0.334883 secs using 399% CPU
Optimizing NNI: done in 0.274724 secs using 399.8% CPU
Optimizing NNI: done in 0.469375 secs using 398.9% CPU
110  JTT+I+R10     105304.288   554 211716.577   826656.577   213946.906
Optimizing NNI: done in 0.601871 secs using 399.2% CPU
TREE SEARCH COMPLETED AFTER 124 ITERATIONS / Time: 0h:0m:50s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35526.573
Optimal log-likelihood: -35526.573
Proportion of invariable sites: 0.027
Gamma shape alpha: 2.431
Parameters optimization took 1 rounds (0.046 sec)
BEST SCORE FOUND : -35526.573
Total tree length: 19.615

Total number of iterations: 124
CPU time used for tree search: 197.293 sec (0h:3m:17s)
Wall-clock time used for tree search: 50.309 sec (0h:0m:50s)
Total CPU time used: 199.727 sec (0h:3m:19s)
Total wall-clock time used: 50.885 sec (0h:0m:50s)

===> START BOOTSTRAP REPLICATE NUMBER 25

Creating bootstrap alignment (seed: 956184)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36946.704
2. Current log-likelihood: -36100.624
3. Current log-likelihood: -36084.590
4. Current log-likelihood: -36084.291
Optimal log-likelihood: -36084.241
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.646
Parameters optimization took 4 rounds (0.269 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0817771 secs using 399.8% CPU
Computing ML distances took 0.081921 sec (of wall-clock time) 0.327368 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000149012 secs using 438.2% CPU
Constructing RapidNJ tree: done in 0.00214195 secs using 485.5% CPU
Computing RapidNJ tree took 0.002344 sec (of wall-clock time) 0.011885 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36631.802
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.474 second
715  mtART+R8      62826.466    317 126286.932   127445.622   127617.850
Computing log-likelihood of 98 initial trees ... 1.587 seconds
Current best score: -36084.241

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.185572 secs using 400.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36070.994
Optimizing NNI: done in 0.24018 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36068.161
Optimizing NNI: done in 0.277626 secs using 399.2% CPU
Optimizing NNI: done in 0.24695 secs using 398.3% CPU
Optimizing NNI: done in 0.229827 secs using 399.1% CPU
Optimizing NNI: done in 0.234469 secs using 399.6% CPU
Optimizing NNI: done in 0.28388 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -36059.001
Optimizing NNI: done in 0.262054 secs using 399.2% CPU
Optimizing NNI: done in 0.22979 secs using 400.7% CPU
Optimizing NNI: done in 0.279366 secs using 399.8% CPU
Iteration 10 / LogL: -36068.247 / Time: 0h:0m:6s
Optimizing NNI: done in 0.271924 secs using 399.6% CPU
Optimizing NNI: done in 0.228227 secs using 399.5% CPU
240  DCMut+F+R8    196826.536   1020 395693.071   2478533.071  400134.529
Optimizing NNI: done in 0.288395 secs using 399.2% CPU
Optimizing NNI: done in 0.273538 secs using 399.2% CPU
Optimizing NNI: done in 0.228435 secs using 399.5% CPU
Optimizing NNI: done in 0.226184 secs using 399.7% CPU
Optimizing NNI: done in 0.246484 secs using 398.6% CPU
Optimizing NNI: done in 0.232167 secs using 399.7% CPU
Optimizing NNI: done in 0.250297 secs using 399.1% CPU
Optimizing NNI: done in 0.286422 secs using 399.2% CPU
Iteration 20 / LogL: -36070.587 / Time: 0h:0m:8s
Finish initializing candidate tree set (13)
Current best tree score: -36059.001 / CPU time: 8.308
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.316716 secs using 399.2% CPU
Optimizing NNI: done in 0.363491 secs using 399.1% CPU
Optimizing NNI: done in 0.367296 secs using 399.6% CPU
Optimizing NNI: done in 0.320764 secs using 399.3% CPU
Optimizing NNI: done in 0.337301 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36058.949
Optimizing NNI: done in 0.344118 secs using 399.9% CPU
Optimizing NNI: done in 0.397469 secs using 398.6% CPU
Optimizing NNI: done in 0.34157 secs using 399.3% CPU
Optimizing NNI: done in 0.418097 secs using 399.1% CPU
Optimizing NNI: done in 0.268363 secs using 399.7% CPU
Iteration 30 / LogL: -36058.997 / Time: 0h:0m:12s (0h:0m:32s left)
Optimizing NNI: done in 0.301638 secs using 399.8% CPU
Optimizing NNI: done in 0.417994 secs using 399% CPU
Optimizing NNI: done in 0.360897 secs using 399.9% CPU
Optimizing NNI: done in 0.403638 secs using 399.6% CPU
Optimizing NNI: done in 0.403448 secs using 399.6% CPU
Optimizing NNI: done in 0.400788 secs using 399.3% CPU
Optimizing NNI: done in 0.491277 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 37: -36058.365
Optimizing NNI: done in 0.320077 secs using 399.9% CPU
Optimizing NNI: done in 0.304082 secs using 399.8% CPU
Optimizing NNI: done in 0.430442 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36058.133
Iteration 40 / LogL: -36058.133 / Time: 0h:0m:16s (0h:0m:40s left)
Optimizing NNI: done in 0.303435 secs using 399.6% CPU
Optimizing NNI: done in 0.338934 secs using 399% CPU
131  JTT+F+I+R9    105426.506   571 211995.011   865219.011   214293.781
Optimizing NNI: done in 0.426385 secs using 399.3% CPU
Optimizing NNI: done in 0.345779 secs using 399.5% CPU
Optimizing NNI: done in 0.458853 secs using 399.4% CPU
Optimizing NNI: done in 0.529035 secs using 399.7% CPU
Optimizing NNI: done in 0.348202 secs using 399.4% CPU
Optimizing NNI: done in 0.360209 secs using 399.8% CPU
Optimizing NNI: done in 0.422359 secs using 399.7% CPU
241  DCMut+F+R9    196816.360   1022 395676.721   2486688.721  400126.887
Optimizing NNI: done in 0.350177 secs using 399.8% CPU
Iteration 50 / LogL: -36061.417 / Time: 0h:0m:20s (0h:0m:36s left)
Optimizing NNI: done in 0.28216 secs using 399.2% CPU
Optimizing NNI: done in 0.360658 secs using 399.6% CPU
Optimizing NNI: done in 0.460244 secs using 399.9% CPU
Optimizing NNI: done in 0.341509 secs using 399.6% CPU
722  mtART+I+R6    62854.881    314 126337.762   127455.389   127656.085
Optimizing NNI: done in 0.447016 secs using 399.6% CPU
Optimizing NNI: done in 0.448451 secs using 399.7% CPU
Optimizing NNI: done in 0.310772 secs using 399.6% CPU
Optimizing NNI: done in 0.47404 secs using 398.6% CPU
Optimizing NNI: done in 0.299235 secs using 400% CPU
Optimizing NNI: done in 0.377076 secs using 399.7% CPU
Iteration 60 / LogL: -36060.795 / Time: 0h:0m:24s (0h:0m:31s left)
Optimizing NNI: done in 0.53283 secs using 399.3% CPU
Optimizing NNI: done in 0.539701 secs using 399.1% CPU
Optimizing NNI: done in 0.298444 secs using 399.6% CPU
Optimizing NNI: done in 0.387461 secs using 399.9% CPU
Optimizing NNI: done in 0.376575 secs using 399.7% CPU
Optimizing NNI: done in 0.302829 secs using 398.8% CPU
Optimizing NNI: done in 0.375816 secs using 399.1% CPU
Optimizing NNI: done in 0.294824 secs using 399.6% CPU
Optimizing NNI: done in 0.516904 secs using 399.3% CPU
Optimizing NNI: done in 0.446093 secs using 399.5% CPU
Iteration 70 / LogL: -36078.406 / Time: 0h:0m:28s (0h:0m:27s left)
Optimizing NNI: done in 0.425105 secs using 399.2% CPU
Optimizing NNI: done in 0.414007 secs using 398.4% CPU
Optimizing NNI: done in 0.377305 secs using 398.9% CPU
Optimizing NNI: done in 0.347457 secs using 399.6% CPU
Optimizing NNI: done in 0.381495 secs using 398.8% CPU
Optimizing NNI: done in 0.436792 secs using 400.1% CPU
Optimizing NNI: done in 0.73995 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36058.059
Optimizing NNI: done in 0.325622 secs using 399.8% CPU
Optimizing NNI: done in 0.353352 secs using 399.6% CPU
Optimizing NNI: done in 0.393258 secs using 399.9% CPU
Iteration 80 / LogL: -36058.205 / Time: 0h:0m:32s (0h:0m:23s left)
Optimizing NNI: done in 0.506185 secs using 398.7% CPU
Optimizing NNI: done in 0.520156 secs using 399.3% CPU
Optimizing NNI: done in 0.385948 secs using 399.3% CPU
Optimizing NNI: done in 0.339473 secs using 399.3% CPU
Optimizing NNI: done in 0.333332 secs using 398.6% CPU
Optimizing NNI: done in 0.507212 secs using 400.2% CPU
Optimizing NNI: done in 0.430727 secs using 399.7% CPU
Optimizing NNI: done in 0.298204 secs using 398.1% CPU
Optimizing NNI: done in 0.413728 secs using 399.4% CPU
Optimizing NNI: done in 0.387096 secs using 399.7% CPU
Iteration 90 / LogL: -36058.160 / Time: 0h:0m:36s (0h:0m:19s left)
Optimizing NNI: done in 0.318461 secs using 399.9% CPU
Optimizing NNI: done in 0.371436 secs using 399.3% CPU
Optimizing NNI: done in 0.495134 secs using 399.9% CPU
Optimizing NNI: done in 0.469801 secs using 399.7% CPU
Optimizing NNI: done in 0.385179 secs using 398.9% CPU
Optimizing NNI: done in 0.356288 secs using 399% CPU
Optimizing NNI: done in 0.340958 secs using 399.3% CPU
Optimizing NNI: done in 0.330183 secs using 399.6% CPU
Optimizing NNI: done in 0.353901 secs using 399.3% CPU
Optimizing NNI: done in 0.346589 secs using 399.3% CPU
Iteration 100 / LogL: -36058.628 / Time: 0h:0m:40s (0h:0m:15s left)
Optimizing NNI: done in 0.427422 secs using 399.2% CPU
Optimizing NNI: done in 0.352519 secs using 399.8% CPU
Optimizing NNI: done in 0.373544 secs using 399.4% CPU
Optimizing NNI: done in 0.48496 secs using 399.5% CPU
Optimizing NNI: done in 0.300713 secs using 399.2% CPU
Optimizing NNI: done in 0.428116 secs using 399% CPU
Optimizing NNI: done in 0.438657 secs using 399.7% CPU
Optimizing NNI: done in 0.331173 secs using 399.3% CPU
Optimizing NNI: done in 0.279209 secs using 399.5% CPU
Optimizing NNI: done in 0.410388 secs using 398.6% CPU
Iteration 110 / LogL: -36058.468 / Time: 0h:0m:44s (0h:0m:10s left)
Optimizing NNI: done in 0.411573 secs using 399.7% CPU
Optimizing NNI: done in 0.401659 secs using 399.8% CPU
Optimizing NNI: done in 0.379496 secs using 399.6% CPU
723  mtART+I+R7    62832.267    316 126296.533   127441.356   127623.252
Optimizing NNI: done in 0.451744 secs using 399.2% CPU
Optimizing NNI: done in 0.321347 secs using 399.7% CPU
Optimizing NNI: done in 0.486205 secs using 399.6% CPU
Optimizing NNI: done in 0.423104 secs using 399.9% CPU
Optimizing NNI: done in 0.373664 secs using 399.6% CPU
Optimizing NNI: done in 0.340521 secs using 398.9% CPU
Optimizing NNI: done in 0.343283 secs using 399.8% CPU
Iteration 120 / LogL: -36058.606 / Time: 0h:0m:48s (0h:0m:6s left)
Optimizing NNI: done in 0.418429 secs using 399.8% CPU
Optimizing NNI: done in 0.37732 secs using 399.9% CPU
Optimizing NNI: done in 0.340668 secs using 399.9% CPU
Optimizing NNI: done in 0.272944 secs using 398.4% CPU
Optimizing NNI: done in 0.335904 secs using 398.9% CPU
242  DCMut+F+R10   196813.450   1024 395674.901   2494874.901  400133.775
Optimizing NNI: done in 0.364025 secs using 400.3% CPU
Optimizing NNI: done in 0.368657 secs using 399% CPU
Optimizing NNI: done in 0.340774 secs using 399% CPU
Optimizing NNI: done in 0.309389 secs using 399.6% CPU
Optimizing NNI: done in 0.483844 secs using 399.9% CPU
Iteration 130 / LogL: -36061.362 / Time: 0h:0m:51s (0h:0m:2s left)
Optimizing NNI: done in 0.385385 secs using 399% CPU
Optimizing NNI: done in 0.440038 secs using 400.2% CPU
Optimizing NNI: done in 0.453463 secs using 398.8% CPU
Optimizing NNI: done in 0.326712 secs using 398.6% CPU
Optimizing NNI: done in 0.392311 secs using 399.3% CPU
Optimizing NNI: done in 0.43792 secs using 399.6% CPU
Optimizing NNI: done in 0.348674 secs using 399.8% CPU
Optimizing NNI: done in 0.450229 secs using 399.4% CPU
TREE SEARCH COMPLETED AFTER 138 ITERATIONS / Time: 0h:0m:55s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36058.059
Optimal log-likelihood: -36058.058
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.621
Parameters optimization took 1 rounds (0.050 sec)
BEST SCORE FOUND : -36058.058
Total tree length: 19.388

Total number of iterations: 138
CPU time used for tree search: 214.681 sec (0h:3m:34s)
Wall-clock time used for tree search: 54.708 sec (0h:0m:54s)
Total CPU time used: 217.266 sec (0h:3m:37s)
Total wall-clock time used: 55.315 sec (0h:0m:55s)

===> START BOOTSTRAP REPLICATE NUMBER 26

Creating bootstrap alignment (seed: 956185)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36689.602
2. Current log-likelihood: -35766.212
3. Current log-likelihood: -35741.842
4. Current log-likelihood: -35741.412
Optimal log-likelihood: -35741.373
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.355
Parameters optimization took 4 rounds (0.282 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0765169 secs using 400% CPU
Computing ML distances took 0.076655 sec (of wall-clock time) 0.306443 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00018692 secs using 432.3% CPU
Constructing RapidNJ tree: done in 0.00223899 secs using 428.4% CPU
Computing RapidNJ tree took 0.002493 sec (of wall-clock time) 0.011651 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36247.744
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 735  mtART+F+R6    61003.545    332 122671.091   124061.732   124064.986
1.498 second
Computing log-likelihood of 98 initial trees ... 1.666 seconds
Current best score: -35741.373

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.163405 secs using 395.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35728.731
Optimizing NNI: done in 0.227893 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35713.627
Optimizing NNI: done in 0.227891 secs using 399.4% CPU
Optimizing NNI: done in 0.257564 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -35701.203
Optimizing NNI: done in 0.252662 secs using 399.9% CPU
Optimizing NNI: done in 0.267904 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -35699.004
Optimizing NNI: done in 0.228497 secs using 399% CPU
Optimizing NNI: done in 0.262828 secs using 399.2% CPU
Optimizing NNI: done in 0.250026 secs using 398.7% CPU
Optimizing NNI: done in 0.271843 secs using 400% CPU
Iteration 10 / LogL: -35700.982 / Time: 0h:0m:6s
Optimizing NNI: done in 0.256203 secs using 399.4% CPU
Optimizing NNI: done in 0.24436 secs using 399.9% CPU
Optimizing NNI: done in 0.259123 secs using 398.7% CPU
Optimizing NNI: done in 0.292524 secs using 399.9% CPU
Optimizing NNI: done in 0.257746 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 15: -35698.926
Optimizing NNI: done in 0.256066 secs using 399.9% CPU
Optimizing NNI: done in 0.247449 secs using 399.1% CPU
Optimizing NNI: done in 0.261084 secs using 400.7% CPU
Optimizing NNI: done in 0.248012 secs using 398.7% CPU
Optimizing NNI: done in 0.247146 secs using 399.5% CPU
Iteration 20 / LogL: -35712.026 / Time: 0h:0m:8s
Finish initializing candidate tree set (10)
Current best tree score: -35698.926 / CPU time: 8.494
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.365997 secs using 399.6% CPU
Optimizing NNI: done in 0.413936 secs using 399.6% CPU
Optimizing NNI: done in 0.376203 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35698.861
Optimizing NNI: done in 0.39438 secs using 399.6% CPU
Optimizing NNI: done in 0.468845 secs using 399.6% CPU
Optimizing NNI: done in 0.298228 secs using 398.2% CPU
Optimizing NNI: done in 0.348587 secs using 399.6% CPU
Optimizing NNI: done in 0.521209 secs using 399.8% CPU
Optimizing NNI: done in 0.349145 secs using 399% CPU
Optimizing NNI: done in 0.40034 secs using 400.1% CPU
Iteration 30 / LogL: -35698.884 / Time: 0h:0m:13s (0h:0m:38s left)
736  mtART+F+R7    60985.523    334 122639.045   124064.396   124041.337
Optimizing NNI: done in 0.361045 secs using 398.7% CPU
Optimizing NNI: done in 0.318954 secs using 399.4% CPU
Optimizing NNI: done in 0.362572 secs using 399.3% CPU
Optimizing NNI: done in 0.348537 secs using 398.7% CPU
Optimizing NNI: done in 0.489299 secs using 399.5% CPU
Optimizing NNI: done in 0.372315 secs using 399.8% CPU
Optimizing NNI: done in 0.371196 secs using 399.6% CPU
Optimizing NNI: done in 0.493064 secs using 398.4% CPU
Optimizing NNI: done in 0.46884 secs using 399.6% CPU
Optimizing NNI: done in 0.424552 secs using 399.4% CPU
Iteration 40 / LogL: -35699.344 / Time: 0h:0m:17s (0h:0m:32s left)
Optimizing NNI: done in 0.386524 secs using 400% CPU
Optimizing NNI: done in 0.388335 secs using 399.9% CPU
Optimizing NNI: done in 0.332099 secs using 399.9% CPU
Optimizing NNI: done in 0.455205 secs using 399.6% CPU
Optimizing NNI: done in 0.316751 secs using 399.3% CPU
Optimizing NNI: done in 0.349935 secs using 399.3% CPU
737  mtART+F+R8    60983.078    336 122638.155   124099.213   124048.844
Optimizing NNI: done in 0.408455 secs using 400.1% CPU
Optimizing NNI: done in 0.325846 secs using 399.6% CPU
Optimizing NNI: done in 0.498536 secs using 399.8% CPU
Optimizing NNI: done in 0.460594 secs using 399.9% CPU
Iteration 50 / LogL: -35699.427 / Time: 0h:0m:21s (0h:0m:27s left)
Optimizing NNI: done in 0.338025 secs using 399.6% CPU
Optimizing NNI: done in 0.440879 secs using 399.6% CPU
Optimizing NNI: done in 0.444692 secs using 399.1% CPU
Optimizing NNI: done in 0.464155 secs using 399.2% CPU
Optimizing NNI: done in 0.351991 secs using 399.3% CPU
Optimizing NNI: done in 0.335979 secs using 398.6% CPU
251  VT+R8         196235.054   1001 394472.109   2400476.109  398830.833
Optimizing NNI: done in 0.385557 secs using 399.8% CPU
Optimizing NNI: done in 0.474679 secs using 399.1% CPU
Optimizing NNI: done in 0.37731 secs using 398.2% CPU
Optimizing NNI: done in 0.305215 secs using 399.9% CPU
Iteration 60 / LogL: -35699.511 / Time: 0h:0m:24s (0h:0m:23s left)
Optimizing NNI: done in 0.428487 secs using 399.6% CPU
Optimizing NNI: done in 0.41883 secs using 399.6% CPU
Optimizing NNI: done in 0.464668 secs using 399.7% CPU
Optimizing NNI: done in 0.476943 secs using 399.3% CPU
Optimizing NNI: done in 0.300326 secs using 399.9% CPU
Optimizing NNI: done in 0.380164 secs using 399.9% CPU
Optimizing NNI: done in 0.473718 secs using 399% CPU
Optimizing NNI: done in 0.680109 secs using 399.9% CPU
Optimizing NNI: done in 0.502166 secs using 398.9% CPU
Optimizing NNI: done in 0.408887 secs using 398.7% CPU
Iteration 70 / LogL: -35702.704 / Time: 0h:0m:29s (0h:0m:19s left)
Optimizing NNI: done in 0.303011 secs using 399.9% CPU
Optimizing NNI: done in 0.31146 secs using 398.9% CPU
Optimizing NNI: done in 0.333368 secs using 399.4% CPU
Optimizing NNI: done in 0.345817 secs using 400% CPU
Optimizing NNI: done in 0.387657 secs using 398.9% CPU
Optimizing NNI: done in 0.319607 secs using 399.3% CPU
Optimizing NNI: done in 0.297469 secs using 399.6% CPU
Optimizing NNI: done in 0.456266 secs using 398.6% CPU
Optimizing NNI: done in 0.350665 secs using 399% CPU
Optimizing NNI: done in 0.401637 secs using 400.3% CPU
Iteration 80 / LogL: -35714.003 / Time: 0h:0m:33s (0h:0m:14s left)
Optimizing NNI: done in 0.412883 secs using 398.4% CPU
Optimizing NNI: done in 0.563413 secs using 399.5% CPU
Optimizing NNI: done in 0.41231 secs using 398.7% CPU
744  mtART+F+I+R6  61003.257    333 122672.514   124080.387   124070.607
Optimizing NNI: done in 0.488007 secs using 399.9% CPU
Optimizing NNI: done in 0.398617 secs using 399.1% CPU
Optimizing NNI: done in 0.312529 secs using 399.5% CPU
Optimizing NNI: done in 0.276881 secs using 399.4% CPU
Optimizing NNI: done in 0.389731 secs using 399.9% CPU
Optimizing NNI: done in 0.314827 secs using 399.5% CPU
Optimizing NNI: done in 0.465609 secs using 399.5% CPU
Iteration 90 / LogL: -35702.634 / Time: 0h:0m:37s (0h:0m:10s left)
Optimizing NNI: done in 0.355621 secs using 399.5% CPU
Optimizing NNI: done in 0.327145 secs using 399.2% CPU
Optimizing NNI: done in 0.429535 secs using 399.4% CPU
Optimizing NNI: done in 0.40768 secs using 399.4% CPU
Optimizing NNI: done in 0.465892 secs using 399.2% CPU
Optimizing NNI: done in 0.563963 secs using 399.5% CPU
Optimizing NNI: done in 0.445803 secs using 399.2% CPU
Optimizing NNI: done in 0.380072 secs using 399.8% CPU
Optimizing NNI: done in 0.352343 secs using 399.5% CPU
Optimizing NNI: done in 0.373911 secs using 399.4% CPU
Iteration 100 / LogL: -35699.031 / Time: 0h:0m:41s (0h:0m:6s left)
Optimizing NNI: done in 0.368755 secs using 399.6% CPU
Optimizing NNI: done in 0.30012 secs using 399.1% CPU
Optimizing NNI: done in 0.315091 secs using 399.9% CPU
Optimizing NNI: done in 0.431786 secs using 399.6% CPU
Optimizing NNI: done in 0.35971 secs using 399.9% CPU
Optimizing NNI: done in 0.408896 secs using 399.2% CPU
Optimizing NNI: done in 0.387401 secs using 399.4% CPU
Optimizing NNI: done in 0.438286 secs using 399.4% CPU
Optimizing NNI: done in 0.372513 secs using 399.3% CPU
Optimizing NNI: done in 0.353977 secs using 399.9% CPU
Iteration 110 / LogL: -35704.452 / Time: 0h:0m:45s (0h:0m:2s left)
Optimizing NNI: done in 0.388214 secs using 399.9% CPU
Optimizing NNI: done in 0.337593 secs using 399.2% CPU
Optimizing NNI: done in 0.384508 secs using 399.9% CPU
Optimizing NNI: done in 0.370238 secs using 399.1% CPU
Optimizing NNI: done in 0.370247 secs using 397.7% CPU
Optimizing NNI: done in 0.292362 secs using 399.4% CPU
TREE SEARCH COMPLETED AFTER 116 ITERATIONS / Time: 0h:0m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35698.861
Optimal log-likelihood: -35698.860
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.331
Parameters optimization took 1 rounds (0.047 sec)
BEST SCORE FOUND : -35698.860
Total tree length: 19.833

Total number of iterations: 116
CPU time used for tree search: 183.007 sec (0h:3m:3s)
Wall-clock time used for tree search: 46.776 sec (0h:0m:46s)
Total CPU time used: 185.231 sec (0h:3m:5s)
Total wall-clock time used: 47.311 sec (0h:0m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 27

Creating bootstrap alignment (seed: 956186)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.020 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36470.288
2. Current log-likelihood: -35630.485
3. Current log-likelihood: -35602.955
4. Current log-likelihood: -35602.488
Optimal log-likelihood: -35602.419
Proportion of invariable sites: 0.022
Gamma shape alpha: 2.345
Parameters optimization took 4 rounds (0.260 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0768821 secs using 399.9% CPU
Computing ML distances took 0.077013 sec (of wall-clock time) 0.307815 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000168085 secs using 612.8% CPU
Constructing RapidNJ tree: done in 0.00214696 secs using 489.8% CPU
Computing RapidNJ tree took 0.002373 sec (of wall-clock time) 0.012056 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36307.903
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.543 second
Computing log-likelihood of 98 initial trees ... 1.579 seconds
Current best score: -35591.352

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.289034 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35543.695
Optimizing NNI: done in 0.248062 secs using 399.4% CPU
Optimizing NNI: done in 0.236044 secs using 399.9% CPU
Optimizing NNI: done in 0.236085 secs using 399.8% CPU
Optimizing NNI: done in 0.234512 secs using 399% CPU
Optimizing NNI: done in 0.251866 secs using 398.6% CPU
Optimizing NNI: done in 0.218337 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -35543.441
Optimizing NNI: done in 0.237772 secs using 399.8% CPU
Optimizing NNI: done in 0.236845 secs using 399% CPU
Optimizing NNI: done in 0.247551 secs using 398.9% CPU
Iteration 10 / LogL: -35546.574 / Time: 0h:0m:6s
Optimizing NNI: done in 0.207977 secs using 398.6% CPU
Optimizing NNI: done in 0.221876 secs using 399.2% CPU
745  mtART+F+I+R7  60985.504    335 122641.009   124084.086   124047.499
Optimizing NNI: done in 0.248412 secs using 399.7% CPU
Optimizing NNI: done in 0.203255 secs using 398.8% CPU
Optimizing NNI: done in 0.220537 secs using 399.8% CPU
Optimizing NNI: done in 0.207731 secs using 399.1% CPU
Optimizing NNI: done in 0.226039 secs using 400% CPU
Optimizing NNI: done in 0.210525 secs using 400% CPU
Optimizing NNI: done in 0.237457 secs using 399.9% CPU
Optimizing NNI: done in 0.209945 secs using 398.9% CPU
Iteration 20 / LogL: -35546.890 / Time: 0h:0m:8s
Finish initializing candidate tree set (4)
Current best tree score: -35543.441 / CPU time: 7.935
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.36311 secs using 399.9% CPU
Optimizing NNI: done in 0.45155 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -35535.149
Optimizing NNI: done in 0.396869 secs using 399% CPU
Optimizing NNI: done in 0.415674 secs using 399.9% CPU
Optimizing NNI: done in 0.359696 secs using 399.8% CPU
Optimizing NNI: done in 0.313599 secs using 399.3% CPU
Optimizing NNI: done in 0.361133 secs using 399.3% CPU
757  mtZOA+R6      61377.869    313 123381.738   124486.030   124695.861
Optimizing NNI: done in 0.346258 secs using 399.8% CPU
Optimizing NNI: done in 0.326998 secs using 399.2% CPU
Optimizing NNI: done in 0.357333 secs using 399.5% CPU
Iteration 30 / LogL: -35538.325 / Time: 0h:0m:12s (0h:0m:38s left)
Optimizing NNI: done in 0.342605 secs using 399.9% CPU
Optimizing NNI: done in 0.45461 secs using 399.4% CPU
Optimizing NNI: done in 0.339496 secs using 399.6% CPU
Optimizing NNI: done in 0.318528 secs using 399.2% CPU
Optimizing NNI: done in 0.313375 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35535.122
Optimizing NNI: done in 0.376994 secs using 399.8% CPU
Optimizing NNI: done in 0.326375 secs using 398.9% CPU
Optimizing NNI: done in 0.533986 secs using 399.1% CPU
Optimizing NNI: done in 0.372818 secs using 399% CPU
Optimizing NNI: done in 0.301356 secs using 399.2% CPU
Iteration 40 / LogL: -35535.826 / Time: 0h:0m:16s (0h:0m:33s left)
Optimizing NNI: done in 0.412593 secs using 399.6% CPU
Optimizing NNI: done in 0.39777 secs using 399.9% CPU
Optimizing NNI: done in 0.274609 secs using 399.4% CPU
Optimizing NNI: done in 0.418202 secs using 398.2% CPU
Optimizing NNI: done in 0.46786 secs using 399.2% CPU
Optimizing NNI: done in 0.495187 secs using 399.4% CPU
Optimizing NNI: done in 0.322494 secs using 399% CPU
132  JTT+F+I+R10   105419.794   573 211985.587   869789.587   214292.408
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.374013 secs using 399.8% CPU
Optimizing NNI: done in 0.338455 secs using 399.9% CPU
Optimizing NNI: done in 0.275798 secs using 399.8% CPU
Iteration 50 / LogL: -35535.271 / Time: 0h:0m:19s (0h:0m:29s left)
758  mtZOA+R7      61368.510    315 123367.020   124498.156   124689.541
Optimizing NNI: done in 0.434004 secs using 399.9% CPU
Optimizing NNI: done in 0.486239 secs using 399.3% CPU
Optimizing NNI: done in 0.348888 secs using 398.8% CPU
Optimizing NNI: done in 0.331851 secs using 399.9% CPU
Optimizing NNI: done in 0.420179 secs using 398.9% CPU
Optimizing NNI: done in 0.421818 secs using 399.8% CPU
Optimizing NNI: done in 0.407029 secs using 399.4% CPU
Optimizing NNI: done in 0.385853 secs using 398.8% CPU
Optimizing NNI: done in 0.387702 secs using 399.5% CPU
Optimizing NNI: done in 0.360287 secs using 399% CPU
Iteration 60 / LogL: -35535.220 / Time: 0h:0m:23s (0h:0m:25s left)
Optimizing NNI: done in 0.346972 secs using 398.4% CPU
Optimizing NNI: done in 0.332266 secs using 399.3% CPU
Optimizing NNI: done in 0.344673 secs using 398.7% CPU
Optimizing NNI: done in 0.369258 secs using 398.4% CPU
Optimizing NNI: done in 0.38315 secs using 399.9% CPU
Optimizing NNI: done in 0.445405 secs using 399% CPU
Optimizing NNI: done in 0.414803 secs using 399.6% CPU
252  VT+R9         196229.175   1003 394464.350   2408488.350  398831.783
Optimizing NNI: done in 0.319132 secs using 399.7% CPU
Optimizing NNI: done in 0.401746 secs using 399.4% CPU
Optimizing NNI: done in 0.303974 secs using 399.5% CPU
Iteration 70 / LogL: -35535.326 / Time: 0h:0m:27s (0h:0m:20s left)
Optimizing NNI: done in 0.441342 secs using 400.3% CPU
Optimizing NNI: done in 0.342778 secs using 398.5% CPU
Optimizing NNI: done in 0.437747 secs using 399.4% CPU
Optimizing NNI: done in 0.37074 secs using 398.8% CPU
Optimizing NNI: done in 0.339148 secs using 398.8% CPU
Optimizing NNI: done in 0.345876 secs using 398.3% CPU
Optimizing NNI: done in 0.352916 secs using 400% CPU
Optimizing NNI: done in 0.422816 secs using 398.7% CPU
Optimizing NNI: done in 0.294679 secs using 399.2% CPU
153  Q.pfam+I+R9   105267.588   552 211639.175   822151.175   213861.453
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.354719 secs using 399.2% CPU
Iteration 80 / LogL: -35535.145 / Time: 0h:0m:31s (0h:0m:16s left)
Optimizing NNI: done in 0.358367 secs using 399.2% CPU
Optimizing NNI: done in 0.442678 secs using 399.3% CPU
Optimizing NNI: done in 0.44812 secs using 399.5% CPU
759  mtZOA+R8      61356.530    317 123347.060   124505.750   124677.978
Optimizing NNI: done in 0.385256 secs using 399.3% CPU
Optimizing NNI: done in 0.39534 secs using 398.5% CPU
Optimizing NNI: done in 0.314354 secs using 399.5% CPU
Optimizing NNI: done in 0.434503 secs using 397.9% CPU
Optimizing NNI: done in 0.329847 secs using 399.2% CPU
Optimizing NNI: done in 0.402343 secs using 398.2% CPU
Optimizing NNI: done in 0.374021 secs using 398.4% CPU
Iteration 90 / LogL: -35535.556 / Time: 0h:0m:35s (0h:0m:12s left)
Optimizing NNI: done in 0.284498 secs using 398.5% CPU
Optimizing NNI: done in 0.337932 secs using 398.9% CPU
Optimizing NNI: done in 0.38765 secs using 399.5% CPU
Optimizing NNI: done in 0.40799 secs using 398.7% CPU
Optimizing NNI: done in 0.394423 secs using 399% CPU
Optimizing NNI: done in 0.378536 secs using 399.5% CPU
Optimizing NNI: done in 0.389274 secs using 399.5% CPU
Optimizing NNI: done in 0.390663 secs using 399.5% CPU
Optimizing NNI: done in 0.455924 secs using 399.1% CPU
Optimizing NNI: done in 0.325296 secs using 399% CPU
Iteration 100 / LogL: -35535.223 / Time: 0h:0m:39s (0h:0m:8s left)
Optimizing NNI: done in 0.346758 secs using 398.6% CPU
Optimizing NNI: done in 0.415558 secs using 399% CPU
Optimizing NNI: done in 0.368572 secs using 399% CPU
Optimizing NNI: done in 0.369629 secs using 399% CPU
Optimizing NNI: done in 0.405838 secs using 397.9% CPU
Optimizing NNI: done in 0.277911 secs using 399.8% CPU
Optimizing NNI: done in 0.428463 secs using 399.7% CPU
Optimizing NNI: done in 0.404536 secs using 399.3% CPU
Optimizing NNI: done in 0.361482 secs using 399.3% CPU
Optimizing NNI: done in 0.265731 secs using 399.5% CPU
Iteration 110 / LogL: -35535.184 / Time: 0h:0m:42s (0h:0m:4s left)
262  VT+F+R8       195084.460   1020 392208.920   2475048.920  396650.377
Optimizing NNI: done in 0.274732 secs using 399.4% CPU
Optimizing NNI: done in 0.335367 secs using 399.2% CPU
Optimizing NNI: done in 0.382843 secs using 399.6% CPU
Optimizing NNI: done in 0.335234 secs using 399.8% CPU
Optimizing NNI: done in 0.41109 secs using 399.4% CPU
Optimizing NNI: done in 0.594461 secs using 398.7% CPU
Optimizing NNI: done in 0.376235 secs using 399.9% CPU
Optimizing NNI: done in 0.404086 secs using 398.9% CPU
Optimizing NNI: done in 0.429517 secs using 399.8% CPU
Optimizing NNI: done in 0.357118 secs using 399.5% CPU
Iteration 120 / LogL: -35535.295 / Time: 0h:0m:46s (0h:0m:0s left)
Optimizing NNI: done in 0.454032 secs using 399.2% CPU
Optimizing NNI: done in 0.328305 secs using 398.6% CPU
Optimizing NNI: done in 0.417434 secs using 399.9% CPU
TREE SEARCH COMPLETED AFTER 123 ITERATIONS / Time: 0h:0m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35535.122
Optimal log-likelihood: -35535.122
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.334
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35535.122
Total tree length: 19.900

Total number of iterations: 123
CPU time used for tree search: 184.986 sec (0h:3m:4s)
Wall-clock time used for tree search: 47.341 sec (0h:0m:47s)
Total CPU time used: 187.443 sec (0h:3m:7s)
Total wall-clock time used: 47.919 sec (0h:0m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 28

Creating bootstrap alignment (seed: 956187)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37253.334
2. Current log-likelihood: -36368.479
3. Current log-likelihood: -36343.535
4. Current log-likelihood: -36342.715
Optimal log-likelihood: -36342.658
Proportion of invariable sites: 0.028
Gamma shape alpha: 2.372
Parameters optimization took 4 rounds (0.284 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0745628 secs using 400% CPU
Computing ML distances took 0.074702 sec (of wall-clock time) 0.298623 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000165939 secs using 442.9% CPU
Constructing RapidNJ tree: done in 0.002285 secs using 458.3% CPU
Computing RapidNJ tree took 0.002520 sec (of wall-clock time) 0.011755 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36879.188
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 760  mtZOA+R9      61356.212    319 123350.424   124537.401   124689.739
1.485 second
Computing log-likelihood of 98 initial trees ... 1.627 seconds
Current best score: -36271.451

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.31838 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36209.557
Optimizing NNI: done in 0.364831 secs using 399.2% CPU
Optimizing NNI: done in 0.363874 secs using 399% CPU
Optimizing NNI: done in 0.361935 secs using 398.1% CPU
Optimizing NNI: done in 0.275758 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -36206.743
Optimizing NNI: done in 0.344142 secs using 399.2% CPU
Optimizing NNI: done in 0.282092 secs using 398.8% CPU
Optimizing NNI: done in 0.336878 secs using 398.8% CPU
Optimizing NNI: done in 0.351585 secs using 399.1% CPU
Optimizing NNI: done in 0.361367 secs using 399.2% CPU
Iteration 10 / LogL: -36213.047 / Time: 0h:0m:7s
Optimizing NNI: done in 0.320758 secs using 398.9% CPU
Optimizing NNI: done in 0.365057 secs using 398.7% CPU
Optimizing NNI: done in 0.26914 secs using 399.2% CPU
Optimizing NNI: done in 0.310034 secs using 399.5% CPU
Optimizing NNI: done in 0.309338 secs using 398.5% CPU
Optimizing NNI: done in 0.315313 secs using 398.8% CPU
Optimizing NNI: done in 0.45591 secs using 398.8% CPU
Optimizing NNI: done in 0.332004 secs using 399.5% CPU
Optimizing NNI: done in 0.348234 secs using 399.2% CPU
Optimizing NNI: done in 0.342158 secs using 399.5% CPU
Iteration 20 / LogL: -36207.200 / Time: 0h:0m:10s
Finish initializing candidate tree set (10)
Current best tree score: -36206.743 / CPU time: 10.038
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.530484 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36203.563
Optimizing NNI: done in 0.346532 secs using 398.6% CPU
Optimizing NNI: done in 0.418337 secs using 399% CPU
Optimizing NNI: done in 0.370111 secs using 399.5% CPU
Optimizing NNI: done in 0.36086 secs using 399.5% CPU
Optimizing NNI: done in 0.51668 secs using 399.3% CPU
Optimizing NNI: done in 0.334682 secs using 398.7% CPU
Optimizing NNI: done in 0.372752 secs using 398.4% CPU
Optimizing NNI: done in 0.471026 secs using 399.5% CPU
Optimizing NNI: done in 0.329932 secs using 399.5% CPU
Iteration 30 / LogL: -36206.553 / Time: 0h:0m:14s (0h:0m:46s left)
Optimizing NNI: done in 0.317615 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36203.488
Optimizing NNI: done in 0.354462 secs using 399.5% CPU
Optimizing NNI: done in 0.417228 secs using 399.8% CPU
Optimizing NNI: done in 0.377944 secs using 399.9% CPU
Optimizing NNI: done in 0.319062 secs using 399.3% CPU
Optimizing NNI: done in 0.271483 secs using 399.9% CPU
Optimizing NNI: done in 0.352312 secs using 399.6% CPU
Optimizing NNI: done in 0.430796 secs using 399.9% CPU
Optimizing NNI: done in 0.295493 secs using 399.5% CPU
Optimizing NNI: done in 0.307595 secs using 399.6% CPU
Iteration 40 / LogL: -36209.330 / Time: 0h:0m:18s (0h:0m:37s left)
Optimizing NNI: done in 0.421628 secs using 399.9% CPU
Optimizing NNI: done in 0.382944 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -36202.080
Optimizing NNI: done in 0.401832 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 43: -36201.702
Optimizing NNI: done in 0.32301 secs using 399.2% CPU
766  mtZOA+I+R6    61377.854    314 123383.708   124501.336   124702.031
Optimizing NNI: done in 0.307691 secs using 399.5% CPU
Optimizing NNI: done in 0.376708 secs using 399.5% CPU
Optimizing NNI: done in 0.402388 secs using 399.2% CPU
Optimizing NNI: done in 0.321862 secs using 399.9% CPU
Optimizing NNI: done in 0.322784 secs using 399.6% CPU
Optimizing NNI: done in 0.371 secs using 399.6% CPU
Iteration 50 / LogL: -36202.123 / Time: 0h:0m:22s (0h:0m:41s left)
Optimizing NNI: done in 0.294409 secs using 398.9% CPU
Optimizing NNI: done in 0.411208 secs using 399.1% CPU
Optimizing NNI: done in 0.370801 secs using 398.8% CPU
Optimizing NNI: done in 0.425613 secs using 399.9% CPU
Optimizing NNI: done in 0.436488 secs using 399% CPU
Optimizing NNI: done in 0.434007 secs using 399.4% CPU
Optimizing NNI: done in 0.43553 secs using 399.2% CPU
Optimizing NNI: done in 0.336393 secs using 399.9% CPU
Optimizing NNI: done in 0.339668 secs using 398.9% CPU
Optimizing NNI: done in 0.502991 secs using 399.6% CPU
Iteration 60 / LogL: -36202.030 / Time: 0h:0m:26s (0h:0m:36s left)
Optimizing NNI: done in 0.337852 secs using 399.3% CPU
Optimizing NNI: done in 0.351676 secs using 400% CPU
Optimizing NNI: done in 0.365128 secs using 399.9% CPU
Optimizing NNI: done in 0.37309 secs using 399.1% CPU
Optimizing NNI: done in 0.411095 secs using 399.4% CPU
Optimizing NNI: done in 0.345548 secs using 399.3% CPU
Optimizing NNI: done in 0.322391 secs using 399.4% CPU
Optimizing NNI: done in 0.46361 secs using 399.5% CPU
Optimizing NNI: done in 0.347129 secs using 398.6% CPU
Optimizing NNI: done in 0.313967 secs using 399.1% CPU
Iteration 70 / LogL: -36206.115 / Time: 0h:0m:29s (0h:0m:31s left)
Optimizing NNI: done in 0.343245 secs using 397.8% CPU
Optimizing NNI: done in 0.429836 secs using 399.3% CPU
Optimizing NNI: done in 0.360421 secs using 399.4% CPU
Optimizing NNI: done in 0.373151 secs using 400.1% CPU
Optimizing NNI: done in 0.375381 secs using 398.9% CPU
Optimizing NNI: done in 0.339481 secs using 399.3% CPU
Optimizing NNI: done in 0.409044 secs using 399.7% CPU
Optimizing NNI: done in 0.350198 secs using 399.7% CPU
Optimizing NNI: done in 0.303442 secs using 398.5% CPU
Optimizing NNI: done in 0.409354 secs using 400% CPU
Iteration 80 / LogL: -36203.124 / Time: 0h:0m:33s (0h:0m:26s left)
Optimizing NNI: done in 0.286634 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -36201.696
Optimizing NNI: done in 0.295737 secs using 399.5% CPU
Optimizing NNI: done in 0.394338 secs using 399.3% CPU
Optimizing NNI: done in 0.334833 secs using 399.6% CPU
Optimizing NNI: done in 0.349835 secs using 398.9% CPU
Optimizing NNI: done in 0.278311 secs using 400.1% CPU
Optimizing NNI: done in 0.316999 secs using 399% CPU
Optimizing NNI: done in 0.3634 secs using 399.8% CPU
Optimizing NNI: done in 0.37852 secs using 399.1% CPU
Optimizing NNI: done in 0.364604 secs using 398.2% CPU
Iteration 90 / LogL: -36203.674 / Time: 0h:0m:36s (0h:0m:21s left)
Optimizing NNI: done in 0.349975 secs using 399.3% CPU
Optimizing NNI: done in 0.381526 secs using 399.6% CPU
Optimizing NNI: done in 0.354316 secs using 399.6% CPU
Optimizing NNI: done in 0.351214 secs using 399.6% CPU
Optimizing NNI: done in 0.365583 secs using 399.3% CPU
Optimizing NNI: done in 0.444915 secs using 399.5% CPU
Optimizing NNI: done in 0.44042 secs using 399.1% CPU
Optimizing NNI: done in 0.448433 secs using 400% CPU
Optimizing NNI: done in 0.352272 secs using 399.1% CPU
Optimizing NNI: done in 0.362867 secs using 398.6% CPU
Iteration 100 / LogL: -36202.032 / Time: 0h:0m:40s (0h:0m:17s left)
Optimizing NNI: done in 0.245687 secs using 399.2% CPU
Optimizing NNI: done in 0.382834 secs using 399.8% CPU
Optimizing NNI: done in 0.336504 secs using 399.6% CPU
263  VT+F+R9       195080.573   1022 392205.145   2483217.145  396655.311
Optimizing NNI: done in 0.464268 secs using 399.8% CPU
Optimizing NNI: done in 0.411163 secs using 399.1% CPU
Optimizing NNI: done in 0.293425 secs using 398.8% CPU
Optimizing NNI: done in 0.45313 secs using 399.5% CPU
Optimizing NNI: done in 0.372163 secs using 399.6% CPU
767  mtZOA+I+R7    61363.311    316 123358.623   124503.446   124685.342
Optimizing NNI: done in 0.372739 secs using 398.5% CPU
Optimizing NNI: done in 0.377209 secs using 399.6% CPU
Iteration 110 / LogL: -36202.073 / Time: 0h:0m:44s (0h:0m:13s left)
Optimizing NNI: done in 0.362798 secs using 399% CPU
Optimizing NNI: done in 0.405485 secs using 399.3% CPU
Optimizing NNI: done in 0.396811 secs using 399% CPU
Optimizing NNI: done in 0.311752 secs using 398.9% CPU
Optimizing NNI: done in 0.293523 secs using 398.3% CPU
Optimizing NNI: done in 0.323267 secs using 400% CPU
Optimizing NNI: done in 0.373713 secs using 399.5% CPU
Optimizing NNI: done in 0.42796 secs using 399.5% CPU
Optimizing NNI: done in 0.385854 secs using 399.6% CPU
Optimizing NNI: done in 0.390495 secs using 399.1% CPU
Iteration 120 / LogL: -36201.771 / Time: 0h:0m:48s (0h:0m:9s left)
Optimizing NNI: done in 0.467794 secs using 399.8% CPU
Optimizing NNI: done in 0.334777 secs using 399.3% CPU
Optimizing NNI: done in 0.329382 secs using 399.3% CPU
Optimizing NNI: done in 0.346972 secs using 399% CPU
Optimizing NNI: done in 0.400254 secs using 399.4% CPU
Optimizing NNI: done in 0.337907 secs using 399.3% CPU
Optimizing NNI: done in 0.480594 secs using 399.2% CPU
Optimizing NNI: done in 0.419422 secs using 398.6% CPU
Optimizing NNI: done in 0.367601 secs using 399.3% CPU
Optimizing NNI: done in 0.248368 secs using 399.6% CPU
Iteration 130 / LogL: -36201.869 / Time: 0h:0m:51s (0h:0m:5s left)
Optimizing NNI: done in 0.326847 secs using 399.3% CPU
Optimizing NNI: done in 0.303944 secs using 398.7% CPU
Optimizing NNI: done in 0.502288 secs using 398.6% CPU
779  mtZOA+F+R6    60214.531    332 121093.062   122483.703   122486.956
Optimizing NNI: done in 0.365741 secs using 399.8% CPU
Optimizing NNI: done in 0.379219 secs using 399.6% CPU
Optimizing NNI: done in 0.414705 secs using 398.5% CPU
Optimizing NNI: done in 0.399186 secs using 399.6% CPU
Optimizing NNI: done in 0.276054 secs using 399.5% CPU
Optimizing NNI: done in 0.35075 secs using 399.7% CPU
Optimizing NNI: done in 0.449937 secs using 399.3% CPU
Iteration 140 / LogL: -36202.105 / Time: 0h:0m:55s (0h:0m:1s left)
Optimizing NNI: done in 0.423239 secs using 398.9% CPU
Optimizing NNI: done in 0.358224 secs using 399% CPU
Optimizing NNI: done in 0.383139 secs using 399.4% CPU
Optimizing NNI: done in 0.360205 secs using 399.6% CPU
TREE SEARCH COMPLETED AFTER 144 ITERATIONS / Time: 0h:0m:57s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36201.696
2. Current log-likelihood: -36201.684
Optimal log-likelihood: -36201.684
Proportion of invariable sites: 0.028
Gamma shape alpha: 2.436
Parameters optimization took 2 rounds (0.089 sec)
BEST SCORE FOUND : -36201.684
Total tree length: 19.760

Total number of iterations: 144
CPU time used for tree search: 223.090 sec (0h:3m:43s)
Wall-clock time used for tree search: 56.827 sec (0h:0m:56s)
Total CPU time used: 225.575 sec (0h:3m:45s)
Total wall-clock time used: 57.423 sec (0h:0m:57s)

===> START BOOTSTRAP REPLICATE NUMBER 29

Creating bootstrap alignment (seed: 956188)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36974.721
2. Current log-likelihood: -36100.261
3. Current log-likelihood: -36075.317
4. Current log-likelihood: -36074.949
Optimal log-likelihood: -36074.924
Proportion of invariable sites: 0.016
Gamma shape alpha: 2.246
Parameters optimization took 4 rounds (0.269 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.078151 secs using 400% CPU
Computing ML distances took 0.078297 sec (of wall-clock time) 0.312976 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000149012 secs using 435.5% CPU
Constructing RapidNJ tree: done in 0.00220013 secs using 498.2% CPU
Computing RapidNJ tree took 0.002402 sec (of wall-clock time) 0.012140 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36672.131
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.606 second
Computing log-likelihood of 98 initial trees ... 1.621 seconds
Current best score: -36074.924

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.233087 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36039.852
Optimizing NNI: done in 0.173247 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36031.488
Optimizing NNI: done in 0.227004 secs using 399.6% CPU
Optimizing NNI: done in 0.240972 secs using 399.3% CPU
Optimizing NNI: done in 0.240982 secs using 399.4% CPU
Optimizing NNI: done in 0.26354 secs using 399.9% CPU
Optimizing NNI: done in 0.247271 secs using 399.7% CPU
Optimizing NNI: done in 0.243798 secs using 399.8% CPU
Optimizing NNI: done in 0.225651 secs using 399.2% CPU
Optimizing NNI: done in 0.22582 secs using 399.8% CPU
Iteration 10 / LogL: -36039.996 / Time: 0h:0m:6s
Optimizing NNI: done in 0.258266 secs using 398.7% CPU
Optimizing NNI: done in 0.242599 secs using 399.7% CPU
Optimizing NNI: done in 0.260806 secs using 399% CPU
Optimizing NNI: done in 0.221747 secs using 398% CPU
Optimizing NNI: done in 0.248314 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 15: -36031.024
Optimizing NNI: done in 0.258336 secs using 399.3% CPU
Optimizing NNI: done in 0.215652 secs using 399.7% CPU
Optimizing NNI: done in 0.243532 secs using 399% CPU
Optimizing NNI: done in 0.255752 secs using 398.7% CPU
Optimizing NNI: done in 0.22884 secs using 399.8% CPU
Iteration 20 / LogL: -36037.951 / Time: 0h:0m:8s
Finish initializing candidate tree set (6)
Current best tree score: -36031.024 / CPU time: 8.229
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.533605 secs using 399.6% CPU
780  mtZOA+F+R7    60195.212    334 121058.424   122483.774   122460.715
Optimizing NNI: done in 0.408752 secs using 399% CPU
Optimizing NNI: done in 0.47152 secs using 399.5% CPU
Optimizing NNI: done in 0.40114 secs using 399.3% CPU
Optimizing NNI: done in 0.399653 secs using 399.2% CPU
Optimizing NNI: done in 0.45702 secs using 399.7% CPU
Optimizing NNI: done in 0.425701 secs using 399.6% CPU
Optimizing NNI: done in 0.382404 secs using 399.3% CPU
Optimizing NNI: done in 0.349258 secs using 399.9% CPU
Optimizing NNI: done in 0.260505 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36030.954
Iteration 30 / LogL: -36030.954 / Time: 0h:0m:12s (0h:0m:37s left)
Optimizing NNI: done in 0.422224 secs using 398.9% CPU
Optimizing NNI: done in 0.382657 secs using 398.6% CPU
Optimizing NNI: done in 0.449569 secs using 399.6% CPU
Optimizing NNI: done in 0.371646 secs using 399.9% CPU
Optimizing NNI: done in 0.48687 secs using 399.3% CPU
Optimizing NNI: done in 0.338206 secs using 399.5% CPU
Optimizing NNI: done in 0.359466 secs using 399.9% CPU
Optimizing NNI: done in 0.486572 secs using 399.4% CPU
Optimizing NNI: done in 0.3836 secs using 399.3% CPU
Optimizing NNI: done in 0.538567 secs using 398.8% CPU
Iteration 40 / LogL: -36044.118 / Time: 0h:0m:17s (0h:0m:33s left)
781  mtZOA+F+R8    60191.888    336 121055.776   122516.834   122466.465
Optimizing NNI: done in 0.4245 secs using 399.1% CPU
273  PMB+R8        197315.374   1001 396632.748   2402636.748  400991.472
Optimizing NNI: done in 0.419988 secs using 399% CPU
Optimizing NNI: done in 0.376168 secs using 398.3% CPU
Optimizing NNI: done in 0.443783 secs using 399.7% CPU
Optimizing NNI: done in 0.368201 secs using 399.9% CPU
Optimizing NNI: done in 0.411649 secs using 399.8% CPU
Optimizing NNI: done in 0.298247 secs using 399% CPU
Optimizing NNI: done in 0.439702 secs using 399.5% CPU
Optimizing NNI: done in 0.333821 secs using 398.6% CPU
Optimizing NNI: done in 0.373581 secs using 398.7% CPU
Iteration 50 / LogL: -36031.110 / Time: 0h:0m:21s (0h:0m:28s left)
Optimizing NNI: done in 0.314707 secs using 399.9% CPU
Optimizing NNI: done in 0.372966 secs using 399.6% CPU
Optimizing NNI: done in 0.382101 secs using 399.5% CPU
Optimizing NNI: done in 0.515733 secs using 399.9% CPU
Optimizing NNI: done in 0.378498 secs using 399.6% CPU
Optimizing NNI: done in 0.319035 secs using 399.8% CPU
Optimizing NNI: done in 0.483964 secs using 399.5% CPU
154  Q.pfam+I+R10  105264.967   554 211637.934   826577.934   213868.264
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.483115 secs using 398.9% CPU
Optimizing NNI: done in 0.400754 secs using 400.4% CPU
Optimizing NNI: done in 0.297628 secs using 399.6% CPU
Iteration 60 / LogL: -36030.996 / Time: 0h:0m:25s (0h:0m:23s left)
Optimizing NNI: done in 0.311771 secs using 399.5% CPU
Optimizing NNI: done in 0.423609 secs using 399.2% CPU
Optimizing NNI: done in 0.357271 secs using 399.1% CPU
Optimizing NNI: done in 0.419847 secs using 398.9% CPU
Optimizing NNI: done in 0.387306 secs using 400.5% CPU
Optimizing NNI: done in 0.411628 secs using 397.7% CPU
Optimizing NNI: done in 0.461436 secs using 398.6% CPU
Optimizing NNI: done in 0.363698 secs using 399.2% CPU
Optimizing NNI: done in 0.312888 secs using 399.2% CPU
Optimizing NNI: done in 0.356797 secs using 399% CPU
Iteration 70 / LogL: -36041.021 / Time: 0h:0m:28s (0h:0m:18s left)
Optimizing NNI: done in 0.370302 secs using 400.3% CPU
Optimizing NNI: done in 0.400892 secs using 399.5% CPU
Optimizing NNI: done in 0.461606 secs using 399.6% CPU
Optimizing NNI: done in 0.446386 secs using 399.3% CPU
Optimizing NNI: done in 0.411096 secs using 398.8% CPU
788  mtZOA+F+I+R6  60213.763    333 121093.525   122501.399   122491.619
Optimizing NNI: done in 0.608217 secs using 400.1% CPU
Optimizing NNI: done in 0.356741 secs using 399.5% CPU
Optimizing NNI: done in 0.431741 secs using 399.4% CPU
Optimizing NNI: done in 0.36115 secs using 398.7% CPU
Optimizing NNI: done in 0.253215 secs using 399.7% CPU
Iteration 80 / LogL: -36034.536 / Time: 0h:0m:33s (0h:0m:14s left)
Optimizing NNI: done in 0.339996 secs using 399.5% CPU
Optimizing NNI: done in 0.362696 secs using 399.2% CPU
Optimizing NNI: done in 0.384482 secs using 399.6% CPU
Optimizing NNI: done in 0.358337 secs using 399.9% CPU
Optimizing NNI: done in 0.348413 secs using 399% CPU
Optimizing NNI: done in 0.371143 secs using 399.5% CPU
Optimizing NNI: done in 0.409085 secs using 399.5% CPU
Optimizing NNI: done in 0.468768 secs using 399.9% CPU
Optimizing NNI: done in 0.386413 secs using 399.1% CPU
Optimizing NNI: done in 0.350867 secs using 399.6% CPU
Iteration 90 / LogL: -36031.555 / Time: 0h:0m:36s (0h:0m:10s left)
Optimizing NNI: done in 0.533337 secs using 399.6% CPU
175  Q.pfam+F+I+R9 105603.423   571 212348.847   865572.847   214647.616
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.337052 secs using 399% CPU
Optimizing NNI: done in 0.34805 secs using 400.3% CPU
Optimizing NNI: done in 0.347662 secs using 399.9% CPU
Optimizing NNI: done in 0.372001 secs using 399.6% CPU
Optimizing NNI: done in 0.439049 secs using 399.8% CPU
Optimizing NNI: done in 0.32665 secs using 399.8% CPU
Optimizing NNI: done in 0.330941 secs using 398.9% CPU
Optimizing NNI: done in 0.336399 secs using 399.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -36030.949
Optimizing NNI: done in 0.351919 secs using 399.2% CPU
Iteration 100 / LogL: -36031.589 / Time: 0h:0m:40s (0h:0m:6s left)
Optimizing NNI: done in 0.28896 secs using 399.8% CPU
Optimizing NNI: done in 0.47478 secs using 399.6% CPU
Optimizing NNI: done in 0.505648 secs using 398.4% CPU
Optimizing NNI: done in 0.480039 secs using 398.5% CPU
Optimizing NNI: done in 0.321562 secs using 398.4% CPU
Optimizing NNI: done in 0.370656 secs using 398% CPU
Optimizing NNI: done in 0.435103 secs using 398.9% CPU
Optimizing NNI: done in 0.452591 secs using 398.8% CPU
Optimizing NNI: done in 0.423068 secs using 398.2% CPU
Optimizing NNI: done in 0.35253 secs using 398.5% CPU
Iteration 110 / LogL: -36033.122 / Time: 0h:0m:44s (0h:0m:2s left)
Optimizing NNI: done in 0.417944 secs using 398.2% CPU
Optimizing NNI: done in 0.276876 secs using 399.2% CPU
Optimizing NNI: done in 0.314695 secs using 399.1% CPU
Optimizing NNI: done in 0.354973 secs using 398.7% CPU
Optimizing NNI: done in 0.477921 secs using 397.3% CPU
Optimizing NNI: done in 0.361962 secs using 399.5% CPU
TREE SEARCH COMPLETED AFTER 116 ITERATIONS / Time: 0h:0m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36030.949
Optimal log-likelihood: -36030.946
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.266
Parameters optimization took 1 rounds (0.046 sec)
BEST SCORE FOUND : -36030.946
Total tree length: 20.211

Total number of iterations: 116
CPU time used for tree search: 181.515 sec (0h:3m:1s)
Wall-clock time used for tree search: 46.527 sec (0h:0m:46s)
Total CPU time used: 184.163 sec (0h:3m:4s)
Total wall-clock time used: 47.144 sec (0h:0m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 30

Creating bootstrap alignment (seed: 956189)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37301.255
2. Current log-likelihood: -36423.568
3. Current log-likelihood: -36411.462
4. Current log-likelihood: -36411.171
Optimal log-likelihood: -36411.123
Proportion of invariable sites: 0.031
Gamma shape alpha: 2.323
Parameters optimization took 4 rounds (0.280 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0872979 secs using 400% CPU
Computing ML distances took 0.087431 sec (of wall-clock time) 0.349539 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000170946 secs using 428.2% CPU
Constructing RapidNJ tree: done in 0.00230098 secs using 455.5% CPU
Computing RapidNJ tree took 0.002551 sec (of wall-clock time) 0.011823 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37089.359
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.550 second
789  mtZOA+F+I+R7  60194.708    335 121059.417   122502.494   122465.907
Computing log-likelihood of 98 initial trees ... 1.670 seconds
Current best score: -36411.123

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.232383 secs using 400% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36368.409
Optimizing NNI: done in 0.237743 secs using 399.3% CPU
Optimizing NNI: done in 0.22467 secs using 399.7% CPU
Optimizing NNI: done in 0.242962 secs using 399.4% CPU
Optimizing NNI: done in 0.224063 secs using 399.4% CPU
Optimizing NNI: done in 0.247202 secs using 399% CPU
Optimizing NNI: done in 0.234647 secs using 399.4% CPU
Optimizing NNI: done in 0.252544 secs using 397.8% CPU
Optimizing NNI: done in 0.235142 secs using 399.4% CPU
Optimizing NNI: done in 0.248584 secs using 400% CPU
Iteration 10 / LogL: -36368.506 / Time: 0h:0m:6s
Optimizing NNI: done in 0.240964 secs using 398.5% CPU
Optimizing NNI: done in 0.213569 secs using 397.9% CPU
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Optimizing NNI: done in 0.232013 secs using 398.1% CPU
Iteration 20 / LogL: -36368.462 / Time: 0h:0m:8s
Finish initializing candidate tree set (2)
Current best tree score: -36368.409 / CPU time: 8.082
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.448964 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36363.620
Optimizing NNI: done in 0.400697 secs using 398.6% CPU
Optimizing NNI: done in 0.52196 secs using 399.3% CPU
274  PMB+R9        197308.918   1003 396623.836   2410647.836  400991.269
801  mtMet+R6      62101.921    313 124829.842   125934.134   126143.966
Optimizing NNI: done in 0.454091 secs using 398.3% CPU
Optimizing NNI: done in 0.533512 secs using 399.6% CPU
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Iteration 30 / LogL: -36400.871 / Time: 0h:0m:13s (0h:0m:42s left)
Optimizing NNI: done in 0.645971 secs using 399.5% CPU
Optimizing NNI: done in 0.383242 secs using 399.3% CPU
Optimizing NNI: done in 0.397734 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36363.557
Optimizing NNI: done in 0.46703 secs using 400% CPU
802  mtMet+R7      62093.666    315 124817.332   125948.468   126139.853
Optimizing NNI: done in 0.368284 secs using 399.5% CPU
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Iteration 40 / LogL: -36363.577 / Time: 0h:0m:18s (0h:0m:38s left)
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Iteration 50 / LogL: -36363.656 / Time: 0h:0m:22s (0h:0m:32s left)
Optimizing NNI: done in 0.352504 secs using 399.8% CPU
Optimizing NNI: done in 0.429694 secs using 399.3% CPU
803  mtMet+R8      62081.311    317 124796.622   125955.312   126127.540
Optimizing NNI: done in 0.553093 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 53: -36363.502
Optimizing NNI: done in 0.383728 secs using 399.1% CPU
Optimizing NNI: done in 0.584391 secs using 399.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -36363.500
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Iteration 60 / LogL: -36363.760 / Time: 0h:0m:27s (0h:0m:43s left)
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Iteration 70 / LogL: -36367.045 / Time: 0h:0m:31s (0h:0m:38s left)
Optimizing NNI: done in 0.404177 secs using 399.5% CPU
Optimizing NNI: done in 0.321086 secs using 399.6% CPU
275  PMB+R10       197306.392   1005 396622.785   2418682.785  400998.926
Optimizing NNI: done in 0.506459 secs using 399.3% CPU
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Iteration 80 / LogL: -36363.890 / Time: 0h:0m:36s (0h:0m:33s left)
Optimizing NNI: done in 0.369268 secs using 399% CPU
Optimizing NNI: done in 0.513205 secs using 398.4% CPU
BETTER TREE FOUND at iteration 82: -36363.493
Optimizing NNI: done in 0.319607 secs using 397.8% CPU
Optimizing NNI: done in 0.528908 secs using 399.1% CPU
804  mtMet+R9      62081.351    319 124800.702   125987.679   126140.017
Optimizing NNI: done in 0.444004 secs using 399.3% CPU
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Iteration 90 / LogL: -36363.583 / Time: 0h:0m:40s (0h:0m:42s left)
Optimizing NNI: done in 0.510383 secs using 398.5% CPU
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Iteration 100 / LogL: -36364.275 / Time: 0h:0m:45s (0h:0m:37s left)
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Iteration 110 / LogL: -36363.503 / Time: 0h:0m:50s (0h:0m:33s left)
Optimizing NNI: done in 0.540049 secs using 398.1% CPU
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Iteration 120 / LogL: -36364.056 / Time: 0h:0m:55s (0h:0m:28s left)
284  PMB+F+R8      197173.281   1020 396386.563   2479226.563  400828.020
Optimizing NNI: done in 0.303757 secs using 400.1% CPU
810  mtMet+I+R6    62101.693    314 124831.386   125949.013   126149.708
Optimizing NNI: done in 0.481578 secs using 399.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -36363.493
Optimizing NNI: done in 0.430977 secs using 398.7% CPU
Optimizing NNI: done in 0.450277 secs using 398.7% CPU
Optimizing NNI: done in 0.619009 secs using 398.3% CPU
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Iteration 130 / LogL: -36363.503 / Time: 0h:0m:59s (0h:0m:24s left)
Optimizing NNI: done in 0.526864 secs using 397.9% CPU
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Iteration 140 / LogL: -36364.656 / Time: 0h:1m:4s (0h:0m:19s left)
Optimizing NNI: done in 0.42485 secs using 399% CPU
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Optimizing NNI: done in 0.343732 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -36363.493
Iteration 150 / LogL: -36363.493 / Time: 0h:1m:8s (0h:0m:14s left)
Optimizing NNI: done in 0.394611 secs using 399.1% CPU
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811  mtMet+I+R7    62094.240    316 124820.481   125965.304   126147.200
Optimizing NNI: done in 0.413306 secs using 399.4% CPU
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Iteration 160 / LogL: -36365.914 / Time: 0h:1m:13s (0h:0m:10s left)
Optimizing NNI: done in 0.701988 secs using 399.3% CPU
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Iteration 170 / LogL: -36365.938 / Time: 0h:1m:19s (0h:0m:5s left)
Optimizing NNI: done in 0.32193 secs using 399.5% CPU
Optimizing NNI: done in 0.473893 secs using 399.7% CPU
823  mtMet+F+R6    60455.726    332 121575.452   122966.093   122969.347
Optimizing NNI: done in 0.351088 secs using 399.3% CPU
Optimizing NNI: done in 0.617352 secs using 399% CPU
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Iteration 180 / LogL: -36363.876 / Time: 0h:1m:23s (0h:0m:0s left)
Optimizing NNI: done in 0.559217 secs using 399.5% CPU
Optimizing NNI: done in 0.423583 secs using 399.2% CPU
Optimizing NNI: done in 0.461532 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 183 ITERATIONS / Time: 0h:1m:25s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36363.493
Optimal log-likelihood: -36363.492
Proportion of invariable sites: 0.031
Gamma shape alpha: 2.299
Parameters optimization took 1 rounds (0.047 sec)
BEST SCORE FOUND : -36363.492
Total tree length: 20.678

Total number of iterations: 183
CPU time used for tree search: 332.009 sec (0h:5m:32s)
Wall-clock time used for tree search: 84.250 sec (0h:1m:24s)
Total CPU time used: 335.498 sec (0h:5m:35s)
Total wall-clock time used: 85.077 sec (0h:1m:25s)

===> START BOOTSTRAP REPLICATE NUMBER 31

Creating bootstrap alignment (seed: 956190)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36985.367
2. Current log-likelihood: -36059.728
3. Current log-likelihood: -36036.318
4. Current log-likelihood: -36035.872
Optimal log-likelihood: -36035.797
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.572
Parameters optimization took 4 rounds (0.275 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0797188 secs using 400% CPU
Computing ML distances took 0.079862 sec (of wall-clock time) 0.319250 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000166893 secs using 430.8% CPU
Constructing RapidNJ tree: done in 0.00233293 secs using 492.6% CPU
Computing RapidNJ tree took 0.002564 sec (of wall-clock time) 0.012947 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36889.267
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.430 second
Computing log-likelihood of 98 initial trees ... 1.649 seconds
Current best score: -36035.797

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.153702 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35977.936
Optimizing NNI: done in 0.267106 secs using 397.4% CPU
Optimizing NNI: done in 0.268337 secs using 398.9% CPU
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824  mtMet+F+R7    60437.393    334 121542.787   122968.137   122945.078
Optimizing NNI: done in 0.248005 secs using 398.7% CPU
Iteration 10 / LogL: -35992.761 / Time: 0h:0m:6s
Optimizing NNI: done in 0.233341 secs using 398.6% CPU
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Optimizing NNI: done in 0.211306 secs using 397.8% CPU
Iteration 20 / LogL: -35977.983 / Time: 0h:0m:8s
Finish initializing candidate tree set (5)
Current best tree score: -35977.936 / CPU time: 8.263
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.351549 secs using 396.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -35977.325
Optimizing NNI: done in 0.386387 secs using 398.5% CPU
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Iteration 30 / LogL: -35992.740 / Time: 0h:0m:12s (0h:0m:39s left)
Optimizing NNI: done in 0.316041 secs using 398.8% CPU
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Iteration 40 / LogL: -35982.444 / Time: 0h:0m:16s (0h:0m:33s left)
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285  PMB+F+R9      197172.042   1022 396388.084   2487400.084  400838.251
Optimizing NNI: done in 0.364131 secs using 398.8% CPU
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Iteration 50 / LogL: -35977.438 / Time: 0h:0m:19s (0h:0m:28s left)
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825  mtMet+F+R8    60433.088    336 121538.177   122999.235   122948.866
Optimizing NNI: done in 0.353047 secs using 398.4% CPU
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Iteration 60 / LogL: -35978.567 / Time: 0h:0m:23s (0h:0m:24s left)
Optimizing NNI: done in 0.299873 secs using 399.6% CPU
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Iteration 70 / LogL: -35991.944 / Time: 0h:0m:26s (0h:0m:19s left)
Optimizing NNI: done in 0.323924 secs using 399.7% CPU
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Iteration 80 / LogL: -35977.346 / Time: 0h:0m:30s (0h:0m:15s left)
Optimizing NNI: done in 0.386016 secs using 399.8% CPU
Optimizing NNI: done in 0.378911 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35977.305
Optimizing NNI: done in 0.331625 secs using 399.3% CPU
Optimizing NNI: done in 0.320648 secs using 399.2% CPU
Optimizing NNI: done in 0.331949 secs using 399.6% CPU
Optimizing NNI: done in 0.252893 secs using 398.9% CPU
Optimizing NNI: done in 0.35999 secs using 399.6% CPU
Optimizing NNI: done in 0.422446 secs using 399.6% CPU
832  mtMet+F+I+R6  60453.915    333 121573.829   122981.703   122971.923
Optimizing NNI: done in 0.325153 secs using 398.8% CPU
Optimizing NNI: done in 0.275074 secs using 399.3% CPU
Iteration 90 / LogL: -35977.390 / Time: 0h:0m:34s (0h:0m:11s left)
Optimizing NNI: done in 0.375674 secs using 399.2% CPU
Optimizing NNI: done in 0.506776 secs using 400.2% CPU
Optimizing NNI: done in 0.308897 secs using 399.5% CPU
Optimizing NNI: done in 0.348541 secs using 399% CPU
Optimizing NNI: done in 0.317166 secs using 399.6% CPU
Optimizing NNI: done in 0.360684 secs using 399.4% CPU
Optimizing NNI: done in 0.301475 secs using 399.4% CPU
Optimizing NNI: done in 0.36741 secs using 399.2% CPU
Optimizing NNI: done in 0.356366 secs using 399.5% CPU
Optimizing NNI: done in 0.334909 secs using 399.2% CPU
Iteration 100 / LogL: -36082.008 / Time: 0h:0m:37s (0h:0m:7s left)
Optimizing NNI: done in 0.333912 secs using 399.3% CPU
Optimizing NNI: done in 0.450724 secs using 399% CPU
Optimizing NNI: done in 0.361957 secs using 399.4% CPU
Optimizing NNI: done in 0.453095 secs using 399.7% CPU
176  Q.pfam+F+I+R10 105598.601   573 212343.203   870147.203   214650.024
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.401078 secs using 399.3% CPU
Optimizing NNI: done in 0.325195 secs using 399.3% CPU
Optimizing NNI: done in 0.305038 secs using 399.9% CPU
Optimizing NNI: done in 0.3775 secs using 399.6% CPU
Optimizing NNI: done in 0.336022 secs using 399.9% CPU
Optimizing NNI: done in 0.409861 secs using 399.9% CPU
Iteration 110 / LogL: -35977.331 / Time: 0h:0m:41s (0h:0m:4s left)
Optimizing NNI: done in 0.373838 secs using 399.6% CPU
Optimizing NNI: done in 0.458189 secs using 399% CPU
295  Blosum62+R8   197539.412   1001 397080.824   2403084.824  401439.549
Optimizing NNI: done in 0.420627 secs using 398.9% CPU
Optimizing NNI: done in 0.387768 secs using 399.1% CPU
Optimizing NNI: done in 0.467465 secs using 399.7% CPU
Optimizing NNI: done in 0.313015 secs using 399.9% CPU
Optimizing NNI: done in 0.365251 secs using 399.4% CPU
Optimizing NNI: done in 0.322238 secs using 399.6% CPU
Optimizing NNI: done in 0.404256 secs using 399.7% CPU
Optimizing NNI: done in 0.312227 secs using 399.6% CPU
Iteration 120 / LogL: -35977.310 / Time: 0h:0m:45s (0h:0m:0s left)
Optimizing NNI: done in 0.34341 secs using 399.5% CPU
Optimizing NNI: done in 0.366984 secs using 399.7% CPU
TREE SEARCH COMPLETED AFTER 122 ITERATIONS / Time: 0h:0m:46s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35977.305
Optimal log-likelihood: -35977.305
Proportion of invariable sites: 0.018
Gamma shape alpha: 2.560
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35977.305
Total tree length: 19.461

Total number of iterations: 122
CPU time used for tree search: 177.708 sec (0h:2m:57s)
Wall-clock time used for tree search: 45.453 sec (0h:0m:45s)
Total CPU time used: 180.252 sec (0h:3m:0s)
Total wall-clock time used: 46.050 sec (0h:0m:46s)

===> START BOOTSTRAP REPLICATE NUMBER 32

Creating bootstrap alignment (seed: 956191)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.019 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36875.973
2. Current log-likelihood: -36046.169
3. Current log-likelihood: -35996.025
4. Current log-likelihood: -35994.393
Optimal log-likelihood: -35994.271
Proportion of invariable sites: 0.012
Gamma shape alpha: 2.227
Parameters optimization took 4 rounds (0.263 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0749319 secs using 400.1% CPU
Computing ML distances took 0.075075 sec (of wall-clock time) 0.300094 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000157118 secs using 426.4% CPU
Constructing RapidNJ tree: done in 0.00214195 secs using 467.7% CPU
Computing RapidNJ tree took 0.002357 sec (of wall-clock time) 0.011957 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36558.346
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.536 second
Computing log-likelihood of 98 initial trees ... 1.516 seconds
Current best score: -35991.612

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.287836 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35940.315
833  mtMet+F+I+R7  60435.792    335 121541.585   122984.662   122948.075
Optimizing NNI: done in 0.193643 secs using 399.2% CPU
Optimizing NNI: done in 0.264091 secs using 399.5% CPU
Optimizing NNI: done in 0.265517 secs using 399.8% CPU
Optimizing NNI: done in 0.271806 secs using 398.8% CPU
Optimizing NNI: done in 0.262229 secs using 398.7% CPU
Optimizing NNI: done in 0.235963 secs using 399.4% CPU
Optimizing NNI: done in 0.299924 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 8: -35932.902
Optimizing NNI: done in 0.259861 secs using 397.5% CPU
Optimizing NNI: done in 0.260226 secs using 398% CPU
Iteration 10 / LogL: -35940.316 / Time: 0h:0m:6s
Optimizing NNI: done in 0.259139 secs using 397.9% CPU
Optimizing NNI: done in 0.24924 secs using 398.7% CPU
Optimizing NNI: done in 0.263059 secs using 399.5% CPU
Optimizing NNI: done in 0.274738 secs using 399.9% CPU
Optimizing NNI: done in 0.248708 secs using 398.7% CPU
Optimizing NNI: done in 0.249027 secs using 399.5% CPU
Optimizing NNI: done in 0.288995 secs using 399.3% CPU
Optimizing NNI: done in 0.262065 secs using 400.6% CPU
Optimizing NNI: done in 0.247534 secs using 398.7% CPU
Optimizing NNI: done in 0.288562 secs using 399.6% CPU
Iteration 20 / LogL: -35940.313 / Time: 0h:0m:9s
Finish initializing candidate tree set (4)
Current best tree score: -35932.902 / CPU time: 8.435
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
197  Q.bird+I+R9   105984.100   552 213072.201   823584.201   215294.479
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.448883 secs using 399.2% CPU
Optimizing NNI: done in 0.436452 secs using 399.5% CPU
Optimizing NNI: done in 0.470644 secs using 399.3% CPU
Optimizing NNI: done in 0.430592 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -35932.773
Optimizing NNI: done in 0.285718 secs using 399.5% CPU
Optimizing NNI: done in 0.495175 secs using 398.9% CPU
Optimizing NNI: done in 0.409268 secs using 399.9% CPU
Optimizing NNI: done in 0.333955 secs using 399.6% CPU
Optimizing NNI: done in 0.416097 secs using 399.9% CPU
Optimizing NNI: done in 0.44117 secs using 399.6% CPU
Iteration 30 / LogL: -35937.652 / Time: 0h:0m:13s (0h:0m:43s left)
Optimizing NNI: done in 0.381318 secs using 399.4% CPU
Optimizing NNI: done in 0.311026 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -35932.768
Optimizing NNI: done in 0.29238 secs using 399.2% CPU
Optimizing NNI: done in 0.458185 secs using 398.4% CPU
Optimizing NNI: done in 0.374742 secs using 399.6% CPU
Optimizing NNI: done in 0.413907 secs using 399.5% CPU
Optimizing NNI: done in 0.335963 secs using 399.6% CPU
Optimizing NNI: done in 0.564471 secs using 399% CPU
Optimizing NNI: done in 0.329292 secs using 399.3% CPU
Optimizing NNI: done in 0.419914 secs using 399.5% CPU
Iteration 40 / LogL: -35936.570 / Time: 0h:0m:17s (0h:0m:37s left)
Optimizing NNI: done in 0.348039 secs using 399.9% CPU
Optimizing NNI: done in 0.393566 secs using 399.5% CPU
Optimizing NNI: done in 0.422169 secs using 399.6% CPU
Optimizing NNI: done in 0.387382 secs using 398.1% CPU
Optimizing NNI: done in 0.428312 secs using 399.5% CPU
Optimizing NNI: done in 0.386002 secs using 399% CPU
845  mtVer+R6      62797.259    313 126220.518   127324.811   127534.642
Optimizing NNI: done in 0.391358 secs using 398.6% CPU
Optimizing NNI: done in 0.40472 secs using 399.6% CPU
Optimizing NNI: done in 0.497597 secs using 399.4% CPU
Optimizing NNI: done in 0.409065 secs using 399.2% CPU
Iteration 50 / LogL: -35934.680 / Time: 0h:0m:21s (0h:0m:32s left)
Optimizing NNI: done in 0.388476 secs using 399.3% CPU
Optimizing NNI: done in 0.446524 secs using 398.5% CPU
Optimizing NNI: done in 0.36901 secs using 399.2% CPU
Optimizing NNI: done in 0.285333 secs using 399.8% CPU
Optimizing NNI: done in 0.319756 secs using 399.3% CPU
Optimizing NNI: done in 0.420345 secs using 399.6% CPU
Optimizing NNI: done in 0.479799 secs using 398.8% CPU
Optimizing NNI: done in 0.351187 secs using 399.6% CPU
Optimizing NNI: done in 0.4328 secs using 399.3% CPU
Optimizing NNI: done in 0.40003 secs using 399.7% CPU
Iteration 60 / LogL: -35936.011 / Time: 0h:0m:25s (0h:0m:27s left)
Optimizing NNI: done in 0.299186 secs using 399.7% CPU
Optimizing NNI: done in 0.346616 secs using 399.6% CPU
Optimizing NNI: done in 0.331241 secs using 399.9% CPU
Optimizing NNI: done in 0.431005 secs using 399.6% CPU
Optimizing NNI: done in 0.300713 secs using 399.5% CPU
Optimizing NNI: done in 0.416991 secs using 399% CPU
Optimizing NNI: done in 0.300535 secs using 398.9% CPU
Optimizing NNI: done in 0.475076 secs using 398.2% CPU
Optimizing NNI: done in 0.411432 secs using 399.7% CPU
296  Blosum62+R9   197530.232   1003 397066.464   2411090.464  401433.897
Optimizing NNI: done in 0.458239 secs using 399.2% CPU
Iteration 70 / LogL: -35932.889 / Time: 0h:0m:29s (0h:0m:22s left)
Optimizing NNI: done in 0.42123 secs using 399.9% CPU
Optimizing NNI: done in 0.401812 secs using 399.3% CPU
Optimizing NNI: done in 0.414248 secs using 398.7% CPU
Optimizing NNI: done in 0.414374 secs using 399.7% CPU
Optimizing NNI: done in 0.424942 secs using 398.9% CPU
Optimizing NNI: done in 0.368647 secs using 398.5% CPU
Optimizing NNI: done in 0.355452 secs using 399.9% CPU
Optimizing NNI: done in 0.387638 secs using 399.6% CPU
Optimizing NNI: done in 0.396275 secs using 399.3% CPU
Optimizing NNI: done in 0.487864 secs using 399.4% CPU
Iteration 80 / LogL: -35932.884 / Time: 0h:0m:33s (0h:0m:18s left)
Optimizing NNI: done in 0.439008 secs using 399.5% CPU
Optimizing NNI: done in 0.38802 secs using 399.3% CPU
Optimizing NNI: done in 0.37581 secs using 399.1% CPU
Optimizing NNI: done in 0.320205 secs using 399.8% CPU
Optimizing NNI: done in 0.49911 secs using 399.1% CPU
846  mtVer+R7      62780.850    315 126191.700   127322.836   127514.221
Optimizing NNI: done in 0.386435 secs using 399.4% CPU
Optimizing NNI: done in 0.449499 secs using 399.3% CPU
Optimizing NNI: done in 0.313328 secs using 399.6% CPU
Optimizing NNI: done in 0.403758 secs using 398.9% CPU
Optimizing NNI: done in 0.327894 secs using 399% CPU
Iteration 90 / LogL: -36382.780 / Time: 0h:0m:37s (0h:0m:14s left)
Optimizing NNI: done in 0.304748 secs using 399.7% CPU
Optimizing NNI: done in 0.407269 secs using 399.2% CPU
Optimizing NNI: done in 0.368824 secs using 399.4% CPU
Optimizing NNI: done in 0.348658 secs using 399.9% CPU
Optimizing NNI: done in 0.307448 secs using 399.6% CPU
Optimizing NNI: done in 0.379215 secs using 399.4% CPU
Optimizing NNI: done in 0.578171 secs using 399.7% CPU
Optimizing NNI: done in 0.35449 secs using 399.7% CPU
Optimizing NNI: done in 0.313259 secs using 399.6% CPU
Optimizing NNI: done in 0.377307 secs using 399.9% CPU
Iteration 100 / LogL: -35932.820 / Time: 0h:0m:41s (0h:0m:9s left)
Optimizing NNI: done in 0.418747 secs using 399.5% CPU
Optimizing NNI: done in 0.468511 secs using 399.3% CPU
Optimizing NNI: done in 0.353868 secs using 398.8% CPU
Optimizing NNI: done in 0.432185 secs using 399.6% CPU
Optimizing NNI: done in 0.366257 secs using 398.7% CPU
Optimizing NNI: done in 0.369219 secs using 398.6% CPU
Optimizing NNI: done in 0.480395 secs using 399.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -35932.764
Optimizing NNI: done in 0.371538 secs using 399.6% CPU
Optimizing NNI: done in 0.408789 secs using 399.4% CPU
Optimizing NNI: done in 0.344346 secs using 399% CPU
Iteration 110 / LogL: -35932.773 / Time: 0h:0m:45s (0h:0m:5s left)
Optimizing NNI: done in 0.565705 secs using 399.2% CPU
Optimizing NNI: done in 0.465289 secs using 399.2% CPU
Optimizing NNI: done in 0.409638 secs using 399.5% CPU
Optimizing NNI: done in 0.384901 secs using 398.8% CPU
Optimizing NNI: done in 0.40589 secs using 399.2% CPU
Optimizing NNI: done in 0.367672 secs using 399.7% CPU
Optimizing NNI: done in 0.367392 secs using 399.6% CPU
Optimizing NNI: done in 0.455596 secs using 399.6% CPU
Optimizing NNI: done in 0.434279 secs using 399.5% CPU
UPDATE BEST LOG-LIKELIHOOD: -35932.758
Optimizing NNI: done in 0.405679 secs using 399.2% CPU
Iteration 120 / LogL: -35933.012 / Time: 0h:0m:49s (0h:0m:1s left)
Optimizing NNI: done in 0.253605 secs using 399.9% CPU
Optimizing NNI: done in 0.410721 secs using 399.7% CPU
Optimizing NNI: done in 0.303882 secs using 399.2% CPU
Optimizing NNI: done in 0.348741 secs using 399.4% CPU
Optimizing NNI: done in 0.388649 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 125 ITERATIONS / Time: 0h:0m:51s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35932.758
Optimal log-likelihood: -35932.757
Proportion of invariable sites: 0.013
Gamma shape alpha: 2.177
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35932.757
Total tree length: 20.592

Total number of iterations: 125
CPU time used for tree search: 197.055 sec (0h:3m:17s)
Wall-clock time used for tree search: 50.363 sec (0h:0m:50s)
Total CPU time used: 200.426 sec (0h:3m:20s)
Total wall-clock time used: 51.161 sec (0h:0m:51s)

===> START BOOTSTRAP REPLICATE NUMBER 33

Creating bootstrap alignment (seed: 956192)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36697.621
2. Current log-likelihood: -35820.129
3. Current log-likelihood: -35808.862
4. Current log-likelihood: -35807.604
5. Current log-likelihood: -35807.367
Optimal log-likelihood: -35807.364
Proportion of invariable sites: 0.033
Gamma shape alpha: 2.350
Parameters optimization took 5 rounds (0.313 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0745211 secs using 400% CPU
Computing ML distances took 0.074650 sec (of wall-clock time) 0.298390 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000154018 secs using 430.5% CPU
Constructing RapidNJ tree: done in 0.00209093 secs using 459.3% CPU
Computing RapidNJ tree took 0.002302 sec (of wall-clock time) 0.011563 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36499.314
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.480 second
Computing log-likelihood of 98 initial trees ... 1.595 seconds
Current best score: -35807.364

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.218723 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35792.957
Optimizing NNI: done in 0.213791 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35791.164
Optimizing NNI: done in 0.209967 secs using 399.9% CPU
Optimizing NNI: done in 0.222038 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -35789.528
Optimizing NNI: done in 0.235597 secs using 399.3% CPU
Optimizing NNI: done in 0.221039 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -35786.636
Optimizing NNI: done in 0.247156 secs using 399.8% CPU
Optimizing NNI: done in 0.214481 secs using 399% CPU
Optimizing NNI: done in 0.231153 secs using 399.9% CPU
Optimizing NNI: done in 0.254164 secs using 399.5% CPU
Iteration 10 / LogL: -35789.682 / Time: 0h:0m:6s
Optimizing NNI: done in 0.246927 secs using 398.2% CPU
Optimizing NNI: done in 0.247082 secs using 399.7% CPU
Optimizing NNI: done in 0.270117 secs using 399.5% CPU
Optimizing NNI: done in 0.246723 secs using 399.7% CPU
Optimizing NNI: done in 0.250904 secs using 399.9% CPU
Optimizing NNI: done in 0.221057 secs using 399.2% CPU
Optimizing NNI: done in 0.257865 secs using 399.9% CPU
Optimizing NNI: done in 0.250279 secs using 397.8% CPU
Optimizing NNI: done in 0.201083 secs using 400.2% CPU
Optimizing NNI: done in 0.29728 secs using 399.4% CPU
Iteration 20 / LogL: -35789.430 / Time: 0h:0m:8s
Finish initializing candidate tree set (13)
Current best tree score: -35786.636 / CPU time: 8.081
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.375907 secs using 399.7% CPU
Optimizing NNI: done in 0.472883 secs using 399.4% CPU
Optimizing NNI: done in 0.432546 secs using 399.3% CPU
Optimizing NNI: done in 0.379953 secs using 399.5% CPU
Optimizing NNI: done in 0.235291 secs using 399.9% CPU
Optimizing NNI: done in 0.380929 secs using 399.1% CPU
Optimizing NNI: done in 0.349399 secs using 399.3% CPU
Optimizing NNI: done in 0.296359 secs using 399.9% CPU
Optimizing NNI: done in 0.328499 secs using 399.7% CPU
Optimizing NNI: done in 0.367881 secs using 399.5% CPU
Iteration 30 / LogL: -35786.742 / Time: 0h:0m:12s (0h:0m:32s left)
Optimizing NNI: done in 0.339112 secs using 399.2% CPU
847  mtVer+R8      62768.302    317 126170.604   127329.294   127501.522
Optimizing NNI: done in 0.439446 secs using 400.4% CPU
297  Blosum62+R10  197526.017   1005 397062.034   2419122.034  401438.175
Optimizing NNI: done in 0.329139 secs using 399.4% CPU
Optimizing NNI: done in 0.385508 secs using 399.3% CPU
Optimizing NNI: done in 0.371948 secs using 399.3% CPU
Optimizing NNI: done in 0.316783 secs using 398.6% CPU
Optimizing NNI: done in 0.350082 secs using 398.9% CPU
Optimizing NNI: done in 0.247439 secs using 399.5% CPU
Optimizing NNI: done in 0.297656 secs using 399.1% CPU
Optimizing NNI: done in 0.429039 secs using 399.7% CPU
Iteration 40 / LogL: -35789.908 / Time: 0h:0m:16s (0h:0m:27s left)
Optimizing NNI: done in 0.400283 secs using 399.5% CPU
Optimizing NNI: done in 0.300233 secs using 399.8% CPU
Optimizing NNI: done in 0.352852 secs using 399.2% CPU
Optimizing NNI: done in 0.449885 secs using 399.3% CPU
Optimizing NNI: done in 0.436914 secs using 399.7% CPU
Optimizing NNI: done in 0.462433 secs using 399.5% CPU
Optimizing NNI: done in 0.406267 secs using 399.4% CPU
Optimizing NNI: done in 0.500872 secs using 399.6% CPU
Optimizing NNI: done in 0.423711 secs using 399.7% CPU
Optimizing NNI: done in 0.385185 secs using 399.1% CPU
Iteration 50 / LogL: -36101.434 / Time: 0h:0m:20s (0h:0m:23s left)
Optimizing NNI: done in 0.392474 secs using 399% CPU
Optimizing NNI: done in 0.421335 secs using 399.2% CPU
Optimizing NNI: done in 0.420868 secs using 399.4% CPU
Optimizing NNI: done in 0.320283 secs using 399.6% CPU
Optimizing NNI: done in 0.339854 secs using 399.7% CPU
Optimizing NNI: done in 0.456675 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35786.577
Optimizing NNI: done in 0.332569 secs using 399.9% CPU
Optimizing NNI: done in 0.376038 secs using 398.7% CPU
Optimizing NNI: done in 0.322585 secs using 399.5% CPU
Optimizing NNI: done in 0.373437 secs using 399.2% CPU
Iteration 60 / LogL: -35793.065 / Time: 0h:0m:24s (0h:0m:18s left)
Optimizing NNI: done in 0.266262 secs using 399.1% CPU
Optimizing NNI: done in 0.335254 secs using 399.5% CPU
Optimizing NNI: done in 0.317339 secs using 399.5% CPU
Optimizing NNI: done in 0.381854 secs using 399.1% CPU
Optimizing NNI: done in 0.308907 secs using 398.5% CPU
Optimizing NNI: done in 0.35382 secs using 399.6% CPU
Optimizing NNI: done in 0.324615 secs using 399.9% CPU
Optimizing NNI: done in 0.397541 secs using 398.8% CPU
Optimizing NNI: done in 0.503586 secs using 399.3% CPU
Optimizing NNI: done in 0.498278 secs using 399.8% CPU
Iteration 70 / LogL: -35786.650 / Time: 0h:0m:27s (0h:0m:14s left)
Optimizing NNI: done in 0.400669 secs using 398.9% CPU
Optimizing NNI: done in 0.372103 secs using 399.2% CPU
Optimizing NNI: done in 0.382147 secs using 399.5% CPU
Optimizing NNI: done in 0.395108 secs using 398.8% CPU
Optimizing NNI: done in 0.306718 secs using 399.2% CPU
Optimizing NNI: done in 0.362383 secs using 399.3% CPU
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Optimizing NNI: done in 0.411447 secs using 399.4% CPU
Optimizing NNI: done in 0.28475 secs using 399.5% CPU
Optimizing NNI: done in 0.357013 secs using 398.6% CPU
Iteration 80 / LogL: -35789.448 / Time: 0h:0m:31s (0h:0m:10s left)
Optimizing NNI: done in 0.392987 secs using 399.3% CPU
Optimizing NNI: done in 0.322214 secs using 398.9% CPU
Optimizing NNI: done in 0.318643 secs using 399.3% CPU
Optimizing NNI: done in 0.35634 secs using 398.9% CPU
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Optimizing NNI: done in 0.42974 secs using 399.2% CPU
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Optimizing NNI: done in 0.385413 secs using 399.8% CPU
Optimizing NNI: done in 0.390395 secs using 399.3% CPU
Iteration 90 / LogL: -35792.895 / Time: 0h:0m:35s (0h:0m:6s left)
Optimizing NNI: done in 0.365047 secs using 399.7% CPU
Optimizing NNI: done in 0.358432 secs using 399% CPU
Optimizing NNI: done in 0.523167 secs using 399.6% CPU
Optimizing NNI: done in 0.429776 secs using 398.2% CPU
Optimizing NNI: done in 0.410016 secs using 399.8% CPU
Optimizing NNI: done in 0.391849 secs using 399.3% CPU
Optimizing NNI: done in 0.39817 secs using 399.1% CPU
Optimizing NNI: done in 0.417242 secs using 399.1% CPU
Optimizing NNI: done in 0.393922 secs using 399.7% CPU
Optimizing NNI: done in 0.335059 secs using 399.2% CPU
Iteration 100 / LogL: -35787.041 / Time: 0h:0m:39s (0h:0m:2s left)
Optimizing NNI: done in 0.351117 secs using 399.5% CPU
Optimizing NNI: done in 0.389876 secs using 399.3% CPU
Optimizing NNI: done in 0.402479 secs using 399.4% CPU
Optimizing NNI: done in 0.278295 secs using 398.9% CPU
Optimizing NNI: done in 0.348615 secs using 399.7% CPU
306  Blosum62+F+R8 196901.090   1020 395842.180   2478682.180  400283.637
Optimizing NNI: done in 0.424952 secs using 399.4% CPU
Optimizing NNI: done in 0.386269 secs using 399.6% CPU
TREE SEARCH COMPLETED AFTER 107 ITERATIONS / Time: 0h:0m:41s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35786.577
Optimal log-likelihood: -35786.566
Proportion of invariable sites: 0.033
Gamma shape alpha: 2.367
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35786.566
Total tree length: 20.140

Total number of iterations: 107
CPU time used for tree search: 160.857 sec (0h:2m:40s)
Wall-clock time used for tree search: 41.255 sec (0h:0m:41s)
Total CPU time used: 164.114 sec (0h:2m:44s)
Total wall-clock time used: 42.022 sec (0h:0m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 34

Creating bootstrap alignment (seed: 956193)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36276.800
2. Current log-likelihood: -35372.297
3. Current log-likelihood: -35357.257
4. Current log-likelihood: -35357.059
Optimal log-likelihood: -35357.042
Proportion of invariable sites: 0.046
Gamma shape alpha: 2.491
Parameters optimization took 4 rounds (0.262 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.07793 secs using 399.9% CPU
Computing ML distances took 0.078064 sec (of wall-clock time) 0.312014 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000153065 secs using 437.1% CPU
Constructing RapidNJ tree: done in 0.00220895 secs using 460.1% CPU
Computing RapidNJ tree took 0.002430 sec (of wall-clock time) 0.012214 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36037.586
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.468 second
Computing log-likelihood of 98 initial trees ... 1.613 seconds
Current best score: -35348.871

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.330678 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35295.909
Optimizing NNI: done in 0.326651 secs using 400.1% CPU
Optimizing NNI: done in 0.350723 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -35293.747
Optimizing NNI: done in 0.325802 secs using 399.8% CPU
Optimizing NNI: done in 0.319425 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -35292.905
Optimizing NNI: done in 0.31761 secs using 399.6% CPU
Optimizing NNI: done in 0.318215 secs using 399.9% CPU
Optimizing NNI: done in 0.321589 secs using 399.1% CPU
Optimizing NNI: done in 0.316375 secs using 399.7% CPU
Optimizing NNI: done in 0.32215 secs using 399.9% CPU
Iteration 10 / LogL: -35293.768 / Time: 0h:0m:7s
Optimizing NNI: done in 0.247455 secs using 399.8% CPU
Optimizing NNI: done in 0.22962 secs using 399.8% CPU
Optimizing NNI: done in 0.279091 secs using 399.9% CPU
Optimizing NNI: done in 0.267383 secs using 398.3% CPU
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Optimizing NNI: done in 0.259771 secs using 399.5% CPU
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Optimizing NNI: done in 0.21669 secs using 399.9% CPU
Optimizing NNI: done in 0.230435 secs using 399.8% CPU
Iteration 20 / LogL: -35298.105 / Time: 0h:0m:9s
Finish initializing candidate tree set (6)
Current best tree score: -35292.905 / CPU time: 8.994
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.524206 secs using 399.6% CPU
Optimizing NNI: done in 0.431097 secs using 399.2% CPU
Optimizing NNI: done in 0.511612 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -35292.766
Optimizing NNI: done in 0.413361 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -35292.095
848  mtVer+R9      62764.125    319 126166.251   127353.228   127505.566
Optimizing NNI: done in 0.428027 secs using 398.7% CPU
Optimizing NNI: done in 0.529361 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -35291.870
Optimizing NNI: done in 0.266807 secs using 399.5% CPU
Optimizing NNI: done in 0.450092 secs using 398.9% CPU
Optimizing NNI: done in 0.475686 secs using 399.4% CPU
Optimizing NNI: done in 0.359718 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35291.825
Iteration 30 / LogL: -35291.825 / Time: 0h:0m:14s (0h:0m:46s left)
Optimizing NNI: done in 0.429161 secs using 399.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -35291.817
Optimizing NNI: done in 0.330994 secs using 399.2% CPU
Optimizing NNI: done in 0.398637 secs using 399.6% CPU
Optimizing NNI: done in 0.387586 secs using 399.1% CPU
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Optimizing NNI: done in 0.326757 secs using 399% CPU
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Optimizing NNI: done in 0.364973 secs using 398.9% CPU
Iteration 40 / LogL: -35292.665 / Time: 0h:0m:18s (0h:0m:39s left)
Optimizing NNI: done in 0.384684 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35291.696
Optimizing NNI: done in 0.379052 secs using 398.8% CPU
Optimizing NNI: done in 0.41224 secs using 399% CPU
Optimizing NNI: done in 0.422353 secs using 399% CPU
Optimizing NNI: done in 0.575879 secs using 399.3% CPU
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Optimizing NNI: done in 0.511705 secs using 399.1% CPU
Optimizing NNI: done in 0.302707 secs using 399.7% CPU
Iteration 50 / LogL: -35291.834 / Time: 0h:0m:22s (0h:0m:34s left)
Optimizing NNI: done in 0.472832 secs using 398.9% CPU
Optimizing NNI: done in 0.32121 secs using 399.9% CPU
Optimizing NNI: done in 0.509954 secs using 399% CPU
Optimizing NNI: done in 0.429083 secs using 398.9% CPU
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Optimizing NNI: done in 0.371172 secs using 399.1% CPU
Optimizing NNI: done in 0.300238 secs using 398.8% CPU
Iteration 60 / LogL: -35291.898 / Time: 0h:0m:26s (0h:0m:29s left)
Optimizing NNI: done in 0.443206 secs using 399.5% CPU
Optimizing NNI: done in 0.423164 secs using 399.1% CPU
Optimizing NNI: done in 0.654069 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35291.679
Optimizing NNI: done in 0.388937 secs using 399.3% CPU
Optimizing NNI: done in 0.440845 secs using 399.9% CPU
Optimizing NNI: done in 0.534634 secs using 399% CPU
Optimizing NNI: done in 0.404375 secs using 399.9% CPU
Optimizing NNI: done in 0.690141 secs using 398.5% CPU
Optimizing NNI: done in 0.297617 secs using 399.9% CPU
Optimizing NNI: done in 0.511667 secs using 398.5% CPU
Iteration 70 / LogL: -35291.691 / Time: 0h:0m:31s (0h:0m:25s left)
Optimizing NNI: done in 0.331789 secs using 399.1% CPU
Optimizing NNI: done in 0.308054 secs using 399.4% CPU
Optimizing NNI: done in 0.288833 secs using 399.9% CPU
Optimizing NNI: done in 0.392177 secs using 399.1% CPU
Optimizing NNI: done in 0.363113 secs using 399.6% CPU
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Optimizing NNI: done in 0.393018 secs using 398.5% CPU
Optimizing NNI: done in 0.352982 secs using 399.6% CPU
Iteration 80 / LogL: -35291.961 / Time: 0h:0m:35s (0h:0m:20s left)
Optimizing NNI: done in 0.404249 secs using 399.4% CPU
Optimizing NNI: done in 0.393365 secs using 399.5% CPU
Optimizing NNI: done in 0.729743 secs using 399.1% CPU
Optimizing NNI: done in 0.401032 secs using 399.6% CPU
Optimizing NNI: done in 0.373879 secs using 398.9% CPU
Optimizing NNI: done in 0.382011 secs using 400% CPU
Optimizing NNI: done in 0.461248 secs using 399.3% CPU
Optimizing NNI: done in 0.471071 secs using 398.8% CPU
Optimizing NNI: done in 0.431484 secs using 398.9% CPU
Optimizing NNI: done in 0.455824 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 90: -35290.723
Iteration 90 / LogL: -35290.723 / Time: 0h:0m:39s (0h:0m:44s left)
Optimizing NNI: done in 0.583802 secs using 399.6% CPU
Optimizing NNI: done in 0.35846 secs using 399.1% CPU
Optimizing NNI: done in 0.301714 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35290.142
Optimizing NNI: done in 0.338953 secs using 398.4% CPU
Optimizing NNI: done in 0.415609 secs using 399.8% CPU
Optimizing NNI: done in 0.355444 secs using 399.6% CPU
Optimizing NNI: done in 0.308576 secs using 399.6% CPU
Optimizing NNI: done in 0.341825 secs using 399.2% CPU
Optimizing NNI: done in 0.667799 secs using 398.6% CPU
Optimizing NNI: done in 0.476598 secs using 399.6% CPU
Iteration 100 / LogL: -35291.944 / Time: 0h:0m:43s (0h:0m:39s left)
Optimizing NNI: done in 0.392937 secs using 399.7% CPU
Optimizing NNI: done in 0.472146 secs using 399.5% CPU
Optimizing NNI: done in 0.558003 secs using 398.3% CPU
854  mtVer+I+R6    62797.426    314 126222.852   127340.479   127541.174
Optimizing NNI: done in 0.375084 secs using 399.6% CPU
Optimizing NNI: done in 0.310197 secs using 399.6% CPU
Optimizing NNI: done in 0.349432 secs using 398.7% CPU
Optimizing NNI: done in 0.421274 secs using 399.6% CPU
Optimizing NNI: done in 0.509505 secs using 399.5% CPU
Optimizing NNI: done in 0.359111 secs using 399.4% CPU
Optimizing NNI: done in 0.409441 secs using 399.3% CPU
Iteration 110 / LogL: -35291.711 / Time: 0h:0m:48s (0h:0m:35s left)
Optimizing NNI: done in 0.646829 secs using 399.1% CPU
Optimizing NNI: done in 0.250483 secs using 399.3% CPU
Optimizing NNI: done in 0.716389 secs using 399.2% CPU
Optimizing NNI: done in 0.458851 secs using 397.7% CPU
Optimizing NNI: done in 0.326171 secs using 399.8% CPU
Optimizing NNI: done in 0.363881 secs using 399% CPU
Optimizing NNI: done in 0.579192 secs using 398.8% CPU
Optimizing NNI: done in 0.411885 secs using 399.4% CPU
Optimizing NNI: done in 0.456317 secs using 398.4% CPU
Optimizing NNI: done in 0.518026 secs using 399.5% CPU
Iteration 120 / LogL: -35293.564 / Time: 0h:0m:52s (0h:0m:31s left)
Optimizing NNI: done in 0.2819 secs using 399.2% CPU
Optimizing NNI: done in 0.329224 secs using 399.3% CPU
Optimizing NNI: done in 0.387251 secs using 398.5% CPU
Optimizing NNI: done in 0.28517 secs using 399.2% CPU
Optimizing NNI: done in 0.277632 secs using 399.9% CPU
Optimizing NNI: done in 0.317793 secs using 399.5% CPU
Optimizing NNI: done in 0.555942 secs using 399.6% CPU
Optimizing NNI: done in 0.412841 secs using 399.7% CPU
Optimizing NNI: done in 0.391982 secs using 399.4% CPU
Optimizing NNI: done in 0.377205 secs using 399.9% CPU
Iteration 130 / LogL: -35290.178 / Time: 0h:0m:56s (0h:0m:26s left)
Optimizing NNI: done in 0.489321 secs using 398.1% CPU
Optimizing NNI: done in 0.355346 secs using 399.4% CPU
Optimizing NNI: done in 0.299275 secs using 399.4% CPU
Optimizing NNI: done in 0.276477 secs using 399.8% CPU
Optimizing NNI: done in 0.479331 secs using 399.6% CPU
Optimizing NNI: done in 0.544521 secs using 399.9% CPU
Optimizing NNI: done in 0.341142 secs using 398.9% CPU
Optimizing NNI: done in 0.697576 secs using 399.3% CPU
Optimizing NNI: done in 0.417556 secs using 399.1% CPU
Optimizing NNI: done in 0.564674 secs using 399.8% CPU
Iteration 140 / LogL: -35291.687 / Time: 0h:1m:1s (0h:0m:21s left)
Optimizing NNI: done in 0.349093 secs using 399.3% CPU
Optimizing NNI: done in 0.496715 secs using 399.1% CPU
Optimizing NNI: done in 0.33467 secs using 399.8% CPU
Optimizing NNI: done in 0.321875 secs using 399.9% CPU
Optimizing NNI: done in 0.329593 secs using 398.3% CPU
Optimizing NNI: done in 0.295068 secs using 399.6% CPU
Optimizing NNI: done in 0.360049 secs using 399.7% CPU
Optimizing NNI: done in 0.380366 secs using 399.6% CPU
Optimizing NNI: done in 0.401359 secs using 399.1% CPU
Optimizing NNI: done in 0.41198 secs using 399.7% CPU
Iteration 150 / LogL: -35291.651 / Time: 0h:1m:4s (0h:0m:17s left)
Optimizing NNI: done in 0.235527 secs using 399.3% CPU
Optimizing NNI: done in 0.311037 secs using 399.4% CPU
Optimizing NNI: done in 0.407582 secs using 399.3% CPU
Optimizing NNI: done in 0.32387 secs using 399.3% CPU
198  Q.bird+I+R10  105976.901   554 213061.802   828001.802   215292.132
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.469643 secs using 399.9% CPU
Optimizing NNI: done in 0.341659 secs using 399.3% CPU
Optimizing NNI: done in 0.318384 secs using 399% CPU
Optimizing NNI: done in 0.329798 secs using 399.9% CPU
Optimizing NNI: done in 0.403959 secs using 399.9% CPU
Optimizing NNI: done in 0.3665 secs using 399.6% CPU
Iteration 160 / LogL: -35291.709 / Time: 0h:1m:8s (0h:0m:12s left)
Optimizing NNI: done in 0.365145 secs using 398.8% CPU
Optimizing NNI: done in 0.636961 secs using 399.1% CPU
Optimizing NNI: done in 0.418935 secs using 399.5% CPU
Optimizing NNI: done in 0.370476 secs using 399.9% CPU
Optimizing NNI: done in 0.256898 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35290.118
307  Blosum62+F+R9 196899.776   1022 395843.552   2486855.552  400293.718
Optimizing NNI: done in 0.276043 secs using 399.6% CPU
Optimizing NNI: done in 0.49459 secs using 398.6% CPU
855  mtVer+I+R7    62781.330    316 126194.660   127339.483   127521.379
Optimizing NNI: done in 0.275138 secs using 399.7% CPU
Optimizing NNI: done in 0.346025 secs using 399.1% CPU
Optimizing NNI: done in 0.457899 secs using 399.7% CPU
Iteration 170 / LogL: -35307.434 / Time: 0h:1m:12s (0h:0m:8s left)
Optimizing NNI: done in 0.357331 secs using 399.8% CPU
Optimizing NNI: done in 0.329267 secs using 399.2% CPU
Optimizing NNI: done in 0.328506 secs using 400.4% CPU
Optimizing NNI: done in 0.32151 secs using 399.5% CPU
Optimizing NNI: done in 0.333379 secs using 399.7% CPU
Optimizing NNI: done in 0.354924 secs using 399% CPU
Optimizing NNI: done in 0.388724 secs using 399.7% CPU
Optimizing NNI: done in 0.389219 secs using 399.6% CPU
Optimizing NNI: done in 0.539013 secs using 399.6% CPU
Optimizing NNI: done in 0.432052 secs using 399.9% CPU
Iteration 180 / LogL: -35290.647 / Time: 0h:1m:16s (0h:0m:4s left)
Optimizing NNI: done in 0.293425 secs using 398.9% CPU
Optimizing NNI: done in 0.468026 secs using 399.4% CPU
Optimizing NNI: done in 0.379913 secs using 398.8% CPU
Optimizing NNI: done in 0.322604 secs using 399.6% CPU
Optimizing NNI: done in 0.307698 secs using 399.3% CPU
Optimizing NNI: done in 0.312378 secs using 399.7% CPU
Optimizing NNI: done in 0.36174 secs using 398.5% CPU
Optimizing NNI: done in 0.401104 secs using 398.9% CPU
Optimizing NNI: done in 0.420616 secs using 399.4% CPU
Optimizing NNI: done in 0.369989 secs using 398.7% CPU
Iteration 190 / LogL: -35291.040 / Time: 0h:1m:19s (0h:0m:0s left)
Optimizing NNI: done in 0.323353 secs using 399.8% CPU
TREE SEARCH COMPLETED AFTER 191 ITERATIONS / Time: 0h:1m:20s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35290.118
Optimal log-likelihood: -35290.112
Proportion of invariable sites: 0.046
Gamma shape alpha: 2.574
Parameters optimization took 1 rounds (0.049 sec)
BEST SCORE FOUND : -35290.112
Total tree length: 20.440

Total number of iterations: 191
CPU time used for tree search: 313.622 sec (0h:5m:13s)
Wall-clock time used for tree search: 79.511 sec (0h:1m:19s)
Total CPU time used: 316.408 sec (0h:5m:16s)
Total wall-clock time used: 80.161 sec (0h:1m:20s)

===> START BOOTSTRAP REPLICATE NUMBER 35

Creating bootstrap alignment (seed: 956194)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37745.656
2. Current log-likelihood: -36840.765
3. Current log-likelihood: -36824.674
4. Current log-likelihood: -36823.791
5. Current log-likelihood: -36823.346
6. Current log-likelihood: -36823.145
Optimal log-likelihood: -36822.998
Proportion of invariable sites: 0.029
Gamma shape alpha: 2.507
Parameters optimization took 6 rounds (0.355 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0774179 secs using 399.9% CPU
Computing ML distances took 0.077545 sec (of wall-clock time) 0.309913 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000150204 secs using 434.7% CPU
Constructing RapidNJ tree: done in 0.00214195 secs using 470.5% CPU
Computing RapidNJ tree took 0.002347 sec (of wall-clock time) 0.011823 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37233.267
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 867  mtVer+F+R6    61347.538    332 123359.076   124749.718   124752.971
1.484 second
Computing log-likelihood of 98 initial trees ... 1.509 seconds
Current best score: -36822.998

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.27794 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36778.801
Optimizing NNI: done in 0.274347 secs using 400.7% CPU
Optimizing NNI: done in 0.31482 secs using 399.9% CPU
Optimizing NNI: done in 0.306033 secs using 398.8% CPU
Optimizing NNI: done in 0.435611 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -36778.530
Optimizing NNI: done in 0.320036 secs using 399.7% CPU
Optimizing NNI: done in 0.341886 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -36777.915
Optimizing NNI: done in 0.299681 secs using 399.8% CPU
Optimizing NNI: done in 0.319017 secs using 399.2% CPU
Optimizing NNI: done in 0.335103 secs using 398.8% CPU
Iteration 10 / LogL: -36778.486 / Time: 0h:0m:6s
Optimizing NNI: done in 0.292565 secs using 399.8% CPU
Optimizing NNI: done in 0.333083 secs using 399.5% CPU
Optimizing NNI: done in 0.415422 secs using 399.6% CPU
Optimizing NNI: done in 0.255707 secs using 399.5% CPU
Optimizing NNI: done in 0.279326 secs using 399.8% CPU
Optimizing NNI: done in 0.30393 secs using 399.5% CPU
Optimizing NNI: done in 0.400205 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 17: -36777.743
Optimizing NNI: done in 0.324732 secs using 399.3% CPU
Optimizing NNI: done in 0.309705 secs using 399.9% CPU
Optimizing NNI: done in 0.405341 secs using 398.7% CPU
Iteration 20 / LogL: -36777.865 / Time: 0h:0m:10s
Finish initializing candidate tree set (10)
Current best tree score: -36777.743 / CPU time: 9.801
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.388981 secs using 399.9% CPU
Optimizing NNI: done in 0.373451 secs using 399.1% CPU
Optimizing NNI: done in 0.399576 secs using 399.6% CPU
Optimizing NNI: done in 0.371288 secs using 399.9% CPU
Optimizing NNI: done in 0.459721 secs using 399.2% CPU
Optimizing NNI: done in 0.526751 secs using 399.2% CPU
Optimizing NNI: done in 0.461856 secs using 398.4% CPU
Optimizing NNI: done in 0.331338 secs using 399.9% CPU
Optimizing NNI: done in 0.33121 secs using 399.9% CPU
Optimizing NNI: done in 0.398337 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36777.664
Iteration 30 / LogL: -36777.664 / Time: 0h:0m:14s (0h:0m:43s left)
Optimizing NNI: done in 0.51512 secs using 399.4% CPU
Optimizing NNI: done in 0.337229 secs using 399.9% CPU
Optimizing NNI: done in 0.346598 secs using 399.3% CPU
Optimizing NNI: done in 0.438123 secs using 399.2% CPU
Optimizing NNI: done in 0.403587 secs using 399.3% CPU
Optimizing NNI: done in 0.3194 secs using 399.9% CPU
Optimizing NNI: done in 0.378887 secs using 398.7% CPU
Optimizing NNI: done in 0.410561 secs using 400% CPU
Optimizing NNI: done in 0.48057 secs using 398.9% CPU
Optimizing NNI: done in 0.37125 secs using 399.3% CPU
Iteration 40 / LogL: -36778.776 / Time: 0h:0m:18s (0h:0m:36s left)
Optimizing NNI: done in 0.431326 secs using 399.8% CPU
Optimizing NNI: done in 0.404733 secs using 399.4% CPU
Optimizing NNI: done in 0.44038 secs using 399.6% CPU
Optimizing NNI: done in 0.410216 secs using 399.6% CPU
Optimizing NNI: done in 0.355065 secs using 399% CPU
Optimizing NNI: done in 0.307356 secs using 398.9% CPU
Optimizing NNI: done in 0.341229 secs using 398.7% CPU
Optimizing NNI: done in 0.261863 secs using 399.4% CPU
Optimizing NNI: done in 0.4894 secs using 398.9% CPU
Optimizing NNI: done in 0.435382 secs using 398.8% CPU
Iteration 50 / LogL: -36777.810 / Time: 0h:0m:22s (0h:0m:30s left)
Optimizing NNI: done in 0.499576 secs using 398.7% CPU
Optimizing NNI: done in 0.342917 secs using 399.6% CPU
Optimizing NNI: done in 0.39905 secs using 398.1% CPU
Optimizing NNI: done in 0.410248 secs using 399.8% CPU
Optimizing NNI: done in 0.384261 secs using 399.9% CPU
Optimizing NNI: done in 0.310341 secs using 399.9% CPU
Optimizing NNI: done in 0.306752 secs using 399.5% CPU
868  mtVer+F+R7    61329.959    334 123327.919   124753.269   124730.211
Optimizing NNI: done in 0.39965 secs using 399.8% CPU
Optimizing NNI: done in 0.403746 secs using 399.9% CPU
Optimizing NNI: done in 0.295997 secs using 399.5% CPU
Iteration 60 / LogL: -36778.195 / Time: 0h:0m:26s (0h:0m:25s left)
Optimizing NNI: done in 0.676602 secs using 399.3% CPU
Optimizing NNI: done in 0.517173 secs using 399.7% CPU
Optimizing NNI: done in 0.426429 secs using 399.7% CPU
Optimizing NNI: done in 0.260182 secs using 399.9% CPU
Optimizing NNI: done in 0.440031 secs using 399.9% CPU
Optimizing NNI: done in 0.37643 secs using 399.5% CPU
Optimizing NNI: done in 0.456293 secs using 399.9% CPU
Optimizing NNI: done in 0.482681 secs using 398.7% CPU
Optimizing NNI: done in 0.421048 secs using 398.8% CPU
Optimizing NNI: done in 0.433015 secs using 399.3% CPU
Iteration 70 / LogL: -36778.456 / Time: 0h:0m:30s (0h:0m:20s left)
Optimizing NNI: done in 0.440004 secs using 399.6% CPU
Optimizing NNI: done in 0.375784 secs using 399.8% CPU
Optimizing NNI: done in 0.459523 secs using 399.7% CPU
Optimizing NNI: done in 0.42113 secs using 399.2% CPU
Optimizing NNI: done in 0.264407 secs using 399.8% CPU
Optimizing NNI: done in 0.232416 secs using 398.8% CPU
Optimizing NNI: done in 0.482113 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36777.643
Optimizing NNI: done in 0.369434 secs using 398.9% CPU
Optimizing NNI: done in 0.421672 secs using 398.5% CPU
Optimizing NNI: done in 0.300002 secs using 399% CPU
Iteration 80 / LogL: -36778.802 / Time: 0h:0m:34s (0h:0m:16s left)
Optimizing NNI: done in 0.357269 secs using 399.8% CPU
Optimizing NNI: done in 0.340037 secs using 398.6% CPU
Optimizing NNI: done in 0.289816 secs using 399.9% CPU
Optimizing NNI: done in 0.491205 secs using 399.4% CPU
Optimizing NNI: done in 0.466436 secs using 399.9% CPU
Optimizing NNI: done in 0.351994 secs using 399.5% CPU
Optimizing NNI: done in 0.428952 secs using 399.1% CPU
Optimizing NNI: done in 0.360948 secs using 400.4% CPU
Optimizing NNI: done in 0.381822 secs using 399.9% CPU
Optimizing NNI: done in 0.415683 secs using 399.7% CPU
Iteration 90 / LogL: -36779.073 / Time: 0h:0m:38s (0h:0m:11s left)
Optimizing NNI: done in 0.304582 secs using 399.8% CPU
Optimizing NNI: done in 0.386806 secs using 399.9% CPU
Optimizing NNI: done in 0.299327 secs using 399.1% CPU
Optimizing NNI: done in 0.523614 secs using 399.5% CPU
Optimizing NNI: done in 0.449128 secs using 399.9% CPU
Optimizing NNI: done in 0.404636 secs using 398.5% CPU
Optimizing NNI: done in 0.356821 secs using 399.7% CPU
Optimizing NNI: done in 0.38189 secs using 399.8% CPU
Optimizing NNI: done in 0.402089 secs using 399.4% CPU
Optimizing NNI: done in 0.439074 secs using 399.7% CPU
Iteration 100 / LogL: -36777.732 / Time: 0h:0m:42s (0h:0m:7s left)
Optimizing NNI: done in 0.463222 secs using 399.4% CPU
Optimizing NNI: done in 0.542618 secs using 399.7% CPU
Optimizing NNI: done in 0.377003 secs using 398.8% CPU
Optimizing NNI: done in 0.383437 secs using 400.4% CPU
317  Dayhoff+R8    198852.273   1001 399706.545   2405710.545  404065.270
Optimizing NNI: done in 0.314414 secs using 399.3% CPU
Optimizing NNI: done in 0.319216 secs using 399.9% CPU
Optimizing NNI: done in 0.29609 secs using 399.2% CPU
Optimizing NNI: done in 0.440304 secs using 398.9% CPU
Optimizing NNI: done in 0.474428 secs using 399.7% CPU
Optimizing NNI: done in 0.451501 secs using 400.2% CPU
Iteration 110 / LogL: -36923.689 / Time: 0h:0m:46s (0h:0m:2s left)
Optimizing NNI: done in 0.329961 secs using 398.6% CPU
Optimizing NNI: done in 0.371963 secs using 399.8% CPU
Optimizing NNI: done in 0.351643 secs using 399.9% CPU
Optimizing NNI: done in 0.381665 secs using 398.8% CPU
Optimizing NNI: done in 0.409123 secs using 398.6% CPU
Optimizing NNI: done in 0.295879 secs using 399.6% CPU
219  Q.bird+F+I+R9 106707.128   571 214556.255   867780.255   216855.025
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.419089 secs using 399.7% CPU
Optimizing NNI: done in 0.410601 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 118 ITERATIONS / Time: 0h:0m:49s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36777.643
Optimal log-likelihood: -36777.641
Proportion of invariable sites: 0.029
Gamma shape alpha: 2.498
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -36777.641
Total tree length: 20.318

Total number of iterations: 118
CPU time used for tree search: 192.123 sec (0h:3m:12s)
Wall-clock time used for tree search: 49.046 sec (0h:0m:49s)
Total CPU time used: 194.618 sec (0h:3m:14s)
Total wall-clock time used: 49.647 sec (0h:0m:49s)

===> START BOOTSTRAP REPLICATE NUMBER 36

Creating bootstrap alignment (seed: 956195)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37178.132
2. Current log-likelihood: -36296.057
3. Current log-likelihood: -36278.117
4. Current log-likelihood: -36277.233
5. Current log-likelihood: -36277.048
Optimal log-likelihood: -36276.963
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.599
Parameters optimization took 5 rounds (0.306 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.074888 secs using 399.8% CPU
Computing ML distances took 0.075010 sec (of wall-clock time) 0.299755 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000153065 secs using 433.2% CPU
Constructing RapidNJ tree: done in 0.00219202 secs using 484.9% CPU
Computing RapidNJ tree took 0.002475 sec (of wall-clock time) 0.012506 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36614.017
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.445 second
869  mtVer+F+R8    61323.177    336 123318.354   124779.412   124729.043
Computing log-likelihood of 98 initial trees ... 1.528 seconds
Current best score: -36234.926

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.264619 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36174.575
Optimizing NNI: done in 0.292304 secs using 399.6% CPU
Optimizing NNI: done in 0.215266 secs using 398.6% CPU
Optimizing NNI: done in 0.272905 secs using 399.6% CPU
Optimizing NNI: done in 0.258246 secs using 399.9% CPU
Optimizing NNI: done in 0.262335 secs using 399.5% CPU
Optimizing NNI: done in 0.246937 secs using 398.6% CPU
Optimizing NNI: done in 0.27788 secs using 400.5% CPU
Optimizing NNI: done in 0.275869 secs using 399.2% CPU
Optimizing NNI: done in 0.289163 secs using 399.2% CPU
Iteration 10 / LogL: -36174.583 / Time: 0h:0m:6s
Optimizing NNI: done in 0.288426 secs using 399.2% CPU
Optimizing NNI: done in 0.288382 secs using 398.5% CPU
Optimizing NNI: done in 0.25956 secs using 399.9% CPU
Optimizing NNI: done in 0.299562 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 14: -36168.512
Optimizing NNI: done in 0.388765 secs using 399.6% CPU
Optimizing NNI: done in 0.204681 secs using 399.4% CPU
Optimizing NNI: done in 0.307356 secs using 398.9% CPU
Optimizing NNI: done in 0.230551 secs using 400% CPU
Optimizing NNI: done in 0.205875 secs using 400% CPU
Optimizing NNI: done in 0.257673 secs using 399.1% CPU
Iteration 20 / LogL: -36174.597 / Time: 0h:0m:9s
Finish initializing candidate tree set (7)
Current best tree score: -36168.512 / CPU time: 8.509
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.425932 secs using 399.9% CPU
Optimizing NNI: done in 0.433128 secs using 399.2% CPU
Optimizing NNI: done in 0.398851 secs using 399.4% CPU
Optimizing NNI: done in 0.342154 secs using 398.7% CPU
Optimizing NNI: done in 0.336668 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -36167.633
Optimizing NNI: done in 0.416019 secs using 398.8% CPU
Optimizing NNI: done in 0.440378 secs using 399.5% CPU
Optimizing NNI: done in 0.454235 secs using 399.5% CPU
Optimizing NNI: done in 0.48251 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -36165.196
Optimizing NNI: done in 0.277222 secs using 399.1% CPU
Iteration 30 / LogL: -36165.201 / Time: 0h:0m:13s (0h:0m:45s left)
Optimizing NNI: done in 0.341313 secs using 399.6% CPU
Optimizing NNI: done in 0.417079 secs using 399.7% CPU
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Optimizing NNI: done in 0.318543 secs using 399.6% CPU
Optimizing NNI: done in 0.364776 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36164.197
Optimizing NNI: done in 0.36412 secs using 399.6% CPU
Iteration 40 / LogL: -36165.184 / Time: 0h:0m:17s (0h:0m:38s left)
Optimizing NNI: done in 0.186576 secs using 399.9% CPU
Optimizing NNI: done in 0.249368 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36164.071
Optimizing NNI: done in 0.370604 secs using 399.6% CPU
Optimizing NNI: done in 0.301883 secs using 399.3% CPU
Optimizing NNI: done in 0.280664 secs using 399.9% CPU
Optimizing NNI: done in 0.42387 secs using 399.4% CPU
Optimizing NNI: done in 0.299776 secs using 399.6% CPU
Optimizing NNI: done in 0.305745 secs using 398.9% CPU
Optimizing NNI: done in 0.277232 secs using 399.5% CPU
Optimizing NNI: done in 0.357112 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36163.917
Iteration 50 / LogL: -36163.917 / Time: 0h:0m:20s (0h:0m:32s left)
Optimizing NNI: done in 0.316912 secs using 399.5% CPU
Optimizing NNI: done in 0.390638 secs using 399.2% CPU
Optimizing NNI: done in 0.339422 secs using 400.2% CPU
318  Dayhoff+R9    198844.881   1003 399695.761   2413719.761  404063.195
Optimizing NNI: done in 0.410939 secs using 399.9% CPU
Optimizing NNI: done in 0.324136 secs using 399.9% CPU
Optimizing NNI: done in 0.435083 secs using 399.5% CPU
Optimizing NNI: done in 0.358239 secs using 400% CPU
Optimizing NNI: done in 0.383832 secs using 399.4% CPU
Optimizing NNI: done in 0.335341 secs using 399.8% CPU
Optimizing NNI: done in 0.311454 secs using 399.6% CPU
Iteration 60 / LogL: -36164.923 / Time: 0h:0m:23s (0h:0m:27s left)
Optimizing NNI: done in 0.369028 secs using 399.1% CPU
Optimizing NNI: done in 0.249973 secs using 399.5% CPU
Optimizing NNI: done in 0.235883 secs using 399.5% CPU
Optimizing NNI: done in 0.275233 secs using 400% CPU
Optimizing NNI: done in 0.284408 secs using 398.1% CPU
Optimizing NNI: done in 0.384949 secs using 399.9% CPU
Optimizing NNI: done in 0.359156 secs using 400% CPU
Optimizing NNI: done in 0.322073 secs using 399.3% CPU
Optimizing NNI: done in 0.316464 secs using 399.9% CPU
Optimizing NNI: done in 0.326846 secs using 399.9% CPU
Iteration 70 / LogL: -36256.949 / Time: 0h:0m:27s (0h:0m:23s left)
Optimizing NNI: done in 0.350997 secs using 399.9% CPU
Optimizing NNI: done in 0.331618 secs using 398.8% CPU
Optimizing NNI: done in 0.389267 secs using 400.3% CPU
Optimizing NNI: done in 0.334767 secs using 399.6% CPU
Optimizing NNI: done in 0.293265 secs using 399.8% CPU
Optimizing NNI: done in 0.351682 secs using 399.4% CPU
Optimizing NNI: done in 0.311613 secs using 399% CPU
Optimizing NNI: done in 0.266525 secs using 399.4% CPU
Optimizing NNI: done in 0.350232 secs using 399.8% CPU
Optimizing NNI: done in 0.349502 secs using 399.6% CPU
Iteration 80 / LogL: -36164.039 / Time: 0h:0m:30s (0h:0m:18s left)
Optimizing NNI: done in 0.389334 secs using 399.6% CPU
Optimizing NNI: done in 0.373724 secs using 398.9% CPU
Optimizing NNI: done in 0.311726 secs using 399.3% CPU
Optimizing NNI: done in 0.329133 secs using 399.2% CPU
Optimizing NNI: done in 0.345469 secs using 399% CPU
Optimizing NNI: done in 0.302352 secs using 398.8% CPU
Optimizing NNI: done in 0.332353 secs using 398.7% CPU
Optimizing NNI: done in 0.32113 secs using 399.6% CPU
Optimizing NNI: done in 0.283433 secs using 399.5% CPU
Optimizing NNI: done in 0.390606 secs using 399.4% CPU
Iteration 90 / LogL: -36164.703 / Time: 0h:0m:33s (0h:0m:14s left)
Optimizing NNI: done in 0.238208 secs using 399.9% CPU
Optimizing NNI: done in 0.273858 secs using 398.4% CPU
Optimizing NNI: done in 0.307898 secs using 400.7% CPU
870  mtVer+F+R9    61321.918    338 123319.836   124817.640   124738.922
Optimizing NNI: done in 0.290618 secs using 399.7% CPU
Optimizing NNI: done in 0.287322 secs using 399.9% CPU
Optimizing NNI: done in 0.3615 secs using 399.3% CPU
Optimizing NNI: done in 0.37916 secs using 399.9% CPU
Optimizing NNI: done in 0.362275 secs using 398.8% CPU
Optimizing NNI: done in 0.287319 secs using 399.2% CPU
Optimizing NNI: done in 0.352621 secs using 400.2% CPU
Iteration 100 / LogL: -36165.841 / Time: 0h:0m:37s (0h:0m:10s left)
Optimizing NNI: done in 0.290233 secs using 399.7% CPU
Optimizing NNI: done in 0.427368 secs using 399.6% CPU
Optimizing NNI: done in 0.469779 secs using 399.2% CPU
Optimizing NNI: done in 0.451452 secs using 399.1% CPU
Optimizing NNI: done in 0.304277 secs using 399.3% CPU
Optimizing NNI: done in 0.432975 secs using 399.6% CPU
Optimizing NNI: done in 0.296703 secs using 398% CPU
Optimizing NNI: done in 0.345827 secs using 399.6% CPU
Optimizing NNI: done in 0.317775 secs using 399.9% CPU
Optimizing NNI: done in 0.475055 secs using 399% CPU
Iteration 110 / LogL: -36169.051 / Time: 0h:0m:40s (0h:0m:7s left)
Optimizing NNI: done in 0.419842 secs using 399.6% CPU
Optimizing NNI: done in 0.271631 secs using 399.9% CPU
Optimizing NNI: done in 0.407437 secs using 399.6% CPU
Optimizing NNI: done in 0.437386 secs using 399.5% CPU
Optimizing NNI: done in 0.326934 secs using 399.3% CPU
Optimizing NNI: done in 0.451255 secs using 399% CPU
Optimizing NNI: done in 0.296519 secs using 400% CPU
319  Dayhoff+R10   198842.886   1005 399695.772   2421755.772  404071.914
Optimizing NNI: done in 0.27691 secs using 398.7% CPU
Optimizing NNI: done in 0.249872 secs using 399.4% CPU
Optimizing NNI: done in 0.314355 secs using 399.3% CPU
Iteration 120 / LogL: -36165.994 / Time: 0h:0m:44s (0h:0m:3s left)
Optimizing NNI: done in 0.354752 secs using 399.4% CPU
Optimizing NNI: done in 0.39448 secs using 398.9% CPU
Optimizing NNI: done in 0.302984 secs using 398.5% CPU
Optimizing NNI: done in 0.288367 secs using 399.2% CPU
Optimizing NNI: done in 0.450266 secs using 399.4% CPU
Optimizing NNI: done in 0.421237 secs using 399.9% CPU
Optimizing NNI: done in 0.260139 secs using 398.7% CPU
Optimizing NNI: done in 0.371502 secs using 399.6% CPU
Optimizing NNI: done in 0.309011 secs using 399.9% CPU
Optimizing NNI: done in 0.382235 secs using 399.6% CPU
Iteration 130 / LogL: -36264.132 / Time: 0h:0m:47s (0h:0m:-1s left)
TREE SEARCH COMPLETED AFTER 130 ITERATIONS / Time: 0h:0m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36163.917
Optimal log-likelihood: -36163.916
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.655
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -36163.916
Total tree length: 19.267

Total number of iterations: 130
CPU time used for tree search: 185.239 sec (0h:3m:5s)
Wall-clock time used for tree search: 47.322 sec (0h:0m:47s)
Total CPU time used: 188.002 sec (0h:3m:8s)
Total wall-clock time used: 47.968 sec (0h:0m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 37

Creating bootstrap alignment (seed: 956196)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36827.903
876  mtVer+F+I+R6  61343.147    333 123352.293   124760.166   124750.386
2. Current log-likelihood: -35886.802
3. Current log-likelihood: -35873.286
4. Current log-likelihood: -35873.178
Optimal log-likelihood: -35873.146
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.499
Parameters optimization took 4 rounds (0.209 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0743809 secs using 398.6% CPU
Computing ML distances took 0.074528 sec (of wall-clock time) 0.296851 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000154972 secs using 431% CPU
Constructing RapidNJ tree: done in 0.00229621 secs using 468.6% CPU
Computing RapidNJ tree took 0.002509 sec (of wall-clock time) 0.012626 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36720.758
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.510 second
Computing log-likelihood of 98 initial trees ... 1.569 seconds
Current best score: -35873.146

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.17717 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35834.561
Optimizing NNI: done in 0.261491 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35821.015
Optimizing NNI: done in 0.267474 secs using 399.5% CPU
Optimizing NNI: done in 0.235931 secs using 399.9% CPU
Optimizing NNI: done in 0.239259 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -35816.055
Optimizing NNI: done in 0.235628 secs using 398.5% CPU
Optimizing NNI: done in 0.243612 secs using 399.9% CPU
Optimizing NNI: done in 0.238435 secs using 399.1% CPU
Optimizing NNI: done in 0.248191 secs using 399.1% CPU
Optimizing NNI: done in 0.2482 secs using 399.5% CPU
Iteration 10 / LogL: -35821.043 / Time: 0h:0m:6s
Optimizing NNI: done in 0.266562 secs using 398.9% CPU
Optimizing NNI: done in 0.246186 secs using 399.7% CPU
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Optimizing NNI: done in 0.230449 secs using 399% CPU
Iteration 20 / LogL: -35822.282 / Time: 0h:0m:8s
Finish initializing candidate tree set (7)
Current best tree score: -35816.055 / CPU time: 8.169
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.309113 secs using 400.3% CPU
Optimizing NNI: done in 0.413602 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -35815.468
Optimizing NNI: done in 0.424763 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -35806.416
Optimizing NNI: done in 0.418021 secs using 398.6% CPU
Optimizing NNI: done in 0.425752 secs using 399.4% CPU
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Optimizing NNI: done in 0.348899 secs using 399.6% CPU
Iteration 30 / LogL: -35808.551 / Time: 0h:0m:12s (0h:0m:40s left)
Optimizing NNI: done in 0.32657 secs using 399.9% CPU
Optimizing NNI: done in 0.307012 secs using 399.9% CPU
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Optimizing NNI: done in 0.480618 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -35804.467
Optimizing NNI: done in 0.213363 secs using 398.4% CPU
Optimizing NNI: done in 0.334966 secs using 399.9% CPU
Optimizing NNI: done in 0.493388 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35804.453
Optimizing NNI: done in 0.443697 secs using 399.8% CPU
Optimizing NNI: done in 0.382661 secs using 399.7% CPU
Iteration 40 / LogL: -35805.093 / Time: 0h:0m:16s (0h:0m:39s left)
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Iteration 50 / LogL: -35805.291 / Time: 0h:0m:20s (0h:0m:35s left)
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Optimizing NNI: done in 0.324108 secs using 399.9% CPU
Optimizing NNI: done in 0.391951 secs using 398.9% CPU
328  Dayhoff+F+R8  196817.472   1020 395674.945   2478514.945  400116.402
Optimizing NNI: done in 0.349625 secs using 399% CPU
Optimizing NNI: done in 0.334074 secs using 399.3% CPU
877  mtVer+F+I+R7  61326.325    335 123322.650   124765.727   124729.140
Optimizing NNI: done in 0.461841 secs using 399.4% CPU
Optimizing NNI: done in 0.24791 secs using 399% CPU
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Iteration 60 / LogL: -35805.621 / Time: 0h:0m:24s (0h:0m:30s left)
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Optimizing NNI: done in 0.470646 secs using 399.3% CPU
Optimizing NNI: done in 0.487121 secs using 399.7% CPU
889  mtInv+R6      62323.205    313 125272.410   126376.702   126586.534
Optimizing NNI: done in 0.493061 secs using 398.9% CPU
Optimizing NNI: done in 0.461001 secs using 399.9% CPU
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Optimizing NNI: done in 0.419122 secs using 399.4% CPU
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Optimizing NNI: done in 0.344528 secs using 399% CPU
Optimizing NNI: done in 0.397263 secs using 399.6% CPU
Iteration 70 / LogL: -36060.039 / Time: 0h:0m:28s (0h:0m:26s left)
Optimizing NNI: done in 0.371013 secs using 399.9% CPU
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Optimizing NNI: done in 0.363304 secs using 399.3% CPU
Iteration 80 / LogL: -35806.314 / Time: 0h:0m:32s (0h:0m:22s left)
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Optimizing NNI: done in 0.482518 secs using 400.1% CPU
329  Dayhoff+F+R9  196807.436   1022 395658.873   2486670.873  400109.039
Optimizing NNI: done in 0.410337 secs using 399.2% CPU
Optimizing NNI: done in 0.286445 secs using 399.6% CPU
Iteration 90 / LogL: -35805.681 / Time: 0h:0m:36s (0h:0m:18s left)
Optimizing NNI: done in 0.394895 secs using 399.4% CPU
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Iteration 100 / LogL: -35807.902 / Time: 0h:0m:40s (0h:0m:14s left)
Optimizing NNI: done in 0.532064 secs using 399.2% CPU
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890  mtInv+R7      62309.931    315 125249.862   126380.998   126572.383
Optimizing NNI: done in 0.389818 secs using 399.9% CPU
Optimizing NNI: done in 0.467368 secs using 399.6% CPU
Optimizing NNI: done in 0.419796 secs using 399.9% CPU
Iteration 110 / LogL: -35805.167 / Time: 0h:0m:45s (0h:0m:10s left)
Optimizing NNI: done in 0.381102 secs using 399.7% CPU
220  Q.bird+F+I+R10 106704.495   573 214554.990   872358.990   216861.811
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.448211 secs using 399.8% CPU
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Optimizing NNI: done in 0.3139 secs using 399% CPU
Iteration 120 / LogL: -35804.463 / Time: 0h:0m:49s (0h:0m:6s left)
Optimizing NNI: done in 0.347469 secs using 399.6% CPU
Optimizing NNI: done in 0.413116 secs using 399.6% CPU
Optimizing NNI: done in 0.443919 secs using 399.3% CPU
891  mtInv+R8      62308.746    317 125251.492   126410.182   126582.410
Optimizing NNI: done in 0.461776 secs using 399.7% CPU
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Iteration 130 / LogL: -35806.212 / Time: 0h:0m:53s (0h:0m:2s left)
Optimizing NNI: done in 0.469601 secs using 399.1% CPU
Optimizing NNI: done in 0.417386 secs using 399.9% CPU
Optimizing NNI: done in 0.498684 secs using 399.5% CPU
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Optimizing NNI: done in 0.406958 secs using 399.9% CPU
Optimizing NNI: done in 0.530136 secs using 399.9% CPU
TREE SEARCH COMPLETED AFTER 136 ITERATIONS / Time: 0h:0m:56s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35804.453
Optimal log-likelihood: -35804.453
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.562
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -35804.453
Total tree length: 20.169

Total number of iterations: 136
CPU time used for tree search: 221.120 sec (0h:3m:41s)
Wall-clock time used for tree search: 56.329 sec (0h:0m:56s)
Total CPU time used: 223.093 sec (0h:3m:43s)
Total wall-clock time used: 56.797 sec (0h:0m:56s)

===> START BOOTSTRAP REPLICATE NUMBER 38

Creating bootstrap alignment (seed: 956197)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36496.887
2. Current log-likelihood: -35642.561
3. Current log-likelihood: -35628.964
4. Current log-likelihood: -35628.602
Optimal log-likelihood: -35628.496
Proportion of invariable sites: 0.034
Gamma shape alpha: 2.120
Parameters optimization took 4 rounds (0.250 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.076324 secs using 398.7% CPU
Computing ML distances took 0.076459 sec (of wall-clock time) 0.304599 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00016284 secs using 351.3% CPU
Constructing RapidNJ tree: done in 0.00208902 secs using 370% CPU
Computing RapidNJ tree took 0.002308 sec (of wall-clock time) 0.008692 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36029.244
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.453 second
Computing log-likelihood of 98 initial trees ... 1.510 seconds
Current best score: -35534.479

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.253895 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35463.260
Optimizing NNI: done in 0.277217 secs using 399.9% CPU
Optimizing NNI: done in 0.26546 secs using 399.5% CPU
241  Q.mammal+I+R9 105497.779   552 212099.558   822611.558   214321.836
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.242782 secs using 399.9% CPU
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898  mtInv+I+R6    62323.080    314 125274.161   126391.788   126592.483
Optimizing NNI: done in 0.308629 secs using 399.9% CPU
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Iteration 10 / LogL: -35463.405 / Time: 0h:0m:6s
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330  Dayhoff+F+R10 196804.461   1024 395656.923   2494856.923  400115.798
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Iteration 20 / LogL: -35465.998 / Time: 0h:0m:9s
Finish initializing candidate tree set (9)
Current best tree score: -35463.260 / CPU time: 8.925
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 30 / LogL: -35475.773 / Time: 0h:0m:14s (0h:0m:34s left)
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Optimizing NNI: done in 0.372834 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -35462.187
Optimizing NNI: done in 0.404531 secs using 399.6% CPU
Optimizing NNI: done in 0.341117 secs using 399.9% CPU
Iteration 40 / LogL: -35463.956 / Time: 0h:0m:17s (0h:0m:44s left)
Optimizing NNI: done in 0.546447 secs using 399.9% CPU
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Optimizing NNI: done in 0.338013 secs using 398.1% CPU
Optimizing NNI: done in 0.358236 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35462.057
Optimizing NNI: done in 0.401033 secs using 399.3% CPU
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Iteration 50 / LogL: -35462.865 / Time: 0h:0m:21s (0h:0m:38s left)
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899  mtInv+I+R7    62310.234    316 125252.469   126397.292   126579.188
Optimizing NNI: done in 0.396015 secs using 399.6% CPU
Optimizing NNI: done in 0.287401 secs using 399.6% CPU
339  mtREV+R8      202211.702   1001 406425.405   2412429.405  410784.129
Optimizing NNI: done in 0.509293 secs using 399.5% CPU
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Iteration 60 / LogL: -35462.685 / Time: 0h:0m:25s (0h:0m:33s left)
Optimizing NNI: done in 0.533118 secs using 399.2% CPU
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Iteration 70 / LogL: -35470.473 / Time: 0h:0m:29s (0h:0m:29s left)
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911  mtInv+F+R6    60145.705    332 120955.411   122346.052   122349.306
Optimizing NNI: done in 0.559727 secs using 399.5% CPU
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Iteration 80 / LogL: -35463.253 / Time: 0h:0m:34s (0h:0m:25s left)
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Iteration 90 / LogL: -35462.694 / Time: 0h:0m:38s (0h:0m:20s left)
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Iteration 100 / LogL: -35463.507 / Time: 0h:0m:42s (0h:0m:16s left)
Optimizing NNI: done in 0.342852 secs using 398.8% CPU
912  mtInv+F+R7    60130.008    334 120928.016   122353.366   122330.308
Optimizing NNI: done in 0.339496 secs using 399.8% CPU
Optimizing NNI: done in 0.371882 secs using 399.1% CPU
Optimizing NNI: done in 0.317772 secs using 399.9% CPU
Optimizing NNI: done in 0.443085 secs using 399.8% CPU
Optimizing NNI: done in 0.435868 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35462.042
Optimizing NNI: done in 0.238128 secs using 399.2% CPU
Optimizing NNI: done in 0.387457 secs using 399.7% CPU
Optimizing NNI: done in 0.735426 secs using 399.5% CPU
Optimizing NNI: done in 0.341448 secs using 399.3% CPU
Iteration 110 / LogL: -35468.914 / Time: 0h:0m:46s (0h:0m:11s left)
Optimizing NNI: done in 0.318471 secs using 399.3% CPU
Optimizing NNI: done in 0.323242 secs using 398.3% CPU
Optimizing NNI: done in 0.556217 secs using 400% CPU
Optimizing NNI: done in 0.350342 secs using 399.4% CPU
Optimizing NNI: done in 0.284497 secs using 399.2% CPU
Optimizing NNI: done in 0.3652 secs using 399.7% CPU
Optimizing NNI: done in 0.297728 secs using 398.9% CPU
Optimizing NNI: done in 0.465859 secs using 399% CPU
Optimizing NNI: done in 0.354659 secs using 400.5% CPU
Optimizing NNI: done in 0.380363 secs using 398.6% CPU
Iteration 120 / LogL: -35465.280 / Time: 0h:0m:50s (0h:0m:7s left)
Optimizing NNI: done in 0.253956 secs using 399.5% CPU
Optimizing NNI: done in 0.62955 secs using 399.2% CPU
Optimizing NNI: done in 0.555717 secs using 399.6% CPU
340  mtREV+R9      202203.018   1003 406412.035   2420436.035  410779.468
Optimizing NNI: done in 0.305438 secs using 400.1% CPU
913  mtInv+F+R8    60128.022    336 120928.044   122389.102   122338.733
Optimizing NNI: done in 0.343628 secs using 399.6% CPU
Optimizing NNI: done in 0.448848 secs using 399.9% CPU
Optimizing NNI: done in 0.368461 secs using 399.4% CPU
Optimizing NNI: done in 0.482968 secs using 399.5% CPU
Optimizing NNI: done in 0.312728 secs using 399% CPU
Optimizing NNI: done in 0.373259 secs using 399.7% CPU
Iteration 130 / LogL: -35462.204 / Time: 0h:0m:54s (0h:0m:3s left)
Optimizing NNI: done in 0.336981 secs using 399.9% CPU
Optimizing NNI: done in 0.351409 secs using 399.3% CPU
Optimizing NNI: done in 0.362144 secs using 399.4% CPU
Optimizing NNI: done in 0.320365 secs using 399.6% CPU
Optimizing NNI: done in 0.211468 secs using 399.9% CPU
Optimizing NNI: done in 0.221652 secs using 399.7% CPU
Optimizing NNI: done in 0.3635 secs using 399.7% CPU
Optimizing NNI: done in 0.411014 secs using 399.9% CPU
Optimizing NNI: done in 0.297692 secs using 399.8% CPU
TREE SEARCH COMPLETED AFTER 139 ITERATIONS / Time: 0h:0m:57s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35462.042
Optimal log-likelihood: -35462.042
Proportion of invariable sites: 0.031
Gamma shape alpha: 2.110
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -35462.042
Total tree length: 20.345

Total number of iterations: 139
CPU time used for tree search: 222.401 sec (0h:3m:42s)
Wall-clock time used for tree search: 56.620 sec (0h:0m:56s)
Total CPU time used: 225.868 sec (0h:3m:45s)
Total wall-clock time used: 57.441 sec (0h:0m:57s)

===> START BOOTSTRAP REPLICATE NUMBER 39

Creating bootstrap alignment (seed: 956198)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.024 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37114.678
2. Current log-likelihood: -36225.111
3. Current log-likelihood: -36207.528
4. Current log-likelihood: -36206.064
5. Current log-likelihood: -36205.435
6. Current log-likelihood: -36205.207
Optimal log-likelihood: -36205.201
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.414
Parameters optimization took 6 rounds (0.374 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0754449 secs using 398.6% CPU
Computing ML distances took 0.075587 sec (of wall-clock time) 0.301138 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000145912 secs using 429.7% CPU
Constructing RapidNJ tree: done in 0.00220704 secs using 456.9% CPU
Computing RapidNJ tree took 0.002413 sec (of wall-clock time) 0.011215 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36496.280
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.536 second
Computing log-likelihood of 98 initial trees ... 1.581 seconds
Current best score: -36203.342

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.312675 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36158.086
Optimizing NNI: done in 0.308608 secs using 399.9% CPU
Optimizing NNI: done in 0.214821 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -36155.311
920  mtInv+F+I+R6  60143.730    333 120953.460   122361.333   122351.553
Optimizing NNI: done in 0.303588 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -36154.192
Optimizing NNI: done in 0.237269 secs using 399.8% CPU
Optimizing NNI: done in 0.217327 secs using 400.2% CPU
Optimizing NNI: done in 0.266118 secs using 399.9% CPU
Optimizing NNI: done in 0.297401 secs using 398.6% CPU
Optimizing NNI: done in 0.231116 secs using 399.9% CPU
Optimizing NNI: done in 0.212499 secs using 399.9% CPU
Iteration 10 / LogL: -36154.335 / Time: 0h:0m:6s
Optimizing NNI: done in 0.261114 secs using 399.1% CPU
Optimizing NNI: done in 0.273389 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 12: -36153.691
Optimizing NNI: done in 0.307383 secs using 399.9% CPU
Optimizing NNI: done in 0.237139 secs using 399.5% CPU
Optimizing NNI: done in 0.285125 secs using 399.2% CPU
Optimizing NNI: done in 0.28099 secs using 399.4% CPU
Optimizing NNI: done in 0.307946 secs using 399.9% CPU
Optimizing NNI: done in 0.301542 secs using 399.9% CPU
Optimizing NNI: done in 0.300499 secs using 399.2% CPU
Optimizing NNI: done in 0.250166 secs using 399.5% CPU
Iteration 20 / LogL: -36154.279 / Time: 0h:0m:9s
Finish initializing candidate tree set (7)
Current best tree score: -36153.691 / CPU time: 8.776
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.467165 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36153.244
Optimizing NNI: done in 0.335514 secs using 399.6% CPU
Optimizing NNI: done in 0.420908 secs using 399.7% CPU
Optimizing NNI: done in 0.507128 secs using 399.7% CPU
Optimizing NNI: done in 0.910969 secs using 399.7% CPU
Optimizing NNI: done in 0.401175 secs using 399.2% CPU
Optimizing NNI: done in 0.591501 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -36151.829
Optimizing NNI: done in 0.489595 secs using 399.6% CPU
Optimizing NNI: done in 0.376992 secs using 399.9% CPU
Optimizing NNI: done in 0.359654 secs using 399.9% CPU
Iteration 30 / LogL: -36152.793 / Time: 0h:0m:14s (0h:0m:48s left)
Optimizing NNI: done in 0.452781 secs using 399.5% CPU
Optimizing NNI: done in 0.44414 secs using 399.9% CPU
Optimizing NNI: done in 0.383772 secs using 399.6% CPU
Optimizing NNI: done in 0.49467 secs using 399.9% CPU
Optimizing NNI: done in 0.53666 secs using 399.5% CPU
Optimizing NNI: done in 0.407032 secs using 399.4% CPU
Optimizing NNI: done in 0.296416 secs using 399.9% CPU
Optimizing NNI: done in 0.433226 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36151.689
Optimizing NNI: done in 0.403206 secs using 399.4% CPU
Optimizing NNI: done in 0.864396 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36151.500
Iteration 40 / LogL: -36151.500 / Time: 0h:0m:19s (0h:0m:43s left)
Optimizing NNI: done in 0.422177 secs using 398.8% CPU
Optimizing NNI: done in 0.392489 secs using 399.7% CPU
Optimizing NNI: done in 0.38076 secs using 399.7% CPU
Optimizing NNI: done in 0.344934 secs using 399.4% CPU
921  mtInv+F+I+R7  60128.152    335 120926.304   122369.381   122332.794
Optimizing NNI: done in 0.381638 secs using 400% CPU
Optimizing NNI: done in 0.453485 secs using 399.2% CPU
Optimizing NNI: done in 0.475417 secs using 399.5% CPU
Optimizing NNI: done in 1.0148 secs using 399.2% CPU
Optimizing NNI: done in 0.476024 secs using 399.3% CPU
Optimizing NNI: done in 0.385934 secs using 399.9% CPU
Iteration 50 / LogL: -36169.304 / Time: 0h:0m:24s (0h:0m:37s left)
Optimizing NNI: done in 0.350329 secs using 399.9% CPU
Optimizing NNI: done in 0.38124 secs using 399.6% CPU
Optimizing NNI: done in 0.295298 secs using 399.2% CPU
Optimizing NNI: done in 0.466885 secs using 399.9% CPU
Optimizing NNI: done in 0.372362 secs using 399.8% CPU
Optimizing NNI: done in 1.05481 secs using 399.4% CPU
Optimizing NNI: done in 0.395057 secs using 399.4% CPU
933  mtMAM+R6      63712.112    313 128050.224   129154.516   129364.347
Optimizing NNI: done in 0.346469 secs using 399.9% CPU
Optimizing NNI: done in 0.38409 secs using 399.9% CPU
Optimizing NNI: done in 0.424512 secs using 399.2% CPU
Iteration 60 / LogL: -36152.007 / Time: 0h:0m:28s (0h:0m:32s left)
Optimizing NNI: done in 0.562001 secs using 399.6% CPU
Optimizing NNI: done in 0.329955 secs using 399.6% CPU
Optimizing NNI: done in 0.4048 secs using 399.4% CPU
Optimizing NNI: done in 0.97857 secs using 399.7% CPU
Optimizing NNI: done in 0.329617 secs using 399.9% CPU
Optimizing NNI: done in 0.374601 secs using 399.9% CPU
Optimizing NNI: done in 0.384905 secs using 399.7% CPU
Optimizing NNI: done in 0.289553 secs using 400% CPU
Optimizing NNI: done in 0.419297 secs using 399.5% CPU
Optimizing NNI: done in 0.389153 secs using 399.7% CPU
Iteration 70 / LogL: -36152.367 / Time: 0h:0m:33s (0h:0m:27s left)
Optimizing NNI: done in 0.306698 secs using 399.5% CPU
Optimizing NNI: done in 0.433188 secs using 399.2% CPU
Optimizing NNI: done in 0.412278 secs using 399.6% CPU
Optimizing NNI: done in 0.403542 secs using 400.4% CPU
Optimizing NNI: done in 0.373447 secs using 399.4% CPU
Optimizing NNI: done in 0.373835 secs using 400% CPU
Optimizing NNI: done in 0.370486 secs using 399.6% CPU
Optimizing NNI: done in 0.436679 secs using 399.2% CPU
Optimizing NNI: done in 0.37827 secs using 399.9% CPU
Optimizing NNI: done in 0.337032 secs using 399.3% CPU
Iteration 80 / LogL: -36181.795 / Time: 0h:0m:37s (0h:0m:22s left)
Optimizing NNI: done in 0.376649 secs using 399.1% CPU
Optimizing NNI: done in 0.430215 secs using 399.2% CPU
Optimizing NNI: done in 0.443063 secs using 399.7% CPU
Optimizing NNI: done in 0.398909 secs using 399% CPU
Optimizing NNI: done in 0.39085 secs using 400.2% CPU
Optimizing NNI: done in 0.336662 secs using 399.6% CPU
Optimizing NNI: done in 0.438742 secs using 399.9% CPU
Optimizing NNI: done in 0.515328 secs using 399.7% CPU
341  mtREV+R10     202198.737   1005 406407.475   2428467.475  410783.617
Optimizing NNI: done in 0.465664 secs using 399.9% CPU
Optimizing NNI: done in 0.988579 secs using 398.8% CPU
Iteration 90 / LogL: -36152.067 / Time: 0h:0m:41s (0h:0m:17s left)
Optimizing NNI: done in 0.474479 secs using 399.1% CPU
Optimizing NNI: done in 0.396689 secs using 398.9% CPU
Optimizing NNI: done in 0.569009 secs using 398.7% CPU
Optimizing NNI: done in 0.60248 secs using 399.9% CPU
Optimizing NNI: done in 0.382733 secs using 399.9% CPU
Optimizing NNI: done in 0.462716 secs using 399.4% CPU
Optimizing NNI: done in 0.541765 secs using 399.5% CPU
Optimizing NNI: done in 1.1029 secs using 399.5% CPU
Optimizing NNI: done in 0.598265 secs using 399.4% CPU
Optimizing NNI: done in 0.354722 secs using 399.3% CPU
Iteration 100 / LogL: -36535.173 / Time: 0h:0m:47s (0h:0m:12s left)
Optimizing NNI: done in 0.341935 secs using 399.3% CPU
Optimizing NNI: done in 0.351734 secs using 399.7% CPU
Optimizing NNI: done in 0.395458 secs using 399.2% CPU
Optimizing NNI: done in 0.397601 secs using 398.7% CPU
Optimizing NNI: done in 0.347605 secs using 399.6% CPU
Optimizing NNI: done in 0.344593 secs using 399.5% CPU
Optimizing NNI: done in 0.975107 secs using 399.1% CPU
Optimizing NNI: done in 0.335718 secs using 398.7% CPU
Optimizing NNI: done in 0.629851 secs using 399.3% CPU
Optimizing NNI: done in 0.392611 secs using 399.1% CPU
Iteration 110 / LogL: -36160.336 / Time: 0h:0m:51s (0h:0m:8s left)
Optimizing NNI: done in 0.530157 secs using 399.8% CPU
Optimizing NNI: done in 0.731726 secs using 399.3% CPU
Optimizing NNI: done in 0.386231 secs using 399.6% CPU
Optimizing NNI: done in 0.285985 secs using 399.9% CPU
934  mtMAM+R7      63684.089    315 127998.177   129129.314   129320.698
Optimizing NNI: done in 1.06646 secs using 399.6% CPU
Optimizing NNI: done in 0.421411 secs using 399.9% CPU
Optimizing NNI: done in 0.538878 secs using 399.7% CPU
Optimizing NNI: done in 0.354291 secs using 398.8% CPU
Optimizing NNI: done in 0.458921 secs using 399.9% CPU
Optimizing NNI: done in 1.10479 secs using 399% CPU
Iteration 120 / LogL: -36151.985 / Time: 0h:0m:57s (0h:0m:3s left)
Optimizing NNI: done in 0.550564 secs using 399.1% CPU
Optimizing NNI: done in 0.362681 secs using 398.6% CPU
Optimizing NNI: done in 0.414665 secs using 400% CPU
Optimizing NNI: done in 0.386382 secs using 399.6% CPU
350  mtREV+F+R8    197257.838   1020 396555.675   2479395.675  400997.133
Optimizing NNI: done in 0.427031 secs using 399.8% CPU
Optimizing NNI: done in 0.371327 secs using 399.4% CPU
Optimizing NNI: done in 0.453108 secs using 399% CPU
Optimizing NNI: done in 0.350459 secs using 399.6% CPU
TREE SEARCH COMPLETED AFTER 128 ITERATIONS / Time: 0h:1m:1s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36151.500
Optimal log-likelihood: -36151.499
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.374
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -36151.499
Total tree length: 19.883

Total number of iterations: 128
CPU time used for tree search: 237.462 sec (0h:3m:57s)
Wall-clock time used for tree search: 60.458 sec (0h:1m:0s)
Total CPU time used: 240.959 sec (0h:4m:0s)
Total wall-clock time used: 61.286 sec (0h:1m:1s)

===> START BOOTSTRAP REPLICATE NUMBER 40

Creating bootstrap alignment (seed: 956199)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36412.592
2. Current log-likelihood: -35566.710
3. Current log-likelihood: -35553.058
4. Current log-likelihood: -35552.690
Optimal log-likelihood: -35552.646
Proportion of invariable sites: 0.019
Gamma shape alpha: 2.370
Parameters optimization took 4 rounds (0.260 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0708981 secs using 400% CPU
Computing ML distances took 0.071029 sec (of wall-clock time) 0.283929 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000161886 secs using 450.3% CPU
Constructing RapidNJ tree: done in 0.00224805 secs using 448.9% CPU
Computing RapidNJ tree took 0.002477 sec (of wall-clock time) 0.011496 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36136.540
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.438 second
Computing log-likelihood of 98 initial trees ... 1.574 seconds
Current best score: -35552.646

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.216787 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35526.212
Optimizing NNI: done in 0.285464 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35519.504
Optimizing NNI: done in 0.267425 secs using 400.9% CPU
Optimizing NNI: done in 0.228485 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -35510.918
Optimizing NNI: done in 0.249211 secs using 399.4% CPU
Optimizing NNI: done in 0.258692 secs using 399.8% CPU
Optimizing NNI: done in 0.227135 secs using 399.5% CPU
Optimizing NNI: done in 0.259873 secs using 399.9% CPU
Optimizing NNI: done in 0.286041 secs using 399.9% CPU
Optimizing NNI: done in 0.285037 secs using 398.7% CPU
Iteration 10 / LogL: -35526.475 / Time: 0h:0m:6s
Optimizing NNI: done in 0.261087 secs using 400.1% CPU
Optimizing NNI: done in 0.283215 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 12: -35504.159
Optimizing NNI: done in 0.284819 secs using 399.1% CPU
Optimizing NNI: done in 0.280072 secs using 399.5% CPU
Optimizing NNI: done in 0.285852 secs using 398.5% CPU
Optimizing NNI: done in 0.329786 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 16: -35503.932
Optimizing NNI: done in 0.241224 secs using 399% CPU
Optimizing NNI: done in 0.269981 secs using 399.9% CPU
Optimizing NNI: done in 0.216902 secs using 399.9% CPU
Optimizing NNI: done in 0.231734 secs using 399.9% CPU
Iteration 20 / LogL: -35517.761 / Time: 0h:0m:9s
Finish initializing candidate tree set (11)
Current best tree score: -35503.932 / CPU time: 8.770
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.293691 secs using 398.5% CPU
Optimizing NNI: done in 0.37705 secs using 399.6% CPU
Optimizing NNI: done in 0.476268 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -35499.171
Optimizing NNI: done in 0.358388 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35499.034
Optimizing NNI: done in 0.402269 secs using 400.2% CPU
Optimizing NNI: done in 0.327634 secs using 399.9% CPU
Optimizing NNI: done in 0.430235 secs using 399.6% CPU
Optimizing NNI: done in 0.346259 secs using 399.6% CPU
Optimizing NNI: done in 0.361197 secs using 399.6% CPU
935  mtMAM+R8      63668.492    317 127970.984   129129.674   129301.902
Optimizing NNI: done in 0.319334 secs using 399.3% CPU
Iteration 30 / LogL: -35499.486 / Time: 0h:0m:13s (0h:0m:41s left)
Optimizing NNI: done in 0.370014 secs using 399.9% CPU
Optimizing NNI: done in 0.358004 secs using 398.8% CPU
Optimizing NNI: done in 0.442225 secs using 399% CPU
Optimizing NNI: done in 0.329056 secs using 399.6% CPU
Optimizing NNI: done in 0.332612 secs using 399.3% CPU
Optimizing NNI: done in 0.411077 secs using 399.6% CPU
Optimizing NNI: done in 0.449634 secs using 399.7% CPU
Optimizing NNI: done in 0.383597 secs using 399.6% CPU
Optimizing NNI: done in 0.28273 secs using 399.5% CPU
Optimizing NNI: done in 0.434319 secs using 399.9% CPU
Iteration 40 / LogL: -35499.208 / Time: 0h:0m:16s (0h:0m:35s left)
Optimizing NNI: done in 0.395972 secs using 399.4% CPU
Optimizing NNI: done in 0.338186 secs using 399.9% CPU
Optimizing NNI: done in 0.408497 secs using 399.2% CPU
Optimizing NNI: done in 0.376863 secs using 399.9% CPU
Optimizing NNI: done in 0.400108 secs using 399.7% CPU
Optimizing NNI: done in 0.363333 secs using 399.1% CPU
Optimizing NNI: done in 0.354569 secs using 399.9% CPU
Optimizing NNI: done in 0.390843 secs using 399.3% CPU
Optimizing NNI: done in 0.462748 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35499.012
351  mtREV+F+R9    197248.935   1022 396541.871   2487553.871  400992.037
Optimizing NNI: done in 0.407391 secs using 399.6% CPU
Iteration 50 / LogL: -35499.745 / Time: 0h:0m:20s (0h:0m:31s left)
Optimizing NNI: done in 0.31046 secs using 398.9% CPU
Optimizing NNI: done in 0.361152 secs using 399.9% CPU
Optimizing NNI: done in 0.325717 secs using 399.3% CPU
Optimizing NNI: done in 0.451084 secs using 400% CPU
Optimizing NNI: done in 0.371393 secs using 398.8% CPU
Optimizing NNI: done in 0.350445 secs using 399.6% CPU
Optimizing NNI: done in 0.279417 secs using 399.9% CPU
Optimizing NNI: done in 0.246128 secs using 399.9% CPU
242  Q.mammal+I+R10 105495.683   554 212099.366   827039.366   214329.696
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.736448 secs using 399.2% CPU
Optimizing NNI: done in 0.345229 secs using 399.6% CPU
Iteration 60 / LogL: -35499.440 / Time: 0h:0m:24s (0h:0m:26s left)
Optimizing NNI: done in 0.413163 secs using 399.9% CPU
Optimizing NNI: done in 0.417434 secs using 399.4% CPU
Optimizing NNI: done in 0.461296 secs using 399.7% CPU
Optimizing NNI: done in 0.379033 secs using 399.4% CPU
Optimizing NNI: done in 0.369653 secs using 399.8% CPU
Optimizing NNI: done in 0.422791 secs using 399.9% CPU
Optimizing NNI: done in 0.390613 secs using 399.9% CPU
Optimizing NNI: done in 0.390998 secs using 399.9% CPU
Optimizing NNI: done in 0.364131 secs using 399.6% CPU
Optimizing NNI: done in 0.348292 secs using 399.1% CPU
Iteration 70 / LogL: -35499.372 / Time: 0h:0m:28s (0h:0m:22s left)
Optimizing NNI: done in 0.318988 secs using 400.1% CPU
Optimizing NNI: done in 0.381862 secs using 399.4% CPU
Optimizing NNI: done in 0.318978 secs using 399.9% CPU
Optimizing NNI: done in 0.399825 secs using 399.7% CPU
Optimizing NNI: done in 0.386209 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35498.991
Optimizing NNI: done in 0.372394 secs using 398.3% CPU
Optimizing NNI: done in 0.343195 secs using 400.3% CPU
Optimizing NNI: done in 0.446546 secs using 399.5% CPU
Optimizing NNI: done in 0.43089 secs using 399.7% CPU
Optimizing NNI: done in 0.400599 secs using 399.7% CPU
Iteration 80 / LogL: -35503.477 / Time: 0h:0m:32s (0h:0m:17s left)
Optimizing NNI: done in 0.341765 secs using 399.9% CPU
Optimizing NNI: done in 0.29763 secs using 399.6% CPU
Optimizing NNI: done in 0.376545 secs using 399.6% CPU
Optimizing NNI: done in 0.349817 secs using 399.9% CPU
Optimizing NNI: done in 0.426896 secs using 399.2% CPU
Optimizing NNI: done in 0.432314 secs using 399.4% CPU
Optimizing NNI: done in 0.31432 secs using 399.9% CPU
Optimizing NNI: done in 0.448054 secs using 399.7% CPU
Optimizing NNI: done in 0.469172 secs using 399.5% CPU
Optimizing NNI: done in 0.375114 secs using 399.1% CPU
Iteration 90 / LogL: -35505.146 / Time: 0h:0m:36s (0h:0m:13s left)
Optimizing NNI: done in 0.381041 secs using 399.7% CPU
Optimizing NNI: done in 0.441817 secs using 399.5% CPU
Optimizing NNI: done in 0.404077 secs using 399.6% CPU
Optimizing NNI: done in 0.461665 secs using 399% CPU
Optimizing NNI: done in 0.353632 secs using 399% CPU
Optimizing NNI: done in 0.34679 secs using 399.9% CPU
Optimizing NNI: done in 0.331751 secs using 398.4% CPU
Optimizing NNI: done in 0.455887 secs using 399.1% CPU
263  Q.mammal+F+I+R9 106245.082   571 213632.165   866856.165   215930.934
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.387467 secs using 399.7% CPU
Optimizing NNI: done in 0.325422 secs using 399.9% CPU
Iteration 100 / LogL: -35510.013 / Time: 0h:0m:40s (0h:0m:9s left)
Optimizing NNI: done in 0.463704 secs using 399.9% CPU
Optimizing NNI: done in 0.314869 secs using 399.6% CPU
Optimizing NNI: done in 0.382606 secs using 399.7% CPU
Optimizing NNI: done in 0.388829 secs using 399.5% CPU
Optimizing NNI: done in 0.391674 secs using 400.4% CPU
Optimizing NNI: done in 0.376468 secs using 399.1% CPU
Optimizing NNI: done in 0.403693 secs using 399.4% CPU
Optimizing NNI: done in 0.430006 secs using 399.7% CPU
Optimizing NNI: done in 0.338974 secs using 399.3% CPU
Optimizing NNI: done in 0.35798 secs using 399% CPU
Iteration 110 / LogL: -35509.459 / Time: 0h:0m:44s (0h:0m:5s left)
Optimizing NNI: done in 0.426958 secs using 399.5% CPU
Optimizing NNI: done in 0.411205 secs using 399.9% CPU
Optimizing NNI: done in 0.446359 secs using 399.6% CPU
Optimizing NNI: done in 0.331738 secs using 399.6% CPU
Optimizing NNI: done in 0.371833 secs using 399.1% CPU
Optimizing NNI: done in 0.318946 secs using 399.6% CPU
Optimizing NNI: done in 0.298996 secs using 399.9% CPU
Optimizing NNI: done in 0.318195 secs using 399.9% CPU
Optimizing NNI: done in 0.367412 secs using 399.9% CPU
Optimizing NNI: done in 0.349584 secs using 399.6% CPU
Iteration 120 / LogL: -35499.005 / Time: 0h:0m:47s (0h:0m:1s left)
Optimizing NNI: done in 0.40985 secs using 399.9% CPU
Optimizing NNI: done in 0.362513 secs using 399.8% CPU
Optimizing NNI: done in 0.40725 secs using 399.1% CPU
Optimizing NNI: done in 0.361231 secs using 399.9% CPU
TREE SEARCH COMPLETED AFTER 124 ITERATIONS / Time: 0h:0m:49s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35498.991
Optimal log-likelihood: -35498.990
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.450
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35498.990
Total tree length: 19.184

Total number of iterations: 124
CPU time used for tree search: 192.162 sec (0h:3m:12s)
Wall-clock time used for tree search: 49.021 sec (0h:0m:49s)
Total CPU time used: 194.401 sec (0h:3m:14s)
Total wall-clock time used: 49.552 sec (0h:0m:49s)

===> START BOOTSTRAP REPLICATE NUMBER 41

Creating bootstrap alignment (seed: 956200)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36537.670
2. Current log-likelihood: -35625.876
3. Current log-likelihood: -35613.856
4. Current log-likelihood: -35613.426
Optimal log-likelihood: -35613.336
Proportion of invariable sites: 0.018
Gamma shape alpha: 2.675
Parameters optimization took 4 rounds (0.227 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0742171 secs using 400% CPU
Computing ML distances took 0.074349 sec (of wall-clock time) 0.297206 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000149965 secs using 430.8% CPU
Constructing RapidNJ tree: done in 0.00221014 secs using 498.6% CPU
Computing RapidNJ tree took 0.002419 sec (of wall-clock time) 0.012218 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35961.008
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.480 second
Computing log-likelihood of 98 initial trees ... 1.530 seconds
Current best score: -35579.014

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.212609 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35517.149
Optimizing NNI: done in 0.225027 secs using 399.4% CPU
Optimizing NNI: done in 0.234331 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -35516.715
Optimizing NNI: done in 0.251944 secs using 398.7% CPU
Optimizing NNI: done in 0.239884 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -35512.968
Optimizing NNI: done in 0.244453 secs using 399.4% CPU
Optimizing NNI: done in 0.25698 secs using 399.5% CPU
352  mtREV+F+R10   197245.156   1024 396538.312   2495738.312  400997.187
Optimizing NNI: done in 0.263836 secs using 399.5% CPU
Optimizing NNI: done in 0.244775 secs using 398.8% CPU
Optimizing NNI: done in 0.267464 secs using 401% CPU
Iteration 10 / LogL: -35513.007 / Time: 0h:0m:6s
Optimizing NNI: done in 0.237235 secs using 399.1% CPU
Optimizing NNI: done in 0.265971 secs using 399.5% CPU
936  mtMAM+R9      63668.264    319 127974.528   129161.505   129313.843
Optimizing NNI: done in 0.260484 secs using 399.1% CPU
Optimizing NNI: done in 0.250639 secs using 399.5% CPU
Optimizing NNI: done in 0.307734 secs using 399.3% CPU
Optimizing NNI: done in 0.266493 secs using 398.8% CPU
Optimizing NNI: done in 0.276036 secs using 398.8% CPU
Optimizing NNI: done in 0.253579 secs using 400% CPU
Optimizing NNI: done in 0.227336 secs using 399% CPU
Optimizing NNI: done in 0.2483 secs using 399.5% CPU
Iteration 20 / LogL: -35518.398 / Time: 0h:0m:8s
Finish initializing candidate tree set (8)
Current best tree score: -35512.968 / CPU time: 8.279
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.417234 secs using 399.1% CPU
Optimizing NNI: done in 0.344094 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35512.952
Optimizing NNI: done in 0.411045 secs using 399.9% CPU
Optimizing NNI: done in 0.478276 secs using 399.9% CPU
Optimizing NNI: done in 0.563843 secs using 399.7% CPU
Optimizing NNI: done in 0.326944 secs using 399.6% CPU
Optimizing NNI: done in 0.3511 secs using 399.4% CPU
Optimizing NNI: done in 0.31318 secs using 399.6% CPU
Optimizing NNI: done in 0.339124 secs using 398.1% CPU
Optimizing NNI: done in 0.416066 secs using 399.6% CPU
Iteration 30 / LogL: -35515.823 / Time: 0h:0m:12s (0h:0m:32s left)
Optimizing NNI: done in 0.39816 secs using 398.7% CPU
Optimizing NNI: done in 0.338635 secs using 399.3% CPU
Optimizing NNI: done in 0.368787 secs using 399.6% CPU
Optimizing NNI: done in 0.465491 secs using 399.7% CPU
Optimizing NNI: done in 0.441727 secs using 399.4% CPU
Optimizing NNI: done in 0.601695 secs using 399.6% CPU
Optimizing NNI: done in 0.325152 secs using 399.6% CPU
Optimizing NNI: done in 0.310437 secs using 399.9% CPU
Optimizing NNI: done in 0.33442 secs using 398.7% CPU
Optimizing NNI: done in 0.490584 secs using 399.3% CPU
Iteration 40 / LogL: -35513.068 / Time: 0h:0m:16s (0h:0m:28s left)
Optimizing NNI: done in 0.512262 secs using 399.9% CPU
Optimizing NNI: done in 0.436367 secs using 399.4% CPU
Optimizing NNI: done in 0.283891 secs using 399.9% CPU
Optimizing NNI: done in 0.562972 secs using 399.8% CPU
Optimizing NNI: done in 0.426731 secs using 398.7% CPU
Optimizing NNI: done in 0.502387 secs using 399.2% CPU
Optimizing NNI: done in 0.335825 secs using 399.9% CPU
Optimizing NNI: done in 0.389184 secs using 399.9% CPU
Optimizing NNI: done in 0.354729 secs using 399.6% CPU
Optimizing NNI: done in 0.357729 secs using 399.1% CPU
Iteration 50 / LogL: -35518.824 / Time: 0h:0m:21s (0h:0m:23s left)
942  mtMAM+I+R6    63712.305    314 128052.611   129170.238   129370.933
Optimizing NNI: done in 0.465439 secs using 399.9% CPU
Optimizing NNI: done in 0.325346 secs using 399% CPU
Optimizing NNI: done in 0.330714 secs using 399.6% CPU
Optimizing NNI: done in 0.349017 secs using 399.9% CPU
Optimizing NNI: done in 0.339282 secs using 399.6% CPU
Optimizing NNI: done in 0.332165 secs using 399.9% CPU
Optimizing NNI: done in 0.334117 secs using 399.1% CPU
Optimizing NNI: done in 0.33075 secs using 400.5% CPU
Optimizing NNI: done in 0.329372 secs using 399.3% CPU
Optimizing NNI: done in 0.347584 secs using 399.9% CPU
Iteration 60 / LogL: -35514.009 / Time: 0h:0m:24s (0h:0m:18s left)
Optimizing NNI: done in 0.324153 secs using 399.3% CPU
Optimizing NNI: done in 0.33782 secs using 399.3% CPU
Optimizing NNI: done in 0.409844 secs using 399.9% CPU
Optimizing NNI: done in 0.260377 secs using 399.9% CPU
Optimizing NNI: done in 0.320646 secs using 399.2% CPU
Optimizing NNI: done in 0.429083 secs using 399.2% CPU
Optimizing NNI: done in 0.416648 secs using 399.7% CPU
Optimizing NNI: done in 0.455024 secs using 399.4% CPU
Optimizing NNI: done in 0.408645 secs using 399.1% CPU
Optimizing NNI: done in 0.375271 secs using 400.5% CPU
Iteration 70 / LogL: -35514.436 / Time: 0h:0m:28s (0h:0m:14s left)
Optimizing NNI: done in 0.387629 secs using 399.4% CPU
Optimizing NNI: done in 0.437371 secs using 399.7% CPU
Optimizing NNI: done in 0.402368 secs using 399.9% CPU
Optimizing NNI: done in 0.341885 secs using 399.3% CPU
Optimizing NNI: done in 0.439272 secs using 399% CPU
Optimizing NNI: done in 0.381221 secs using 399.3% CPU
Optimizing NNI: done in 0.372351 secs using 399.9% CPU
Optimizing NNI: done in 0.377967 secs using 399.9% CPU
Optimizing NNI: done in 0.410999 secs using 398.9% CPU
Optimizing NNI: done in 0.414374 secs using 399.1% CPU
Iteration 80 / LogL: -35512.973 / Time: 0h:0m:32s (0h:0m:10s left)
Optimizing NNI: done in 0.379231 secs using 400.2% CPU
Optimizing NNI: done in 0.51727 secs using 399.4% CPU
Optimizing NNI: done in 0.346866 secs using 399.1% CPU
Optimizing NNI: done in 0.368289 secs using 399.1% CPU
Optimizing NNI: done in 0.450319 secs using 398.8% CPU
Optimizing NNI: done in 0.45599 secs using 399.9% CPU
Optimizing NNI: done in 0.338642 secs using 399.3% CPU
Optimizing NNI: done in 0.354978 secs using 399.6% CPU
Optimizing NNI: done in 0.479149 secs using 399.1% CPU
BETTER TREE FOUND at iteration 89: -35512.948
Optimizing NNI: done in 0.307794 secs using 399.6% CPU
Iteration 90 / LogL: -35514.586 / Time: 0h:0m:36s (0h:0m:40s left)
Optimizing NNI: done in 0.40999 secs using 399.7% CPU
Optimizing NNI: done in 0.370703 secs using 399.5% CPU
Optimizing NNI: done in 0.43546 secs using 399.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -35512.948
Optimizing NNI: done in 0.359322 secs using 399.6% CPU
Optimizing NNI: done in 0.374856 secs using 399.9% CPU
Optimizing NNI: done in 0.37244 secs using 399.6% CPU
Optimizing NNI: done in 0.353986 secs using 399.1% CPU
Optimizing NNI: done in 0.408226 secs using 400.4% CPU
Optimizing NNI: done in 0.443693 secs using 399.3% CPU
Optimizing NNI: done in 0.279651 secs using 399.5% CPU
Iteration 100 / LogL: -35512.954 / Time: 0h:0m:40s (0h:0m:36s left)
Optimizing NNI: done in 0.386963 secs using 398.9% CPU
Optimizing NNI: done in 0.510428 secs using 399.3% CPU
Optimizing NNI: done in 0.400407 secs using 399.9% CPU
Optimizing NNI: done in 0.388806 secs using 399.1% CPU
Optimizing NNI: done in 0.43527 secs using 400% CPU
Optimizing NNI: done in 0.476778 secs using 399.9% CPU
Optimizing NNI: done in 0.391133 secs using 399.7% CPU
Optimizing NNI: done in 0.44272 secs using 399% CPU
Optimizing NNI: done in 0.362073 secs using 399.9% CPU
Optimizing NNI: done in 0.409613 secs using 398.7% CPU
Iteration 110 / LogL: -35516.823 / Time: 0h:0m:44s (0h:0m:32s left)
Optimizing NNI: done in 0.320026 secs using 399% CPU
Optimizing NNI: done in 0.556381 secs using 399.4% CPU
Optimizing NNI: done in 0.438756 secs using 399.1% CPU
Optimizing NNI: done in 0.396227 secs using 399.4% CPU
Optimizing NNI: done in 0.482494 secs using 399.9% CPU
Optimizing NNI: done in 0.376387 secs using 399.9% CPU
Optimizing NNI: done in 0.431807 secs using 399.5% CPU
Optimizing NNI: done in 0.313888 secs using 400% CPU
Optimizing NNI: done in 0.390197 secs using 399.6% CPU
Optimizing NNI: done in 0.490269 secs using 398.9% CPU
Iteration 120 / LogL: -35513.675 / Time: 0h:0m:48s (0h:0m:28s left)
Optimizing NNI: done in 0.285439 secs using 399.5% CPU
Optimizing NNI: done in 0.379133 secs using 399.6% CPU
Optimizing NNI: done in 0.343461 secs using 399.9% CPU
Optimizing NNI: done in 0.377941 secs using 399.7% CPU
Optimizing NNI: done in 0.337848 secs using 398.9% CPU
Optimizing NNI: done in 0.484581 secs using 399.5% CPU
Optimizing NNI: done in 0.429175 secs using 399.9% CPU
Optimizing NNI: done in 0.310025 secs using 399.6% CPU
Optimizing NNI: done in 0.391659 secs using 399.7% CPU
Optimizing NNI: done in 0.450309 secs using 399.8% CPU
Iteration 130 / LogL: -35513.060 / Time: 0h:0m:52s (0h:0m:24s left)
Optimizing NNI: done in 0.364813 secs using 399.7% CPU
Optimizing NNI: done in 0.370424 secs using 399.7% CPU
Optimizing NNI: done in 0.357335 secs using 399.1% CPU
Optimizing NNI: done in 0.43457 secs using 399.7% CPU
Optimizing NNI: done in 0.390451 secs using 399.7% CPU
Optimizing NNI: done in 0.388195 secs using 399.1% CPU
Optimizing NNI: done in 0.323746 secs using 399.8% CPU
Optimizing NNI: done in 0.493128 secs using 399.2% CPU
Optimizing NNI: done in 0.356844 secs using 399.3% CPU
Optimizing NNI: done in 0.397449 secs using 399.9% CPU
Iteration 140 / LogL: -35513.160 / Time: 0h:0m:56s (0h:0m:19s left)
Optimizing NNI: done in 0.282219 secs using 400% CPU
Optimizing NNI: done in 0.3437 secs using 399.9% CPU
Optimizing NNI: done in 0.40978 secs using 399% CPU
Optimizing NNI: done in 0.49824 secs using 399.5% CPU
Optimizing NNI: done in 0.4096 secs using 399.7% CPU
Optimizing NNI: done in 0.438809 secs using 398.7% CPU
Optimizing NNI: done in 0.438775 secs using 399.4% CPU
Optimizing NNI: done in 0.370921 secs using 399.9% CPU
361  mtART+R8      203583.239   1001 409168.478   2415172.478  413527.203
Optimizing NNI: done in 0.452525 secs using 399.6% CPU
Optimizing NNI: done in 0.420645 secs using 399.5% CPU
Iteration 150 / LogL: -35516.894 / Time: 0h:1m:0s (0h:0m:15s left)
Optimizing NNI: done in 0.364169 secs using 399.7% CPU
Optimizing NNI: done in 0.285618 secs using 398.7% CPU
Optimizing NNI: done in 0.348968 secs using 399.8% CPU
Optimizing NNI: done in 0.240741 secs using 400% CPU
Optimizing NNI: done in 0.332843 secs using 399.9% CPU
Optimizing NNI: done in 0.459643 secs using 399.7% CPU
Optimizing NNI: done in 0.355461 secs using 399.6% CPU
Optimizing NNI: done in 0.349853 secs using 399.6% CPU
Optimizing NNI: done in 0.575867 secs using 399.2% CPU
Optimizing NNI: done in 0.318122 secs using 399.9% CPU
Iteration 160 / LogL: -35513.301 / Time: 0h:1m:4s (0h:0m:11s left)
Optimizing NNI: done in 0.354632 secs using 399.6% CPU
Optimizing NNI: done in 0.389156 secs using 399.7% CPU
Optimizing NNI: done in 0.497797 secs using 398.9% CPU
Optimizing NNI: done in 0.437194 secs using 399% CPU
Optimizing NNI: done in 0.439658 secs using 399.7% CPU
Optimizing NNI: done in 0.438921 secs using 399.4% CPU
Optimizing NNI: done in 0.453144 secs using 399.9% CPU
Optimizing NNI: done in 0.450694 secs using 399.9% CPU
Optimizing NNI: done in 0.381566 secs using 399.7% CPU
Optimizing NNI: done in 0.444429 secs using 399.7% CPU
Iteration 170 / LogL: -35520.014 / Time: 0h:1m:8s (0h:0m:7s left)
Optimizing NNI: done in 0.323118 secs using 399.9% CPU
Optimizing NNI: done in 0.411404 secs using 398.5% CPU
Optimizing NNI: done in 0.319349 secs using 399% CPU
Optimizing NNI: done in 0.386315 secs using 399.6% CPU
Optimizing NNI: done in 0.511741 secs using 399.7% CPU
Optimizing NNI: done in 0.428232 secs using 399.4% CPU
943  mtMAM+I+R7    63684.235    316 128000.470   129145.293   129327.190
Optimizing NNI: done in 0.328273 secs using 399.9% CPU
Optimizing NNI: done in 0.380059 secs using 399.4% CPU
Optimizing NNI: done in 0.395039 secs using 399.2% CPU
Optimizing NNI: done in 0.351613 secs using 398.4% CPU
Iteration 180 / LogL: -35512.960 / Time: 0h:1m:12s (0h:0m:3s left)
Optimizing NNI: done in 0.36085 secs using 400.2% CPU
Optimizing NNI: done in 0.482454 secs using 398.5% CPU
Optimizing NNI: done in 0.354233 secs using 398.2% CPU
Optimizing NNI: done in 0.428078 secs using 399.7% CPU
Optimizing NNI: done in 0.426463 secs using 399.3% CPU
Optimizing NNI: done in 0.431322 secs using 399.6% CPU
Optimizing NNI: done in 0.426519 secs using 399.2% CPU
Optimizing NNI: done in 0.305712 secs using 399.1% CPU
Optimizing NNI: done in 0.391328 secs using 399.4% CPU
Optimizing NNI: done in 0.396686 secs using 399.4% CPU
Iteration 190 / LogL: -35520.599 / Time: 0h:1m:16s (0h:0m:-1s left)
TREE SEARCH COMPLETED AFTER 190 ITERATIONS / Time: 0h:1m:16s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35512.948
Optimal log-likelihood: -35512.947
Proportion of invariable sites: 0.019
Gamma shape alpha: 2.697
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -35512.947
Total tree length: 19.265

Total number of iterations: 190
CPU time used for tree search: 300.015 sec (0h:5m:0s)
Wall-clock time used for tree search: 76.056 sec (0h:1m:16s)
Total CPU time used: 301.925 sec (0h:5m:1s)
Total wall-clock time used: 76.513 sec (0h:1m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 42

Creating bootstrap alignment (seed: 956201)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36865.185
2. Current log-likelihood: -35944.217
3. Current log-likelihood: -35922.722
4. Current log-likelihood: -35921.664
Optimal log-likelihood: -35921.614
Proportion of invariable sites: 0.011
Gamma shape alpha: 2.094
Parameters optimization took 4 rounds (0.264 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.076565 secs using 400.3% CPU
Computing ML distances took 0.076696 sec (of wall-clock time) 0.306606 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000164032 secs using 1370% CPU
Constructing RapidNJ tree: done in 0.00224209 secs using 479.5% CPU
Computing RapidNJ tree took 0.002462 sec (of wall-clock time) 0.013053 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36337.891
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.403 second
Computing log-likelihood of 98 initial trees ... 1.545 seconds
Current best score: -35915.908

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.251993 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35858.063
Optimizing NNI: done in 0.277954 secs using 399.9% CPU
Optimizing NNI: done in 0.250247 secs using 399.5% CPU
Optimizing NNI: done in 0.251533 secs using 398.3% CPU
Optimizing NNI: done in 0.290795 secs using 399.6% CPU
Optimizing NNI: done in 0.257789 secs using 400.3% CPU
Optimizing NNI: done in 0.260708 secs using 398% CPU
Optimizing NNI: done in 0.2655 secs using 399.5% CPU
Optimizing NNI: done in 0.273407 secs using 398.8% CPU
Optimizing NNI: done in 0.248598 secs using 399.5% CPU
Iteration 10 / LogL: -35868.208 / Time: 0h:0m:6s
955  mtMAM+F+R6    61878.116    332 124420.231   125810.873   125814.126
Optimizing NNI: done in 0.310231 secs using 398.9% CPU
Optimizing NNI: done in 0.25107 secs using 398.8% CPU
Optimizing NNI: done in 0.274678 secs using 399.2% CPU
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Optimizing NNI: done in 0.239298 secs using 398.3% CPU
Optimizing NNI: done in 0.266428 secs using 399.5% CPU
Optimizing NNI: done in 0.255878 secs using 399.5% CPU
Iteration 20 / LogL: -35862.064 / Time: 0h:0m:8s
Finish initializing candidate tree set (5)
Current best tree score: -35858.063 / CPU time: 8.284
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.399104 secs using 398.5% CPU
Optimizing NNI: done in 0.363885 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35857.993
Optimizing NNI: done in 0.392343 secs using 398.8% CPU
Optimizing NNI: done in 0.341663 secs using 399.6% CPU
Optimizing NNI: done in 0.359027 secs using 399.1% CPU
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Optimizing NNI: done in 0.397954 secs using 399.1% CPU
Optimizing NNI: done in 0.318853 secs using 399.6% CPU
Iteration 30 / LogL: -35858.494 / Time: 0h:0m:12s (0h:0m:30s left)
Optimizing NNI: done in 0.328147 secs using 399.5% CPU
Optimizing NNI: done in 0.36034 secs using 399.7% CPU
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Optimizing NNI: done in 0.488562 secs using 399.5% CPU
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Optimizing NNI: done in 0.39798 secs using 399.7% CPU
Iteration 40 / LogL: -35858.245 / Time: 0h:0m:16s (0h:0m:25s left)
Optimizing NNI: done in 0.407259 secs using 399.2% CPU
Optimizing NNI: done in 0.338887 secs using 399.2% CPU
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Optimizing NNI: done in 0.525895 secs using 399.9% CPU
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Optimizing NNI: done in 0.373702 secs using 399.9% CPU
Optimizing NNI: done in 0.314209 secs using 399.2% CPU
956  mtMAM+F+R7    61854.633    334 124377.266   125802.616   125779.558
Optimizing NNI: done in 0.541187 secs using 399.2% CPU
Optimizing NNI: done in 0.526335 secs using 399.4% CPU
Optimizing NNI: done in 0.538092 secs using 400.1% CPU
Iteration 50 / LogL: -35858.388 / Time: 0h:0m:20s (0h:0m:21s left)
Optimizing NNI: done in 0.404828 secs using 399.4% CPU
Optimizing NNI: done in 0.38935 secs using 399.7% CPU
Optimizing NNI: done in 0.41739 secs using 399.5% CPU
Optimizing NNI: done in 0.414017 secs using 399.3% CPU
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Optimizing NNI: done in 0.356568 secs using 399.7% CPU
Optimizing NNI: done in 0.415903 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 59: -35857.355
Optimizing NNI: done in 0.419618 secs using 399% CPU
Iteration 60 / LogL: -35858.115 / Time: 0h:0m:24s (0h:0m:41s left)
Optimizing NNI: done in 0.506701 secs using 398.7% CPU
Optimizing NNI: done in 0.388685 secs using 399.7% CPU
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Optimizing NNI: done in 0.311221 secs using 399% CPU
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Optimizing NNI: done in 0.31954 secs using 399.3% CPU
Optimizing NNI: done in 0.434668 secs using 399.5% CPU
Iteration 70 / LogL: -35857.366 / Time: 0h:0m:28s (0h:0m:37s left)
Optimizing NNI: done in 0.4364 secs using 399.3% CPU
Optimizing NNI: done in 0.446803 secs using 400.1% CPU
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Optimizing NNI: done in 0.490786 secs using 399.3% CPU
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Optimizing NNI: done in 0.449887 secs using 399.5% CPU
Iteration 80 / LogL: -35867.814 / Time: 0h:0m:32s (0h:0m:32s left)
Optimizing NNI: done in 0.331039 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 81: -35856.678
Optimizing NNI: done in 0.277328 secs using 398.5% CPU
957  mtMAM+F+R8    61844.924    336 124361.848   125822.906   125772.537
Optimizing NNI: done in 0.39204 secs using 400.5% CPU
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Optimizing NNI: done in 0.270622 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 90: -35856.336
Iteration 90 / LogL: -35856.336 / Time: 0h:0m:36s (0h:0m:41s left)
Optimizing NNI: done in 0.25775 secs using 399.9% CPU
Optimizing NNI: done in 0.306246 secs using 398.5% CPU
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Optimizing NNI: done in 0.344977 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 99: -35856.308
Optimizing NNI: done in 0.439843 secs using 399% CPU
Iteration 100 / LogL: -35866.559 / Time: 0h:0m:40s (0h:0m:40s left)
Optimizing NNI: done in 0.293104 secs using 399.4% CPU
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Optimizing NNI: done in 0.416739 secs using 399.7% CPU
362  mtART+R9      203529.654   1003 409065.309   2423089.309  413432.742
Optimizing NNI: done in 0.393237 secs using 399.1% CPU
Optimizing NNI: done in 0.518223 secs using 399.6% CPU
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Iteration 110 / LogL: -35856.871 / Time: 0h:0m:43s (0h:0m:35s left)
Optimizing NNI: done in 0.348863 secs using 399.9% CPU
Optimizing NNI: done in 0.43859 secs using 399.6% CPU
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Iteration 120 / LogL: -35859.407 / Time: 0h:0m:47s (0h:0m:31s left)
Optimizing NNI: done in 0.354585 secs using 399.1% CPU
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Iteration 130 / LogL: -35901.213 / Time: 0h:0m:51s (0h:0m:27s left)
Optimizing NNI: done in 0.313361 secs using 400.6% CPU
Optimizing NNI: done in 0.359828 secs using 399.9% CPU
Optimizing NNI: done in 0.344079 secs using 399.3% CPU
958  mtMAM+F+R9    61843.394    338 124362.788   125860.592   125781.874
Optimizing NNI: done in 0.316784 secs using 399.2% CPU
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Iteration 140 / LogL: -35859.244 / Time: 0h:0m:54s (0h:0m:23s left)
Optimizing NNI: done in 0.441807 secs using 399.7% CPU
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Iteration 150 / LogL: -35860.653 / Time: 0h:0m:58s (0h:0m:19s left)
Optimizing NNI: done in 0.465217 secs using 399.7% CPU
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Iteration 160 / LogL: -35857.837 / Time: 0h:1m:2s (0h:0m:15s left)
Optimizing NNI: done in 0.277437 secs using 399.9% CPU
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Iteration 170 / LogL: -35864.580 / Time: 0h:1m:5s (0h:0m:11s left)
Optimizing NNI: done in 0.328229 secs using 399.9% CPU
Optimizing NNI: done in 0.338548 secs using 399.9% CPU
Optimizing NNI: done in 0.412797 secs using 399% CPU
Optimizing NNI: done in 0.329645 secs using 399.8% CPU
Optimizing NNI: done in 0.344623 secs using 399% CPU
964  mtMAM+F+I+R6  61877.208    333 124420.417   125828.290   125818.510
Optimizing NNI: done in 0.299124 secs using 399.2% CPU
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Optimizing NNI: done in 0.462377 secs using 399.7% CPU
Iteration 180 / LogL: -35856.857 / Time: 0h:1m:9s (0h:0m:7s left)
Optimizing NNI: done in 0.330878 secs using 399.6% CPU
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Optimizing NNI: done in 0.283954 secs using 400% CPU
Iteration 190 / LogL: -35858.249 / Time: 0h:1m:13s (0h:0m:3s left)
Optimizing NNI: done in 0.301503 secs using 400% CPU
Optimizing NNI: done in 0.271176 secs using 399.5% CPU
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Optimizing NNI: done in 0.457849 secs using 399.7% CPU
Optimizing NNI: done in 0.332002 secs using 399.9% CPU
Iteration 200 / LogL: -35868.128 / Time: 0h:1m:17s (0h:0m:-1s left)
TREE SEARCH COMPLETED AFTER 200 ITERATIONS / Time: 0h:1m:17s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35856.308
Optimal log-likelihood: -35856.305
Proportion of invariable sites: 0.012
Gamma shape alpha: 2.144
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35856.305
Total tree length: 19.983

Total number of iterations: 200
CPU time used for tree search: 302.946 sec (0h:5m:2s)
Wall-clock time used for tree search: 76.741 sec (0h:1m:16s)
Total CPU time used: 305.407 sec (0h:5m:5s)
Total wall-clock time used: 77.318 sec (0h:1m:17s)

===> START BOOTSTRAP REPLICATE NUMBER 43

Creating bootstrap alignment (seed: 956202)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36719.616
2. Current log-likelihood: -35903.517
3. Current log-likelihood: -35890.278
4. Current log-likelihood: -35889.734
Optimal log-likelihood: -35889.713
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.391
Parameters optimization took 4 rounds (0.259 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.073987 secs using 400% CPU
Computing ML distances took 0.074123 sec (of wall-clock time) 0.296279 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000146151 secs using 424.2% CPU
Constructing RapidNJ tree: done in 0.00217915 secs using 419.7% CPU
Computing RapidNJ tree took 0.002398 sec (of wall-clock time) 0.011033 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36711.628
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.453 second
Computing log-likelihood of 98 initial trees ... 1.498 seconds
Current best score: -35889.713

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.231387 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35859.107
Optimizing NNI: done in 0.256267 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35856.179
Optimizing NNI: done in 0.266177 secs using 398.4% CPU
Optimizing NNI: done in 0.297684 secs using 400% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -35852.356
Optimizing NNI: done in 0.251604 secs using 398.9% CPU
Optimizing NNI: done in 0.283732 secs using 399.2% CPU
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Iteration 10 / LogL: -35861.674 / Time: 0h:0m:6s
Optimizing NNI: done in 0.307051 secs using 399.3% CPU
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Optimizing NNI: done in 0.285543 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 19: -35848.095
Optimizing NNI: done in 0.318661 secs using 399.6% CPU
Iteration 20 / LogL: -35861.906 / Time: 0h:0m:9s
Finish initializing candidate tree set (8)
Current best tree score: -35848.095 / CPU time: 9.034
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.434434 secs using 399.2% CPU
Optimizing NNI: done in 0.421115 secs using 399.4% CPU
965  mtMAM+F+I+R7  61854.353    335 124378.706   125821.783   125785.197
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.336634 secs using 399.6% CPU
Optimizing NNI: done in 0.365707 secs using 399.3% CPU
Optimizing NNI: done in 0.349436 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -35847.425
Optimizing NNI: done in 0.289822 secs using 399.5% CPU
Optimizing NNI: done in 0.373045 secs using 399.5% CPU
UPDATE BEST LOG-LIKELIHOOD: -35847.419
Optimizing NNI: done in 0.333255 secs using 399.3% CPU
Optimizing NNI: done in 0.379642 secs using 399.9% CPU
Optimizing NNI: done in 0.31696 secs using 399.6% CPU
Iteration 30 / LogL: -35850.118 / Time: 0h:0m:13s (0h:0m:43s left)
Optimizing NNI: done in 0.379647 secs using 399.9% CPU
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Optimizing NNI: done in 0.413586 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -35846.909
Optimizing NNI: done in 0.301077 secs using 399.5% CPU
Optimizing NNI: done in 0.481258 secs using 399.9% CPU
Optimizing NNI: done in 0.216379 secs using 399% CPU
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Optimizing NNI: done in 0.332891 secs using 399.6% CPU
Iteration 40 / LogL: -35846.933 / Time: 0h:0m:17s (0h:0m:41s left)
Optimizing NNI: done in 0.328239 secs using 399.6% CPU
Optimizing NNI: done in 0.346546 secs using 399.6% CPU
Optimizing NNI: done in 0.390157 secs using 400% CPU
Optimizing NNI: done in 0.450393 secs using 399.3% CPU
Optimizing NNI: done in 0.354635 secs using 399.8% CPU
Optimizing NNI: done in 0.417003 secs using 399.1% CPU
Optimizing NNI: done in 0.373786 secs using 399.7% CPU
Optimizing NNI: done in 0.307217 secs using 399.6% CPU
Optimizing NNI: done in 0.32063 secs using 399.9% CPU
Optimizing NNI: done in 0.543054 secs using 399.7% CPU
Iteration 50 / LogL: -35847.357 / Time: 0h:0m:20s (0h:0m:36s left)
Optimizing NNI: done in 0.350051 secs using 399.7% CPU
Optimizing NNI: done in 0.371093 secs using 399.9% CPU
Optimizing NNI: done in 0.419601 secs using 399.4% CPU
Optimizing NNI: done in 0.481199 secs using 399.1% CPU
Optimizing NNI: done in 0.355774 secs using 399.3% CPU
Optimizing NNI: done in 0.40967 secs using 399.9% CPU
Optimizing NNI: done in 0.495531 secs using 399.1% CPU
Optimizing NNI: done in 0.337578 secs using 399.6% CPU
Optimizing NNI: done in 0.328111 secs using 398.7% CPU
Optimizing NNI: done in 0.33611 secs using 399.6% CPU
Iteration 60 / LogL: -35847.356 / Time: 0h:0m:24s (0h:0m:31s left)
Optimizing NNI: done in 0.473239 secs using 399.3% CPU
Optimizing NNI: done in 0.395179 secs using 399.5% CPU
Optimizing NNI: done in 0.351864 secs using 398.5% CPU
977  FLAVI+R6      62815.374    313 126256.748   127361.040   127570.872
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.336326 secs using 399.9% CPU
Optimizing NNI: done in 0.426244 secs using 398.7% CPU
Optimizing NNI: done in 0.42719 secs using 399.9% CPU
Optimizing NNI: done in 0.363262 secs using 399.7% CPU
Optimizing NNI: done in 0.295702 secs using 399.9% CPU
Optimizing NNI: done in 0.324812 secs using 399.6% CPU
Optimizing NNI: done in 0.433801 secs using 399.3% CPU
Iteration 70 / LogL: -35847.864 / Time: 0h:0m:28s (0h:0m:26s left)
Optimizing NNI: done in 0.394318 secs using 399.4% CPU
Optimizing NNI: done in 0.285282 secs using 399.9% CPU
Optimizing NNI: done in 0.352034 secs using 398.4% CPU
Optimizing NNI: done in 0.258056 secs using 400.4% CPU
Optimizing NNI: done in 0.423097 secs using 399.9% CPU
Optimizing NNI: done in 0.429563 secs using 399.4% CPU
Optimizing NNI: done in 0.326732 secs using 399.9% CPU
Optimizing NNI: done in 0.300519 secs using 398.9% CPU
Optimizing NNI: done in 0.328736 secs using 399.6% CPU
Optimizing NNI: done in 0.326881 secs using 399.6% CPU
Iteration 80 / LogL: -35852.127 / Time: 0h:0m:32s (0h:0m:22s left)
Optimizing NNI: done in 0.389844 secs using 399.2% CPU
Optimizing NNI: done in 0.351458 secs using 398.9% CPU
Optimizing NNI: done in 0.364234 secs using 397% CPU
264  Q.mammal+F+I+R10 106236.557   573 213619.113   871423.113   215925.934
Optimizing NNI: done in 0.404935 secs using 399.9% CPU
Optimizing NNI: done in 0.390852 secs using 398.8% CPU
Optimizing NNI: done in 0.358507 secs using 399.2% CPU
Optimizing NNI: done in 0.453916 secs using 399% CPU
Optimizing NNI: done in 0.46495 secs using 399.3% CPU
Optimizing NNI: done in 0.381031 secs using 399.3% CPU
Optimizing NNI: done in 0.395589 secs using 399.3% CPU
Iteration 90 / LogL: -35852.223 / Time: 0h:0m:36s (0h:0m:18s left)
Optimizing NNI: done in 0.347665 secs using 399% CPU
Optimizing NNI: done in 0.38275 secs using 399.6% CPU
Optimizing NNI: done in 0.326472 secs using 399.2% CPU
363  mtART+R10     203525.582   1005 409061.164   2431121.164  413437.306
Optimizing NNI: done in 0.358829 secs using 399.2% CPU
Optimizing NNI: done in 0.381013 secs using 399.3% CPU
Optimizing NNI: done in 0.299734 secs using 398.9% CPU
Optimizing NNI: done in 0.428636 secs using 398.7% CPU
Optimizing NNI: done in 0.371626 secs using 399.7% CPU
Optimizing NNI: done in 0.360661 secs using 399% CPU
Optimizing NNI: done in 0.369692 secs using 399% CPU
Iteration 100 / LogL: -35848.207 / Time: 0h:0m:39s (0h:0m:14s left)
978  FLAVI+R7      62789.908    315 126209.816   127340.952   127532.337
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.352089 secs using 397.8% CPU
Optimizing NNI: done in 0.388188 secs using 399.5% CPU
Optimizing NNI: done in 0.322456 secs using 398.9% CPU
Optimizing NNI: done in 0.431031 secs using 398.8% CPU
Optimizing NNI: done in 0.33396 secs using 398.9% CPU
Optimizing NNI: done in 0.27574 secs using 399.2% CPU
Optimizing NNI: done in 0.373149 secs using 398.7% CPU
Optimizing NNI: done in 0.316181 secs using 399.2% CPU
Optimizing NNI: done in 0.321069 secs using 398.5% CPU
Optimizing NNI: done in 0.334622 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -35846.908
Iteration 110 / LogL: -35846.908 / Time: 0h:0m:43s (0h:0m:9s left)
Optimizing NNI: done in 0.386584 secs using 399.3% CPU
Optimizing NNI: done in 0.379352 secs using 399.5% CPU
Optimizing NNI: done in 0.461385 secs using 399.5% CPU
Optimizing NNI: done in 0.325951 secs using 398.9% CPU
979  FLAVI+R8      62785.192    317 126204.383   127363.073   127535.301
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.401735 secs using 398.2% CPU
Optimizing NNI: done in 0.491857 secs using 399.6% CPU
Optimizing NNI: done in 0.517098 secs using 399.1% CPU
285  Q.insect+I+R9 105377.523   552 211859.046   822371.046   214081.324
Optimizing NNI: done in 0.338621 secs using 398.9% CPU
Optimizing NNI: done in 0.528032 secs using 399.3% CPU
Optimizing NNI: done in 0.332292 secs using 398% CPU
Iteration 120 / LogL: -35847.289 / Time: 0h:0m:47s (0h:0m:5s left)
Optimizing NNI: done in 0.368327 secs using 398.7% CPU
Optimizing NNI: done in 0.427274 secs using 399% CPU
Optimizing NNI: done in 0.308824 secs using 399.5% CPU
Optimizing NNI: done in 0.341365 secs using 399.5% CPU
Optimizing NNI: done in 0.436831 secs using 399.5% CPU
Optimizing NNI: done in 0.388675 secs using 399.1% CPU
Optimizing NNI: done in 0.546171 secs using 399.8% CPU
Optimizing NNI: done in 0.337621 secs using 399% CPU
Optimizing NNI: done in 0.383179 secs using 398.5% CPU
Optimizing NNI: done in 0.376514 secs using 399.5% CPU
Iteration 130 / LogL: -35851.319 / Time: 0h:0m:51s (0h:0m:1s left)
Optimizing NNI: done in 0.291622 secs using 399.5% CPU
Optimizing NNI: done in 0.351975 secs using 399.6% CPU
Optimizing NNI: done in 0.4078 secs using 399.5% CPU
Optimizing NNI: done in 0.404954 secs using 399.5% CPU
Optimizing NNI: done in 0.368521 secs using 398.7% CPU
Optimizing NNI: done in 0.399758 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 136 ITERATIONS / Time: 0h:0m:53s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35846.908
Optimal log-likelihood: -35846.905
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.374
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35846.905
Total tree length: 19.522

Total number of iterations: 136
CPU time used for tree search: 208.507 sec (0h:3m:28s)
Wall-clock time used for tree search: 53.159 sec (0h:0m:53s)
Total CPU time used: 210.941 sec (0h:3m:30s)
Total wall-clock time used: 53.731 sec (0h:0m:53s)

===> START BOOTSTRAP REPLICATE NUMBER 44

Creating bootstrap alignment (seed: 956203)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.018 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37879.867
2. Current log-likelihood: -37032.280
3. Current log-likelihood: -37021.413
4. Current log-likelihood: -37021.160
Optimal log-likelihood: -37021.115
Proportion of invariable sites: 0.027
Gamma shape alpha: 2.668
Parameters optimization took 4 rounds (0.229 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0773661 secs using 399.4% CPU
Computing ML distances took 0.077493 sec (of wall-clock time) 0.309224 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000168085 secs using 1630% CPU
Constructing RapidNJ tree: done in 0.00218201 secs using 400.5% CPU
Computing RapidNJ tree took 0.002408 sec (of wall-clock time) 0.011537 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37074.205
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.486 second
Computing log-likelihood of 98 initial trees ... 2.163 seconds
Current best score: -36893.263

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.516755 secs using 397.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36826.038
Optimizing NNI: done in 0.593472 secs using 399% CPU
Optimizing NNI: done in 0.86669 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -36825.937
Optimizing NNI: done in 0.55979 secs using 399.4% CPU
Optimizing NNI: done in 0.438361 secs using 399.1% CPU
Optimizing NNI: done in 0.559235 secs using 398.8% CPU
986  FLAVI+I+R6    62815.031    314 126258.062   127375.689   127576.385
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.581135 secs using 399.4% CPU
Optimizing NNI: done in 0.440649 secs using 398.3% CPU
Optimizing NNI: done in 0.562182 secs using 398.6% CPU
Optimizing NNI: done in 0.7784 secs using 398.8% CPU
Iteration 10 / LogL: -36826.284 / Time: 0h:0m:10s
Optimizing NNI: done in 0.564201 secs using 399.4% CPU
Optimizing NNI: done in 0.569768 secs using 398.4% CPU
Optimizing NNI: done in 0.40851 secs using 398.6% CPU
Optimizing NNI: done in 0.4263 secs using 398.3% CPU
Optimizing NNI: done in 0.562831 secs using 399.2% CPU
Optimizing NNI: done in 0.687521 secs using 399.2% CPU
Optimizing NNI: done in 0.459876 secs using 399.4% CPU
Optimizing NNI: done in 0.561435 secs using 398.9% CPU
372  mtART+F+R8    200433.253   1020 402906.506   2485746.506  407347.964
Optimizing NNI: done in 0.582635 secs using 398.3% CPU
Optimizing NNI: done in 0.734334 secs using 399.2% CPU
Iteration 20 / LogL: -36831.133 / Time: 0h:0m:15s
Finish initializing candidate tree set (9)
Current best tree score: -36825.937 / CPU time: 15.349
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.58108 secs using 399.2% CPU
Optimizing NNI: done in 0.360678 secs using 399.4% CPU
Optimizing NNI: done in 0.311506 secs using 399.1% CPU
Optimizing NNI: done in 0.549783 secs using 397.7% CPU
Optimizing NNI: done in 0.351239 secs using 397.6% CPU
Optimizing NNI: done in 0.564665 secs using 398.5% CPU
Optimizing NNI: done in 0.385209 secs using 397.8% CPU
Optimizing NNI: done in 0.337744 secs using 398.3% CPU
Optimizing NNI: done in 0.402924 secs using 398% CPU
Optimizing NNI: done in 0.34923 secs using 398.3% CPU
Iteration 30 / LogL: -36826.774 / Time: 0h:0m:20s (0h:0m:50s left)
Optimizing NNI: done in 0.374722 secs using 399.1% CPU
Optimizing NNI: done in 0.549017 secs using 399.2% CPU
Optimizing NNI: done in 0.34304 secs using 399.9% CPU
Optimizing NNI: done in 0.462347 secs using 399.5% CPU
Optimizing NNI: done in 0.488251 secs using 399.7% CPU
Optimizing NNI: done in 0.385715 secs using 399.5% CPU
Optimizing NNI: done in 0.579988 secs using 398.8% CPU
Optimizing NNI: done in 0.350186 secs using 399.6% CPU
Optimizing NNI: done in 0.282594 secs using 399.9% CPU
Optimizing NNI: done in 0.394685 secs using 399.5% CPU
Iteration 40 / LogL: -36833.583 / Time: 0h:0m:24s (0h:0m:39s left)
Optimizing NNI: done in 0.330251 secs using 399% CPU
987  FLAVI+I+R7    62789.557    316 126211.114   127355.937   127537.833
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.512081 secs using 399.8% CPU
Optimizing NNI: done in 0.273962 secs using 398.8% CPU
Optimizing NNI: done in 0.393698 secs using 399.7% CPU
Optimizing NNI: done in 0.501686 secs using 399.5% CPU
Optimizing NNI: done in 0.425726 secs using 399.9% CPU
Optimizing NNI: done in 0.262148 secs using 399.2% CPU
Optimizing NNI: done in 0.389369 secs using 399.8% CPU
Optimizing NNI: done in 0.436876 secs using 399.2% CPU
Optimizing NNI: done in 0.315666 secs using 399.3% CPU
Iteration 50 / LogL: -36826.877 / Time: 0h:0m:28s (0h:0m:30s left)
Optimizing NNI: done in 0.52949 secs using 398.5% CPU
Optimizing NNI: done in 0.389097 secs using 399.6% CPU
Optimizing NNI: done in 0.311807 secs using 398.3% CPU
Optimizing NNI: done in 0.4746 secs using 399.5% CPU
Optimizing NNI: done in 0.367583 secs using 399.4% CPU
Optimizing NNI: done in 0.4288 secs using 399.5% CPU
Optimizing NNI: done in 0.316802 secs using 399.9% CPU
Optimizing NNI: done in 0.574611 secs using 399.3% CPU
Optimizing NNI: done in 0.349666 secs using 400.2% CPU
Optimizing NNI: done in 0.370643 secs using 399.9% CPU
Iteration 60 / LogL: -36826.034 / Time: 0h:0m:32s (0h:0m:23s left)
Optimizing NNI: done in 0.363481 secs using 398.5% CPU
Optimizing NNI: done in 0.425139 secs using 398.3% CPU
Optimizing NNI: done in 0.42695 secs using 398.8% CPU
Optimizing NNI: done in 0.33493 secs using 399.4% CPU
Optimizing NNI: done in 0.613506 secs using 399.6% CPU
Optimizing NNI: done in 0.325565 secs using 399.6% CPU
Optimizing NNI: done in 0.323882 secs using 399.9% CPU
Optimizing NNI: done in 0.580478 secs using 399.5% CPU
Optimizing NNI: done in 0.3466 secs using 399% CPU
Optimizing NNI: done in 0.543345 secs using 398.3% CPU
Iteration 70 / LogL: -36826.036 / Time: 0h:0m:36s (0h:0m:17s left)
Optimizing NNI: done in 0.395707 secs using 398.5% CPU
Optimizing NNI: done in 0.51241 secs using 398.5% CPU
Optimizing NNI: done in 0.504712 secs using 399.9% CPU
Optimizing NNI: done in 0.625917 secs using 399.6% CPU
Optimizing NNI: done in 0.349778 secs using 399% CPU
Optimizing NNI: done in 0.372986 secs using 399.9% CPU
Optimizing NNI: done in 0.548683 secs using 399.4% CPU
Optimizing NNI: done in 0.463251 secs using 399% CPU
Optimizing NNI: done in 0.561091 secs using 398.8% CPU
Optimizing NNI: done in 0.519148 secs using 399.3% CPU
Iteration 80 / LogL: -36835.010 / Time: 0h:0m:41s (0h:0m:12s left)
999  FLAVI+F+R6    62636.840    332 125937.679   127328.321   127331.574
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.492419 secs using 399.1% CPU
Optimizing NNI: done in 0.473302 secs using 399.7% CPU
Optimizing NNI: done in 0.400604 secs using 399.6% CPU
Optimizing NNI: done in 0.553615 secs using 398.7% CPU
Optimizing NNI: done in 0.677584 secs using 397.9% CPU
Optimizing NNI: done in 0.554217 secs using 398.5% CPU
Optimizing NNI: done in 0.598351 secs using 399.1% CPU
Optimizing NNI: done in 0.398658 secs using 398.8% CPU
Optimizing NNI: done in 0.371721 secs using 398% CPU
Optimizing NNI: done in 0.337416 secs using 398.1% CPU
Iteration 90 / LogL: -36827.179 / Time: 0h:0m:46s (0h:0m:6s left)
Optimizing NNI: done in 0.262132 secs using 398.3% CPU
Optimizing NNI: done in 0.454821 secs using 397.8% CPU
Optimizing NNI: done in 0.575201 secs using 399.9% CPU
Optimizing NNI: done in 0.498173 secs using 398.9% CPU
Optimizing NNI: done in 0.567291 secs using 397.8% CPU
Optimizing NNI: done in 0.41633 secs using 399.3% CPU
Optimizing NNI: done in 0.446865 secs using 399.2% CPU
Optimizing NNI: done in 0.378223 secs using 398.1% CPU
Optimizing NNI: done in 0.393591 secs using 397.6% CPU
Optimizing NNI: done in 0.383216 secs using 399.5% CPU
Iteration 100 / LogL: -36825.940 / Time: 0h:0m:50s (0h:0m:1s left)
Optimizing NNI: done in 0.571568 secs using 398.4% CPU
Optimizing NNI: done in 0.397054 secs using 399.9% CPU
Optimizing NNI: done in 0.401611 secs using 399.3% CPU
Optimizing NNI: done in 0.487301 secs using 399.7% CPU
TREE SEARCH COMPLETED AFTER 104 ITERATIONS / Time: 0h:0m:52s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36825.937
Optimal log-likelihood: -36825.937
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.625
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36825.937
Total tree length: 20.225

Total number of iterations: 104
CPU time used for tree search: 204.778 sec (0h:3m:24s)
Wall-clock time used for tree search: 52.272 sec (0h:0m:52s)
Total CPU time used: 206.825 sec (0h:3m:26s)
Total wall-clock time used: 52.760 sec (0h:0m:52s)

===> START BOOTSTRAP REPLICATE NUMBER 45

Creating bootstrap alignment (seed: 956204)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36373.887
2. Current log-likelihood: -35478.063
3. Current log-likelihood: -35464.726
4. Current log-likelihood: -35464.189
Optimal log-likelihood: -35464.049
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.533
Parameters optimization took 4 rounds (0.279 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.075783 secs using 398.1% CPU
Computing ML distances took 0.075908 sec (of wall-clock time) 0.302034 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000156879 secs using 423.3% CPU
Constructing RapidNJ tree: done in 0.00225186 secs using 493.4% CPU
Computing RapidNJ tree took 0.002465 sec (of wall-clock time) 0.012335 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36034.747
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.478 second
Computing log-likelihood of 98 initial trees ... 1.625 seconds
Current best score: -35451.488

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.223241 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35399.768
Optimizing NNI: done in 0.221721 secs using 398.5% CPU
Optimizing NNI: done in 0.264803 secs using 397.6% CPU
Estimate model parameters (epsilon = 0.100)
1000  FLAVI+F+R7    62615.110    334 125898.220   127323.570   127300.512
WARNING: Normalizing state frequencies so that sum of them equals to 1
UPDATE BEST LOG-LIKELIHOOD: -35399.711
Optimizing NNI: done in 0.203919 secs using 399.9% CPU
Optimizing NNI: done in 0.236759 secs using 399.9% CPU
Optimizing NNI: done in 0.237096 secs using 399% CPU
Optimizing NNI: done in 0.247951 secs using 399.7% CPU
Optimizing NNI: done in 0.253174 secs using 399% CPU
Optimizing NNI: done in 0.272279 secs using 399.9% CPU
Optimizing NNI: done in 0.229387 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 10: -35399.430
Iteration 10 / LogL: -35399.430 / Time: 0h:0m:6s
Optimizing NNI: done in 0.261529 secs using 398.7% CPU
Optimizing NNI: done in 0.234619 secs using 399.1% CPU
Optimizing NNI: done in 0.225918 secs using 399.9% CPU
Optimizing NNI: done in 0.267561 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35399.381
Optimizing NNI: done in 0.233291 secs using 399.5% CPU
Optimizing NNI: done in 0.209419 secs using 400.7% CPU
Optimizing NNI: done in 0.228587 secs using 399.5% CPU
Optimizing NNI: done in 0.222499 secs using 398.1% CPU
Optimizing NNI: done in 0.224632 secs using 399.9% CPU
Optimizing NNI: done in 0.237829 secs using 399.5% CPU
Iteration 20 / LogL: -35399.775 / Time: 0h:0m:8s
Finish initializing candidate tree set (7)
Current best tree score: -35399.381 / CPU time: 8.091
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.367609 secs using 399.1% CPU
Optimizing NNI: done in 0.333501 secs using 399.3% CPU
Optimizing NNI: done in 0.331904 secs using 399.4% CPU
Optimizing NNI: done in 0.359409 secs using 400% CPU
Optimizing NNI: done in 0.491347 secs using 398.3% CPU
1001  FLAVI+F+R8    62610.598    336 125893.196   127354.254   127303.885
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.366602 secs using 398.8% CPU
Optimizing NNI: done in 0.438229 secs using 398.3% CPU
Optimizing NNI: done in 0.396665 secs using 399.4% CPU
Optimizing NNI: done in 0.388685 secs using 399.3% CPU
Optimizing NNI: done in 0.365026 secs using 399.9% CPU
Iteration 30 / LogL: -35400.202 / Time: 0h:0m:12s (0h:0m:34s left)
Optimizing NNI: done in 0.391318 secs using 399.8% CPU
Optimizing NNI: done in 0.413908 secs using 399.6% CPU
373  mtART+F+R9    200385.741   1022 402815.481   2493827.481  407265.647
Optimizing NNI: done in 0.431584 secs using 398.5% CPU
Optimizing NNI: done in 0.7168 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35399.363
Optimizing NNI: done in 0.328712 secs using 399% CPU
Optimizing NNI: done in 0.403776 secs using 399.3% CPU
Optimizing NNI: done in 0.349301 secs using 399.6% CPU
Optimizing NNI: done in 0.580856 secs using 399.2% CPU
Optimizing NNI: done in 0.317034 secs using 399.9% CPU
Optimizing NNI: done in 0.337596 secs using 399.6% CPU
Iteration 40 / LogL: -35399.398 / Time: 0h:0m:17s (0h:0m:30s left)
Optimizing NNI: done in 0.415563 secs using 399.6% CPU
Optimizing NNI: done in 0.328908 secs using 399.9% CPU
Optimizing NNI: done in 0.377059 secs using 399.9% CPU
Optimizing NNI: done in 0.38767 secs using 399.8% CPU
Optimizing NNI: done in 0.327553 secs using 398.9% CPU
Optimizing NNI: done in 0.478855 secs using 399.9% CPU
Optimizing NNI: done in 0.391147 secs using 399.7% CPU
Optimizing NNI: done in 0.423483 secs using 399.9% CPU
Optimizing NNI: done in 0.335461 secs using 398.5% CPU
Optimizing NNI: done in 0.328351 secs using 398.7% CPU
Iteration 50 / LogL: -35400.196 / Time: 0h:0m:20s (0h:0m:25s left)
Optimizing NNI: done in 0.349173 secs using 399% CPU
Optimizing NNI: done in 0.440302 secs using 398.5% CPU
Optimizing NNI: done in 0.392581 secs using 399.6% CPU
Optimizing NNI: done in 0.310523 secs using 399.6% CPU
Optimizing NNI: done in 0.37387 secs using 399.6% CPU
Optimizing NNI: done in 0.453059 secs using 399% CPU
Optimizing NNI: done in 0.460467 secs using 400.3% CPU
Optimizing NNI: done in 0.433929 secs using 399% CPU
Optimizing NNI: done in 0.455092 secs using 399.4% CPU
Optimizing NNI: done in 0.405193 secs using 399% CPU
Iteration 60 / LogL: -35807.764 / Time: 0h:0m:24s (0h:0m:21s left)
Optimizing NNI: done in 0.447892 secs using 399.3% CPU
Optimizing NNI: done in 0.336854 secs using 400.2% CPU
Optimizing NNI: done in 0.347207 secs using 399.6% CPU
Optimizing NNI: done in 0.338354 secs using 399.8% CPU
Optimizing NNI: done in 0.260324 secs using 399.9% CPU
Optimizing NNI: done in 0.499535 secs using 399.7% CPU
Optimizing NNI: done in 0.339319 secs using 399.6% CPU
1008  FLAVI+F+I+R6  62636.276    333 125938.552   127346.426   127336.646
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.406693 secs using 399.4% CPU
Optimizing NNI: done in 0.462941 secs using 399.3% CPU
Optimizing NNI: done in 0.298847 secs using 399% CPU
Iteration 70 / LogL: -35399.466 / Time: 0h:0m:28s (0h:0m:16s left)
Optimizing NNI: done in 0.29636 secs using 399.7% CPU
Optimizing NNI: done in 0.474235 secs using 399.5% CPU
Optimizing NNI: done in 0.370394 secs using 399.9% CPU
Optimizing NNI: done in 0.319081 secs using 399.9% CPU
Optimizing NNI: done in 0.308809 secs using 399.5% CPU
Optimizing NNI: done in 0.272496 secs using 399% CPU
Optimizing NNI: done in 0.414097 secs using 398.6% CPU
Optimizing NNI: done in 0.387647 secs using 398.4% CPU
Optimizing NNI: done in 0.335787 secs using 399% CPU
Optimizing NNI: done in 0.521934 secs using 398.8% CPU
Iteration 80 / LogL: -35399.817 / Time: 0h:0m:32s (0h:0m:12s left)
Optimizing NNI: done in 0.385914 secs using 399.3% CPU
Optimizing NNI: done in 0.393034 secs using 398.9% CPU
Optimizing NNI: done in 0.444367 secs using 399.9% CPU
Optimizing NNI: done in 0.390506 secs using 399.9% CPU
Optimizing NNI: done in 0.36888 secs using 399.8% CPU
286  Q.insect+I+R10 105372.681   554 211853.361   826793.361   214083.691
Optimizing NNI: done in 0.323193 secs using 399.6% CPU
Optimizing NNI: done in 0.46338 secs using 398.8% CPU
Optimizing NNI: done in 0.457904 secs using 398.3% CPU
Optimizing NNI: done in 0.378845 secs using 399.8% CPU
Optimizing NNI: done in 0.345449 secs using 399.5% CPU
Iteration 90 / LogL: -35399.761 / Time: 0h:0m:36s (0h:0m:8s left)
Optimizing NNI: done in 0.383425 secs using 399.8% CPU
Optimizing NNI: done in 0.385773 secs using 399.5% CPU
Optimizing NNI: done in 0.429592 secs using 398.4% CPU
Optimizing NNI: done in 0.353009 secs using 398.2% CPU
Optimizing NNI: done in 0.299039 secs using 398.6% CPU
Optimizing NNI: done in 0.303812 secs using 399.5% CPU
Optimizing NNI: done in 0.397402 secs using 399.7% CPU
Optimizing NNI: done in 0.361687 secs using 399.7% CPU
Optimizing NNI: done in 0.324422 secs using 399% CPU
Optimizing NNI: done in 0.327205 secs using 399.6% CPU
Iteration 100 / LogL: -35401.001 / Time: 0h:0m:40s (0h:0m:4s left)
Optimizing NNI: done in 0.284747 secs using 399.2% CPU
Optimizing NNI: done in 0.34828 secs using 399.7% CPU
Optimizing NNI: done in 0.436856 secs using 399.9% CPU
Optimizing NNI: done in 0.41582 secs using 399.2% CPU
1009  FLAVI+F+I+R7  62614.816    335 125899.631   127342.708   127306.122
Optimizing NNI: done in 0.382028 secs using 398.6% CPU
Optimizing NNI: done in 0.379451 secs using 399.3% CPU
Optimizing NNI: done in 0.378872 secs using 399.4% CPU
Optimizing NNI: done in 0.409263 secs using 399.3% CPU
Optimizing NNI: done in 0.421281 secs using 400.3% CPU
Optimizing NNI: done in 0.394731 secs using 399.9% CPU
Iteration 110 / LogL: -35399.692 / Time: 0h:0m:43s (0h:0m:0s left)
Optimizing NNI: done in 0.42275 secs using 399.6% CPU
TREE SEARCH COMPLETED AFTER 111 ITERATIONS / Time: 0h:0m:44s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35399.363
Optimal log-likelihood: -35399.363
Proportion of invariable sites: 0.029
Gamma shape alpha: 2.489
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -35399.363
Total tree length: 19.316

Total number of iterations: 111
CPU time used for tree search: 170.643 sec (0h:2m:50s)
Wall-clock time used for tree search: 43.711 sec (0h:0m:43s)
Total CPU time used: 173.704 sec (0h:2m:53s)
Total wall-clock time used: 44.431 sec (0h:0m:44s)

===> START BOOTSTRAP REPLICATE NUMBER 46

Creating bootstrap alignment (seed: 956205)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36591.343
2. Current log-likelihood: -35763.135
3. Current log-likelihood: -35746.782
4. Current log-likelihood: -35745.942
Optimal log-likelihood: -35745.918
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.284
Parameters optimization took 4 rounds (0.256 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.074615 secs using 400% CPU
Computing ML distances took 0.074748 sec (of wall-clock time) 0.298812 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000153065 secs using 420.7% CPU
Constructing RapidNJ tree: done in 0.00219202 secs using 419.4% CPU
Computing RapidNJ tree took 0.002407 sec (of wall-clock time) 0.010165 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36370.431
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.439 second
Computing log-likelihood of 98 initial trees ... 1.568 seconds
Current best score: -35740.133

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.24226 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35681.858
Optimizing NNI: done in 0.28608 secs using 398.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -35681.857
Optimizing NNI: done in 0.274612 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -35681.721
Optimizing NNI: done in 0.225758 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -35681.391
Optimizing NNI: done in 0.260761 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -35681.258
Optimizing NNI: done in 0.260734 secs using 399.5% CPU
Optimizing NNI: done in 0.274686 secs using 399.9% CPU
Optimizing NNI: done in 0.275218 secs using 399.9% CPU
Optimizing NNI: done in 0.255336 secs using 399.4% CPU
Optimizing NNI: done in 0.277463 secs using 399.8% CPU
Iteration 10 / LogL: -35681.740 / Time: 0h:0m:6s
Optimizing NNI: done in 0.273989 secs using 399.2% CPU
Optimizing NNI: done in 0.24469 secs using 397.8% CPU
Optimizing NNI: done in 0.26338 secs using 398.8% CPU
Optimizing NNI: done in 0.264047 secs using 399.2% CPU
Optimizing NNI: done in 0.26097 secs using 398.1% CPU
Optimizing NNI: done in 0.244364 secs using 400.6% CPU
Optimizing NNI: done in 0.275543 secs using 399.5% CPU
Optimizing NNI: done in 0.258349 secs using 399.5% CPU
Optimizing NNI: done in 0.286754 secs using 398.8% CPU
Optimizing NNI: done in 0.271097 secs using 398.1% CPU
Iteration 20 / LogL: -35681.310 / Time: 0h:0m:8s
Finish initializing candidate tree set (4)
Current best tree score: -35681.258 / CPU time: 8.513
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.396365 secs using 398.3% CPU
Optimizing NNI: done in 0.382197 secs using 398.3% CPU
Optimizing NNI: done in 0.372449 secs using 399.8% CPU
Optimizing NNI: done in 0.386653 secs using 399.9% CPU
Optimizing NNI: done in 0.39612 secs using 399.1% CPU
Optimizing NNI: done in 0.386973 secs using 399.7% CPU
Optimizing NNI: done in 0.28233 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -35679.454
Optimizing NNI: done in 0.408572 secs using 398.7% CPU
Optimizing NNI: done in 0.372305 secs using 400.4% CPU
Optimizing NNI: done in 0.374764 secs using 399.9% CPU
Iteration 30 / LogL: -35681.847 / Time: 0h:0m:12s (0h:0m:42s left)
Optimizing NNI: done in 0.412122 secs using 398.7% CPU
Optimizing NNI: done in 0.432072 secs using 398.3% CPU
Optimizing NNI: done in 0.432481 secs using 398.3% CPU
Optimizing NNI: done in 0.385515 secs using 398.8% CPU
1021  HIVb+R6       61602.342    313 123830.684   124934.976   125144.808
Optimizing NNI: done in 0.413619 secs using 398.4% CPU
Optimizing NNI: done in 0.398726 secs using 398.9% CPU
Optimizing NNI: done in 0.456416 secs using 399.5% CPU
Optimizing NNI: done in 0.411718 secs using 399.2% CPU
Optimizing NNI: done in 0.357823 secs using 399.2% CPU
Optimizing NNI: done in 0.340081 secs using 399.9% CPU
Iteration 40 / LogL: -35681.326 / Time: 0h:0m:16s (0h:0m:37s left)
Optimizing NNI: done in 0.305399 secs using 398.9% CPU
307  Q.insect+F+I+R9 105543.746   571 212229.491   865453.491   214528.261
Optimizing NNI: done in 0.401048 secs using 399.6% CPU
Optimizing NNI: done in 0.422407 secs using 399.1% CPU
Optimizing NNI: done in 0.386558 secs using 398.7% CPU
Optimizing NNI: done in 0.374009 secs using 399.5% CPU
Optimizing NNI: done in 0.445949 secs using 400% CPU
Optimizing NNI: done in 0.336344 secs using 399.3% CPU
Optimizing NNI: done in 0.516498 secs using 399.7% CPU
Optimizing NNI: done in 0.386817 secs using 399.7% CPU
1022  HIVb+R7       61598.334    315 123826.667   124957.804   125149.188
Optimizing NNI: done in 0.43508 secs using 399.1% CPU
Iteration 50 / LogL: -35681.755 / Time: 0h:0m:20s (0h:0m:32s left)
Optimizing NNI: done in 0.314327 secs using 399.9% CPU
Optimizing NNI: done in 0.309276 secs using 399.7% CPU
Optimizing NNI: done in 0.436455 secs using 399.9% CPU
Optimizing NNI: done in 0.370658 secs using 400% CPU
Optimizing NNI: done in 0.40349 secs using 399.4% CPU
Optimizing NNI: done in 0.512951 secs using 399.5% CPU
Optimizing NNI: done in 0.329198 secs using 399.3% CPU
Optimizing NNI: done in 0.488097 secs using 399.7% CPU
Optimizing NNI: done in 0.339892 secs using 399.3% CPU
Optimizing NNI: done in 0.422875 secs using 399.3% CPU
Iteration 60 / LogL: -35679.883 / Time: 0h:0m:24s (0h:0m:28s left)
Optimizing NNI: done in 0.41471 secs using 399.2% CPU
Optimizing NNI: done in 0.369616 secs using 399.3% CPU
Optimizing NNI: done in 0.3693 secs using 399.7% CPU
Optimizing NNI: done in 0.227561 secs using 399.1% CPU
Optimizing NNI: done in 0.391955 secs using 399.7% CPU
Optimizing NNI: done in 0.374236 secs using 399.4% CPU
Optimizing NNI: done in 0.319249 secs using 399.8% CPU
Optimizing NNI: done in 0.376839 secs using 399% CPU
Optimizing NNI: done in 0.458129 secs using 399.1% CPU
Optimizing NNI: done in 0.364336 secs using 398.8% CPU
Iteration 70 / LogL: -35679.494 / Time: 0h:0m:28s (0h:0m:23s left)
Optimizing NNI: done in 0.37074 secs using 399.1% CPU
Optimizing NNI: done in 0.3899 secs using 399.3% CPU
Optimizing NNI: done in 0.380054 secs using 399.6% CPU
Optimizing NNI: done in 0.451655 secs using 398.7% CPU
Optimizing NNI: done in 0.366947 secs using 398.8% CPU
Optimizing NNI: done in 0.39689 secs using 397.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -35679.448
Optimizing NNI: done in 0.351914 secs using 398.1% CPU
Optimizing NNI: done in 0.301064 secs using 399.5% CPU
Optimizing NNI: done in 0.399079 secs using 398.1% CPU
Optimizing NNI: done in 0.337068 secs using 398.7% CPU
Iteration 80 / LogL: -35679.534 / Time: 0h:0m:32s (0h:0m:19s left)
Optimizing NNI: done in 0.371355 secs using 397.7% CPU
Optimizing NNI: done in 0.484791 secs using 398.7% CPU
Optimizing NNI: done in 0.385054 secs using 398.8% CPU
374  mtART+F+R10   200379.364   1024 402806.728   2502006.728  407265.603
Optimizing NNI: done in 0.301557 secs using 398.7% CPU
Optimizing NNI: done in 0.370681 secs using 398.6% CPU
Optimizing NNI: done in 0.326727 secs using 400.3% CPU
Optimizing NNI: done in 0.390874 secs using 399.9% CPU
Optimizing NNI: done in 0.388832 secs using 398.6% CPU
Optimizing NNI: done in 0.390609 secs using 399.6% CPU
Optimizing NNI: done in 0.46525 secs using 398.9% CPU
Iteration 90 / LogL: -35679.482 / Time: 0h:0m:36s (0h:0m:15s left)
Optimizing NNI: done in 0.408615 secs using 399% CPU
Optimizing NNI: done in 0.296659 secs using 400% CPU
Optimizing NNI: done in 0.27582 secs using 399.6% CPU
Optimizing NNI: done in 0.367118 secs using 399.9% CPU
Optimizing NNI: done in 0.544347 secs using 398.4% CPU
1030  HIVb+I+R6     61601.684    314 123831.369   124948.996   125149.691
Optimizing NNI: done in 0.481421 secs using 398.8% CPU
Optimizing NNI: done in 0.329955 secs using 400.6% CPU
Optimizing NNI: done in 0.296236 secs using 399.6% CPU
Optimizing NNI: done in 0.372911 secs using 399.9% CPU
Optimizing NNI: done in 0.376977 secs using 399.6% CPU
Iteration 100 / LogL: -35681.394 / Time: 0h:0m:40s (0h:0m:10s left)
Optimizing NNI: done in 0.378926 secs using 399.1% CPU
Optimizing NNI: done in 0.409935 secs using 399.5% CPU
Optimizing NNI: done in 0.371959 secs using 398.9% CPU
Optimizing NNI: done in 0.427095 secs using 399.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -35679.447
Optimizing NNI: done in 0.331906 secs using 399.6% CPU
Optimizing NNI: done in 0.406625 secs using 399.4% CPU
Optimizing NNI: done in 0.463152 secs using 399.3% CPU
Optimizing NNI: done in 0.455081 secs using 399.2% CPU
1031  HIVb+I+R7     61598.003    316 123828.006   124972.828   125154.725
Optimizing NNI: done in 0.352662 secs using 399.6% CPU
Optimizing NNI: done in 0.355715 secs using 399.6% CPU
Iteration 110 / LogL: -35681.336 / Time: 0h:0m:44s (0h:0m:6s left)
Optimizing NNI: done in 0.477641 secs using 399.3% CPU
Optimizing NNI: done in 0.345994 secs using 399% CPU
Optimizing NNI: done in 0.383303 secs using 399.1% CPU
Optimizing NNI: done in 0.376195 secs using 399.2% CPU
Optimizing NNI: done in 0.438322 secs using 399.9% CPU
Optimizing NNI: done in 0.3205 secs using 399% CPU
Optimizing NNI: done in 0.28715 secs using 399.9% CPU
Optimizing NNI: done in 0.334814 secs using 399.9% CPU
Optimizing NNI: done in 0.448568 secs using 399.9% CPU
Optimizing NNI: done in 0.384937 secs using 399.9% CPU
Iteration 120 / LogL: -35681.785 / Time: 0h:0m:47s (0h:0m:2s left)
Optimizing NNI: done in 0.394618 secs using 398.1% CPU
Optimizing NNI: done in 0.312831 secs using 399.7% CPU
Optimizing NNI: done in 0.574104 secs using 399.2% CPU
Optimizing NNI: done in 0.404059 secs using 399.2% CPU
Optimizing NNI: done in 0.318312 secs using 399.4% CPU
Optimizing NNI: done in 0.415687 secs using 399.9% CPU
Optimizing NNI: done in 0.433648 secs using 398.8% CPU
Optimizing NNI: done in 0.461785 secs using 399.5% CPU
TREE SEARCH COMPLETED AFTER 128 ITERATIONS / Time: 0h:0m:51s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35679.447
Optimal log-likelihood: -35679.445
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.295
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35679.445
Total tree length: 19.975

Total number of iterations: 128
CPU time used for tree search: 199.159 sec (0h:3m:19s)
Wall-clock time used for tree search: 50.803 sec (0h:0m:50s)
Total CPU time used: 201.336 sec (0h:3m:21s)
Total wall-clock time used: 51.320 sec (0h:0m:51s)

===> START BOOTSTRAP REPLICATE NUMBER 47

Creating bootstrap alignment (seed: 956206)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36274.731
2. Current log-likelihood: -35508.426
3. Current log-likelihood: -35490.004
4. Current log-likelihood: -35489.385
Optimal log-likelihood: -35489.304
Proportion of invariable sites: 0.026
Gamma shape alpha: 2.398
Parameters optimization took 4 rounds (0.266 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.072994 secs using 400% CPU
Computing ML distances took 0.073126 sec (of wall-clock time) 0.292326 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000138998 secs using 428.1% CPU
Constructing RapidNJ tree: done in 0.00215793 secs using 509.6% CPU
Computing RapidNJ tree took 0.002353 sec (of wall-clock time) 0.011902 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36024.107
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 383  mtZOA+R8      198366.129   1001 398734.257   2404738.257  403092.982
1.532 second
Computing log-likelihood of 98 initial trees ... 1.569 seconds
Current best score: -35469.192

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.239326 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35421.115
Optimizing NNI: done in 0.289613 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35420.076
Optimizing NNI: done in 0.259038 secs using 399.5% CPU
Optimizing NNI: done in 0.283817 secs using 399.6% CPU
Optimizing NNI: done in 0.2977 secs using 399.2% CPU
Optimizing NNI: done in 0.30317 secs using 399.6% CPU
Optimizing NNI: done in 0.296712 secs using 398.6% CPU
Optimizing NNI: done in 0.299563 secs using 399.7% CPU
Optimizing NNI: done in 0.292433 secs using 400% CPU
Optimizing NNI: done in 0.311958 secs using 398.3% CPU
Iteration 10 / LogL: -35420.076 / Time: 0h:0m:6s
Optimizing NNI: done in 0.280842 secs using 399.6% CPU
Optimizing NNI: done in 0.288328 secs using 399.3% CPU
Optimizing NNI: done in 0.282033 secs using 399% CPU
Optimizing NNI: done in 0.288291 secs using 400.2% CPU
Optimizing NNI: done in 0.285253 secs using 399.9% CPU
Optimizing NNI: done in 0.221418 secs using 399.9% CPU
Optimizing NNI: done in 0.238037 secs using 399.8% CPU
Optimizing NNI: done in 0.264042 secs using 399.9% CPU
Optimizing NNI: done in 0.284075 secs using 399.6% CPU
Optimizing NNI: done in 0.281967 secs using 399.9% CPU
Iteration 20 / LogL: -35420.077 / Time: 0h:0m:9s
Finish initializing candidate tree set (3)
Current best tree score: -35420.076 / CPU time: 8.839
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
1043  HIVb+F+R6     61283.289    332 123230.577   124621.219   124624.472
Optimizing NNI: done in 0.365661 secs using 398.9% CPU
Optimizing NNI: done in 0.407068 secs using 400% CPU
Optimizing NNI: done in 0.455795 secs using 398.8% CPU
Optimizing NNI: done in 0.351227 secs using 399.6% CPU
Optimizing NNI: done in 0.338256 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -35419.624
Optimizing NNI: done in 0.298862 secs using 399.9% CPU
Optimizing NNI: done in 0.398413 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -35418.915
Optimizing NNI: done in 0.436283 secs using 399.5% CPU
Optimizing NNI: done in 0.311492 secs using 399.8% CPU
Optimizing NNI: done in 0.304689 secs using 399.9% CPU
Iteration 30 / LogL: -35420.116 / Time: 0h:0m:13s (0h:0m:44s left)
Optimizing NNI: done in 0.414166 secs using 399.2% CPU
Optimizing NNI: done in 0.37338 secs using 399.1% CPU
Optimizing NNI: done in 0.465391 secs using 399.7% CPU
Optimizing NNI: done in 0.399571 secs using 399.9% CPU
Optimizing NNI: done in 0.37117 secs using 399.6% CPU
1044  HIVb+F+R7     61279.972    334 123227.944   124653.294   124630.236
Optimizing NNI: done in 0.309368 secs using 398.9% CPU
Optimizing NNI: done in 0.344242 secs using 399.9% CPU
Optimizing NNI: done in 0.559251 secs using 399.6% CPU
Optimizing NNI: done in 0.333855 secs using 400.1% CPU
Optimizing NNI: done in 0.393701 secs using 399.4% CPU
Iteration 40 / LogL: -35419.111 / Time: 0h:0m:17s (0h:0m:38s left)
Optimizing NNI: done in 0.452179 secs using 399.3% CPU
Optimizing NNI: done in 0.439463 secs using 399.9% CPU
Optimizing NNI: done in 0.516134 secs using 398.9% CPU
Optimizing NNI: done in 0.442475 secs using 399.9% CPU
Optimizing NNI: done in 0.341229 secs using 399.6% CPU
Optimizing NNI: done in 0.533014 secs using 399.3% CPU
Optimizing NNI: done in 0.340755 secs using 399.9% CPU
Optimizing NNI: done in 0.37737 secs using 399.9% CPU
Optimizing NNI: done in 0.378574 secs using 399.9% CPU
Optimizing NNI: done in 0.347729 secs using 399.3% CPU
Iteration 50 / LogL: -35419.590 / Time: 0h:0m:21s (0h:0m:33s left)
Optimizing NNI: done in 0.357756 secs using 399.9% CPU
Optimizing NNI: done in 0.415553 secs using 399.6% CPU
Optimizing NNI: done in 0.350147 secs using 399.6% CPU
Optimizing NNI: done in 0.325538 secs using 399.9% CPU
Optimizing NNI: done in 0.325801 secs using 399.6% CPU
Optimizing NNI: done in 0.297853 secs using 398.5% CPU
Optimizing NNI: done in 0.491013 secs using 399.7% CPU
Optimizing NNI: done in 0.37141 secs using 399.6% CPU
Optimizing NNI: done in 0.384396 secs using 398.3% CPU
Optimizing NNI: done in 0.350062 secs using 399.3% CPU
Iteration 60 / LogL: -35419.316 / Time: 0h:0m:25s (0h:0m:28s left)
Optimizing NNI: done in 0.354689 secs using 399.9% CPU
Optimizing NNI: done in 0.331353 secs using 399.9% CPU
Optimizing NNI: done in 0.389658 secs using 399.2% CPU
Optimizing NNI: done in 0.506707 secs using 399.3% CPU
Optimizing NNI: done in 0.313038 secs using 399.9% CPU
Optimizing NNI: done in 0.321653 secs using 399.6% CPU
Optimizing NNI: done in 0.378379 secs using 399.9% CPU
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Optimizing NNI: done in 0.326563 secs using 399.9% CPU
Optimizing NNI: done in 0.452212 secs using 399% CPU
Iteration 70 / LogL: -35420.088 / Time: 0h:0m:28s (0h:0m:23s left)
Optimizing NNI: done in 0.31534 secs using 399.3% CPU
Optimizing NNI: done in 0.298112 secs using 399.6% CPU
Optimizing NNI: done in 0.286028 secs using 399.7% CPU
Optimizing NNI: done in 0.334117 secs using 399.9% CPU
Optimizing NNI: done in 0.400541 secs using 399.1% CPU
Optimizing NNI: done in 0.408386 secs using 399.9% CPU
Optimizing NNI: done in 0.347971 secs using 399.9% CPU
Optimizing NNI: done in 0.369644 secs using 399.7% CPU
Optimizing NNI: done in 0.249427 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -35418.911
Optimizing NNI: done in 0.343881 secs using 400.2% CPU
Iteration 80 / LogL: -35420.810 / Time: 0h:0m:32s (0h:0m:19s left)
1052  HIVb+F+I+R6   61283.115    333 123232.229   124640.103   124630.323
Optimizing NNI: done in 0.385547 secs using 399.3% CPU
Optimizing NNI: done in 0.31471 secs using 399.6% CPU
Optimizing NNI: done in 0.354479 secs using 399.9% CPU
Optimizing NNI: done in 0.33953 secs using 399.8% CPU
Optimizing NNI: done in 0.266439 secs using 400% CPU
Optimizing NNI: done in 0.364238 secs using 399.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -35418.910
Optimizing NNI: done in 0.45724 secs using 399.4% CPU
384  mtZOA+R9      198360.117   1003 398726.235   2412750.235  403093.668
Optimizing NNI: done in 0.385761 secs using 398.8% CPU
Optimizing NNI: done in 0.309746 secs using 399.2% CPU
Optimizing NNI: done in 0.312364 secs using 398.6% CPU
Iteration 90 / LogL: -35419.382 / Time: 0h:0m:35s (0h:0m:14s left)
Optimizing NNI: done in 0.328653 secs using 399.9% CPU
Optimizing NNI: done in 0.344858 secs using 399.5% CPU
Optimizing NNI: done in 0.348196 secs using 398.7% CPU
Optimizing NNI: done in 0.383647 secs using 398.6% CPU
Optimizing NNI: done in 0.386972 secs using 399.1% CPU
1053  HIVb+F+I+R7   61280.040    335 123230.079   124673.156   124636.570
Optimizing NNI: done in 0.336934 secs using 399.6% CPU
Optimizing NNI: done in 0.269636 secs using 398.5% CPU
Optimizing NNI: done in 0.451804 secs using 399.6% CPU
Optimizing NNI: done in 0.361759 secs using 399.1% CPU
Optimizing NNI: done in 0.317781 secs using 399.5% CPU
Iteration 100 / LogL: -35420.022 / Time: 0h:0m:39s (0h:0m:10s left)
Optimizing NNI: done in 0.343396 secs using 399.6% CPU
Optimizing NNI: done in 0.290277 secs using 399.9% CPU
Optimizing NNI: done in 0.350785 secs using 399.6% CPU
Optimizing NNI: done in 0.408119 secs using 398.4% CPU
Optimizing NNI: done in 0.380447 secs using 400.3% CPU
Optimizing NNI: done in 0.326879 secs using 399.5% CPU
Optimizing NNI: done in 0.358309 secs using 398.5% CPU
Optimizing NNI: done in 0.372925 secs using 399.1% CPU
Optimizing NNI: done in 0.321875 secs using 399.9% CPU
Optimizing NNI: done in 0.386352 secs using 398.9% CPU
Iteration 110 / LogL: -35419.062 / Time: 0h:0m:42s (0h:0m:6s left)
Optimizing NNI: done in 0.431192 secs using 400.3% CPU
Optimizing NNI: done in 0.350185 secs using 399.6% CPU
Optimizing NNI: done in 0.392394 secs using 399.5% CPU
Optimizing NNI: done in 0.376106 secs using 398.4% CPU
Optimizing NNI: done in 0.337441 secs using 398.9% CPU
Optimizing NNI: done in 0.395506 secs using 398.2% CPU
Optimizing NNI: done in 0.389727 secs using 399.3% CPU
Optimizing NNI: done in 0.317852 secs using 398.9% CPU
Optimizing NNI: done in 0.261406 secs using 399.2% CPU
Optimizing NNI: done in 0.428676 secs using 397.8% CPU
Iteration 120 / LogL: -35728.438 / Time: 0h:0m:46s (0h:0m:2s left)
Optimizing NNI: done in 0.289318 secs using 398.8% CPU
Optimizing NNI: done in 0.356049 secs using 398.9% CPU
Optimizing NNI: done in 0.420562 secs using 399.7% CPU
Optimizing NNI: done in 0.227994 secs using 399% CPU
Optimizing NNI: done in 0.356507 secs using 399.9% CPU
Optimizing NNI: done in 0.373897 secs using 399.8% CPU
Optimizing NNI: done in 0.317856 secs using 398.9% CPU
Optimizing NNI: done in 0.277009 secs using 399.5% CPU
TREE SEARCH COMPLETED AFTER 128 ITERATIONS / Time: 0h:0m:49s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35418.910
Optimal log-likelihood: -35418.908
Proportion of invariable sites: 0.026
Gamma shape alpha: 2.424
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35418.908
Total tree length: 18.694

Total number of iterations: 128
CPU time used for tree search: 191.006 sec (0h:3m:11s)
Wall-clock time used for tree search: 48.820 sec (0h:0m:48s)
Total CPU time used: 193.366 sec (0h:3m:13s)
Total wall-clock time used: 49.376 sec (0h:0m:49s)

===> START BOOTSTRAP REPLICATE NUMBER 48

Creating bootstrap alignment (seed: 956207)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -35527.531
2. Current log-likelihood: -34722.731
3. Current log-likelihood: -34691.398
4. Current log-likelihood: -34690.846
Optimal log-likelihood: -34690.797
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.673
Parameters optimization took 4 rounds (0.256 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.084614 secs using 401.7% CPU
Computing ML distances took 0.084742 sec (of wall-clock time) 0.339993 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000153065 secs using 1352% CPU
Constructing RapidNJ tree: done in 0.00221491 secs using 446.3% CPU
Computing RapidNJ tree took 0.002425 sec (of wall-clock time) 0.012012 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35359.980
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.432 second
Computing log-likelihood of 98 initial trees ... 1.562 seconds
Current best score: -34690.797

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.198136 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -34660.679
Optimizing NNI: done in 0.209137 secs using 399.9% CPU
Optimizing NNI: done in 0.185612 secs using 399.3% CPU
Optimizing NNI: done in 0.224562 secs using 399% CPU
Optimizing NNI: done in 0.229029 secs using 398.6% CPU
Optimizing NNI: done in 0.420557 secs using 400.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -34660.628
Optimizing NNI: done in 0.419554 secs using 399.4% CPU
Optimizing NNI: done in 0.24353 secs using 399.9% CPU
Optimizing NNI: done in 0.412057 secs using 399.4% CPU
Optimizing NNI: done in 0.243973 secs using 399.9% CPU
Iteration 10 / LogL: -34660.791 / Time: 0h:0m:6s
Optimizing NNI: done in 0.205122 secs using 399.4% CPU
Optimizing NNI: done in 0.21037 secs using 399.3% CPU
Optimizing NNI: done in 0.231271 secs using 400.4% CPU
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Optimizing NNI: done in 0.223468 secs using 399.9% CPU
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Optimizing NNI: done in 0.216356 secs using 399.9% CPU
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Optimizing NNI: done in 0.253109 secs using 399.1% CPU
Optimizing NNI: done in 0.250703 secs using 397.8% CPU
Iteration 20 / LogL: -34661.087 / Time: 0h:0m:8s
Finish initializing candidate tree set (6)
Current best tree score: -34660.628 / CPU time: 8.308
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.33421 secs using 398.8% CPU
Optimizing NNI: done in 0.374282 secs using 397.9% CPU
Optimizing NNI: done in 0.350441 secs using 399.3% CPU
Optimizing NNI: done in 0.377802 secs using 398.5% CPU
Optimizing NNI: done in 0.394178 secs using 398.8% CPU
Optimizing NNI: done in 0.332606 secs using 398.4% CPU
Optimizing NNI: done in 0.404776 secs using 398.1% CPU
Optimizing NNI: done in 0.636372 secs using 398.4% CPU
Optimizing NNI: done in 0.573034 secs using 398.3% CPU
Optimizing NNI: done in 0.572283 secs using 399.7% CPU
Iteration 30 / LogL: -34660.633 / Time: 0h:0m:13s (0h:0m:34s left)
Optimizing NNI: done in 0.571316 secs using 398.8% CPU
Optimizing NNI: done in 0.401434 secs using 398.8% CPU
Optimizing NNI: done in 0.362471 secs using 399.7% CPU
Optimizing NNI: done in 0.366637 secs using 399.4% CPU
Optimizing NNI: done in 0.369637 secs using 398.1% CPU
Optimizing NNI: done in 0.376609 secs using 399.1% CPU
Optimizing NNI: done in 0.378048 secs using 398.5% CPU
Optimizing NNI: done in 0.33628 secs using 399.6% CPU
Optimizing NNI: done in 0.309417 secs using 400% CPU
1065  HIVw+R6       64522.959    313 129671.919   130776.211   130986.043
Optimizing NNI: done in 0.323058 secs using 399.8% CPU
Iteration 40 / LogL: -34660.736 / Time: 0h:0m:17s (0h:0m:28s left)
Optimizing NNI: done in 0.547028 secs using 398.2% CPU
Optimizing NNI: done in 0.3178 secs using 397.9% CPU
Optimizing NNI: done in 0.662008 secs using 398.4% CPU
Optimizing NNI: done in 0.587977 secs using 398.4% CPU
Optimizing NNI: done in 0.583417 secs using 399.5% CPU
Optimizing NNI: done in 0.575905 secs using 398.7% CPU
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Optimizing NNI: done in 0.342549 secs using 399.4% CPU
Optimizing NNI: done in 0.637128 secs using 398.6% CPU
Iteration 50 / LogL: -34660.630 / Time: 0h:0m:22s (0h:0m:25s left)
Optimizing NNI: done in 0.564456 secs using 399.1% CPU
Optimizing NNI: done in 0.429922 secs using 398% CPU
Optimizing NNI: done in 0.281961 secs using 398.6% CPU
Optimizing NNI: done in 0.65706 secs using 398.5% CPU
Optimizing NNI: done in 0.516056 secs using 399.7% CPU
Optimizing NNI: done in 0.51531 secs using 398.6% CPU
Optimizing NNI: done in 0.415875 secs using 399% CPU
Optimizing NNI: done in 0.628311 secs using 399.5% CPU
Optimizing NNI: done in 0.349524 secs using 398.5% CPU
Optimizing NNI: done in 0.455638 secs using 399.6% CPU
Iteration 60 / LogL: -34664.318 / Time: 0h:0m:27s (0h:0m:21s left)
Optimizing NNI: done in 0.259045 secs using 399.1% CPU
Optimizing NNI: done in 0.433408 secs using 397.1% CPU
Optimizing NNI: done in 0.542935 secs using 398.5% CPU
Optimizing NNI: done in 0.289483 secs using 399% CPU
Optimizing NNI: done in 0.346716 secs using 399.7% CPU
Optimizing NNI: done in 0.314516 secs using 400.4% CPU
Optimizing NNI: done in 0.459544 secs using 399.9% CPU
Optimizing NNI: done in 0.546909 secs using 399.7% CPU
Optimizing NNI: done in 0.363624 secs using 399.6% CPU
Optimizing NNI: done in 0.54797 secs using 399% CPU
Iteration 70 / LogL: -34664.317 / Time: 0h:0m:31s (0h:0m:16s left)
Optimizing NNI: done in 0.346559 secs using 398.5% CPU
Optimizing NNI: done in 0.311428 secs using 397.5% CPU
Optimizing NNI: done in 0.549199 secs using 398.1% CPU
394  mtZOA+F+R8    196919.533   1020 395879.066   2478719.066  400320.523
Optimizing NNI: done in 0.393974 secs using 399.3% CPU
308  Q.insect+F+I+R10 105534.082   573 212214.164   870018.164   214520.985
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.586491 secs using 399.2% CPU
Optimizing NNI: done in 0.381592 secs using 400.3% CPU
Optimizing NNI: done in 0.307236 secs using 399.5% CPU
Optimizing NNI: done in 0.570515 secs using 399.7% CPU
Optimizing NNI: done in 0.450873 secs using 399% CPU
Optimizing NNI: done in 0.608494 secs using 398.8% CPU
Iteration 80 / LogL: -34661.020 / Time: 0h:0m:36s (0h:0m:11s left)
Optimizing NNI: done in 0.381395 secs using 398.5% CPU
Optimizing NNI: done in 0.334135 secs using 398.5% CPU
Optimizing NNI: done in 0.377246 secs using 399.9% CPU
Optimizing NNI: done in 0.357358 secs using 399.9% CPU
Optimizing NNI: done in 0.34462 secs using 399.3% CPU
Optimizing NNI: done in 0.547809 secs using 399.5% CPU
Optimizing NNI: done in 0.280901 secs using 399.9% CPU
Optimizing NNI: done in 0.434363 secs using 398.3% CPU
Optimizing NNI: done in 0.459976 secs using 399.7% CPU
Optimizing NNI: done in 0.523735 secs using 398.9% CPU
Iteration 90 / LogL: -34667.649 / Time: 0h:0m:40s (0h:0m:7s left)
Optimizing NNI: done in 0.406523 secs using 399.7% CPU
Optimizing NNI: done in 0.395354 secs using 399.9% CPU
329  Q.plant+I+R9  105143.380   552 211390.761   821902.761   213613.039
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.544115 secs using 399.1% CPU
Optimizing NNI: done in 0.420497 secs using 399.9% CPU
Optimizing NNI: done in 0.276648 secs using 399.6% CPU
Optimizing NNI: done in 0.567408 secs using 399% CPU
Optimizing NNI: done in 0.290904 secs using 399.9% CPU
Optimizing NNI: done in 0.314874 secs using 399.2% CPU
Optimizing NNI: done in 0.580137 secs using 399.4% CPU
Optimizing NNI: done in 0.359381 secs using 399.6% CPU
Iteration 100 / LogL: -34660.843 / Time: 0h:0m:44s (0h:0m:2s left)
Optimizing NNI: done in 0.320089 secs using 399% CPU
Optimizing NNI: done in 0.327224 secs using 400.3% CPU
Optimizing NNI: done in 0.492815 secs using 398.1% CPU
Optimizing NNI: done in 0.455589 secs using 399.7% CPU
Optimizing NNI: done in 0.554555 secs using 399.9% CPU
Optimizing NNI: done in 0.62256 secs using 399.7% CPU
Optimizing NNI: done in 0.458764 secs using 399.9% CPU
TREE SEARCH COMPLETED AFTER 107 ITERATIONS / Time: 0h:0m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -34660.628
Optimal log-likelihood: -34660.627
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.659
Parameters optimization took 1 rounds (0.047 sec)
BEST SCORE FOUND : -34660.627
Total tree length: 18.098

Total number of iterations: 107
CPU time used for tree search: 183.861 sec (0h:3m:3s)
Wall-clock time used for tree search: 47.009 sec (0h:0m:47s)
Total CPU time used: 186.615 sec (0h:3m:6s)
Total wall-clock time used: 47.651 sec (0h:0m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 49

Creating bootstrap alignment (seed: 956208)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36721.645
2. Current log-likelihood: -35779.334
3. Current log-likelihood: -35766.716
4. Current log-likelihood: -35765.938
Optimal log-likelihood: -35765.778
Proportion of invariable sites: 0.029
Gamma shape alpha: 2.465
Parameters optimization took 4 rounds (0.266 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0752659 secs using 400% CPU
Computing ML distances took 0.075398 sec (of wall-clock time) 0.301419 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000146866 secs using 450.8% CPU
Constructing RapidNJ tree: done in 0.00219703 secs using 454.5% CPU
Computing RapidNJ tree took 0.002398 sec (of wall-clock time) 0.011044 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36260.916
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.493 second
Computing log-likelihood of 98 initial trees ... 1.533 seconds
Current best score: -35765.778

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.28224 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35724.457
Optimizing NNI: done in 0.373877 secs using 400.3% CPU
Optimizing NNI: done in 0.360059 secs using 399.9% CPU
Optimizing NNI: done in 0.391275 secs using 399.4% CPU
Optimizing NNI: done in 0.372067 secs using 399.7% CPU
Optimizing NNI: done in 0.339383 secs using 398.3% CPU
Optimizing NNI: done in 0.311404 secs using 399% CPU
Optimizing NNI: done in 0.320533 secs using 399.2% CPU
Optimizing NNI: done in 0.349601 secs using 399.2% CPU
Optimizing NNI: done in 0.400659 secs using 399.4% CPU
Iteration 10 / LogL: -35724.652 / Time: 0h:0m:7s
Optimizing NNI: done in 0.254162 secs using 399.1% CPU
Optimizing NNI: done in 0.255517 secs using 398.4% CPU
1066  HIVw+R7       64494.595    315 129619.189   130750.326   130941.710
Optimizing NNI: done in 0.386353 secs using 398.6% CPU
Optimizing NNI: done in 0.230577 secs using 399.3% CPU
Optimizing NNI: done in 0.413965 secs using 400.1% CPU
Optimizing NNI: done in 0.396821 secs using 399.1% CPU
Optimizing NNI: done in 0.429808 secs using 399.7% CPU
Optimizing NNI: done in 0.405495 secs using 399.4% CPU
Optimizing NNI: done in 0.274468 secs using 399.6% CPU
Optimizing NNI: done in 0.351006 secs using 399.1% CPU
Iteration 20 / LogL: -35734.740 / Time: 0h:0m:10s
Finish initializing candidate tree set (8)
Current best tree score: -35724.457 / CPU time: 10.032
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.372411 secs using 400.6% CPU
Optimizing NNI: done in 0.427931 secs using 399.6% CPU
Optimizing NNI: done in 0.554382 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -35721.754
Optimizing NNI: done in 0.775149 secs using 398.2% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -35721.164
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Iteration 30 / LogL: -35724.616 / Time: 0h:0m:14s (0h:0m:48s left)
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UPDATE BEST LOG-LIKELIHOOD: -35721.162
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BETTER TREE FOUND at iteration 35: -35720.957
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Iteration 40 / LogL: -35721.493 / Time: 0h:0m:19s (0h:0m:47s left)
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UPDATE BEST LOG-LIKELIHOOD: -35720.957
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Iteration 60 / LogL: -35721.073 / Time: 0h:0m:28s (0h:0m:35s left)
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1067  HIVw+R8       64490.582    317 129615.163   130773.853   130946.081
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Iteration 70 / LogL: -35721.303 / Time: 0h:0m:32s (0h:0m:30s left)
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Iteration 80 / LogL: -35721.188 / Time: 0h:0m:37s (0h:0m:25s left)
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Iteration 90 / LogL: -35721.166 / Time: 0h:0m:42s (0h:0m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 97: -35720.800
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 100: -35720.581
Iteration 100 / LogL: -35720.581 / Time: 0h:0m:46s (0h:0m:46s left)
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1074  HIVw+I+R6     64521.854    314 129671.708   130789.335   130990.030
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Iteration 110 / LogL: -35793.294 / Time: 0h:0m:51s (0h:0m:42s left)
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Iteration 120 / LogL: -35721.014 / Time: 0h:0m:54s (0h:0m:36s left)
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Iteration 130 / LogL: -35721.105 / Time: 0h:0m:59s (0h:0m:32s left)
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UPDATE BEST LOG-LIKELIHOOD: -35720.579
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395  mtZOA+F+R9    196898.434   1022 395840.867   2486852.867  400291.033
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Iteration 150 / LogL: -35720.768 / Time: 0h:1m:8s (0h:0m:22s left)
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UPDATE BEST LOG-LIKELIHOOD: -35720.579
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Iteration 160 / LogL: -35722.236 / Time: 0h:1m:12s (0h:0m:18s left)
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1075  HIVw+I+R7     64493.543    316 129619.086   130763.909   130945.805
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Iteration 170 / LogL: -35721.309 / Time: 0h:1m:17s (0h:0m:13s left)
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Iteration 180 / LogL: -35721.248 / Time: 0h:1m:21s (0h:0m:9s left)
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Iteration 190 / LogL: -35723.317 / Time: 0h:1m:25s (0h:0m:4s left)
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Iteration 200 / LogL: -35720.961 / Time: 0h:1m:29s (0h:0m:0s left)
Optimizing NNI: done in 0.477725 secs using 399.7% CPU
TREE SEARCH COMPLETED AFTER 201 ITERATIONS / Time: 0h:1m:30s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35720.579
Optimal log-likelihood: -35720.579
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.496
Parameters optimization took 1 rounds (0.041 sec)
BEST SCORE FOUND : -35720.579
Total tree length: 19.546

Total number of iterations: 201
CPU time used for tree search: 353.827 sec (0h:5m:53s)
Wall-clock time used for tree search: 89.620 sec (0h:1m:29s)
Total CPU time used: 355.958 sec (0h:5m:55s)
Total wall-clock time used: 90.130 sec (0h:1m:30s)

===> START BOOTSTRAP REPLICATE NUMBER 50

Creating bootstrap alignment (seed: 956209)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds

NOTE: 16 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37115.218
2. Current log-likelihood: -36122.824
3. Current log-likelihood: -36109.144
4. Current log-likelihood: -36108.817
Optimal log-likelihood: -36108.714
Proportion of invariable sites: 0.019
Gamma shape alpha: 2.358
Parameters optimization took 4 rounds (0.249 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.077702 secs using 398.7% CPU
Computing ML distances took 0.077838 sec (of wall-clock time) 0.309900 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000130892 secs using 754.1% CPU
Constructing RapidNJ tree: done in 0.00222993 secs using 283.8% CPU
Computing RapidNJ tree took 0.002422 sec (of wall-clock time) 0.007375 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36547.785
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.523 second
Computing log-likelihood of 98 initial trees ... 1.473 seconds
Current best score: -36108.714

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.150103 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36079.734
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36076.542
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -36076.204
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Iteration 10 / LogL: -36077.380 / Time: 0h:0m:5s
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Iteration 20 / LogL: -36080.183 / Time: 0h:0m:8s
Finish initializing candidate tree set (8)
Current best tree score: -36076.204 / CPU time: 7.596
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Optimizing NNI: done in 0.29449 secs using 400.1% CPU
330  Q.plant+I+R10 105139.439   554 211386.878   826326.878   213617.208
WARNING: Normalizing state frequencies so that sum of them equals to 1
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Estimate model parameters (epsilon = 0.100)
1087  HIVw+F+R6     63532.197    332 127728.394   129119.035   129122.289
BETTER TREE FOUND at iteration 27: -36075.442
Optimizing NNI: done in 0.338707 secs using 399.9% CPU
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Optimizing NNI: done in 0.414252 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36075.347
Iteration 30 / LogL: -36075.347 / Time: 0h:0m:11s (0h:0m:39s left)
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Iteration 40 / LogL: -36081.739 / Time: 0h:0m:15s (0h:0m:34s left)
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Iteration 50 / LogL: -36082.216 / Time: 0h:0m:18s (0h:0m:29s left)
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Iteration 60 / LogL: -36077.226 / Time: 0h:0m:22s (0h:0m:25s left)
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Iteration 70 / LogL: -36107.195 / Time: 0h:0m:25s (0h:0m:21s left)
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Iteration 80 / LogL: -36104.515 / Time: 0h:0m:29s (0h:0m:17s left)
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Optimizing NNI: done in 0.419885 secs using 399.2% CPU
Optimizing NNI: done in 0.307076 secs using 399.9% CPU
Optimizing NNI: done in 0.278233 secs using 399.6% CPU
Optimizing NNI: done in 0.354964 secs using 399.9% CPU
Iteration 90 / LogL: -36075.350 / Time: 0h:0m:33s (0h:0m:13s left)
Optimizing NNI: done in 0.365678 secs using 399.5% CPU
Optimizing NNI: done in 0.324157 secs using 399.9% CPU
Optimizing NNI: done in 0.314873 secs using 399.3% CPU
Optimizing NNI: done in 0.35113 secs using 398.5% CPU
Optimizing NNI: done in 0.304447 secs using 400% CPU
Optimizing NNI: done in 0.383763 secs using 399.6% CPU
Optimizing NNI: done in 0.339909 secs using 399.9% CPU
Optimizing NNI: done in 0.304005 secs using 399.7% CPU
Optimizing NNI: done in 0.337627 secs using 399.7% CPU
Optimizing NNI: done in 0.273507 secs using 399.5% CPU
Iteration 100 / LogL: -36076.953 / Time: 0h:0m:36s (0h:0m:9s left)
Optimizing NNI: done in 0.369883 secs using 399.6% CPU
Optimizing NNI: done in 0.369767 secs using 398.5% CPU
Optimizing NNI: done in 0.286388 secs using 399.6% CPU
351  Q.plant+F+I+R9 105680.023   571 212502.046   865726.046   214800.815
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.389814 secs using 399.9% CPU
Optimizing NNI: done in 0.320334 secs using 399.5% CPU
Optimizing NNI: done in 0.454925 secs using 399.4% CPU
Optimizing NNI: done in 0.257857 secs using 399.1% CPU
Optimizing NNI: done in 0.406642 secs using 399.4% CPU
Optimizing NNI: done in 0.382558 secs using 399.9% CPU
Optimizing NNI: done in 0.320111 secs using 398.6% CPU
Iteration 110 / LogL: -36078.559 / Time: 0h:0m:40s (0h:0m:6s left)
Optimizing NNI: done in 0.266346 secs using 398.8% CPU
Optimizing NNI: done in 0.326443 secs using 399.7% CPU
Optimizing NNI: done in 0.318859 secs using 399.8% CPU
Optimizing NNI: done in 0.312349 secs using 398.9% CPU
Optimizing NNI: done in 0.338094 secs using 399.6% CPU
Optimizing NNI: done in 0.35177 secs using 399.6% CPU
Optimizing NNI: done in 0.387355 secs using 398.3% CPU
Optimizing NNI: done in 0.376545 secs using 399.6% CPU
1088  HIVw+F+R7     63515.599    334 127699.197   129124.548   129101.489
Optimizing NNI: done in 0.413266 secs using 399.5% CPU
Optimizing NNI: done in 0.303018 secs using 399.8% CPU
Iteration 120 / LogL: -36076.877 / Time: 0h:0m:43s (0h:0m:2s left)
Optimizing NNI: done in 0.368246 secs using 399.1% CPU
Optimizing NNI: done in 0.355458 secs using 399.7% CPU
Optimizing NNI: done in 0.309957 secs using 399.9% CPU
Optimizing NNI: done in 0.332166 secs using 398.1% CPU
Optimizing NNI: done in 0.373609 secs using 399.4% CPU
Optimizing NNI: done in 0.359088 secs using 399.1% CPU
Optimizing NNI: done in 0.33901 secs using 399.2% CPU
Optimizing NNI: done in 0.378138 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 128 ITERATIONS / Time: 0h:0m:46s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36075.347
Optimal log-likelihood: -36075.346
Proportion of invariable sites: 0.019
Gamma shape alpha: 2.382
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -36075.346
Total tree length: 21.691

Total number of iterations: 128
CPU time used for tree search: 179.001 sec (0h:2m:59s)
Wall-clock time used for tree search: 45.805 sec (0h:0m:45s)
Total CPU time used: 181.225 sec (0h:3m:1s)
Total wall-clock time used: 46.333 sec (0h:0m:46s)

===> START BOOTSTRAP REPLICATE NUMBER 51

Creating bootstrap alignment (seed: 956210)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37552.197
2. Current log-likelihood: -36639.545
3. Current log-likelihood: -36627.392
4. Current log-likelihood: -36626.797
Optimal log-likelihood: -36626.662
Proportion of invariable sites: 0.015
Gamma shape alpha: 2.679
Parameters optimization took 4 rounds (0.267 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0758338 secs using 399.3% CPU
Computing ML distances took 0.075982 sec (of wall-clock time) 0.303126 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000134945 secs using 458.7% CPU
Constructing RapidNJ tree: done in 0.00125408 secs using 379.8% CPU
Computing RapidNJ tree took 0.001437 sec (of wall-clock time) 0.007295 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37038.825
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.462 second
Computing log-likelihood of 98 initial trees ... 1.624 seconds
Current best score: -36617.515

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.441135 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36572.014
Optimizing NNI: done in 0.384121 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36569.762
Optimizing NNI: done in 0.32953 secs using 399.4% CPU
Optimizing NNI: done in 0.314823 secs using 399.7% CPU
Optimizing NNI: done in 0.326507 secs using 400.2% CPU
Optimizing NNI: done in 0.311754 secs using 399.1% CPU
Optimizing NNI: done in 0.296296 secs using 399.4% CPU
Optimizing NNI: done in 0.445811 secs using 399% CPU
Optimizing NNI: done in 0.383595 secs using 399.2% CPU
Optimizing NNI: done in 0.320428 secs using 398.6% CPU
Iteration 10 / LogL: -36569.763 / Time: 0h:0m:7s
Optimizing NNI: done in 0.319398 secs using 400% CPU
Optimizing NNI: done in 0.282148 secs using 399.2% CPU
Optimizing NNI: done in 0.314766 secs using 399.9% CPU
Optimizing NNI: done in 0.348481 secs using 397% CPU
Optimizing NNI: done in 0.314711 secs using 398.5% CPU
Optimizing NNI: done in 0.328503 secs using 399.8% CPU
Optimizing NNI: done in 0.254188 secs using 399.1% CPU
Optimizing NNI: done in 0.346956 secs using 400.3% CPU
Optimizing NNI: done in 0.293917 secs using 399.7% CPU
Optimizing NNI: done in 0.291149 secs using 399.9% CPU
Iteration 20 / LogL: -36578.498 / Time: 0h:0m:10s
Finish initializing candidate tree set (9)
Current best tree score: -36569.762 / CPU time: 9.890
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.547452 secs using 399.3% CPU
1089  HIVw+F+R8     63509.986    336 127691.972   129153.030   129102.661
Optimizing NNI: done in 0.610845 secs using 399.4% CPU
Optimizing NNI: done in 0.509544 secs using 399.7% CPU
Optimizing NNI: done in 0.508551 secs using 399.5% CPU
Optimizing NNI: done in 0.505011 secs using 399.9% CPU
Optimizing NNI: done in 0.417645 secs using 399.9% CPU
Optimizing NNI: done in 0.465008 secs using 398.8% CPU
Optimizing NNI: done in 0.433926 secs using 399.8% CPU
Optimizing NNI: done in 0.553505 secs using 399.6% CPU
Optimizing NNI: done in 0.502792 secs using 399.3% CPU
Iteration 30 / LogL: -36569.764 / Time: 0h:0m:15s (0h:0m:38s left)
Optimizing NNI: done in 0.52297 secs using 399.5% CPU
Optimizing NNI: done in 0.487438 secs using 399.7% CPU
Optimizing NNI: done in 0.426951 secs using 399.5% CPU
Optimizing NNI: done in 0.489095 secs using 399.3% CPU
Optimizing NNI: done in 0.334877 secs using 399.9% CPU
Optimizing NNI: done in 0.508837 secs using 399.3% CPU
Optimizing NNI: done in 0.461236 secs using 399.7% CPU
Optimizing NNI: done in 0.345512 secs using 399.3% CPU
Optimizing NNI: done in 0.481396 secs using 398.2% CPU
Optimizing NNI: done in 0.439921 secs using 398.3% CPU
Iteration 40 / LogL: -36574.746 / Time: 0h:0m:20s (0h:0m:31s left)
Optimizing NNI: done in 0.402531 secs using 398.9% CPU
Optimizing NNI: done in 0.509105 secs using 399% CPU
396  mtZOA+F+R10   196891.474   1024 395830.948   2495030.948  400289.823
Optimizing NNI: done in 0.519554 secs using 399% CPU
Optimizing NNI: done in 0.618375 secs using 398.6% CPU
Optimizing NNI: done in 0.355518 secs using 399.1% CPU
Optimizing NNI: done in 0.469513 secs using 398.3% CPU
Optimizing NNI: done in 0.461425 secs using 399.5% CPU
Optimizing NNI: done in 0.459346 secs using 399.6% CPU
Optimizing NNI: done in 0.407355 secs using 399.4% CPU
Optimizing NNI: done in 0.433549 secs using 398.5% CPU
Iteration 50 / LogL: -36569.764 / Time: 0h:0m:24s (0h:0m:26s left)
Optimizing NNI: done in 0.491839 secs using 399% CPU
Optimizing NNI: done in 0.509318 secs using 399.1% CPU
Optimizing NNI: done in 0.577407 secs using 399.9% CPU
Optimizing NNI: done in 0.460781 secs using 399% CPU
Optimizing NNI: done in 0.444579 secs using 399.7% CPU
Optimizing NNI: done in 0.494794 secs using 399.9% CPU
Optimizing NNI: done in 0.494015 secs using 399.7% CPU
Optimizing NNI: done in 0.418774 secs using 399.9% CPU
Optimizing NNI: done in 0.348308 secs using 399.3% CPU
Optimizing NNI: done in 0.467968 secs using 399.2% CPU
Iteration 60 / LogL: -36569.763 / Time: 0h:0m:29s (0h:0m:20s left)
Optimizing NNI: done in 0.522026 secs using 399.9% CPU
Optimizing NNI: done in 0.462181 secs using 399.7% CPU
Optimizing NNI: done in 0.436731 secs using 399.9% CPU
Optimizing NNI: done in 0.396774 secs using 398.7% CPU
Optimizing NNI: done in 0.515933 secs using 399.4% CPU
Optimizing NNI: done in 0.534195 secs using 400.2% CPU
Optimizing NNI: done in 0.496004 secs using 399.2% CPU
Optimizing NNI: done in 0.43989 secs using 399.6% CPU
Optimizing NNI: done in 0.459564 secs using 398.8% CPU
Optimizing NNI: done in 0.388507 secs using 399.3% CPU
Iteration 70 / LogL: -36570.136 / Time: 0h:0m:34s (0h:0m:15s left)
Optimizing NNI: done in 0.432741 secs using 399.7% CPU
Optimizing NNI: done in 0.530836 secs using 399.4% CPU
1096  HIVw+F+I+R6   63531.944    333 127729.888   129137.762   129127.982
Optimizing NNI: done in 0.51577 secs using 399% CPU
Optimizing NNI: done in 0.474324 secs using 399.7% CPU
Optimizing NNI: done in 0.376127 secs using 399.9% CPU
Optimizing NNI: done in 0.677125 secs using 399.2% CPU
Optimizing NNI: done in 0.40023 secs using 399.1% CPU
Optimizing NNI: done in 0.542612 secs using 399.2% CPU
Optimizing NNI: done in 0.47643 secs using 399.5% CPU
Optimizing NNI: done in 0.544164 secs using 399.9% CPU
Iteration 80 / LogL: -36590.088 / Time: 0h:0m:39s (0h:0m:10s left)
Optimizing NNI: done in 0.484993 secs using 399.5% CPU
405  mtMet+R8      200042.427   1001 402086.853   2408090.853  406445.578
Optimizing NNI: done in 0.430342 secs using 399.4% CPU
Optimizing NNI: done in 0.404722 secs using 399.9% CPU
Optimizing NNI: done in 0.466545 secs using 399.3% CPU
Optimizing NNI: done in 0.390762 secs using 399.4% CPU
Optimizing NNI: done in 0.56007 secs using 399.2% CPU
Optimizing NNI: done in 0.474756 secs using 399.3% CPU
Optimizing NNI: done in 0.500016 secs using 399.4% CPU
Optimizing NNI: done in 0.505863 secs using 399.9% CPU
Optimizing NNI: done in 0.416361 secs using 399.7% CPU
Iteration 90 / LogL: -36569.764 / Time: 0h:0m:43s (0h:0m:5s left)
Optimizing NNI: done in 0.394588 secs using 399.4% CPU
Optimizing NNI: done in 0.465228 secs using 398.6% CPU
Optimizing NNI: done in 0.508979 secs using 399% CPU
Optimizing NNI: done in 0.394821 secs using 399.3% CPU
Optimizing NNI: done in 0.440029 secs using 399% CPU
Optimizing NNI: done in 0.505165 secs using 399.5% CPU
Optimizing NNI: done in 0.524032 secs using 399.7% CPU
Optimizing NNI: done in 0.504502 secs using 399.2% CPU
Optimizing NNI: done in 0.494828 secs using 397.7% CPU
Optimizing NNI: done in 0.525068 secs using 399.8% CPU
Iteration 100 / LogL: -36569.764 / Time: 0h:0m:48s (0h:0m:0s left)
Optimizing NNI: done in 0.440338 secs using 399.2% CPU
Optimizing NNI: done in 0.440023 secs using 399.4% CPU
Optimizing NNI: done in 0.470908 secs using 400.2% CPU
TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:49s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36569.762
Optimal log-likelihood: -36569.762
Proportion of invariable sites: 0.015
Gamma shape alpha: 2.646
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36569.762
Total tree length: 19.931

Total number of iterations: 103
CPU time used for tree search: 193.837 sec (0h:3m:13s)
Wall-clock time used for tree search: 49.478 sec (0h:0m:49s)
Total CPU time used: 196.136 sec (0h:3m:16s)
Total wall-clock time used: 50.024 sec (0h:0m:50s)

===> START BOOTSTRAP REPLICATE NUMBER 52

Creating bootstrap alignment (seed: 956211)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36726.235
2. Current log-likelihood: -35796.793
3. Current log-likelihood: -35785.476
Optimal log-likelihood: -35785.357
Proportion of invariable sites: 0.015
Gamma shape alpha: 2.427
Parameters optimization took 3 rounds (0.217 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.073153 secs using 400% CPU
Computing ML distances took 0.073292 sec (of wall-clock time) 0.292990 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000133991 secs using 415.7% CPU
Constructing RapidNJ tree: done in 0.00132108 secs using 316.7% CPU
Computing RapidNJ tree took 0.001506 sec (of wall-clock time) 0.006541 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36410.100
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.524 second
Computing log-likelihood of 98 initial trees ... 1.544 seconds
Current best score: -35785.357

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.26198 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35751.919
Optimizing NNI: done in 0.233154 secs using 400% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35749.656
Optimizing NNI: done in 0.24246 secs using 398.7% CPU
Optimizing NNI: done in 0.240309 secs using 398.6% CPU
Optimizing NNI: done in 0.245489 secs using 399.9% CPU
Optimizing NNI: done in 0.346555 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -35749.279
Optimizing NNI: done in 0.268864 secs using 399.9% CPU
1097  HIVw+F+I+R7   63515.653    335 127701.306   129144.383   129107.796
Optimizing NNI: done in 0.346005 secs using 399.6% CPU
Optimizing NNI: done in 0.258958 secs using 399.3% CPU
Optimizing NNI: done in 0.298608 secs using 400% CPU
Iteration 10 / LogL: -35754.318 / Time: 0h:0m:6s
Optimizing NNI: done in 0.238982 secs using 398.7% CPU
Optimizing NNI: done in 0.265813 secs using 399.6% CPU
Optimizing NNI: done in 0.255877 secs using 398.8% CPU
Optimizing NNI: done in 0.382651 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 14: -35748.970
Optimizing NNI: done in 0.266257 secs using 399.5% CPU
Optimizing NNI: done in 0.277457 secs using 399.2% CPU
1109  FLU+R6        61371.791    313 123369.583   124473.875   124683.706
Optimizing NNI: done in 0.256146 secs using 399.9% CPU
Optimizing NNI: done in 0.259816 secs using 399.9% CPU
Optimizing NNI: done in 0.281993 secs using 399.4% CPU
Optimizing NNI: done in 0.29537 secs using 399.1% CPU
Iteration 20 / LogL: -35749.379 / Time: 0h:0m:9s
Finish initializing candidate tree set (7)
Current best tree score: -35748.970 / CPU time: 8.874
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.369978 secs using 399.6% CPU
Optimizing NNI: done in 0.251735 secs using 399.9% CPU
Optimizing NNI: done in 0.367221 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -35748.792
Optimizing NNI: done in 0.37458 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -35746.294
Optimizing NNI: done in 0.477932 secs using 399.9% CPU
Optimizing NNI: done in 0.47156 secs using 399.9% CPU
1110  FLU+R7        61363.433    315 123356.866   124488.002   124679.387
Optimizing NNI: done in 0.49453 secs using 399.7% CPU
Optimizing NNI: done in 0.332309 secs using 398.6% CPU
Optimizing NNI: done in 0.400153 secs using 399.8% CPU
Optimizing NNI: done in 0.469821 secs using 399.5% CPU
Iteration 30 / LogL: -35746.316 / Time: 0h:0m:13s (0h:0m:43s left)
Optimizing NNI: done in 0.500763 secs using 399.3% CPU
Optimizing NNI: done in 0.491012 secs using 398.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -35746.292
Optimizing NNI: done in 0.457275 secs using 398.6% CPU
Optimizing NNI: done in 0.329217 secs using 399.6% CPU
Optimizing NNI: done in 0.406717 secs using 399.4% CPU
Optimizing NNI: done in 0.462762 secs using 399% CPU
1111  FLU+R8        61354.945    317 123343.891   124502.580   124674.808
Optimizing NNI: done in 0.443948 secs using 399.6% CPU
Optimizing NNI: done in 0.474135 secs using 399.4% CPU
Optimizing NNI: done in 0.47002 secs using 399.5% CPU
Optimizing NNI: done in 0.415282 secs using 398.9% CPU
Iteration 40 / LogL: -35748.935 / Time: 0h:0m:18s (0h:0m:38s left)
Optimizing NNI: done in 0.467026 secs using 398.9% CPU
Optimizing NNI: done in 0.441914 secs using 399.5% CPU
Optimizing NNI: done in 0.443788 secs using 399.4% CPU
Optimizing NNI: done in 0.470181 secs using 399.7% CPU
Optimizing NNI: done in 0.466282 secs using 399.2% CPU
Optimizing NNI: done in 0.468983 secs using 399.2% CPU
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Optimizing NNI: done in 0.402806 secs using 398.9% CPU
Optimizing NNI: done in 0.381486 secs using 400.5% CPU
Optimizing NNI: done in 0.374396 secs using 399.1% CPU
Iteration 50 / LogL: -35767.641 / Time: 0h:0m:22s (0h:0m:33s left)
Optimizing NNI: done in 0.413068 secs using 399.9% CPU
Optimizing NNI: done in 0.384382 secs using 399.9% CPU
Optimizing NNI: done in 0.427803 secs using 399.9% CPU
Optimizing NNI: done in 0.385615 secs using 399.2% CPU
Optimizing NNI: done in 0.443128 secs using 400.5% CPU
Optimizing NNI: done in 0.428698 secs using 399.3% CPU
Optimizing NNI: done in 0.347322 secs using 398.9% CPU
Optimizing NNI: done in 0.318512 secs using 398.9% CPU
Optimizing NNI: done in 0.575712 secs using 398.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -35746.290
Optimizing NNI: done in 0.46097 secs using 398.9% CPU
Iteration 60 / LogL: -35749.135 / Time: 0h:0m:26s (0h:0m:28s left)
Optimizing NNI: done in 0.367996 secs using 399.4% CPU
Optimizing NNI: done in 0.447154 secs using 399.9% CPU
Optimizing NNI: done in 0.434277 secs using 399.5% CPU
Optimizing NNI: done in 0.31684 secs using 399.3% CPU
Optimizing NNI: done in 0.477533 secs using 399.7% CPU
Optimizing NNI: done in 0.429422 secs using 399.2% CPU
Optimizing NNI: done in 0.435021 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 67: -35746.071
406  mtMet+R9      200019.941   1003 402045.882   2416069.882  406413.316
Optimizing NNI: done in 0.53671 secs using 399.3% CPU
Optimizing NNI: done in 0.50208 secs using 399.4% CPU
Optimizing NNI: done in 0.401684 secs using 399.9% CPU
Iteration 70 / LogL: -35748.786 / Time: 0h:0m:31s (0h:0m:43s left)
Optimizing NNI: done in 0.359992 secs using 399.9% CPU
1112  FLU+R9        61352.112    319 123342.224   124529.201   124681.539
Optimizing NNI: done in 0.416719 secs using 399.7% CPU
Optimizing NNI: done in 0.501251 secs using 399.7% CPU
Optimizing NNI: done in 0.389966 secs using 399% CPU
Optimizing NNI: done in 0.349759 secs using 400.2% CPU
Optimizing NNI: done in 0.392707 secs using 399.7% CPU
Optimizing NNI: done in 0.411568 secs using 399.2% CPU
Optimizing NNI: done in 0.367285 secs using 399.6% CPU
Optimizing NNI: done in 0.33474 secs using 399.6% CPU
Optimizing NNI: done in 0.481753 secs using 398.4% CPU
Iteration 80 / LogL: -35746.325 / Time: 0h:0m:35s (0h:0m:38s left)
Optimizing NNI: done in 0.468654 secs using 399.9% CPU
Optimizing NNI: done in 0.350793 secs using 399.4% CPU
Optimizing NNI: done in 0.464773 secs using 398.7% CPU
Optimizing NNI: done in 0.332132 secs using 397.4% CPU
Optimizing NNI: done in 0.376534 secs using 398.2% CPU
1118  FLU+I+R6      61367.705    314 123363.411   124481.038   124681.733
Optimizing NNI: done in 0.512817 secs using 399.1% CPU
Optimizing NNI: done in 0.391369 secs using 399.3% CPU
Optimizing NNI: done in 0.37625 secs using 399.6% CPU
Optimizing NNI: done in 0.477027 secs using 398.2% CPU
Optimizing NNI: done in 0.393513 secs using 399.6% CPU
Iteration 90 / LogL: -35829.994 / Time: 0h:0m:39s (0h:0m:34s left)
Optimizing NNI: done in 0.308711 secs using 399.9% CPU
Optimizing NNI: done in 0.384522 secs using 399.9% CPU
Optimizing NNI: done in 0.349258 secs using 399.9% CPU
Optimizing NNI: done in 0.396727 secs using 399.1% CPU
Optimizing NNI: done in 0.428065 secs using 399.9% CPU
Optimizing NNI: done in 0.326284 secs using 399.9% CPU
Optimizing NNI: done in 0.476096 secs using 399.5% CPU
Optimizing NNI: done in 0.530234 secs using 399.7% CPU
Optimizing NNI: done in 0.387526 secs using 399.7% CPU
Optimizing NNI: done in 0.421991 secs using 398.6% CPU
Iteration 100 / LogL: -35746.312 / Time: 0h:0m:43s (0h:0m:29s left)
1119  FLU+I+R7      61361.082    316 123354.164   124498.987   124680.883
Optimizing NNI: done in 0.373336 secs using 398.2% CPU
Optimizing NNI: done in 0.408684 secs using 399.9% CPU
Optimizing NNI: done in 0.451958 secs using 399.4% CPU
Optimizing NNI: done in 0.47338 secs using 398.9% CPU
Optimizing NNI: done in 0.426333 secs using 399.8% CPU
Optimizing NNI: done in 0.372099 secs using 399.7% CPU
1131  FLU+F+R6      61080.692    332 122825.383   124216.025   124219.278
Optimizing NNI: done in 0.378189 secs using 399.1% CPU
Optimizing NNI: done in 0.488839 secs using 399.5% CPU
Optimizing NNI: done in 0.348514 secs using 398.6% CPU
Optimizing NNI: done in 0.466301 secs using 399.3% CPU
Iteration 110 / LogL: -35746.082 / Time: 0h:0m:47s (0h:0m:24s left)
Optimizing NNI: done in 0.400731 secs using 399.9% CPU
Optimizing NNI: done in 0.441212 secs using 399.5% CPU
Optimizing NNI: done in 0.412066 secs using 400.1% CPU
1132  FLU+F+R7      61074.901    334 122817.802   124243.152   124220.094
Optimizing NNI: done in 0.32254 secs using 399.9% CPU
Optimizing NNI: done in 0.352597 secs using 399.6% CPU
Optimizing NNI: done in 0.344348 secs using 399.9% CPU
Optimizing NNI: done in 0.381505 secs using 399.9% CPU
Optimizing NNI: done in 0.324601 secs using 399.7% CPU
Optimizing NNI: done in 0.442413 secs using 400.1% CPU
Optimizing NNI: done in 0.51749 secs using 399.9% CPU
Iteration 120 / LogL: -35748.987 / Time: 0h:0m:51s (0h:0m:20s left)
Optimizing NNI: done in 0.407498 secs using 399.7% CPU
Optimizing NNI: done in 0.450045 secs using 398.8% CPU
Optimizing NNI: done in 0.462832 secs using 397.9% CPU
Optimizing NNI: done in 0.535143 secs using 399.2% CPU
Optimizing NNI: done in 0.468678 secs using 399.4% CPU
Optimizing NNI: done in 0.42313 secs using 399.6% CPU
Optimizing NNI: done in 0.394313 secs using 399.9% CPU
1140  FLU+F+I+R6    61079.005    333 122824.009   124231.883   124222.103
Optimizing NNI: done in 0.368448 secs using 399.1% CPU
Optimizing NNI: done in 0.418791 secs using 399.7% CPU
Optimizing NNI: done in 0.362419 secs using 399% CPU
Iteration 130 / LogL: -35764.172 / Time: 0h:0m:55s (0h:0m:16s left)
352  Q.plant+F+I+R10 105676.627   573 212499.255   870303.255   214806.076
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.379645 secs using 399% CPU
Optimizing NNI: done in 0.445534 secs using 399.3% CPU
Optimizing NNI: done in 0.480367 secs using 399.6% CPU
Optimizing NNI: done in 0.399381 secs using 400.3% CPU
Optimizing NNI: done in 0.317201 secs using 398.6% CPU
Optimizing NNI: done in 0.480168 secs using 399.9% CPU
Optimizing NNI: done in 0.451413 secs using 399.7% CPU
Optimizing NNI: done in 0.328181 secs using 399.9% CPU
Optimizing NNI: done in 0.540651 secs using 399.6% CPU
Optimizing NNI: done in 0.476275 secs using 399.7% CPU
Iteration 140 / LogL: -35746.368 / Time: 0h:1m:0s (0h:0m:11s left)
Optimizing NNI: done in 0.50053 secs using 399.1% CPU
1141  FLU+F+I+R7    61074.340    335 122818.679   124261.756   124225.169
Optimizing NNI: done in 0.664536 secs using 399.5% CPU
Optimizing NNI: done in 0.45063 secs using 399.7% CPU
Optimizing NNI: done in 0.459752 secs using 399.7% CPU
Optimizing NNI: done in 0.469501 secs using 399.7% CPU
Optimizing NNI: done in 0.441767 secs using 399.3% CPU
1153  rtREV+R6      60257.949    313 121141.898   122246.191   122456.022
Optimizing NNI: done in 0.537695 secs using 399.5% CPU
Optimizing NNI: done in 0.591789 secs using 399.3% CPU
Optimizing NNI: done in 0.414618 secs using 399.2% CPU
Optimizing NNI: done in 0.538263 secs using 399.2% CPU
Iteration 150 / LogL: -35749.290 / Time: 0h:1m:5s (0h:0m:7s left)
Optimizing NNI: done in 0.482721 secs using 399.7% CPU
Optimizing NNI: done in 0.501223 secs using 399.8% CPU
1154  rtREV+R7      60251.101    315 121132.202   122263.338   122454.723
Optimizing NNI: done in 0.38955 secs using 398.3% CPU
Optimizing NNI: done in 0.404828 secs using 399.4% CPU
Optimizing NNI: done in 0.575141 secs using 399.4% CPU
Optimizing NNI: done in 0.487602 secs using 399.5% CPU
Optimizing NNI: done in 0.392706 secs using 399.7% CPU
Optimizing NNI: done in 0.372158 secs using 398.9% CPU
373  Q.yeast+I+R9  105701.686   552 212507.373   823019.373   214729.651
WARNING: Normalizing state frequencies so that sum of them equals to 1
1155  rtREV+R8      60244.011    317 121122.022   122280.712   122452.940
Optimizing NNI: done in 0.512169 secs using 398.8% CPU
Optimizing NNI: done in 0.434026 secs using 399.9% CPU
Iteration 160 / LogL: -35748.810 / Time: 0h:1m:9s (0h:0m:3s left)
Optimizing NNI: done in 0.32121 secs using 399.6% CPU
Optimizing NNI: done in 0.450866 secs using 399.1% CPU
Optimizing NNI: done in 0.47497 secs using 399.4% CPU
Optimizing NNI: done in 0.511459 secs using 399.5% CPU
Optimizing NNI: done in 0.356602 secs using 398.5% CPU
Optimizing NNI: done in 0.369173 secs using 399.1% CPU
Optimizing NNI: done in 0.372641 secs using 399.1% CPU
Optimizing NNI: done in 0.497981 secs using 399.9% CPU
TREE SEARCH COMPLETED AFTER 168 ITERATIONS / Time: 0h:1m:13s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35746.071
Optimal log-likelihood: -35746.070
Proportion of invariable sites: 0.015
Gamma shape alpha: 2.454
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -35746.070
Total tree length: 19.640

Total number of iterations: 168
CPU time used for tree search: 286.881 sec (0h:4m:46s)
Wall-clock time used for tree search: 72.842 sec (0h:1m:12s)
Total CPU time used: 289.282 sec (0h:4m:49s)
Total wall-clock time used: 73.398 sec (0h:1m:13s)

===> START BOOTSTRAP REPLICATE NUMBER 53

Creating bootstrap alignment (seed: 956212)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.018 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36831.049
2. Current log-likelihood: -35938.729
3. Current log-likelihood: -35931.083
4. Current log-likelihood: -35930.899
Optimal log-likelihood: -35930.864
Proportion of invariable sites: 0.026
Gamma shape alpha: 2.476
Parameters optimization took 4 rounds (0.234 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0832481 secs using 397.6% CPU
Computing ML distances took 0.083385 sec (of wall-clock time) 0.331295 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000133991 secs using 429.1% CPU
Constructing RapidNJ tree: done in 0.00126314 secs using 167.5% CPU
Computing RapidNJ tree took 0.001449 sec (of wall-clock time) 0.005376 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36511.538
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.513 second
Computing log-likelihood of 98 initial trees ... 1.607 seconds
Current best score: -35930.864

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.187109 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35908.021
Optimizing NNI: done in 0.281063 secs using 400.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35902.199
Optimizing NNI: done in 0.231941 secs using 399.9% CPU
Optimizing NNI: done in 0.232096 secs using 398.1% CPU
Optimizing NNI: done in 0.385427 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35902.186
Optimizing NNI: done in 0.271539 secs using 399.5% CPU
Optimizing NNI: done in 0.419905 secs using 399.2% CPU
Optimizing NNI: done in 0.43959 secs using 399.2% CPU
Optimizing NNI: done in 0.432595 secs using 399.5% CPU
Optimizing NNI: done in 0.221802 secs using 398.9% CPU
Iteration 10 / LogL: -35908.127 / Time: 0h:0m:6s
Optimizing NNI: done in 0.397351 secs using 399.6% CPU
Optimizing NNI: done in 0.277176 secs using 399.8% CPU
Optimizing NNI: done in 0.285291 secs using 399.9% CPU
Optimizing NNI: done in 0.275492 secs using 398.2% CPU
Optimizing NNI: done in 0.408448 secs using 399% CPU
Optimizing NNI: done in 0.405289 secs using 398.9% CPU
Optimizing NNI: done in 0.244224 secs using 398.3% CPU
Optimizing NNI: done in 0.216797 secs using 398.5% CPU
1156  rtREV+R9      60243.349    319 121124.699   122311.675   122464.013
Optimizing NNI: done in 0.407288 secs using 398.7% CPU
Optimizing NNI: done in 0.492123 secs using 398.9% CPU
Iteration 20 / LogL: -35908.703 / Time: 0h:0m:10s
Finish initializing candidate tree set (6)
Current best tree score: -35902.186 / CPU time: 9.881
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.520478 secs using 398.7% CPU
Optimizing NNI: done in 0.433702 secs using 399.6% CPU
Optimizing NNI: done in 0.607322 secs using 399.7% CPU
Optimizing NNI: done in 0.418722 secs using 399.4% CPU
Optimizing NNI: done in 0.26128 secs using 399.6% CPU
Optimizing NNI: done in 0.402061 secs using 399.7% CPU
Optimizing NNI: done in 0.254504 secs using 399.9% CPU
Optimizing NNI: done in 0.551232 secs using 399.5% CPU
Optimizing NNI: done in 0.558158 secs using 399.8% CPU
Optimizing NNI: done in 0.54011 secs using 398.7% CPU
Iteration 30 / LogL: -35906.223 / Time: 0h:0m:14s (0h:0m:37s left)
Optimizing NNI: done in 0.455824 secs using 400.4% CPU
Optimizing NNI: done in 0.418972 secs using 399.4% CPU
Optimizing NNI: done in 0.55058 secs using 399.5% CPU
Optimizing NNI: done in 0.451636 secs using 399.5% CPU
1162  rtREV+I+R6    60257.784    314 121143.568   122261.195   122461.890
Optimizing NNI: done in 0.467691 secs using 399.9% CPU
Optimizing NNI: done in 0.497781 secs using 398.8% CPU
Optimizing NNI: done in 0.392723 secs using 398.4% CPU
Optimizing NNI: done in 0.502581 secs using 397.9% CPU
Optimizing NNI: done in 0.487753 secs using 399.3% CPU
Optimizing NNI: done in 0.424793 secs using 399.6% CPU
Iteration 40 / LogL: -35902.982 / Time: 0h:0m:19s (0h:0m:31s left)
Optimizing NNI: done in 0.437131 secs using 399.1% CPU
Optimizing NNI: done in 0.510511 secs using 398.2% CPU
Optimizing NNI: done in 0.357025 secs using 399.6% CPU
Optimizing NNI: done in 0.501195 secs using 399.9% CPU
Optimizing NNI: done in 0.334605 secs using 399.9% CPU
Optimizing NNI: done in 0.495844 secs using 399.7% CPU
Optimizing NNI: done in 0.435089 secs using 399.4% CPU
Optimizing NNI: done in 0.607496 secs using 398.5% CPU
Optimizing NNI: done in 0.416608 secs using 397.9% CPU
Optimizing NNI: done in 0.411258 secs using 399.2% CPU
Iteration 50 / LogL: -35911.940 / Time: 0h:0m:24s (0h:0m:25s left)
1163  rtREV+I+R7    60251.370    316 121134.740   122279.563   122461.460
Optimizing NNI: done in 0.527484 secs using 397.9% CPU
Optimizing NNI: done in 0.244116 secs using 398.7% CPU
Optimizing NNI: done in 0.670657 secs using 398.4% CPU
Optimizing NNI: done in 0.469611 secs using 397.9% CPU
1175  rtREV+F+R6    59892.087    332 120448.174   121838.816   121842.069
Optimizing NNI: done in 0.549799 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 55: -35901.958
Optimizing NNI: done in 0.585634 secs using 398.3% CPU
Optimizing NNI: done in 0.60503 secs using 399.3% CPU
Optimizing NNI: done in 0.602264 secs using 399.4% CPU
1176  rtREV+F+R7    59885.038    334 120438.076   121863.426   121840.368
Optimizing NNI: done in 0.329785 secs using 399% CPU
Optimizing NNI: done in 0.512335 secs using 398.5% CPU
Iteration 60 / LogL: -35903.379 / Time: 0h:0m:29s (0h:0m:47s left)
Optimizing NNI: done in 0.344009 secs using 398.4% CPU
Optimizing NNI: done in 0.665537 secs using 397.9% CPU
Optimizing NNI: done in 0.404154 secs using 398.9% CPU
Optimizing NNI: done in 0.42745 secs using 398.6% CPU
1177  rtREV+F+R8    59876.997    336 120425.993   121887.051   121836.682
Optimizing NNI: done in 0.605798 secs using 399.6% CPU
Optimizing NNI: done in 0.280685 secs using 399.9% CPU
Optimizing NNI: done in 0.361754 secs using 399.1% CPU
Optimizing NNI: done in 0.379922 secs using 399.1% CPU
Optimizing NNI: done in 0.534018 secs using 399.7% CPU
Optimizing NNI: done in 0.552152 secs using 399.3% CPU
Iteration 70 / LogL: -35902.817 / Time: 0h:0m:33s (0h:0m:41s left)
Optimizing NNI: done in 0.419996 secs using 399.7% CPU
Optimizing NNI: done in 0.58621 secs using 399.2% CPU
Optimizing NNI: done in 0.282503 secs using 400.8% CPU
Optimizing NNI: done in 0.448383 secs using 399.7% CPU
Optimizing NNI: done in 0.641572 secs using 399.1% CPU
Optimizing NNI: done in 0.764358 secs using 399.4% CPU
Optimizing NNI: done in 0.268096 secs using 400.3% CPU
Optimizing NNI: done in 0.306953 secs using 398.2% CPU
Optimizing NNI: done in 0.378771 secs using 398.8% CPU
Optimizing NNI: done in 0.333912 secs using 398.6% CPU
Iteration 80 / LogL: -35902.505 / Time: 0h:0m:38s (0h:0m:36s left)
Optimizing NNI: done in 0.391787 secs using 398.3% CPU
Optimizing NNI: done in 0.422584 secs using 398.7% CPU
Optimizing NNI: done in 0.373556 secs using 399.6% CPU
Optimizing NNI: done in 0.385719 secs using 399.9% CPU
Optimizing NNI: done in 0.478328 secs using 399.3% CPU
Optimizing NNI: done in 0.444662 secs using 399.7% CPU
Optimizing NNI: done in 0.463103 secs using 399.3% CPU
Optimizing NNI: done in 0.521699 secs using 399.3% CPU
Optimizing NNI: done in 0.484169 secs using 399.4% CPU
Optimizing NNI: done in 0.530182 secs using 399.1% CPU
Iteration 90 / LogL: -35908.975 / Time: 0h:0m:42s (0h:0m:31s left)
Optimizing NNI: done in 0.382574 secs using 399.9% CPU
Optimizing NNI: done in 0.579537 secs using 399.9% CPU
Optimizing NNI: done in 0.510122 secs using 399.8% CPU
Optimizing NNI: done in 0.321604 secs using 399.8% CPU
1178  rtREV+F+R9    59876.123    338 120428.246   121926.050   121847.332
Optimizing NNI: done in 0.49442 secs using 399.7% CPU
Optimizing NNI: done in 0.341467 secs using 399.5% CPU
Optimizing NNI: done in 0.382348 secs using 399.6% CPU
Optimizing NNI: done in 0.568523 secs using 399.6% CPU
Optimizing NNI: done in 0.346571 secs using 398.2% CPU
Optimizing NNI: done in 0.573673 secs using 397.9% CPU
Iteration 100 / LogL: -35902.430 / Time: 0h:0m:47s (0h:0m:26s left)
Optimizing NNI: done in 0.519283 secs using 397.9% CPU
Optimizing NNI: done in 0.289482 secs using 399.3% CPU
Optimizing NNI: done in 0.2982 secs using 400.2% CPU
Optimizing NNI: done in 0.374031 secs using 398.8% CPU
Optimizing NNI: done in 0.378263 secs using 399.1% CPU
Optimizing NNI: done in 0.609055 secs using 399.9% CPU
Optimizing NNI: done in 0.498761 secs using 399.2% CPU
Optimizing NNI: done in 0.448167 secs using 400.3% CPU
Optimizing NNI: done in 0.45608 secs using 398.4% CPU
Optimizing NNI: done in 0.410155 secs using 399.4% CPU
Iteration 110 / LogL: -35902.052 / Time: 0h:0m:51s (0h:0m:21s left)
Optimizing NNI: done in 0.365339 secs using 399.6% CPU
Optimizing NNI: done in 0.531516 secs using 399.7% CPU
Optimizing NNI: done in 0.644835 secs using 398.6% CPU
Optimizing NNI: done in 0.315878 secs using 399.9% CPU
Optimizing NNI: done in 0.78658 secs using 398.5% CPU
Optimizing NNI: done in 0.493368 secs using 399.2% CPU
Optimizing NNI: done in 0.520248 secs using 399.5% CPU
Optimizing NNI: done in 0.491862 secs using 399.3% CPU
1184  rtREV+F+I+R6  59891.586    333 120449.172   121857.045   121847.265
Optimizing NNI: done in 0.388973 secs using 399.9% CPU
Optimizing NNI: done in 0.34302 secs using 398.7% CPU
Iteration 120 / LogL: -35908.142 / Time: 0h:0m:56s (0h:0m:16s left)
Optimizing NNI: done in 0.52278 secs using 399.1% CPU
Optimizing NNI: done in 0.365758 secs using 399.5% CPU
Optimizing NNI: done in 0.286455 secs using 398.2% CPU
Optimizing NNI: done in 0.50044 secs using 398.5% CPU
Optimizing NNI: done in 0.410102 secs using 398.6% CPU
Optimizing NNI: done in 0.454165 secs using 398.5% CPU
Optimizing NNI: done in 0.343632 secs using 398.7% CPU
Optimizing NNI: done in 0.410752 secs using 397.9% CPU
Optimizing NNI: done in 0.392478 secs using 399.9% CPU
Optimizing NNI: done in 0.461045 secs using 399.9% CPU
Iteration 130 / LogL: -35902.044 / Time: 0h:1m:0s (0h:0m:11s left)
Optimizing NNI: done in 0.49725 secs using 399.5% CPU
Optimizing NNI: done in 0.491232 secs using 399.4% CPU
Optimizing NNI: done in 0.615866 secs using 399.3% CPU
Optimizing NNI: done in 0.477576 secs using 398.8% CPU
Optimizing NNI: done in 0.503074 secs using 399.8% CPU
Optimizing NNI: done in 0.429436 secs using 399.6% CPU
Optimizing NNI: done in 0.521712 secs using 399.7% CPU
Optimizing NNI: done in 0.417183 secs using 399.5% CPU
Optimizing NNI: done in 0.650199 secs using 399.3% CPU
1185  rtREV+F+I+R7  59884.896    335 120439.792   121882.869   121846.282
Optimizing NNI: done in 0.60227 secs using 399.3% CPU
Iteration 140 / LogL: -35909.656 / Time: 0h:1m:6s (0h:0m:7s left)
Optimizing NNI: done in 0.64052 secs using 399.3% CPU
Optimizing NNI: done in 0.464235 secs using 399.7% CPU
Optimizing NNI: done in 0.522832 secs using 399.1% CPU
Optimizing NNI: done in 0.428358 secs using 399.2% CPU
Optimizing NNI: done in 0.332912 secs using 400% CPU
1197  cpREV+R6      60125.526    313 120877.052   121981.344   122191.176
Optimizing NNI: done in 0.343643 secs using 399.3% CPU
Optimizing NNI: done in 0.401965 secs using 399.9% CPU
Optimizing NNI: done in 0.506855 secs using 399.5% CPU
Optimizing NNI: done in 0.266084 secs using 399.9% CPU
Optimizing NNI: done in 0.566227 secs using 399.4% CPU
Iteration 150 / LogL: -35902.429 / Time: 0h:1m:10s (0h:0m:2s left)
Optimizing NNI: done in 0.433695 secs using 399.7% CPU
Optimizing NNI: done in 0.400136 secs using 399% CPU
Optimizing NNI: done in 0.322337 secs using 399.6% CPU
Optimizing NNI: done in 0.322288 secs using 399.8% CPU
Optimizing NNI: done in 0.314155 secs using 399.9% CPU
Optimizing NNI: done in 0.556969 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 156 ITERATIONS / Time: 0h:1m:13s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35901.958
Optimal log-likelihood: -35901.957
Proportion of invariable sites: 0.026
Gamma shape alpha: 2.467
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35901.957
Total tree length: 19.803

Total number of iterations: 156
CPU time used for tree search: 285.780 sec (0h:4m:45s)
Wall-clock time used for tree search: 72.584 sec (0h:1m:12s)
Total CPU time used: 288.156 sec (0h:4m:48s)
Total wall-clock time used: 73.142 sec (0h:1m:13s)

===> START BOOTSTRAP REPLICATE NUMBER 54

Creating bootstrap alignment (seed: 956213)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36466.671
2. Current log-likelihood: -35601.955
3. Current log-likelihood: -35589.606
4. Current log-likelihood: -35588.884
5. Current log-likelihood: -35588.678
Optimal log-likelihood: -35588.561
Proportion of invariable sites: 0.036
Gamma shape alpha: 2.444
Parameters optimization took 5 rounds (0.304 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.075758 secs using 400% CPU
Computing ML distances took 0.075880 sec (of wall-clock time) 0.303345 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000133038 secs using 466% CPU
Constructing RapidNJ tree: done in 0.00118589 secs using 238% CPU
Computing RapidNJ tree took 0.001374 sec (of wall-clock time) 0.006039 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36187.887
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|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.557 second
1198  cpREV+R7      60114.354    315 120858.707   121989.843   122181.228
Computing log-likelihood of 98 initial trees ... 1.558 seconds
Current best score: -35588.561

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.363696 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35544.752
Optimizing NNI: done in 0.255822 secs using 399.9% CPU
Optimizing NNI: done in 0.300131 secs using 399.2% CPU
Optimizing NNI: done in 0.298516 secs using 398.5% CPU
Optimizing NNI: done in 0.312487 secs using 399.6% CPU
Optimizing NNI: done in 0.266265 secs using 399.9% CPU
Optimizing NNI: done in 0.306674 secs using 399.4% CPU
Optimizing NNI: done in 0.274065 secs using 399.1% CPU
Optimizing NNI: done in 0.294253 secs using 400.6% CPU
Optimizing NNI: done in 0.288525 secs using 399.6% CPU
Iteration 10 / LogL: -35546.723 / Time: 0h:0m:6s
Optimizing NNI: done in 0.289787 secs using 399.8% CPU
Optimizing NNI: done in 0.297979 secs using 399.1% CPU
Optimizing NNI: done in 0.293143 secs using 399.5% CPU
Optimizing NNI: done in 0.297878 secs using 398.8% CPU
Optimizing NNI: done in 0.224314 secs using 399% CPU
Optimizing NNI: done in 0.30896 secs using 399.2% CPU
Optimizing NNI: done in 0.264781 secs using 400.6% CPU
Optimizing NNI: done in 0.269197 secs using 398.7% CPU
Optimizing NNI: done in 0.290891 secs using 399.1% CPU
Optimizing NNI: done in 0.266087 secs using 399.9% CPU
Iteration 20 / LogL: -35550.603 / Time: 0h:0m:9s
Finish initializing candidate tree set (5)
Current best tree score: -35544.752 / CPU time: 9.014
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 0.32879 secs using 399.5% CPU
Optimizing NNI: done in 0.300567 secs using 399.2% CPU
Optimizing NNI: done in 0.422424 secs using 399% CPU
Optimizing NNI: done in 0.359942 secs using 399.9% CPU
Optimizing NNI: done in 0.395173 secs using 398.4% CPU
Optimizing NNI: done in 0.319086 secs using 399.3% CPU
Optimizing NNI: done in 0.423363 secs using 399.6% CPU
1199  cpREV+R8      60110.898    317 120855.795   122014.485   122186.713
Optimizing NNI: done in 0.345994 secs using 399.5% CPU
Optimizing NNI: done in 0.382324 secs using 399.9% CPU
Optimizing NNI: done in 0.45453 secs using 398.3% CPU
Iteration 30 / LogL: -35546.338 / Time: 0h:0m:13s (0h:0m:32s left)
Optimizing NNI: done in 0.343037 secs using 399.9% CPU
Optimizing NNI: done in 0.458798 secs using 399.6% CPU
Optimizing NNI: done in 0.402489 secs using 398.9% CPU
Optimizing NNI: done in 0.388755 secs using 399.1% CPU
Optimizing NNI: done in 0.430915 secs using 399.7% CPU
Optimizing NNI: done in 0.375257 secs using 399.6% CPU
Optimizing NNI: done in 0.405914 secs using 399.9% CPU
Optimizing NNI: done in 0.387264 secs using 398.8% CPU
Optimizing NNI: done in 0.311787 secs using 398.8% CPU
Optimizing NNI: done in 0.343651 secs using 398.4% CPU
Iteration 40 / LogL: -35546.301 / Time: 0h:0m:17s (0h:0m:27s left)
Optimizing NNI: done in 0.395842 secs using 400.1% CPU
Optimizing NNI: done in 0.375726 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35544.705
1206  cpREV+I+R6    60123.873    314 120875.747   121993.374   122194.069
Optimizing NNI: done in 0.4116 secs using 398.9% CPU
Optimizing NNI: done in 0.352277 secs using 398.1% CPU
Optimizing NNI: done in 0.475773 secs using 398.8% CPU
Optimizing NNI: done in 0.319024 secs using 397.5% CPU
Optimizing NNI: done in 0.344057 secs using 398.8% CPU
Optimizing NNI: done in 0.444023 secs using 398.5% CPU
Optimizing NNI: done in 0.402074 secs using 398.5% CPU
Optimizing NNI: done in 0.441901 secs using 398.8% CPU
Iteration 50 / LogL: -35544.736 / Time: 0h:0m:21s (0h:0m:22s left)
Optimizing NNI: done in 0.388701 secs using 398.3% CPU
Optimizing NNI: done in 0.342209 secs using 400.4% CPU
Optimizing NNI: done in 0.308627 secs using 399.3% CPU
Optimizing NNI: done in 0.43477 secs using 399% CPU
Optimizing NNI: done in 0.352132 secs using 399.9% CPU
Optimizing NNI: done in 0.570255 secs using 398.7% CPU
Optimizing NNI: done in 0.387526 secs using 398.4% CPU
Optimizing NNI: done in 0.425931 secs using 399.8% CPU
Optimizing NNI: done in 0.344537 secs using 399.9% CPU
Optimizing NNI: done in 0.409173 secs using 399.4% CPU
Iteration 60 / LogL: -35545.154 / Time: 0h:0m:25s (0h:0m:17s left)
Optimizing NNI: done in 0.371468 secs using 399.6% CPU
Optimizing NNI: done in 0.493774 secs using 399% CPU
Optimizing NNI: done in 0.260662 secs using 400.6% CPU
Optimizing NNI: done in 0.445358 secs using 399.2% CPU
374  Q.yeast+I+R10 105699.440   554 212506.880   827446.880   214737.210
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.444109 secs using 399.7% CPU
1207  cpREV+I+R7    60114.273    316 120860.546   122005.369   122187.266
Optimizing NNI: done in 0.486067 secs using 399.2% CPU
Optimizing NNI: done in 0.328634 secs using 399.6% CPU
Optimizing NNI: done in 0.363393 secs using 399.5% CPU
Optimizing NNI: done in 0.577798 secs using 398% CPU
Optimizing NNI: done in 0.349301 secs using 399.9% CPU
Iteration 70 / LogL: -35560.097 / Time: 0h:0m:29s (0h:0m:13s left)
Optimizing NNI: done in 0.398748 secs using 398.8% CPU
Optimizing NNI: done in 0.396611 secs using 398.8% CPU
1219  cpREV+F+R6    59920.197    332 120504.394   121895.036   121898.289
Optimizing NNI: done in 0.282532 secs using 399.9% CPU
Optimizing NNI: done in 0.455586 secs using 399.7% CPU
Optimizing NNI: done in 0.265856 secs using 399.2% CPU
Optimizing NNI: done in 0.475503 secs using 399.5% CPU
Optimizing NNI: done in 0.392897 secs using 399.9% CPU
Optimizing NNI: done in 0.444639 secs using 399.9% CPU
Optimizing NNI: done in 0.304288 secs using 399.1% CPU
Optimizing NNI: done in 0.397445 secs using 399.4% CPU
Iteration 80 / LogL: -35544.723 / Time: 0h:0m:33s (0h:0m:8s left)
Optimizing NNI: done in 0.440302 secs using 399.2% CPU
Optimizing NNI: done in 0.414284 secs using 398.9% CPU
Optimizing NNI: done in 0.398703 secs using 398.9% CPU
Optimizing NNI: done in 0.446382 secs using 398.8% CPU
Optimizing NNI: done in 0.376218 secs using 399.4% CPU
Optimizing NNI: done in 0.644192 secs using 398.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -35544.705
Optimizing NNI: done in 0.412379 secs using 398.5% CPU
Optimizing NNI: done in 0.338288 secs using 398.1% CPU
Optimizing NNI: done in 0.415624 secs using 399.7% CPU
Optimizing NNI: done in 0.591474 secs using 398.8% CPU
Iteration 90 / LogL: -35545.824 / Time: 0h:0m:37s (0h:0m:4s left)
Optimizing NNI: done in 0.374908 secs using 399% CPU
Optimizing NNI: done in 0.358623 secs using 398.9% CPU
Optimizing NNI: done in 0.509138 secs using 397.5% CPU
UPDATE BEST LOG-LIKELIHOOD: -35544.704
Optimizing NNI: done in 0.348952 secs using 398.6% CPU
Optimizing NNI: done in 0.483106 secs using 398.5% CPU
Optimizing NNI: done in 0.380193 secs using 398.8% CPU
Optimizing NNI: done in 0.528064 secs using 399.9% CPU
Optimizing NNI: done in 0.376723 secs using 399.1% CPU
Optimizing NNI: done in 0.613595 secs using 398.5% CPU
Optimizing NNI: done in 0.447309 secs using 399.1% CPU
Iteration 100 / LogL: -35545.158 / Time: 0h:0m:42s (0h:0m:0s left)
Optimizing NNI: done in 0.478636 secs using 398.5% CPU
Optimizing NNI: done in 0.440843 secs using 398.3% CPU
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:43s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35544.704
Optimal log-likelihood: -35544.703
Proportion of invariable sites: 0.036
Gamma shape alpha: 2.508
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35544.703
Total tree length: 19.190

Total number of iterations: 102
CPU time used for tree search: 166.032 sec (0h:2m:46s)
Wall-clock time used for tree search: 42.626 sec (0h:0m:42s)
Total CPU time used: 169.135 sec (0h:2m:49s)
Total wall-clock time used: 43.357 sec (0h:0m:43s)

===> START BOOTSTRAP REPLICATE NUMBER 55

Creating bootstrap alignment (seed: 956214)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37493.245
2. Current log-likelihood: -36649.380
3. Current log-likelihood: -36637.931
4. Current log-likelihood: -36637.648
Optimal log-likelihood: -36637.583
Proportion of invariable sites: 0.014
Gamma shape alpha: 2.279
Parameters optimization took 4 rounds (0.218 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0739031 secs using 398% CPU
Computing ML distances took 0.074043 sec (of wall-clock time) 0.294466 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000133991 secs using 458.2% CPU
Constructing RapidNJ tree: done in 0.00130677 secs using 331.4% CPU
Computing RapidNJ tree took 0.001491 sec (of wall-clock time) 0.006686 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37273.714
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.531 second
Computing log-likelihood of 98 initial trees ... 1.466 seconds
Current best score: -36637.583

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.164657 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36595.428
Optimizing NNI: done in 0.229429 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36593.082
Optimizing NNI: done in 0.259344 secs using 399.9% CPU
Optimizing NNI: done in 0.24444 secs using 399.5% CPU
Optimizing NNI: done in 0.2572 secs using 399.6% CPU
Optimizing NNI: done in 0.260957 secs using 399.5% CPU
Optimizing NNI: done in 0.258116 secs using 398.8% CPU
Optimizing NNI: done in 0.245103 secs using 399.9% CPU
Optimizing NNI: done in 0.271451 secs using 399.9% CPU
Optimizing NNI: done in 0.256629 secs using 398.7% CPU
Iteration 10 / LogL: -36595.431 / Time: 0h:0m:6s
Optimizing NNI: done in 0.27759 secs using 398.7% CPU
Optimizing NNI: done in 0.274737 secs using 398.4% CPU
Optimizing NNI: done in 0.259983 secs using 397.5% CPU
Optimizing NNI: done in 0.288172 secs using 395% CPU
Optimizing NNI: done in 0.266993 secs using 396.9% CPU
Optimizing NNI: done in 0.274226 secs using 398.1% CPU
Optimizing NNI: done in 0.26901 secs using 398.5% CPU
1220  cpREV+F+R7    59900.106    334 120468.213   121893.563   121870.505
Optimizing NNI: done in 0.274439 secs using 398.7% CPU
Optimizing NNI: done in 0.25814 secs using 397.9% CPU
Optimizing NNI: done in 0.263147 secs using 399.1% CPU
Iteration 20 / LogL: -36595.427 / Time: 0h:0m:8s
Finish initializing candidate tree set (4)
Current best tree score: -36593.082 / CPU time: 8.338
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.4327 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36592.233
Optimizing NNI: done in 0.429622 secs using 398.7% CPU
Optimizing NNI: done in 0.376095 secs using 398.4% CPU
Optimizing NNI: done in 0.318886 secs using 399.8% CPU
Optimizing NNI: done in 0.367106 secs using 399.3% CPU
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Optimizing NNI: done in 0.401735 secs using 399.4% CPU
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Optimizing NNI: done in 0.363878 secs using 399.1% CPU
Optimizing NNI: done in 0.373945 secs using 398.9% CPU
Iteration 30 / LogL: -36592.506 / Time: 0h:0m:12s (0h:0m:40s left)
Optimizing NNI: done in 0.330389 secs using 399.9% CPU
Optimizing NNI: done in 0.285824 secs using 399.2% CPU
Optimizing NNI: done in 0.354699 secs using 399.6% CPU
Optimizing NNI: done in 0.234023 secs using 398.7% CPU
Optimizing NNI: done in 0.381485 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -36591.442
Optimizing NNI: done in 0.251651 secs using 399.5% CPU
Optimizing NNI: done in 0.343715 secs using 399.3% CPU
Optimizing NNI: done in 0.315611 secs using 398.3% CPU
Optimizing NNI: done in 0.358923 secs using 397.7% CPU
WARNING: Log-likelihood -200050 of mtMet+R10 worse than mtMet+R9 -200020
407  mtMet+R10     200049.839   1005 402109.679   2424169.679  406485.821
Optimizing NNI: done in 0.333021 secs using 396.6% CPU
Iteration 40 / LogL: -36592.993 / Time: 0h:0m:16s (0h:0m:39s left)
Optimizing NNI: done in 0.390216 secs using 399.4% CPU
Optimizing NNI: done in 0.364087 secs using 398.4% CPU
Optimizing NNI: done in 0.351229 secs using 398.7% CPU
1221  cpREV+F+R8    59898.397    336 120468.794   121929.852   121879.483
Optimizing NNI: done in 0.398428 secs using 399.1% CPU
Optimizing NNI: done in 0.422551 secs using 399.4% CPU
Optimizing NNI: done in 0.42835 secs using 399.2% CPU
Optimizing NNI: done in 0.367209 secs using 400.6% CPU
Optimizing NNI: done in 0.295483 secs using 399.9% CPU
Optimizing NNI: done in 0.344191 secs using 399.9% CPU
Optimizing NNI: done in 0.326729 secs using 399.6% CPU
Iteration 50 / LogL: -36591.458 / Time: 0h:0m:19s (0h:0m:34s left)
Optimizing NNI: done in 0.334203 secs using 399.5% CPU
Optimizing NNI: done in 0.45046 secs using 399.3% CPU
Optimizing NNI: done in 0.317545 secs using 400.5% CPU
Optimizing NNI: done in 0.399303 secs using 399.3% CPU
Optimizing NNI: done in 0.42935 secs using 398.9% CPU
Optimizing NNI: done in 0.363452 secs using 399.9% CPU
Optimizing NNI: done in 0.351181 secs using 399.9% CPU
Optimizing NNI: done in 0.410749 secs using 399.1% CPU
Optimizing NNI: done in 0.343423 secs using 399.8% CPU
395  Q.yeast+F+I+R9 105573.456   571 212288.913   865512.913   214587.682
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.438311 secs using 398.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -36591.436
Iteration 60 / LogL: -36591.436 / Time: 0h:0m:23s (0h:0m:30s left)
1228  cpREV+F+I+R6  59916.314    333 120498.627   121906.501   121896.721
Optimizing NNI: done in 0.416445 secs using 399.9% CPU
Optimizing NNI: done in 0.433695 secs using 399.9% CPU
Optimizing NNI: done in 0.324834 secs using 399.9% CPU
Optimizing NNI: done in 0.458588 secs using 399.7% CPU
Optimizing NNI: done in 0.409479 secs using 398.7% CPU
Optimizing NNI: done in 0.401127 secs using 399.9% CPU
Optimizing NNI: done in 0.353287 secs using 399.3% CPU
Optimizing NNI: done in 0.330681 secs using 399.6% CPU
Optimizing NNI: done in 0.352471 secs using 399.4% CPU
Optimizing NNI: done in 0.243804 secs using 399.5% CPU
Iteration 70 / LogL: -36591.537 / Time: 0h:0m:27s (0h:0m:25s left)
Optimizing NNI: done in 0.408988 secs using 398.7% CPU
Optimizing NNI: done in 0.384325 secs using 399.4% CPU
Optimizing NNI: done in 0.433464 secs using 399% CPU
Optimizing NNI: done in 0.35479 secs using 398.8% CPU
Optimizing NNI: done in 0.361351 secs using 399% CPU
Optimizing NNI: done in 0.437126 secs using 399% CPU
Optimizing NNI: done in 0.37842 secs using 399.8% CPU
Optimizing NNI: done in 0.389154 secs using 398.8% CPU
Optimizing NNI: done in 0.392169 secs using 399% CPU
416  mtMet+F+R8    196455.394   1020 394950.789   2477790.789  399392.246
Optimizing NNI: done in 0.462484 secs using 399.7% CPU
Iteration 80 / LogL: -36594.885 / Time: 0h:0m:31s (0h:0m:21s left)
Optimizing NNI: done in 0.382895 secs using 398.8% CPU
Optimizing NNI: done in 0.186077 secs using 399.7% CPU
Optimizing NNI: done in 0.389774 secs using 398.5% CPU
Optimizing NNI: done in 0.327784 secs using 399% CPU
Optimizing NNI: done in 0.368297 secs using 398.7% CPU
Optimizing NNI: done in 0.335906 secs using 398.1% CPU
Optimizing NNI: done in 0.378569 secs using 398.6% CPU
Optimizing NNI: done in 0.29428 secs using 399.5% CPU
Optimizing NNI: done in 0.450138 secs using 399.6% CPU
Optimizing NNI: done in 0.341226 secs using 398.9% CPU
Iteration 90 / LogL: -36591.829 / Time: 0h:0m:35s (0h:0m:17s left)
Optimizing NNI: done in 0.286966 secs using 399.3% CPU
Optimizing NNI: done in 0.292459 secs using 399.9% CPU
Optimizing NNI: done in 0.33205 secs using 398.9% CPU
Optimizing NNI: done in 0.304895 secs using 399.6% CPU
Optimizing NNI: done in 0.321341 secs using 399.8% CPU
Optimizing NNI: done in 0.487837 secs using 399.1% CPU
Optimizing NNI: done in 0.405328 secs using 399.6% CPU
Optimizing NNI: done in 0.38477 secs using 399.3% CPU
Optimizing NNI: done in 0.315505 secs using 398.5% CPU
Optimizing NNI: done in 0.408969 secs using 398.2% CPU
Iteration 100 / LogL: -36591.483 / Time: 0h:0m:38s (0h:0m:13s left)
Optimizing NNI: done in 0.332973 secs using 400% CPU
Optimizing NNI: done in 0.431187 secs using 398% CPU
Optimizing NNI: done in 0.367915 secs using 399.4% CPU
Optimizing NNI: done in 0.343869 secs using 399.8% CPU
Optimizing NNI: done in 0.390093 secs using 399% CPU
Optimizing NNI: done in 0.309256 secs using 399.2% CPU
Optimizing NNI: done in 0.3426 secs using 399.6% CPU
Optimizing NNI: done in 0.370443 secs using 399.8% CPU
Optimizing NNI: done in 0.338977 secs using 399.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -36591.434
Optimizing NNI: done in 0.411844 secs using 399% CPU
Iteration 110 / LogL: -36591.796 / Time: 0h:0m:42s (0h:0m:9s left)
Optimizing NNI: done in 0.427034 secs using 399.3% CPU
Optimizing NNI: done in 0.425269 secs using 399.3% CPU
Optimizing NNI: done in 0.334348 secs using 399% CPU
1229  cpREV+F+I+R7  59900.315    335 120470.631   121913.708   121877.121
Akaike Information Criterion:           LG+R8
Corrected Akaike Information Criterion: LG+R6
Bayesian Information Criterion:         LG+R8
Best-fit model: LG+R8 chosen according to BIC

All model information printed to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.model.gz
CPU time for ModelFinder: 10601.448 seconds (2h:56m:41s)
Wall-clock time for ModelFinder: 3585.764 seconds (0h:59m:45s)

===> START BOOTSTRAP REPLICATE NUMBER 1

Creating bootstrap alignment (seed: 956250)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.051 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60011.302
Optimizing NNI: done in 0.343532 secs using 397.7% CPU
Optimizing NNI: done in 0.391664 secs using 397.2% CPU
Optimizing NNI: done in 0.34801 secs using 397.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 116: -36589.293
2. Current log-likelihood: -59405.489
Optimizing NNI: done in 0.45687 secs using 399.4% CPU
Optimizing NNI: done in 0.388741 secs using 399.4% CPU
Optimizing NNI: done in 0.401477 secs using 399.8% CPU
3. Current log-likelihood: -59398.328
Optimizing NNI: done in 0.431123 secs using 398.8% CPU
Iteration 120 / LogL: -36589.386 / Time: 0h:0m:46s (0h:0m:37s left)
Optimizing NNI: done in 0.330825 secs using 399.2% CPU
Optimizing NNI: done in 0.321247 secs using 399.1% CPU
4. Current log-likelihood: -59397.614
Optimizing NNI: done in 0.387144 secs using 399.4% CPU
Optimizing NNI: done in 0.304744 secs using 399.9% CPU
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5. Current log-likelihood: -59397.172
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6. Current log-likelihood: -59396.907
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Optimizing NNI: done in 0.311267 secs using 399.3% CPU
Iteration 130 / LogL: -36589.302 / Time: 0h:0m:49s (0h:0m:33s left)
Optimizing NNI: done in 0.342016 secs using 399.6% CPU
7. Current log-likelihood: -59396.720
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8. Current log-likelihood: -59396.574
Optimizing NNI: done in 0.363137 secs using 398.9% CPU
Optimizing NNI: done in 0.270744 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36589.270
Optimizing NNI: done in 0.279017 secs using 399.5% CPU
9. Current log-likelihood: -59396.454
Optimizing NNI: done in 0.378555 secs using 399.6% CPU
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Optimizing NNI: done in 0.351381 secs using 399.3% CPU
Iteration 140 / LogL: -36590.005 / Time: 0h:0m:53s (0h:0m:29s left)
10. Current log-likelihood: -59396.351
Optimizing NNI: done in 0.278233 secs using 398.8% CPU
Optimizing NNI: done in 0.371159 secs using 399.8% CPU
Optimizing NNI: done in 0.294679 secs using 398.7% CPU
Optimal log-likelihood: -59396.257
Site proportion and rates:  (0.114,0.070) (0.110,0.186) (0.162,0.379) (0.190,0.634) (0.186,1.048) (0.108,1.842) (0.104,2.446) (0.026,5.433)
Parameters optimization took 10 rounds (10.352 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 0.360659 secs using 400.1% CPU
Optimizing NNI: done in 0.381161 secs using 398.5% CPU
Optimizing NNI: done in 0.321225 secs using 399% CPU
Optimizing NNI: done in 0.44914 secs using 399.4% CPU
Calculating distance matrix: done in 1.5014 secs using 299.8% CPU
Computing ML distances took 1.501629 sec (of wall-clock time) 4.501974 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000509024 secs
Constructing RapidNJ tree: done in 0.00395107 secs using 368.2% CPU
Computing RapidNJ tree took 0.004520 sec (of wall-clock time) 0.015573 sec (of CPU time)
Optimizing NNI: done in 0.295915 secs using 399.2% CPU
Log-likelihood of RapidNJ tree: -59600.385
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 0.309355 secs using 398.9% CPU
Optimizing NNI: done in 0.332497 secs using 400.4% CPU
Iteration 150 / LogL: -36589.692 / Time: 0h:0m:56s (0h:0m:25s left)
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Iteration 160 / LogL: -36589.370 / Time: 0h:1m:0s (0h:0m:21s left)
Optimizing NNI: done in 0.3435 secs using 399.3% CPU
Optimizing NNI: done in 0.375487 secs using 399.6% CPU
5.000 second
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Iteration 170 / LogL: -36589.302 / Time: 0h:1m:3s (0h:0m:17s left)
Optimizing NNI: done in 0.291938 secs using 399.9% CPU
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Iteration 180 / LogL: -36589.686 / Time: 0h:1m:7s (0h:0m:13s left)
Optimizing NNI: done in 0.295036 secs using 400% CPU
Optimizing NNI: done in 0.276297 secs using 399.1% CPU
Optimizing NNI: done in 0.409186 secs using 399% CPU
Computing log-likelihood of 98 initial trees ... 7.263 seconds
Current best score: -59396.257

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.392383 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
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Iteration 190 / LogL: -36603.514 / Time: 0h:1m:10s (0h:0m:9s left)
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BETTER TREE FOUND at iteration 1: -59228.903
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Iteration 200 / LogL: -36590.583 / Time: 0h:1m:14s (0h:0m:5s left)
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417  mtMet+F+R9    196440.615   1022 394925.229   2485937.229  399375.395
Optimizing NNI: done in 0.316322 secs using 399.2% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.357271 secs using 399.3% CPU
Iteration 210 / LogL: -36589.303 / Time: 0h:1m:17s (0h:0m:2s left)
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BETTER TREE FOUND at iteration 3: -59214.667
Optimizing NNI: done in 0.289392 secs using 399.2% CPU
Optimizing NNI: done in 0.319878 secs using 399.6% CPU
TREE SEARCH COMPLETED AFTER 217 ITERATIONS / Time: 0h:1m:19s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36589.270
Optimal log-likelihood: -36589.268
Proportion of invariable sites: 0.015
Gamma shape alpha: 2.347
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -36589.268
Total tree length: 19.335

Total number of iterations: 217
CPU time used for tree search: 312.689 sec (0h:5m:12s)
Wall-clock time used for tree search: 79.351 sec (0h:1m:19s)
Total CPU time used: 315.145 sec (0h:5m:15s)
Total wall-clock time used: 79.920 sec (0h:1m:19s)

===> START BOOTSTRAP REPLICATE NUMBER 56

Creating bootstrap alignment (seed: 956215)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36671.018
2. Current log-likelihood: -35819.551
3. Current log-likelihood: -35803.206
4. Current log-likelihood: -35802.582
Optimal log-likelihood: -35802.564
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.784
Parameters optimization took 4 rounds (0.262 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.079895 secs using 400% CPU
Computing ML distances took 0.080061 sec (of wall-clock time) 0.319986 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000127792 secs using 201.1% CPU
Constructing RapidNJ tree: done in 0.00118685 secs using 148.8% CPU
Computing RapidNJ tree took 0.001366 sec (of wall-clock time) 0.002969 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36262.791
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.81462 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
1.561 second
Computing log-likelihood of 98 initial trees ... 1.629 seconds
Current best score: -35802.564

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35752.357
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BETTER TREE FOUND at iteration 4: -59213.568
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Iteration 10 / LogL: -35752.987 / Time: 0h:0m:6s
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Iteration 20 / LogL: -35752.582 / Time: 0h:0m:8s
Finish initializing candidate tree set (2)
Current best tree score: -35752.357 / CPU time: 8.038
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35752.337
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BETTER TREE FOUND at iteration 6: -59200.711
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Iteration 30 / LogL: -35761.063 / Time: 0h:0m:12s (0h:0m:31s left)
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Iteration 40 / LogL: -35753.894 / Time: 0h:0m:16s (0h:0m:26s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 50 / LogL: -35752.397 / Time: 0h:0m:20s (0h:0m:21s left)
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BETTER TREE FOUND at iteration 9: -59191.858
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Iteration 60 / LogL: -35752.380 / Time: 0h:0m:24s (0h:0m:17s left)
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Iteration 10 / LogL: -59228.199 / Time: 0h:1m:2s
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Iteration 70 / LogL: -35783.395 / Time: 0h:0m:29s (0h:0m:13s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 75: -35750.252
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35750.193
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Iteration 80 / LogL: -35909.998 / Time: 0h:0m:33s (0h:0m:40s left)
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Iteration 90 / LogL: -35751.617 / Time: 0h:0m:37s (0h:0m:35s left)
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Iteration 100 / LogL: -35750.423 / Time: 0h:0m:41s (0h:0m:31s left)
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Iteration 110 / LogL: -35751.549 / Time: 0h:0m:45s (0h:0m:27s left)
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Iteration 20 / LogL: -59261.046 / Time: 0h:1m:23s
Finish initializing candidate tree set (20)
Current best tree score: -59191.858 / CPU time: 71.171
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 0.331124 secs using 398.9% CPU
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Iteration 120 / LogL: -35750.929 / Time: 0h:0m:49s (0h:0m:22s left)
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Iteration 130 / LogL: -35750.993 / Time: 0h:0m:52s (0h:0m:18s left)
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Iteration 140 / LogL: -35758.530 / Time: 0h:0m:56s (0h:0m:14s left)
Optimizing NNI: done in 2.30668 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.419718 secs using 399.8% CPU
Optimizing NNI: done in 0.289645 secs using 399.9% CPU
Optimizing NNI: done in 0.322709 secs using 399.3% CPU
Optimizing NNI: done in 0.392179 secs using 399.4% CPU
BETTER TREE FOUND at iteration 24: -59177.881
Optimizing NNI: done in 0.41843 secs using 399.1% CPU
Optimizing NNI: done in 0.263277 secs using 399.5% CPU
Optimizing NNI: done in 0.429267 secs using 399.7% CPU
Optimizing NNI: done in 0.432111 secs using 398.3% CPU
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Optimizing NNI: done in 2.04117 secs using 299.6% CPU
Optimizing NNI: done in 0.459595 secs using 399.3% CPU
Iteration 150 / LogL: -35753.586 / Time: 0h:0m:59s (0h:0m:10s left)
Optimizing NNI: done in 0.451778 secs using 399.3% CPU
Optimizing NNI: done in 0.344282 secs using 397.8% CPU
Optimizing NNI: done in 0.315358 secs using 399.8% CPU
Optimizing NNI: done in 0.235303 secs using 399.4% CPU
Optimizing NNI: done in 0.381113 secs using 398.9% CPU
Optimizing NNI: done in 1.84882 secs using 299.7% CPU
Optimizing NNI: done in 0.386819 secs using 399.7% CPU
Optimizing NNI: done in 0.383051 secs using 399.4% CPU
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Optimizing NNI: done in 0.384147 secs using 399.3% CPU
Optimizing NNI: done in 0.312946 secs using 398.9% CPU
Iteration 160 / LogL: -35754.335 / Time: 0h:1m:3s (0h:0m:5s left)
Optimizing NNI: done in 0.364543 secs using 399.4% CPU
Optimizing NNI: done in 2.2226 secs using 299.5% CPU
Optimizing NNI: done in 0.421698 secs using 399.6% CPU
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Optimizing NNI: done in 0.577894 secs using 398.9% CPU
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Optimizing NNI: done in 1.6844 secs using 299.7% CPU
Optimizing NNI: done in 0.378174 secs using 398.7% CPU
Optimizing NNI: done in 0.413218 secs using 396.7% CPU
Optimizing NNI: done in 0.3443 secs using 398.7% CPU
Optimizing NNI: done in 0.379298 secs using 399.5% CPU
Optimizing NNI: done in 0.267726 secs using 399.9% CPU
Iteration 170 / LogL: -35750.243 / Time: 0h:1m:7s (0h:0m:1s left)
Optimizing NNI: done in 0.38498 secs using 399.9% CPU
Optimizing NNI: done in 2.39325 secs using 299.4% CPU
Optimizing NNI: done in 0.383399 secs using 399.4% CPU
Optimizing NNI: done in 0.447146 secs using 398.8% CPU
Optimizing NNI: done in 0.600245 secs using 398.6% CPU
Optimizing NNI: done in 0.575721 secs using 399.6% CPU
Optimizing NNI: done in 0.261499 secs using 401% CPU
TREE SEARCH COMPLETED AFTER 176 ITERATIONS / Time: 0h:1m:10s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35750.193
Optimal log-likelihood: -35750.193
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.797
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -35750.193
Total tree length: 18.634

Total number of iterations: 176
CPU time used for tree search: 273.436 sec (0h:4m:33s)
Wall-clock time used for tree search: 69.515 sec (0h:1m:9s)
Total CPU time used: 275.953 sec (0h:4m:35s)
Total wall-clock time used: 70.106 sec (0h:1m:10s)

===> START BOOTSTRAP REPLICATE NUMBER 57

Creating bootstrap alignment (seed: 956216)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36527.168
2. Current log-likelihood: -35577.852
3. Current log-likelihood: -35564.242
4. Current log-likelihood: -35563.905
Optimal log-likelihood: -35563.803
Proportion of invariable sites: 0.018
Gamma shape alpha: 2.504
Parameters optimization took 4 rounds (0.252 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0754991 secs using 398% CPU
Computing ML distances took 0.075638 sec (of wall-clock time) 0.300851 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000134945 secs using 449.1% CPU
Constructing RapidNJ tree: done in 0.00127602 secs using 407.4% CPU
Computing RapidNJ tree took 0.001473 sec (of wall-clock time) 0.006358 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36011.358
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.52406 secs using 299.5% CPU
Iteration 30 / LogL: -59192.986 / Time: 0h:1m:46s (0h:5m:46s left)
1.439 second
Optimizing NNI: done in 1.94552 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
Computing log-likelihood of 98 initial trees ... 1.558 seconds
Current best score: -35553.465

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.21987 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35511.157
Optimizing NNI: done in 0.23338 secs using 398.9% CPU
BETTER TREE FOUND at iteration 31: -59172.341
Optimizing NNI: done in 0.223607 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -35510.821
Optimizing NNI: done in 0.189555 secs using 399.3% CPU
Optimizing NNI: done in 0.189836 secs using 399.3% CPU
Optimizing NNI: done in 0.21837 secs using 399.7% CPU
Optimizing NNI: done in 0.254116 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -35509.199
Optimizing NNI: done in 0.25366 secs using 398.8% CPU
Optimizing NNI: done in 0.252341 secs using 399.5% CPU
Optimizing NNI: done in 0.250144 secs using 398.7% CPU
Iteration 10 / LogL: -35510.107 / Time: 0h:0m:6s
Optimizing NNI: done in 2.10167 secs using 299.6% CPU
Optimizing NNI: done in 0.217478 secs using 398.5% CPU
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Optimizing NNI: done in 0.235244 secs using 397.8% CPU
Optimizing NNI: done in 0.268002 secs using 399.5% CPU
Optimizing NNI: done in 0.252118 secs using 399.6% CPU
Optimizing NNI: done in 0.292084 secs using 399.6% CPU
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Optimizing NNI: done in 0.234161 secs using 399.9% CPU
Optimizing NNI: done in 2.10073 secs using 299.5% CPU
396  Q.yeast+F+I+R10 105564.485   573 212274.969   870078.969   214581.791
Optimizing NNI: done in 0.24454 secs using 399.1% CPU
Iteration 20 / LogL: -35523.055 / Time: 0h:0m:8s
Finish initializing candidate tree set (7)
Current best tree score: -35509.199 / CPU time: 8.044
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.438396 secs using 399.9% CPU
Optimizing NNI: done in 0.435871 secs using 399.4% CPU
Optimizing NNI: done in 0.426602 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -35503.632
Optimizing NNI: done in 0.374494 secs using 399% CPU
Optimizing NNI: done in 2.0677 secs using 299.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.336368 secs using 399.1% CPU
Optimizing NNI: done in 0.393939 secs using 399.3% CPU
Optimizing NNI: done in 0.418134 secs using 399.4% CPU
BETTER TREE FOUND at iteration 34: -59162.013
Optimizing NNI: done in 0.395854 secs using 399.9% CPU
Optimizing NNI: done in 0.523458 secs using 399.9% CPU
Optimizing NNI: done in 0.348181 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35503.558
Iteration 30 / LogL: -35503.558 / Time: 0h:0m:12s (0h:0m:40s left)
Optimizing NNI: done in 0.417558 secs using 398.6% CPU
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Optimizing NNI: done in 0.348238 secs using 398.1% CPU
Iteration 40 / LogL: -35504.373 / Time: 0h:0m:16s (0h:0m:35s left)
Optimizing NNI: done in 0.341988 secs using 399% CPU
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Optimizing NNI: done in 2.33103 secs using 299.1% CPU
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Optimizing NNI: done in 0.402876 secs using 400% CPU
Optimizing NNI: done in 1.89432 secs using 299.5% CPU
Optimizing NNI: done in 0.315586 secs using 399.9% CPU
Iteration 50 / LogL: -35508.059 / Time: 0h:0m:20s (0h:0m:30s left)
Optimizing NNI: done in 0.42037 secs using 399.6% CPU
Optimizing NNI: done in 0.275835 secs using 399.5% CPU
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Optimizing NNI: done in 0.442116 secs using 398.7% CPU
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Optimizing NNI: done in 0.360132 secs using 399.9% CPU
417  JTTDCMut+I+R9 105350.171   552 211804.343   822316.343   214026.621
Optimizing NNI: done in 0.307527 secs using 399% CPU
Iteration 60 / LogL: -35575.544 / Time: 0h:0m:24s (0h:0m:25s left)
Optimizing NNI: done in 0.278267 secs using 398.8% CPU
Optimizing NNI: done in 2.11642 secs using 299.6% CPU
Iteration 40 / LogL: -59168.815 / Time: 0h:2m:10s (0h:5m:14s left)
Optimizing NNI: done in 0.327073 secs using 398.6% CPU
Optimizing NNI: done in 0.401155 secs using 398.8% CPU
Optimizing NNI: done in 0.381396 secs using 399.1% CPU
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Optimizing NNI: done in 1.79373 secs using 299.5% CPU
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Optimizing NNI: done in 0.287197 secs using 399.4% CPU
Optimizing NNI: done in 0.365348 secs using 396.9% CPU
Optimizing NNI: done in 0.327858 secs using 399.6% CPU
Iteration 70 / LogL: -35503.579 / Time: 0h:0m:27s (0h:0m:21s left)
Optimizing NNI: done in 0.292495 secs using 399.2% CPU
Optimizing NNI: done in 0.480555 secs using 398.1% CPU
Optimizing NNI: done in 2.28896 secs using 299.7% CPU
Optimizing NNI: done in 0.454143 secs using 399% CPU
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Optimizing NNI: done in 0.364058 secs using 399.6% CPU
Optimizing NNI: done in 0.350051 secs using 399.7% CPU
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Optimizing NNI: done in 0.37153 secs using 399.4% CPU
Optimizing NNI: done in 0.374068 secs using 398% CPU
Iteration 80 / LogL: -35503.759 / Time: 0h:0m:31s (0h:0m:17s left)
Optimizing NNI: done in 0.573892 secs using 399% CPU
Optimizing NNI: done in 0.390728 secs using 398.9% CPU
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Optimizing NNI: done in 2.16318 secs using 297.7% CPU
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Optimizing NNI: done in 0.315325 secs using 398.9% CPU
Optimizing NNI: done in 2.1809 secs using 298.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.436474 secs using 399.5% CPU
Iteration 90 / LogL: -36305.434 / Time: 0h:0m:35s (0h:0m:12s left)
Optimizing NNI: done in 0.367574 secs using 399.3% CPU
Optimizing NNI: done in 0.397026 secs using 398.5% CPU
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Optimizing NNI: done in 0.272006 secs using 397.5% CPU
Optimizing NNI: done in 0.280703 secs using 397.9% CPU
BETTER TREE FOUND at iteration 45: -59156.220
Optimizing NNI: done in 0.360118 secs using 397.7% CPU
Optimizing NNI: done in 0.363544 secs using 397.7% CPU
Optimizing NNI: done in 0.37784 secs using 399.5% CPU
Optimizing NNI: done in 0.378151 secs using 397.5% CPU
Optimizing NNI: done in 0.341881 secs using 398.9% CPU
Iteration 100 / LogL: -35503.728 / Time: 0h:0m:38s (0h:0m:8s left)
Optimizing NNI: done in 0.374879 secs using 399.3% CPU
Optimizing NNI: done in 0.349388 secs using 399.5% CPU
Optimizing NNI: done in 2.3727 secs using 298.2% CPU
Optimizing NNI: done in 0.454672 secs using 399.4% CPU
Optimizing NNI: done in 0.361418 secs using 398.5% CPU
Optimizing NNI: done in 0.40266 secs using 399.6% CPU
Optimizing NNI: done in 0.322839 secs using 398.7% CPU
Optimizing NNI: done in 0.266288 secs using 399.6% CPU
Optimizing NNI: done in 1.80914 secs using 297.8% CPU
Optimizing NNI: done in 0.31733 secs using 399% CPU
Optimizing NNI: done in 0.312946 secs using 399.3% CPU
Optimizing NNI: done in 0.35537 secs using 400.3% CPU
Iteration 110 / LogL: -35504.667 / Time: 0h:0m:42s (0h:0m:5s left)
Optimizing NNI: done in 0.353954 secs using 399% CPU
418  mtMet+F+R10   196431.320   1024 394910.641   2494110.641  399369.516
Optimizing NNI: done in 0.332252 secs using 399.9% CPU
Optimizing NNI: done in 0.327221 secs using 399.6% CPU
Optimizing NNI: done in 1.84538 secs using 298.3% CPU
Optimizing NNI: done in 0.37544 secs using 399.3% CPU
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Optimizing NNI: done in 0.402048 secs using 399.9% CPU
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Optimizing NNI: done in 0.380009 secs using 399.2% CPU
Optimizing NNI: done in 2.43401 secs using 298.5% CPU
Optimizing NNI: done in 0.281528 secs using 398.5% CPU
Iteration 120 / LogL: -35508.329 / Time: 0h:0m:45s (0h:0m:1s left)
Optimizing NNI: done in 0.370223 secs using 399.9% CPU
Optimizing NNI: done in 0.364811 secs using 398.8% CPU
Optimizing NNI: done in 0.276098 secs using 399.5% CPU
Optimizing NNI: done in 0.321224 secs using 399.9% CPU
TREE SEARCH COMPLETED AFTER 124 ITERATIONS / Time: 0h:0m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35503.558
Optimal log-likelihood: -35503.557
Proportion of invariable sites: 0.018
Gamma shape alpha: 2.520
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -35503.557
Total tree length: 20.286

Total number of iterations: 124
CPU time used for tree search: 182.123 sec (0h:3m:2s)
Wall-clock time used for tree search: 46.560 sec (0h:0m:46s)
Total CPU time used: 184.397 sec (0h:3m:4s)
Total wall-clock time used: 47.098 sec (0h:0m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 58

Creating bootstrap alignment (seed: 956217)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.010 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37227.440
2. Current log-likelihood: -36261.073
3. Current log-likelihood: -36247.330
4. Current log-likelihood: -36247.136
Optimal log-likelihood: -36247.124
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.516
Parameters optimization took 4 rounds (0.259 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0737472 secs using 397.3% CPU
Computing ML distances took 0.073899 sec (of wall-clock time) 0.293414 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000136852 secs using 447.2% CPU
Constructing RapidNJ tree: done in 0.00128794 secs using 509.8% CPU
Computing RapidNJ tree took 0.001474 sec (of wall-clock time) 0.007422 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36549.707
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.17684 secs using 299.5% CPU
Iteration 50 / LogL: -59160.543 / Time: 0h:2m:34s (0h:4m:58s left)
1.458 second
Optimizing NNI: done in 2.39416 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
Computing log-likelihood of 98 initial trees ... 1.590 seconds
Current best score: -36225.843

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.376879 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36156.454
BETTER TREE FOUND at iteration 51: -59154.119
Optimizing NNI: done in 0.376209 secs using 398.7% CPU
Optimizing NNI: done in 0.434535 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36156.364
Optimizing NNI: done in 0.439787 secs using 398.6% CPU
Optimizing NNI: done in 0.319485 secs using 397.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -36155.671
Optimizing NNI: done in 0.43345 secs using 397.6% CPU
Optimizing NNI: done in 2.11132 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.428586 secs using 397.1% CPU
Optimizing NNI: done in 0.465961 secs using 397.7% CPU
BETTER TREE FOUND at iteration 52: -59152.071
Optimizing NNI: done in 0.428155 secs using 398.1% CPU
Optimizing NNI: done in 0.312205 secs using 398.5% CPU
Iteration 10 / LogL: -36157.700 / Time: 0h:0m:7s
Optimizing NNI: done in 0.269213 secs using 397.7% CPU
Optimizing NNI: done in 0.378588 secs using 399.1% CPU
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Optimizing NNI: done in 1.87596 secs using 298.7% CPU
Optimizing NNI: done in 0.449458 secs using 399.7% CPU
Iteration 20 / LogL: -36156.366 / Time: 0h:0m:11s
Finish initializing candidate tree set (10)
Current best tree score: -36155.671 / CPU time: 11.077
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.445744 secs using 399.6% CPU
Optimizing NNI: done in 0.410362 secs using 399.2% CPU
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Optimizing NNI: done in 2.12379 secs using 299.3% CPU
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Optimizing NNI: done in 0.501154 secs using 399.9% CPU
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Optimizing NNI: done in 2.29518 secs using 299.5% CPU
Optimizing NNI: done in 0.540505 secs using 399.2% CPU
BETTER TREE FOUND at iteration 30: -36155.670
Iteration 30 / LogL: -36155.670 / Time: 0h:0m:16s (0h:0m:55s left)
Optimizing NNI: done in 0.401138 secs using 399.9% CPU
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Optimizing NNI: done in 2.02687 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.519838 secs using 397.4% CPU
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Optimizing NNI: done in 0.43938 secs using 398.1% CPU
Optimizing NNI: done in 0.466109 secs using 399.3% CPU
BETTER TREE FOUND at iteration 57: -59150.169
Optimizing NNI: done in 0.468787 secs using 398.2% CPU
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Iteration 40 / LogL: -36155.672 / Time: 0h:0m:20s (0h:0m:47s left)
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427  mtVer+R8      203014.713   1001 408031.426   2414035.426  412390.150
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 73: -59148.080
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Iteration 120 / LogL: -36156.327 / Time: 0h:0m:56s (0h:0m:4s left)
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Iteration 130 / LogL: -36161.683 / Time: 0h:1m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.461622 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 131 ITERATIONS / Time: 0h:1m:1s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36155.670
Optimal log-likelihood: -36155.669
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.519
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36155.669
Total tree length: 19.707

Total number of iterations: 131
CPU time used for tree search: 238.076 sec (0h:3m:58s)
Wall-clock time used for tree search: 60.593 sec (0h:1m:0s)
Total CPU time used: 240.471 sec (0h:4m:0s)
Total wall-clock time used: 61.156 sec (0h:1m:1s)

===> START BOOTSTRAP REPLICATE NUMBER 59

Creating bootstrap alignment (seed: 956218)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37348.048
2. Current log-likelihood: -36402.461
3. Current log-likelihood: -36388.873
4. Current log-likelihood: -36387.714
5. Current log-likelihood: -36387.178
6. Current log-likelihood: -36386.882
Optimal log-likelihood: -36386.872
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.441
Parameters optimization took 6 rounds (0.388 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0753832 secs using 400% CPU
Computing ML distances took 0.075527 sec (of wall-clock time) 0.301907 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000146151 secs using 458.4% CPU
Constructing RapidNJ tree: done in 0.001302 secs using 498.6% CPU
Computing RapidNJ tree took 0.001498 sec (of wall-clock time) 0.007606 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36759.344
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.99953 secs using 298.9% CPU
1.507 second
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Computing log-likelihood of 98 initial trees ... 1.596 seconds
Current best score: -36386.872

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36313.602
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36308.638
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -36299.581
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Iteration 10 / LogL: -36313.830 / Time: 0h:0m:6s
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 15: -36295.132
BETTER TREE FOUND at iteration 80: -59148.023
Iteration 80 / LogL: -59148.023 / Time: 0h:3m:42s (0h:4m:41s left)
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Iteration 20 / LogL: -36299.085 / Time: 0h:0m:9s
Finish initializing candidate tree set (15)
Current best tree score: -36295.132 / CPU time: 8.732
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -36294.828
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -36292.286
Iteration 30 / LogL: -36292.286 / Time: 0h:0m:13s (0h:0m:45s left)
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428  mtVer+R9      203008.014   1003 408022.029   2422046.029  412389.462
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Iteration 40 / LogL: -36309.659 / Time: 0h:0m:17s (0h:0m:40s left)
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Iteration 50 / LogL: -36293.278 / Time: 0h:0m:21s (0h:0m:35s left)
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BETTER TREE FOUND at iteration 52: -36292.119
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Iteration 90 / LogL: -36292.849 / Time: 0h:0m:38s (0h:0m:26s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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418  JTTDCMut+I+R10 105350.266   554 211808.533   826748.533   214038.862
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Optimizing NNI: done in 2.18631 secs using 299.5% CPU
Iteration 100 / LogL: -59160.510 / Time: 0h:4m:28s (0h:4m:17s left)
Optimizing NNI: done in 0.373047 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -36291.813
Optimizing NNI: done in 0.328 secs using 399.2% CPU
Optimizing NNI: done in 0.362567 secs using 399.9% CPU
Optimizing NNI: done in 0.451806 secs using 399.4% CPU
Optimizing NNI: done in 0.329389 secs using 399.9% CPU
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Optimizing NNI: done in 2.1585 secs using 299.1% CPU
Optimizing NNI: done in 0.377902 secs using 399.9% CPU
Optimizing NNI: done in 0.447186 secs using 399.7% CPU
Optimizing NNI: done in 0.397706 secs using 398.6% CPU
Iteration 140 / LogL: -36301.563 / Time: 0h:0m:57s (0h:0m:5s left)
Optimizing NNI: done in 0.459736 secs using 398.6% CPU
Optimizing NNI: done in 1.73426 secs using 299.2% CPU
Optimizing NNI: done in 0.533703 secs using 399.3% CPU
Optimizing NNI: done in 0.312691 secs using 399.5% CPU
439  JTTDCMut+F+I+R9 105462.410   571 212066.820   865290.820   214365.589
Optimizing NNI: done in 0.309918 secs using 399.6% CPU
Optimizing NNI: done in 0.336091 secs using 399.6% CPU
Optimizing NNI: done in 1.74137 secs using 299.5% CPU
Optimizing NNI: done in 0.393639 secs using 399.8% CPU
Optimizing NNI: done in 0.367021 secs using 399.9% CPU
Optimizing NNI: done in 0.393603 secs using 399.9% CPU
Optimizing NNI: done in 0.31943 secs using 398.3% CPU
Optimizing NNI: done in 0.360966 secs using 399.1% CPU
Iteration 150 / LogL: -36291.839 / Time: 0h:1m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.460844 secs using 399.1% CPU
Optimizing NNI: done in 2.23411 secs using 299.6% CPU
Optimizing NNI: done in 0.397129 secs using 398.9% CPU
Optimizing NNI: done in 0.339963 secs using 399.8% CPU
Optimizing NNI: done in 0.379172 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 154 ITERATIONS / Time: 0h:1m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36291.813
Optimal log-likelihood: -36291.812
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.466
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -36291.812
Total tree length: 20.529

Total number of iterations: 154
CPU time used for tree search: 245.689 sec (0h:4m:5s)
Wall-clock time used for tree search: 62.520 sec (0h:1m:2s)
Total CPU time used: 248.448 sec (0h:4m:8s)
Total wall-clock time used: 63.180 sec (0h:1m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 60

Creating bootstrap alignment (seed: 956219)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37048.066
2. Current log-likelihood: -36163.132
3. Current log-likelihood: -36141.255
4. Current log-likelihood: -36140.671
Optimal log-likelihood: -36140.655
Proportion of invariable sites: 0.029
Gamma shape alpha: 2.661
Parameters optimization took 4 rounds (0.252 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.07424 secs using 398% CPU
Computing ML distances took 0.074387 sec (of wall-clock time) 0.295797 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000133991 secs using 460.5% CPU
Constructing RapidNJ tree: done in 0.00123 secs using 508.4% CPU
Computing RapidNJ tree took 0.001419 sec (of wall-clock time) 0.007243 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36528.077
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.9344 secs using 299.5% CPU
1.424 second
Computing log-likelihood of 98 initial trees ... 1.600 seconds
Current best score: -36135.039

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.417422 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36068.075
Optimizing NNI: done in 3.1316 secs using 299.2% CPU
Optimizing NNI: done in 0.369828 secs using 399.1% CPU
Optimizing NNI: done in 0.464962 secs using 398.4% CPU
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Optimizing NNI: done in 0.463734 secs using 397% CPU
Optimizing NNI: done in 0.457889 secs using 398.2% CPU
Optimizing NNI: done in 0.44749 secs using 398.3% CPU
Optimizing NNI: done in 2.63776 secs using 299.3% CPU
Optimizing NNI: done in 0.519832 secs using 398.9% CPU
Optimizing NNI: done in 0.438647 secs using 398.1% CPU
Optimizing NNI: done in 0.559641 secs using 398.5% CPU
Iteration 10 / LogL: -36079.387 / Time: 0h:0m:8s
Optimizing NNI: done in 0.447821 secs using 399.7% CPU
Optimizing NNI: done in 0.447334 secs using 397.5% CPU
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Optimizing NNI: done in 3.31172 secs using 299.1% CPU
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Optimizing NNI: done in 0.509017 secs using 399% CPU
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Optimizing NNI: done in 0.430356 secs using 398.7% CPU
Optimizing NNI: done in 0.499394 secs using 399.3% CPU
Optimizing NNI: done in 0.45831 secs using 398.2% CPU
Iteration 20 / LogL: -36078.283 / Time: 0h:0m:12s
Finish initializing candidate tree set (9)
Current best tree score: -36068.075 / CPU time: 12.222
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.49136 secs using 299.6% CPU
Optimizing NNI: done in 1.04542 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36068.018
Optimizing NNI: done in 0.923087 secs using 398.7% CPU
Optimizing NNI: done in 2.48767 secs using 299.6% CPU
Iteration 110 / LogL: -59152.167 / Time: 0h:4m:52s (0h:3m:48s left)
Optimizing NNI: done in 0.742311 secs using 398.8% CPU
Optimizing NNI: done in 0.543935 secs using 398.6% CPU
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Optimizing NNI: done in 1.84931 secs using 299.2% CPU
Optimizing NNI: done in 0.98792 secs using 398.4% CPU
Optimizing NNI: done in 0.61746 secs using 398.7% CPU
Optimizing NNI: done in 0.822433 secs using 398.1% CPU
Optimizing NNI: done in 1.9854 secs using 299.1% CPU
Optimizing NNI: done in 1.03151 secs using 399.2% CPU
Optimizing NNI: done in 0.841877 secs using 398.8% CPU
Iteration 30 / LogL: -36071.243 / Time: 0h:0m:20s (0h:1m:5s left)
Optimizing NNI: done in 2.4072 secs using 299.3% CPU
Optimizing NNI: done in 0.744038 secs using 399.3% CPU
Optimizing NNI: done in 0.558601 secs using 398.1% CPU
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Optimizing NNI: done in 2.05595 secs using 299% CPU
Optimizing NNI: done in 0.910622 secs using 398.8% CPU
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Optimizing NNI: done in 2.20891 secs using 299.1% CPU
Optimizing NNI: done in 0.725233 secs using 398.5% CPU
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Optimizing NNI: done in 2.01922 secs using 299.4% CPU
Optimizing NNI: done in 0.815856 secs using 398.5% CPU
Iteration 40 / LogL: -36068.200 / Time: 0h:0m:27s (0h:0m:58s left)
Optimizing NNI: done in 1.07185 secs using 398.9% CPU
Optimizing NNI: done in 0.948303 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -36063.937
Optimizing NNI: done in 2.20757 secs using 299% CPU
Optimizing NNI: done in 0.504397 secs using 399.3% CPU
Optimizing NNI: done in 0.739643 secs using 398.3% CPU
Optimizing NNI: done in 0.327042 secs using 399.3% CPU
Optimizing NNI: done in 0.310125 secs using 399.9% CPU
Optimizing NNI: done in 0.435808 secs using 399.5% CPU
BETTER TREE FOUND at iteration 47: -36063.937
Optimizing NNI: done in 2.31912 secs using 299.4% CPU
Optimizing NNI: done in 0.384403 secs using 399.9% CPU
Optimizing NNI: done in 0.4433 secs using 399.2% CPU
Optimizing NNI: done in 0.429183 secs using 399.9% CPU
Iteration 50 / LogL: -36068.431 / Time: 0h:0m:33s (0h:1m:6s left)
Optimizing NNI: done in 0.582601 secs using 398.9% CPU
Optimizing NNI: done in 1.96934 secs using 299.3% CPU
Optimizing NNI: done in 0.432739 secs using 398% CPU
Optimizing NNI: done in 0.385825 secs using 399.7% CPU
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Optimizing NNI: done in 1.70762 secs using 299.2% CPU
Iteration 120 / LogL: -59170.156 / Time: 0h:5m:13s (0h:3m:17s left)
Optimizing NNI: done in 0.445455 secs using 399.5% CPU
Optimizing NNI: done in 0.445087 secs using 398.6% CPU
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Optimizing NNI: done in 1.76342 secs using 299.5% CPU
Optimizing NNI: done in 0.269698 secs using 397.8% CPU
Iteration 60 / LogL: -36064.142 / Time: 0h:0m:37s (0h:0m:55s left)
Optimizing NNI: done in 0.614872 secs using 398.1% CPU
Optimizing NNI: done in 0.532601 secs using 399.2% CPU
Optimizing NNI: done in 0.512169 secs using 398.9% CPU
Optimizing NNI: done in 1.93781 secs using 299.3% CPU
Optimizing NNI: done in 0.399576 secs using 399% CPU
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Optimizing NNI: done in 0.267553 secs using 398.4% CPU
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Optimizing NNI: done in 1.97435 secs using 299.5% CPU
Optimizing NNI: done in 0.334951 secs using 398.7% CPU
Optimizing NNI: done in 0.338099 secs using 399.6% CPU
Iteration 70 / LogL: -36068.231 / Time: 0h:0m:42s (0h:0m:47s left)
Optimizing NNI: done in 0.404269 secs using 399.4% CPU
Optimizing NNI: done in 0.680994 secs using 399% CPU
Optimizing NNI: done in 0.43957 secs using 399.4% CPU
Optimizing NNI: done in 2.04635 secs using 298.9% CPU
Optimizing NNI: done in 0.472619 secs using 398.2% CPU
Optimizing NNI: done in 0.314333 secs using 398.4% CPU
Optimizing NNI: done in 0.43424 secs using 399.2% CPU
Optimizing NNI: done in 0.403986 secs using 399.7% CPU
Optimizing NNI: done in 2.00689 secs using 299.3% CPU
Optimizing NNI: done in 0.54209 secs using 398.7% CPU
Optimizing NNI: done in 0.514706 secs using 399.5% CPU
Optimizing NNI: done in 0.521656 secs using 398.2% CPU
Iteration 80 / LogL: -36063.939 / Time: 0h:0m:47s (0h:0m:39s left)
Optimizing NNI: done in 0.299442 secs using 399.6% CPU
Optimizing NNI: done in 0.524304 secs using 398.6% CPU
Optimizing NNI: done in 0.411505 secs using 399.9% CPU
Optimizing NNI: done in 2.5627 secs using 298.3% CPU
Optimizing NNI: done in 0.377652 secs using 399.4% CPU
Optimizing NNI: done in 0.451937 secs using 399.2% CPU
Optimizing NNI: done in 0.330983 secs using 399.8% CPU
Optimizing NNI: done in 0.429089 secs using 399% CPU
Optimizing NNI: done in 0.459071 secs using 397.9% CPU
Optimizing NNI: done in 2.14184 secs using 299.3% CPU
Optimizing NNI: done in 0.373023 secs using 398.1% CPU
Optimizing NNI: done in 0.335594 secs using 397% CPU
Iteration 90 / LogL: -36063.943 / Time: 0h:0m:51s (0h:0m:32s left)
Optimizing NNI: done in 0.214264 secs using 399% CPU
Optimizing NNI: done in 0.567819 secs using 399.2% CPU
Optimizing NNI: done in 0.460949 secs using 399% CPU
Optimizing NNI: done in 0.380357 secs using 399.4% CPU
Optimizing NNI: done in 0.360745 secs using 399.7% CPU
Optimizing NNI: done in 2.60579 secs using 299.3% CPU
Optimizing NNI: done in 0.288113 secs using 398.5% CPU
Optimizing NNI: done in 0.472515 secs using 399.4% CPU
Optimizing NNI: done in 0.452031 secs using 399.4% CPU
429  mtVer+R10     202969.843   1005 407949.685   2430009.685  412325.827
Optimizing NNI: done in 0.531378 secs using 399.2% CPU
Optimizing NNI: done in 1.94609 secs using 299.5% CPU
Optimizing NNI: done in 0.393398 secs using 399.9% CPU
Iteration 100 / LogL: -36063.969 / Time: 0h:0m:55s (0h:0m:26s left)
Optimizing NNI: done in 0.414961 secs using 399.1% CPU
Optimizing NNI: done in 0.248668 secs using 399.9% CPU
Optimizing NNI: done in 0.507793 secs using 399.3% CPU
Optimizing NNI: done in 0.433647 secs using 399.7% CPU
Optimizing NNI: done in 0.370706 secs using 399.1% CPU
Optimizing NNI: done in 2.18288 secs using 299.4% CPU
Iteration 130 / LogL: -59181.492 / Time: 0h:5m:35s (0h:2m:48s left)
Optimizing NNI: done in 0.500867 secs using 398.7% CPU
Optimizing NNI: done in 0.348839 secs using 399.6% CPU
Optimizing NNI: done in 0.616652 secs using 399.7% CPU
Optimizing NNI: done in 0.361237 secs using 398.3% CPU
Optimizing NNI: done in 2.02379 secs using 299.4% CPU
Optimizing NNI: done in 0.414664 secs using 399.1% CPU
Iteration 110 / LogL: -36104.448 / Time: 0h:0m:59s (0h:0m:20s left)
Optimizing NNI: done in 0.44863 secs using 399.2% CPU
Optimizing NNI: done in 0.531393 secs using 399.7% CPU
Optimizing NNI: done in 0.422632 secs using 399.4% CPU
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Optimizing NNI: done in 2.22806 secs using 299.3% CPU
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Optimizing NNI: done in 0.514192 secs using 400.3% CPU
Iteration 120 / LogL: -36067.676 / Time: 0h:1m:4s (0h:0m:14s left)
Optimizing NNI: done in 0.478227 secs using 399.7% CPU
Optimizing NNI: done in 0.563884 secs using 399.4% CPU
Optimizing NNI: done in 0.400522 secs using 399.7% CPU
Optimizing NNI: done in 2.21958 secs using 299.5% CPU
Optimizing NNI: done in 0.469455 secs using 399.4% CPU
Optimizing NNI: done in 0.394763 secs using 399.8% CPU
Optimizing NNI: done in 0.303975 secs using 398.4% CPU
Optimizing NNI: done in 0.456591 secs using 398.7% CPU
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Optimizing NNI: done in 0.473147 secs using 398.8% CPU
Optimizing NNI: done in 0.44607 secs using 399.6% CPU
Optimizing NNI: done in 0.506976 secs using 400.5% CPU
Iteration 130 / LogL: -36071.881 / Time: 0h:1m:8s (0h:0m:9s left)
Optimizing NNI: done in 0.402236 secs using 399.6% CPU
Optimizing NNI: done in 0.424482 secs using 399.4% CPU
Optimizing NNI: done in 2.17619 secs using 299.6% CPU
Optimizing NNI: done in 0.53311 secs using 398.6% CPU
Optimizing NNI: done in 0.396014 secs using 398% CPU
Optimizing NNI: done in 0.364171 secs using 398.6% CPU
438  mtVer+F+R8    198883.127   1020 399806.254   2482646.254  404247.711
Optimizing NNI: done in 0.341826 secs using 399% CPU
Optimizing NNI: done in 2.03455 secs using 299.5% CPU
Optimizing NNI: done in 0.573753 secs using 397.9% CPU
Optimizing NNI: done in 0.343524 secs using 396.9% CPU
Optimizing NNI: done in 0.593243 secs using 397.8% CPU
Optimizing NNI: done in 0.426449 secs using 399.8% CPU
Iteration 140 / LogL: -36063.996 / Time: 0h:1m:13s (0h:0m:3s left)
Optimizing NNI: done in 1.74234 secs using 299.7% CPU
Optimizing NNI: done in 0.492938 secs using 399% CPU
Optimizing NNI: done in 0.486266 secs using 399.5% CPU
Optimizing NNI: done in 0.505197 secs using 398.3% CPU
Optimizing NNI: done in 0.511151 secs using 398.5% CPU
Optimizing NNI: done in 1.97862 secs using 299% CPU
Optimizing NNI: done in 0.374229 secs using 398.6% CPU
Optimizing NNI: done in 0.596709 secs using 398.9% CPU
Optimizing NNI: done in 0.314022 secs using 399.6% CPU
Optimizing NNI: done in 0.297329 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 148 ITERATIONS / Time: 0h:1m:16s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36063.937
Optimal log-likelihood: -36063.936
Proportion of invariable sites: 0.029
Gamma shape alpha: 2.742
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -36063.936
Total tree length: 19.116

Total number of iterations: 148
CPU time used for tree search: 300.686 sec (0h:5m:0s)
Wall-clock time used for tree search: 76.290 sec (0h:1m:16s)
Total CPU time used: 302.893 sec (0h:5m:2s)
Total wall-clock time used: 76.814 sec (0h:1m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 61

Creating bootstrap alignment (seed: 956220)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36645.640
2. Current log-likelihood: -35706.600
3. Current log-likelihood: -35685.149
4. Current log-likelihood: -35683.663
Optimal log-likelihood: -35683.647
Proportion of invariable sites: 0.011
Gamma shape alpha: 2.550
Parameters optimization took 4 rounds (0.230 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0730391 secs using 401.5% CPU
Computing ML distances took 0.073175 sec (of wall-clock time) 0.293367 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000134945 secs using 1645% CPU
Constructing RapidNJ tree: done in 0.0012641 secs using 449.2% CPU
Computing RapidNJ tree took 0.001453 sec (of wall-clock time) 0.007951 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36433.037
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.16365 secs using 299.4% CPU
Iteration 140 / LogL: -59176.448 / Time: 0h:5m:55s (0h:2m:20s left)
1.507 second
Optimizing NNI: done in 1.93901 secs using 299.4% CPU
Computing log-likelihood of 98 initial trees ... 1.504 seconds
Current best score: -35644.495

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.17908 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35599.604
Optimizing NNI: done in 0.175381 secs using 399.3% CPU
Optimizing NNI: done in 0.186482 secs using 399.4% CPU
Optimizing NNI: done in 0.236207 secs using 398.9% CPU
Optimizing NNI: done in 0.230632 secs using 399.4% CPU
Optimizing NNI: done in 0.204719 secs using 398.6% CPU
Optimizing NNI: done in 2.01896 secs using 299.5% CPU
Optimizing NNI: done in 0.1869 secs using 400.9% CPU
Optimizing NNI: done in 0.244774 secs using 395.4% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35599.580
Optimizing NNI: done in 0.183512 secs using 399.9% CPU
Optimizing NNI: done in 0.179071 secs using 399.4% CPU
Iteration 10 / LogL: -35599.661 / Time: 0h:0m:5s
Optimizing NNI: done in 0.17999 secs using 398.8% CPU
Optimizing NNI: done in 0.199041 secs using 399.8% CPU
Optimizing NNI: done in 0.234054 secs using 398.9% CPU
Optimizing NNI: done in 0.178454 secs using 399% CPU
Optimizing NNI: done in 0.189244 secs using 398.3% CPU
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Optimizing NNI: done in 0.220911 secs using 398.5% CPU
Optimizing NNI: done in 0.219236 secs using 398.8% CPU
Optimizing NNI: done in 0.196117 secs using 399.8% CPU
Optimizing NNI: done in 0.180209 secs using 398.8% CPU
Optimizing NNI: done in 0.219282 secs using 399.9% CPU
Iteration 20 / LogL: -35605.967 / Time: 0h:0m:7s
Finish initializing candidate tree set (4)
Current best tree score: -35599.580 / CPU time: 7.242
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.412953 secs using 398.4% CPU
Optimizing NNI: done in 0.290058 secs using 399.9% CPU
Optimizing NNI: done in 1.86478 secs using 299.3% CPU
Optimizing NNI: done in 0.547821 secs using 398.8% CPU
UPDATE BEST LOG-LIKELIHOOD: -35599.578
Optimizing NNI: done in 0.415677 secs using 399.2% CPU
Optimizing NNI: done in 0.341781 secs using 399.3% CPU
Optimizing NNI: done in 0.514315 secs using 399.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -35599.578
Optimizing NNI: done in 1.87389 secs using 299.3% CPU
Optimizing NNI: done in 0.369918 secs using 399.6% CPU
Optimizing NNI: done in 0.525841 secs using 398.9% CPU
Optimizing NNI: done in 0.260745 secs using 399.6% CPU
Optimizing NNI: done in 0.354147 secs using 399.9% CPU
Iteration 30 / LogL: -35600.617 / Time: 0h:0m:11s (0h:0m:28s left)
Optimizing NNI: done in 0.419484 secs using 399.9% CPU
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Iteration 40 / LogL: -35628.295 / Time: 0h:0m:15s (0h:0m:24s left)
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Iteration 50 / LogL: -35599.680 / Time: 0h:0m:19s (0h:0m:20s left)
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Iteration 150 / LogL: -59162.196 / Time: 0h:6m:15s (0h:1m:53s left)
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UPDATE BEST LOG-LIKELIHOOD: -35599.577
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Iteration 60 / LogL: -35609.180 / Time: 0h:0m:24s (0h:0m:17s left)
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Iteration 70 / LogL: -35627.380 / Time: 0h:0m:28s (0h:0m:12s left)
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440  JTTDCMut+F+I+R10 105455.664   573 212057.328   869861.328   214364.149
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Iteration 80 / LogL: -35600.183 / Time: 0h:0m:32s (0h:0m:8s left)
Optimizing NNI: done in 1.57348 secs using 299.7% CPU
Optimizing NNI: done in 0.298213 secs using 399.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -35599.577
439  mtVer+F+R9    198874.584   1022 399793.168   2490805.168  404243.334
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Iteration 90 / LogL: -35599.578 / Time: 0h:0m:36s (0h:0m:4s left)
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Iteration 160 / LogL: -59180.914 / Time: 0h:6m:34s (0h:1m:26s left)
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Iteration 100 / LogL: -35625.992 / Time: 0h:0m:41s (0h:0m:0s left)
Optimizing NNI: done in 0.534107 secs using 399.3% CPU
Optimizing NNI: done in 1.71581 secs using 299.8% CPU
BETTER TREE FOUND at iteration 161: -59144.746
Optimizing NNI: done in 0.54563 secs using 399.5% CPU
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:42s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35599.577
Optimal log-likelihood: -35599.577
Proportion of invariable sites: 0.011
Gamma shape alpha: 2.658
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -35599.577
Total tree length: 19.012

Total number of iterations: 102
CPU time used for tree search: 162.537 sec (0h:2m:42s)
Wall-clock time used for tree search: 41.671 sec (0h:0m:41s)
Total CPU time used: 164.532 sec (0h:2m:44s)
Total wall-clock time used: 42.147 sec (0h:0m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 62

Creating bootstrap alignment (seed: 956221)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.023 seconds

NOTE: 16 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -38335.346
2. Current log-likelihood: -37393.593
3. Current log-likelihood: -37382.834
4. Current log-likelihood: -37382.546
Optimal log-likelihood: -37382.500
Proportion of invariable sites: 0.013
Gamma shape alpha: 2.294
Parameters optimization took 4 rounds (0.249 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0765412 secs using 397.8% CPU
Computing ML distances took 0.076685 sec (of wall-clock time) 0.307572 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000149965 secs using 1534% CPU
Constructing RapidNJ tree: done in 0.00125504 secs using 279% CPU
Computing RapidNJ tree took 0.001456 sec (of wall-clock time) 0.005827 sec (of CPU time)
Log-likelihood of RapidNJ tree: -38151.094
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.12519 secs using 299.1% CPU
1.492 second
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Computing log-likelihood of 98 initial trees ... 1.481 seconds
Current best score: -37382.500

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -37343.030
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -37338.842
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -37338.789
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -37338.747
Iteration 10 / LogL: -37338.747 / Time: 0h:0m:6s
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Iteration 20 / LogL: -37339.507 / Time: 0h:0m:9s
Finish initializing candidate tree set (4)
Current best tree score: -37338.747 / CPU time: 8.528
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 30 / LogL: -37340.220 / Time: 0h:0m:12s (0h:0m:33s left)
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Iteration 40 / LogL: -37356.965 / Time: 0h:0m:16s (0h:0m:27s left)
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Iteration 170 / LogL: -59171.732 / Time: 0h:6m:53s (0h:3m:42s left)
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Iteration 50 / LogL: -37339.731 / Time: 0h:0m:20s (0h:0m:23s left)
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461  DCMut+I+R9    106802.944   552 214709.888   825221.888   216932.166
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Iteration 60 / LogL: -37338.781 / Time: 0h:0m:25s (0h:0m:19s left)
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440  mtVer+F+R10   198869.999   1024 399787.998   2498987.998  404246.873
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Iteration 70 / LogL: -37339.735 / Time: 0h:0m:28s (0h:0m:14s left)
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Iteration 80 / LogL: -37343.034 / Time: 0h:0m:32s (0h:0m:10s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 89: -37338.707
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Iteration 90 / LogL: -37365.662 / Time: 0h:0m:37s (0h:0m:41s left)
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449  mtInv+R8      200418.426   1001 402838.852   2408842.852  407197.577
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Iteration 180 / LogL: -59372.766 / Time: 0h:7m:15s (0h:3m:17s left)
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Iteration 100 / LogL: -37338.768 / Time: 0h:0m:41s (0h:0m:37s left)
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Iteration 110 / LogL: -37339.207 / Time: 0h:0m:45s (0h:0m:33s left)
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Iteration 120 / LogL: -37339.761 / Time: 0h:0m:49s (0h:0m:28s left)
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Iteration 130 / LogL: -37343.168 / Time: 0h:0m:53s (0h:0m:24s left)
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Iteration 140 / LogL: -37340.886 / Time: 0h:0m:57s (0h:0m:20s left)
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Iteration 190 / LogL: -59166.816 / Time: 0h:7m:36s (0h:2m:51s left)
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Iteration 150 / LogL: -37342.766 / Time: 0h:1m:2s (0h:0m:16s left)
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Iteration 160 / LogL: -37339.027 / Time: 0h:1m:6s (0h:0m:12s left)
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Iteration 170 / LogL: -37340.403 / Time: 0h:1m:10s (0h:0m:7s left)
Optimizing NNI: done in 0.306166 secs using 399.9% CPU
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Iteration 180 / LogL: -37360.782 / Time: 0h:1m:14s (0h:0m:3s left)
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Optimizing NNI: done in 0.402402 secs using 399.9% CPU
Iteration 190 / LogL: -37339.053 / Time: 0h:1m:18s (0h:0m:-1s left)
TREE SEARCH COMPLETED AFTER 190 ITERATIONS / Time: 0h:1m:18s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -37338.707
Optimal log-likelihood: -37338.707
Proportion of invariable sites: 0.014
Gamma shape alpha: 2.365
Parameters optimization took 1 rounds (0.041 sec)
BEST SCORE FOUND : -37338.707
Total tree length: 20.386

Total number of iterations: 190
CPU time used for tree search: 307.634 sec (0h:5m:7s)
Wall-clock time used for tree search: 78.040 sec (0h:1m:18s)
Total CPU time used: 310.656 sec (0h:5m:10s)
Total wall-clock time used: 78.749 sec (0h:1m:18s)

===> START BOOTSTRAP REPLICATE NUMBER 63

Creating bootstrap alignment (seed: 956222)...

Optimizing NNI: done in 1.67689 secs using 299.5% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36446.530
2. Current log-likelihood: -35584.223
3. Current log-likelihood: -35570.641
4. Current log-likelihood: -35570.114
Optimal log-likelihood: -35570.036
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.631
Parameters optimization took 4 rounds (0.272 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0712402 secs using 400% CPU
Computing ML distances took 0.071376 sec (of wall-clock time) 0.285293 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000148058 secs using 278.9% CPU
Constructing RapidNJ tree: done in 0.00122905 secs using 227.8% CPU
Computing RapidNJ tree took 0.001427 sec (of wall-clock time) 0.004246 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35803.383
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.80172 secs using 299.4% CPU
Iteration 200 / LogL: -59150.501 / Time: 0h:7m:57s (0h:2m:26s left)
1.587 second
450  mtInv+R9      200410.477   1003 402826.954   2416850.954  407194.387
Computing log-likelihood of 98 initial trees ... 1.528 seconds
Current best score: -35570.036

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.251499 secs using 396.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35534.162
Optimizing NNI: done in 0.186905 secs using 399.4% CPU
Optimizing NNI: done in 2.33237 secs using 299.5% CPU
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Iteration 10 / LogL: -35542.088 / Time: 0h:0m:6s
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Iteration 20 / LogL: -35536.588 / Time: 0h:0m:8s
Finish initializing candidate tree set (11)
Current best tree score: -35534.162 / CPU time: 8.457
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.326981 secs using 399.4% CPU
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Optimizing NNI: done in 0.331255 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -35533.496
Optimizing NNI: done in 0.341988 secs using 398.7% CPU
Optimizing NNI: done in 0.465047 secs using 399.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -35533.486
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Iteration 30 / LogL: -35534.800 / Time: 0h:0m:12s (0h:0m:41s left)
Optimizing NNI: done in 0.367236 secs using 399.6% CPU
Optimizing NNI: done in 0.32704 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -35532.189
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Iteration 40 / LogL: -35534.235 / Time: 0h:0m:17s (0h:0m:40s left)
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Iteration 50 / LogL: -35548.346 / Time: 0h:0m:21s (0h:0m:36s left)
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Iteration 210 / LogL: -59144.810 / Time: 0h:8m:20s (0h:2m:2s left)
Optimizing NNI: done in 0.387646 secs using 398.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -35532.188
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Iteration 60 / LogL: -35533.528 / Time: 0h:0m:25s (0h:0m:31s left)
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Iteration 70 / LogL: -35534.193 / Time: 0h:0m:30s (0h:0m:26s left)
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Iteration 80 / LogL: -35533.319 / Time: 0h:0m:34s (0h:0m:22s left)
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Optimizing NNI: done in 0.506368 secs using 400.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 88: -35531.951
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Optimizing NNI: done in 0.382589 secs using 399.9% CPU
Iteration 90 / LogL: -35531.962 / Time: 0h:0m:38s (0h:0m:42s left)
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Iteration 100 / LogL: -35536.464 / Time: 0h:0m:42s (0h:0m:38s left)
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Iteration 220 / LogL: -59169.291 / Time: 0h:8m:41s (0h:1m:37s left)
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Iteration 110 / LogL: -35531.951 / Time: 0h:0m:47s (0h:0m:34s left)
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Iteration 120 / LogL: -35532.195 / Time: 0h:0m:52s (0h:0m:29s left)
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Iteration 130 / LogL: -35532.736 / Time: 0h:0m:56s (0h:0m:25s left)
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Iteration 140 / LogL: -35532.192 / Time: 0h:1m:0s (0h:0m:20s left)
Optimizing NNI: done in 2.31325 secs using 299.7% CPU
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Optimizing NNI: done in 0.445992 secs using 398.9% CPU
451  mtInv+R10     200408.596   1005 402827.192   2424887.192  407203.334
Optimizing NNI: done in 0.423865 secs using 399.8% CPU
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Iteration 150 / LogL: -35533.868 / Time: 0h:1m:4s (0h:0m:16s left)
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Iteration 230 / LogL: -59176.474 / Time: 0h:9m:2s (0h:1m:13s left)
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Iteration 160 / LogL: -35531.956 / Time: 0h:1m:8s (0h:0m:12s left)
Optimizing NNI: done in 1.91288 secs using 299.7% CPU
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Iteration 170 / LogL: -35533.993 / Time: 0h:1m:13s (0h:0m:7s left)
Optimizing NNI: done in 2.29532 secs using 299.4% CPU
Optimizing NNI: done in 0.406886 secs using 399.4% CPU
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460  mtInv+F+R8    195221.172   1020 392482.344   2475322.344  396923.802
Optimizing NNI: done in 0.453369 secs using 398.8% CPU
Optimizing NNI: done in 0.536384 secs using 398.2% CPU
Iteration 180 / LogL: -35531.952 / Time: 0h:1m:17s (0h:0m:3s left)
Optimizing NNI: done in 2.34476 secs using 299.8% CPU
Optimizing NNI: done in 0.389077 secs using 398.6% CPU
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Optimizing NNI: done in 0.480657 secs using 399.9% CPU
TREE SEARCH COMPLETED AFTER 189 ITERATIONS / Time: 0h:1m:21s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35531.951
Optimal log-likelihood: -35531.950
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.663
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -35531.950
Total tree length: 19.426

Total number of iterations: 189
CPU time used for tree search: 318.838 sec (0h:5m:18s)
Wall-clock time used for tree search: 80.933 sec (0h:1m:20s)
Total CPU time used: 321.085 sec (0h:5m:21s)
Total wall-clock time used: 81.468 sec (0h:1m:21s)

===> START BOOTSTRAP REPLICATE NUMBER 64

Creating bootstrap alignment (seed: 956223)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37543.235
Optimizing NNI: done in 2.23408 secs using 299.1% CPU
2. Current log-likelihood: -36661.279
3. Current log-likelihood: -36641.992
4. Current log-likelihood: -36641.322
Optimal log-likelihood: -36641.190
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.797
Parameters optimization took 4 rounds (0.269 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.075278 secs using 400% CPU
Computing ML distances took 0.075407 sec (of wall-clock time) 0.301439 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00014019 secs using 492.9% CPU
Constructing RapidNJ tree: done in 0.00118399 secs using 312.8% CPU
Computing RapidNJ tree took 0.001370 sec (of wall-clock time) 0.007088 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37092.652
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.88792 secs using 299.5% CPU
1.564 second
Computing log-likelihood of 98 initial trees ... 1.598 seconds
Current best score: -36641.190

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.84091 secs using 299.6% CPU
Optimizing NNI: done in 0.21967 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36594.092
Optimizing NNI: done in 0.242709 secs using 397.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36586.572
Optimizing NNI: done in 0.204354 secs using 399.8% CPU
Optimizing NNI: done in 0.270596 secs using 399.8% CPU
Optimizing NNI: done in 0.272575 secs using 399.9% CPU
Optimizing NNI: done in 0.278444 secs using 399.9% CPU
Optimizing NNI: done in 0.277886 secs using 399.5% CPU
Optimizing NNI: done in 0.212306 secs using 399.5% CPU
Optimizing NNI: done in 0.23341 secs using 398.2% CPU
Optimizing NNI: done in 2.14704 secs using 299.6% CPU
Iteration 240 / LogL: -59161.287 / Time: 0h:9m:22s (0h:0m:49s left)
Optimizing NNI: done in 0.201902 secs using 399.5% CPU
Iteration 10 / LogL: -36586.711 / Time: 0h:0m:6s
Optimizing NNI: done in 0.214948 secs using 399.3% CPU
Optimizing NNI: done in 0.232365 secs using 399% CPU
Optimizing NNI: done in 0.281601 secs using 399.5% CPU
Optimizing NNI: done in 0.200718 secs using 399.4% CPU
Optimizing NNI: done in 0.285611 secs using 399.9% CPU
Optimizing NNI: done in 0.227457 secs using 399.9% CPU
Optimizing NNI: done in 1.78305 secs using 299.2% CPU
Optimizing NNI: done in 0.208481 secs using 399.2% CPU
Optimizing NNI: done in 0.243029 secs using 398.3% CPU
Optimizing NNI: done in 0.209282 secs using 399.4% CPU
Optimizing NNI: done in 0.261714 secs using 399.8% CPU
Iteration 20 / LogL: -36586.705 / Time: 0h:0m:8s
Finish initializing candidate tree set (7)
Current best tree score: -36586.572 / CPU time: 8.101
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.472014 secs using 399.1% CPU
Optimizing NNI: done in 1.59598 secs using 299.4% CPU
Optimizing NNI: done in 0.53215 secs using 398.5% CPU
Optimizing NNI: done in 0.41563 secs using 398.3% CPU
Optimizing NNI: done in 0.355205 secs using 398.8% CPU
Optimizing NNI: done in 0.399554 secs using 398% CPU
Optimizing NNI: done in 0.356745 secs using 398.7% CPU
Optimizing NNI: done in 2.02123 secs using 299.5% CPU
Optimizing NNI: done in 0.55895 secs using 398.6% CPU
Optimizing NNI: done in 0.433663 secs using 399.5% CPU
Optimizing NNI: done in 0.522935 secs using 399.5% CPU
Optimizing NNI: done in 0.388911 secs using 399.4% CPU
Iteration 30 / LogL: -36586.597 / Time: 0h:0m:13s (0h:0m:32s left)
Optimizing NNI: done in 1.78976 secs using 299.3% CPU
Optimizing NNI: done in 0.478468 secs using 399.1% CPU
Optimizing NNI: done in 0.332543 secs using 400.2% CPU
Optimizing NNI: done in 0.408319 secs using 399.3% CPU
Optimizing NNI: done in 0.481746 secs using 399% CPU
Optimizing NNI: done in 0.409067 secs using 398.2% CPU
Optimizing NNI: done in 2.02523 secs using 299.1% CPU
Optimizing NNI: done in 0.40322 secs using 398.7% CPU
Optimizing NNI: done in 0.359474 secs using 398.5% CPU
Optimizing NNI: done in 0.524484 secs using 397.4% CPU
Optimizing NNI: done in 0.412355 secs using 398.4% CPU
Optimizing NNI: done in 0.434741 secs using 398.9% CPU
Iteration 40 / LogL: -36586.690 / Time: 0h:0m:17s (0h:0m:27s left)
Optimizing NNI: done in 2.16103 secs using 299.4% CPU
Optimizing NNI: done in 0.423464 secs using 398.3% CPU
Optimizing NNI: done in 0.331478 secs using 399.3% CPU
Optimizing NNI: done in 0.425981 secs using 399.4% CPU
Optimizing NNI: done in 0.461987 secs using 399% CPU
Optimizing NNI: done in 0.311118 secs using 399.3% CPU
Optimizing NNI: done in 0.36013 secs using 399.4% CPU
Optimizing NNI: done in 2.28405 secs using 299.1% CPU
Optimizing NNI: done in 0.365591 secs using 398.9% CPU
Optimizing NNI: done in 0.414585 secs using 399.7% CPU
Optimizing NNI: done in 0.345394 secs using 399.3% CPU
Optimizing NNI: done in 0.473977 secs using 399.5% CPU
Iteration 50 / LogL: -36586.894 / Time: 0h:0m:21s (0h:0m:22s left)
Optimizing NNI: done in 1.70977 secs using 299.3% CPU
Optimizing NNI: done in 0.364964 secs using 399.6% CPU
Optimizing NNI: done in 0.412191 secs using 399.3% CPU
Optimizing NNI: done in 0.453126 secs using 398.6% CPU
Optimizing NNI: done in 0.349339 secs using 397.2% CPU
Optimizing NNI: done in 0.442449 secs using 399.1% CPU
Optimizing NNI: done in 0.397277 secs using 398.9% CPU
Optimizing NNI: done in 2.23004 secs using 299.2% CPU
Optimizing NNI: done in 0.447616 secs using 399.9% CPU
Optimizing NNI: done in 0.286039 secs using 398.7% CPU
Optimizing NNI: done in 0.574708 secs using 399.4% CPU
Optimizing NNI: done in 0.408531 secs using 399% CPU
Iteration 60 / LogL: -36586.818 / Time: 0h:0m:25s (0h:0m:18s left)
Optimizing NNI: done in 1.85456 secs using 299.5% CPU
Iteration 250 / LogL: -59152.130 / Time: 0h:9m:42s (0h:0m:25s left)
Optimizing NNI: done in 0.484524 secs using 398% CPU
Optimizing NNI: done in 0.35514 secs using 398.4% CPU
Optimizing NNI: done in 0.386428 secs using 398.3% CPU
Optimizing NNI: done in 0.409512 secs using 399.6% CPU
Optimizing NNI: done in 0.312845 secs using 397.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -36586.567
Optimizing NNI: done in 0.436347 secs using 398.7% CPU
Optimizing NNI: done in 2.29459 secs using 299.4% CPU
Optimizing NNI: done in 0.451498 secs using 398.9% CPU
Optimizing NNI: done in 0.338398 secs using 399.6% CPU
Optimizing NNI: done in 0.523978 secs using 399.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -36586.565
Optimizing NNI: done in 0.289022 secs using 399.2% CPU
Iteration 70 / LogL: -36587.081 / Time: 0h:0m:29s (0h:0m:13s left)
Optimizing NNI: done in 0.333845 secs using 399.3% CPU
Optimizing NNI: done in 2.14863 secs using 299.4% CPU
Optimizing NNI: done in 0.442655 secs using 398.4% CPU
Optimizing NNI: done in 0.297156 secs using 399.3% CPU
Optimizing NNI: done in 0.295337 secs using 399.6% CPU
Optimizing NNI: done in 0.251332 secs using 398.7% CPU
Optimizing NNI: done in 0.371651 secs using 399.4% CPU
Optimizing NNI: done in 0.331047 secs using 399.4% CPU
Optimizing NNI: done in 0.326186 secs using 399.3% CPU
Optimizing NNI: done in 2.16494 secs using 299.3% CPU
Optimizing NNI: done in 0.395089 secs using 399.6% CPU
Optimizing NNI: done in 0.360748 secs using 399.3% CPU
Iteration 80 / LogL: -36589.154 / Time: 0h:0m:32s (0h:0m:9s left)
Optimizing NNI: done in 0.346453 secs using 399.6% CPU
Optimizing NNI: done in 0.254123 secs using 398.8% CPU
Optimizing NNI: done in 0.347594 secs using 399.7% CPU
Optimizing NNI: done in 1.78948 secs using 299.5% CPU
Optimizing NNI: done in 0.318247 secs using 399.6% CPU
Optimizing NNI: done in 0.276703 secs using 399.9% CPU
Optimizing NNI: done in 0.439845 secs using 399.2% CPU
Optimizing NNI: done in 0.343984 secs using 399.9% CPU
Optimizing NNI: done in 0.331888 secs using 398.9% CPU
Optimizing NNI: done in 1.76599 secs using 299.4% CPU
Optimizing NNI: done in 0.417544 secs using 399.3% CPU
Optimizing NNI: done in 0.285276 secs using 399.2% CPU
Iteration 90 / LogL: -36586.857 / Time: 0h:0m:36s (0h:0m:4s left)
Optimizing NNI: done in 0.363576 secs using 399.3% CPU
Optimizing NNI: done in 0.328419 secs using 399.6% CPU
Optimizing NNI: done in 0.356113 secs using 398.8% CPU
Optimizing NNI: done in 0.382619 secs using 399.1% CPU
Optimizing NNI: done in 0.451357 secs using 399.2% CPU
Optimizing NNI: done in 2.38871 secs using 299.4% CPU
Optimizing NNI: done in 0.377376 secs using 399.6% CPU
Optimizing NNI: done in 0.37627 secs using 399.1% CPU
Optimizing NNI: done in 0.341808 secs using 398.7% CPU
Optimizing NNI: done in 0.404751 secs using 399.4% CPU
Optimizing NNI: done in 0.351697 secs using 399.4% CPU
Iteration 100 / LogL: -36589.685 / Time: 0h:0m:40s (0h:0m:0s left)
Optimizing NNI: done in 2.07863 secs using 299.3% CPU
Optimizing NNI: done in 0.34496 secs using 399.3% CPU
Optimizing NNI: done in 0.314436 secs using 399.6% CPU
Optimizing NNI: done in 0.374843 secs using 399.9% CPU
TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:41s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36586.565
Optimal log-likelihood: -36586.565
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.791
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -36586.565
Total tree length: 19.600

Total number of iterations: 103
CPU time used for tree search: 158.334 sec (0h:2m:38s)
Wall-clock time used for tree search: 40.689 sec (0h:0m:40s)
Total CPU time used: 160.588 sec (0h:2m:40s)
Total wall-clock time used: 41.226 sec (0h:0m:41s)

===> START BOOTSTRAP REPLICATE NUMBER 65

Creating bootstrap alignment (seed: 956224)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36101.724
2. Current log-likelihood: -35188.410
3. Current log-likelihood: -35175.440
4. Current log-likelihood: -35175.112
Optimal log-likelihood: -35175.018
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.343
Parameters optimization took 4 rounds (0.254 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0738759 secs using 400% CPU
Computing ML distances took 0.074012 sec (of wall-clock time) 0.295848 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000128984 secs using 441.9% CPU
Constructing RapidNJ tree: done in 0.00122309 secs using 325.6% CPU
Computing RapidNJ tree took 0.001405 sec (of wall-clock time) 0.006030 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35673.512
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.00406 secs using 299.6% CPU
1.439 second
Optimizing NNI: done in 2.0271 secs using 299.2% CPU
Computing log-likelihood of 98 initial trees ... 1.530 seconds
Current best score: -35175.018

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.250446 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35142.510
Optimizing NNI: done in 0.29447 secs using 399.1% CPU
Optimizing NNI: done in 0.281818 secs using 399.5% CPU
Optimizing NNI: done in 0.28984 secs using 399.5% CPU
Optimizing NNI: done in 0.292452 secs using 398.9% CPU
Optimizing NNI: done in 0.294012 secs using 398.8% CPU
Optimizing NNI: done in 0.270112 secs using 398.8% CPU
Optimizing NNI: done in 2.39642 secs using 299.1% CPU
Iteration 260 / LogL: -59163.404 / Time: 0h:10m:3s (0h:0m:2s left)
Optimizing NNI: done in 0.275086 secs using 399.9% CPU
Optimizing NNI: done in 0.273233 secs using 399.5% CPU
Optimizing NNI: done in 0.286498 secs using 399.5% CPU
Iteration 10 / LogL: -35144.301 / Time: 0h:0m:6s
Optimizing NNI: done in 0.276002 secs using 399.1% CPU
Optimizing NNI: done in 0.313029 secs using 398.6% CPU
Optimizing NNI: done in 0.276418 secs using 398.9% CPU
Optimizing NNI: done in 0.275039 secs using 398.5% CPU
Optimizing NNI: done in 1.97819 secs using 299.2% CPU
Optimizing NNI: done in 0.278989 secs using 399.3% CPU
Optimizing NNI: done in 0.279418 secs using 399.7% CPU
Optimizing NNI: done in 0.273256 secs using 399.9% CPU
Optimizing NNI: done in 0.289553 secs using 399.5% CPU
Optimizing NNI: done in 0.286143 secs using 399.9% CPU
Optimizing NNI: done in 0.291932 secs using 399.9% CPU
Iteration 20 / LogL: -35144.309 / Time: 0h:0m:9s
Finish initializing candidate tree set (3)
Current best tree score: -35142.510 / CPU time: 8.724
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.432492 secs using 399.4% CPU
Optimizing NNI: done in 2.04827 secs using 298.9% CPU
TREE SEARCH COMPLETED AFTER 262 ITERATIONS / Time: 0h:10m:7s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59144.746
Optimizing NNI: done in 0.366762 secs using 399.5% CPU
UPDATE BEST LOG-LIKELIHOOD: -35142.506
Optimizing NNI: done in 0.336243 secs using 399.8% CPU
2. Current log-likelihood: -59144.732
Optimizing NNI: done in 0.403939 secs using 398.9% CPU
461  mtInv+F+R9    195216.017   1022 392476.033   2483488.033  396926.199
Optimizing NNI: done in 0.3819 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35142.445
Optimizing NNI: done in 0.397451 secs using 399.4% CPU
Optimal log-likelihood: -59144.722
Site proportion and rates:  (0.107,0.067) (0.112,0.179) (0.143,0.364) (0.211,0.615) (0.188,1.025) (0.146,1.914) (0.066,2.687) (0.026,5.416)
Parameters optimization took 2 rounds (2.057 sec)
BEST SCORE FOUND : -59144.722
Total tree length: 44.182

Total number of iterations: 262
CPU time used for tree search: 1772.316 sec (0h:29m:32s)
Wall-clock time used for tree search: 595.395 sec (0h:9m:55s)
Total CPU time used: 1815.931 sec (0h:30m:15s)
Total wall-clock time used: 609.933 sec (0h:10m:9s)

===> START BOOTSTRAP REPLICATE NUMBER 2

Creating bootstrap alignment (seed: 956251)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.046 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61051.220
Optimizing NNI: done in 0.326508 secs using 398.7% CPU
Optimizing NNI: done in 0.491994 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -35141.669
Optimizing NNI: done in 0.290903 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -35140.026
2. Current log-likelihood: -60532.049
Optimizing NNI: done in 0.421276 secs using 399.6% CPU
Iteration 30 / LogL: -35208.491 / Time: 0h:0m:13s (0h:0m:45s left)
Optimizing NNI: done in 0.444474 secs using 399.5% CPU
Optimizing NNI: done in 0.459302 secs using 399.5% CPU
3. Current log-likelihood: -60526.054
Optimizing NNI: done in 0.377521 secs using 399.2% CPU
Optimizing NNI: done in 0.364772 secs using 399.5% CPU
Optimizing NNI: done in 0.251489 secs using 398.3% CPU
4. Current log-likelihood: -60521.525
Optimizing NNI: done in 0.344741 secs using 399.3% CPU
Optimizing NNI: done in 0.270421 secs using 399.9% CPU
Optimizing NNI: done in 0.325197 secs using 398.1% CPU
5. Current log-likelihood: -60511.908
Optimizing NNI: done in 0.467609 secs using 399.5% CPU
Optimizing NNI: done in 0.275936 secs using 399.2% CPU
Iteration 40 / LogL: -35146.801 / Time: 0h:0m:16s (0h:0m:38s left)
Optimizing NNI: done in 0.405882 secs using 399.4% CPU
Optimizing NNI: done in 0.406022 secs using 398.9% CPU
6. Current log-likelihood: -60499.285
Optimizing NNI: done in 0.363057 secs using 399.6% CPU
Optimizing NNI: done in 0.41147 secs using 399.2% CPU
Optimizing NNI: done in 0.320235 secs using 399.6% CPU
7. Current log-likelihood: -60494.903
Optimizing NNI: done in 0.399612 secs using 399.2% CPU
Optimizing NNI: done in 0.292074 secs using 399.2% CPU
Optimizing NNI: done in 0.316952 secs using 397.7% CPU
8. Current log-likelihood: -60494.780
Optimizing NNI: done in 0.271563 secs using 399.5% CPU
Optimizing NNI: done in 0.392341 secs using 399.4% CPU
Iteration 50 / LogL: -35154.204 / Time: 0h:0m:20s (0h:0m:32s left)
Optimizing NNI: done in 0.46252 secs using 399.7% CPU
Optimal log-likelihood: -60494.769
Site proportion and rates:  (0.079,0.058) (0.129,0.192) (0.068,0.361) (0.148,0.500) (0.172,0.710) (0.199,1.183) (0.185,2.176) (0.019,5.729)
Parameters optimization took 8 rounds (9.220 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 0.307903 secs using 399.5% CPU
Optimizing NNI: done in 0.253778 secs using 398.3% CPU
Optimizing NNI: done in 0.405532 secs using 399.7% CPU
Optimizing NNI: done in 0.341064 secs using 399.4% CPU
Calculating distance matrix: done in 1.52411 secs using 299.5% CPU
Computing ML distances took 1.524393 sec (of wall-clock time) 4.564546 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000495195 secs using 286.8% CPU
Constructing RapidNJ tree: done in 0.00417089 secs using 240.6% CPU
Computing RapidNJ tree took 0.004736 sec (of wall-clock time) 0.012037 sec (of CPU time)
Optimizing NNI: done in 0.392808 secs using 399.3% CPU
Optimizing NNI: done in 0.313369 secs using 399.3% CPU
Log-likelihood of RapidNJ tree: -60592.432
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 0.300451 secs using 399.2% CPU
Optimizing NNI: done in 0.261473 secs using 398.5% CPU
Optimizing NNI: done in 0.401528 secs using 398.6% CPU
Iteration 60 / LogL: -35140.048 / Time: 0h:0m:23s (0h:0m:27s left)
Optimizing NNI: done in 0.374164 secs using 399.6% CPU
Optimizing NNI: done in 0.398189 secs using 399.6% CPU
Optimizing NNI: done in 0.283827 secs using 399.9% CPU
Optimizing NNI: done in 0.291134 secs using 398.5% CPU
Optimizing NNI: done in 0.279829 secs using 398.4% CPU
Optimizing NNI: done in 0.526788 secs using 400% CPU
Optimizing NNI: done in 0.271502 secs using 399.5% CPU
Optimizing NNI: done in 0.420161 secs using 397.5% CPU
Optimizing NNI: done in 0.342783 secs using 397.7% CPU
Optimizing NNI: done in 0.44546 secs using 399.2% CPU
Iteration 70 / LogL: -35140.251 / Time: 0h:0m:27s (0h:0m:23s left)
Optimizing NNI: done in 0.264598 secs using 398.6% CPU
Optimizing NNI: done in 0.30087 secs using 400.3% CPU
5.301 second
Optimizing NNI: done in 0.3631 secs using 399.1% CPU
Optimizing NNI: done in 0.45753 secs using 397.7% CPU
Optimizing NNI: done in 0.400378 secs using 399.6% CPU
Optimizing NNI: done in 0.441235 secs using 398.7% CPU
Optimizing NNI: done in 0.519834 secs using 399.6% CPU
Optimizing NNI: done in 0.303094 secs using 398.5% CPU
Optimizing NNI: done in 0.297135 secs using 399.6% CPU
Optimizing NNI: done in 0.395621 secs using 399.4% CPU
Iteration 80 / LogL: -35152.084 / Time: 0h:0m:31s (0h:0m:19s left)
Optimizing NNI: done in 0.307782 secs using 399.5% CPU
Optimizing NNI: done in 0.33278 secs using 399.3% CPU
Optimizing NNI: done in 0.35292 secs using 399.9% CPU
Optimizing NNI: done in 0.326988 secs using 398.9% CPU
Optimizing NNI: done in 0.410339 secs using 398.8% CPU
Optimizing NNI: done in 0.291912 secs using 399.6% CPU
Optimizing NNI: done in 0.423497 secs using 398.9% CPU
Optimizing NNI: done in 0.406101 secs using 399.6% CPU
Optimizing NNI: done in 0.344714 secs using 399.3% CPU
Optimizing NNI: done in 0.340365 secs using 399.3% CPU
Iteration 90 / LogL: -35152.119 / Time: 0h:0m:34s (0h:0m:15s left)
Optimizing NNI: done in 0.509272 secs using 399.6% CPU
Computing log-likelihood of 98 initial trees ... 7.324 seconds
Current best score: -60404.559

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.384087 secs using 399.6% CPU
Optimizing NNI: done in 0.359731 secs using 399.7% CPU
Optimizing NNI: done in 0.469156 secs using 399.7% CPU
Optimizing NNI: done in 0.432529 secs using 398.9% CPU
Optimizing NNI: done in 1.63036 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.455546 secs using 399.4% CPU
Optimizing NNI: done in 0.416958 secs using 399.9% CPU
Optimizing NNI: done in 0.417823 secs using 399.2% CPU
Optimizing NNI: done in 0.419003 secs using 399.1% CPU
Optimizing NNI: done in 0.364056 secs using 400.4% CPU
Iteration 100 / LogL: -35140.156 / Time: 0h:0m:39s (0h:0m:11s left)
Optimizing NNI: done in 0.413171 secs using 398.4% CPU
Optimizing NNI: done in 0.272046 secs using 398.5% CPU
Optimizing NNI: done in 0.46407 secs using 398.1% CPU
Optimizing NNI: done in 0.312728 secs using 398% CPU
Optimizing NNI: done in 0.404187 secs using 397.7% CPU
Optimizing NNI: done in 0.35491 secs using 398.5% CPU
Optimizing NNI: done in 0.293837 secs using 399% CPU
471  mtMAM+R8      207137.637   1001 416277.273   2422281.273  420635.998
Optimizing NNI: done in 0.517184 secs using 399.7% CPU
Optimizing NNI: done in 0.317751 secs using 399.6% CPU
Optimizing NNI: done in 0.282357 secs using 399.2% CPU
Iteration 110 / LogL: -35141.321 / Time: 0h:0m:42s (0h:0m:7s left)
Optimizing NNI: done in 0.374899 secs using 397.6% CPU
Optimizing NNI: done in 0.455615 secs using 399.3% CPU
Optimizing NNI: done in 0.307291 secs using 399.3% CPU
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Optimizing NNI: done in 0.297254 secs using 399.6% CPU
Optimizing NNI: done in 0.364797 secs using 399.7% CPU
462  DCMut+I+R10   106797.301   554 214702.602   829642.602   216932.931
Optimizing NNI: done in 0.345412 secs using 399.9% CPU
Iteration 120 / LogL: -35148.597 / Time: 0h:0m:46s (0h:0m:3s left)
Optimizing NNI: done in 0.426463 secs using 399.5% CPU
Optimizing NNI: done in 0.377414 secs using 398.4% CPU
Optimizing NNI: done in 0.354336 secs using 399% CPU
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Optimizing NNI: done in 0.376737 secs using 398.5% CPU
Optimizing NNI: done in 0.451427 secs using 396.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -35140.025
Optimizing NNI: done in 0.46044 secs using 397.6% CPU
BETTER TREE FOUND at iteration 1: -60173.292
Optimizing NNI: done in 0.482266 secs using 397.9% CPU
Optimizing NNI: done in 0.450803 secs using 399.9% CPU
Iteration 130 / LogL: -35140.805 / Time: 0h:0m:50s (0h:0m:-1s left)
TREE SEARCH COMPLETED AFTER 130 ITERATIONS / Time: 0h:0m:50s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35140.025
Optimal log-likelihood: -35140.015
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.368
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -35140.015
Total tree length: 20.503

Total number of iterations: 130
CPU time used for tree search: 196.071 sec (0h:3m:16s)
Wall-clock time used for tree search: 50.047 sec (0h:0m:50s)
Total CPU time used: 198.290 sec (0h:3m:18s)
Total wall-clock time used: 50.574 sec (0h:0m:50s)

===> START BOOTSTRAP REPLICATE NUMBER 66

Creating bootstrap alignment (seed: 956225)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37107.260
2. Current log-likelihood: -36213.015
3. Current log-likelihood: -36201.963
4. Current log-likelihood: -36201.468
Optimal log-likelihood: -36201.403
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.436
Parameters optimization took 4 rounds (0.270 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.07304 secs using 400% CPU
Computing ML distances took 0.073170 sec (of wall-clock time) 0.292444 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000138044 secs using 462.9% CPU
Constructing RapidNJ tree: done in 0.00127101 secs using 434.7% CPU
Computing RapidNJ tree took 0.001460 sec (of wall-clock time) 0.006429 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36445.875
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.84914 secs using 298.8% CPU
1.544 second
Optimizing NNI: done in 1.78478 secs using 299.3% CPU
Computing log-likelihood of 98 initial trees ... 1.592 seconds
Current best score: -36200.643

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.226056 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36156.713
Optimizing NNI: done in 0.152452 secs using 401.8% CPU
Optimizing NNI: done in 0.229143 secs using 399.9% CPU
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Optimizing NNI: done in 2.00059 secs using 299.5% CPU
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Optimizing NNI: done in 0.229498 secs using 399.9% CPU
Optimizing NNI: done in 0.243202 secs using 399.9% CPU
Iteration 10 / LogL: -36161.556 / Time: 0h:0m:5s
Optimizing NNI: done in 0.239761 secs using 398.9% CPU
Optimizing NNI: done in 1.58465 secs using 299.1% CPU
Optimizing NNI: done in 0.239332 secs using 400.9% CPU
Optimizing NNI: done in 0.243006 secs using 399.9% CPU
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Optimizing NNI: done in 0.236965 secs using 399.5% CPU
483  DCMut+F+I+R9  106295.007   571 213732.014   866956.014   216030.784
Optimizing NNI: done in 1.73303 secs using 298.9% CPU
Optimizing NNI: done in 0.254904 secs using 399.8% CPU
Optimizing NNI: done in 0.252699 secs using 397.8% CPU
Iteration 20 / LogL: -36160.032 / Time: 0h:0m:8s
Finish initializing candidate tree set (9)
Current best tree score: -36156.713 / CPU time: 7.914
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.39965 secs using 400.4% CPU
Optimizing NNI: done in 0.427481 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -36155.665
Optimizing NNI: done in 0.39532 secs using 399.4% CPU
Optimizing NNI: done in 1.74711 secs using 299.2% CPU
Optimizing NNI: done in 0.330344 secs using 399.1% CPU
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Optimizing NNI: done in 0.280567 secs using 399.8% CPU
Optimizing NNI: done in 1.74688 secs using 299% CPU
Optimizing NNI: done in 0.388003 secs using 399.1% CPU
Iteration 30 / LogL: -36156.907 / Time: 0h:0m:11s (0h:0m:37s left)
Optimizing NNI: done in 0.316529 secs using 399.5% CPU
Optimizing NNI: done in 0.388698 secs using 399.9% CPU
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Optimizing NNI: done in 1.94168 secs using 298.8% CPU
Iteration 10 / LogL: -60230.869 / Time: 0h:0m:54s
Optimizing NNI: done in 0.369634 secs using 398.4% CPU
Iteration 40 / LogL: -36157.202 / Time: 0h:0m:15s (0h:0m:33s left)
Optimizing NNI: done in 0.369801 secs using 398.7% CPU
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Optimizing NNI: done in 0.332327 secs using 399.3% CPU
Iteration 50 / LogL: -36156.689 / Time: 0h:0m:19s (0h:0m:28s left)
Optimizing NNI: done in 0.421195 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36155.590
Optimizing NNI: done in 0.417073 secs using 397.1% CPU
Optimizing NNI: done in 0.384116 secs using 398.2% CPU
Optimizing NNI: done in 1.93861 secs using 299.6% CPU
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Optimizing NNI: done in 0.41447 secs using 399.6% CPU
Iteration 60 / LogL: -36156.809 / Time: 0h:0m:23s (0h:0m:24s left)
Optimizing NNI: done in 0.354004 secs using 399.3% CPU
Optimizing NNI: done in 0.394264 secs using 399.7% CPU
Optimizing NNI: done in 1.69611 secs using 299.3% CPU
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Optimizing NNI: done in 0.326005 secs using 398.9% CPU
Iteration 70 / LogL: -36161.524 / Time: 0h:0m:27s (0h:0m:20s left)
Optimizing NNI: done in 0.316907 secs using 399.6% CPU
Optimizing NNI: done in 0.380715 secs using 399.9% CPU
Optimizing NNI: done in 1.26428 secs using 299.5% CPU
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Optimizing NNI: done in 1.98374 secs using 299% CPU
Optimizing NNI: done in 0.285982 secs using 398.8% CPU
Optimizing NNI: done in 0.339913 secs using 398.6% CPU
Optimizing NNI: done in 0.441741 secs using 398.5% CPU
Iteration 80 / LogL: -36158.805 / Time: 0h:0m:30s (0h:0m:16s left)
Optimizing NNI: done in 0.295926 secs using 399.5% CPU
Optimizing NNI: done in 0.421929 secs using 399.4% CPU
Optimizing NNI: done in 1.84159 secs using 299.7% CPU
Optimizing NNI: done in 0.34332 secs using 399.8% CPU
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Optimizing NNI: done in 0.396133 secs using 399.4% CPU
Optimizing NNI: done in 1.95065 secs using 299.4% CPU
Iteration 20 / LogL: -60293.986 / Time: 0h:1m:12s
Finish initializing candidate tree set (20)
Current best tree score: -60173.292 / CPU time: 61.425
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.265895 secs using 399.4% CPU
Optimizing NNI: done in 0.442402 secs using 399.4% CPU
Iteration 90 / LogL: -36155.766 / Time: 0h:0m:34s (0h:0m:12s left)
Optimizing NNI: done in 0.37753 secs using 399.4% CPU
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Optimizing NNI: done in 0.411413 secs using 399.4% CPU
Optimizing NNI: done in 0.286954 secs using 399.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -36155.581
Iteration 100 / LogL: -36155.581 / Time: 0h:0m:38s (0h:0m:8s left)
Optimizing NNI: done in 0.314803 secs using 398.3% CPU
Optimizing NNI: done in 2.30061 secs using 299.3% CPU
Optimizing NNI: done in 0.399211 secs using 399.4% CPU
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Optimizing NNI: done in 0.437227 secs using 399% CPU
Optimizing NNI: done in 0.293215 secs using 398.8% CPU
Optimizing NNI: done in 0.421387 secs using 400% CPU
Iteration 110 / LogL: -36156.973 / Time: 0h:0m:42s (0h:0m:4s left)
Optimizing NNI: done in 0.292013 secs using 399.2% CPU
Optimizing NNI: done in 0.454454 secs using 398.3% CPU
Optimizing NNI: done in 1.746 secs using 299.3% CPU
Optimizing NNI: done in 0.390512 secs using 398% CPU
Optimizing NNI: done in 0.457156 secs using 397.7% CPU
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Optimizing NNI: done in 0.459127 secs using 399.1% CPU
Optimizing NNI: done in 1.90608 secs using 298.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.361532 secs using 397.7% CPU
Optimizing NNI: done in 0.417226 secs using 399% CPU
Optimizing NNI: done in 0.432957 secs using 399% CPU
Optimizing NNI: done in 0.506107 secs using 398.9% CPU
Iteration 120 / LogL: -36156.221 / Time: 0h:0m:46s (0h:0m:0s left)
Optimizing NNI: done in 0.429242 secs using 398.8% CPU
BETTER TREE FOUND at iteration 25: -60157.992
Optimizing NNI: done in 0.370117 secs using 399.9% CPU
Optimizing NNI: done in 0.395682 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 123 ITERATIONS / Time: 0h:0m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36155.581
Optimal log-likelihood: -36155.578
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.449
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -36155.578
Total tree length: 19.548

Total number of iterations: 123
CPU time used for tree search: 184.099 sec (0h:3m:4s)
Wall-clock time used for tree search: 47.110 sec (0h:0m:47s)
Total CPU time used: 186.140 sec (0h:3m:6s)
Total wall-clock time used: 47.604 sec (0h:0m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 67

Creating bootstrap alignment (seed: 956226)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.020 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37455.866
2. Current log-likelihood: -36553.190
3. Current log-likelihood: -36526.883
4. Current log-likelihood: -36525.912
Optimal log-likelihood: -36525.887
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.629
Parameters optimization took 4 rounds (0.270 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0747402 secs using 400% CPU
Computing ML distances took 0.074866 sec (of wall-clock time) 0.299274 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000136137 secs using 465% CPU
Constructing RapidNJ tree: done in 0.00120592 secs using 313.7% CPU
Computing RapidNJ tree took 0.001390 sec (of wall-clock time) 0.007084 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36919.180
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.42172 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -60155.060
1.450 second
Computing log-likelihood of 98 initial trees ... 1.541 seconds
Current best score: -36525.887

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.246412 secs using 397.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36507.310
Optimizing NNI: done in 0.281394 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.20753 secs using 299.3% CPU
BETTER TREE FOUND at iteration 2: -36503.109
Optimizing NNI: done in 0.258545 secs using 399% CPU
Optimizing NNI: done in 0.264031 secs using 397.6% CPU
Optimizing NNI: done in 0.241679 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -36502.499
Optimizing NNI: done in 0.232147 secs using 399.2% CPU
Optimizing NNI: done in 0.242555 secs using 400.4% CPU
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Optimizing NNI: done in 0.257779 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36502.316
Optimizing NNI: done in 0.256243 secs using 399.9% CPU
Iteration 10 / LogL: -36508.047 / Time: 0h:0m:6s
Optimizing NNI: done in 2.10289 secs using 299.4% CPU
Optimizing NNI: done in 0.271479 secs using 399.1% CPU
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Optimizing NNI: done in 1.96718 secs using 299.4% CPU
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Optimizing NNI: done in 0.241628 secs using 399.5% CPU
Optimizing NNI: done in 0.2331 secs using 399.9% CPU
Iteration 20 / LogL: -36508.228 / Time: 0h:0m:8s
Finish initializing candidate tree set (8)
Current best tree score: -36502.316 / CPU time: 8.310
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.412373 secs using 398.9% CPU
Optimizing NNI: done in 0.389117 secs using 399.4% CPU
Optimizing NNI: done in 0.435565 secs using 400% CPU
Optimizing NNI: done in 0.376556 secs using 399.6% CPU
Optimizing NNI: done in 2.23258 secs using 298.9% CPU
Iteration 30 / LogL: -60160.055 / Time: 0h:1m:36s (0h:5m:20s left)
Optimizing NNI: done in 0.271957 secs using 399.9% CPU
Optimizing NNI: done in 0.400696 secs using 399.7% CPU
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Optimizing NNI: done in 0.398669 secs using 399.7% CPU
Optimizing NNI: done in 1.49301 secs using 299.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.433278 secs using 399% CPU
Optimizing NNI: done in 0.425565 secs using 399.4% CPU
Iteration 30 / LogL: -36505.142 / Time: 0h:0m:12s (0h:0m:32s left)
Optimizing NNI: done in 0.41107 secs using 398.7% CPU
Optimizing NNI: done in 0.426848 secs using 399.8% CPU
Optimizing NNI: done in 0.435464 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -60139.100
BETTER TREE FOUND at iteration 33: -36502.264
Optimizing NNI: done in 0.445277 secs using 400.4% CPU
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472  mtMAM+R9      207095.777   1003 416197.555   2430221.555  420564.988
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BETTER TREE FOUND at iteration 39: -60124.450
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Iteration 130 / LogL: -36502.669 / Time: 0h:0m:56s (0h:0m:1s left)
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BETTER TREE FOUND at iteration 49: -60108.730
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TREE SEARCH COMPLETED AFTER 134 ITERATIONS / Time: 0h:0m:58s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36502.264
Optimal log-likelihood: -36502.264
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.663
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -36502.264
Total tree length: 19.703

Total number of iterations: 134
CPU time used for tree search: 226.801 sec (0h:3m:46s)
Wall-clock time used for tree search: 57.758 sec (0h:0m:57s)
Total CPU time used: 229.182 sec (0h:3m:49s)
Total wall-clock time used: 58.321 sec (0h:0m:58s)

===> START BOOTSTRAP REPLICATE NUMBER 68

Creating bootstrap alignment (seed: 956227)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36685.305
2. Current log-likelihood: -35799.339
3. Current log-likelihood: -35781.659
4. Current log-likelihood: -35781.433
Optimal log-likelihood: -35781.412
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.447
Parameters optimization took 4 rounds (0.256 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.075676 secs using 402.3% CPU
Computing ML distances took 0.075819 sec (of wall-clock time) 0.304703 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000137091 secs using 455.9% CPU
Constructing RapidNJ tree: done in 0.001297 secs using 430.7% CPU
Computing RapidNJ tree took 0.001485 sec (of wall-clock time) 0.006488 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36436.567
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.01142 secs using 299.4% CPU
Iteration 50 / LogL: -60131.999 / Time: 0h:2m:25s (0h:4m:54s left)
1.544 second
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Computing log-likelihood of 98 initial trees ... 1.543 seconds
Current best score: -35781.412

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 19: -35733.272
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Iteration 20 / LogL: -35738.334 / Time: 0h:0m:8s
Finish initializing candidate tree set (4)
Current best tree score: -35733.272 / CPU time: 7.987
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -35733.098
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -35730.761
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -35729.429
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Iteration 40 / LogL: -35730.767 / Time: 0h:0m:16s (0h:0m:39s left)
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UPDATE BEST LOG-LIKELIHOOD: -35729.425
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UPDATE BEST LOG-LIKELIHOOD: -35729.421
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Iteration 100 / LogL: -35739.966 / Time: 0h:0m:39s (0h:0m:13s left)
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Iteration 70 / LogL: -60119.706 / Time: 0h:3m:7s (0h:3m:34s left)
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Iteration 110 / LogL: -35729.503 / Time: 0h:0m:42s (0h:0m:9s left)
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484  DCMut+F+I+R10 106292.780   573 213731.560   871535.560   216038.381
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Iteration 130 / LogL: -35730.038 / Time: 0h:0m:50s (0h:0m:1s left)
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Optimizing NNI: done in 0.331326 secs using 398.7% CPU
Optimizing NNI: done in 0.274094 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 134 ITERATIONS / Time: 0h:0m:51s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35729.421
Optimal log-likelihood: -35729.417
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.515
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35729.417
Total tree length: 19.585

Total number of iterations: 134
CPU time used for tree search: 200.586 sec (0h:3m:20s)
Wall-clock time used for tree search: 51.276 sec (0h:0m:51s)
Total CPU time used: 203.517 sec (0h:3m:23s)
Total wall-clock time used: 51.963 sec (0h:0m:51s)

===> START BOOTSTRAP REPLICATE NUMBER 69

Creating bootstrap alignment (seed: 956228)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.023 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36858.667
2. Current log-likelihood: -36024.231
3. Current log-likelihood: -36010.232
4. Current log-likelihood: -36009.531
Optimal log-likelihood: -36009.377
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.386
Parameters optimization took 4 rounds (0.265 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.07217 secs using 398% CPU
Computing ML distances took 0.072293 sec (of wall-clock time) 0.287520 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000135899 secs using 463.6% CPU
Constructing RapidNJ tree: done in 0.001302 secs using 483.7% CPU
Computing RapidNJ tree took 0.001487 sec (of wall-clock time) 0.007474 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36683.439
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.29301 secs using 299.5% CPU
Estimate model parameters (epsilon = 0.100)
1.544 second
BETTER TREE FOUND at iteration 75: -60107.477
Computing log-likelihood of 98 initial trees ... 1.602 seconds
Current best score: -36009.377

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.177755 secs using 400% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35981.371
Optimizing NNI: done in 0.257869 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35981.258
Optimizing NNI: done in 0.278175 secs using 399.1% CPU
Optimizing NNI: done in 0.222031 secs using 399.9% CPU
Optimizing NNI: done in 0.245236 secs using 399.5% CPU
Optimizing NNI: done in 0.247183 secs using 399.9% CPU
Optimizing NNI: done in 1.91587 secs using 299.5% CPU
Optimizing NNI: done in 0.247359 secs using 397.9% CPU
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Optimizing NNI: done in 0.247506 secs using 399.5% CPU
Optimizing NNI: done in 0.247577 secs using 400.2% CPU
Iteration 10 / LogL: -35981.271 / Time: 0h:0m:6s
Optimizing NNI: done in 0.213228 secs using 399.5% CPU
Optimizing NNI: done in 0.228572 secs using 399.9% CPU
Optimizing NNI: done in 0.206731 secs using 399.9% CPU
Optimizing NNI: done in 0.257072 secs using 399.1% CPU
UPDATE BEST LOG-LIKELIHOOD: -35981.257
Optimizing NNI: done in 0.242071 secs using 398.7% CPU
Optimizing NNI: done in 2.1817 secs using 299.2% CPU
Optimizing NNI: done in 0.226548 secs using 399.5% CPU
Optimizing NNI: done in 0.216627 secs using 399.9% CPU
505  VT+I+R9       105830.002   552 212764.005   823276.005   214986.283
Optimizing NNI: done in 0.215512 secs using 399.5% CPU
Optimizing NNI: done in 0.229231 secs using 399.8% CPU
Optimizing NNI: done in 0.196544 secs using 399.4% CPU
Iteration 20 / LogL: -35981.287 / Time: 0h:0m:8s
Finish initializing candidate tree set (3)
Current best tree score: -35981.257 / CPU time: 7.971
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.283118 secs using 399.8% CPU
Optimizing NNI: done in 0.367208 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -35980.708
Optimizing NNI: done in 1.97459 secs using 299.4% CPU
Optimizing NNI: done in 0.473769 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -35974.027
Optimizing NNI: done in 0.369643 secs using 398.9% CPU
Optimizing NNI: done in 0.396018 secs using 398% CPU
Optimizing NNI: done in 0.418955 secs using 400.2% CPU
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Optimizing NNI: done in 2.19341 secs using 299.3% CPU
Optimizing NNI: done in 0.397688 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35973.341
Optimizing NNI: done in 0.38315 secs using 399.3% CPU
Iteration 30 / LogL: -35981.393 / Time: 0h:0m:12s (0h:0m:39s left)
Optimizing NNI: done in 0.249664 secs using 399.7% CPU
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Optimizing NNI: done in 2.12241 secs using 299.2% CPU
Iteration 80 / LogL: -60125.974 / Time: 0h:3m:30s (0h:4m:13s left)
Optimizing NNI: done in 0.36831 secs using 399.7% CPU
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Iteration 40 / LogL: -35979.524 / Time: 0h:0m:15s (0h:0m:33s left)
Optimizing NNI: done in 2.20667 secs using 298.6% CPU
Optimizing NNI: done in 0.347077 secs using 398.8% CPU
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Optimizing NNI: done in 2.24517 secs using 299% CPU
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Optimizing NNI: done in 0.350842 secs using 399.5% CPU
Iteration 50 / LogL: -35979.524 / Time: 0h:0m:19s (0h:0m:29s left)
Optimizing NNI: done in 0.454845 secs using 399.3% CPU
Optimizing NNI: done in 2.09932 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.373969 secs using 399.2% CPU
Optimizing NNI: done in 0.389601 secs using 399.5% CPU
Optimizing NNI: done in 0.429865 secs using 399.5% CPU
BETTER TREE FOUND at iteration 83: -60107.409
Optimizing NNI: done in 0.432611 secs using 399.4% CPU
Optimizing NNI: done in 0.365111 secs using 398.8% CPU
Optimizing NNI: done in 0.382803 secs using 399.2% CPU
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Optimizing NNI: done in 0.399057 secs using 399.7% CPU
Optimizing NNI: done in 0.423512 secs using 399.4% CPU
Iteration 60 / LogL: -35973.761 / Time: 0h:0m:23s (0h:0m:25s left)
Optimizing NNI: done in 2.48778 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.439896 secs using 399.8% CPU
Optimizing NNI: done in 0.319288 secs using 397.7% CPU
Optimizing NNI: done in 0.337881 secs using 399.7% CPU
BETTER TREE FOUND at iteration 84: -60107.040
Optimizing NNI: done in 0.439246 secs using 399.6% CPU
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Optimizing NNI: done in 0.56102 secs using 399.3% CPU
Optimizing NNI: done in 1.8474 secs using 299.3% CPU
Optimizing NNI: done in 0.303387 secs using 398.9% CPU
Optimizing NNI: done in 0.412546 secs using 398.4% CPU
Optimizing NNI: done in 0.437976 secs using 399.3% CPU
Iteration 70 / LogL: -35974.177 / Time: 0h:0m:28s (0h:0m:21s left)
Optimizing NNI: done in 0.509556 secs using 398.2% CPU
473  mtMAM+R10     207079.072   1005 416168.143   2438228.143  420544.285
Optimizing NNI: done in 1.89064 secs using 298.6% CPU
BETTER TREE FOUND at iteration 86: -60107.039
Optimizing NNI: done in 0.385516 secs using 398.7% CPU
Optimizing NNI: done in 0.416968 secs using 399.1% CPU
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Optimizing NNI: done in 2.33364 secs using 298.7% CPU
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Optimizing NNI: done in 0.370975 secs using 398.1% CPU
Optimizing NNI: done in 0.45078 secs using 398.6% CPU
Iteration 80 / LogL: -35973.509 / Time: 0h:0m:32s (0h:0m:17s left)
Optimizing NNI: done in 0.352697 secs using 398.2% CPU
Optimizing NNI: done in 0.38146 secs using 399.2% CPU
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Optimizing NNI: done in 0.322075 secs using 399.5% CPU
Optimizing NNI: done in 0.377143 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -35973.336
Optimizing NNI: done in 0.283675 secs using 399.4% CPU
Optimizing NNI: done in 0.287217 secs using 399.3% CPU
Optimizing NNI: done in 0.42978 secs using 399.4% CPU
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Optimizing NNI: done in 2.28783 secs using 298.5% CPU
Optimizing NNI: done in 0.358357 secs using 399.1% CPU
Iteration 90 / LogL: -35973.478 / Time: 0h:0m:36s (0h:0m:13s left)
Optimizing NNI: done in 0.369541 secs using 399.7% CPU
Optimizing NNI: done in 0.339159 secs using 399.5% CPU
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Optimizing NNI: done in 0.463252 secs using 399% CPU
Optimizing NNI: done in 2.47589 secs using 298.7% CPU
Iteration 90 / LogL: -60107.041 / Time: 0h:3m:55s (0h:4m:13s left)
Optimizing NNI: done in 0.422804 secs using 399.5% CPU
Optimizing NNI: done in 0.378767 secs using 397.5% CPU
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Optimizing NNI: done in 0.438883 secs using 399.5% CPU
Optimizing NNI: done in 0.387727 secs using 399.6% CPU
Iteration 100 / LogL: -35974.306 / Time: 0h:0m:40s (0h:0m:9s left)
Optimizing NNI: done in 0.295792 secs using 399.2% CPU
Optimizing NNI: done in 2.20402 secs using 298.6% CPU
Optimizing NNI: done in 0.377868 secs using 399% CPU
Optimizing NNI: done in 0.433114 secs using 398.9% CPU
Optimizing NNI: done in 0.446808 secs using 399.6% CPU
Optimizing NNI: done in 0.428745 secs using 398.9% CPU
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Optimizing NNI: done in 2.24594 secs using 298.7% CPU
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Optimizing NNI: done in 0.409122 secs using 396.9% CPU
Optimizing NNI: done in 0.386687 secs using 399.1% CPU
Optimizing NNI: done in 0.348058 secs using 399.3% CPU
Iteration 110 / LogL: -35973.547 / Time: 0h:0m:44s (0h:0m:5s left)
Optimizing NNI: done in 0.41688 secs using 398.5% CPU
Optimizing NNI: done in 0.444079 secs using 397.1% CPU
Optimizing NNI: done in 2.07785 secs using 298.9% CPU
Optimizing NNI: done in 0.346742 secs using 398.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -35973.335
Optimizing NNI: done in 0.345301 secs using 399.5% CPU
Optimizing NNI: done in 0.450165 secs using 399.1% CPU
Optimizing NNI: done in 0.342187 secs using 398.7% CPU
Optimizing NNI: done in 0.353729 secs using 398.8% CPU
Optimizing NNI: done in 2.18249 secs using 299.1% CPU
BETTER TREE FOUND at iteration 94: -60107.039
Optimizing NNI: done in 0.411072 secs using 399.5% CPU
Optimizing NNI: done in 0.419516 secs using 399.4% CPU
Optimizing NNI: done in 0.35522 secs using 399.1% CPU
Iteration 120 / LogL: -35978.273 / Time: 0h:0m:47s (0h:0m:1s left)
Optimizing NNI: done in 0.500229 secs using 399.7% CPU
Optimizing NNI: done in 0.434278 secs using 399.8% CPU
Optimizing NNI: done in 2.02622 secs using 299.3% CPU
Optimizing NNI: done in 0.338272 secs using 399.5% CPU
Optimizing NNI: done in 0.362296 secs using 399.6% CPU
TREE SEARCH COMPLETED AFTER 124 ITERATIONS / Time: 0h:0m:49s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35973.335
Optimal log-likelihood: -35973.330
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.381
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35973.330
Total tree length: 19.283

Total number of iterations: 124
CPU time used for tree search: 191.604 sec (0h:3m:11s)
Wall-clock time used for tree search: 49.031 sec (0h:0m:49s)
Total CPU time used: 194.346 sec (0h:3m:14s)
Total wall-clock time used: 49.671 sec (0h:0m:49s)

===> START BOOTSTRAP REPLICATE NUMBER 70

Creating bootstrap alignment (seed: 956229)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36306.774
2. Current log-likelihood: -35459.667
3. Current log-likelihood: -35448.825
4. Current log-likelihood: -35448.376
Optimal log-likelihood: -35448.280
Proportion of invariable sites: 0.018
Gamma shape alpha: 2.235
Parameters optimization took 4 rounds (0.233 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0749421 secs using 399.9% CPU
Computing ML distances took 0.075092 sec (of wall-clock time) 0.300111 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000134945 secs using 458% CPU
Constructing RapidNJ tree: done in 0.00134897 secs using 294.2% CPU
Computing RapidNJ tree took 0.001537 sec (of wall-clock time) 0.005443 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35929.888
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.03849 secs using 299.1% CPU
1.496 second
Computing log-likelihood of 98 initial trees ... 1.587 seconds
Current best score: -35432.097

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.29212 secs using 298.9% CPU
Optimizing NNI: done in 0.29514 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35396.902
Optimizing NNI: done in 0.23904 secs using 398.6% CPU
Optimizing NNI: done in 0.266092 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -35393.893
Optimizing NNI: done in 0.248297 secs using 399.5% CPU
Optimizing NNI: done in 0.280645 secs using 398.5% CPU
Optimizing NNI: done in 0.264716 secs using 398.9% CPU
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Optimizing NNI: done in 2.34315 secs using 298.9% CPU
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Iteration 10 / LogL: -35394.012 / Time: 0h:0m:6s
Optimizing NNI: done in 0.232867 secs using 399.5% CPU
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Optimizing NNI: done in 0.242058 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 20: -35385.072
Iteration 20 / LogL: -35385.072 / Time: 0h:0m:9s
Finish initializing candidate tree set (4)
Current best tree score: -35385.072 / CPU time: 8.447
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.465764 secs using 399.7% CPU
Optimizing NNI: done in 0.371268 secs using 399.8% CPU
Optimizing NNI: done in 0.348156 secs using 399.5% CPU
Optimizing NNI: done in 0.455804 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.20395 secs using 299.1% CPU
Iteration 100 / LogL: -60107.043 / Time: 0h:4m:17s (0h:4m:3s left)
BETTER TREE FOUND at iteration 24: -35384.505
Optimizing NNI: done in 0.576257 secs using 399.4% CPU
Optimizing NNI: done in 0.427776 secs using 399.4% CPU
Optimizing NNI: done in 0.330541 secs using 399.7% CPU
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Optimizing NNI: done in 2.19619 secs using 298.9% CPU
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Iteration 30 / LogL: -35386.323 / Time: 0h:0m:13s (0h:0m:42s left)
Optimizing NNI: done in 0.298259 secs using 399.6% CPU
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Iteration 40 / LogL: -35393.654 / Time: 0h:0m:16s (0h:0m:36s left)
Optimizing NNI: done in 0.412805 secs using 398.6% CPU
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Iteration 50 / LogL: -35384.756 / Time: 0h:0m:20s (0h:0m:31s left)
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Iteration 60 / LogL: -35384.927 / Time: 0h:0m:24s (0h:0m:26s left)
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Iteration 70 / LogL: -35384.704 / Time: 0h:0m:28s (0h:0m:22s left)
Optimizing NNI: done in 0.446902 secs using 399.3% CPU
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Optimizing NNI: done in 0.382774 secs using 398.8% CPU
Optimizing NNI: done in 0.321834 secs using 399.6% CPU
Iteration 80 / LogL: -35384.656 / Time: 0h:0m:32s (0h:0m:17s left)
Optimizing NNI: done in 0.340422 secs using 399.3% CPU
Optimizing NNI: done in 2.20582 secs using 298.6% CPU
Iteration 110 / LogL: -60113.212 / Time: 0h:4m:38s (0h:3m:34s left)
Optimizing NNI: done in 0.405296 secs using 398.8% CPU
Optimizing NNI: done in 0.293621 secs using 399.6% CPU
Optimizing NNI: done in 0.32654 secs using 399.3% CPU
Optimizing NNI: done in 0.434913 secs using 399.3% CPU
Optimizing NNI: done in 0.376913 secs using 399.6% CPU
Optimizing NNI: done in 0.308577 secs using 399.2% CPU
Optimizing NNI: done in 2.30349 secs using 298.9% CPU
Optimizing NNI: done in 0.395184 secs using 398.8% CPU
Optimizing NNI: done in 0.344691 secs using 399% CPU
Optimizing NNI: done in 0.297545 secs using 399.2% CPU
Iteration 90 / LogL: -35384.677 / Time: 0h:0m:35s (0h:0m:13s left)
Optimizing NNI: done in 0.369878 secs using 398.8% CPU
UPDATE BEST LOG-LIKELIHOOD: -35384.501
Optimizing NNI: done in 0.399557 secs using 398.7% CPU
Optimizing NNI: done in 0.350887 secs using 399.9% CPU
Optimizing NNI: done in 2.24715 secs using 298.7% CPU
Optimizing NNI: done in 0.367599 secs using 399.3% CPU
Optimizing NNI: done in 0.315272 secs using 399.2% CPU
Optimizing NNI: done in 0.388173 secs using 398.6% CPU
Optimizing NNI: done in 0.371578 secs using 399% CPU
Optimizing NNI: done in 0.343758 secs using 397.7% CPU
Optimizing NNI: done in 0.354341 secs using 399.6% CPU
Optimizing NNI: done in 2.16938 secs using 299.1% CPU
Optimizing NNI: done in 0.352569 secs using 399% CPU
Iteration 100 / LogL: -35384.532 / Time: 0h:0m:39s (0h:0m:9s left)
Optimizing NNI: done in 0.281839 secs using 399.6% CPU
Optimizing NNI: done in 0.397691 secs using 398.8% CPU
Optimizing NNI: done in 0.354623 secs using 398.4% CPU
Optimizing NNI: done in 0.373917 secs using 399.4% CPU
Optimizing NNI: done in 0.310758 secs using 399.4% CPU
Optimizing NNI: done in 0.358779 secs using 399.6% CPU
Optimizing NNI: done in 2.27652 secs using 298.9% CPU
Optimizing NNI: done in 0.390809 secs using 398.8% CPU
Optimizing NNI: done in 0.379703 secs using 399.3% CPU
Optimizing NNI: done in 0.573544 secs using 399.4% CPU
Optimizing NNI: done in 0.358531 secs using 399% CPU
Iteration 110 / LogL: -35384.909 / Time: 0h:0m:43s (0h:0m:5s left)
Optimizing NNI: done in 0.307578 secs using 399.5% CPU
Optimizing NNI: done in 0.284547 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35384.485
Optimizing NNI: done in 2.3458 secs using 299% CPU
Optimizing NNI: done in 0.358591 secs using 397.9% CPU
Optimizing NNI: done in 0.341641 secs using 398.4% CPU
Optimizing NNI: done in 0.423227 secs using 399.6% CPU
Optimizing NNI: done in 0.336433 secs using 398.5% CPU
Optimizing NNI: done in 0.389954 secs using 398.9% CPU
Optimizing NNI: done in 0.284918 secs using 399% CPU
Optimizing NNI: done in 0.45383 secs using 399.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -35384.484
Optimizing NNI: done in 2.52478 secs using 299% CPU
Optimizing NNI: done in 0.370069 secs using 398.7% CPU
Iteration 120 / LogL: -35385.303 / Time: 0h:0m:46s (0h:0m:1s left)
Optimizing NNI: done in 0.374571 secs using 399.4% CPU
Optimizing NNI: done in 0.360736 secs using 398.2% CPU
Optimizing NNI: done in 0.354699 secs using 400.3% CPU
Optimizing NNI: done in 0.416768 secs using 399.2% CPU
Optimizing NNI: done in 0.461038 secs using 398.1% CPU
TREE SEARCH COMPLETED AFTER 125 ITERATIONS / Time: 0h:0m:48s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35384.484
Optimal log-likelihood: -35384.483
Proportion of invariable sites: 0.019
Gamma shape alpha: 2.242
Parameters optimization took 1 rounds (0.051 sec)
BEST SCORE FOUND : -35384.483
Total tree length: 19.527

Total number of iterations: 125
CPU time used for tree search: 188.364 sec (0h:3m:8s)
Wall-clock time used for tree search: 48.178 sec (0h:0m:48s)
Total CPU time used: 191.026 sec (0h:3m:11s)
Total wall-clock time used: 48.798 sec (0h:0m:48s)

===> START BOOTSTRAP REPLICATE NUMBER 71

Creating bootstrap alignment (seed: 956230)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36418.593
Optimizing NNI: done in 2.36803 secs using 299.2% CPU
2. Current log-likelihood: -35564.487
3. Current log-likelihood: -35547.796
4. Current log-likelihood: -35546.524
Optimal log-likelihood: -35546.493
Proportion of invariable sites: 0.018
Gamma shape alpha: 2.350
Parameters optimization took 4 rounds (0.286 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0754819 secs using 398.6% CPU
Computing ML distances took 0.075624 sec (of wall-clock time) 0.301216 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000126123 secs using 453.5% CPU
Constructing RapidNJ tree: done in 0.00128198 secs using 492.1% CPU
Computing RapidNJ tree took 0.001460 sec (of wall-clock time) 0.007342 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36021.669
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.538 second
Optimizing NNI: done in 2.19536 secs using 299.3% CPU
Computing log-likelihood of 98 initial trees ... 1.593 seconds
Current best score: -35546.493

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.208422 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35528.714
Optimizing NNI: done in 0.220768 secs using 397.4% CPU
Optimizing NNI: done in 2.12382 secs using 298.9% CPU
Optimizing NNI: done in 0.274401 secs using 399.4% CPU
Optimizing NNI: done in 0.245228 secs using 399.7% CPU
Optimizing NNI: done in 0.298413 secs using 399.7% CPU
Optimizing NNI: done in 0.226971 secs using 398.3% CPU
Optimizing NNI: done in 0.243317 secs using 399.7% CPU
Optimizing NNI: done in 0.282579 secs using 399.4% CPU
Optimizing NNI: done in 0.253122 secs using 399.7% CPU
Optimizing NNI: done in 0.289379 secs using 399% CPU
Iteration 10 / LogL: -35533.205 / Time: 0h:0m:6s
Optimizing NNI: done in 0.254628 secs using 399.3% CPU
482  mtMAM+F+R8    202259.202   1020 406558.403   2489398.403  410999.861
Optimizing NNI: done in 0.267733 secs using 398.2% CPU
Optimizing NNI: done in 2.62031 secs using 298.9% CPU
Iteration 120 / LogL: -60114.694 / Time: 0h:5m:2s (0h:3m:7s left)
Optimizing NNI: done in 0.257352 secs using 398.9% CPU
Optimizing NNI: done in 0.272582 secs using 399.4% CPU
Optimizing NNI: done in 0.248608 secs using 399.5% CPU
Optimizing NNI: done in 0.2527 secs using 400.2% CPU
Optimizing NNI: done in 0.2289 secs using 399.3% CPU
Optimizing NNI: done in 0.238089 secs using 398.3% CPU
Optimizing NNI: done in 0.276066 secs using 399% CPU
Optimizing NNI: done in 0.274909 secs using 399.3% CPU
Iteration 20 / LogL: -35533.303 / Time: 0h:0m:8s
Finish initializing candidate tree set (5)
Current best tree score: -35528.714 / CPU time: 8.401
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.348874 secs using 399.4% CPU
Optimizing NNI: done in 2.29637 secs using 298.9% CPU
Optimizing NNI: done in 0.642887 secs using 399.4% CPU
Optimizing NNI: done in 0.317372 secs using 399.2% CPU
Optimizing NNI: done in 0.421261 secs using 399.3% CPU
Optimizing NNI: done in 0.432195 secs using 399.1% CPU
Optimizing NNI: done in 0.310848 secs using 399.2% CPU
Optimizing NNI: done in 2.38889 secs using 298.5% CPU
Optimizing NNI: done in 0.374749 secs using 399.7% CPU
Optimizing NNI: done in 0.436559 secs using 398.9% CPU
Optimizing NNI: done in 0.448653 secs using 399% CPU
Optimizing NNI: done in 0.455736 secs using 399.4% CPU
Iteration 30 / LogL: -35532.024 / Time: 0h:0m:13s (0h:0m:32s left)
Optimizing NNI: done in 0.40278 secs using 399.6% CPU
Optimizing NNI: done in 0.426916 secs using 399% CPU
Optimizing NNI: done in 2.58579 secs using 298.9% CPU
Optimizing NNI: done in 0.382764 secs using 399.6% CPU
Optimizing NNI: done in 0.401207 secs using 398.4% CPU
Optimizing NNI: done in 0.482768 secs using 398.7% CPU
Optimizing NNI: done in 0.51166 secs using 398.2% CPU
Optimizing NNI: done in 0.362947 secs using 399.3% CPU
Optimizing NNI: done in 0.338507 secs using 399.2% CPU
Optimizing NNI: done in 2.40347 secs using 298.8% CPU
Optimizing NNI: done in 0.455077 secs using 399.5% CPU
Optimizing NNI: done in 0.429008 secs using 399.1% CPU
Iteration 40 / LogL: -35528.900 / Time: 0h:0m:17s (0h:0m:27s left)
Optimizing NNI: done in 0.561869 secs using 398.5% CPU
Optimizing NNI: done in 0.463874 secs using 398.9% CPU
Optimizing NNI: done in 0.325766 secs using 399% CPU
Optimizing NNI: done in 2.08098 secs using 297.3% CPU
Optimizing NNI: done in 0.443173 secs using 399.8% CPU
Optimizing NNI: done in 0.376299 secs using 399.3% CPU
Optimizing NNI: done in 0.437919 secs using 399.4% CPU
Optimizing NNI: done in 0.397806 secs using 398.8% CPU
Optimizing NNI: done in 0.60399 secs using 398.7% CPU
Optimizing NNI: done in 2.19356 secs using 297.7% CPU
Optimizing NNI: done in 0.45502 secs using 399.1% CPU
Optimizing NNI: done in 0.40597 secs using 399.1% CPU
Iteration 50 / LogL: -35530.274 / Time: 0h:0m:21s (0h:0m:22s left)
506  VT+I+R10      105823.454   554 212754.907   827694.907   214985.237
Optimizing NNI: done in 0.440418 secs using 398.9% CPU
Optimizing NNI: done in 0.412253 secs using 398.8% CPU
Optimizing NNI: done in 0.306025 secs using 399.2% CPU
Optimizing NNI: done in 2.06026 secs using 297.5% CPU
Optimizing NNI: done in 0.439269 secs using 399.3% CPU
Optimizing NNI: done in 0.354169 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 55: -35528.550
Optimizing NNI: done in 0.513234 secs using 398.4% CPU
Optimizing NNI: done in 0.499002 secs using 398.8% CPU
Optimizing NNI: done in 0.35565 secs using 399.3% CPU
Optimizing NNI: done in 2.39379 secs using 286.7% CPU
Optimizing NNI: done in 0.430652 secs using 398.9% CPU
Optimizing NNI: done in 0.527947 secs using 399.4% CPU
Iteration 60 / LogL: -35530.380 / Time: 0h:0m:26s (0h:0m:42s left)
Optimizing NNI: done in 0.434585 secs using 398.7% CPU
Optimizing NNI: done in 0.454378 secs using 399.6% CPU
Optimizing NNI: done in 0.413218 secs using 398.9% CPU
Optimizing NNI: done in 2.22471 secs using 298.9% CPU
Optimizing NNI: done in 0.383967 secs using 399.7% CPU
Optimizing NNI: done in 0.50681 secs using 398.6% CPU
Optimizing NNI: done in 0.515667 secs using 399.4% CPU
Optimizing NNI: done in 0.478165 secs using 399.4% CPU
Optimizing NNI: done in 0.43555 secs using 399.4% CPU
Optimizing NNI: done in 2.51731 secs using 299.2% CPU
Iteration 130 / LogL: -60155.553 / Time: 0h:5m:25s (0h:2m:41s left)
Optimizing NNI: done in 0.471809 secs using 399% CPU
Optimizing NNI: done in 0.341599 secs using 399.4% CPU
Iteration 70 / LogL: -35528.767 / Time: 0h:0m:30s (0h:0m:37s left)
Optimizing NNI: done in 0.56457 secs using 399.5% CPU
Optimizing NNI: done in 0.398305 secs using 399.7% CPU
Optimizing NNI: done in 0.320572 secs using 398.5% CPU
Optimizing NNI: done in 0.451742 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35528.486
Optimizing NNI: done in 2.30727 secs using 298.8% CPU
Optimizing NNI: done in 0.501574 secs using 399.6% CPU
Optimizing NNI: done in 0.414512 secs using 399% CPU
Optimizing NNI: done in 0.330943 secs using 399% CPU
Optimizing NNI: done in 0.363273 secs using 398.9% CPU
Optimizing NNI: done in 0.308274 secs using 400% CPU
Optimizing NNI: done in 2.05161 secs using 299.5% CPU
Optimizing NNI: done in 0.347814 secs using 399.3% CPU
Iteration 80 / LogL: -35535.653 / Time: 0h:0m:34s (0h:0m:33s left)
527  VT+F+I+R9     105879.182   571 212900.364   866124.364   215199.134
Optimizing NNI: done in 0.403744 secs using 398.9% CPU
Optimizing NNI: done in 0.577162 secs using 399.3% CPU
Optimizing NNI: done in 0.401428 secs using 398.7% CPU
Optimizing NNI: done in 0.321113 secs using 398.5% CPU
Optimizing NNI: done in 0.331882 secs using 399.4% CPU
Optimizing NNI: done in 0.37144 secs using 399.6% CPU
Optimizing NNI: done in 2.49492 secs using 299% CPU
Optimizing NNI: done in 0.368085 secs using 398.9% CPU
Optimizing NNI: done in 0.341264 secs using 398.4% CPU
Optimizing NNI: done in 0.442402 secs using 398.3% CPU
Optimizing NNI: done in 0.294182 secs using 399.3% CPU
Iteration 90 / LogL: -35528.568 / Time: 0h:0m:38s (0h:0m:28s left)
Optimizing NNI: done in 0.430397 secs using 399.7% CPU
Optimizing NNI: done in 2.25643 secs using 299% CPU
Optimizing NNI: done in 0.453244 secs using 399% CPU
Optimizing NNI: done in 0.530097 secs using 398.5% CPU
Optimizing NNI: done in 0.390198 secs using 398.6% CPU
Optimizing NNI: done in 0.343799 secs using 398.7% CPU
Optimizing NNI: done in 0.373693 secs using 399.9% CPU
Optimizing NNI: done in 1.98904 secs using 298.6% CPU
Optimizing NNI: done in 0.415345 secs using 399.4% CPU
Optimizing NNI: done in 0.386931 secs using 399.3% CPU
Optimizing NNI: done in 0.433605 secs using 399.2% CPU
Optimizing NNI: done in 0.501071 secs using 399% CPU
Iteration 100 / LogL: -35529.137 / Time: 0h:0m:43s (0h:0m:23s left)
Optimizing NNI: done in 0.490531 secs using 399.1% CPU
Optimizing NNI: done in 2.1622 secs using 299.2% CPU
Optimizing NNI: done in 0.416675 secs using 399.4% CPU
Optimizing NNI: done in 0.326143 secs using 399.7% CPU
Optimizing NNI: done in 0.389222 secs using 399.4% CPU
Optimizing NNI: done in 0.424397 secs using 399.2% CPU
Optimizing NNI: done in 0.420542 secs using 399.2% CPU
Optimizing NNI: done in 0.401277 secs using 398.9% CPU
Optimizing NNI: done in 2.31489 secs using 299.1% CPU
Optimizing NNI: done in 0.352808 secs using 399.4% CPU
Optimizing NNI: done in 0.410143 secs using 399.1% CPU
Optimizing NNI: done in 0.512817 secs using 399.7% CPU
Iteration 110 / LogL: -35529.174 / Time: 0h:0m:47s (0h:0m:19s left)
Optimizing NNI: done in 0.314149 secs using 399.6% CPU
Optimizing NNI: done in 0.336051 secs using 399.8% CPU
Optimizing NNI: done in 0.343322 secs using 399.1% CPU
Optimizing NNI: done in 0.373294 secs using 398.8% CPU
Optimizing NNI: done in 2.61114 secs using 298.6% CPU
Optimizing NNI: done in 0.356624 secs using 399.4% CPU
Optimizing NNI: done in 0.580009 secs using 399.3% CPU
Optimizing NNI: done in 0.370158 secs using 399.6% CPU
Optimizing NNI: done in 0.368588 secs using 399.1% CPU
Optimizing NNI: done in 0.375424 secs using 399.3% CPU
Optimizing NNI: done in 0.348379 secs using 399% CPU
Iteration 120 / LogL: -35535.164 / Time: 0h:0m:51s (0h:0m:14s left)
Optimizing NNI: done in 2.3848 secs using 299.1% CPU
Optimizing NNI: done in 0.324386 secs using 399.6% CPU
Optimizing NNI: done in 0.297584 secs using 399.6% CPU
Optimizing NNI: done in 0.418131 secs using 398.7% CPU
Optimizing NNI: done in 0.383249 secs using 399.9% CPU
Optimizing NNI: done in 0.521113 secs using 399.5% CPU
Optimizing NNI: done in 0.532312 secs using 398.8% CPU
Optimizing NNI: done in 2.44857 secs using 299.2% CPU
Iteration 140 / LogL: -60116.347 / Time: 0h:5m:48s (0h:2m:15s left)
Optimizing NNI: done in 0.436073 secs using 399.2% CPU
Optimizing NNI: done in 0.32697 secs using 399.3% CPU
Optimizing NNI: done in 0.533628 secs using 399.4% CPU
Optimizing NNI: done in 0.355377 secs using 398.5% CPU
Iteration 130 / LogL: -35528.694 / Time: 0h:0m:55s (0h:0m:10s left)
Optimizing NNI: done in 0.437893 secs using 399.6% CPU
Optimizing NNI: done in 2.08553 secs using 299.2% CPU
Optimizing NNI: done in 0.335545 secs using 399.8% CPU
Optimizing NNI: done in 0.534032 secs using 399.3% CPU
Optimizing NNI: done in 0.563196 secs using 399.5% CPU
Optimizing NNI: done in 0.402323 secs using 399.2% CPU
Optimizing NNI: done in 1.94312 secs using 298.5% CPU
Optimizing NNI: done in 0.316478 secs using 399.6% CPU
Optimizing NNI: done in 0.422437 secs using 399.1% CPU
Optimizing NNI: done in 0.397108 secs using 398.6% CPU
Optimizing NNI: done in 0.399367 secs using 400% CPU
Optimizing NNI: done in 0.46781 secs using 399% CPU
Iteration 140 / LogL: -35528.659 / Time: 0h:0m:59s (0h:0m:6s left)
Optimizing NNI: done in 0.371481 secs using 398.9% CPU
Optimizing NNI: done in 2.36863 secs using 299.1% CPU
Optimizing NNI: done in 0.395002 secs using 398.9% CPU
Optimizing NNI: done in 0.345081 secs using 399.1% CPU
Optimizing NNI: done in 0.426588 secs using 399.2% CPU
Optimizing NNI: done in 0.430661 secs using 399.2% CPU
Optimizing NNI: done in 0.395207 secs using 399.1% CPU
Optimizing NNI: done in 1.93382 secs using 299% CPU
Optimizing NNI: done in 0.533065 secs using 398.9% CPU
Optimizing NNI: done in 0.486931 secs using 399.3% CPU
Optimizing NNI: done in 0.286963 secs using 399.7% CPU
Optimizing NNI: done in 0.412753 secs using 400.1% CPU
Iteration 150 / LogL: -35528.684 / Time: 0h:1m:3s (0h:0m:2s left)
Optimizing NNI: done in 0.292195 secs using 399.7% CPU
Optimizing NNI: done in 1.98903 secs using 299.1% CPU
Optimizing NNI: done in 0.379706 secs using 399.1% CPU
Optimizing NNI: done in 0.33922 secs using 399.6% CPU
Optimizing NNI: done in 0.426424 secs using 399.6% CPU
483  mtMAM+F+R9    202225.832   1022 406495.663   2497507.663  410945.830
Optimizing NNI: done in 0.500633 secs using 399% CPU
Optimizing NNI: done in 0.391706 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 156 ITERATIONS / Time: 0h:1m:5s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35528.486
Optimal log-likelihood: -35528.474
Proportion of invariable sites: 0.018
Gamma shape alpha: 2.369
Parameters optimization took 1 rounds (0.046 sec)
BEST SCORE FOUND : -35528.474
Total tree length: 19.463

Total number of iterations: 156
CPU time used for tree search: 257.256 sec (0h:4m:17s)
Wall-clock time used for tree search: 65.448 sec (0h:1m:5s)
Total CPU time used: 259.635 sec (0h:4m:19s)
Total wall-clock time used: 66.015 sec (0h:1m:6s)

===> START BOOTSTRAP REPLICATE NUMBER 72

Creating bootstrap alignment (seed: 956231)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36282.217
2. Current log-likelihood: -35480.989
3. Current log-likelihood: -35464.164
4. Current log-likelihood: -35463.679
Optimal log-likelihood: -35463.619
Proportion of invariable sites: 0.022
Gamma shape alpha: 2.324
Parameters optimization took 4 rounds (0.283 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.39406 secs using 298.8% CPU
Calculating distance matrix: done in 0.074877 secs using 398.6% CPU
Computing ML distances took 0.075023 sec (of wall-clock time) 0.298821 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000127077 secs using 423.4% CPU
Constructing RapidNJ tree: done in 0.00126195 secs using 346% CPU
Computing RapidNJ tree took 0.001440 sec (of wall-clock time) 0.007276 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35861.552
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.458 second
Optimizing NNI: done in 2.18755 secs using 299.2% CPU
Computing log-likelihood of 98 initial trees ... 1.689 seconds
Current best score: -35454.286

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.259686 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35421.396
Optimizing NNI: done in 0.23189 secs using 398.7% CPU
Optimizing NNI: done in 0.261677 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -35421.150
Optimizing NNI: done in 1.99675 secs using 298.9% CPU
Optimizing NNI: done in 0.217601 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35421.126
Optimizing NNI: done in 0.227372 secs using 398.7% CPU
Optimizing NNI: done in 0.266776 secs using 399.3% CPU
Optimizing NNI: done in 0.165429 secs using 398.5% CPU
Optimizing NNI: done in 0.228288 secs using 398.4% CPU
Optimizing NNI: done in 0.258616 secs using 398.4% CPU
Optimizing NNI: done in 0.280603 secs using 400.3% CPU
Iteration 10 / LogL: -35421.126 / Time: 0h:0m:6s
Optimizing NNI: done in 1.9186 secs using 299.3% CPU
Optimizing NNI: done in 0.23273 secs using 399.6% CPU
Optimizing NNI: done in 0.224772 secs using 398.8% CPU
Optimizing NNI: done in 0.360592 secs using 398.9% CPU
BETTER TREE FOUND at iteration 13: -35421.125
Optimizing NNI: done in 0.207794 secs using 399.4% CPU
Optimizing NNI: done in 0.321291 secs using 397.8% CPU
Optimizing NNI: done in 0.230194 secs using 398.4% CPU
Optimizing NNI: done in 0.21534 secs using 399.2% CPU
Optimizing NNI: done in 0.217296 secs using 398.4% CPU
Optimizing NNI: done in 0.225325 secs using 399.7% CPU
Optimizing NNI: done in 0.262599 secs using 399.7% CPU
Iteration 20 / LogL: -35421.129 / Time: 0h:0m:8s
Finish initializing candidate tree set (5)
Current best tree score: -35421.125 / CPU time: 8.304
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.37258 secs using 299.1% CPU
Iteration 150 / LogL: -60111.611 / Time: 0h:6m:10s (0h:1m:49s left)
Optimizing NNI: done in 0.421494 secs using 399.4% CPU
Optimizing NNI: done in 0.296346 secs using 399.6% CPU
Optimizing NNI: done in 0.361348 secs using 399.7% CPU
Optimizing NNI: done in 0.60787 secs using 399.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -35421.123
Optimizing NNI: done in 0.582624 secs using 398.9% CPU
Optimizing NNI: done in 2.24649 secs using 299% CPU
Optimizing NNI: done in 0.571476 secs using 398.5% CPU
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Optimizing NNI: done in 2.25966 secs using 298.9% CPU
Optimizing NNI: done in 0.629922 secs using 399.2% CPU
Iteration 30 / LogL: -35424.272 / Time: 0h:0m:13s (0h:0m:38s left)
Optimizing NNI: done in 0.457209 secs using 399.2% CPU
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Optimizing NNI: done in 2.23293 secs using 299% CPU
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Optimizing NNI: done in 2.18831 secs using 299.3% CPU
Optimizing NNI: done in 0.334736 secs using 399.6% CPU
Iteration 40 / LogL: -35426.314 / Time: 0h:0m:18s (0h:0m:33s left)
Optimizing NNI: done in 0.5744 secs using 399.3% CPU
Optimizing NNI: done in 0.452194 secs using 399.4% CPU
Optimizing NNI: done in 0.412761 secs using 399.7% CPU
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Optimizing NNI: done in 0.348069 secs using 398.5% CPU
Iteration 50 / LogL: -35421.349 / Time: 0h:0m:22s (0h:0m:29s left)
Optimizing NNI: done in 0.394788 secs using 399.2% CPU
Optimizing NNI: done in 0.356914 secs using 399.7% CPU
Optimizing NNI: done in 0.469056 secs using 399.4% CPU
Optimizing NNI: done in 2.2761 secs using 298.6% CPU
Optimizing NNI: done in 0.516442 secs using 399.6% CPU
Optimizing NNI: done in 0.414693 secs using 399.4% CPU
Optimizing NNI: done in 0.322731 secs using 399.1% CPU
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Optimizing NNI: done in 1.91452 secs using 298.9% CPU
Optimizing NNI: done in 0.539271 secs using 399.9% CPU
Optimizing NNI: done in 0.470934 secs using 398.5% CPU
Iteration 60 / LogL: -35425.514 / Time: 0h:0m:27s (0h:0m:24s left)
Optimizing NNI: done in 0.350113 secs using 399.1% CPU
Optimizing NNI: done in 0.464423 secs using 399.5% CPU
Optimizing NNI: done in 2.18598 secs using 299.1% CPU
Optimizing NNI: done in 0.540024 secs using 399.7% CPU
Optimizing NNI: done in 0.469025 secs using 399.4% CPU
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Optimizing NNI: done in 2.14743 secs using 299.3% CPU
Iteration 160 / LogL: -60122.620 / Time: 0h:6m:31s (0h:1m:23s left)
Optimizing NNI: done in 0.415233 secs using 399.1% CPU
Optimizing NNI: done in 0.391441 secs using 399.3% CPU
Optimizing NNI: done in 0.377844 secs using 399.1% CPU
Iteration 70 / LogL: -35424.754 / Time: 0h:0m:31s (0h:0m:19s left)
Optimizing NNI: done in 0.302524 secs using 399% CPU
Optimizing NNI: done in 0.246565 secs using 399.6% CPU
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Optimizing NNI: done in 2.24879 secs using 298.8% CPU
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Optimizing NNI: done in 0.265759 secs using 399.1% CPU
Optimizing NNI: done in 0.345296 secs using 399.1% CPU
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Optimizing NNI: done in 1.78269 secs using 299.1% CPU
Optimizing NNI: done in 0.38863 secs using 399.1% CPU
Optimizing NNI: done in 0.348059 secs using 399.8% CPU
Iteration 80 / LogL: -35422.625 / Time: 0h:0m:35s (0h:0m:14s left)
Optimizing NNI: done in 0.490142 secs using 399.3% CPU
Optimizing NNI: done in 0.42366 secs using 399.1% CPU
Optimizing NNI: done in 0.513825 secs using 398.9% CPU
Optimizing NNI: done in 2.28182 secs using 299.1% CPU
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Optimizing NNI: done in 0.411423 secs using 398.9% CPU
Optimizing NNI: done in 0.57223 secs using 398.9% CPU
Optimizing NNI: done in 0.303115 secs using 399.6% CPU
Optimizing NNI: done in 1.8623 secs using 299.1% CPU
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Optimizing NNI: done in 0.369311 secs using 398.9% CPU
Optimizing NNI: done in 0.339642 secs using 400.2% CPU
Iteration 90 / LogL: -35426.762 / Time: 0h:0m:39s (0h:0m:10s left)
Optimizing NNI: done in 0.339724 secs using 399.6% CPU
Optimizing NNI: done in 0.622816 secs using 399.3% CPU
Optimizing NNI: done in 1.98891 secs using 299.3% CPU
Optimizing NNI: done in 0.395108 secs using 399.6% CPU
Optimizing NNI: done in 0.396644 secs using 398.9% CPU
Optimizing NNI: done in 0.649297 secs using 399.1% CPU
Optimizing NNI: done in 1.80026 secs using 299.4% CPU
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Optimizing NNI: done in 0.391668 secs using 399% CPU
Optimizing NNI: done in 0.29128 secs using 399.6% CPU
Iteration 100 / LogL: -35429.284 / Time: 0h:0m:44s (0h:0m:5s left)
Optimizing NNI: done in 1.78421 secs using 298.7% CPU
Optimizing NNI: done in 0.523743 secs using 399.4% CPU
Optimizing NNI: done in 0.457376 secs using 399.2% CPU
Optimizing NNI: done in 0.363147 secs using 399.4% CPU
Optimizing NNI: done in 0.380776 secs using 398.9% CPU
Optimizing NNI: done in 0.48798 secs using 399.5% CPU
Optimizing NNI: done in 2.23066 secs using 299.1% CPU
Optimizing NNI: done in 0.362378 secs using 398.9% CPU
Optimizing NNI: done in 0.437316 secs using 399.2% CPU
Optimizing NNI: done in 0.357116 secs using 398.7% CPU
Optimizing NNI: done in 0.499578 secs using 399% CPU
Optimizing NNI: done in 0.294843 secs using 399% CPU
Iteration 110 / LogL: -35421.264 / Time: 0h:0m:48s (0h:0m:1s left)
Optimizing NNI: done in 0.481723 secs using 399.6% CPU
Optimizing NNI: done in 2.26284 secs using 299.2% CPU
Optimizing NNI: done in 0.569208 secs using 399.5% CPU
Optimizing NNI: done in 0.331616 secs using 399.7% CPU
Optimizing NNI: done in 0.627382 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 114 ITERATIONS / Time: 0h:0m:50s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35421.123
Optimal log-likelihood: -35421.122
Proportion of invariable sites: 0.022
Gamma shape alpha: 2.396
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -35421.122
Total tree length: 18.714

Total number of iterations: 114
CPU time used for tree search: 195.503 sec (0h:3m:15s)
Wall-clock time used for tree search: 49.916 sec (0h:0m:49s)
Total CPU time used: 197.858 sec (0h:3m:17s)
Total wall-clock time used: 50.476 sec (0h:0m:50s)

===> START BOOTSTRAP REPLICATE NUMBER 73

Creating bootstrap alignment (seed: 956232)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.018 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36487.515
2. Current log-likelihood: -35648.650
3. Current log-likelihood: -35636.724
4. Current log-likelihood: -35635.754
5. Current log-likelihood: -35635.594
Optimal log-likelihood: -35635.589
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.254
Parameters optimization took 5 rounds (0.323 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0782828 secs using 398.6% CPU
Computing ML distances took 0.078426 sec (of wall-clock time) 0.312428 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000138998 secs using 460.4% CPU
Constructing RapidNJ tree: done in 0.00127697 secs using 302% CPU
Computing RapidNJ tree took 0.001478 sec (of wall-clock time) 0.005475 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36373.210
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.46539 secs using 299% CPU
Iteration 170 / LogL: -60107.040 / Time: 0h:6m:52s (0h:0m:58s left)
1.562 second
Optimizing NNI: done in 2.01795 secs using 299.1% CPU
Computing log-likelihood of 98 initial trees ... 1.636 seconds
Current best score: -35635.589

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.234528 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35582.627
Optimizing NNI: done in 0.262415 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35582.434
Optimizing NNI: done in 0.231228 secs using 399.1% CPU
Optimizing NNI: done in 0.389682 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35582.419
Optimizing NNI: done in 2.3274 secs using 298.9% CPU
Optimizing NNI: done in 0.287745 secs using 399.4% CPU
Optimizing NNI: done in 0.399466 secs using 399.7% CPU
Optimizing NNI: done in 0.340341 secs using 398.7% CPU
Optimizing NNI: done in 0.471061 secs using 398.8% CPU
Optimizing NNI: done in 0.30584 secs using 400.5% CPU
Optimizing NNI: done in 0.411596 secs using 398.5% CPU
Iteration 10 / LogL: -35584.987 / Time: 0h:0m:7s
Optimizing NNI: done in 2.14139 secs using 299% CPU
Optimizing NNI: done in 0.288604 secs using 399.3% CPU
484  mtMAM+F+R10   202217.624   1024 406483.248   2505683.248  410942.123
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.378994 secs using 399.2% CPU
528  VT+F+I+R10    105877.337   573 212900.674   870704.674   215207.495
Optimizing NNI: done in 0.269526 secs using 399.5% CPU
Optimizing NNI: done in 0.247006 secs using 399.8% CPU
Optimizing NNI: done in 0.384769 secs using 399.1% CPU
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Optimizing NNI: done in 2.21906 secs using 299.1% CPU
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Optimizing NNI: done in 0.341892 secs using 399.6% CPU
Optimizing NNI: done in 0.314706 secs using 399.4% CPU
Iteration 20 / LogL: -35582.642 / Time: 0h:0m:10s
Finish initializing candidate tree set (9)
Current best tree score: -35582.419 / CPU time: 10.029
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.492529 secs using 399.3% CPU
Optimizing NNI: done in 0.28557 secs using 398.4% CPU
Optimizing NNI: done in 2.19182 secs using 299.5% CPU
Optimizing NNI: done in 0.557089 secs using 398.6% CPU
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Optimizing NNI: done in 0.616411 secs using 399.5% CPU
Optimizing NNI: done in 0.461117 secs using 399.2% CPU
Iteration 30 / LogL: -35582.884 / Time: 0h:0m:15s (0h:0m:37s left)
Optimizing NNI: done in 0.333866 secs using 398.9% CPU
Optimizing NNI: done in 0.297365 secs using 399.9% CPU
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Optimizing NNI: done in 0.498226 secs using 399.7% CPU
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Optimizing NNI: done in 2.147 secs using 299.5% CPU
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Optimizing NNI: done in 0.403654 secs using 399.4% CPU
Iteration 40 / LogL: -35582.713 / Time: 0h:0m:19s (0h:0m:30s left)
Optimizing NNI: done in 0.336837 secs using 398.7% CPU
Optimizing NNI: done in 1.96876 secs using 299.2% CPU
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Optimizing NNI: done in 0.38982 secs using 399.5% CPU
Optimizing NNI: done in 2.33958 secs using 299.3% CPU
Iteration 180 / LogL: -60123.670 / Time: 0h:7m:14s (0h:0m:33s left)
Optimizing NNI: done in 0.524768 secs using 399.9% CPU
Optimizing NNI: done in 0.411263 secs using 399.1% CPU
Optimizing NNI: done in 0.379603 secs using 399.4% CPU
Optimizing NNI: done in 0.518412 secs using 399.4% CPU
Iteration 50 / LogL: -35582.421 / Time: 0h:0m:23s (0h:0m:25s left)
Optimizing NNI: done in 0.528394 secs using 398.6% CPU
549  PMB+I+R9      106510.426   552 214124.851   824636.851   216347.129
Optimizing NNI: done in 2.19174 secs using 299.3% CPU
Optimizing NNI: done in 0.400741 secs using 399.5% CPU
Optimizing NNI: done in 0.543756 secs using 399.3% CPU
Optimizing NNI: done in 0.539398 secs using 399.3% CPU
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Optimizing NNI: done in 0.398499 secs using 399.6% CPU
Optimizing NNI: done in 2.33021 secs using 298.9% CPU
Optimizing NNI: done in 0.388034 secs using 399.6% CPU
Optimizing NNI: done in 0.580804 secs using 399.5% CPU
Optimizing NNI: done in 0.381205 secs using 398.9% CPU
Optimizing NNI: done in 0.326811 secs using 399.4% CPU
Iteration 60 / LogL: -35880.302 / Time: 0h:0m:28s (0h:0m:20s left)
Optimizing NNI: done in 0.435081 secs using 399.4% CPU
Optimizing NNI: done in 2.21958 secs using 299% CPU
Optimizing NNI: done in 0.508089 secs using 399.4% CPU
Optimizing NNI: done in 0.334373 secs using 397.9% CPU
Optimizing NNI: done in 0.293277 secs using 399.4% CPU
493  FLAVI+R8      202777.540   1001 407557.080   2413561.080  411915.804
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.408892 secs using 399.6% CPU
Optimizing NNI: done in 0.321762 secs using 399.8% CPU
Optimizing NNI: done in 0.298146 secs using 398.7% CPU
Optimizing NNI: done in 0.328012 secs using 400.2% CPU
Optimizing NNI: done in 2.51493 secs using 298.9% CPU
Optimizing NNI: done in 0.417057 secs using 398.8% CPU
Optimizing NNI: done in 0.342647 secs using 399.8% CPU
Iteration 70 / LogL: -35590.676 / Time: 0h:0m:32s (0h:0m:14s left)
Optimizing NNI: done in 0.299104 secs using 399.7% CPU
Optimizing NNI: done in 0.255471 secs using 398.1% CPU
Optimizing NNI: done in 0.443269 secs using 399.1% CPU
Optimizing NNI: done in 0.603612 secs using 399.6% CPU
Optimizing NNI: done in 2.16207 secs using 299.1% CPU
Optimizing NNI: done in 0.407539 secs using 398.6% CPU
Optimizing NNI: done in 0.50106 secs using 399.6% CPU
Optimizing NNI: done in 0.331121 secs using 398.1% CPU
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Optimizing NNI: done in 2.13602 secs using 299.1% CPU
Optimizing NNI: done in 0.482987 secs using 399.5% CPU
Iteration 80 / LogL: -35583.040 / Time: 0h:0m:36s (0h:0m:10s left)
Optimizing NNI: done in 0.539338 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -35582.419
Optimizing NNI: done in 0.344169 secs using 399.8% CPU
Optimizing NNI: done in 0.342245 secs using 399.6% CPU
Optimizing NNI: done in 0.450639 secs using 399.3% CPU
Optimizing NNI: done in 2.2006 secs using 299.2% CPU
Optimizing NNI: done in 0.421981 secs using 398.5% CPU
Optimizing NNI: done in 0.524154 secs using 399.6% CPU
Optimizing NNI: done in 0.391394 secs using 399.7% CPU
Optimizing NNI: done in 0.394203 secs using 399% CPU
Optimizing NNI: done in 0.478845 secs using 399.3% CPU
Optimizing NNI: done in 2.33308 secs using 299.2% CPU
Optimizing NNI: done in 0.560763 secs using 399.5% CPU
Iteration 90 / LogL: -35582.422 / Time: 0h:0m:40s (0h:0m:5s left)
Optimizing NNI: done in 0.523652 secs using 398.8% CPU
Optimizing NNI: done in 0.376223 secs using 399.4% CPU
Optimizing NNI: done in 0.507503 secs using 398.9% CPU
Optimizing NNI: done in 0.307453 secs using 399% CPU
Optimizing NNI: done in 1.90503 secs using 299.1% CPU
Optimizing NNI: done in 0.438461 secs using 399.9% CPU
Optimizing NNI: done in 0.318436 secs using 399.5% CPU
Optimizing NNI: done in 0.454995 secs using 399.4% CPU
Optimizing NNI: done in 0.372764 secs using 398.6% CPU
Optimizing NNI: done in 0.427298 secs using 399.7% CPU
Optimizing NNI: done in 1.95926 secs using 299.2% CPU
Iteration 190 / LogL: -60107.041 / Time: 0h:7m:36s (0h:0m:9s left)
Optimizing NNI: done in 0.532277 secs using 399.4% CPU
Iteration 100 / LogL: -35584.796 / Time: 0h:0m:45s (0h:0m:0s left)
Optimizing NNI: done in 0.581744 secs using 399.6% CPU
Optimizing NNI: done in 0.311842 secs using 398.9% CPU
Optimizing NNI: done in 0.509061 secs using 399.8% CPU
TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:46s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35582.419
Optimal log-likelihood: -35582.412
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.284
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35582.412
Total tree length: 18.860

Total number of iterations: 103
CPU time used for tree search: 178.989 sec (0h:2m:58s)
Wall-clock time used for tree search: 45.859 sec (0h:0m:45s)
Total CPU time used: 182.041 sec (0h:3m:2s)
Total wall-clock time used: 46.576 sec (0h:0m:46s)

===> START BOOTSTRAP REPLICATE NUMBER 74

Creating bootstrap alignment (seed: 956233)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37244.718
2. Current log-likelihood: -36374.271
3. Current log-likelihood: -36359.018
4. Current log-likelihood: -36358.797
Optimal log-likelihood: -36358.776
Proportion of invariable sites: 0.019
Gamma shape alpha: 2.504
Parameters optimization took 4 rounds (0.264 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0722549 secs using 398.5% CPU
Computing ML distances took 0.072385 sec (of wall-clock time) 0.288261 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000138998 secs using 468.4% CPU
Constructing RapidNJ tree: done in 0.00132203 secs using 389.1% CPU
Computing RapidNJ tree took 0.001511 sec (of wall-clock time) 0.006774 sec (of CPU time)
Optimizing NNI: done in 2.50913 secs using 299.2% CPU
Log-likelihood of RapidNJ tree: -37048.972
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.461 second
Optimizing NNI: done in 2.02286 secs using 299.1% CPU
494  FLAVI+R9      202768.495   1003 407542.991   2421566.991  411910.424
WARNING: Normalizing state frequencies so that sum of them equals to 1
Computing log-likelihood of 98 initial trees ... 1.577 seconds
Current best score: -36358.776

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.260863 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36311.492
Optimizing NNI: done in 0.320705 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36305.425
Optimizing NNI: done in 0.248614 secs using 399.6% CPU
Optimizing NNI: done in 2.12263 secs using 299.4% CPU
Optimizing NNI: done in 0.213256 secs using 399.7% CPU
Optimizing NNI: done in 0.234561 secs using 399.6% CPU
Optimizing NNI: done in 0.237822 secs using 399.3% CPU
Optimizing NNI: done in 0.278666 secs using 399.7% CPU
Optimizing NNI: done in 0.239016 secs using 399.8% CPU
Optimizing NNI: done in 0.231731 secs using 399.6% CPU
Optimizing NNI: done in 0.306787 secs using 398.6% CPU
Iteration 10 / LogL: -36313.361 / Time: 0h:0m:6s
Optimizing NNI: done in 0.291607 secs using 399.3% CPU
Optimizing NNI: done in 2.12202 secs using 299.3% CPU
Optimizing NNI: done in 0.262774 secs using 400.6% CPU
Optimizing NNI: done in 0.249285 secs using 399.8% CPU
Optimizing NNI: done in 0.27689 secs using 398.6% CPU
Optimizing NNI: done in 0.282481 secs using 399.7% CPU
Optimizing NNI: done in 0.257574 secs using 399.5% CPU
Optimizing NNI: done in 0.258818 secs using 398.8% CPU
Optimizing NNI: done in 0.275918 secs using 398.9% CPU
Optimizing NNI: done in 2.02712 secs using 299.2% CPU
TREE SEARCH COMPLETED AFTER 195 ITERATIONS / Time: 0h:7m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60107.039
Optimizing NNI: done in 0.389213 secs using 398.8% CPU
Optimal log-likelihood: -60107.038
Site proportion and rates:  (0.088,0.061) (0.128,0.203) (0.122,0.393) (0.227,0.642) (0.177,1.048) (0.118,1.632) (0.121,2.375) (0.019,5.737)
Parameters optimization took 1 rounds (0.238 sec)
BEST SCORE FOUND : -60107.038
Total tree length: 43.649

Total number of iterations: 195
CPU time used for tree search: 1352.379 sec (0h:22m:32s)
Wall-clock time used for tree search: 455.738 sec (0h:7m:35s)
Total CPU time used: 1387.142 sec (0h:23m:7s)
Total wall-clock time used: 467.358 sec (0h:7m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 3

Creating bootstrap alignment (seed: 956252)...

Optimizing NNI: done in 0.262648 secs using 400.2% CPU
Iteration 20 / LogL: -36325.388 / Time: 0h:0m:9s
Finish initializing candidate tree set (9)
Current best tree score: -36305.425 / CPU time: 8.618
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.052 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60198.193
Optimizing NNI: done in 0.391496 secs using 399.3% CPU
Optimizing NNI: done in 0.466201 secs using 399.2% CPU
2. Current log-likelihood: -59625.528
Optimizing NNI: done in 0.54583 secs using 399.5% CPU
Optimizing NNI: done in 0.405877 secs using 399.2% CPU
Optimizing NNI: done in 0.367874 secs using 399.4% CPU
3. Current log-likelihood: -59622.463
Optimizing NNI: done in 0.39145 secs using 399.8% CPU
Optimizing NNI: done in 0.467825 secs using 399.3% CPU
Optimal log-likelihood: -59622.402
Site proportion and rates:  (0.078,0.056) (0.120,0.179) (0.079,0.346) (0.165,0.506) (0.128,0.737) (0.153,0.965) (0.124,1.542) (0.153,2.818)
Parameters optimization took 3 rounds (3.244 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 0.46786 secs using 399.6% CPU
Optimizing NNI: done in 0.30776 secs using 399.7% CPU
Optimizing NNI: done in 0.432452 secs using 398.8% CPU
Iteration 30 / LogL: -36306.527 / Time: 0h:0m:13s (0h:0m:33s left)
Calculating distance matrix: done in 1.48629 secs using 299.6% CPU
Computing ML distances took 1.486494 sec (of wall-clock time) 4.453698 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000552177 secs using 313.8% CPU
Constructing RapidNJ tree: done in 0.00381303 secs using 378.7% CPU
Computing RapidNJ tree took 0.004440 sec (of wall-clock time) 0.017358 sec (of CPU time)
Optimizing NNI: done in 0.510752 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -36305.424
Optimizing NNI: done in 0.540618 secs using 399.4% CPU
Optimizing NNI: done in 0.311575 secs using 399.8% CPU
UPDATE BEST LOG-LIKELIHOOD: -36305.418
Log-likelihood of RapidNJ tree: -59636.308
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 0.395415 secs using 399.6% CPU
Optimizing NNI: done in 0.453455 secs using 399.1% CPU
Optimizing NNI: done in 0.470784 secs using 399.7% CPU
Optimizing NNI: done in 0.603177 secs using 399.4% CPU
Optimizing NNI: done in 0.370207 secs using 398.8% CPU
Optimizing NNI: done in 0.331499 secs using 399.3% CPU
Optimizing NNI: done in 0.422264 secs using 399% CPU
Iteration 40 / LogL: -36310.918 / Time: 0h:0m:17s (0h:0m:28s left)
Optimizing NNI: done in 0.447843 secs using 399.3% CPU
Optimizing NNI: done in 0.413574 secs using 399.3% CPU
Optimizing NNI: done in 0.345365 secs using 398.4% CPU
Optimizing NNI: done in 0.375885 secs using 398.8% CPU
Optimizing NNI: done in 0.479184 secs using 399% CPU
5.065 second
Optimizing NNI: done in 0.422761 secs using 399.8% CPU
UPDATE BEST LOG-LIKELIHOOD: -36305.417
Optimizing NNI: done in 0.487249 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 47: -36305.287
Optimizing NNI: done in 0.402575 secs using 399.1% CPU
Optimizing NNI: done in 0.34456 secs using 398.5% CPU
Optimizing NNI: done in 0.432195 secs using 398.9% CPU
Iteration 50 / LogL: -36306.568 / Time: 0h:0m:22s (0h:0m:43s left)
Optimizing NNI: done in 0.338496 secs using 399.5% CPU
Optimizing NNI: done in 0.292659 secs using 399.8% CPU
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Optimizing NNI: done in 0.325544 secs using 399.8% CPU
Optimizing NNI: done in 0.493263 secs using 399.9% CPU
Iteration 60 / LogL: -36310.082 / Time: 0h:0m:26s (0h:0m:38s left)
Optimizing NNI: done in 0.462287 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36305.145
Optimizing NNI: done in 0.439072 secs using 399.9% CPU
Computing log-likelihood of 98 initial trees ... 7.135 seconds
Current best score: -59615.947

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.398513 secs using 399.4% CPU
Optimizing NNI: done in 0.480467 secs using 399.5% CPU
Optimizing NNI: done in 0.385557 secs using 399.7% CPU
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Optimizing NNI: done in 0.378241 secs using 399.6% CPU
Optimizing NNI: done in 2.67474 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.448244 secs using 399.5% CPU
Optimizing NNI: done in 0.368899 secs using 398.9% CPU
Iteration 70 / LogL: -36306.478 / Time: 0h:0m:30s (0h:0m:33s left)
Optimizing NNI: done in 0.473384 secs using 399.2% CPU
Optimizing NNI: done in 0.495526 secs using 399.4% CPU
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Optimizing NNI: done in 0.326014 secs using 399.2% CPU
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Optimizing NNI: done in 0.296183 secs using 399% CPU
Optimizing NNI: done in 0.534081 secs using 399.3% CPU
Optimizing NNI: done in 0.411004 secs using 398.2% CPU
Optimizing NNI: done in 0.593525 secs using 399.7% CPU
Iteration 80 / LogL: -36305.769 / Time: 0h:0m:34s (0h:0m:29s left)
Optimizing NNI: done in 0.281119 secs using 399.8% CPU
Optimizing NNI: done in 0.500967 secs using 399% CPU
Optimizing NNI: done in 0.4712 secs using 399.5% CPU
BETTER TREE FOUND at iteration 1: -59413.772
Optimizing NNI: done in 0.489166 secs using 399.4% CPU
Optimizing NNI: done in 0.372313 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36305.083
Optimizing NNI: done in 0.523096 secs using 399.3% CPU
Optimizing NNI: done in 1.2323 secs using 299.5% CPU
Optimizing NNI: done in 0.408919 secs using 399.5% CPU
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Optimizing NNI: done in 0.425278 secs using 398.8% CPU
Optimizing NNI: done in 0.499739 secs using 399.6% CPU
Iteration 90 / LogL: -36306.491 / Time: 0h:0m:39s (0h:0m:25s left)
Optimizing NNI: done in 1.70877 secs using 299.4% CPU
Optimizing NNI: done in 0.376032 secs using 399.5% CPU
Optimizing NNI: done in 0.523017 secs using 398.9% CPU
Optimizing NNI: done in 0.432357 secs using 400.3% CPU
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Optimizing NNI: done in 1.69658 secs using 299.3% CPU
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Optimizing NNI: done in 0.401241 secs using 399.6% CPU
Optimizing NNI: done in 1.55926 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.484204 secs using 399.1% CPU
Optimizing NNI: done in 0.324021 secs using 399.9% CPU
Iteration 100 / LogL: -36309.304 / Time: 0h:0m:43s (0h:0m:20s left)
Optimizing NNI: done in 0.403514 secs using 399.3% CPU
Optimizing NNI: done in 0.443012 secs using 399.3% CPU
Optimizing NNI: done in 0.43985 secs using 399.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -36305.077
BETTER TREE FOUND at iteration 5: -59403.080
Optimizing NNI: done in 0.402261 secs using 399.3% CPU
Optimizing NNI: done in 0.462766 secs using 399.1% CPU
Optimizing NNI: done in 0.49095 secs using 398.7% CPU
Optimizing NNI: done in 1.69431 secs using 298.9% CPU
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Optimizing NNI: done in 0.399419 secs using 399.4% CPU
Iteration 110 / LogL: -36306.426 / Time: 0h:0m:47s (0h:0m:16s left)
Optimizing NNI: done in 0.392475 secs using 398.4% CPU
Optimizing NNI: done in 1.75543 secs using 298.9% CPU
Optimizing NNI: done in 0.331328 secs using 399.6% CPU
Optimizing NNI: done in 0.481794 secs using 399.3% CPU
Optimizing NNI: done in 0.352044 secs using 399.1% CPU
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Optimizing NNI: done in 1.64556 secs using 299.4% CPU
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Optimizing NNI: done in 0.508553 secs using 400% CPU
Iteration 120 / LogL: -36305.785 / Time: 0h:0m:51s (0h:0m:11s left)
Optimizing NNI: done in 2.12648 secs using 299.4% CPU
Optimizing NNI: done in 0.485047 secs using 399.7% CPU
Optimizing NNI: done in 0.397993 secs using 397.6% CPU
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Optimizing NNI: done in 0.240205 secs using 397.6% CPU
Optimizing NNI: done in 1.64363 secs using 299% CPU
Iteration 10 / LogL: -59449.850 / Time: 0h:0m:44s
Optimizing NNI: done in 0.459123 secs using 400.1% CPU
Optimizing NNI: done in 0.450493 secs using 398.3% CPU
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Optimizing NNI: done in 0.451053 secs using 398.3% CPU
Optimizing NNI: done in 1.9851 secs using 299% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.406978 secs using 399.5% CPU
Iteration 130 / LogL: -36306.142 / Time: 0h:0m:55s (0h:0m:7s left)
Optimizing NNI: done in 0.365902 secs using 398.9% CPU
Optimizing NNI: done in 0.385743 secs using 399.1% CPU
Optimizing NNI: done in 0.451387 secs using 399.4% CPU
BETTER TREE FOUND at iteration 11: -59393.484
Optimizing NNI: done in 0.532121 secs using 399.3% CPU
Optimizing NNI: done in 0.449381 secs using 398.9% CPU
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Optimizing NNI: done in 1.65486 secs using 299.1% CPU
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Optimizing NNI: done in 0.335754 secs using 398.9% CPU
Optimizing NNI: done in 0.3369 secs using 398.7% CPU
Iteration 140 / LogL: -36305.154 / Time: 0h:1m:0s (0h:0m:3s left)
Optimizing NNI: done in 0.575108 secs using 399.7% CPU
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Optimizing NNI: done in 1.85007 secs using 299.4% CPU
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Optimizing NNI: done in 0.307168 secs using 398.4% CPU
Optimizing NNI: done in 0.534098 secs using 398% CPU
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Optimizing NNI: done in 1.59392 secs using 299.3% CPU
Optimizing NNI: done in 0.577817 secs using 399.2% CPU
550  PMB+I+R10     106510.250   554 214128.500   829068.500   216358.829
Optimizing NNI: done in 0.51293 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 148 ITERATIONS / Time: 0h:1m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36305.077
Optimal log-likelihood: -36305.076
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.565
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -36305.076
Total tree length: 19.665

Total number of iterations: 148
CPU time used for tree search: 248.513 sec (0h:4m:8s)
Wall-clock time used for tree search: 63.199 sec (0h:1m:3s)
Total CPU time used: 251.145 sec (0h:4m:11s)
Total wall-clock time used: 63.810 sec (0h:1m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 75

Creating bootstrap alignment (seed: 956234)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36233.362
2. Current log-likelihood: -35484.449
3. Current log-likelihood: -35467.232
4. Current log-likelihood: -35466.795
Optimal log-likelihood: -35466.755
Proportion of invariable sites: 0.014
Gamma shape alpha: 2.221
Parameters optimization took 4 rounds (0.257 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0779169 secs using 399.8% CPU
Computing ML distances took 0.078052 sec (of wall-clock time) 0.311832 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000152826 secs using 348.1% CPU
Constructing RapidNJ tree: done in 0.00120807 secs using 154.1% CPU
Computing RapidNJ tree took 0.001416 sec (of wall-clock time) 0.003302 sec (of CPU time)
Optimizing NNI: done in 1.63117 secs using 299.3% CPU
Log-likelihood of RapidNJ tree: -36010.157
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.44602 secs using 299.5% CPU
1.499 second
Computing log-likelihood of 98 initial trees ... 1.524 seconds
Current best score: -35335.195

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.205896 secs using 397.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.91304 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35290.679
Optimizing NNI: done in 0.254234 secs using 399.2% CPU
Optimizing NNI: done in 0.252201 secs using 397.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -35287.974
Optimizing NNI: done in 0.255662 secs using 399.3% CPU
Optimizing NNI: done in 0.251192 secs using 398.9% CPU
Optimizing NNI: done in 0.245296 secs using 400.1% CPU
Optimizing NNI: done in 0.238884 secs using 398.6% CPU
Optimizing NNI: done in 0.240561 secs using 399% CPU
BETTER TREE FOUND at iteration 17: -59389.159
Optimizing NNI: done in 0.216489 secs using 398.4% CPU
Optimizing NNI: done in 0.222331 secs using 399.3% CPU
Iteration 10 / LogL: -35290.828 / Time: 0h:0m:6s
Optimizing NNI: done in 0.22384 secs using 398.9% CPU
Optimizing NNI: done in 0.270772 secs using 399.3% CPU
Optimizing NNI: done in 0.299544 secs using 399% CPU
Optimizing NNI: done in 0.295348 secs using 398.2% CPU
571  PMB+F+I+R9    106865.141   571 214872.283   868096.283   217171.052
Optimizing NNI: done in 0.260234 secs using 399.4% CPU
Optimizing NNI: done in 1.77054 secs using 299.2% CPU
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Optimizing NNI: done in 0.230573 secs using 399.6% CPU
Optimizing NNI: done in 0.236025 secs using 398.4% CPU
Iteration 20 / LogL: -35290.754 / Time: 0h:0m:8s
Finish initializing candidate tree set (4)
Current best tree score: -35287.974 / CPU time: 8.155
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.355342 secs using 398.9% CPU
Optimizing NNI: done in 0.279799 secs using 396.8% CPU
Optimizing NNI: done in 1.87348 secs using 299.1% CPU
Optimizing NNI: done in 0.381608 secs using 398.6% CPU
Optimizing NNI: done in 0.282292 secs using 398.7% CPU
Optimizing NNI: done in 0.458166 secs using 399% CPU
Optimizing NNI: done in 1.29291 secs using 299.6% CPU
Iteration 20 / LogL: -59455.296 / Time: 0h:1m:5s
Finish initializing candidate tree set (20)
Current best tree score: -59389.159 / CPU time: 59.796
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.393328 secs using 398.7% CPU
Optimizing NNI: done in 0.318225 secs using 398.7% CPU
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Optimizing NNI: done in 1.7868 secs using 299% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.362272 secs using 399.1% CPU
Iteration 30 / LogL: -35291.453 / Time: 0h:0m:12s (0h:0m:32s left)
Optimizing NNI: done in 0.389707 secs using 399.1% CPU
Optimizing NNI: done in 0.395031 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35287.890
Optimizing NNI: done in 0.321491 secs using 396.4% CPU
Optimizing NNI: done in 0.248295 secs using 398.8% CPU
Optimizing NNI: done in 0.335158 secs using 398.2% CPU
BETTER TREE FOUND at iteration 21: -59383.846
Optimizing NNI: done in 0.396071 secs using 398.3% CPU
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Optimizing NNI: done in 0.344236 secs using 398.6% CPU
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Optimizing NNI: done in 0.335866 secs using 397.9% CPU
Iteration 40 / LogL: -35290.752 / Time: 0h:0m:16s (0h:0m:26s left)
Optimizing NNI: done in 0.38858 secs using 399.2% CPU
Optimizing NNI: done in 2.04118 secs using 299.3% CPU
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Optimizing NNI: done in 0.409164 secs using 399.4% CPU
Optimizing NNI: done in 0.327724 secs using 398.7% CPU
Optimizing NNI: done in 2.42075 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.401962 secs using 399.9% CPU
Optimizing NNI: done in 0.47892 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -35287.888
Iteration 50 / LogL: -35287.888 / Time: 0h:0m:20s (0h:0m:21s left)
Optimizing NNI: done in 0.313719 secs using 399.2% CPU
Optimizing NNI: done in 0.320539 secs using 399% CPU
Optimizing NNI: done in 0.595703 secs using 400.2% CPU
Optimizing NNI: done in 0.34145 secs using 398.9% CPU
Optimizing NNI: done in 0.419432 secs using 399.6% CPU
BETTER TREE FOUND at iteration 23: -59365.072
Optimizing NNI: done in 0.316903 secs using 398.9% CPU
Optimizing NNI: done in 0.342433 secs using 399.3% CPU
Optimizing NNI: done in 0.307055 secs using 398.5% CPU
Optimizing NNI: done in 0.368853 secs using 400% CPU
Optimizing NNI: done in 1.42164 secs using 299.5% CPU
Optimizing NNI: done in 0.299647 secs using 399.5% CPU
Iteration 60 / LogL: -35288.443 / Time: 0h:0m:23s (0h:0m:17s left)
Optimizing NNI: done in 0.385852 secs using 399.9% CPU
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Optimizing NNI: done in 0.399281 secs using 399.8% CPU
Optimizing NNI: done in 0.322913 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35287.653
Optimizing NNI: done in 2.17263 secs using 299.2% CPU
Optimizing NNI: done in 0.423354 secs using 399.5% CPU
Optimizing NNI: done in 0.368079 secs using 399.6% CPU
Optimizing NNI: done in 0.378073 secs using 399.3% CPU
Optimizing NNI: done in 0.307425 secs using 399.9% CPU
Optimizing NNI: done in 0.265806 secs using 398.6% CPU
Iteration 70 / LogL: -35290.618 / Time: 0h:0m:27s (0h:0m:13s left)
Optimizing NNI: done in 0.392934 secs using 400.2% CPU
Optimizing NNI: done in 1.99594 secs using 299.2% CPU
Optimizing NNI: done in 0.360986 secs using 399.9% CPU
Optimizing NNI: done in 0.464781 secs using 399.2% CPU
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Optimizing NNI: done in 0.377944 secs using 398.8% CPU
Iteration 80 / LogL: -35288.000 / Time: 0h:0m:31s (0h:0m:9s left)
Optimizing NNI: done in 0.324622 secs using 399.2% CPU
Optimizing NNI: done in 2.07522 secs using 299.6% CPU
Optimizing NNI: done in 0.396908 secs using 399.4% CPU
Optimizing NNI: done in 0.29087 secs using 399.3% CPU
495  FLAVI+R10     202753.049   1005 407516.099   2429576.099  411892.240
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.405256 secs using 399.6% CPU
Optimizing NNI: done in 0.274844 secs using 399.9% CPU
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Optimizing NNI: done in 1.73406 secs using 299.2% CPU
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Optimizing NNI: done in 0.462943 secs using 400% CPU
Optimizing NNI: done in 0.355899 secs using 398.6% CPU
Iteration 90 / LogL: -35290.590 / Time: 0h:0m:34s (0h:0m:5s left)
Optimizing NNI: done in 0.297671 secs using 399.5% CPU
Optimizing NNI: done in 1.91048 secs using 299.4% CPU
Iteration 30 / LogL: -59369.503 / Time: 0h:1m:29s (0h:4m:48s left)
Optimizing NNI: done in 0.334934 secs using 399.6% CPU
Optimizing NNI: done in 0.286675 secs using 399.6% CPU
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Optimizing NNI: done in 0.475304 secs using 399.9% CPU
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Optimizing NNI: done in 0.40259 secs using 399.9% CPU
Optimizing NNI: done in 0.304483 secs using 399.7% CPU
Iteration 100 / LogL: -35292.195 / Time: 0h:0m:38s (0h:0m:1s left)
Optimizing NNI: done in 0.392877 secs using 399% CPU
Optimizing NNI: done in 1.7834 secs using 299.7% CPU
Optimizing NNI: done in 0.334528 secs using 399% CPU
Optimizing NNI: done in 0.340347 secs using 399.9% CPU
Optimizing NNI: done in 0.322458 secs using 399.9% CPU
TREE SEARCH COMPLETED AFTER 104 ITERATIONS / Time: 0h:0m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35287.653
Optimal log-likelihood: -35287.645
Proportion of invariable sites: 0.011
Gamma shape alpha: 2.211
Parameters optimization took 1 rounds (0.042 sec)
BEST SCORE FOUND : -35287.645
Total tree length: 20.360

Total number of iterations: 104
CPU time used for tree search: 152.436 sec (0h:2m:32s)
Wall-clock time used for tree search: 39.177 sec (0h:0m:39s)
Total CPU time used: 155.614 sec (0h:2m:35s)
Total wall-clock time used: 39.927 sec (0h:0m:39s)

===> START BOOTSTRAP REPLICATE NUMBER 76

Creating bootstrap alignment (seed: 956235)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -35184.960
2. Current log-likelihood: -34355.746
3. Current log-likelihood: -34343.249
4. Current log-likelihood: -34342.968
Optimal log-likelihood: -34342.942
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.214
Parameters optimization took 4 rounds (0.259 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.073185 secs using 400% CPU
Computing ML distances took 0.073342 sec (of wall-clock time) 0.293157 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000133991 secs using 432.1% CPU
Constructing RapidNJ tree: done in 0.00118399 secs using 387.5% CPU
Computing RapidNJ tree took 0.001380 sec (of wall-clock time) 0.007046 sec (of CPU time)
Log-likelihood of RapidNJ tree: -34616.772
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.95852 secs using 299.7% CPU
1.482 second
Optimizing NNI: done in 1.94122 secs using 299.6% CPU
Computing log-likelihood of 98 initial trees ... 1.551 seconds
Current best score: -34340.317

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.311192 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -34284.652
Optimizing NNI: done in 0.306165 secs using 399.2% CPU
Optimizing NNI: done in 0.321019 secs using 399.6% CPU
Optimizing NNI: done in 0.304651 secs using 399.3% CPU
Optimizing NNI: done in 2.01065 secs using 298.9% CPU
Optimizing NNI: done in 0.319764 secs using 399.2% CPU
Optimizing NNI: done in 0.311146 secs using 400.6% CPU
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Optimizing NNI: done in 0.325784 secs using 399.3% CPU
Optimizing NNI: done in 0.366684 secs using 399.9% CPU
Iteration 10 / LogL: -34290.363 / Time: 0h:0m:6s
Optimizing NNI: done in 0.204619 secs using 398.9% CPU
Optimizing NNI: done in 1.99529 secs using 299% CPU
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Optimizing NNI: done in 0.311597 secs using 397.9% CPU
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Optimizing NNI: done in 0.292308 secs using 399.9% CPU
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Optimizing NNI: done in 1.86239 secs using 299.3% CPU
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Optimizing NNI: done in 0.257164 secs using 399.9% CPU
Optimizing NNI: done in 0.299098 secs using 399.2% CPU
Iteration 20 / LogL: -34284.671 / Time: 0h:0m:9s
Finish initializing candidate tree set (8)
Current best tree score: -34284.652 / CPU time: 9.288
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.44306 secs using 400.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -34282.491
Optimizing NNI: done in 0.369039 secs using 399.6% CPU
Optimizing NNI: done in 0.420896 secs using 399.2% CPU
Optimizing NNI: done in 2.05923 secs using 299.3% CPU
Optimizing NNI: done in 0.437291 secs using 399.6% CPU
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Optimizing NNI: done in 0.343307 secs using 399.4% CPU
Iteration 30 / LogL: -34282.655 / Time: 0h:0m:14s (0h:0m:44s left)
Optimizing NNI: done in 0.381397 secs using 400.2% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -34282.470
Optimizing NNI: done in 1.81319 secs using 299.3% CPU
Iteration 40 / LogL: -59370.201 / Time: 0h:1m:49s (0h:3m:52s left)
Optimizing NNI: done in 0.527221 secs using 399.3% CPU
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Optimizing NNI: done in 0.447676 secs using 399.9% CPU
Iteration 40 / LogL: -34734.839 / Time: 0h:0m:18s (0h:0m:38s left)
Optimizing NNI: done in 1.68234 secs using 299.4% CPU
504  FLAVI+F+R8    202442.661   1020 406925.322   2489765.322  411366.780
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.521779 secs using 399.8% CPU
Optimizing NNI: done in 0.423683 secs using 399.8% CPU
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Optimizing NNI: done in 2.02362 secs using 299% CPU
Optimizing NNI: done in 0.50148 secs using 399.1% CPU
Iteration 50 / LogL: -34282.477 / Time: 0h:0m:22s (0h:0m:33s left)
Optimizing NNI: done in 0.486915 secs using 399.8% CPU
Optimizing NNI: done in 0.50823 secs using 399.5% CPU
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Optimizing NNI: done in 2.05926 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.363899 secs using 398.6% CPU
Optimizing NNI: done in 0.592843 secs using 398.9% CPU
Optimizing NNI: done in 0.428862 secs using 399.9% CPU
Optimizing NNI: done in 0.506891 secs using 399.6% CPU
Optimizing NNI: done in 0.363348 secs using 399.6% CPU
BETTER TREE FOUND at iteration 45: -59364.487
Optimizing NNI: done in 0.517069 secs using 399.5% CPU
Optimizing NNI: done in 0.396384 secs using 399.3% CPU
Iteration 60 / LogL: -34282.495 / Time: 0h:0m:27s (0h:0m:28s left)
Optimizing NNI: done in 0.452896 secs using 399.8% CPU
Optimizing NNI: done in 0.469475 secs using 399.4% CPU
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Optimizing NNI: done in 0.388938 secs using 399.6% CPU
Optimizing NNI: done in 0.371849 secs using 399.3% CPU
Iteration 70 / LogL: -34282.534 / Time: 0h:0m:31s (0h:0m:23s left)
Optimizing NNI: done in 0.42135 secs using 399% CPU
Optimizing NNI: done in 0.535781 secs using 399.5% CPU
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Optimizing NNI: done in 1.99977 secs using 299.3% CPU
Optimizing NNI: done in 0.4773 secs using 399.4% CPU
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Optimizing NNI: done in 0.426659 secs using 398.8% CPU
Optimizing NNI: done in 0.450214 secs using 399.6% CPU
Iteration 80 / LogL: -34284.682 / Time: 0h:0m:36s (0h:0m:18s left)
Optimizing NNI: done in 0.396021 secs using 399.9% CPU
Optimizing NNI: done in 1.88924 secs using 299.4% CPU
Iteration 50 / LogL: -59366.969 / Time: 0h:2m:11s (0h:4m:15s left)
Optimizing NNI: done in 0.42628 secs using 399.7% CPU
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Optimizing NNI: done in 0.435316 secs using 399.4% CPU
Optimizing NNI: done in 0.568746 secs using 399.6% CPU
Iteration 90 / LogL: -34282.634 / Time: 0h:0m:41s (0h:0m:14s left)
Optimizing NNI: done in 2.09824 secs using 299.2% CPU
Optimizing NNI: done in 0.407911 secs using 399.1% CPU
Optimizing NNI: done in 0.427433 secs using 399.7% CPU
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Optimizing NNI: done in 1.62772 secs using 299.4% CPU
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Optimizing NNI: done in 0.485327 secs using 399.5% CPU
Optimizing NNI: done in 2.03196 secs using 299.2% CPU
BETTER TREE FOUND at iteration 54: -59364.483
Optimizing NNI: done in 0.510214 secs using 399.5% CPU
Optimizing NNI: done in 0.503139 secs using 399.1% CPU
505  FLAVI+F+R9    202434.692   1022 406913.384   2497925.384  411363.551
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 0.302776 secs using 399.8% CPU
Iteration 100 / LogL: -34282.481 / Time: 0h:0m:46s (0h:0m:9s left)
Optimizing NNI: done in 0.484877 secs using 398.7% CPU
Optimizing NNI: done in 1.73121 secs using 299.5% CPU
Optimizing NNI: done in 0.493716 secs using 399.9% CPU
Optimizing NNI: done in 0.335228 secs using 399.8% CPU
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Optimizing NNI: done in 1.57465 secs using 299.1% CPU
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Optimizing NNI: done in 0.528057 secs using 399% CPU
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Optimizing NNI: done in 1.74966 secs using 299.4% CPU
Optimizing NNI: done in 0.568613 secs using 399.5% CPU
Optimizing NNI: done in 0.601239 secs using 399.6% CPU
Iteration 110 / LogL: -34288.272 / Time: 0h:0m:51s (0h:0m:5s left)
Optimizing NNI: done in 0.419841 secs using 399.9% CPU
Optimizing NNI: done in 1.77256 secs using 299% CPU
Optimizing NNI: done in 0.491686 secs using 399.9% CPU
Optimizing NNI: done in 0.45524 secs using 399.7% CPU
Optimizing NNI: done in 0.425068 secs using 399.9% CPU
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Optimizing NNI: done in 1.57758 secs using 299.3% CPU
Optimizing NNI: done in 0.441612 secs using 399.4% CPU
Optimizing NNI: done in 0.417307 secs using 399.9% CPU
Optimizing NNI: done in 0.515547 secs using 399.7% CPU
Optimizing NNI: done in 0.536234 secs using 399.7% CPU
Optimizing NNI: done in 1.91239 secs using 299.6% CPU
Iteration 60 / LogL: -59376.316 / Time: 0h:2m:30s (0h:3m:59s left)
Optimizing NNI: done in 0.349033 secs using 399.6% CPU
Iteration 120 / LogL: -34282.476 / Time: 0h:0m:55s (0h:0m:0s left)
Optimizing NNI: done in 0.540471 secs using 399.3% CPU
Optimizing NNI: done in 0.508483 secs using 400% CPU
TREE SEARCH COMPLETED AFTER 122 ITERATIONS / Time: 0h:0m:56s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -34282.470
Optimal log-likelihood: -34282.470
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.288
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -34282.470
Total tree length: 18.725

Total number of iterations: 122
CPU time used for tree search: 221.366 sec (0h:3m:41s)
Wall-clock time used for tree search: 56.362 sec (0h:0m:56s)
Total CPU time used: 223.482 sec (0h:3m:43s)
Total wall-clock time used: 56.867 sec (0h:0m:56s)

===> START BOOTSTRAP REPLICATE NUMBER 77

Creating bootstrap alignment (seed: 956236)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36272.794
2. Current log-likelihood: -35392.237
3. Current log-likelihood: -35380.466
4. Current log-likelihood: -35380.205
Optimal log-likelihood: -35380.117
Proportion of invariable sites: 0.019
Gamma shape alpha: 2.296
Parameters optimization took 4 rounds (0.262 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0757799 secs using 400% CPU
Computing ML distances took 0.075919 sec (of wall-clock time) 0.303442 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000137091 secs using 461.7% CPU
Constructing RapidNJ tree: done in 0.00129485 secs using 485.8% CPU
Computing RapidNJ tree took 0.001480 sec (of wall-clock time) 0.007519 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35865.174
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.94523 secs using 299.4% CPU
1.520 second
Optimizing NNI: done in 1.61337 secs using 299.4% CPU
Computing log-likelihood of 98 initial trees ... 1.569 seconds
Current best score: -35379.658

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.346842 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35332.859
Optimizing NNI: done in 0.335143 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35329.910
Optimizing NNI: done in 1.98114 secs using 299.6% CPU
Optimizing NNI: done in 0.336435 secs using 399.3% CPU
Optimizing NNI: done in 0.282494 secs using 399.8% CPU
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Optimizing NNI: done in 0.332414 secs using 399.6% CPU
Optimizing NNI: done in 0.327413 secs using 399.6% CPU
Iteration 10 / LogL: -35332.620 / Time: 0h:0m:6s
Optimizing NNI: done in 0.347881 secs using 399.9% CPU
Optimizing NNI: done in 0.235573 secs using 399.1% CPU
Optimizing NNI: done in 0.318509 secs using 399.9% CPU
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Optimizing NNI: done in 2.1367 secs using 299.4% CPU
Optimizing NNI: done in 0.32547 secs using 398.4% CPU
Optimizing NNI: done in 0.328565 secs using 400.2% CPU
Optimizing NNI: done in 0.219181 secs using 399.5% CPU
Optimizing NNI: done in 0.244653 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 18: -35325.486
Optimizing NNI: done in 0.232986 secs using 399.9% CPU
Optimizing NNI: done in 0.340565 secs using 399.3% CPU
Iteration 20 / LogL: -35332.611 / Time: 0h:0m:9s
Finish initializing candidate tree set (8)
Current best tree score: -35325.486 / CPU time: 9.315
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -35320.522
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BETTER TREE FOUND at iteration 39: -35320.342
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BETTER TREE FOUND at iteration 47: -35319.334
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506  FLAVI+F+R10   202428.582   1024 406905.164   2506105.164  411364.039
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Iteration 80 / LogL: -35323.224 / Time: 0h:0m:34s (0h:0m:29s left)
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Iteration 90 / LogL: -35319.384 / Time: 0h:0m:38s (0h:0m:24s left)
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Iteration 110 / LogL: -35322.040 / Time: 0h:0m:46s (0h:0m:15s left)
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UPDATE BEST LOG-LIKELIHOOD: -35319.330
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Iteration 120 / LogL: -35319.412 / Time: 0h:0m:50s (0h:0m:11s left)
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WARNING: Log-likelihood -106867 of PMB+F+I+R10 worse than PMB+F+I+R9 -106865
572  PMB+F+I+R10   106867.386   573 214880.773   872684.773   217187.594
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Iteration 130 / LogL: -35422.243 / Time: 0h:0m:54s (0h:0m:7s left)
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Iteration 140 / LogL: -35319.617 / Time: 0h:0m:59s (0h:0m:2s left)
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Iteration 90 / LogL: -59385.775 / Time: 0h:3m:31s (0h:2m:31s left)
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515  HIVb+R8       200393.670   1001 402789.341   2408793.341  407148.065
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TREE SEARCH COMPLETED AFTER 148 ITERATIONS / Time: 0h:1m:2s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35319.330
Optimal log-likelihood: -35319.327
Proportion of invariable sites: 0.019
Gamma shape alpha: 2.280
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -35319.327
Total tree length: 19.768

Total number of iterations: 148
CPU time used for tree search: 243.300 sec (0h:4m:3s)
Wall-clock time used for tree search: 61.890 sec (0h:1m:1s)
Total CPU time used: 245.448 sec (0h:4m:5s)
Total wall-clock time used: 62.403 sec (0h:1m:2s)

===> START BOOTSTRAP REPLICATE NUMBER 78

Creating bootstrap alignment (seed: 956237)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37799.101
2. Current log-likelihood: -36823.307
3. Current log-likelihood: -36809.635
4. Current log-likelihood: -36809.442
Optimal log-likelihood: -36809.354
Proportion of invariable sites: 0.007
Gamma shape alpha: 2.671
Parameters optimization took 4 rounds (0.257 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0764771 secs using 398.7% CPU
Computing ML distances took 0.076608 sec (of wall-clock time) 0.305218 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00013423 secs using 464.9% CPU
Constructing RapidNJ tree: done in 0.00125813 secs using 325.8% CPU
Computing RapidNJ tree took 0.001445 sec (of wall-clock time) 0.007397 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37226.701
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.74526 secs using 299.4% CPU
1.678 second
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Computing log-likelihood of 98 initial trees ... 1.546 seconds
Current best score: -36809.354

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36772.639
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593  Blosum62+I+R9 106740.093   552 214584.185   825096.185   216806.463
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Iteration 10 / LogL: -36773.259 / Time: 0h:0m:6s
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Iteration 20 / LogL: -36772.645 / Time: 0h:0m:9s
Finish initializing candidate tree set (4)
Current best tree score: -36772.639 / CPU time: 9.332
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36772.595
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -36764.549
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -36763.702
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36763.683
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Iteration 30 / LogL: -36763.936 / Time: 0h:0m:15s (0h:0m:48s left)
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Iteration 100 / LogL: -59371.483 / Time: 0h:3m:50s (0h:2m:5s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 40 / LogL: -36763.934 / Time: 0h:0m:19s (0h:0m:42s left)
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UPDATE BEST LOG-LIKELIHOOD: -36763.682
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BETTER TREE FOUND at iteration 101: -59363.472
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516  HIVb+R9       200381.791   1003 402769.582   2416793.582  407137.016
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Iteration 60 / LogL: -36763.684 / Time: 0h:0m:29s (0h:0m:31s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 105: -59360.756
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Iteration 70 / LogL: -36764.410 / Time: 0h:0m:33s (0h:0m:26s left)
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Iteration 110 / LogL: -59364.263 / Time: 0h:4m:16s (0h:3m:43s left)
Optimizing NNI: done in 0.415279 secs using 399.7% CPU
Optimizing NNI: done in 0.399779 secs using 399.6% CPU
Iteration 90 / LogL: -36763.936 / Time: 0h:0m:43s (0h:0m:16s left)
Optimizing NNI: done in 0.496294 secs using 399.1% CPU
Optimizing NNI: done in 0.484887 secs using 399.3% CPU
Optimizing NNI: done in 0.466836 secs using 399.9% CPU
Optimizing NNI: done in 2.47066 secs using 299.5% CPU
Optimizing NNI: done in 0.680385 secs using 398.5% CPU
Optimizing NNI: done in 0.349752 secs using 399.9% CPU
Optimizing NNI: done in 0.62978 secs using 399.9% CPU
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Optimizing NNI: done in 0.38459 secs using 399.6% CPU
Optimizing NNI: done in 2.42594 secs using 299.5% CPU
Optimizing NNI: done in 0.524375 secs using 399.9% CPU
Optimizing NNI: done in 0.37747 secs using 399.4% CPU
Iteration 100 / LogL: -36763.691 / Time: 0h:0m:48s (0h:0m:11s left)
Optimizing NNI: done in 0.557666 secs using 399.4% CPU
Optimizing NNI: done in 0.365775 secs using 399.1% CPU
Optimizing NNI: done in 2.00843 secs using 299% CPU
Optimizing NNI: done in 0.43978 secs using 399.4% CPU
Optimizing NNI: done in 0.758622 secs using 399% CPU
Optimizing NNI: done in 0.483234 secs using 399.6% CPU
Optimizing NNI: done in 0.515057 secs using 399.3% CPU
Optimizing NNI: done in 2.11299 secs using 299.3% CPU
Optimizing NNI: done in 0.355961 secs using 399.9% CPU
Optimizing NNI: done in 0.542843 secs using 398.6% CPU
Optimizing NNI: done in 0.441062 secs using 399.9% CPU
Optimizing NNI: done in 0.41568 secs using 399.9% CPU
Iteration 110 / LogL: -36772.598 / Time: 0h:0m:53s (0h:0m:6s left)
Optimizing NNI: done in 0.403833 secs using 399.9% CPU
Optimizing NNI: done in 1.91695 secs using 299.4% CPU
Optimizing NNI: done in 0.534004 secs using 399.8% CPU
Optimizing NNI: done in 0.558067 secs using 399.7% CPU
Optimizing NNI: done in 0.390233 secs using 399.9% CPU
Optimizing NNI: done in 0.416552 secs using 399.4% CPU
Optimizing NNI: done in 2.01235 secs using 299.3% CPU
Optimizing NNI: done in 0.354031 secs using 399.4% CPU
Optimizing NNI: done in 0.31084 secs using 399.5% CPU
Optimizing NNI: done in 0.495495 secs using 399.9% CPU
Optimizing NNI: done in 0.519814 secs using 399.4% CPU
Optimizing NNI: done in 0.379338 secs using 399.9% CPU
Iteration 120 / LogL: -36763.938 / Time: 0h:0m:57s (0h:0m:1s left)
Optimizing NNI: done in 2.17168 secs using 299.4% CPU
Optimizing NNI: done in 0.359522 secs using 399.4% CPU
Optimizing NNI: done in 0.466028 secs using 399.9% CPU
Optimizing NNI: done in 0.672272 secs using 399% CPU
Optimizing NNI: done in 0.511379 secs using 399.9% CPU
TREE SEARCH COMPLETED AFTER 124 ITERATIONS / Time: 0h:0m:59s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36763.682
Optimal log-likelihood: -36763.681
Proportion of invariable sites: 0.007
Gamma shape alpha: 2.693
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -36763.681
Total tree length: 20.456

Total number of iterations: 124
CPU time used for tree search: 231.955 sec (0h:3m:51s)
Wall-clock time used for tree search: 59.159 sec (0h:0m:59s)
Total CPU time used: 234.062 sec (0h:3m:54s)
Total wall-clock time used: 59.664 sec (0h:0m:59s)

===> START BOOTSTRAP REPLICATE NUMBER 79

Creating bootstrap alignment (seed: 956238)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37589.971
2. Current log-likelihood: -36736.148
3. Current log-likelihood: -36699.373
4. Current log-likelihood: -36698.566
Optimal log-likelihood: -36698.506
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.651
Parameters optimization took 4 rounds (0.273 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.076015 secs using 397.6% CPU
Computing ML distances took 0.076148 sec (of wall-clock time) 0.302386 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000137091 secs using 454.4% CPU
Constructing RapidNJ tree: done in 0.00121403 secs using 336.9% CPU
Computing RapidNJ tree took 0.001398 sec (of wall-clock time) 0.007107 sec (of CPU time)
Optimizing NNI: done in 2.34943 secs using 299.5% CPU
Log-likelihood of RapidNJ tree: -37256.672
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.518 second
Optimizing NNI: done in 2.12882 secs using 299.1% CPU
Computing log-likelihood of 98 initial trees ... 1.557 seconds
Current best score: -36698.506

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.280589 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36637.416
Optimizing NNI: done in 0.323803 secs using 400.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.7126 secs using 299.3% CPU
Iteration 120 / LogL: -59375.612 / Time: 0h:4m:37s (0h:3m:18s left)
BETTER TREE FOUND at iteration 2: -36634.260
Optimizing NNI: done in 0.32485 secs using 399.9% CPU
Optimizing NNI: done in 0.281817 secs using 398.9% CPU
Optimizing NNI: done in 0.279318 secs using 399.9% CPU
Optimizing NNI: done in 0.293848 secs using 399.8% CPU
Optimizing NNI: done in 1.5264 secs using 299.6% CPU
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Optimizing NNI: done in 0.280671 secs using 399.1% CPU
Optimizing NNI: done in 0.295902 secs using 399.9% CPU
Optimizing NNI: done in 0.283085 secs using 399.5% CPU
Iteration 10 / LogL: -36638.908 / Time: 0h:0m:6s
Optimizing NNI: done in 0.296658 secs using 399.6% CPU
Optimizing NNI: done in 0.302066 secs using 399.6% CPU
Optimizing NNI: done in 1.80142 secs using 299.3% CPU
Optimizing NNI: done in 0.315034 secs using 399.8% CPU
Optimizing NNI: done in 0.261811 secs using 399.9% CPU
Optimizing NNI: done in 0.259388 secs using 399.8% CPU
Optimizing NNI: done in 0.261564 secs using 399.7% CPU
Optimizing NNI: done in 0.252658 secs using 400.5% CPU
Optimizing NNI: done in 0.282977 secs using 399.5% CPU
Optimizing NNI: done in 0.346196 secs using 399.6% CPU
Optimizing NNI: done in 1.80426 secs using 299.6% CPU
Optimizing NNI: done in 0.310227 secs using 399.2% CPU
Iteration 20 / LogL: -36634.422 / Time: 0h:0m:9s
Finish initializing candidate tree set (7)
Current best tree score: -36634.260 / CPU time: 9.102
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.385398 secs using 399.3% CPU
Optimizing NNI: done in 0.435823 secs using 399.1% CPU
Optimizing NNI: done in 0.480149 secs using 399.5% CPU
Optimizing NNI: done in 0.502335 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36634.067
Optimizing NNI: done in 2.23795 secs using 299.5% CPU
Optimizing NNI: done in 0.351409 secs using 399.6% CPU
Optimizing NNI: done in 0.315553 secs using 399.5% CPU
Optimizing NNI: done in 0.554441 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36634.014
Optimizing NNI: done in 0.360891 secs using 399.8% CPU
Optimizing NNI: done in 0.328424 secs using 399.6% CPU
Optimizing NNI: done in 0.335616 secs using 399.7% CPU
Iteration 30 / LogL: -36638.054 / Time: 0h:0m:13s (0h:0m:34s left)
Optimizing NNI: done in 2.29575 secs using 299% CPU
Optimizing NNI: done in 0.273828 secs using 399.9% CPU
Optimizing NNI: done in 0.296695 secs using 399.9% CPU
Optimizing NNI: done in 0.40652 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -36632.404
Optimizing NNI: done in 0.435538 secs using 399.7% CPU
Optimizing NNI: done in 0.391648 secs using 399.1% CPU
Optimizing NNI: done in 1.90254 secs using 299.3% CPU
Optimizing NNI: done in 0.508997 secs using 399.9% CPU
Optimizing NNI: done in 0.520597 secs using 399.7% CPU
Optimizing NNI: done in 0.382457 secs using 399.9% CPU
Optimizing NNI: done in 0.422622 secs using 399.9% CPU
Optimizing NNI: done in 0.351244 secs using 399.3% CPU
Iteration 40 / LogL: -36634.856 / Time: 0h:0m:18s (0h:0m:43s left)
Optimizing NNI: done in 2.16297 secs using 299.2% CPU
Optimizing NNI: done in 0.478676 secs using 398.5% CPU
Optimizing NNI: done in 0.273893 secs using 399.2% CPU
Optimizing NNI: done in 0.489572 secs using 398.6% CPU
Optimizing NNI: done in 0.46276 secs using 399.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -36632.388
Optimizing NNI: done in 1.94991 secs using 299.3% CPU
Optimizing NNI: done in 0.569491 secs using 398.9% CPU
BETTER TREE FOUND at iteration 45: -36632.386
Optimizing NNI: done in 0.427814 secs using 399.6% CPU
Optimizing NNI: done in 0.277264 secs using 399.8% CPU
Optimizing NNI: done in 0.427604 secs using 399.7% CPU
Optimizing NNI: done in 0.337773 secs using 399% CPU
Optimizing NNI: done in 0.377891 secs using 400.6% CPU
Iteration 50 / LogL: -36632.481 / Time: 0h:0m:22s (0h:0m:43s left)
Optimizing NNI: done in 2.10043 secs using 299.4% CPU
Optimizing NNI: done in 0.326432 secs using 399.8% CPU
Optimizing NNI: done in 0.411942 secs using 399.6% CPU
Optimizing NNI: done in 0.43857 secs using 399.7% CPU
Optimizing NNI: done in 0.488176 secs using 399.1% CPU
Optimizing NNI: done in 0.580491 secs using 399.6% CPU
Optimizing NNI: done in 2.44048 secs using 299.3% CPU
Iteration 130 / LogL: -59370.237 / Time: 0h:4m:58s (0h:2m:53s left)
Optimizing NNI: done in 0.410436 secs using 398.1% CPU
Optimizing NNI: done in 0.528437 secs using 399.9% CPU
517  HIVb+R10      200371.459   1005 402752.918   2424812.918  407129.060
Optimizing NNI: done in 0.605031 secs using 399.5% CPU
Optimizing NNI: done in 0.399222 secs using 399.9% CPU
Optimizing NNI: done in 0.346033 secs using 399.6% CPU
Iteration 60 / LogL: -36632.405 / Time: 0h:0m:26s (0h:0m:38s left)
Optimizing NNI: done in 0.327153 secs using 399.9% CPU
Optimizing NNI: done in 2.50448 secs using 299.3% CPU
Optimizing NNI: done in 0.537799 secs using 399.9% CPU
Optimizing NNI: done in 0.438981 secs using 399.7% CPU
Optimizing NNI: done in 0.266216 secs using 398.9% CPU
Optimizing NNI: done in 1.56585 secs using 299.4% CPU
Optimizing NNI: done in 0.55801 secs using 399.7% CPU
Optimizing NNI: done in 0.519474 secs using 399.1% CPU
Optimizing NNI: done in 0.471949 secs using 398.6% CPU
Optimizing NNI: done in 0.432827 secs using 399.2% CPU
Optimizing NNI: done in 1.98454 secs using 299.5% CPU
Optimizing NNI: done in 0.553005 secs using 399.4% CPU
Optimizing NNI: done in 0.34946 secs using 399.3% CPU
Iteration 70 / LogL: -36632.405 / Time: 0h:0m:31s (0h:0m:34s left)
Optimizing NNI: done in 0.615406 secs using 398.7% CPU
Optimizing NNI: done in 0.351721 secs using 399.9% CPU
Optimizing NNI: done in 0.358723 secs using 399.6% CPU
Optimizing NNI: done in 1.73874 secs using 299.2% CPU
Optimizing NNI: done in 0.421013 secs using 399.9% CPU
Optimizing NNI: done in 0.492376 secs using 399.7% CPU
Optimizing NNI: done in 0.239057 secs using 399.5% CPU
Optimizing NNI: done in 0.569295 secs using 399.9% CPU
Optimizing NNI: done in 1.92322 secs using 299.6% CPU
Optimizing NNI: done in 0.37773 secs using 399.8% CPU
Optimizing NNI: done in 0.497727 secs using 399.7% CPU
Optimizing NNI: done in 0.505549 secs using 398.3% CPU
Iteration 80 / LogL: -36632.388 / Time: 0h:0m:35s (0h:0m:29s left)
Optimizing NNI: done in 0.617956 secs using 399.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -36632.386
Optimizing NNI: done in 0.42473 secs using 399.9% CPU
Optimizing NNI: done in 2.27697 secs using 299.4% CPU
Optimizing NNI: done in 0.364518 secs using 399.4% CPU
Optimizing NNI: done in 0.383338 secs using 399.6% CPU
Optimizing NNI: done in 0.308946 secs using 399.9% CPU
Optimizing NNI: done in 0.342653 secs using 398.7% CPU
Optimizing NNI: done in 0.486552 secs using 399.2% CPU
594  Blosum62+I+R10 106740.114   554 214588.228   829528.228   216818.558
Optimizing NNI: done in 1.99048 secs using 299.7% CPU
Optimizing NNI: done in 0.502104 secs using 398.9% CPU
Optimizing NNI: done in 0.472718 secs using 399.5% CPU
Optimizing NNI: done in 0.395216 secs using 399.2% CPU
Iteration 90 / LogL: -36632.892 / Time: 0h:0m:40s (0h:0m:24s left)
Optimizing NNI: done in 0.365328 secs using 399.9% CPU
Optimizing NNI: done in 0.473326 secs using 399.9% CPU
Optimizing NNI: done in 0.321017 secs using 399.3% CPU
Optimizing NNI: done in 2.35877 secs using 299.6% CPU
526  HIVb+F+R8     198771.236   1020 399582.473   2482422.473  404023.930
Optimizing NNI: done in 0.264276 secs using 399.5% CPU
Optimizing NNI: done in 0.58475 secs using 399.6% CPU
Optimizing NNI: done in 0.478851 secs using 399.2% CPU
Optimizing NNI: done in 0.503672 secs using 399.1% CPU
Optimizing NNI: done in 2.26863 secs using 299.6% CPU
Optimizing NNI: done in 0.475158 secs using 399.7% CPU
Optimizing NNI: done in 0.396643 secs using 399.4% CPU
Optimizing NNI: done in 0.505609 secs using 399.8% CPU
Iteration 100 / LogL: -36632.392 / Time: 0h:0m:44s (0h:0m:20s left)
Optimizing NNI: done in 0.441554 secs using 399% CPU
Optimizing NNI: done in 0.550977 secs using 399.9% CPU
Optimizing NNI: done in 0.301995 secs using 397.3% CPU
Optimizing NNI: done in 2.29184 secs using 299.2% CPU
Iteration 140 / LogL: -59372.356 / Time: 0h:5m:19s (0h:2m:29s left)
Optimizing NNI: done in 0.591427 secs using 399.9% CPU
Optimizing NNI: done in 0.408056 secs using 399.6% CPU
Optimizing NNI: done in 0.51773 secs using 399.3% CPU
615  Blosum62+F+I+R9 106803.750   571 214749.499   867973.499   217048.269
Optimizing NNI: done in 0.583769 secs using 399.8% CPU
Optimizing NNI: done in 2.21218 secs using 299.4% CPU
Optimizing NNI: done in 0.579238 secs using 399.4% CPU
Optimizing NNI: done in 0.498655 secs using 399.9% CPU
Optimizing NNI: done in 0.425857 secs using 399.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -36632.386
Iteration 110 / LogL: -36632.386 / Time: 0h:0m:49s (0h:0m:15s left)
Optimizing NNI: done in 0.512829 secs using 399% CPU
Optimizing NNI: done in 1.9975 secs using 299.3% CPU
Optimizing NNI: done in 0.475633 secs using 399.7% CPU
Optimizing NNI: done in 0.360757 secs using 399.2% CPU
Optimizing NNI: done in 0.502288 secs using 399.5% CPU
Optimizing NNI: done in 0.46194 secs using 399.7% CPU
Optimizing NNI: done in 2.09468 secs using 299.6% CPU
Optimizing NNI: done in 0.469043 secs using 399.1% CPU
Optimizing NNI: done in 0.406414 secs using 399.4% CPU
Optimizing NNI: done in 0.399567 secs using 399.6% CPU
Optimizing NNI: done in 0.405196 secs using 399.2% CPU
Optimizing NNI: done in 0.370441 secs using 399.3% CPU
Iteration 120 / LogL: -36632.899 / Time: 0h:0m:53s (0h:0m:11s left)
Optimizing NNI: done in 1.83757 secs using 299.4% CPU
Optimizing NNI: done in 0.590185 secs using 399.6% CPU
Optimizing NNI: done in 0.449352 secs using 399.4% CPU
Optimizing NNI: done in 0.574704 secs using 399.9% CPU
Optimizing NNI: done in 0.435008 secs using 399.7% CPU
Optimizing NNI: done in 0.26388 secs using 399.9% CPU
Optimizing NNI: done in 2.08948 secs using 299.3% CPU
Optimizing NNI: done in 0.511486 secs using 398.5% CPU
Optimizing NNI: done in 0.43227 secs using 399.2% CPU
Optimizing NNI: done in 0.514215 secs using 399.3% CPU
Optimizing NNI: done in 0.455743 secs using 399.9% CPU
Optimizing NNI: done in 2.18866 secs using 299.5% CPU
Optimizing NNI: done in 0.608073 secs using 399.4% CPU
Iteration 130 / LogL: -36632.387 / Time: 0h:0m:58s (0h:0m:6s left)
Optimizing NNI: done in 0.458125 secs using 399% CPU
Optimizing NNI: done in 0.539649 secs using 399.7% CPU
Optimizing NNI: done in 0.4475 secs using 399.7% CPU
Optimizing NNI: done in 0.462769 secs using 399% CPU
Optimizing NNI: done in 2.33988 secs using 299.5% CPU
Optimizing NNI: done in 0.328409 secs using 399.6% CPU
Optimizing NNI: done in 0.571804 secs using 399.5% CPU
Optimizing NNI: done in 0.192724 secs using 399% CPU
Optimizing NNI: done in 1.38415 secs using 299.4% CPU
Optimizing NNI: done in 0.480403 secs using 400.2% CPU
Optimizing NNI: done in 0.454933 secs using 399.7% CPU
Optimizing NNI: done in 0.408602 secs using 399.7% CPU
Iteration 140 / LogL: -36632.394 / Time: 0h:1m:3s (0h:0m:2s left)
Optimizing NNI: done in 0.457619 secs using 398.8% CPU
Optimizing NNI: done in 1.74849 secs using 299.4% CPU
Optimizing NNI: done in 0.549602 secs using 399.6% CPU
Optimizing NNI: done in 0.368447 secs using 400% CPU
Optimizing NNI: done in 0.493568 secs using 399.6% CPU
Optimizing NNI: done in 0.464042 secs using 399.9% CPU
Optimizing NNI: done in 0.399097 secs using 399.7% CPU
TREE SEARCH COMPLETED AFTER 146 ITERATIONS / Time: 0h:1m:5s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36632.386
Optimizing NNI: done in 1.93309 secs using 299.5% CPU
Iteration 150 / LogL: -59363.527 / Time: 0h:5m:39s (0h:2m:5s left)
Optimal log-likelihood: -36632.385
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.615
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -36632.385
Total tree length: 19.937

Total number of iterations: 146
CPU time used for tree search: 256.446 sec (0h:4m:16s)
Wall-clock time used for tree search: 65.201 sec (0h:1m:5s)
Total CPU time used: 259.669 sec (0h:4m:19s)
Total wall-clock time used: 65.962 sec (0h:1m:5s)

===> START BOOTSTRAP REPLICATE NUMBER 80

Creating bootstrap alignment (seed: 956239)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37205.927
2. Current log-likelihood: -36229.262
3. Current log-likelihood: -36215.378
4. Current log-likelihood: -36214.360
Optimal log-likelihood: -36214.350
Proportion of invariable sites: 0.017
Gamma shape alpha: 2.582
Parameters optimization took 4 rounds (0.264 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0713439 secs using 399.4% CPU
Computing ML distances took 0.071492 sec (of wall-clock time) 0.288086 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000137091 secs using 1396% CPU
Constructing RapidNJ tree: done in 0.00127101 secs using 501% CPU
Computing RapidNJ tree took 0.001463 sec (of wall-clock time) 0.008336 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36648.876
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 527  HIVb+F+R9     198764.928   1022 399573.855   2490585.855  404024.021
1.503 second
Optimizing NNI: done in 2.0479 secs using 299.5% CPU
Computing log-likelihood of 98 initial trees ... 1.537 seconds
Current best score: -36214.350

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.212473 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36168.583
Optimizing NNI: done in 0.226905 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36168.568
Optimizing NNI: done in 2.07099 secs using 299.5% CPU
Optimizing NNI: done in 0.206732 secs using 396% CPU
Optimizing NNI: done in 0.23801 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -36168.341
Optimizing NNI: done in 0.220762 secs using 397.5% CPU
Optimizing NNI: done in 0.218223 secs using 399.7% CPU
Optimizing NNI: done in 0.249375 secs using 398.5% CPU
Optimizing NNI: done in 0.223923 secs using 399% CPU
Optimizing NNI: done in 0.284687 secs using 398.3% CPU
Optimizing NNI: done in 0.244385 secs using 399.3% CPU
Iteration 10 / LogL: -36169.246 / Time: 0h:0m:6s
Optimizing NNI: done in 1.94123 secs using 299.4% CPU
Optimizing NNI: done in 0.238268 secs using 399.1% CPU
Optimizing NNI: done in 0.268144 secs using 398.8% CPU
Optimizing NNI: done in 0.252448 secs using 398.7% CPU
Optimizing NNI: done in 0.253519 secs using 398.6% CPU
Optimizing NNI: done in 0.220865 secs using 400.1% CPU
Optimizing NNI: done in 0.23697 secs using 399.5% CPU
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Optimizing NNI: done in 0.235645 secs using 398.9% CPU
Iteration 20 / LogL: -36169.056 / Time: 0h:0m:8s
Finish initializing candidate tree set (5)
Current best tree score: -36168.341 / CPU time: 7.992
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.376028 secs using 398.7% CPU
Optimizing NNI: done in 0.410981 secs using 398.8% CPU
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Optimizing NNI: done in 2.01321 secs using 299.4% CPU
Optimizing NNI: done in 0.300794 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36168.298
Optimizing NNI: done in 0.362907 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -36168.297
Optimizing NNI: done in 0.429897 secs using 398.8% CPU
Optimizing NNI: done in 0.445075 secs using 399% CPU
Optimizing NNI: done in 0.366927 secs using 400.1% CPU
Optimizing NNI: done in 0.287187 secs using 398.6% CPU
Iteration 30 / LogL: -36168.855 / Time: 0h:0m:12s (0h:0m:31s left)
Optimizing NNI: done in 2.10371 secs using 299.6% CPU
Optimizing NNI: done in 0.352087 secs using 397.9% CPU
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Optimizing NNI: done in 0.385104 secs using 397.9% CPU
Optimizing NNI: done in 0.41486 secs using 398.6% CPU
537  HIVw+R8       209399.096   1001 420800.192   2426804.192  425158.916
Optimizing NNI: done in 0.320118 secs using 398.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -36168.289
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Optimizing NNI: done in 0.311058 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -36168.284
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Optimizing NNI: done in 0.301506 secs using 398% CPU
Iteration 40 / LogL: -36175.949 / Time: 0h:0m:15s (0h:0m:26s left)
Optimizing NNI: done in 1.75384 secs using 299.4% CPU
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Iteration 160 / LogL: -59362.493 / Time: 0h:5m:59s (0h:1m:41s left)
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Iteration 50 / LogL: -36168.629 / Time: 0h:0m:20s (0h:0m:22s left)
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Iteration 60 / LogL: -36169.087 / Time: 0h:0m:23s (0h:0m:17s left)
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Iteration 70 / LogL: -36169.071 / Time: 0h:0m:27s (0h:0m:13s left)
Optimizing NNI: done in 0.347039 secs using 399.6% CPU
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Iteration 80 / LogL: -36170.110 / Time: 0h:0m:30s (0h:0m:9s left)
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Optimizing NNI: done in 0.43678 secs using 397.9% CPU
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Optimizing NNI: done in 0.231985 secs using 400.1% CPU
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Optimizing NNI: done in 0.385941 secs using 398.8% CPU
UPDATE BEST LOG-LIKELIHOOD: -36168.283
Optimizing NNI: done in 2.24933 secs using 299.1% CPU
Optimizing NNI: done in 0.340111 secs using 398.7% CPU
Optimizing NNI: done in 0.429904 secs using 398.9% CPU
Iteration 90 / LogL: -36168.373 / Time: 0h:0m:34s (0h:0m:5s left)
Optimizing NNI: done in 0.341929 secs using 399.3% CPU
Optimizing NNI: done in 0.445975 secs using 399% CPU
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Optimizing NNI: done in 0.37185 secs using 398.1% CPU
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Optimizing NNI: done in 0.308366 secs using 399% CPU
Optimizing NNI: done in 0.432555 secs using 398.1% CPU
Iteration 100 / LogL: -36168.800 / Time: 0h:0m:38s (0h:0m:1s left)
Optimizing NNI: done in 2.22204 secs using 299.6% CPU
Optimizing NNI: done in 0.396548 secs using 398.1% CPU
Optimizing NNI: done in 0.39512 secs using 398.9% CPU
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Optimizing NNI: done in 0.412581 secs using 399.3% CPU
Optimizing NNI: done in 2.0042 secs using 299.5% CPU
Iteration 170 / LogL: -59362.464 / Time: 0h:6m:19s (0h:1m:18s left)
Optimizing NNI: done in 0.4383 secs using 399.4% CPU
TREE SEARCH COMPLETED AFTER 105 ITERATIONS / Time: 0h:0m:40s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36168.283
Optimal log-likelihood: -36168.282
Proportion of invariable sites: 0.018
Gamma shape alpha: 2.566
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -36168.282
Total tree length: 19.855

Total number of iterations: 105
CPU time used for tree search: 154.239 sec (0h:2m:34s)
Wall-clock time used for tree search: 39.655 sec (0h:0m:39s)
Total CPU time used: 156.534 sec (0h:2m:36s)
Total wall-clock time used: 40.197 sec (0h:0m:40s)

===> START BOOTSTRAP REPLICATE NUMBER 81

Creating bootstrap alignment (seed: 956240)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.019 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37367.671
2. Current log-likelihood: -36461.094
3. Current log-likelihood: -36438.944
4. Current log-likelihood: -36437.794
Optimal log-likelihood: -36437.720
Proportion of invariable sites: 0.016
Gamma shape alpha: 2.394
Parameters optimization took 4 rounds (0.262 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0736082 secs using 399.9% CPU
Computing ML distances took 0.073741 sec (of wall-clock time) 0.294711 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000138998 secs using 452.5% CPU
Constructing RapidNJ tree: done in 0.00131202 secs using 335% CPU
Computing RapidNJ tree took 0.001503 sec (of wall-clock time) 0.006772 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37112.870
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.69598 secs using 299.8% CPU
1.450 second
Computing log-likelihood of 98 initial trees ... 1.526 seconds
Current best score: -36437.720

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.96704 secs using 299.2% CPU
Optimizing NNI: done in 0.231967 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36393.266
Optimizing NNI: done in 0.294643 secs using 398.3% CPU
Optimizing NNI: done in 0.332257 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -36388.632
Optimizing NNI: done in 0.255991 secs using 398.5% CPU
Optimizing NNI: done in 0.271884 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -36387.850
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Optimizing NNI: done in 0.49059 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -36383.577
Optimizing NNI: done in 0.296676 secs using 398.3% CPU
Iteration 10 / LogL: -36393.304 / Time: 0h:0m:6s
Optimizing NNI: done in 0.292646 secs using 399.2% CPU
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Iteration 20 / LogL: -36383.618 / Time: 0h:0m:9s
Finish initializing candidate tree set (11)
Current best tree score: -36383.577 / CPU time: 9.292
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.26635 secs using 299.2% CPU
Optimizing NNI: done in 0.4992 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36383.548
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BETTER TREE FOUND at iteration 28: -36383.541
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Iteration 30 / LogL: -36410.353 / Time: 0h:0m:14s (0h:0m:48s left)
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BETTER TREE FOUND at iteration 34: -36383.538
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Iteration 40 / LogL: -36383.564 / Time: 0h:0m:18s (0h:0m:45s left)
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Iteration 180 / LogL: -59378.635 / Time: 0h:6m:40s (0h:0m:55s left)
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Iteration 50 / LogL: -36383.576 / Time: 0h:0m:24s (0h:0m:41s left)
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Iteration 60 / LogL: -36383.700 / Time: 0h:0m:29s (0h:0m:36s left)
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Iteration 70 / LogL: -36383.563 / Time: 0h:0m:34s (0h:0m:32s left)
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Iteration 80 / LogL: -36384.728 / Time: 0h:0m:39s (0h:0m:26s left)
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Iteration 190 / LogL: -59391.706 / Time: 0h:7m:0s (0h:0m:33s left)
Optimizing NNI: done in 0.452532 secs using 399% CPU
Optimizing NNI: done in 0.504819 secs using 398.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -36383.538
Optimizing NNI: done in 0.659457 secs using 399.1% CPU
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Iteration 90 / LogL: -36383.866 / Time: 0h:0m:44s (0h:0m:22s left)
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Iteration 100 / LogL: -36383.576 / Time: 0h:0m:49s (0h:0m:16s left)
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Iteration 110 / LogL: -36469.938 / Time: 0h:0m:54s (0h:0m:11s left)
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Iteration 120 / LogL: -36383.969 / Time: 0h:0m:59s (0h:0m:6s left)
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Iteration 200 / LogL: -59372.148 / Time: 0h:7m:21s (0h:0m:11s left)
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Iteration 130 / LogL: -36384.687 / Time: 0h:1m:4s (0h:0m:1s left)
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Optimizing NNI: done in 0.404179 secs using 399.3% CPU
Optimizing NNI: done in 0.46419 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 135 ITERATIONS / Time: 0h:1m:7s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36383.538
Optimal log-likelihood: -36383.533
Proportion of invariable sites: 0.016
Gamma shape alpha: 2.395
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36383.533
Total tree length: 20.445

Total number of iterations: 135
CPU time used for tree search: 261.037 sec (0h:4m:21s)
Wall-clock time used for tree search: 66.412 sec (0h:1m:6s)
Total CPU time used: 263.974 sec (0h:4m:23s)
Total wall-clock time used: 67.101 sec (0h:1m:7s)

===> START BOOTSTRAP REPLICATE NUMBER 82

Creating bootstrap alignment (seed: 956241)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36313.801
2. Current log-likelihood: -35506.429
3. Current log-likelihood: -35488.189
4. Current log-likelihood: -35487.446
Optimal log-likelihood: -35487.314
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.580
Parameters optimization took 4 rounds (0.273 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0730641 secs using 397.9% CPU
Computing ML distances took 0.073192 sec (of wall-clock time) 0.291015 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000121117 secs using 456.6% CPU
Constructing RapidNJ tree: done in 0.00119305 secs using 305.7% CPU
Computing RapidNJ tree took 0.001363 sec (of wall-clock time) 0.006798 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36225.035
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.80957 secs using 299.3% CPU
1.640 second
Optimizing NNI: done in 2.49558 secs using 299.4% CPU
Computing log-likelihood of 98 initial trees ... 1.574 seconds
Current best score: -35487.314

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.315189 secs using 396.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35448.083
Optimizing NNI: done in 0.2251 secs using 400.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35443.270
Optimizing NNI: done in 0.229394 secs using 398.7% CPU
Optimizing NNI: done in 0.243755 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -35442.635
Optimizing NNI: done in 1.91936 secs using 299.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.2743 secs using 398.5% CPU
Optimizing NNI: done in 0.216632 secs using 399% CPU
Optimizing NNI: done in 0.279165 secs using 397.6% CPU
Optimizing NNI: done in 0.220584 secs using 398.6% CPU
BETTER TREE FOUND at iteration 205: -59360.061
Optimizing NNI: done in 0.27098 secs using 397.8% CPU
Optimizing NNI: done in 0.284472 secs using 398.8% CPU
Iteration 10 / LogL: -35448.152 / Time: 0h:0m:6s
Optimizing NNI: done in 0.266251 secs using 400.5% CPU
Optimizing NNI: done in 0.39485 secs using 399.4% CPU
Optimizing NNI: done in 0.218771 secs using 399.7% CPU
Optimizing NNI: done in 0.280608 secs using 398.9% CPU
Optimizing NNI: done in 0.269755 secs using 398.8% CPU
Optimizing NNI: done in 1.95284 secs using 299.2% CPU
Optimizing NNI: done in 0.383725 secs using 398.4% CPU
Optimizing NNI: done in 0.383242 secs using 398.8% CPU
Optimizing NNI: done in 0.390514 secs using 398.7% CPU
Optimizing NNI: done in 0.381475 secs using 398.5% CPU
538  HIVw+R9       209380.617   1003 420767.234   2434791.234  425134.668
Optimizing NNI: done in 0.386723 secs using 399.1% CPU
Iteration 20 / LogL: -35448.106 / Time: 0h:0m:9s
Finish initializing candidate tree set (4)
Current best tree score: -35442.635 / CPU time: 9.331
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.95055 secs using 299.5% CPU
Optimizing NNI: done in 0.355882 secs using 398.8% CPU
Optimizing NNI: done in 0.312686 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -35441.563
Optimizing NNI: done in 0.382593 secs using 399.6% CPU
Optimizing NNI: done in 0.455346 secs using 398.7% CPU
Optimizing NNI: done in 1.69256 secs using 299.4% CPU
Optimizing NNI: done in 0.415713 secs using 399% CPU
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Optimizing NNI: done in 0.59082 secs using 398.6% CPU
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Optimizing NNI: done in 0.275919 secs using 398.6% CPU
Optimizing NNI: done in 0.371642 secs using 398.7% CPU
Iteration 30 / LogL: -35445.426 / Time: 0h:0m:13s (0h:0m:43s left)
Optimizing NNI: done in 2.28597 secs using 299.3% CPU
Optimizing NNI: done in 0.355382 secs using 399.6% CPU
Optimizing NNI: done in 0.46566 secs using 398.5% CPU
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Optimizing NNI: done in 0.540108 secs using 399.4% CPU
Optimizing NNI: done in 1.89489 secs using 299.1% CPU
Iteration 210 / LogL: -59388.040 / Time: 0h:7m:42s (0h:3m:30s left)
Optimizing NNI: done in 0.527112 secs using 398.6% CPU
Optimizing NNI: done in 0.372036 secs using 398.8% CPU
Optimizing NNI: done in 0.552823 secs using 398.4% CPU
Optimizing NNI: done in 0.438898 secs using 398.2% CPU
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Optimizing NNI: done in 2.25704 secs using 299.4% CPU
Optimizing NNI: done in 0.407477 secs using 398.4% CPU
Iteration 40 / LogL: -35441.838 / Time: 0h:0m:18s (0h:0m:38s left)
WARNING: Log-likelihood -106805 of Blosum62+F+I+R10 worse than Blosum62+F+I+R9 -106804
616  Blosum62+F+I+R10 106805.470   573 214756.940   872560.940   217063.761
Optimizing NNI: done in 0.392247 secs using 398.3% CPU
Optimizing NNI: done in 0.33136 secs using 398.1% CPU
Optimizing NNI: done in 0.294979 secs using 398.5% CPU
Optimizing NNI: done in 0.4177 secs using 398.8% CPU
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Optimizing NNI: done in 0.32986 secs using 399.3% CPU
Optimizing NNI: done in 0.280576 secs using 398.6% CPU
Optimizing NNI: done in 2.59775 secs using 299.4% CPU
Optimizing NNI: done in 0.360966 secs using 399.6% CPU
Optimizing NNI: done in 0.360763 secs using 397.8% CPU
Optimizing NNI: done in 0.428002 secs using 399.3% CPU
Iteration 50 / LogL: -35441.647 / Time: 0h:0m:21s (0h:0m:32s left)
Optimizing NNI: done in 0.319602 secs using 399.9% CPU
Optimizing NNI: done in 0.271976 secs using 398.8% CPU
Optimizing NNI: done in 1.75588 secs using 299.5% CPU
Optimizing NNI: done in 0.352879 secs using 398.9% CPU
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Optimizing NNI: done in 0.324689 secs using 399.2% CPU
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Optimizing NNI: done in 0.32237 secs using 399.6% CPU
Optimizing NNI: done in 2.03248 secs using 299.4% CPU
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Optimizing NNI: done in 0.360517 secs using 399.6% CPU
Optimizing NNI: done in 0.358339 secs using 398.9% CPU
Iteration 60 / LogL: -35442.655 / Time: 0h:0m:25s (0h:0m:26s left)
Optimizing NNI: done in 0.496097 secs using 398.7% CPU
Optimizing NNI: done in 0.399592 secs using 398.9% CPU
Optimizing NNI: done in 0.275175 secs using 399.9% CPU
Optimizing NNI: done in 0.273247 secs using 397.8% CPU
Optimizing NNI: done in 2.34545 secs using 299.2% CPU
Optimizing NNI: done in 0.37554 secs using 399.4% CPU
Optimizing NNI: done in 0.360525 secs using 398.9% CPU
Optimizing NNI: done in 0.480284 secs using 398.7% CPU
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Optimizing NNI: done in 1.64005 secs using 299.4% CPU
Optimizing NNI: done in 0.362892 secs using 398.5% CPU
Optimizing NNI: done in 0.337447 secs using 398.8% CPU
Iteration 70 / LogL: -35442.773 / Time: 0h:0m:29s (0h:0m:21s left)
Optimizing NNI: done in 0.310364 secs using 398.2% CPU
Optimizing NNI: done in 0.352239 secs using 399.2% CPU
Optimizing NNI: done in 0.337809 secs using 399% CPU
Optimizing NNI: done in 0.271753 secs using 399.4% CPU
Optimizing NNI: done in 0.36503 secs using 398.1% CPU
Optimizing NNI: done in 2.33157 secs using 299.2% CPU
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Optimizing NNI: done in 0.370287 secs using 398.9% CPU
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Optimizing NNI: done in 0.450199 secs using 398.3% CPU
Optimizing NNI: done in 0.391539 secs using 398.8% CPU
Iteration 80 / LogL: -35441.584 / Time: 0h:0m:32s (0h:0m:17s left)
Optimizing NNI: done in 1.98884 secs using 299.4% CPU
Optimizing NNI: done in 0.362864 secs using 397.8% CPU
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Optimizing NNI: done in 0.279201 secs using 398.2% CPU
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Optimizing NNI: done in 0.470665 secs using 398.7% CPU
Optimizing NNI: done in 0.320119 secs using 399.1% CPU
Iteration 90 / LogL: -35441.608 / Time: 0h:0m:36s (0h:0m:12s left)
Optimizing NNI: done in 0.569303 secs using 398.4% CPU
Optimizing NNI: done in 1.88174 secs using 299.4% CPU
Iteration 220 / LogL: -59362.093 / Time: 0h:8m:3s (0h:3m:7s left)
Optimizing NNI: done in 0.429249 secs using 397.9% CPU
Optimizing NNI: done in 0.338019 secs using 397.9% CPU
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Optimizing NNI: done in 0.315758 secs using 399.7% CPU
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Optimizing NNI: done in 2.03848 secs using 299.2% CPU
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Optimizing NNI: done in 0.303166 secs using 398.9% CPU
Optimizing NNI: done in 0.392423 secs using 398.4% CPU
Optimizing NNI: done in 0.46559 secs using 399.2% CPU
Iteration 100 / LogL: -35441.629 / Time: 0h:0m:39s (0h:0m:8s left)
Optimizing NNI: done in 0.269509 secs using 399.2% CPU
Optimizing NNI: done in 0.301067 secs using 398.6% CPU
Optimizing NNI: done in 2.1708 secs using 299.6% CPU
Optimizing NNI: done in 0.490958 secs using 399.4% CPU
Optimizing NNI: done in 0.417908 secs using 399.4% CPU
Optimizing NNI: done in 0.386362 secs using 399% CPU
Optimizing NNI: done in 0.312004 secs using 398.5% CPU
Optimizing NNI: done in 0.332242 secs using 397.6% CPU
Optimizing NNI: done in 1.81172 secs using 299.7% CPU
Optimizing NNI: done in 0.317032 secs using 399.4% CPU
Optimizing NNI: done in 0.347562 secs using 398.5% CPU
Optimizing NNI: done in 0.343247 secs using 399.3% CPU
Iteration 110 / LogL: -35441.594 / Time: 0h:0m:43s (0h:0m:4s left)
Optimizing NNI: done in 0.281512 secs using 399.2% CPU
Optimizing NNI: done in 0.386653 secs using 399.2% CPU
Optimizing NNI: done in 0.311743 secs using 398.8% CPU
Optimizing NNI: done in 1.99416 secs using 299.5% CPU
Optimizing NNI: done in 0.485041 secs using 398.9% CPU
Optimizing NNI: done in 0.314725 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35441.523
Optimizing NNI: done in 0.401822 secs using 399.4% CPU
Optimizing NNI: done in 0.326989 secs using 398.3% CPU
Optimizing NNI: done in 0.352997 secs using 397.5% CPU
Optimizing NNI: done in 1.69462 secs using 299.5% CPU
Optimizing NNI: done in 0.388653 secs using 398.8% CPU
Optimizing NNI: done in 0.26816 secs using 399.1% CPU
Iteration 120 / LogL: -35582.696 / Time: 0h:0m:47s (0h:0m:0s left)
Optimizing NNI: done in 0.268429 secs using 398.5% CPU
Optimizing NNI: done in 0.389272 secs using 397.7% CPU
Optimizing NNI: done in 0.276639 secs using 399.4% CPU
TREE SEARCH COMPLETED AFTER 123 ITERATIONS / Time: 0h:0m:48s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35441.523
Optimal log-likelihood: -35441.521
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.593
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35441.521
Total tree length: 18.999

Total number of iterations: 123
CPU time used for tree search: 185.255 sec (0h:3m:5s)
Wall-clock time used for tree search: 47.526 sec (0h:0m:47s)
Total CPU time used: 187.583 sec (0h:3m:7s)
Total wall-clock time used: 48.080 sec (0h:0m:48s)

===> START BOOTSTRAP REPLICATE NUMBER 83

Creating bootstrap alignment (seed: 956242)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.020 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37280.916
2. Current log-likelihood: -36377.705
3. Current log-likelihood: -36368.635
4. Current log-likelihood: -36367.804
Optimizing NNI: done in 1.84348 secs using 299.1% CPU
5. Current log-likelihood: -36367.407
Optimal log-likelihood: -36367.350
Proportion of invariable sites: 0.021
Gamma shape alpha: 2.434
Parameters optimization took 5 rounds (0.328 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.075124 secs using 397.6% CPU
Computing ML distances took 0.075258 sec (of wall-clock time) 0.298900 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000135183 secs using 1213% CPU
Constructing RapidNJ tree: done in 0.00134706 secs using 512.4% CPU
Computing RapidNJ tree took 0.001545 sec (of wall-clock time) 0.008606 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37075.919
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.0425 secs using 299.2% CPU
1.595 second
539  HIVw+R10      209376.097   1005 420762.193   2442822.193  425138.335
Computing log-likelihood of 98 initial trees ... 1.614 seconds
Current best score: -36367.350

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.225169 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36325.313
Optimizing NNI: done in 1.9475 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.224625 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36318.689
Optimizing NNI: done in 0.21764 secs using 397.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -36318.197
Optimizing NNI: done in 0.237398 secs using 399.5% CPU
Optimizing NNI: done in 0.236702 secs using 400% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -36318.043
BETTER TREE FOUND at iteration 228: -59356.091
Optimizing NNI: done in 0.253151 secs using 399.2% CPU
Optimizing NNI: done in 0.220376 secs using 398.9% CPU
Optimizing NNI: done in 0.261872 secs using 399.6% CPU
Optimizing NNI: done in 0.223073 secs using 396.5% CPU
Optimizing NNI: done in 0.242265 secs using 398.8% CPU
Iteration 10 / LogL: -36325.988 / Time: 0h:0m:6s
Optimizing NNI: done in 0.333105 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 11: -36317.069
Optimizing NNI: done in 0.238445 secs using 398% CPU
Optimizing NNI: done in 2.09365 secs using 299.5% CPU
Optimizing NNI: done in 0.286899 secs using 400.5% CPU
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Optimizing NNI: done in 0.236555 secs using 398.4% CPU
Optimizing NNI: done in 0.255674 secs using 398.3% CPU
Iteration 20 / LogL: -36318.216 / Time: 0h:0m:9s
Finish initializing candidate tree set (10)
Current best tree score: -36317.069 / CPU time: 8.525
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.9482 secs using 299.7% CPU
Iteration 230 / LogL: -59363.792 / Time: 0h:8m:24s (0h:3m:35s left)
Optimizing NNI: done in 0.550314 secs using 399% CPU
Optimizing NNI: done in 0.373054 secs using 398.7% CPU
Optimizing NNI: done in 0.401778 secs using 399.1% CPU
Optimizing NNI: done in 0.476622 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -36316.536
Optimizing NNI: done in 0.379467 secs using 398.7% CPU
Optimizing NNI: done in 2.18394 secs using 299.3% CPU
Optimizing NNI: done in 0.442258 secs using 399.5% CPU
637  Dayhoff+I+R9  106797.666   552 214699.332   825211.332   216921.610
Optimizing NNI: done in 0.523201 secs using 398.1% CPU
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Optimizing NNI: done in 1.77903 secs using 299.6% CPU
Optimizing NNI: done in 0.378998 secs using 398.6% CPU
Iteration 30 / LogL: -36696.345 / Time: 0h:0m:13s (0h:0m:44s left)
Optimizing NNI: done in 0.452649 secs using 398.9% CPU
Optimizing NNI: done in 0.348197 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -36316.373
Optimizing NNI: done in 0.388969 secs using 399.1% CPU
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Optimizing NNI: done in 0.612119 secs using 398.7% CPU
Optimizing NNI: done in 0.399328 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -36316.246
Optimizing NNI: done in 0.374982 secs using 398.2% CPU
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Optimizing NNI: done in 0.506993 secs using 398.8% CPU
Optimizing NNI: done in 0.463536 secs using 398.6% CPU
Iteration 40 / LogL: -36318.493 / Time: 0h:0m:18s (0h:0m:44s left)
Optimizing NNI: done in 0.517216 secs using 398.6% CPU
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Optimizing NNI: done in 0.37434 secs using 399.5% CPU
548  HIVw+F+R8     204961.158   1020 411962.315   2494802.315  416403.773
Optimizing NNI: done in 0.408791 secs using 398.9% CPU
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Iteration 50 / LogL: -36320.250 / Time: 0h:0m:22s (0h:0m:39s left)
Optimizing NNI: done in 0.423036 secs using 398.9% CPU
Optimizing NNI: done in 0.544245 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.672 secs using 299.1% CPU
BETTER TREE FOUND at iteration 52: -36316.166
Optimizing NNI: done in 0.363468 secs using 398.3% CPU
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Iteration 60 / LogL: -36316.167 / Time: 0h:0m:26s (0h:0m:41s left)
Optimizing NNI: done in 2.00991 secs using 299.4% CPU
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Optimizing NNI: done in 1.82606 secs using 299.2% CPU
Iteration 240 / LogL: -59361.397 / Time: 0h:8m:43s (0h:3m:12s left)
Optimizing NNI: done in 0.418115 secs using 398.4% CPU
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Optimizing NNI: done in 2.02495 secs using 299.3% CPU
Optimizing NNI: done in 0.385455 secs using 399.4% CPU
Iteration 70 / LogL: -36316.458 / Time: 0h:0m:31s (0h:0m:36s left)
Optimizing NNI: done in 0.459442 secs using 396.8% CPU
Optimizing NNI: done in 0.327163 secs using 398.6% CPU
Optimizing NNI: done in 0.338335 secs using 399.1% CPU
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Optimizing NNI: done in 0.57055 secs using 399.1% CPU
Optimizing NNI: done in 2.11421 secs using 299.4% CPU
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Optimizing NNI: done in 0.451124 secs using 399.6% CPU
Optimizing NNI: done in 2.24889 secs using 299.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.470605 secs using 398.8% CPU
Iteration 80 / LogL: -36320.341 / Time: 0h:0m:35s (0h:0m:32s left)
Optimizing NNI: done in 0.568654 secs using 399.2% CPU
BETTER TREE FOUND at iteration 243: -59355.954
Optimizing NNI: done in 0.491837 secs using 399% CPU
Optimizing NNI: done in 0.424268 secs using 399.3% CPU
Optimizing NNI: done in 0.455714 secs using 398.5% CPU
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Optimizing NNI: done in 1.80626 secs using 299.1% CPU
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Optimizing NNI: done in 1.78873 secs using 299.7% CPU
Optimizing NNI: done in 0.539098 secs using 398.9% CPU
Iteration 90 / LogL: -36318.308 / Time: 0h:0m:40s (0h:0m:28s left)
Optimizing NNI: done in 0.467545 secs using 399.1% CPU
Optimizing NNI: done in 0.355015 secs using 399.6% CPU
549  HIVw+F+R9     204951.516   1022 411947.031   2502959.031  416397.198
Optimizing NNI: done in 0.567202 secs using 399.2% CPU
Optimizing NNI: done in 1.93501 secs using 299.5% CPU
Optimizing NNI: done in 0.377004 secs using 398.6% CPU
Optimizing NNI: done in 0.346045 secs using 398.8% CPU
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Optimizing NNI: done in 0.651091 secs using 399.2% CPU
Optimizing NNI: done in 0.549 secs using 399.3% CPU
Iteration 100 / LogL: -36319.512 / Time: 0h:0m:45s (0h:0m:23s left)
Optimizing NNI: done in 0.368965 secs using 398.5% CPU
Optimizing NNI: done in 0.418751 secs using 399.4% CPU
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Optimizing NNI: done in 0.483849 secs using 398.4% CPU
Iteration 110 / LogL: -36320.427 / Time: 0h:0m:49s (0h:0m:19s left)
Optimizing NNI: done in 0.471987 secs using 398.7% CPU
Optimizing NNI: done in 2.24335 secs using 299.4% CPU
Iteration 250 / LogL: -59358.694 / Time: 0h:9m:5s (0h:3m:23s left)
Optimizing NNI: done in 0.397206 secs using 398.4% CPU
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Optimizing NNI: done in 0.365628 secs using 398.6% CPU
Optimizing NNI: done in 0.572899 secs using 398.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -36316.166
Optimizing NNI: done in 0.273143 secs using 397.5% CPU
Optimizing NNI: done in 2.05476 secs using 299.5% CPU
Optimizing NNI: done in 0.523369 secs using 399.2% CPU
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Optimizing NNI: done in 0.469105 secs using 398.2% CPU
Optimizing NNI: done in 0.515829 secs using 399.3% CPU
Iteration 120 / LogL: -36316.229 / Time: 0h:0m:53s (0h:0m:14s left)
Optimizing NNI: done in 0.434891 secs using 398.3% CPU
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Optimizing NNI: done in 1.74682 secs using 299.4% CPU
Optimizing NNI: done in 0.618366 secs using 398.7% CPU
Iteration 130 / LogL: -36317.023 / Time: 0h:0m:58s (0h:0m:9s left)
Optimizing NNI: done in 0.444251 secs using 399% CPU
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Optimizing NNI: done in 0.360015 secs using 398.2% CPU
Iteration 140 / LogL: -36317.396 / Time: 0h:1m:2s (0h:0m:5s left)
Optimizing NNI: done in 0.297897 secs using 398.8% CPU
Optimizing NNI: done in 0.407254 secs using 399.8% CPU
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Optimizing NNI: done in 2.17434 secs using 299.5% CPU
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Optimizing NNI: done in 1.83318 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.674866 secs using 398% CPU
Iteration 150 / LogL: -36316.468 / Time: 0h:1m:6s (0h:0m:0s left)
Optimizing NNI: done in 0.270583 secs using 398.5% CPU
Optimizing NNI: done in 0.563929 secs using 397.4% CPU
Optimizing NNI: done in 0.376154 secs using 398% CPU
TREE SEARCH COMPLETED AFTER 153 ITERATIONS / Time: 0h:1m:8s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36316.166
BETTER TREE FOUND at iteration 258: -59355.219
Optimal log-likelihood: -36316.165
Proportion of invariable sites: 0.021
Gamma shape alpha: 2.399
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -36316.165
Total tree length: 20.611

Total number of iterations: 153
CPU time used for tree search: 263.988 sec (0h:4m:23s)
Wall-clock time used for tree search: 67.257 sec (0h:1m:7s)
Total CPU time used: 267.356 sec (0h:4m:27s)
Total wall-clock time used: 68.053 sec (0h:1m:8s)

===> START BOOTSTRAP REPLICATE NUMBER 84

Creating bootstrap alignment (seed: 956243)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -35987.249
2. Current log-likelihood: -35116.181
3. Current log-likelihood: -35103.465
4. Current log-likelihood: -35103.135
Optimal log-likelihood: -35103.061
Proportion of invariable sites: 0.013
Gamma shape alpha: 2.377
Parameters optimization took 4 rounds (0.266 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0777678 secs using 399.8% CPU
Computing ML distances took 0.077922 sec (of wall-clock time) 0.311327 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000130892 secs using 466% CPU
Constructing RapidNJ tree: done in 0.00120497 secs using 307.7% CPU
Computing RapidNJ tree took 0.001402 sec (of wall-clock time) 0.005080 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35621.230
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.438 second
Optimizing NNI: done in 1.98562 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 259: -59352.598
Computing log-likelihood of 98 initial trees ... 1.557 seconds
Current best score: -35103.061

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.205052 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35082.034
Optimizing NNI: done in 0.243301 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35079.993
Optimizing NNI: done in 0.27888 secs using 399.2% CPU
Optimizing NNI: done in 0.268258 secs using 398.9% CPU
Optimizing NNI: done in 0.274705 secs using 398.2% CPU
Optimizing NNI: done in 2.13525 secs using 299.4% CPU
Iteration 260 / LogL: -59361.544 / Time: 0h:9m:28s (0h:3m:37s left)
Optimizing NNI: done in 0.259373 secs using 399% CPU
Optimizing NNI: done in 0.272846 secs using 399.3% CPU
Optimizing NNI: done in 0.33349 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 8: -35073.378
Optimizing NNI: done in 0.333993 secs using 398.5% CPU
Optimizing NNI: done in 0.259779 secs using 399.3% CPU
Iteration 10 / LogL: -35081.408 / Time: 0h:0m:6s
Optimizing NNI: done in 0.273366 secs using 398.9% CPU
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Optimizing NNI: done in 0.218419 secs using 398.9% CPU
Iteration 20 / LogL: -35082.101 / Time: 0h:0m:9s
Finish initializing candidate tree set (7)
Current best tree score: -35073.378 / CPU time: 8.628
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.02527 secs using 299.1% CPU
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Optimizing NNI: done in 0.719086 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -35064.665
Optimizing NNI: done in 0.387305 secs using 398.8% CPU
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Iteration 30 / LogL: -35075.908 / Time: 0h:0m:13s (0h:0m:45s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -35064.291
Optimizing NNI: done in 0.393123 secs using 397.6% CPU
550  HIVw+F+R10    204945.555   1024 411939.109   2511139.109  416397.984
Optimizing NNI: done in 0.343392 secs using 398.2% CPU
Optimizing NNI: done in 0.399806 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35064.209
Optimizing NNI: done in 0.357138 secs using 399% CPU
Optimizing NNI: done in 1.96715 secs using 299.3% CPU
Optimizing NNI: done in 0.412701 secs using 399.6% CPU
Iteration 40 / LogL: -35525.555 / Time: 0h:0m:17s (0h:0m:42s left)
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UPDATE BEST LOG-LIKELIHOOD: -35064.202
Optimizing NNI: done in 0.464144 secs using 399.4% CPU
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Optimizing NNI: done in 0.325177 secs using 399.1% CPU
Iteration 50 / LogL: -35065.897 / Time: 0h:0m:21s (0h:0m:37s left)
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Optimizing NNI: done in 0.334888 secs using 399.1% CPU
Iteration 60 / LogL: -35066.966 / Time: 0h:0m:25s (0h:0m:32s left)
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Optimizing NNI: done in 1.80444 secs using 299.4% CPU
Iteration 270 / LogL: -59355.954 / Time: 0h:9m:48s (0h:3m:14s left)
Optimizing NNI: done in 0.453992 secs using 398.9% CPU
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Optimizing NNI: done in 0.391749 secs using 399.1% CPU
Iteration 70 / LogL: -35070.626 / Time: 0h:0m:29s (0h:0m:27s left)
Optimizing NNI: done in 1.8463 secs using 299.3% CPU
Optimizing NNI: done in 0.379361 secs using 399.4% CPU
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Optimizing NNI: done in 0.277688 secs using 399% CPU
Optimizing NNI: done in 0.391734 secs using 397.2% CPU
559  FLU+R8        200582.056   1001 403166.112   2409170.112  407524.836
Optimizing NNI: done in 0.625544 secs using 398.2% CPU
Optimizing NNI: done in 0.444367 secs using 399.1% CPU
Optimizing NNI: done in 0.398814 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35064.188
Optimizing NNI: done in 0.396727 secs using 399.1% CPU
Optimizing NNI: done in 2.52414 secs using 299.2% CPU
Optimizing NNI: done in 0.500404 secs using 398.4% CPU
Iteration 80 / LogL: -35072.726 / Time: 0h:0m:34s (0h:0m:24s left)
Optimizing NNI: done in 0.400686 secs using 399.6% CPU
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Optimizing NNI: done in 0.661557 secs using 397.9% CPU
Iteration 90 / LogL: -35066.416 / Time: 0h:0m:38s (0h:0m:19s left)
Optimizing NNI: done in 0.326941 secs using 399% CPU
Optimizing NNI: done in 0.261992 secs using 399.2% CPU
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Iteration 100 / LogL: -35064.361 / Time: 0h:0m:42s (0h:0m:14s left)
Optimizing NNI: done in 0.370301 secs using 398.5% CPU
Optimizing NNI: done in 2.22117 secs using 299.3% CPU
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Optimizing NNI: done in 0.349464 secs using 397.5% CPU
Iteration 110 / LogL: -35069.391 / Time: 0h:0m:46s (0h:0m:10s left)
Optimizing NNI: done in 1.93435 secs using 299.6% CPU
Iteration 280 / LogL: -59376.584 / Time: 0h:10m:9s (0h:2m:52s left)
Optimizing NNI: done in 0.455688 secs using 399.1% CPU
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Optimizing NNI: done in 0.311844 secs using 398.7% CPU
Optimizing NNI: done in 0.549626 secs using 399.3% CPU
Iteration 120 / LogL: -35065.048 / Time: 0h:0m:50s (0h:0m:6s left)
Optimizing NNI: done in 2.02417 secs using 298.8% CPU
Optimizing NNI: done in 0.362315 secs using 399.2% CPU
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Optimizing NNI: done in 0.272864 secs using 399.3% CPU
Iteration 130 / LogL: -35065.854 / Time: 0h:0m:54s (0h:0m:2s left)
Optimizing NNI: done in 1.97517 secs using 299.2% CPU
Optimizing NNI: done in 0.345806 secs using 398.9% CPU
Optimizing NNI: done in 0.396138 secs using 399.5% CPU
Optimizing NNI: done in 0.281004 secs using 399.3% CPU
Optimizing NNI: done in 0.405044 secs using 398.4% CPU
560  FLU+R9        200563.618   1003 403133.235   2417157.235  407500.668
Optimizing NNI: done in 1.5229 secs using 299.4% CPU
Optimizing NNI: done in 0.3303 secs using 398% CPU
Optimizing NNI: done in 0.447027 secs using 398.3% CPU
TREE SEARCH COMPLETED AFTER 136 ITERATIONS / Time: 0h:0m:56s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35064.188
Optimal log-likelihood: -35064.187
Proportion of invariable sites: 0.013
Gamma shape alpha: 2.379
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35064.187
Total tree length: 19.157

Total number of iterations: 136
CPU time used for tree search: 221.255 sec (0h:3m:41s)
Wall-clock time used for tree search: 56.407 sec (0h:0m:56s)
Total CPU time used: 223.619 sec (0h:3m:43s)
Total wall-clock time used: 56.967 sec (0h:0m:56s)

===> START BOOTSTRAP REPLICATE NUMBER 85

Creating bootstrap alignment (seed: 956244)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37591.740
2. Current log-likelihood: -36709.434
3. Current log-likelihood: -36690.021
4. Current log-likelihood: -36689.144
Optimal log-likelihood: -36689.095
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.647
Parameters optimization took 4 rounds (0.277 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.074667 secs using 399.3% CPU
Computing ML distances took 0.074796 sec (of wall-clock time) 0.298482 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000138998 secs using 466.2% CPU
Constructing RapidNJ tree: done in 0.00129104 secs using 435.7% CPU
Computing RapidNJ tree took 0.001484 sec (of wall-clock time) 0.007588 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37297.009
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.15833 secs using 299.5% CPU
1.552 second
Optimizing NNI: done in 1.41796 secs using 299.4% CPU
Computing log-likelihood of 98 initial trees ... 1.589 seconds
Current best score: -36689.095

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.211239 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36671.937
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36667.607
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -36665.567
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Iteration 10 / LogL: -36667.491 / Time: 0h:0m:6s
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Iteration 290 / LogL: -59355.955 / Time: 0h:10m:27s (0h:2m:29s left)
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Iteration 20 / LogL: -36667.775 / Time: 0h:0m:9s
Finish initializing candidate tree set (15)
Current best tree score: -36665.567 / CPU time: 8.641
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.382666 secs using 397.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36658.070
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -36656.717
Optimizing NNI: done in 0.322977 secs using 399.3% CPU
Optimizing NNI: done in 0.325452 secs using 398.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -36656.707
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Iteration 30 / LogL: -36666.052 / Time: 0h:0m:12s (0h:0m:41s left)
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Iteration 40 / LogL: -36660.437 / Time: 0h:0m:16s (0h:0m:36s left)
Optimizing NNI: done in 0.463126 secs using 398.4% CPU
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Optimizing NNI: done in 0.420647 secs using 397.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -36656.614
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Iteration 50 / LogL: -36656.936 / Time: 0h:0m:21s (0h:0m:40s left)
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Iteration 60 / LogL: -36672.635 / Time: 0h:0m:25s (0h:0m:36s left)
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Iteration 300 / LogL: -59359.376 / Time: 0h:10m:46s (0h:2m:7s left)
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Iteration 70 / LogL: -36656.786 / Time: 0h:0m:30s (0h:0m:32s left)
Optimizing NNI: done in 0.319782 secs using 399.3% CPU
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Iteration 80 / LogL: -36658.253 / Time: 0h:0m:33s (0h:0m:27s left)
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Iteration 90 / LogL: -36664.184 / Time: 0h:0m:38s (0h:0m:23s left)
Optimizing NNI: done in 0.292948 secs using 399% CPU
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Optimizing NNI: done in 0.353259 secs using 398.3% CPU
Iteration 100 / LogL: -36656.831 / Time: 0h:0m:42s (0h:0m:18s left)
561  FLU+R10       200558.394   1005 403126.789   2425186.789  407502.931
Optimizing NNI: done in 1.78986 secs using 299.2% CPU
Optimizing NNI: done in 0.460404 secs using 399.6% CPU
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Optimizing NNI: done in 1.80915 secs using 299.3% CPU
Iteration 310 / LogL: -59353.969 / Time: 0h:11m:5s (0h:1m:45s left)
Optimizing NNI: done in 0.568241 secs using 398.6% CPU
Iteration 110 / LogL: -36656.888 / Time: 0h:0m:46s (0h:0m:14s left)
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Iteration 120 / LogL: -36656.885 / Time: 0h:0m:50s (0h:0m:10s left)
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Iteration 130 / LogL: -36656.886 / Time: 0h:0m:53s (0h:0m:5s left)
Optimizing NNI: done in 2.30066 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.371908 secs using 399.3% CPU
Optimizing NNI: done in 0.436984 secs using 399.6% CPU
BETTER TREE FOUND at iteration 314: -59352.488
Optimizing NNI: done in 0.513372 secs using 398.9% CPU
Optimizing NNI: done in 0.368754 secs using 399% CPU
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Optimizing NNI: done in 0.24471 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36656.579
Optimizing NNI: done in 0.325814 secs using 399.5% CPU
Optimizing NNI: done in 1.94275 secs using 299.4% CPU
Optimizing NNI: done in 0.45168 secs using 398.7% CPU
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Optimizing NNI: done in 0.407271 secs using 398.4% CPU
Iteration 140 / LogL: -36657.311 / Time: 0h:0m:57s (0h:0m:1s left)
Optimizing NNI: done in 0.434333 secs using 399.4% CPU
Optimizing NNI: done in 0.412754 secs using 399.3% CPU
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Optimizing NNI: done in 0.425067 secs using 399.6% CPU
Optimizing NNI: done in 0.389269 secs using 399.5% CPU
TREE SEARCH COMPLETED AFTER 145 ITERATIONS / Time: 0h:0m:59s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36656.579
Optimal log-likelihood: -36656.576
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.650
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -36656.576
Total tree length: 20.191

Total number of iterations: 145
CPU time used for tree search: 231.926 sec (0h:3m:51s)
Wall-clock time used for tree search: 59.178 sec (0h:0m:59s)
Total CPU time used: 234.735 sec (0h:3m:54s)
Total wall-clock time used: 59.835 sec (0h:0m:59s)

===> START BOOTSTRAP REPLICATE NUMBER 86

Creating bootstrap alignment (seed: 956245)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37899.832
2. Current log-likelihood: -37070.197
3. Current log-likelihood: -37033.538
4. Current log-likelihood: -37032.407
5. Current log-likelihood: -37032.205
Optimal log-likelihood: -37032.071
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.687
Parameters optimization took 5 rounds (0.317 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0828052 secs using 399.3% CPU
Computing ML distances took 0.082938 sec (of wall-clock time) 0.330975 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000132084 secs using 452.7% CPU
Constructing RapidNJ tree: done in 0.00120592 secs using 394.6% CPU
Computing RapidNJ tree took 0.001400 sec (of wall-clock time) 0.006142 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37637.346
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.09061 secs using 299.3% CPU
1.480 second
Optimizing NNI: done in 1.54701 secs using 299.2% CPU
Computing log-likelihood of 98 initial trees ... 1.557 seconds
Current best score: -37032.071

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.380261 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36983.099
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36977.753
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -36963.781
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -36961.748
Optimizing NNI: done in 0.236035 secs using 398.8% CPU
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Optimizing NNI: done in 1.72982 secs using 299.4% CPU
Iteration 320 / LogL: -59362.189 / Time: 0h:11m:26s (0h:3m:22s left)
Optimizing NNI: done in 0.438416 secs using 398.5% CPU
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Iteration 10 / LogL: -36988.616 / Time: 0h:0m:7s
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Iteration 20 / LogL: -36975.064 / Time: 0h:0m:11s
Finish initializing candidate tree set (9)
Current best tree score: -36961.748 / CPU time: 11.084
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 0.480491 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -36960.490
570  FLU+F+R8      199008.285   1020 400056.570   2482896.570  404498.027
Optimizing NNI: done in 2.03041 secs using 299.1% CPU
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Iteration 30 / LogL: -36962.459 / Time: 0h:0m:16s (0h:0m:53s left)
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Iteration 40 / LogL: -37077.549 / Time: 0h:0m:20s (0h:0m:44s left)
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Iteration 50 / LogL: -36960.568 / Time: 0h:0m:24s (0h:0m:38s left)
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Iteration 330 / LogL: -59356.122 / Time: 0h:11m:46s (0h:3m:0s left)
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Iteration 70 / LogL: -36962.889 / Time: 0h:0m:33s (0h:0m:26s left)
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571  FLU+F+R9      198994.222   1022 400032.445   2491044.445  404482.611
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Iteration 90 / LogL: -36960.526 / Time: 0h:0m:42s (0h:0m:16s left)
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Iteration 100 / LogL: -36960.492 / Time: 0h:0m:46s (0h:0m:11s left)
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Iteration 340 / LogL: -59373.265 / Time: 0h:12m:6s (0h:2m:38s left)
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Iteration 110 / LogL: -36960.690 / Time: 0h:0m:50s (0h:0m:6s left)
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Iteration 120 / LogL: -36988.601 / Time: 0h:0m:55s (0h:0m:2s left)
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638  Dayhoff+I+R10 106791.925   554 214691.850   829631.850   216922.179
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TREE SEARCH COMPLETED AFTER 126 ITERATIONS / Time: 0h:0m:57s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36960.490
Optimal log-likelihood: -36960.490
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.701
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -36960.490
Total tree length: 20.227

Total number of iterations: 126
CPU time used for tree search: 224.763 sec (0h:3m:44s)
Wall-clock time used for tree search: 57.280 sec (0h:0m:57s)
Total CPU time used: 227.462 sec (0h:3m:47s)
Total wall-clock time used: 57.917 sec (0h:0m:57s)

===> START BOOTSTRAP REPLICATE NUMBER 87

Creating bootstrap alignment (seed: 956246)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.010 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37110.556
2. Current log-likelihood: -36244.395
3. Current log-likelihood: -36235.656
4. Current log-likelihood: -36235.378
Optimal log-likelihood: -36235.324
Proportion of invariable sites: 0.014
Gamma shape alpha: 2.166
Parameters optimization took 4 rounds (0.235 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0833881 secs using 400.1% CPU
Computing ML distances took 0.083524 sec (of wall-clock time) 0.333928 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000118017 secs using 472.8% CPU
Constructing RapidNJ tree: done in 0.00126791 secs using 513.2% CPU
Computing RapidNJ tree took 0.001436 sec (of wall-clock time) 0.007326 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36595.661
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.87083 secs using 299.4% CPU
1.429 second
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Computing log-likelihood of 98 initial trees ... 1.605 seconds
Current best score: -36225.917

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36168.745
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -36165.548
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Iteration 10 / LogL: -36169.210 / Time: 0h:0m:6s
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Iteration 350 / LogL: -59352.489 / Time: 0h:12m:26s (0h:2m:16s left)
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Iteration 20 / LogL: -36167.193 / Time: 0h:0m:9s
Finish initializing candidate tree set (11)
Current best tree score: -36165.548 / CPU time: 8.779
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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659  Dayhoff+F+I+R9 106289.136   571 213720.272   866944.272   216019.042
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Iteration 30 / LogL: -36167.197 / Time: 0h:0m:14s (0h:0m:36s left)
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Iteration 40 / LogL: -36173.810 / Time: 0h:0m:19s (0h:0m:31s left)
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572  FLU+F+R10     198990.836   1024 400029.672   2499229.672  404488.547
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Iteration 50 / LogL: -36172.316 / Time: 0h:0m:24s (0h:0m:26s left)
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Iteration 360 / LogL: -59358.092 / Time: 0h:12m:45s (0h:1m:55s left)
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Iteration 60 / LogL: -36172.374 / Time: 0h:0m:29s (0h:0m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 67: -36164.807
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Iteration 70 / LogL: -36167.478 / Time: 0h:0m:33s (0h:0m:47s left)
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36164.784
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581  rtREV+R8      198734.452   1001 399470.904   2405474.904  403829.628
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Iteration 80 / LogL: -36166.761 / Time: 0h:0m:38s (0h:0m:42s left)
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Iteration 90 / LogL: -36166.867 / Time: 0h:0m:43s (0h:0m:37s left)
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Iteration 100 / LogL: -36172.403 / Time: 0h:0m:47s (0h:0m:32s left)
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582  rtREV+R9      198720.690   1003 399447.380   2413471.380  403814.813
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Iteration 130 / LogL: -36166.034 / Time: 0h:1m:1s (0h:0m:17s left)
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Iteration 140 / LogL: -36170.417 / Time: 0h:1m:5s (0h:0m:12s left)
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Iteration 380 / LogL: -59353.702 / Time: 0h:13m:26s (0h:1m:12s left)
Optimizing NNI: done in 0.41811 secs using 398.6% CPU
Iteration 150 / LogL: -36164.907 / Time: 0h:1m:8s (0h:0m:7s left)
Optimizing NNI: done in 0.47213 secs using 399.7% CPU
Optimizing NNI: done in 0.422309 secs using 399.9% CPU
Optimizing NNI: done in 0.518101 secs using 399.4% CPU
Optimizing NNI: done in 1.9935 secs using 298.9% CPU
Optimizing NNI: done in 0.617957 secs using 399.6% CPU
Optimizing NNI: done in 0.396669 secs using 399.6% CPU
Optimizing NNI: done in 0.288867 secs using 399.6% CPU
Optimizing NNI: done in 0.496972 secs using 399.2% CPU
Optimizing NNI: done in 1.71761 secs using 298.6% CPU
Optimizing NNI: done in 0.413113 secs using 399.6% CPU
Optimizing NNI: done in 0.349948 secs using 399.8% CPU
Optimizing NNI: done in 0.539004 secs using 399.8% CPU
Iteration 160 / LogL: -36166.224 / Time: 0h:1m:13s (0h:0m:3s left)
Optimizing NNI: done in 0.388694 secs using 399.1% CPU
Optimizing NNI: done in 0.341288 secs using 399.7% CPU
Optimizing NNI: done in 0.510005 secs using 399.6% CPU
Optimizing NNI: done in 2.51426 secs using 298.9% CPU
Optimizing NNI: done in 0.440741 secs using 399.8% CPU
Optimizing NNI: done in 0.454485 secs using 399.6% CPU
Optimizing NNI: done in 0.368825 secs using 399.5% CPU
Optimizing NNI: done in 0.371609 secs using 399.8% CPU
Optimizing NNI: done in 0.386917 secs using 399.2% CPU
TREE SEARCH COMPLETED AFTER 168 ITERATIONS / Time: 0h:1m:16s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36164.784
Optimal log-likelihood: -36164.783
Proportion of invariable sites: 0.014
Gamma shape alpha: 2.172
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36164.783
Total tree length: 20.458

Total number of iterations: 168
CPU time used for tree search: 301.312 sec (0h:5m:1s)
Wall-clock time used for tree search: 76.349 sec (0h:1m:16s)
Total CPU time used: 303.328 sec (0h:5m:3s)
Total wall-clock time used: 76.831 sec (0h:1m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 88

Creating bootstrap alignment (seed: 956247)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.010 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37566.901
2. Current log-likelihood: -36628.350
3. Current log-likelihood: -36614.226
4. Current log-likelihood: -36612.727
5. Current log-likelihood: -36612.084
Optimal log-likelihood: -36612.073
Proportion of invariable sites: 0.028
Gamma shape alpha: 2.308
Parameters optimization took 5 rounds (0.321 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0797849 secs using 397.5% CPU
Computing ML distances took 0.079914 sec (of wall-clock time) 0.317460 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000121117 secs using 452.5% CPU
Constructing RapidNJ tree: done in 0.00118089 secs using 285.9% CPU
Computing RapidNJ tree took 0.001354 sec (of wall-clock time) 0.006868 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36916.470
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.3495 secs using 299.2% CPU
1.534 second
Optimizing NNI: done in 1.90499 secs using 299.1% CPU
Computing log-likelihood of 98 initial trees ... 1.539 seconds
Current best score: -36612.073

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.207143 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36586.199
Optimizing NNI: done in 0.223233 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36576.850
Optimizing NNI: done in 1.89922 secs using 299.6% CPU
Optimizing NNI: done in 0.583996 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36576.702
Optimizing NNI: done in 0.255322 secs using 399.4% CPU
Optimizing NNI: done in 0.221252 secs using 398.6% CPU
Optimizing NNI: done in 0.246598 secs using 401% CPU
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Optimizing NNI: done in 0.275639 secs using 399.5% CPU
Optimizing NNI: done in 0.611158 secs using 399.5% CPU
Iteration 10 / LogL: -36576.712 / Time: 0h:0m:7s
Optimizing NNI: done in 0.225385 secs using 399.9% CPU
Optimizing NNI: done in 0.584537 secs using 399.4% CPU
Optimizing NNI: done in 0.587532 secs using 399.2% CPU
Optimizing NNI: done in 2.24198 secs using 299.3% CPU
Optimizing NNI: done in 0.292357 secs using 399.2% CPU
583  rtREV+R10     198718.347   1005 399446.693   2421506.693  403822.835
Optimizing NNI: done in 0.314788 secs using 399.5% CPU
Optimizing NNI: done in 0.311965 secs using 399.5% CPU
Optimizing NNI: done in 0.324855 secs using 399.3% CPU
Optimizing NNI: done in 0.30238 secs using 399.5% CPU
Optimizing NNI: done in 0.295131 secs using 399.9% CPU
Optimizing NNI: done in 1.87446 secs using 299.6% CPU
Optimizing NNI: done in 0.305956 secs using 399.6% CPU
Iteration 20 / LogL: -36577.081 / Time: 0h:0m:10s
Finish initializing candidate tree set (3)
Current best tree score: -36576.702 / CPU time: 10.031
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.516785 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36576.004
Optimizing NNI: done in 0.323246 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36575.923
Optimizing NNI: done in 0.32841 secs using 399.9% CPU
Optimizing NNI: done in 0.397587 secs using 399.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -36568.132
Optimizing NNI: done in 2.09562 secs using 299.3% CPU
Iteration 390 / LogL: -59364.625 / Time: 0h:13m:47s (0h:0m:51s left)
Optimizing NNI: done in 0.511386 secs using 398.3% CPU
Optimizing NNI: done in 0.523129 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36567.986
Optimizing NNI: done in 0.79848 secs using 399% CPU
Optimizing NNI: done in 0.354278 secs using 400.3% CPU
Optimizing NNI: done in 2.12595 secs using 299.1% CPU
Optimizing NNI: done in 0.417294 secs using 399.3% CPU
Optimizing NNI: done in 0.403544 secs using 398.6% CPU
Iteration 30 / LogL: -36568.152 / Time: 0h:0m:15s (0h:0m:49s left)
Optimizing NNI: done in 0.862683 secs using 399.2% CPU
Optimizing NNI: done in 1.84225 secs using 298.8% CPU
Optimizing NNI: done in 0.76762 secs using 399.2% CPU
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Optimizing NNI: done in 1.9616 secs using 298.8% CPU
Optimizing NNI: done in 0.557575 secs using 399.7% CPU
592  rtREV+F+R8    196515.045   1020 395070.090   2477910.090  399511.547
Optimizing NNI: done in 0.437167 secs using 399.1% CPU
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Optimizing NNI: done in 0.329486 secs using 399.5% CPU
Optimizing NNI: done in 1.99276 secs using 299.1% CPU
Optimizing NNI: done in 0.347663 secs using 398% CPU
Iteration 40 / LogL: -36568.264 / Time: 0h:0m:20s (0h:0m:44s left)
Optimizing NNI: done in 0.634881 secs using 398.9% CPU
Optimizing NNI: done in 0.659477 secs using 399% CPU
Optimizing NNI: done in 0.425032 secs using 398.7% CPU
Optimizing NNI: done in 2.14496 secs using 299.3% CPU
Optimizing NNI: done in 0.458647 secs using 399.4% CPU
Optimizing NNI: done in 0.534736 secs using 399.3% CPU
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Optimizing NNI: done in 1.89979 secs using 299.4% CPU
Optimizing NNI: done in 0.633489 secs using 398.9% CPU
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Optimizing NNI: done in 0.284375 secs using 399.5% CPU
Iteration 50 / LogL: -36570.352 / Time: 0h:0m:25s (0h:0m:38s left)
Optimizing NNI: done in 0.381425 secs using 398.9% CPU
Optimizing NNI: done in 0.626964 secs using 399.4% CPU
Optimizing NNI: done in 2.16838 secs using 299.4% CPU
Optimizing NNI: done in 0.361328 secs using 399.6% CPU
Optimizing NNI: done in 0.517109 secs using 399.2% CPU
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Optimizing NNI: done in 0.37489 secs using 399.8% CPU
Optimizing NNI: done in 0.514417 secs using 399.8% CPU
Optimizing NNI: done in 2.25417 secs using 299.2% CPU
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Optimizing NNI: done in 0.522574 secs using 399.5% CPU
Optimizing NNI: done in 0.331619 secs using 400% CPU
Iteration 60 / LogL: -36568.346 / Time: 0h:0m:30s (0h:0m:32s left)
Optimizing NNI: done in 0.451385 secs using 398.5% CPU
Optimizing NNI: done in 0.430777 secs using 399.5% CPU
Optimizing NNI: done in 2.14401 secs using 299.5% CPU
Optimizing NNI: done in 0.432884 secs using 399.6% CPU
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Optimizing NNI: done in 0.336642 secs using 398.9% CPU
Optimizing NNI: done in 0.405826 secs using 399.8% CPU
Optimizing NNI: done in 0.368786 secs using 399.5% CPU
Optimizing NNI: done in 2.09278 secs using 299.2% CPU
Iteration 400 / LogL: -59441.430 / Time: 0h:14m:7s (0h:0m:29s left)
Optimizing NNI: done in 0.714535 secs using 399.7% CPU
Optimizing NNI: done in 0.286025 secs using 399.5% CPU
Optimizing NNI: done in 0.336985 secs using 400% CPU
Iteration 70 / LogL: -36570.722 / Time: 0h:0m:34s (0h:0m:27s left)
Optimizing NNI: done in 0.629604 secs using 398.9% CPU
Optimizing NNI: done in 0.288453 secs using 398.8% CPU
Optimizing NNI: done in 2.01645 secs using 299.3% CPU
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Optimizing NNI: done in 0.553403 secs using 398.5% CPU
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Optimizing NNI: done in 2.0848 secs using 298.9% CPU
Optimizing NNI: done in 0.440302 secs using 398.3% CPU
Optimizing NNI: done in 0.403454 secs using 399.9% CPU
Optimizing NNI: done in 0.528378 secs using 399.6% CPU
Optimizing NNI: done in 0.52654 secs using 398.7% CPU
Iteration 80 / LogL: -36569.734 / Time: 0h:0m:39s (0h:0m:21s left)
Optimizing NNI: done in 0.533275 secs using 399.5% CPU
Optimizing NNI: done in 2.10237 secs using 299.3% CPU
Optimizing NNI: done in 0.405456 secs using 399.1% CPU
Optimizing NNI: done in 0.662276 secs using 399.4% CPU
Optimizing NNI: done in 0.461544 secs using 399% CPU
Optimizing NNI: done in 0.213477 secs using 399.7% CPU
Optimizing NNI: done in 1.69316 secs using 298.8% CPU
Optimizing NNI: done in 0.624118 secs using 399.2% CPU
Optimizing NNI: done in 0.386253 secs using 399.6% CPU
Optimizing NNI: done in 0.501582 secs using 398.4% CPU
Optimizing NNI: done in 1.88838 secs using 299.4% CPU
Optimizing NNI: done in 0.627715 secs using 398.6% CPU
Optimizing NNI: done in 0.360177 secs using 398.8% CPU
Iteration 90 / LogL: -36568.255 / Time: 0h:0m:43s (0h:0m:16s left)
Optimizing NNI: done in 0.3831 secs using 399.4% CPU
Optimizing NNI: done in 0.288916 secs using 398.9% CPU
Optimizing NNI: done in 0.49963 secs using 398.8% CPU
Optimizing NNI: done in 1.84589 secs using 298.9% CPU
Optimizing NNI: done in 0.429162 secs using 399.2% CPU
Optimizing NNI: done in 0.233504 secs using 399.3% CPU
Optimizing NNI: done in 0.386413 secs using 399.4% CPU
Optimizing NNI: done in 0.64281 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 97: -36566.869
Optimizing NNI: done in 2.03644 secs using 299.3% CPU
Optimizing NNI: done in 0.74768 secs using 398.6% CPU
Optimizing NNI: done in 0.492905 secs using 399.6% CPU
Optimizing NNI: done in 0.444978 secs using 399.1% CPU
Iteration 100 / LogL: -36659.022 / Time: 0h:0m:48s (0h:0m:47s left)
Optimizing NNI: done in 0.386263 secs using 399.4% CPU
Optimizing NNI: done in 1.92217 secs using 299.4% CPU
Optimizing NNI: done in 0.380657 secs using 398.9% CPU
Optimizing NNI: done in 0.336213 secs using 399.3% CPU
Optimizing NNI: done in 0.371497 secs using 399.7% CPU
Optimizing NNI: done in 0.308387 secs using 399.2% CPU
Optimizing NNI: done in 0.446919 secs using 398.9% CPU
Optimizing NNI: done in 1.75949 secs using 299.3% CPU
Optimizing NNI: done in 0.227102 secs using 399.1% CPU
Optimizing NNI: done in 0.32769 secs using 399.3% CPU
Optimizing NNI: done in 0.405456 secs using 399.6% CPU
Optimizing NNI: done in 0.451525 secs using 399.7% CPU
Iteration 110 / LogL: -36567.985 / Time: 0h:0m:52s (0h:0m:41s left)
593  rtREV+F+R9    196508.638   1022 395061.277   2486073.277  399511.443
Optimizing NNI: done in 0.541326 secs using 399.6% CPU
Optimizing NNI: done in 1.87341 secs using 299.1% CPU
Iteration 410 / LogL: -59352.610 / Time: 0h:14m:27s (0h:0m:8s left)
Optimizing NNI: done in 0.339103 secs using 399.5% CPU
Optimizing NNI: done in 0.522144 secs using 399.6% CPU
Optimizing NNI: done in 0.493973 secs using 399% CPU
Optimizing NNI: done in 0.368452 secs using 399.5% CPU
Optimizing NNI: done in 0.35786 secs using 398.3% CPU
Optimizing NNI: done in 2.04666 secs using 298.9% CPU
Optimizing NNI: done in 0.537254 secs using 398.9% CPU
Optimizing NNI: done in 0.548713 secs using 398.2% CPU
Optimizing NNI: done in 0.631735 secs using 399.2% CPU
Optimizing NNI: done in 1.88112 secs using 299% CPU
Optimizing NNI: done in 0.343096 secs using 399.6% CPU
Iteration 120 / LogL: -36570.725 / Time: 0h:0m:56s (0h:0m:36s left)
Optimizing NNI: done in 0.323553 secs using 398.9% CPU
Optimizing NNI: done in 0.315744 secs using 398.6% CPU
Optimizing NNI: done in 0.665767 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -36566.867
Optimizing NNI: done in 0.466091 secs using 398.9% CPU
Optimizing NNI: done in 1.92234 secs using 299% CPU
Optimizing NNI: done in 0.513954 secs using 398.7% CPU
Optimizing NNI: done in 0.673754 secs using 398.6% CPU
Optimizing NNI: done in 0.585492 secs using 398.8% CPU
Optimizing NNI: done in 1.76815 secs using 298.4% CPU
Optimizing NNI: done in 0.598197 secs using 398.9% CPU
Optimizing NNI: done in 0.375676 secs using 398.6% CPU
Optimizing NNI: done in 0.501734 secs using 398.4% CPU
Iteration 130 / LogL: -36567.988 / Time: 0h:1m:2s (0h:0m:32s left)
Optimizing NNI: done in 0.336594 secs using 399.9% CPU
Optimizing NNI: done in 1.99989 secs using 299.1% CPU
TREE SEARCH COMPLETED AFTER 415 ITERATIONS / Time: 0h:14m:37s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59352.488
Optimizing NNI: done in 0.357177 secs using 398.5% CPU
Optimal log-likelihood: -59352.488
Site proportion and rates:  (0.101,0.062) (0.125,0.207) (0.130,0.410) (0.191,0.613) (0.159,0.886) (0.129,1.339) (0.131,2.355) (0.035,5.059)
Parameters optimization took 1 rounds (0.226 sec)
BEST SCORE FOUND : -59352.488
Total tree length: 46.011

Total number of iterations: 415
CPU time used for tree search: 2597.595 sec (0h:43m:17s)
Wall-clock time used for tree search: 871.228 sec (0h:14m:31s)
Total CPU time used: 2615.932 sec (0h:43m:35s)
Total wall-clock time used: 877.310 sec (0h:14m:37s)

===> START BOOTSTRAP REPLICATE NUMBER 4

Creating bootstrap alignment (seed: 956253)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60842.021
Optimizing NNI: done in 0.330224 secs using 399.2% CPU
Optimizing NNI: done in 0.275498 secs using 399.9% CPU
2. Current log-likelihood: -60264.620
Optimizing NNI: done in 0.629433 secs using 398.8% CPU
Optimizing NNI: done in 0.579415 secs using 399.9% CPU
3. Current log-likelihood: -60261.377
Optimizing NNI: done in 0.576897 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 137: -36566.845
Optimizing NNI: done in 0.542123 secs using 399.3% CPU
4. Current log-likelihood: -60260.035
Optimizing NNI: done in 0.534151 secs using 399.3% CPU
Optimizing NNI: done in 0.377907 secs using 399.4% CPU
Iteration 140 / LogL: -36573.552 / Time: 0h:1m:6s (0h:0m:46s left)
Optimizing NNI: done in 0.293557 secs using 399.5% CPU
5. Current log-likelihood: -60258.284
Optimizing NNI: done in 0.417966 secs using 399.7% CPU
Optimizing NNI: done in 0.494203 secs using 399.7% CPU
6. Current log-likelihood: -60255.998
Optimizing NNI: done in 0.580005 secs using 399.5% CPU
7. Current log-likelihood: -60254.409
Optimizing NNI: done in 0.604277 secs using 399.7% CPU
Optimizing NNI: done in 0.491723 secs using 398.6% CPU
8. Current log-likelihood: -60253.527
Optimizing NNI: done in 0.549426 secs using 399% CPU
Optimizing NNI: done in 0.411343 secs using 399.9% CPU
Optimizing NNI: done in 0.318953 secs using 399.3% CPU
9. Current log-likelihood: -60252.801
Optimizing NNI: done in 0.353524 secs using 399.3% CPU
Iteration 150 / LogL: -36570.639 / Time: 0h:1m:11s (0h:0m:41s left)
Optimizing NNI: done in 0.317759 secs using 399.9% CPU
Optimizing NNI: done in 0.305397 secs using 398.3% CPU
10. Current log-likelihood: -60251.997
Optimizing NNI: done in 0.490136 secs using 399.4% CPU
Optimizing NNI: done in 0.302103 secs using 399.9% CPU
11. Current log-likelihood: -60250.854
Optimizing NNI: done in 0.332969 secs using 398.7% CPU
Optimizing NNI: done in 0.483066 secs using 399.3% CPU
Optimizing NNI: done in 0.35937 secs using 399% CPU
12. Current log-likelihood: -60249.143
Optimizing NNI: done in 0.63467 secs using 399.1% CPU
13. Current log-likelihood: -60246.800
Optimizing NNI: done in 0.626569 secs using 399% CPU
Optimizing NNI: done in 0.675566 secs using 398.7% CPU
Iteration 160 / LogL: -36567.988 / Time: 0h:1m:15s (0h:0m:36s left)
14. Current log-likelihood: -60246.522
Optimizing NNI: done in 0.301209 secs using 398.6% CPU
Optimizing NNI: done in 0.278712 secs using 399.9% CPU
Optimal log-likelihood: -60246.493
Site proportion and rates:  (0.116,0.054) (0.106,0.172) (0.076,0.403) (0.088,0.428) (0.241,0.725) (0.171,1.215) (0.179,2.315) (0.022,5.002)
Parameters optimization took 14 rounds (13.536 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 0.293871 secs using 399.2% CPU
Optimizing NNI: done in 0.613145 secs using 398.9% CPU
Optimizing NNI: done in 0.607837 secs using 399% CPU
Calculating distance matrix: done in 1.5084 secs using 299.9% CPU
Computing ML distances took 1.508618 sec (of wall-clock time) 4.524888 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000468969 secs using 83.8% CPU
Constructing RapidNJ tree: done in 0.0039289 secs using 230.5% CPU
Computing RapidNJ tree took 0.004468 sec (of wall-clock time) 0.010439 sec (of CPU time)
Optimizing NNI: done in 0.531618 secs using 398.9% CPU
Log-likelihood of RapidNJ tree: -60367.779
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 0.638301 secs using 399.4% CPU
Optimizing NNI: done in 0.404463 secs using 399.8% CPU
Optimizing NNI: done in 0.603289 secs using 399.2% CPU
Optimizing NNI: done in 0.320843 secs using 398.7% CPU
Iteration 170 / LogL: -36566.996 / Time: 0h:1m:20s (0h:0m:31s left)
Optimizing NNI: done in 0.367564 secs using 399.1% CPU
Optimizing NNI: done in 0.28898 secs using 399.9% CPU
Optimizing NNI: done in 0.377484 secs using 399.4% CPU
Optimizing NNI: done in 0.296997 secs using 399.8% CPU
594  rtREV+F+R10   196506.672   1024 395061.344   2494261.344  399520.219
660  Dayhoff+F+I+R10 106286.856   573 213719.713   871523.713   216026.534
Optimizing NNI: done in 0.448822 secs using 399.4% CPU
Optimizing NNI: done in 0.707918 secs using 399.2% CPU
Optimizing NNI: done in 0.462176 secs using 399.5% CPU
Optimizing NNI: done in 0.604685 secs using 399.1% CPU
5.298 second
Optimizing NNI: done in 0.368921 secs using 399% CPU
Optimizing NNI: done in 0.42573 secs using 399.6% CPU
Iteration 180 / LogL: -36566.847 / Time: 0h:1m:24s (0h:0m:26s left)
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Optimizing NNI: done in 0.468355 secs using 399.4% CPU
Optimizing NNI: done in 0.53483 secs using 399.7% CPU
Optimizing NNI: done in 0.578924 secs using 399.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -36566.845
Optimizing NNI: done in 0.548271 secs using 399.3% CPU
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Optimizing NNI: done in 0.590202 secs using 398.7% CPU
Iteration 190 / LogL: -36566.846 / Time: 0h:1m:29s (0h:0m:22s left)
Optimizing NNI: done in 0.298393 secs using 399.1% CPU
Optimizing NNI: done in 0.664613 secs using 399.8% CPU
Optimizing NNI: done in 0.437597 secs using 399.7% CPU
Computing log-likelihood of 98 initial trees ... 6.963 seconds
Current best score: -60165.763

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.491906 secs using 398.5% CPU
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 0.717257 secs using 399.2% CPU
Iteration 200 / LogL: -36566.846 / Time: 0h:1m:34s (0h:0m:17s left)
BETTER TREE FOUND at iteration 1: -59945.578
Optimizing NNI: done in 0.624908 secs using 399.7% CPU
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Estimate model parameters (epsilon = 0.100)
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681  mtREV+I+R9    110333.742   552 221771.483   832283.483   223993.761
Optimizing NNI: done in 0.364392 secs using 399.3% CPU
BETTER TREE FOUND at iteration 2: -59897.191
603  cpREV+R8      196528.431   1001 395058.861   2401062.861  399417.586
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Iteration 210 / LogL: -36567.597 / Time: 0h:1m:39s (0h:0m:12s left)
Optimizing NNI: done in 0.335793 secs using 399.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -36566.842
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Iteration 220 / LogL: -36573.229 / Time: 0h:1m:43s (0h:0m:8s left)
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36566.757
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Optimizing NNI: done in 0.603798 secs using 399.2% CPU
Iteration 230 / LogL: -36573.939 / Time: 0h:1m:48s (0h:0m:3s left)
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Iteration 10 / LogL: -59982.916 / Time: 0h:0m:47s
Optimizing NNI: done in 0.565274 secs using 399.5% CPU
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Optimizing NNI: done in 0.726115 secs using 399.7% CPU
TREE SEARCH COMPLETED AFTER 238 ITERATIONS / Time: 0h:1m:52s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36566.757
2. Current log-likelihood: -36566.732
Optimal log-likelihood: -36566.719
Proportion of invariable sites: 0.028
Gamma shape alpha: 2.338
Parameters optimization took 2 rounds (0.084 sec)
BEST SCORE FOUND : -36566.719
Total tree length: 20.602

Total number of iterations: 238
CPU time used for tree search: 444.876 sec (0h:7m:24s)
Wall-clock time used for tree search: 112.428 sec (0h:1m:52s)
Total CPU time used: 447.622 sec (0h:7m:27s)
Total wall-clock time used: 113.083 sec (0h:1m:53s)

===> START BOOTSTRAP REPLICATE NUMBER 89

Creating bootstrap alignment (seed: 956248)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36215.439
2. Current log-likelihood: -35369.041
3. Current log-likelihood: -35349.816
4. Current log-likelihood: -35349.236
Optimal log-likelihood: -35349.130
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.655
Parameters optimization took 4 rounds (0.272 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0720949 secs using 399.9% CPU
Computing ML distances took 0.072245 sec (of wall-clock time) 0.288732 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000134945 secs using 452.8% CPU
Constructing RapidNJ tree: done in 0.00135398 secs using 365.9% CPU
Computing RapidNJ tree took 0.001540 sec (of wall-clock time) 0.007612 sec (of CPU time)
Optimizing NNI: done in 1.61009 secs using 299.5% CPU
Log-likelihood of RapidNJ tree: -36067.117
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.26483 secs using 299.5% CPU
1.433 second
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Computing log-likelihood of 98 initial trees ... 1.587 seconds
Current best score: -35349.130

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35335.686
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35335.618
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UPDATE BEST LOG-LIKELIHOOD: -35335.613
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Iteration 10 / LogL: -35336.640 / Time: 0h:0m:6s
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Iteration 20 / LogL: -35336.871 / Time: 0h:0m:8s
Finish initializing candidate tree set (7)
Current best tree score: -35335.613 / CPU time: 7.819
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -35334.614
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Iteration 20 / LogL: -59947.185 / Time: 0h:1m:2s
Finish initializing candidate tree set (20)
Current best tree score: -59897.191 / CPU time: 46.400
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
604  cpREV+R9      196515.402   1003 395036.804   2409060.804  399404.237
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Iteration 30 / LogL: -35336.826 / Time: 0h:0m:12s (0h:0m:40s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 21: -59884.797
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Iteration 40 / LogL: -35335.047 / Time: 0h:0m:16s (0h:0m:36s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -35334.408
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BETTER TREE FOUND at iteration 22: -59874.754
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Iteration 50 / LogL: -35334.944 / Time: 0h:0m:20s (0h:0m:39s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -35333.864
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Iteration 60 / LogL: -35335.149 / Time: 0h:0m:24s (0h:0m:38s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 26: -59868.655
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Iteration 70 / LogL: -35345.396 / Time: 0h:0m:29s (0h:0m:34s left)
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Iteration 80 / LogL: -35334.114 / Time: 0h:0m:32s (0h:0m:29s left)
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Iteration 30 / LogL: -59870.296 / Time: 0h:1m:26s (0h:4m:45s left)
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Iteration 100 / LogL: -35336.061 / Time: 0h:0m:41s (0h:0m:21s left)
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Iteration 110 / LogL: -35335.769 / Time: 0h:0m:45s (0h:0m:17s left)
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Iteration 120 / LogL: -35334.009 / Time: 0h:0m:49s (0h:0m:12s left)
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605  cpREV+R10     196510.888   1005 395031.776   2417091.776  399407.918
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Iteration 40 / LogL: -59893.171 / Time: 0h:1m:43s (0h:3m:48s left)
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Iteration 130 / LogL: -35341.927 / Time: 0h:0m:53s (0h:0m:8s left)
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Iteration 140 / LogL: -35333.878 / Time: 0h:0m:58s (0h:0m:4s left)
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Iteration 150 / LogL: -35334.847 / Time: 0h:1m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.48908 secs using 399% CPU
Optimizing NNI: done in 1.93853 secs using 299.5% CPU
Optimizing NNI: done in 0.516571 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 152 ITERATIONS / Time: 0h:1m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35333.864
Optimal log-likelihood: -35333.836
Proportion of invariable sites: 0.023
Gamma shape alpha: 2.607
Parameters optimization took 1 rounds (0.056 sec)
BEST SCORE FOUND : -35333.836
Total tree length: 18.852

Total number of iterations: 152
CPU time used for tree search: 245.992 sec (0h:4m:5s)
Wall-clock time used for tree search: 62.623 sec (0h:1m:2s)
Total CPU time used: 249.190 sec (0h:4m:9s)
Total wall-clock time used: 63.377 sec (0h:1m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 90

Creating bootstrap alignment (seed: 956249)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.019 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36627.113
WARNING: Log-likelihood -110344 of mtREV+I+R10 worse than mtREV+I+R9 -110334
2. Current log-likelihood: -35784.777
682  mtREV+I+R10   110344.459   554 221796.917   836736.917   224027.247
3. Current log-likelihood: -35770.203
4. Current log-likelihood: -35769.039
5. Current log-likelihood: -35768.432
Optimal log-likelihood: -35768.352
Proportion of invariable sites: 0.014
Gamma shape alpha: 2.172
Parameters optimization took 5 rounds (0.316 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.075722 secs using 398.5% CPU
Computing ML distances took 0.075862 sec (of wall-clock time) 0.302088 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000127077 secs
Constructing RapidNJ tree: done in 0.00127578 secs using 377.9% CPU
Computing RapidNJ tree took 0.001455 sec (of wall-clock time) 0.006257 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36239.607
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.36342 secs using 298.7% CPU
1.531 second
Optimizing NNI: done in 1.72227 secs using 299.3% CPU
Computing log-likelihood of 98 initial trees ... 1.532 seconds
Current best score: -35738.183

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.192947 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35698.440
Optimizing NNI: done in 0.278927 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35698.362
Optimizing NNI: done in 1.49982 secs using 299.7% CPU
Optimizing NNI: done in 0.285962 secs using 399% CPU
Optimizing NNI: done in 0.18356 secs using 399.7% CPU
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Optimizing NNI: done in 0.243535 secs using 398% CPU
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Optimizing NNI: done in 0.181261 secs using 398.4% CPU
Optimizing NNI: done in 0.182112 secs using 397.7% CPU
Iteration 10 / LogL: -35699.612 / Time: 0h:0m:5s
Optimizing NNI: done in 1.73787 secs using 299.5% CPU
Optimizing NNI: done in 0.184583 secs using 398.4% CPU
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Optimizing NNI: done in 0.211771 secs using 399.1% CPU
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Optimizing NNI: done in 0.206653 secs using 398.9% CPU
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Optimizing NNI: done in 0.23766 secs using 398.6% CPU
Optimizing NNI: done in 0.180432 secs using 398.9% CPU
Optimizing NNI: done in 0.224854 secs using 397.5% CPU
Optimizing NNI: done in 1.89805 secs using 299.1% CPU
Iteration 50 / LogL: -59880.031 / Time: 0h:2m:1s (0h:3m:8s left)
Optimizing NNI: done in 0.264014 secs using 398.5% CPU
Iteration 20 / LogL: -35699.901 / Time: 0h:0m:8s
Finish initializing candidate tree set (11)
Current best tree score: -35698.362 / CPU time: 7.560
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.31508 secs using 398.2% CPU
Optimizing NNI: done in 0.416995 secs using 397.8% CPU
Optimizing NNI: done in 0.436542 secs using 398.5% CPU
Optimizing NNI: done in 0.429559 secs using 398.5% CPU
Optimizing NNI: done in 1.84412 secs using 299.4% CPU
Optimizing NNI: done in 0.402204 secs using 398.3% CPU
Optimizing NNI: done in 0.389413 secs using 398.3% CPU
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Optimizing NNI: done in 0.404955 secs using 399.4% CPU
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Optimizing NNI: done in 1.97794 secs using 299.3% CPU
Optimizing NNI: done in 0.351255 secs using 398.1% CPU
Iteration 30 / LogL: -35700.130 / Time: 0h:0m:12s (0h:0m:29s left)
Optimizing NNI: done in 0.5383 secs using 398.4% CPU
Optimizing NNI: done in 0.54786 secs using 398.6% CPU
Optimizing NNI: done in 1.74849 secs using 299.3% CPU
Optimizing NNI: done in 0.469992 secs using 399.5% CPU
Optimizing NNI: done in 0.435515 secs using 398.4% CPU
Optimizing NNI: done in 0.525452 secs using 398.4% CPU
Optimizing NNI: done in 0.382213 secs using 399% CPU
Optimizing NNI: done in 1.68897 secs using 299.6% CPU
Optimizing NNI: done in 0.384355 secs using 399.4% CPU
Optimizing NNI: done in 0.309025 secs using 399.5% CPU
Optimizing NNI: done in 0.357778 secs using 398.8% CPU
Optimizing NNI: done in 0.349408 secs using 398.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -35698.359
Iteration 40 / LogL: -35698.359 / Time: 0h:0m:16s (0h:0m:25s left)
Optimizing NNI: done in 0.311702 secs using 399.3% CPU
Optimizing NNI: done in 0.402574 secs using 398.8% CPU
Optimizing NNI: done in 1.97109 secs using 298.9% CPU
Optimizing NNI: done in 0.372149 secs using 398.1% CPU
Optimizing NNI: done in 0.532841 secs using 398.2% CPU
Optimizing NNI: done in 0.235382 secs using 398.3% CPU
Optimizing NNI: done in 0.617943 secs using 398.3% CPU
Optimizing NNI: done in 1.69782 secs using 299.4% CPU
Optimizing NNI: done in 0.419825 secs using 398.7% CPU
Optimizing NNI: done in 0.347066 secs using 399.5% CPU
Optimizing NNI: done in 0.323745 secs using 398.5% CPU
Optimizing NNI: done in 0.281564 secs using 400.4% CPU
Iteration 50 / LogL: -35699.011 / Time: 0h:0m:20s (0h:0m:21s left)
614  cpREV+F+R8    195115.409   1020 392270.817   2475110.817  396712.275
Optimizing NNI: done in 0.415281 secs using 399.1% CPU
Optimizing NNI: done in 1.78832 secs using 299.5% CPU
Optimizing NNI: done in 0.478504 secs using 399.4% CPU
Optimizing NNI: done in 0.454726 secs using 398.4% CPU
Optimizing NNI: done in 0.365365 secs using 399.2% CPU
703  mtREV+F+I+R9  107399.759   571 215941.518   869165.518   218240.288
Optimizing NNI: done in 0.430421 secs using 399% CPU
Optimizing NNI: done in 1.8323 secs using 299.3% CPU
Optimizing NNI: done in 0.334237 secs using 399.6% CPU
Optimizing NNI: done in 0.597154 secs using 398.5% CPU
Optimizing NNI: done in 0.35062 secs using 399% CPU
Optimizing NNI: done in 0.378675 secs using 398.9% CPU
Optimizing NNI: done in 1.62188 secs using 299.2% CPU
Optimizing NNI: done in 0.509784 secs using 399.2% CPU
Iteration 60 / LogL: -35698.863 / Time: 0h:0m:24s (0h:0m:17s left)
Optimizing NNI: done in 0.246992 secs using 399.1% CPU
Optimizing NNI: done in 0.396891 secs using 399.2% CPU
Optimizing NNI: done in 0.602756 secs using 398% CPU
Optimizing NNI: done in 1.77293 secs using 299.4% CPU
Iteration 60 / LogL: -59870.325 / Time: 0h:2m:19s (0h:2m:36s left)
Optimizing NNI: done in 0.487871 secs using 399.5% CPU
Optimizing NNI: done in 0.310821 secs using 398.9% CPU
Optimizing NNI: done in 0.363786 secs using 399.4% CPU
Optimizing NNI: done in 0.314934 secs using 398% CPU
Optimizing NNI: done in 0.358714 secs using 399.3% CPU
Optimizing NNI: done in 1.9182 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.466904 secs using 399.4% CPU
Optimizing NNI: done in 0.324526 secs using 398.3% CPU
Iteration 70 / LogL: -35699.190 / Time: 0h:0m:28s (0h:0m:13s left)
BETTER TREE FOUND at iteration 61: -59868.187
Optimizing NNI: done in 0.45186 secs using 398.4% CPU
Optimizing NNI: done in 0.455123 secs using 399.8% CPU
Optimizing NNI: done in 0.429209 secs using 399.4% CPU
Optimizing NNI: done in 0.262423 secs using 398.1% CPU
Optimizing NNI: done in 0.479977 secs using 398.8% CPU
Optimizing NNI: done in 1.80529 secs using 299% CPU
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Optimizing NNI: done in 0.299763 secs using 397.9% CPU
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Optimizing NNI: done in 0.357508 secs using 398.5% CPU
Optimizing NNI: done in 0.468821 secs using 398% CPU
Iteration 80 / LogL: -35699.294 / Time: 0h:0m:32s (0h:0m:9s left)
Optimizing NNI: done in 1.95623 secs using 299.1% CPU
Optimizing NNI: done in 0.320334 secs using 399.6% CPU
Optimizing NNI: done in 0.514068 secs using 398.6% CPU
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Optimizing NNI: done in 1.53449 secs using 299.2% CPU
Optimizing NNI: done in 0.529644 secs using 398% CPU
Optimizing NNI: done in 0.439151 secs using 399% CPU
Optimizing NNI: done in 0.310948 secs using 398.4% CPU
Optimizing NNI: done in 0.536512 secs using 398.7% CPU
Optimizing NNI: done in 1.63324 secs using 299.4% CPU
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Optimizing NNI: done in 0.376899 secs using 399% CPU
Optimizing NNI: done in 0.454457 secs using 399.4% CPU
Iteration 90 / LogL: -35698.437 / Time: 0h:0m:36s (0h:0m:4s left)
Optimizing NNI: done in 0.360341 secs using 399.1% CPU
Optimizing NNI: done in 0.402971 secs using 398.5% CPU
Optimizing NNI: done in 1.89965 secs using 299.1% CPU
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Optimizing NNI: done in 1.97894 secs using 299.6% CPU
Optimizing NNI: done in 0.518884 secs using 399.4% CPU
Optimizing NNI: done in 0.398223 secs using 399.6% CPU
Optimizing NNI: done in 0.593503 secs using 399% CPU
Optimizing NNI: done in 0.297661 secs using 398.9% CPU
Iteration 100 / LogL: -35701.365 / Time: 0h:0m:41s (0h:0m:0s left)
Optimizing NNI: done in 0.456406 secs using 399.4% CPU
Optimizing NNI: done in 2.00172 secs using 299.5% CPU
Optimizing NNI: done in 0.398994 secs using 399.1% CPU
Optimizing NNI: done in 0.555843 secs using 399.5% CPU
TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:42s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35698.359
Optimal log-likelihood: -35698.350
Proportion of invariable sites: 0.014
Gamma shape alpha: 2.168
Parameters optimization took 1 rounds (0.046 sec)
BEST SCORE FOUND : -35698.350
Total tree length: 19.989

Total number of iterations: 103
CPU time used for tree search: 163.735 sec (0h:2m:43s)
Wall-clock time used for tree search: 42.050 sec (0h:0m:42s)
Total CPU time used: 166.242 sec (0h:2m:46s)
Total wall-clock time used: 42.649 sec (0h:0m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 91

Creating bootstrap alignment (seed: 956250)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.021 seconds

NOTE: 18 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37191.729
2. Current log-likelihood: -36356.352
3. Current log-likelihood: -36342.828
4. Current log-likelihood: -36342.631
Optimal log-likelihood: -36342.625
Proportion of invariable sites: 0.028
Gamma shape alpha: 2.774
Parameters optimization took 4 rounds (0.263 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0766239 secs using 396.8% CPU
Computing ML distances took 0.076768 sec (of wall-clock time) 0.304409 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000146866 secs using 106.2% CPU
Constructing RapidNJ tree: done in 0.00119901 secs
Computing RapidNJ tree took 0.001394 sec (of wall-clock time) 0.000974 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36514.864
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.51892 secs using 299.4% CPU
1.590 second
Computing log-likelihood of 98 initial trees ... 1.613 seconds
Current best score: -36251.268

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.224603 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36181.193
Optimizing NNI: done in 2.32537 secs using 298.9% CPU
Iteration 70 / LogL: -59874.284 / Time: 0h:2m:40s (0h:3m:31s left)
Optimizing NNI: done in 0.20362 secs using 399.9% CPU
Optimizing NNI: done in 0.222837 secs using 398.8% CPU
Optimizing NNI: done in 0.237319 secs using 399.6% CPU
Optimizing NNI: done in 0.452151 secs using 397.8% CPU
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Optimizing NNI: done in 0.58724 secs using 398.9% CPU
Optimizing NNI: done in 2.25657 secs using 298.8% CPU
Optimizing NNI: done in 0.23264 secs using 400.5% CPU
Optimizing NNI: done in 0.589619 secs using 399.1% CPU
Iteration 10 / LogL: -36185.119 / Time: 0h:0m:7s
Optimizing NNI: done in 0.210878 secs using 399.1% CPU
Optimizing NNI: done in 0.394671 secs using 399.4% CPU
Optimizing NNI: done in 0.239875 secs using 399.7% CPU
Optimizing NNI: done in 0.292536 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36181.119
Optimizing NNI: done in 0.362176 secs using 397.9% CPU
Optimizing NNI: done in 2.20633 secs using 299.1% CPU
Optimizing NNI: done in 0.31704 secs using 400% CPU
Optimizing NNI: done in 0.214952 secs using 399.1% CPU
Optimizing NNI: done in 0.255771 secs using 398.1% CPU
Optimizing NNI: done in 0.262938 secs using 399.6% CPU
Optimizing NNI: done in 0.246321 secs using 399.6% CPU
Iteration 20 / LogL: -36181.277 / Time: 0h:0m:9s
Finish initializing candidate tree set (10)
Current best tree score: -36181.119 / CPU time: 9.402
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.444347 secs using 399.3% CPU
Optimizing NNI: done in 0.400367 secs using 399% CPU
Optimizing NNI: done in 2.45594 secs using 298.5% CPU
Optimizing NNI: done in 0.351473 secs using 399.1% CPU
Optimizing NNI: done in 0.297625 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36180.977
Optimizing NNI: done in 0.425292 secs using 397.7% CPU
Optimizing NNI: done in 0.449425 secs using 398.9% CPU
Optimizing NNI: done in 0.508317 secs using 398.2% CPU
Optimizing NNI: done in 2.0616 secs using 298.9% CPU
Optimizing NNI: done in 0.38961 secs using 399.1% CPU
Optimizing NNI: done in 0.563291 secs using 399% CPU
Optimizing NNI: done in 0.419944 secs using 398.8% CPU
Iteration 30 / LogL: -36186.760 / Time: 0h:0m:14s (0h:0m:34s left)
Optimizing NNI: done in 0.401831 secs using 398.1% CPU
Optimizing NNI: done in 1.70927 secs using 298.8% CPU
Optimizing NNI: done in 0.398103 secs using 397.5% CPU
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Optimizing NNI: done in 0.531467 secs using 399.9% CPU
Optimizing NNI: done in 0.391304 secs using 399.1% CPU
Iteration 40 / LogL: -36185.265 / Time: 0h:0m:18s (0h:0m:28s left)
Optimizing NNI: done in 2.03523 secs using 299.3% CPU
Optimizing NNI: done in 0.578292 secs using 399.3% CPU
Optimizing NNI: done in 0.588354 secs using 399.1% CPU
BETTER TREE FOUND at iteration 42: -36180.975
Optimizing NNI: done in 0.38218 secs using 399.3% CPU
Optimizing NNI: done in 1.70246 secs using 298.8% CPU
Optimizing NNI: done in 0.335946 secs using 399.6% CPU
Optimizing NNI: done in 0.535852 secs using 399% CPU
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Optimizing NNI: done in 0.415824 secs using 399.6% CPU
Optimizing NNI: done in 0.468163 secs using 398.3% CPU
Iteration 50 / LogL: -36181.267 / Time: 0h:0m:22s (0h:0m:42s left)
Optimizing NNI: done in 0.377021 secs using 399.4% CPU
Optimizing NNI: done in 1.50572 secs using 299.3% CPU
Iteration 80 / LogL: -59870.507 / Time: 0h:2m:59s (0h:3m:3s left)
Optimizing NNI: done in 0.269042 secs using 398.5% CPU
Optimizing NNI: done in 0.45819 secs using 398.2% CPU
Optimizing NNI: done in 0.296323 secs using 398.8% CPU
Optimizing NNI: done in 0.422614 secs using 399.9% CPU
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Optimizing NNI: done in 2.09477 secs using 299.1% CPU
Optimizing NNI: done in 0.654749 secs using 398.1% CPU
Optimizing NNI: done in 0.418222 secs using 399% CPU
Optimizing NNI: done in 0.317898 secs using 399% CPU
Optimizing NNI: done in 0.485812 secs using 399.6% CPU
Iteration 60 / LogL: -36217.731 / Time: 0h:0m:26s (0h:0m:37s left)
Optimizing NNI: done in 0.358248 secs using 398.7% CPU
Optimizing NNI: done in 2.04964 secs using 299.4% CPU
Optimizing NNI: done in 0.346195 secs using 398.7% CPU
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Optimizing NNI: done in 0.355155 secs using 400% CPU
Optimizing NNI: done in 1.60407 secs using 299.5% CPU
BETTER TREE FOUND at iteration 83: -59868.180
Optimizing NNI: done in 0.373383 secs using 399.4% CPU
Optimizing NNI: done in 0.459721 secs using 399.3% CPU
Optimizing NNI: done in 0.540664 secs using 397.4% CPU
Optimizing NNI: done in 0.337504 secs using 398% CPU
615  cpREV+F+R9    195110.262   1022 392264.525   2483276.525  396714.691
Akaike Information Criterion:           LG+F+R9
Corrected Akaike Information Criterion: LG+G4
Bayesian Information Criterion:         LG+F+R8
Best-fit model: LG+F+R8 chosen according to BIC

All model information printed to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz
CPU time for ModelFinder: 22365.098 seconds (6h:12m:45s)
Wall-clock time for ModelFinder: 5727.319 seconds (1h:35m:27s)

===> START BOOTSTRAP REPLICATE NUMBER 1

Creating bootstrap alignment (seed: 958747)...

Optimizing NNI: done in 0.302736 secs using 398.9% CPU
Iteration 70 / LogL: -36186.453 / Time: 0h:0m:30s (0h:0m:32s left)
Optimizing NNI: done in 1.96342 secs using 299.1% CPU
Optimizing NNI: done in 0.294519 secs using 399.3% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.357 seconds

NOTE: 242 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -195367.583
Optimizing NNI: done in 0.261212 secs using 399.2% CPU
Optimizing NNI: done in 0.490212 secs using 398.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -36180.972
Optimizing NNI: done in 0.423206 secs using 398.5% CPU
Optimizing NNI: done in 1.87985 secs using 299.7% CPU
Optimizing NNI: done in 0.459761 secs using 398.4% CPU
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Optimizing NNI: done in 0.420335 secs using 398.1% CPU
Optimizing NNI: done in 2.04872 secs using 299.2% CPU
2. Current log-likelihood: -193003.246
Optimizing NNI: done in 0.52551 secs using 397.7% CPU
Iteration 80 / LogL: -36181.189 / Time: 0h:0m:35s (0h:0m:27s left)
Optimizing NNI: done in 0.307763 secs using 399.9% CPU
Optimizing NNI: done in 0.384653 secs using 399.6% CPU
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Optimizing NNI: done in 1.89088 secs using 299.3% CPU
Optimizing NNI: done in 0.372796 secs using 398.4% CPU
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Optimizing NNI: done in 1.76968 secs using 299.3% CPU
Optimizing NNI: done in 0.293324 secs using 398.7% CPU
3. Current log-likelihood: -192991.571
Optimizing NNI: done in 0.350652 secs using 398.4% CPU
Iteration 90 / LogL: -36211.346 / Time: 0h:0m:39s (0h:0m:22s left)
Optimizing NNI: done in 0.459276 secs using 398.4% CPU
Optimizing NNI: done in 0.413415 secs using 399.6% CPU
Optimizing NNI: done in 1.76405 secs using 299.2% CPU
Optimizing NNI: done in 0.41215 secs using 399.5% CPU
Optimizing NNI: done in 0.355546 secs using 399.1% CPU
Optimizing NNI: done in 0.413572 secs using 399.3% CPU
Optimizing NNI: done in 0.517225 secs using 398.9% CPU
Optimizing NNI: done in 0.495724 secs using 399% CPU
Optimizing NNI: done in 1.99612 secs using 299.5% CPU
Estimate model parameters (epsilon = 0.100)
4. Current log-likelihood: -192991.238
Optimizing NNI: done in 0.385157 secs using 397.4% CPU
Optimizing NNI: done in 0.341886 secs using 397.9% CPU
Optimizing NNI: done in 0.346768 secs using 397.4% CPU
Iteration 100 / LogL: -36181.115 / Time: 0h:0m:43s (0h:0m:18s left)
Optimizing NNI: done in 0.554212 secs using 398% CPU
Optimizing NNI: done in 0.468449 secs using 399.4% CPU
BETTER TREE FOUND at iteration 90: -59867.818
Iteration 90 / LogL: -59867.818 / Time: 0h:3m:20s (0h:3m:45s left)
Optimizing NNI: done in 0.396747 secs using 399.1% CPU
Optimizing NNI: done in 0.395347 secs using 399.5% CPU
Optimal log-likelihood: -192991.093
Site proportion and rates:  (0.018,0.104) (0.039,0.246) (0.115,0.360) (0.235,0.548) (0.166,0.764) (0.182,1.098) (0.158,1.654) (0.087,2.657)
Parameters optimization took 4 rounds (13.981 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 0.459335 secs using 398.9% CPU
Optimizing NNI: done in 0.471117 secs using 397.8% CPU
Optimizing NNI: done in 1.81356 secs using 299.3% CPU
Optimizing NNI: done in 0.542854 secs using 398.7% CPU
Optimizing NNI: done in 0.370824 secs using 398% CPU
Optimizing NNI: done in 0.464645 secs using 398.2% CPU
Optimizing NNI: done in 0.305194 secs using 398.3% CPU
Iteration 110 / LogL: -36185.135 / Time: 0h:0m:47s (0h:0m:13s left)
Optimizing NNI: done in 1.57562 secs using 299.2% CPU
Optimizing NNI: done in 0.430837 secs using 399.4% CPU
Optimizing NNI: done in 0.605588 secs using 399% CPU
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Optimizing NNI: done in 1.637 secs using 299.3% CPU
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Optimizing NNI: done in 0.350278 secs using 397.9% CPU
Optimizing NNI: done in 0.546947 secs using 398.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -36180.972
Optimizing NNI: done in 0.322445 secs using 399.5% CPU
Optimizing NNI: done in 0.340021 secs using 399.1% CPU
Optimizing NNI: done in 1.9621 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.454135 secs using 398.4% CPU
Optimizing NNI: done in 0.334297 secs using 398.3% CPU
Iteration 120 / LogL: -36181.129 / Time: 0h:0m:51s (0h:0m:9s left)
BETTER TREE FOUND at iteration 94: -59867.091
Optimizing NNI: done in 0.477094 secs using 398.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -36180.970
Optimizing NNI: done in 0.335453 secs using 398.5% CPU
Optimizing NNI: done in 0.397229 secs using 397.9% CPU
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Optimizing NNI: done in 1.79876 secs using 299.4% CPU
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Optimizing NNI: done in 1.62592 secs using 299.5% CPU
Optimizing NNI: done in 0.359859 secs using 397.9% CPU
Iteration 130 / LogL: -36182.498 / Time: 0h:0m:55s (0h:0m:5s left)
Optimizing NNI: done in 0.4796 secs using 398.5% CPU
Optimizing NNI: done in 0.370397 secs using 398.1% CPU
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Optimizing NNI: done in 1.67955 secs using 299.1% CPU
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Optimizing NNI: done in 1.59588 secs using 299.2% CPU
Optimizing NNI: done in 0.415831 secs using 399% CPU
Optimizing NNI: done in 0.461929 secs using 399.6% CPU
Iteration 140 / LogL: -36182.583 / Time: 0h:0m:59s (0h:0m:0s left)
Optimizing NNI: done in 0.463203 secs using 398.3% CPU
Optimizing NNI: done in 0.337382 secs using 399.6% CPU
Optimizing NNI: done in 1.58497 secs using 299.2% CPU
Calculating distance matrix: done in 15.687 secs using 399.8% CPU
Computing ML distances took 15.687634 sec (of wall-clock time) 62.725427 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00230908 secs using 198.8% CPU
Constructing RapidNJ tree: done in 0.0322878 secs using 487.2% CPU
Computing RapidNJ tree took 0.034699 sec (of wall-clock time) 0.162680 sec (of CPU time)
Optimizing NNI: done in 0.453339 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 143 ITERATIONS / Time: 0h:1m:1s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36180.970
Optimal log-likelihood: -36180.970
Proportion of invariable sites: 0.026
Gamma shape alpha: 2.743
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -36180.970
Total tree length: 20.090

Total number of iterations: 143
CPU time used for tree search: 237.271 sec (0h:3m:57s)
Wall-clock time used for tree search: 60.535 sec (0h:1m:0s)
Total CPU time used: 239.499 sec (0h:3m:59s)
Total wall-clock time used: 61.070 sec (0h:1m:1s)

===> START BOOTSTRAP REPLICATE NUMBER 92

Creating bootstrap alignment (seed: 956251)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36777.784
2. Current log-likelihood: -35896.694
3. Current log-likelihood: -35880.240
4. Current log-likelihood: -35879.584
Optimal log-likelihood: -35879.574
Proportion of invariable sites: 0.028
Gamma shape alpha: 2.703
Parameters optimization took 4 rounds (0.260 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0746801 secs using 399.3% CPU
Computing ML distances took 0.074808 sec (of wall-clock time) 0.298512 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000130892 secs using 459.2% CPU
Constructing RapidNJ tree: done in 0.00128317 secs using 347% CPU
Computing RapidNJ tree took 0.001463 sec (of wall-clock time) 0.006697 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36339.626
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.03145 secs using 299.4% CPU
Iteration 100 / LogL: -59868.130 / Time: 0h:3m:39s (0h:3m:27s left)
1.572 second
Log-likelihood of RapidNJ tree: -198263.680
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Computing log-likelihood of 98 initial trees ... 1.587 seconds
Current best score: -35879.574

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.325157 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35854.184
Optimizing NNI: done in 2.55697 secs using 299.2% CPU
Optimizing NNI: done in 0.284488 secs using 398.5% CPU
Optimizing NNI: done in 0.291662 secs using 398.6% CPU
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Optimizing NNI: done in 2.21256 secs using 299.7% CPU
Optimizing NNI: done in 0.291793 secs using 399.7% CPU
Optimizing NNI: done in 0.285603 secs using 399.3% CPU
Iteration 10 / LogL: -35854.185 / Time: 0h:0m:6s
Optimizing NNI: done in 0.271382 secs using 398.7% CPU
Optimizing NNI: done in 0.276745 secs using 397.9% CPU
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Optimizing NNI: done in 0.294384 secs using 398.9% CPU
Iteration 20 / LogL: -35854.186 / Time: 0h:0m:9s
Finish initializing candidate tree set (1)
Current best tree score: -35854.184 / CPU time: 9.019
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.9226 secs using 299.2% CPU
Optimizing NNI: done in 0.619973 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -35849.997
Optimizing NNI: done in 0.276831 secs using 397.7% CPU
Optimizing NNI: done in 0.434361 secs using 399.2% CPU
Optimizing NNI: done in 0.620177 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -35849.343
Optimizing NNI: done in 1.80424 secs using 299.2% CPU
Optimizing NNI: done in 0.267102 secs using 400.2% CPU
Optimizing NNI: done in 0.330361 secs using 398.5% CPU
Optimizing NNI: done in 0.434763 secs using 398.5% CPU
Optimizing NNI: done in 0.392944 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -35849.339
Optimizing NNI: done in 1.77959 secs using 299.4% CPU
Optimizing NNI: done in 0.642803 secs using 397.6% CPU
Optimizing NNI: done in 0.355237 secs using 398.3% CPU
Iteration 30 / LogL: -35862.064 / Time: 0h:0m:14s (0h:0m:46s left)
Optimizing NNI: done in 0.346754 secs using 399.4% CPU
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Optimizing NNI: done in 1.73809 secs using 299.5% CPU
Optimizing NNI: done in 0.484093 secs using 399.2% CPU
Iteration 40 / LogL: -35849.352 / Time: 0h:0m:18s (0h:0m:40s left)
Optimizing NNI: done in 0.534047 secs using 398.7% CPU
Optimizing NNI: done in 0.496214 secs using 399% CPU
Optimizing NNI: done in 1.57603 secs using 299.1% CPU
Iteration 110 / LogL: -59890.527 / Time: 0h:3m:57s (0h:3m:2s left)
Optimizing NNI: done in 0.395396 secs using 399.4% CPU
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Optimizing NNI: done in 0.6123 secs using 398.6% CPU
Iteration 50 / LogL: -35849.380 / Time: 0h:0m:23s (0h:0m:35s left)
Optimizing NNI: done in 1.82419 secs using 299.4% CPU
Optimizing NNI: done in 0.422052 secs using 398.9% CPU
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Optimizing NNI: done in 0.427137 secs using 399.4% CPU
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Optimizing NNI: done in 1.69468 secs using 299.3% CPU
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Optimizing NNI: done in 1.44199 secs using 299.3% CPU
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Optimizing NNI: done in 0.373831 secs using 398.6% CPU
Iteration 60 / LogL: -35849.868 / Time: 0h:0m:27s (0h:0m:30s left)
Optimizing NNI: done in 1.26704 secs using 299.5% CPU
Optimizing NNI: done in 0.472168 secs using 397.6% CPU
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Optimizing NNI: done in 1.86112 secs using 299.4% CPU
Optimizing NNI: done in 0.468401 secs using 398.5% CPU
Optimizing NNI: done in 0.511763 secs using 398.6% CPU
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Optimizing NNI: done in 1.41681 secs using 299.3% CPU
Optimizing NNI: done in 0.522203 secs using 398.9% CPU
Optimizing NNI: done in 0.355503 secs using 398.8% CPU
Iteration 70 / LogL: -35856.935 / Time: 0h:0m:32s (0h:0m:25s left)
Optimizing NNI: done in 0.553346 secs using 399.1% CPU
Optimizing NNI: done in 0.425556 secs using 398.8% CPU
Optimizing NNI: done in 1.71592 secs using 299.3% CPU
30.541 second
Optimizing NNI: done in 0.593604 secs using 399.1% CPU
Optimizing NNI: done in 0.577615 secs using 399.6% CPU
Optimizing NNI: done in 0.521875 secs using 399% CPU
Optimizing NNI: done in 1.75596 secs using 299.6% CPU
Optimizing NNI: done in 0.431678 secs using 398.7% CPU
Optimizing NNI: done in 0.55218 secs using 399.4% CPU
Optimizing NNI: done in 0.582224 secs using 398.5% CPU
Optimizing NNI: done in 1.61202 secs using 299.3% CPU
Iteration 120 / LogL: -59868.227 / Time: 0h:4m:13s (0h:2m:37s left)
Optimizing NNI: done in 0.45661 secs using 399.1% CPU
Optimizing NNI: done in 0.480604 secs using 399.2% CPU
Iteration 80 / LogL: -35850.984 / Time: 0h:0m:37s (0h:0m:20s left)
Optimizing NNI: done in 0.425887 secs using 398.5% CPU
Optimizing NNI: done in 0.559544 secs using 399.3% CPU
Optimizing NNI: done in 1.79929 secs using 299.6% CPU
Optimizing NNI: done in 0.496861 secs using 397.1% CPU
704  mtREV+F+I+R10 107397.701   573 215941.402   873745.402   218248.223
Optimizing NNI: done in 0.721797 secs using 398.4% CPU
Optimizing NNI: done in 0.366855 secs using 398.5% CPU
Optimizing NNI: done in 1.63397 secs using 299.3% CPU
Optimizing NNI: done in 0.333683 secs using 399.3% CPU
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Optimizing NNI: done in 0.567098 secs using 398.4% CPU
Optimizing NNI: done in 1.48082 secs using 299.4% CPU
Optimizing NNI: done in 0.50681 secs using 399.4% CPU
Optimizing NNI: done in 0.40857 secs using 398.4% CPU
Iteration 90 / LogL: -35849.416 / Time: 0h:0m:42s (0h:0m:16s left)
Optimizing NNI: done in 0.487133 secs using 399% CPU
Optimizing NNI: done in 0.376844 secs using 398.9% CPU
Optimizing NNI: done in 1.69206 secs using 299.2% CPU
Optimizing NNI: done in 0.526147 secs using 399.7% CPU
Optimizing NNI: done in 0.544346 secs using 398.4% CPU
Optimizing NNI: done in 0.424038 secs using 397.9% CPU
Optimizing NNI: done in 0.498975 secs using 398% CPU
Optimizing NNI: done in 1.90747 secs using 299.6% CPU
Optimizing NNI: done in 0.322829 secs using 399.2% CPU
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Optimizing NNI: done in 0.469491 secs using 399.1% CPU
Optimizing NNI: done in 0.417093 secs using 398.7% CPU
Iteration 100 / LogL: -35849.838 / Time: 0h:0m:46s (0h:0m:11s left)
Optimizing NNI: done in 1.90937 secs using 299.1% CPU
Optimizing NNI: done in 0.44406 secs using 399.1% CPU
Optimizing NNI: done in 0.510949 secs using 399.4% CPU
Optimizing NNI: done in 0.423684 secs using 399.1% CPU
Optimizing NNI: done in 0.553641 secs using 399.6% CPU
Optimizing NNI: done in 1.63407 secs using 299.1% CPU
Optimizing NNI: done in 0.441836 secs using 398.3% CPU
Optimizing NNI: done in 0.605031 secs using 398.1% CPU
Optimizing NNI: done in 0.417864 secs using 399.2% CPU
Optimizing NNI: done in 1.69013 secs using 299.5% CPU
Optimizing NNI: done in 0.566286 secs using 398.8% CPU
Optimizing NNI: done in 0.584205 secs using 399.1% CPU
Optimizing NNI: done in 0.34044 secs using 399.4% CPU
Iteration 110 / LogL: -35852.246 / Time: 0h:0m:51s (0h:0m:6s left)
Optimizing NNI: done in 0.357981 secs using 399.7% CPU
Optimizing NNI: done in 1.8504 secs using 299.5% CPU
Optimizing NNI: done in 0.449079 secs using 399.1% CPU
Optimizing NNI: done in 0.427776 secs using 399.3% CPU
Optimizing NNI: done in 0.426153 secs using 398.7% CPU
725  mtART+I+R9    111293.317   552 223690.634   834202.634   225912.912
Optimizing NNI: done in 0.376539 secs using 399% CPU
Optimizing NNI: done in 1.69082 secs using 299.1% CPU
Iteration 130 / LogL: -59883.485 / Time: 0h:4m:31s (0h:2m:14s left)
Optimizing NNI: done in 0.350639 secs using 398.5% CPU
Optimizing NNI: done in 0.364192 secs using 400% CPU
Optimizing NNI: done in 0.424278 secs using 398.8% CPU
Optimizing NNI: done in 0.297139 secs using 398.5% CPU
Optimizing NNI: done in 0.506066 secs using 399.2% CPU
Iteration 120 / LogL: -35849.358 / Time: 0h:0m:55s (0h:0m:1s left)
Optimizing NNI: done in 2.1161 secs using 299.6% CPU
Optimizing NNI: done in 0.448971 secs using 398.9% CPU
Optimizing NNI: done in 0.55314 secs using 399% CPU
Optimizing NNI: done in 0.430555 secs using 399.2% CPU
Optimizing NNI: done in 0.559016 secs using 397.4% CPU
Computing log-likelihood of 98 initial trees ... 24.545 seconds
Current best score: -192991.093

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.75562 secs using 299.6% CPU
Optimizing NNI: done in 0.349014 secs using 398.3% CPU
TREE SEARCH COMPLETED AFTER 125 ITERATIONS / Time: 0h:0m:58s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35849.339
Optimal log-likelihood: -35849.338
Proportion of invariable sites: 0.029
Gamma shape alpha: 2.726
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -35849.338
Total tree length: 20.028

Total number of iterations: 125
CPU time used for tree search: 224.542 sec (0h:3m:44s)
Wall-clock time used for tree search: 57.339 sec (0h:0m:57s)
Total CPU time used: 227.776 sec (0h:3m:47s)
Total wall-clock time used: 58.102 sec (0h:0m:58s)

===> START BOOTSTRAP REPLICATE NUMBER 93

Creating bootstrap alignment (seed: 956252)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36735.670
2. Current log-likelihood: -35800.419
3. Current log-likelihood: -35790.789
4. Current log-likelihood: -35790.518
Optimal log-likelihood: -35790.435
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.229
Parameters optimization took 4 rounds (0.259 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0763521 secs using 398.1% CPU
Computing ML distances took 0.076492 sec (of wall-clock time) 0.304215 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000133991 secs using 1209% CPU
Constructing RapidNJ tree: done in 0.001261 secs using 186.4% CPU
Computing RapidNJ tree took 0.001443 sec (of wall-clock time) 0.004019 sec (of CPU time)
Log-likelihood of RapidNJ tree: -35975.182
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.78489 secs using 299.7% CPU
1.450 second
Optimizing NNI: done in 1.53053 secs using 299.4% CPU
Computing log-likelihood of 98 initial trees ... 1.551 seconds
Current best score: -35790.435

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.255662 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35738.746
Optimizing NNI: done in 0.285083 secs using 396.4% CPU
Optimizing NNI: done in 0.301904 secs using 398.5% CPU
Optimizing NNI: done in 1.65029 secs using 299.1% CPU
Optimizing NNI: done in 0.302621 secs using 397.4% CPU
Optimizing NNI: done in 5.31883 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.328935 secs using 399.1% CPU
Optimizing NNI: done in 0.300401 secs using 398.2% CPU
Optimizing NNI: done in 0.339954 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -35726.735
Optimizing NNI: done in 0.346023 secs using 398.6% CPU
Optimizing NNI: done in 1.55467 secs using 299.5% CPU
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Iteration 10 / LogL: -35726.749 / Time: 0h:0m:6s
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BETTER TREE FOUND at iteration 1: -192418.078
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Iteration 20 / LogL: -35743.709 / Time: 0h:0m:9s
Finish initializing candidate tree set (11)
Current best tree score: -35726.735 / CPU time: 9.244
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -35726.616
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UPDATE BEST LOG-LIKELIHOOD: -35726.473
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BETTER TREE FOUND at iteration 2: -192358.930
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Iteration 90 / LogL: -35728.257 / Time: 0h:0m:41s (0h:0m:14s left)
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Iteration 160 / LogL: -59877.101 / Time: 0h:5m:25s (0h:1m:9s left)
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Iteration 110 / LogL: -35726.640 / Time: 0h:0m:50s (0h:0m:5s left)
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Iteration 120 / LogL: -35726.471 / Time: 0h:0m:54s (0h:0m:0s left)
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TREE SEARCH COMPLETED AFTER 122 ITERATIONS / Time: 0h:0m:55s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35726.470
Optimal log-likelihood: -35726.470
Proportion of invariable sites: 0.020
Gamma shape alpha: 2.273
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35726.470
Total tree length: 20.167

Total number of iterations: 122
CPU time used for tree search: 214.458 sec (0h:3m:34s)
Wall-clock time used for tree search: 54.714 sec (0h:0m:54s)
Total CPU time used: 217.438 sec (0h:3m:37s)
Total wall-clock time used: 55.414 sec (0h:0m:55s)

===> START BOOTSTRAP REPLICATE NUMBER 94

Creating bootstrap alignment (seed: 956253)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37771.931
2. Current log-likelihood: -36847.242
3. Current log-likelihood: -36831.578
4. Current log-likelihood: -36830.571
5. Current log-likelihood: -36830.218
Optimal log-likelihood: -36830.101
Proportion of invariable sites: 0.031
Gamma shape alpha: 2.558
Parameters optimization took 5 rounds (0.318 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.075438 secs using 399.9% CPU
Computing ML distances took 0.075573 sec (of wall-clock time) 0.301999 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000133038 secs using 449.5% CPU
Constructing RapidNJ tree: done in 0.00140095 secs using 354.5% CPU
Computing RapidNJ tree took 0.001586 sec (of wall-clock time) 0.005721 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37410.988
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.79537 secs using 298.9% CPU
1.498 second
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Optimizing NNI: done in 1.72721 secs using 298.8% CPU
Computing log-likelihood of 98 initial trees ... 1.572 seconds
Current best score: -36830.101

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.46952 secs using 397.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36777.173
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36775.435
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Iteration 10 / LogL: -36775.806 / Time: 0h:0m:6s
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36775.354
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BETTER TREE FOUND at iteration 167: -59858.383
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Iteration 20 / LogL: -36776.209 / Time: 0h:0m:9s
Finish initializing candidate tree set (3)
Current best tree score: -36775.354 / CPU time: 9.037
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Optimizing NNI: done in 0.366199 secs using 399% CPU
WARNING: Log-likelihood -111305 of mtART+I+R10 worse than mtART+I+R9 -111293
726  mtART+I+R10   111304.898   554 223717.796   838657.796   225948.126
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Iteration 170 / LogL: -59859.315 / Time: 0h:5m:44s (0h:3m:17s left)
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Iteration 30 / LogL: -36775.450 / Time: 0h:0m:14s (0h:0m:35s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -36774.650
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Iteration 10 / LogL: -192395.847 / Time: 0h:2m:39s
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Iteration 40 / LogL: -36893.616 / Time: 0h:0m:18s (0h:0m:44s left)
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Iteration 50 / LogL: -36775.818 / Time: 0h:0m:23s (0h:0m:38s left)
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Iteration 60 / LogL: -36775.512 / Time: 0h:0m:27s (0h:0m:33s left)
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UPDATE BEST LOG-LIKELIHOOD: -36774.650
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Iteration 70 / LogL: -36776.168 / Time: 0h:0m:32s (0h:0m:28s left)
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Iteration 180 / LogL: -59900.029 / Time: 0h:6m:3s (0h:2m:56s left)
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747  mtART+F+I+R9  108943.465   571 219028.929   872252.929   221327.699
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Iteration 80 / LogL: -36774.652 / Time: 0h:0m:36s (0h:0m:23s left)
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Iteration 90 / LogL: -36775.956 / Time: 0h:0m:40s (0h:0m:18s left)
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Iteration 100 / LogL: -36776.263 / Time: 0h:0m:43s (0h:0m:13s left)
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BETTER TREE FOUND at iteration 187: -59858.377
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Iteration 110 / LogL: -36775.978 / Time: 0h:0m:47s (0h:0m:9s left)
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Iteration 190 / LogL: -59863.622 / Time: 0h:6m:19s (0h:3m:14s left)
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Iteration 120 / LogL: -36776.151 / Time: 0h:0m:51s (0h:0m:4s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 192: -59857.229
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Iteration 130 / LogL: -36774.650 / Time: 0h:0m:56s (0h:0m:0s left)
Optimizing NNI: done in 0.364677 secs using 400% CPU
Optimizing NNI: done in 1.5175 secs using 298.8% CPU
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TREE SEARCH COMPLETED AFTER 132 ITERATIONS / Time: 0h:0m:57s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36774.650
Optimal log-likelihood: -36774.649
Proportion of invariable sites: 0.031
Gamma shape alpha: 2.627
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -36774.649
Total tree length: 20.530

Total number of iterations: 132
CPU time used for tree search: 220.780 sec (0h:3m:40s)
Wall-clock time used for tree search: 56.332 sec (0h:0m:56s)
Total CPU time used: 223.930 sec (0h:3m:43s)
Total wall-clock time used: 57.073 sec (0h:0m:57s)

===> START BOOTSTRAP REPLICATE NUMBER 95

Creating bootstrap alignment (seed: 956254)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36987.351
2. Current log-likelihood: -36080.350
3. Current log-likelihood: -36062.515
4. Current log-likelihood: -36061.758
5. Current log-likelihood: -36061.447
Optimal log-likelihood: -36061.335
Proportion of invariable sites: 0.018
Gamma shape alpha: 2.587
Parameters optimization took 5 rounds (0.327 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.075937 secs using 398.5% CPU
Computing ML distances took 0.076063 sec (of wall-clock time) 0.302928 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000135899 secs
Constructing RapidNJ tree: done in 0.00121689 secs using 410.3% CPU
Computing RapidNJ tree took 0.001404 sec (of wall-clock time) 0.006237 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36630.513
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.77439 secs using 299.5% CPU
Optimizing NNI: done in 5.90781 secs using 398.1% CPU
1.431 second
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Computing log-likelihood of 98 initial trees ... 1.540 seconds
Current best score: -36056.607

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.271166 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36012.560
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -36011.859
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Iteration 10 / LogL: -36012.578 / Time: 0h:0m:6s
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 20: -36011.715
Iteration 20 / LogL: -36011.715 / Time: 0h:0m:8s
Finish initializing candidate tree set (8)
Current best tree score: -36011.715 / CPU time: 8.277
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
BETTER TREE FOUND at iteration 199: -59855.747
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Iteration 200 / LogL: -59857.180 / Time: 0h:6m:38s (0h:3m:18s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -36009.146
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -36008.555
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -36008.189
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36008.152
Iteration 30 / LogL: -36008.152 / Time: 0h:0m:13s (0h:0m:45s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -36008.018
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 35: -36006.679
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Iteration 40 / LogL: -36025.273 / Time: 0h:0m:17s (0h:0m:43s left)
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Iteration 20 / LogL: -192495.557 / Time: 0h:3m:41s
Finish initializing candidate tree set (20)
Current best tree score: -192358.930 / CPU time: 188.062
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 50 / LogL: -36008.219 / Time: 0h:0m:22s (0h:0m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -36006.175
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BETTER TREE FOUND at iteration 54: -36006.165
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36006.004
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Iteration 60 / LogL: -36008.249 / Time: 0h:0m:26s (0h:0m:41s left)
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Iteration 210 / LogL: -59864.304 / Time: 0h:6m:55s (0h:2m:56s left)
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Iteration 70 / LogL: -36006.728 / Time: 0h:0m:30s (0h:0m:36s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 80 / LogL: -36025.217 / Time: 0h:0m:34s (0h:0m:32s left)
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Iteration 90 / LogL: -36006.182 / Time: 0h:0m:38s (0h:0m:27s left)
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748  mtART+F+I+R10 108903.574   573 218953.147   876757.147   221259.968
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Estimate model parameters (epsilon = 0.100)
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Iteration 100 / LogL: -36006.704 / Time: 0h:0m:42s (0h:0m:23s left)
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -36005.984
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Iteration 110 / LogL: -36006.776 / Time: 0h:0m:46s (0h:0m:18s left)
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Iteration 220 / LogL: -59854.664 / Time: 0h:7m:14s (0h:3m:2s left)
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Iteration 120 / LogL: -36006.253 / Time: 0h:0m:50s (0h:0m:14s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 223: -59853.692
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769  mtZOA+I+R9    108399.040   552 217902.080   828414.080   220124.358
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BETTER TREE FOUND at iteration 23: -192357.236
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Iteration 130 / LogL: -36005.984 / Time: 0h:0m:54s (0h:0m:10s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 225: -59853.405
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Iteration 140 / LogL: -36006.047 / Time: 0h:0m:58s (0h:0m:5s left)
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Iteration 150 / LogL: -36006.153 / Time: 0h:1m:2s (0h:0m:1s left)
Optimizing NNI: done in 1.6425 secs using 299.4% CPU
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Optimizing NNI: done in 0.399802 secs using 399% CPU
Optimizing NNI: done in 0.467037 secs using 398.5% CPU
TREE SEARCH COMPLETED AFTER 155 ITERATIONS / Time: 0h:1m:4s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36005.984
Optimal log-likelihood: -36005.983
Proportion of invariable sites: 0.018
Gamma shape alpha: 2.596
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36005.983
Total tree length: 20.388

Total number of iterations: 155
CPU time used for tree search: 249.432 sec (0h:4m:9s)
Wall-clock time used for tree search: 63.465 sec (0h:1m:3s)
Total CPU time used: 252.261 sec (0h:4m:12s)
Total wall-clock time used: 64.130 sec (0h:1m:4s)

===> START BOOTSTRAP REPLICATE NUMBER 96

Creating bootstrap alignment (seed: 956255)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -37654.770
2. Current log-likelihood: -36669.644
Optimizing NNI: done in 2.05032 secs using 299.3% CPU
3. Current log-likelihood: -36646.024
4. Current log-likelihood: -36645.647
Optimal log-likelihood: -36645.603
Proportion of invariable sites: 0.016
Gamma shape alpha: 2.612
Parameters optimization took 4 rounds (0.284 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0734699 secs using 398.4% CPU
Computing ML distances took 0.073622 sec (of wall-clock time) 0.293076 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000134945 secs using 460.9% CPU
Constructing RapidNJ tree: done in 0.00128698 secs using 364.9% CPU
Computing RapidNJ tree took 0.001471 sec (of wall-clock time) 0.007467 sec (of CPU time)
Log-likelihood of RapidNJ tree: -37516.973
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|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.74344 secs using 299.2% CPU
Iteration 230 / LogL: -59854.106 / Time: 0h:7m:34s (0h:3m:8s left)
1.552 second
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Optimizing NNI: done in 1.6976 secs using 299.7% CPU
Computing log-likelihood of 98 initial trees ... 1.556 seconds
Current best score: -36645.603

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -36611.949
Optimizing NNI: done in 0.260485 secs using 397.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -36603.843
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 8: -36597.770
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Iteration 10 / LogL: -36611.188 / Time: 0h:0m:6s
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Iteration 20 / LogL: -36611.194 / Time: 0h:0m:9s
Finish initializing candidate tree set (10)
Current best tree score: -36597.770 / CPU time: 8.902
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 0.468801 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -36595.733
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UPDATE BEST LOG-LIKELIHOOD: -36595.733
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Iteration 30 / LogL: -36600.462 / Time: 0h:0m:13s (0h:0m:42s left)
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BETTER TREE FOUND at iteration 237: -59853.401
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Iteration 40 / LogL: -36599.640 / Time: 0h:0m:17s (0h:0m:37s left)
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Iteration 240 / LogL: -59853.727 / Time: 0h:7m:51s (0h:3m:11s left)
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Iteration 50 / LogL: -36652.412 / Time: 0h:0m:22s (0h:0m:32s left)
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Optimizing NNI: done in 0.627635 secs using 398.1% CPU
UPDATE BEST LOG-LIKELIHOOD: -36595.733
Optimizing NNI: done in 0.421424 secs using 399.1% CPU
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Iteration 60 / LogL: -36597.800 / Time: 0h:0m:26s (0h:0m:27s left)
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Iteration 70 / LogL: -36598.164 / Time: 0h:0m:30s (0h:0m:22s left)
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Iteration 80 / LogL: -36596.517 / Time: 0h:0m:34s (0h:0m:18s left)
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Iteration 30 / LogL: -192411.783 / Time: 0h:5m:0s (0h:16m:2s left)
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Iteration 250 / LogL: -59868.005 / Time: 0h:8m:8s (0h:2m:50s left)
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Iteration 90 / LogL: -36597.798 / Time: 0h:0m:38s (0h:0m:13s left)
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Iteration 100 / LogL: -36598.157 / Time: 0h:0m:42s (0h:0m:9s left)
Optimizing NNI: done in 0.429899 secs using 398.6% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.377171 secs using 398.1% CPU
Iteration 110 / LogL: -36598.588 / Time: 0h:0m:47s (0h:0m:4s left)
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BETTER TREE FOUND at iteration 256: -59853.142
Optimizing NNI: done in 0.326388 secs using 399.6% CPU
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Iteration 120 / LogL: -36599.052 / Time: 0h:0m:51s (0h:0m:0s left)
Optimizing NNI: done in 1.78011 secs using 299.3% CPU
Optimizing NNI: done in 0.420701 secs using 398.7% CPU
Optimizing NNI: done in 0.455719 secs using 398.6% CPU
TREE SEARCH COMPLETED AFTER 122 ITERATIONS / Time: 0h:0m:52s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -36595.733
Optimal log-likelihood: -36595.732
Proportion of invariable sites: 0.016
Gamma shape alpha: 2.527
Parameters optimization took 1 rounds (0.045 sec)
BEST SCORE FOUND : -36595.732
Total tree length: 20.742

Total number of iterations: 122
CPU time used for tree search: 202.804 sec (0h:3m:22s)
Wall-clock time used for tree search: 51.891 sec (0h:0m:51s)
Total CPU time used: 205.605 sec (0h:3m:25s)
Total wall-clock time used: 52.548 sec (0h:0m:52s)

===> START BOOTSTRAP REPLICATE NUMBER 97

Creating bootstrap alignment (seed: 956256)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36822.082
2. Current log-likelihood: -35881.220
3. Current log-likelihood: -35863.956
4. Current log-likelihood: -35862.782
5. Current log-likelihood: -35862.395
Optimal log-likelihood: -35862.277
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.761
Parameters optimization took 5 rounds (0.332 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.073235 secs using 399.7% CPU
Computing ML distances took 0.073368 sec (of wall-clock time) 0.293043 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000149012 secs using 215.4% CPU
Constructing RapidNJ tree: done in 0.00123715 secs using 147% CPU
Computing RapidNJ tree took 0.001438 sec (of wall-clock time) 0.003281 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36424.064
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.17236 secs using 299% CPU
Optimizing NNI: done in 6.46301 secs using 398.2% CPU
1.564 second
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Iteration 260 / LogL: -59934.770 / Time: 0h:8m:27s (0h:3m:8s left)
Computing log-likelihood of 98 initial trees ... 1.543 seconds
Current best score: -35862.277

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.301047 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35794.960
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Iteration 10 / LogL: -35794.988 / Time: 0h:0m:6s
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -35795.594 / Time: 0h:0m:9s
Finish initializing candidate tree set (5)
Current best tree score: -35794.960 / CPU time: 9.063
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 30 / LogL: -35797.862 / Time: 0h:0m:13s (0h:0m:33s left)
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Iteration 40 / LogL: -35795.678 / Time: 0h:0m:17s (0h:0m:27s left)
BETTER TREE FOUND at iteration 34: -192347.602
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Iteration 270 / LogL: -59871.304 / Time: 0h:8m:45s (0h:2m:47s left)
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Iteration 50 / LogL: -35795.912 / Time: 0h:0m:21s (0h:0m:21s left)
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Iteration 60 / LogL: -35795.235 / Time: 0h:0m:24s (0h:0m:17s left)
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Iteration 70 / LogL: -35795.134 / Time: 0h:0m:27s (0h:0m:12s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 275: -59850.046
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Optimizing NNI: done in 0.365174 secs using 399.5% CPU
Iteration 80 / LogL: -35795.244 / Time: 0h:0m:31s (0h:0m:8s left)
Optimizing NNI: done in 0.443868 secs using 399.1% CPU
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Optimizing NNI: done in 0.343498 secs using 399.7% CPU
Iteration 90 / LogL: -35794.984 / Time: 0h:0m:35s (0h:0m:4s left)
Optimizing NNI: done in 0.377336 secs using 399.6% CPU
Optimizing NNI: done in 0.327219 secs using 398.8% CPU
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Optimizing NNI: done in 0.396036 secs using 399.3% CPU
Optimizing NNI: done in 1.76025 secs using 299.5% CPU
Iteration 280 / LogL: -59855.143 / Time: 0h:9m:2s (0h:3m:4s left)
Optimizing NNI: done in 0.332029 secs using 399.1% CPU
Optimizing NNI: done in 0.382288 secs using 399.4% CPU
Iteration 100 / LogL: -35803.715 / Time: 0h:0m:38s (0h:0m:0s left)
Optimizing NNI: done in 0.335286 secs using 399.4% CPU
Optimizing NNI: done in 0.33092 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35794.960
Optimal log-likelihood: -35794.953
Proportion of invariable sites: 0.025
Gamma shape alpha: 2.683
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35794.953
Total tree length: 19.260

Total number of iterations: 102
CPU time used for tree search: 149.155 sec (0h:2m:29s)
Wall-clock time used for tree search: 38.425 sec (0h:0m:38s)
Total CPU time used: 152.313 sec (0h:2m:32s)
Total wall-clock time used: 39.171 sec (0h:0m:39s)

===> START BOOTSTRAP REPLICATE NUMBER 98

Creating bootstrap alignment (seed: 956257)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.010 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36386.918
2. Current log-likelihood: -35463.017
3. Current log-likelihood: -35452.059
4. Current log-likelihood: -35451.854
Optimal log-likelihood: -35451.827
Proportion of invariable sites: 0.018
Gamma shape alpha: 2.549
Parameters optimization took 4 rounds (0.219 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.073287 secs using 396.9% CPU
Computing ML distances took 0.073411 sec (of wall-clock time) 0.291179 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000152111 secs using 389.8% CPU
Constructing RapidNJ tree: done in 0.00128007 secs using 297.8% CPU
Computing RapidNJ tree took 0.001481 sec (of wall-clock time) 0.005426 sec (of CPU time)
Optimizing NNI: done in 1.6408 secs using 299.4% CPU
Log-likelihood of RapidNJ tree: -36083.815
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.52801 secs using 299.4% CPU
1.479 second
Computing log-likelihood of 98 initial trees ... 1.540 seconds
Current best score: -35450.666

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.94325 secs using 299.4% CPU
Optimizing NNI: done in 0.38511 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35378.760
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Optimizing NNI: done in 0.225865 secs using 399.2% CPU
Optimizing NNI: done in 0.377583 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -35377.687
Optimizing NNI: done in 7.08588 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.382784 secs using 398.6% CPU
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Iteration 10 / LogL: -35377.761 / Time: 0h:0m:7s
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Optimizing NNI: done in 0.387104 secs using 399.2% CPU
Iteration 20 / LogL: -35378.815 / Time: 0h:0m:10s
Finish initializing candidate tree set (7)
Current best tree score: -35377.687 / CPU time: 9.886
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Optimizing NNI: done in 0.434183 secs using 398.8% CPU
BETTER TREE FOUND at iteration 38: -192329.259
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Optimizing NNI: done in 0.416241 secs using 399.1% CPU
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Optimizing NNI: done in 1.76259 secs using 298.9% CPU
Optimizing NNI: done in 0.449511 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35377.646
Optimizing NNI: done in 0.35942 secs using 399.3% CPU
Iteration 30 / LogL: -35378.701 / Time: 0h:0m:15s (0h:0m:38s left)
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Optimizing NNI: done in 1.7092 secs using 299.6% CPU
Iteration 290 / LogL: -59860.689 / Time: 0h:9m:20s (0h:2m:44s left)
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Optimizing NNI: done in 0.351133 secs using 399.2% CPU
Optimizing NNI: done in 1.57455 secs using 299.4% CPU
770  mtZOA+I+R10   108387.466   554 217882.932   832822.932   220113.262
Optimizing NNI: done in 0.471391 secs using 398.4% CPU
Optimizing NNI: done in 0.46486 secs using 397.9% CPU
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Iteration 40 / LogL: -35381.982 / Time: 0h:0m:19s (0h:0m:31s left)
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BETTER TREE FOUND at iteration 42: -35377.643
Optimizing NNI: done in 0.384273 secs using 398.3% CPU
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Optimizing NNI: done in 1.62329 secs using 299.1% CPU
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Iteration 50 / LogL: -35379.169 / Time: 0h:0m:23s (0h:0m:43s left)
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Optimizing NNI: done in 6.64119 secs using 398.5% CPU
Iteration 40 / LogL: -192444.462 / Time: 0h:6m:22s (0h:15m:59s left)
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Optimizing NNI: done in 0.431977 secs using 398.3% CPU
Optimizing NNI: done in 1.83818 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 0.292149 secs using 398.8% CPU
Optimizing NNI: done in 0.454549 secs using 398.6% CPU
BETTER TREE FOUND at iteration 296: -59849.988
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Iteration 60 / LogL: -35377.670 / Time: 0h:0m:27s (0h:0m:38s left)
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Optimizing NNI: done in 1.68884 secs using 299.6% CPU
791  mtZOA+F+I+R9  107159.024   571 215460.047   868684.047   217758.817
Optimizing NNI: done in 0.438758 secs using 398.8% CPU
Optimizing NNI: done in 0.365694 secs using 398.3% CPU
Optimizing NNI: done in 0.477308 secs using 398.6% CPU
Iteration 70 / LogL: -35377.666 / Time: 0h:0m:31s (0h:0m:33s left)
Optimizing NNI: done in 0.435404 secs using 398.7% CPU
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Optimizing NNI: done in 1.73488 secs using 299.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -59849.987
Iteration 300 / LogL: -59849.987 / Time: 0h:9m:38s (0h:3m:5s left)
Optimizing NNI: done in 0.464001 secs using 398.7% CPU
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Iteration 80 / LogL: -35377.780 / Time: 0h:0m:36s (0h:0m:28s left)
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Iteration 90 / LogL: -35380.163 / Time: 0h:0m:40s (0h:0m:23s left)
Optimizing NNI: done in 0.473815 secs using 399.2% CPU
Optimizing NNI: done in 1.71658 secs using 299.3% CPU
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Optimizing NNI: done in 0.472584 secs using 398.1% CPU
Iteration 100 / LogL: -35385.851 / Time: 0h:0m:44s (0h:0m:18s left)
Optimizing NNI: done in 2.10493 secs using 298.7% CPU
Optimizing NNI: done in 0.404271 secs using 398.8% CPU
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Optimizing NNI: done in 6.5482 secs using 397.8% CPU
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Optimizing NNI: done in 0.457805 secs using 398.5% CPU
Iteration 110 / LogL: -35377.691 / Time: 0h:0m:48s (0h:0m:14s left)
Optimizing NNI: done in 0.50049 secs using 397.9% CPU
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Iteration 310 / LogL: -59853.634 / Time: 0h:9m:55s (0h:2m:45s left)
Optimizing NNI: done in 0.456381 secs using 399.5% CPU
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Iteration 120 / LogL: -35377.711 / Time: 0h:0m:53s (0h:0m:9s left)
Optimizing NNI: done in 1.68934 secs using 299.3% CPU
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Iteration 130 / LogL: -35377.748 / Time: 0h:0m:58s (0h:0m:5s left)
Optimizing NNI: done in 0.369453 secs using 399.1% CPU
Optimizing NNI: done in 1.64508 secs using 299.3% CPU
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Iteration 140 / LogL: -35378.791 / Time: 0h:1m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.359658 secs using 399.1% CPU
Optimizing NNI: done in 0.450238 secs using 398.2% CPU
Optimizing NNI: done in 1.76214 secs using 299.3% CPU
Optimizing NNI: done in 0.461944 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 143 ITERATIONS / Time: 0h:1m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35377.643
Optimal log-likelihood: -35377.643
Proportion of invariable sites: 0.019
Gamma shape alpha: 2.555
Parameters optimization took 1 rounds (0.048 sec)
BEST SCORE FOUND : -35377.643
Total tree length: 19.238

Total number of iterations: 143
CPU time used for tree search: 248.570 sec (0h:4m:8s)
Wall-clock time used for tree search: 63.295 sec (0h:1m:3s)
Total CPU time used: 251.569 sec (0h:4m:11s)
Total wall-clock time used: 64.001 sec (0h:1m:4s)

===> START BOOTSTRAP REPLICATE NUMBER 99

Creating bootstrap alignment (seed: 956258)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36652.182
2. Current log-likelihood: -35799.418
3. Current log-likelihood: -35781.690
4. Current log-likelihood: -35781.134
Optimal log-likelihood: -35781.066
Proportion of invariable sites: 0.021
Gamma shape alpha: 2.797
Parameters optimization took 4 rounds (0.266 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.073149 secs using 399.7% CPU
Computing ML distances took 0.073275 sec (of wall-clock time) 0.292713 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000133991 secs using 462.7% CPU
Constructing RapidNJ tree: done in 0.001194 secs using 287.1% CPU
Computing RapidNJ tree took 0.001380 sec (of wall-clock time) 0.007102 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36346.513
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.60011 secs using 299% CPU
1.435 second
Optimizing NNI: done in 6.83273 secs using 398.5% CPU
Optimizing NNI: done in 1.57166 secs using 299.6% CPU
Computing log-likelihood of 98 initial trees ... 1.529 seconds
Current best score: -35781.066

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.230527 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35713.696
Optimizing NNI: done in 0.224424 secs using 398.8% CPU
Optimizing NNI: done in 0.275326 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -35713.299
Optimizing NNI: done in 1.39831 secs using 299.3% CPU
Iteration 320 / LogL: -59858.501 / Time: 0h:10m:12s (0h:2m:25s left)
Optimizing NNI: done in 0.241297 secs using 398.3% CPU
Optimizing NNI: done in 0.2946 secs using 397.7% CPU
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Iteration 10 / LogL: -35720.187 / Time: 0h:0m:6s
Optimizing NNI: done in 0.261046 secs using 398.2% CPU
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Optimizing NNI: done in 0.232785 secs using 397.3% CPU
Iteration 20 / LogL: -35720.921 / Time: 0h:0m:8s
Finish initializing candidate tree set (10)
Current best tree score: -35713.299 / CPU time: 8.299
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 30 / LogL: -35713.313 / Time: 0h:0m:12s (0h:0m:31s left)
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Iteration 40 / LogL: -35713.315 / Time: 0h:0m:16s (0h:0m:26s left)
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Iteration 50 / LogL: -35713.304 / Time: 0h:0m:19s (0h:0m:21s left)
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Iteration 330 / LogL: -59875.389 / Time: 0h:10m:29s (0h:2m:6s left)
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Iteration 60 / LogL: -35713.309 / Time: 0h:0m:23s (0h:0m:17s left)
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792  mtZOA+F+I+R10 107152.590   573 215451.180   873255.180   217758.001
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Iteration 70 / LogL: -35713.502 / Time: 0h:0m:27s (0h:0m:13s left)
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Iteration 80 / LogL: -35724.401 / Time: 0h:0m:30s (0h:0m:8s left)
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Iteration 50 / LogL: -192336.579 / Time: 0h:7m:31s (0h:13m:30s left)
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Iteration 90 / LogL: -35713.417 / Time: 0h:0m:34s (0h:0m:5s left)
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Iteration 100 / LogL: -35714.636 / Time: 0h:0m:37s (0h:0m:1s left)
Optimizing NNI: done in 6.66394 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.87688 secs using 299.1% CPU
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Optimizing NNI: done in 0.356825 secs using 399.5% CPU
TREE SEARCH COMPLETED AFTER 104 ITERATIONS / Time: 0h:0m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35713.299
Optimal log-likelihood: -35713.296
Proportion of invariable sites: 0.021
Gamma shape alpha: 2.835
Parameters optimization took 1 rounds (0.044 sec)
BEST SCORE FOUND : -35713.296
Total tree length: 18.445

Total number of iterations: 104
CPU time used for tree search: 150.766 sec (0h:2m:30s)
Wall-clock time used for tree search: 38.721 sec (0h:0m:38s)
Total CPU time used: 152.958 sec (0h:2m:32s)
Total wall-clock time used: 39.246 sec (0h:0m:39s)

===> START BOOTSTRAP REPLICATE NUMBER 100

Creating bootstrap alignment (seed: 956259)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.013 seconds

NOTE: 17 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36784.322
2. Current log-likelihood: -35880.993
3. Current log-likelihood: -35866.346
4. Current log-likelihood: -35865.833
Optimal log-likelihood: -35865.787
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.440
Parameters optimization took 4 rounds (0.270 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0784271 secs using 399.2% CPU
Computing ML distances took 0.078577 sec (of wall-clock time) 0.313420 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000133991 secs using 471.7% CPU
Constructing RapidNJ tree: done in 0.00125408 secs using 468.7% CPU
Computing RapidNJ tree took 0.001436 sec (of wall-clock time) 0.007258 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36671.286
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.84145 secs using 299% CPU
Iteration 340 / LogL: -59925.421 / Time: 0h:10m:47s (0h:1m:46s left)
1.396 second
Optimizing NNI: done in 2.07576 secs using 299.1% CPU
Computing log-likelihood of 98 initial trees ... 1.496 seconds
Current best score: -35865.787

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.249124 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -35826.459
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -35825.878
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BETTER TREE FOUND at iteration 51: -192324.967
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -35819.105
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Iteration 10 / LogL: -35821.347 / Time: 0h:0m:6s
Optimizing NNI: done in 1.53823 secs using 298.9% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 15: -35816.317
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Iteration 20 / LogL: -35819.776 / Time: 0h:0m:9s
Finish initializing candidate tree set (6)
Current best tree score: -35816.317 / CPU time: 8.516
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 30 / LogL: -35819.773 / Time: 0h:0m:13s (0h:0m:39s left)
813  mtMet+I+R9    109392.783   552 219889.565   830401.565   222111.843
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Iteration 40 / LogL: -35819.775 / Time: 0h:0m:17s (0h:0m:33s left)
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Iteration 350 / LogL: -59850.281 / Time: 0h:11m:5s (0h:1m:27s left)
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35816.292
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Iteration 50 / LogL: -35816.369 / Time: 0h:0m:21s (0h:0m:28s left)
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Iteration 60 / LogL: -35820.978 / Time: 0h:0m:25s (0h:0m:23s left)
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Iteration 70 / LogL: -35816.553 / Time: 0h:0m:29s (0h:0m:19s left)
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Iteration 80 / LogL: -35817.254 / Time: 0h:0m:33s (0h:0m:14s left)
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Iteration 360 / LogL: -59867.198 / Time: 0h:11m:23s (0h:1m:8s left)
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Iteration 90 / LogL: -35818.243 / Time: 0h:0m:36s (0h:0m:10s left)
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Iteration 100 / LogL: -35816.313 / Time: 0h:0m:40s (0h:0m:6s left)
Optimizing NNI: done in 0.425734 secs using 398.9% CPU
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Iteration 110 / LogL: -35816.694 / Time: 0h:0m:44s (0h:0m:2s left)
Optimizing NNI: done in 0.361245 secs using 399.4% CPU
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Optimizing NNI: done in 0.385312 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 116 ITERATIONS / Time: 0h:0m:46s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35816.292
Optimal log-likelihood: -35816.291
Proportion of invariable sites: 0.030
Gamma shape alpha: 2.475
Parameters optimization took 1 rounds (0.043 sec)
BEST SCORE FOUND : -35816.291
Total tree length: 20.401

Total number of iterations: 116
CPU time used for tree search: 179.212 sec (0h:2m:59s)
Wall-clock time used for tree search: 45.828 sec (0h:0m:45s)
Total CPU time used: 181.677 sec (0h:3m:1s)
Total wall-clock time used: 46.409 sec (0h:0m:46s)

===> COMPUTE CONSENSUS TREE FROM 100 BOOTSTRAP TREES

Reading tree(s) file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.boottrees ...
100 tree(s) loaded (0 rooted and 100 unrooted)
0 split(s) discarded because frequency <= -1.000
244 splits found
Consensus tree written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.contree

===> START ANALYSIS ON THE ORIGINAL ALIGNMENT


NOTE: 27 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -36083.822
Optimizing NNI: done in 7.21908 secs using 398.5% CPU
Optimizing NNI: done in 1.35317 secs using 299% CPU
2. Current log-likelihood: -35974.114
3. Current log-likelihood: -35971.095
Optimal log-likelihood: -35971.073
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.466
Parameters optimization took 3 rounds (0.318 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.07546 secs using 401.4% CPU
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Constructing RapidNJ tree: done in 0.00128317 secs using 353% CPU
Computing RapidNJ tree took 0.001479 sec (of wall-clock time) 0.006673 sec (of CPU time)
Log-likelihood of RapidNJ tree: -36335.664
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.82859 secs using 299.3% CPU
1.371 second
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Computing log-likelihood of 98 initial trees ... 2.264 seconds
Current best score: -35971.073

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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -35969.926 / Time: 0h:0m:11s
Finish initializing candidate tree set (10)
Current best tree score: -35964.051 / CPU time: 11.177
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -35964.018
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 64: -192322.635
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Iteration 90 / LogL: -35964.184 / Time: 0h:0m:53s (0h:0m:10s left)
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Optimizing NNI: done in 1.96798 secs using 297% CPU
TREE SEARCH COMPLETED AFTER 397 ITERATIONS / Time: 0h:12m:27s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59849.987
Optimal log-likelihood: -59849.976
Site proportion and rates:  (0.111,0.051) (0.123,0.174) (0.086,0.447) (0.103,0.447) (0.206,0.744) (0.179,1.234) (0.171,2.373) (0.021,5.152)
Parameters optimization took 1 rounds (0.445 sec)
BEST SCORE FOUND : -59849.976
Total tree length: 44.385

Total number of iterations: 397
CPU time used for tree search: 2178.567 sec (0h:36m:18s)
Wall-clock time used for tree search: 731.606 sec (0h:12m:11s)
Total CPU time used: 2228.070 sec (0h:37m:8s)
Total wall-clock time used: 748.114 sec (0h:12m:28s)

===> START BOOTSTRAP REPLICATE NUMBER 5

Creating bootstrap alignment (seed: 956254)...

Optimizing NNI: done in 0.624029 secs using 399.4% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61077.316
Optimizing NNI: done in 0.512487 secs using 399.2% CPU
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2. Current log-likelihood: -60430.961
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3. Current log-likelihood: -60422.963
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4. Current log-likelihood: -60415.651
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Iteration 100 / LogL: -35964.069 / Time: 0h:0m:59s (0h:0m:4s left)
5. Current log-likelihood: -60404.550
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6. Current log-likelihood: -60401.237
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7. Current log-likelihood: -60398.425
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8. Current log-likelihood: -60395.989
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9. Current log-likelihood: -60395.139
Optimizing NNI: done in 0.435382 secs using 398.6% CPU
TREE SEARCH COMPLETED AFTER 108 ITERATIONS / Time: 0h:1m:3s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -35964.016
Optimal log-likelihood: -35964.015
Proportion of invariable sites: 0.024
Gamma shape alpha: 2.464
Parameters optimization took 1 rounds (0.064 sec)
BEST SCORE FOUND : -35964.015
Total tree length: 20.009

Total number of iterations: 108
CPU time used for tree search: 248.469 sec (0h:4m:8s)
Wall-clock time used for tree search: 63.175 sec (0h:1m:3s)
Total CPU time used: 251.331 sec (0h:4m:11s)
Total wall-clock time used: 63.847 sec (0h:1m:3s)
Reading input trees file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.contree
Log-likelihood of consensus tree: -35964.849

===> ASSIGN BOOTSTRAP SUPPORTS TO THE TREE FROM ORIGINAL ALIGNMENT

Reading tree /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.treefile ...
unrooted tree detected
Reading tree(s) file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.boottrees ...
100 tree(s) loaded (0 rooted and 100 unrooted)
Rescaling split weights by 1.000
244 splits found
Creating bootstrap support values...
Tree with assigned support written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.treefile

Analysis results written to: 
  IQ-TREE report:                /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.iqtree
  Maximum-likelihood tree:       /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.treefile
  Likelihood distances:          /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.mldist
  Screen log file:               /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.log

Performing transfer bootstrap expectation...
TBE tree written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.tbe.tree
TBE statistic written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.tbe.stat

Total CPU time for bootstrap: 24346.547 seconds.
Total wall-clock time for bootstrap: 6298.218 seconds.

Non-parametric bootstrap results written to:
  Bootstrap trees:          /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.boottrees
  Consensus tree:           /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/catabolism.contree

Date and Time: Mon Jul  7 14:58:12 2025
10. Current log-likelihood: -60394.933
Optimal log-likelihood: -60394.890
Site proportion and rates:  (0.096,0.059) (0.111,0.195) (0.114,0.339) (0.204,0.531) (0.194,0.931) (0.139,1.526) (0.103,2.293) (0.038,5.102)
Parameters optimization took 10 rounds (10.941 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.48989 secs using 299.9% CPU
Computing ML distances took 1.490097 sec (of wall-clock time) 4.468141 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000460148 secs using 297.3% CPU
Constructing RapidNJ tree: done in 0.00387907 secs using 273.6% CPU
Computing RapidNJ tree took 0.004407 sec (of wall-clock time) 0.013262 sec (of CPU time)
Optimizing NNI: done in 6.87538 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
Log-likelihood of RapidNJ tree: -60583.091
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... BETTER TREE FOUND at iteration 66: -192309.105
5.027 second
Optimizing NNI: done in 5.90512 secs using 398.6% CPU
Computing log-likelihood of 98 initial trees ... 6.959 seconds
Current best score: -60346.030

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -60135.730
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814  mtMet+I+R10   109391.265   554 219890.530   834830.530   222120.860
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Estimate model parameters (epsilon = 0.100)
835  mtMet+F+I+R9  106644.835   571 214431.669   867655.669   216730.439
BETTER TREE FOUND at iteration 7: -60130.700
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Iteration 10 / LogL: -60143.553 / Time: 0h:0m:53s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 72: -192304.951
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Iteration 20 / LogL: -60137.177 / Time: 0h:1m:14s
Finish initializing candidate tree set (20)
Current best tree score: -60130.700 / CPU time: 60.837
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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836  mtMet+F+I+R10 106639.711   573 214425.421   872229.421   216732.243
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Iteration 30 / LogL: -60120.906 / Time: 0h:1m:37s (0h:5m:20s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 80 / LogL: -192349.263 / Time: 0h:11m:12s (0h:13m:2s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
857  mtVer+I+R9    110573.542   552 222251.083   832763.083   224473.361
BETTER TREE FOUND at iteration 82: -192303.438
BETTER TREE FOUND at iteration 38: -60116.844
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -60112.614
Iteration 40 / LogL: -60112.614 / Time: 0h:2m:19s (0h:5m:57s left)
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Estimate model parameters (epsilon = 0.100)
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WARNING: Log-likelihood -110592 of mtVer+I+R10 worse than mtVer+I+R9 -110574
858  mtVer+I+R10   110591.635   554 222291.271   837231.271   224521.600
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879  mtVer+F+I+R9  107890.054   571 216922.107   870146.107   219220.877
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WARNING: Log-likelihood -107914 of mtVer+F+I+R10 worse than mtVer+F+I+R9 -107890
880  mtVer+F+I+R10 107913.725   573 216973.450   874777.450   219280.272
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UPDATE BEST LOG-LIKELIHOOD: -60097.560
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901  mtInv+I+R9    109951.118   552 221006.236   831518.236   223228.514
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Iteration 130 / LogL: -60098.095 / Time: 0h:5m:44s (0h:4m:19s left)
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BETTER TREE FOUND at iteration 133: -60095.248
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BETTER TREE FOUND at iteration 134: -60094.975
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902  mtInv+I+R10   109947.923   554 221003.845   835943.845   223234.175
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923  mtInv+F+I+R9  106062.363   571 213266.725   866490.725   215565.494
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -60094.943
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Iteration 210 / LogL: -60097.210 / Time: 0h:8m:24s (0h:0m:57s left)
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Iteration 220 / LogL: -60095.084 / Time: 0h:8m:42s (0h:0m:33s left)
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Iteration 230 / LogL: -60097.839 / Time: 0h:9m:3s (0h:0m:9s left)
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TREE SEARCH COMPLETED AFTER 235 ITERATIONS / Time: 0h:9m:13s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60094.943
Optimal log-likelihood: -60094.929
Site proportion and rates:  (0.092,0.058) (0.128,0.198) (0.169,0.395) (0.177,0.619) (0.182,1.029) (0.146,1.678) (0.074,2.534) (0.032,5.364)
Parameters optimization took 1 rounds (0.549 sec)
BEST SCORE FOUND : -60094.929
Total tree length: 46.575

Total number of iterations: 235
CPU time used for tree search: 1605.997 sec (0h:26m:45s)
Wall-clock time used for tree search: 540.036 sec (0h:9m:0s)
Total CPU time used: 1648.092 sec (0h:27m:28s)
Total wall-clock time used: 554.102 sec (0h:9m:14s)

===> START BOOTSTRAP REPLICATE NUMBER 6

Creating bootstrap alignment (seed: 956255)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.045 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60748.633
2. Current log-likelihood: -60148.564
3. Current log-likelihood: -60138.276
4. Current log-likelihood: -60137.822
5. Current log-likelihood: -60137.529
Optimizing NNI: done in 6.1669 secs using 398.5% CPU
6. Current log-likelihood: -60137.268
7. Current log-likelihood: -60136.913
8. Current log-likelihood: -60135.960
9. Current log-likelihood: -60131.266
10. Current log-likelihood: -60129.676
11. Current log-likelihood: -60129.287
12. Current log-likelihood: -60128.954
13. Current log-likelihood: -60128.838
Optimizing NNI: done in 6.98233 secs using 398.3% CPU
Optimal log-likelihood: -60128.814
Site proportion and rates:  (0.083,0.061) (0.111,0.198) (0.128,0.390) (0.081,0.409) (0.239,0.678) (0.203,1.275) (0.123,2.316) (0.033,5.646)
Parameters optimization took 13 rounds (12.837 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.53465 secs using 299.8% CPU
Computing ML distances took 1.534850 sec (of wall-clock time) 4.601885 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000447989 secs using 278.4% CPU
Constructing RapidNJ tree: done in 0.00390887 secs using 229.2% CPU
Computing RapidNJ tree took 0.004439 sec (of wall-clock time) 0.011329 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60082.625
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 6.35557 secs using 398.7% CPU
4.957 second
Optimizing NNI: done in 7.142 secs using 398.5% CPU
Iteration 150 / LogL: -192351.968 / Time: 0h:19m:0s (0h:8m:9s left)
Computing log-likelihood of 98 initial trees ... 6.759 seconds
Current best score: -60003.904

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.80335 secs using 299.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 7.1518 secs using 398.3% CPU
BETTER TREE FOUND at iteration 1: -59728.369
Optimizing NNI: done in 2.0766 secs using 299.3% CPU
Optimizing NNI: done in 2.04137 secs using 299.1% CPU
Optimizing NNI: done in 7.26662 secs using 398.3% CPU
Optimizing NNI: done in 2.48016 secs using 299.3% CPU
Optimizing NNI: done in 2.15437 secs using 299.1% CPU
Optimizing NNI: done in 1.80808 secs using 299.3% CPU
Optimizing NNI: done in 6.28715 secs using 398.2% CPU
Optimizing NNI: done in 2.0475 secs using 299.1% CPU
Optimizing NNI: done in 2.1339 secs using 299.6% CPU
Optimizing NNI: done in 2.2706 secs using 299.1% CPU
Optimizing NNI: done in 6.32787 secs using 398.5% CPU
Optimizing NNI: done in 2.21066 secs using 299.1% CPU
Iteration 10 / LogL: -59789.515 / Time: 0h:0m:54s
Optimizing NNI: done in 1.8546 secs using 299.3% CPU
Optimizing NNI: done in 1.67185 secs using 299.6% CPU
Optimizing NNI: done in 6.56573 secs using 398.7% CPU
Optimizing NNI: done in 2.05802 secs using 299.3% CPU
Optimizing NNI: done in 2.12836 secs using 299.1% CPU
Optimizing NNI: done in 2.44381 secs using 299.1% CPU
Optimizing NNI: done in 5.6472 secs using 398.6% CPU
Optimizing NNI: done in 1.9274 secs using 299.1% CPU
Optimizing NNI: done in 2.56788 secs using 299.1% CPU
Optimizing NNI: done in 6.18835 secs using 398.4% CPU
Optimizing NNI: done in 2.54549 secs using 299.6% CPU
Optimizing NNI: done in 2.03373 secs using 298.7% CPU
Optimizing NNI: done in 1.95678 secs using 299.4% CPU
Iteration 20 / LogL: -59761.738 / Time: 0h:1m:16s
Finish initializing candidate tree set (20)
Current best tree score: -59728.369 / CPU time: 60.862
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 2.20999 secs using 299.3% CPU
Optimizing NNI: done in 6.78939 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.10185 secs using 298.9% CPU
BETTER TREE FOUND at iteration 158: -192290.646
Optimizing NNI: done in 2.01783 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -59727.731
Optimizing NNI: done in 2.10136 secs using 299.1% CPU
Optimizing NNI: done in 2.01002 secs using 299% CPU
Optimizing NNI: done in 6.60142 secs using 398.3% CPU
Optimizing NNI: done in 2.29967 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -59720.719
Optimizing NNI: done in 2.63125 secs using 299.3% CPU
Optimizing NNI: done in 6.68924 secs using 398% CPU
Iteration 160 / LogL: -192311.240 / Time: 0h:20m:10s (0h:12m:25s left)
Optimizing NNI: done in 2.80659 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.6308 secs using 398.4% CPU
Optimizing NNI: done in 6.34192 secs using 398.6% CPU
BETTER TREE FOUND at iteration 28: -59688.001
Optimizing NNI: done in 1.72592 secs using 299.1% CPU
Optimizing NNI: done in 1.4704 secs using 299.5% CPU
Iteration 30 / LogL: -59720.996 / Time: 0h:1m:51s (0h:6m:15s left)
Optimizing NNI: done in 6.1946 secs using 398.5% CPU
Optimizing NNI: done in 2.1111 secs using 299.4% CPU
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Optimizing NNI: done in 1.73738 secs using 299.3% CPU
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Optimizing NNI: done in 2.12107 secs using 299% CPU
Iteration 40 / LogL: -59696.700 / Time: 0h:2m:10s (0h:4m:53s left)
Optimizing NNI: done in 6.91658 secs using 397.8% CPU
Optimizing NNI: done in 2.20255 secs using 299.2% CPU
Optimizing NNI: done in 1.78383 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -59687.912
Optimizing NNI: done in 2.00975 secs using 299.2% CPU
Optimizing NNI: done in 5.67746 secs using 398.2% CPU
Optimizing NNI: done in 1.95807 secs using 299.4% CPU
Optimizing NNI: done in 2.30734 secs using 299.6% CPU
Optimizing NNI: done in 1.69134 secs using 299.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 46: -59677.754
Optimizing NNI: done in 7.9411 secs using 398.4% CPU
Optimizing NNI: done in 2.08725 secs using 299.4% CPU
Optimizing NNI: done in 2.03963 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 48: -59675.380
Optimizing NNI: done in 6.09373 secs using 398.2% CPU
Optimizing NNI: done in 1.85699 secs using 299.4% CPU
Optimizing NNI: done in 1.59634 secs using 299% CPU
Iteration 50 / LogL: -59682.869 / Time: 0h:2m:34s (0h:5m:9s left)
Optimizing NNI: done in 1.69571 secs using 299.2% CPU
Optimizing NNI: done in 1.92831 secs using 299.5% CPU
Optimizing NNI: done in 6.96159 secs using 398% CPU
Iteration 170 / LogL: -192309.019 / Time: 0h:21m:14s (0h:11m:3s left)
Optimizing NNI: done in 1.87861 secs using 299.1% CPU
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Optimizing NNI: done in 6.39106 secs using 397.9% CPU
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Optimizing NNI: done in 1.91642 secs using 298.4% CPU
Optimizing NNI: done in 1.79041 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 60: -59669.780
Iteration 60 / LogL: -59669.780 / Time: 0h:2m:55s (0h:4m:56s left)
Optimizing NNI: done in 2.03966 secs using 299.3% CPU
Optimizing NNI: done in 6.22531 secs using 398.6% CPU
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Optimizing NNI: done in 1.58317 secs using 299% CPU
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Optimizing NNI: done in 1.89492 secs using 299.2% CPU
Optimizing NNI: done in 1.80079 secs using 298.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 70: -59667.221
Iteration 70 / LogL: -59667.221 / Time: 0h:3m:15s (0h:4m:43s left)
Optimizing NNI: done in 6.83346 secs using 398.3% CPU
Optimizing NNI: done in 1.95054 secs using 299.6% CPU
Optimizing NNI: done in 1.62399 secs using 298.9% CPU
Optimizing NNI: done in 1.95725 secs using 299.1% CPU
Optimizing NNI: done in 1.78239 secs using 299% CPU
Optimizing NNI: done in 6.93973 secs using 398.3% CPU
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Optimizing NNI: done in 1.64035 secs using 298.6% CPU
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Optimizing NNI: done in 1.63433 secs using 299.2% CPU
Optimizing NNI: done in 1.53649 secs using 299.1% CPU
924  mtInv+F+I+R10 106055.190   573 213256.380   871060.380   215563.202
Optimizing NNI: done in 1.64175 secs using 299.3% CPU
Iteration 80 / LogL: -59681.090 / Time: 0h:3m:33s (0h:4m:3s left)
Optimizing NNI: done in 1.28521 secs using 299.7% CPU
Optimizing NNI: done in 6.29432 secs using 398.3% CPU
Optimizing NNI: done in 2.13534 secs using 299.4% CPU
Optimizing NNI: done in 1.73506 secs using 299.3% CPU
Optimizing NNI: done in 1.97898 secs using 299.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 84: -59659.780
Optimizing NNI: done in 6.52375 secs using 398.7% CPU
Iteration 180 / LogL: -192303.082 / Time: 0h:22m:18s (0h:9m:42s left)
Optimizing NNI: done in 2.02382 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 85: -59658.278
Optimizing NNI: done in 1.37497 secs using 298.8% CPU
Optimizing NNI: done in 6.20238 secs using 398.6% CPU
Optimizing NNI: done in 1.79114 secs using 299.4% CPU
Optimizing NNI: done in 1.7 secs using 299.2% CPU
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Optimizing NNI: done in 1.79126 secs using 299.3% CPU
Iteration 90 / LogL: -59704.459 / Time: 0h:3m:55s (0h:4m:11s left)
Optimizing NNI: done in 6.79677 secs using 398.8% CPU
Optimizing NNI: done in 1.43612 secs using 299.5% CPU
Optimizing NNI: done in 1.63122 secs using 299.3% CPU
Optimizing NNI: done in 1.791 secs using 299.6% CPU
Optimizing NNI: done in 1.87614 secs using 299.6% CPU
Optimizing NNI: done in 6.05316 secs using 398.7% CPU
Optimizing NNI: done in 2.02839 secs using 299.7% CPU
Optimizing NNI: done in 2.202 secs using 299.4% CPU
Optimizing NNI: done in 2.1553 secs using 299.4% CPU
Optimizing NNI: done in 7.1982 secs using 398.6% CPU
Optimizing NNI: done in 1.93324 secs using 299.6% CPU
945  mtMAM+I+R9    112629.743   552 226363.485   836875.485   228585.763
Optimizing NNI: done in 1.85355 secs using 299% CPU
Optimizing NNI: done in 1.84378 secs using 299.2% CPU
Iteration 100 / LogL: -59659.315 / Time: 0h:4m:14s (0h:3m:38s left)
Optimizing NNI: done in 1.72139 secs using 299.5% CPU
Optimizing NNI: done in 6.785 secs using 398.3% CPU
Optimizing NNI: done in 2.04994 secs using 299.6% CPU
Optimizing NNI: done in 2.50874 secs using 299.5% CPU
Optimizing NNI: done in 2.07642 secs using 299.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 6.86091 secs using 398.5% CPU
BETTER TREE FOUND at iteration 104: -59656.831
Optimizing NNI: done in 1.90677 secs using 299.3% CPU
Optimizing NNI: done in 1.76201 secs using 299.3% CPU
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Optimizing NNI: done in 1.90318 secs using 299.4% CPU
Optimizing NNI: done in 1.68399 secs using 299.5% CPU
Iteration 110 / LogL: -59658.324 / Time: 0h:4m:34s (0h:3m:56s left)
Optimizing NNI: done in 1.78631 secs using 299.3% CPU
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Optimizing NNI: done in 1.80578 secs using 299.5% CPU
Optimizing NNI: done in 6.59593 secs using 398.3% CPU
Iteration 190 / LogL: -192326.017 / Time: 0h:23m:24s (0h:8m:25s left)
Optimizing NNI: done in 1.59952 secs using 299.5% CPU
Optimizing NNI: done in 1.68489 secs using 299.4% CPU
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Iteration 120 / LogL: -59672.778 / Time: 0h:4m:52s (0h:3m:26s left)
Optimizing NNI: done in 1.85023 secs using 299.2% CPU
Optimizing NNI: done in 6.25252 secs using 398.5% CPU
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Optimizing NNI: done in 5.44377 secs using 398.6% CPU
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Optimizing NNI: done in 2.0136 secs using 299.3% CPU
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Optimizing NNI: done in 6.29189 secs using 398.8% CPU
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Optimizing NNI: done in 1.70969 secs using 299.4% CPU
Iteration 130 / LogL: -59674.448 / Time: 0h:5m:11s (0h:2m:58s left)
Optimizing NNI: done in 6.39086 secs using 398.5% CPU
946  mtMAM+I+R10   112577.907   554 226263.813   841203.813   228494.143
Optimizing NNI: done in 2.35022 secs using 299.3% CPU
Optimizing NNI: done in 1.61659 secs using 299.3% CPU
BETTER TREE FOUND at iteration 132: -59656.829
Optimizing NNI: done in 2.03209 secs using 299.3% CPU
Optimizing NNI: done in 5.79028 secs using 398.4% CPU
Optimizing NNI: done in 2.3337 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 134: -59656.077
Optimizing NNI: done in 1.5643 secs using 299.2% CPU
Optimizing NNI: done in 1.67633 secs using 299.2% CPU
Optimizing NNI: done in 6.58482 secs using 398.6% CPU
Optimizing NNI: done in 1.71895 secs using 298.9% CPU
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Optimizing NNI: done in 1.4389 secs using 299.5% CPU
Optimizing NNI: done in 1.91867 secs using 299.1% CPU
BETTER TREE FOUND at iteration 140: -59656.073
Iteration 140 / LogL: -59656.073 / Time: 0h:5m:31s (0h:3m:58s left)
Optimizing NNI: done in 6.73133 secs using 398.3% CPU
Optimizing NNI: done in 1.95816 secs using 298.6% CPU
BETTER TREE FOUND at iteration 141: -59656.071
Optimizing NNI: done in 1.6239 secs using 299.6% CPU
Optimizing NNI: done in 1.76189 secs using 299.3% CPU
Optimizing NNI: done in 5.79145 secs using 398.8% CPU
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Optimizing NNI: done in 1.88113 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 146: -59652.901
Optimizing NNI: done in 6.2079 secs using 398.9% CPU
Optimizing NNI: done in 1.83845 secs using 299.5% CPU
Optimizing NNI: done in 1.80078 secs using 299% CPU
Optimizing NNI: done in 1.77786 secs using 299.3% CPU
Optimizing NNI: done in 5.37889 secs using 398.7% CPU
Iteration 200 / LogL: -192293.374 / Time: 0h:24m:25s (0h:7m:7s left)
Optimizing NNI: done in 2.12766 secs using 299.4% CPU
Iteration 150 / LogL: -59724.203 / Time: 0h:5m:51s (0h:3m:46s left)
Optimizing NNI: done in 1.84385 secs using 299.5% CPU
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Optimizing NNI: done in 1.78995 secs using 299.2% CPU
Optimizing NNI: done in 5.65929 secs using 398.5% CPU
967  mtMAM+F+I+R9  109645.183   571 220432.366   873656.366   222731.135
Optimizing NNI: done in 1.67197 secs using 298.8% CPU
Optimizing NNI: done in 1.80672 secs using 299.3% CPU
Optimizing NNI: done in 2.3364 secs using 299.3% CPU
Optimizing NNI: done in 6.78425 secs using 398.4% CPU
Optimizing NNI: done in 1.80383 secs using 299.6% CPU
BETTER TREE FOUND at iteration 160: -59652.898
Iteration 160 / LogL: -59652.898 / Time: 0h:6m:11s (0h:3m:53s left)
Optimizing NNI: done in 1.91055 secs using 299.3% CPU
Optimizing NNI: done in 2.15543 secs using 299.5% CPU
Optimizing NNI: done in 5.89732 secs using 398.7% CPU
Optimizing NNI: done in 2.06741 secs using 299.3% CPU
Optimizing NNI: done in 1.7321 secs using 299.2% CPU
Optimizing NNI: done in 1.66359 secs using 299.4% CPU
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Optimizing NNI: done in 6.54667 secs using 398.6% CPU
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Optimizing NNI: done in 5.88736 secs using 398.9% CPU
Optimizing NNI: done in 1.46381 secs using 299.2% CPU
Iteration 170 / LogL: -59654.192 / Time: 0h:6m:30s (0h:3m:27s left)
Optimizing NNI: done in 2.10319 secs using 299.4% CPU
BETTER TREE FOUND at iteration 171: -59652.897
Optimizing NNI: done in 2.04268 secs using 299.5% CPU
Optimizing NNI: done in 6.49405 secs using 398.6% CPU
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Optimizing NNI: done in 1.78372 secs using 299.3% CPU
Iteration 180 / LogL: -59670.615 / Time: 0h:6m:50s (0h:3m:28s left)
Optimizing NNI: done in 1.63554 secs using 299.6% CPU
Optimizing NNI: done in 2.34431 secs using 299.1% CPU
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Optimizing NNI: done in 8.09461 secs using 398.6% CPU
Iteration 210 / LogL: -192553.780 / Time: 0h:25m:31s (0h:5m:51s left)
Optimizing NNI: done in 1.80493 secs using 299.6% CPU
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Optimizing NNI: done in 1.33128 secs using 299.3% CPU
Optimizing NNI: done in 1.99216 secs using 299.3% CPU
Optimizing NNI: done in 2.02859 secs using 299% CPU
Iteration 190 / LogL: -59672.921 / Time: 0h:7m:8s (0h:3m:3s left)
Optimizing NNI: done in 6.72409 secs using 398.8% CPU
Optimizing NNI: done in 1.77951 secs using 299.4% CPU
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Optimizing NNI: done in 2.15267 secs using 299.4% CPU
Optimizing NNI: done in 1.94858 secs using 298.9% CPU
WARNING: Log-likelihood -109689 of mtMAM+F+I+R10 worse than mtMAM+F+I+R9 -109645
968  mtMAM+F+I+R10 109689.206   573 220524.412   878328.412   222831.233
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 1.85752 secs using 299.5% CPU
Iteration 200 / LogL: -59658.867 / Time: 0h:7m:27s (0h:2m:39s left)
Optimizing NNI: done in 7.00768 secs using 398.3% CPU
Optimizing NNI: done in 1.55754 secs using 299.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.00769 secs using 299.3% CPU
Optimizing NNI: done in 1.68282 secs using 299.3% CPU
BETTER TREE FOUND at iteration 217: -192285.690
Optimizing NNI: done in 1.79913 secs using 299.4% CPU
Optimizing NNI: done in 1.61594 secs using 299.2% CPU
Iteration 210 / LogL: -59678.088 / Time: 0h:7m:46s (0h:2m:16s left)
Optimizing NNI: done in 2.00138 secs using 299.5% CPU
Optimizing NNI: done in 5.80383 secs using 398.5% CPU
Optimizing NNI: done in 1.85425 secs using 299.4% CPU
989  FLAVI+I+R9    108200.132   552 217504.263   828016.263   219726.541
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 1.88417 secs using 299.5% CPU
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Optimizing NNI: done in 1.77755 secs using 299.2% CPU
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Iteration 220 / LogL: -192381.833 / Time: 0h:26m:38s (0h:11m:47s left)
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Iteration 220 / LogL: -59662.937 / Time: 0h:8m:5s (0h:1m:53s left)
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Iteration 230 / LogL: -59687.929 / Time: 0h:8m:24s (0h:1m:30s left)
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Iteration 240 / LogL: -59690.823 / Time: 0h:8m:43s (0h:1m:7s left)
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Optimizing NNI: done in 1.81867 secs using 299% CPU
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Optimizing NNI: done in 5.91288 secs using 397.9% CPU
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BETTER TREE FOUND at iteration 246: -59652.896
Optimizing NNI: done in 1.54232 secs using 299.2% CPU
Optimizing NNI: done in 1.48409 secs using 299.3% CPU
Optimizing NNI: done in 1.91132 secs using 298.8% CPU
Optimizing NNI: done in 5.86822 secs using 398.7% CPU
Optimizing NNI: done in 1.97075 secs using 298.9% CPU
Iteration 250 / LogL: -59653.857 / Time: 0h:9m:1s (0h:3m:28s left)
WARNING: Log-likelihood -108225 of FLAVI+I+R10 worse than FLAVI+I+R9 -108200
990  FLAVI+I+R10   108225.002   554 217558.003   832498.003   219788.333
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 2.07794 secs using 298.6% CPU
Optimizing NNI: done in 2.24208 secs using 298.9% CPU
Optimizing NNI: done in 6.47356 secs using 397.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.93062 secs using 298.9% CPU
BETTER TREE FOUND at iteration 230: -192281.882
Iteration 230 / LogL: -192281.882 / Time: 0h:27m:44s (0h:12m:6s left)
Optimizing NNI: done in 1.65791 secs using 299.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -59652.896
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Iteration 260 / LogL: -59652.899 / Time: 0h:9m:21s (0h:3m:6s left)
Optimizing NNI: done in 6.72077 secs using 398.5% CPU
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Optimizing NNI: done in 1.83723 secs using 298.5% CPU
BETTER TREE FOUND at iteration 266: -59652.896
Optimizing NNI: done in 6.33033 secs using 398.4% CPU
Optimizing NNI: done in 2.13193 secs using 298.7% CPU
Optimizing NNI: done in 2.08947 secs using 299% CPU
1011  FLAVI+F+I+R9  108324.246   571 217790.492   871014.492   220089.261
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 2.05719 secs using 299% CPU
Optimizing NNI: done in 2.06913 secs using 299.3% CPU
Iteration 270 / LogL: -59660.076 / Time: 0h:9m:41s (0h:3m:27s left)
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Iteration 280 / LogL: -59664.376 / Time: 0h:10m:1s (0h:3m:5s left)
Optimizing NNI: done in 2.32128 secs using 299.2% CPU
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Iteration 240 / LogL: -192291.196 / Time: 0h:28m:48s (0h:10m:50s left)
Optimizing NNI: done in 1.91705 secs using 299% CPU
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Optimizing NNI: done in 1.76667 secs using 298.9% CPU
Iteration 290 / LogL: -59675.425 / Time: 0h:10m:21s (0h:2m:43s left)
Optimizing NNI: done in 2.10312 secs using 299.2% CPU
Optimizing NNI: done in 1.54072 secs using 299.4% CPU
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WARNING: Log-likelihood -108356 of FLAVI+F+I+R10 worse than FLAVI+F+I+R9 -108324
1012  FLAVI+F+I+R10 108356.391   573 217858.782   875662.782   220165.604
Optimizing NNI: done in 1.80569 secs using 299% CPU
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Iteration 300 / LogL: -59652.898 / Time: 0h:10m:40s (0h:2m:21s left)
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Iteration 310 / LogL: -59668.410 / Time: 0h:10m:59s (0h:1m:59s left)
Optimizing NNI: done in 1.70698 secs using 298.9% CPU
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Optimizing NNI: done in 6.72754 secs using 398.3% CPU
Iteration 250 / LogL: -192309.744 / Time: 0h:29m:52s (0h:9m:35s left)
Optimizing NNI: done in 1.96871 secs using 298.7% CPU
Iteration 320 / LogL: -59658.267 / Time: 0h:11m:18s (0h:1m:37s left)
Optimizing NNI: done in 1.95685 secs using 299.1% CPU
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Optimizing NNI: done in 2.03189 secs using 299% CPU
1033  HIVb+I+R9     107329.785   552 215763.570   826275.570   217985.848
Optimizing NNI: done in 1.92437 secs using 299.6% CPU
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Iteration 330 / LogL: -59664.315 / Time: 0h:11m:38s (0h:1m:16s left)
Optimizing NNI: done in 2.15206 secs using 299.1% CPU
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Iteration 340 / LogL: -59667.351 / Time: 0h:11m:59s (0h:0m:55s left)
Optimizing NNI: done in 2.19428 secs using 299.2% CPU
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Iteration 350 / LogL: -59656.711 / Time: 0h:12m:17s (0h:0m:33s left)
Optimizing NNI: done in 1.76772 secs using 298.9% CPU
Optimizing NNI: done in 1.92711 secs using 299.3% CPU
Optimizing NNI: done in 6.24738 secs using 398.7% CPU
Iteration 260 / LogL: -192365.077 / Time: 0h:30m:56s (0h:8m:21s left)
Optimizing NNI: done in 2.10956 secs using 299.3% CPU
Optimizing NNI: done in 1.8714 secs using 299.8% CPU
Optimizing NNI: done in 1.9178 secs using 298.9% CPU
Optimizing NNI: done in 5.3651 secs using 398.6% CPU
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Iteration 360 / LogL: -59652.903 / Time: 0h:12m:37s (0h:0m:12s left)
Optimizing NNI: done in 1.84318 secs using 299.2% CPU
Optimizing NNI: done in 1.83403 secs using 299.2% CPU
Optimizing NNI: done in 6.88147 secs using 398.6% CPU
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Optimizing NNI: done in 5.95651 secs using 398.4% CPU
Optimizing NNI: done in 1.90217 secs using 299.2% CPU
Optimizing NNI: done in 1.96832 secs using 298.7% CPU
TREE SEARCH COMPLETED AFTER 367 ITERATIONS / Time: 0h:12m:49s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59652.896
2. Current log-likelihood: -59652.879
Optimal log-likelihood: -59652.866
Site proportion and rates:  (0.103,0.078) (0.095,0.209) (0.203,0.390) (0.213,0.658) (0.133,0.983) (0.149,1.646) (0.073,2.665) (0.031,5.954)
Parameters optimization took 2 rounds (1.259 sec)
BEST SCORE FOUND : -59652.866
Total tree length: 47.283

Total number of iterations: 367
CPU time used for tree search: 2248.527 sec (0h:37m:28s)
Wall-clock time used for tree search: 754.683 sec (0h:12m:34s)
Total CPU time used: 2298.206 sec (0h:38m:18s)
Total wall-clock time used: 771.242 sec (0h:12m:51s)

===> START BOOTSTRAP REPLICATE NUMBER 7

Creating bootstrap alignment (seed: 956256)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.044 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -57611.343
2. Current log-likelihood: -57124.476
Optimizing NNI: done in 6.52323 secs using 398.2% CPU
3. Current log-likelihood: -57113.353
4. Current log-likelihood: -57082.413
5. Current log-likelihood: -57073.704
6. Current log-likelihood: -57073.301
Optimal log-likelihood: -57073.256
Site proportion and rates:  (0.129,0.059) (0.081,0.181) (0.086,0.411) (0.121,0.419) (0.204,0.775) (0.178,1.222) (0.173,2.173) (0.028,5.029)
Parameters optimization took 6 rounds (6.282 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.45638 secs using 299.7% CPU
Computing ML distances took 1.456595 sec (of wall-clock time) 4.364607 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000447989 secs using 296.4% CPU
Constructing RapidNJ tree: done in 0.00353312 secs using 293.2% CPU
Computing RapidNJ tree took 0.004069 sec (of wall-clock time) 0.012241 sec (of CPU time)
Optimizing NNI: done in 6.05774 secs using 398.5% CPU
Log-likelihood of RapidNJ tree: -57309.170
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 5.052 second
Optimizing NNI: done in 5.87236 secs using 398.5% CPU
Computing log-likelihood of 98 initial trees ... 6.623 seconds
Current best score: -57073.256

Do NNI search on 20 best initial trees
Optimizing NNI: done in 6.2082 secs using 398.6% CPU
Optimizing NNI: done in 1.22196 secs using 298.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -56873.631
Optimizing NNI: done in 1.48005 secs using 298.7% CPU
Optimizing NNI: done in 1.08297 secs using 299.4% CPU
Optimizing NNI: done in 6.6674 secs using 398.3% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -56870.463
Optimizing NNI: done in 1.26902 secs using 299.3% CPU
Optimizing NNI: done in 5.21262 secs using 398.8% CPU
Iteration 270 / LogL: -192307.417 / Time: 0h:31m:58s (0h:7m:7s left)
Optimizing NNI: done in 1.45919 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -56857.886
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Iteration 10 / LogL: -56889.053 / Time: 0h:0m:40s
Optimizing NNI: done in 1.7136 secs using 298.4% CPU
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Optimizing NNI: done in 1.54452 secs using 299.2% CPU
Iteration 20 / LogL: -56863.148 / Time: 0h:0m:54s
Finish initializing candidate tree set (20)
Current best tree score: -56857.886 / CPU time: 46.430
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.3223 secs using 299.7% CPU
Optimizing NNI: done in 6.01723 secs using 398.8% CPU
Optimizing NNI: done in 1.7002 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -56853.071
Optimizing NNI: done in 1.6202 secs using 299% CPU
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Optimizing NNI: done in 5.98207 secs using 398.7% CPU
Optimizing NNI: done in 1.50958 secs using 299.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -56853.070
Optimizing NNI: done in 1.86639 secs using 299% CPU
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Iteration 30 / LogL: -56860.744 / Time: 0h:1m:12s (0h:3m:50s left)
Optimizing NNI: done in 1.51443 secs using 299.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.68904 secs using 398.8% CPU
BETTER TREE FOUND at iteration 31: -56850.032
Optimizing NNI: done in 1.72357 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -56849.702
Optimizing NNI: done in 1.76271 secs using 299.4% CPU
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1034  HIVb+I+R10    107323.844   554 215755.688   830695.688   217986.017
Optimizing NNI: done in 1.48916 secs using 299.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 6.44875 secs using 398.2% CPU
Iteration 280 / LogL: -192443.564 / Time: 0h:32m:59s (0h:5m:54s left)
BETTER TREE FOUND at iteration 40: -56847.732
Iteration 40 / LogL: -56847.732 / Time: 0h:1m:33s (0h:4m:0s left)
Optimizing NNI: done in 1.72214 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 41: -56846.864
Optimizing NNI: done in 1.58834 secs using 299.4% CPU
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Iteration 50 / LogL: -56862.964 / Time: 0h:1m:52s (0h:3m:28s left)
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1055  HIVb+F+I+R9   107152.139   571 215446.278   868670.278   217745.048
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Optimizing NNI: done in 7.26879 secs using 398.1% CPU
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Iteration 60 / LogL: -56852.039 / Time: 0h:2m:8s (0h:2m:56s left)
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Iteration 70 / LogL: -56850.342 / Time: 0h:2m:25s (0h:2m:29s left)
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Optimizing NNI: done in 6.66187 secs using 398.7% CPU
Iteration 290 / LogL: -192318.554 / Time: 0h:34m:5s (0h:4m:43s left)
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Iteration 80 / LogL: -56920.319 / Time: 0h:2m:42s (0h:2m:5s left)
Optimizing NNI: done in 1.64461 secs using 299% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 81: -56845.446
Optimizing NNI: done in 6.91601 secs using 398.4% CPU
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Iteration 90 / LogL: -56872.483 / Time: 0h:3m:0s (0h:3m:4s left)
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BETTER TREE FOUND at iteration 96: -56843.716
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Iteration 100 / LogL: -56861.348 / Time: 0h:3m:20s (0h:3m:14s left)
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BETTER TREE FOUND at iteration 106: -56842.706
Optimizing NNI: done in 2.03763 secs using 299.2% CPU
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Iteration 110 / LogL: -56852.354 / Time: 0h:3m:39s (0h:3m:13s left)
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Iteration 300 / LogL: -192350.799 / Time: 0h:35m:9s (0h:3m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 112: -56840.139
Optimizing NNI: done in 1.30201 secs using 299.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.94296 secs using 398.5% CPU
BETTER TREE FOUND at iteration 115: -56839.806
Optimizing NNI: done in 1.7286 secs using 299.1% CPU
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Iteration 120 / LogL: -56873.768 / Time: 0h:3m:57s (0h:3m:9s left)
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BETTER TREE FOUND at iteration 122: -56834.661
Optimizing NNI: done in 1.83497 secs using 299.2% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 124: -56832.412
Optimizing NNI: done in 6.33475 secs using 398.9% CPU
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Iteration 130 / LogL: -56845.284 / Time: 0h:4m:16s (0h:3m:6s left)
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Iteration 140 / LogL: -56834.659 / Time: 0h:4m:32s (0h:2m:44s left)
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Iteration 310 / LogL: -192312.185 / Time: 0h:36m:12s (0h:2m:20s left)
Optimizing NNI: done in 1.53273 secs using 299.5% CPU
WARNING: Log-likelihood -107163 of HIVb+F+I+R10 worse than HIVb+F+I+R9 -107152
1056  HIVb+F+I+R10  107162.680   573 215471.361   873275.361   217778.182
Optimizing NNI: done in 1.81671 secs using 299.6% CPU
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Iteration 150 / LogL: -56832.413 / Time: 0h:4m:49s (0h:2m:23s left)
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1077  HIVw+I+R9     111396.705   552 223897.411   834409.411   226119.689
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Iteration 160 / LogL: -56855.356 / Time: 0h:5m:6s (0h:2m:3s left)
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Iteration 170 / LogL: -56839.491 / Time: 0h:5m:21s (0h:1m:42s left)
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Iteration 180 / LogL: -56834.976 / Time: 0h:5m:38s (0h:1m:23s left)
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Iteration 320 / LogL: -192292.720 / Time: 0h:37m:15s (0h:1m:10s left)
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Iteration 190 / LogL: -56834.294 / Time: 0h:5m:54s (0h:1m:3s left)
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Iteration 200 / LogL: -56845.563 / Time: 0h:6m:10s (0h:0m:44s left)
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BETTER TREE FOUND at iteration 206: -56832.412
Optimizing NNI: done in 7.08018 secs using 398.8% CPU
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Iteration 210 / LogL: -56847.474 / Time: 0h:6m:27s (0h:2m:57s left)
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Iteration 220 / LogL: -56848.185 / Time: 0h:6m:44s (0h:2m:38s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.69606 secs using 299.3% CPU
Optimizing NNI: done in 1.70978 secs using 299.4% CPU
BETTER TREE FOUND at iteration 330: -192279.937
Iteration 330 / LogL: -192279.937 / Time: 0h:38m:22s (0h:11m:39s left)
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Iteration 230 / LogL: -56849.687 / Time: 0h:7m:1s (0h:2m:19s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.772 secs using 299.5% CPU
BETTER TREE FOUND at iteration 332: -192279.120
Optimizing NNI: done in 1.60579 secs using 299.4% CPU
WARNING: Log-likelihood -111412 of HIVw+I+R10 worse than HIVw+I+R9 -111397
1078  HIVw+I+R10    111412.121   554 223932.242   838872.242   226162.571
Optimizing NNI: done in 1.79743 secs using 299.4% CPU
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Iteration 240 / LogL: -56860.231 / Time: 0h:7m:18s (0h:2m:1s left)
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Iteration 250 / LogL: -56837.879 / Time: 0h:7m:34s (0h:1m:42s left)
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Iteration 260 / LogL: -56837.522 / Time: 0h:7m:49s (0h:1m:23s left)
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1099  HIVw+F+I+R9   109122.085   571 219386.170   872610.170   221684.939
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Iteration 340 / LogL: -192304.730 / Time: 0h:39m:24s (0h:10m:41s left)
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Iteration 270 / LogL: -56839.863 / Time: 0h:8m:5s (0h:1m:4s left)
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BETTER TREE FOUND at iteration 273: -56832.412
Optimizing NNI: done in 6.69041 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 343: -192273.065
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WARNING: Log-likelihood -109128 of HIVw+F+I+R10 worse than HIVw+F+I+R9 -109122
1100  HIVw+F+I+R10  109128.065   573 219402.130   877206.130   221708.951
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1121  FLU+I+R9      107356.081   552 215816.161   826328.161   218038.439
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Iteration 440 / LogL: -56833.040 / Time: 0h:12m:40s (0h:0m:0s left)
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TREE SEARCH COMPLETED AFTER 441 ITERATIONS / Time: 0h:12m:41s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -56832.411
Optimal log-likelihood: -56832.403
Site proportion and rates:  (0.139,0.063) (0.070,0.175) (0.124,0.421) (0.088,0.421) (0.230,0.789) (0.157,1.300) (0.166,2.215) (0.027,5.015)
Parameters optimization took 1 rounds (0.546 sec)
BEST SCORE FOUND : -56832.403
Total tree length: 41.027

Total number of iterations: 441
CPU time used for tree search: 2245.087 sec (0h:37m:25s)
Wall-clock time used for tree search: 753.549 sec (0h:12m:33s)
Total CPU time used: 2271.768 sec (0h:37m:51s)
Total wall-clock time used: 762.420 sec (0h:12m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 8

Creating bootstrap alignment (seed: 956257)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.086 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59112.092
2. Current log-likelihood: -58602.816
3. Current log-likelihood: -58587.146
4. Current log-likelihood: -58572.304
5. Current log-likelihood: -58558.980
Optimizing NNI: done in 7.05039 secs using 398.6% CPU
6. Current log-likelihood: -58558.031
Optimal log-likelihood: -58558.000
Site proportion and rates:  (0.115,0.065) (0.110,0.202) (0.110,0.357) (0.106,0.493) (0.165,0.746) (0.200,1.196) (0.166,2.240) (0.029,5.096)
Parameters optimization took 6 rounds (6.380 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.49424 secs using 299.7% CPU
Computing ML distances took 1.494437 sec (of wall-clock time) 4.478808 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000507116 secs using 404.4% CPU
Constructing RapidNJ tree: done in 0.00391102 secs using 257.3% CPU
Computing RapidNJ tree took 0.004488 sec (of wall-clock time) 0.012179 sec (of CPU time)
Log-likelihood of RapidNJ tree: -58821.604
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 6.80591 secs using 398% CPU
5.311 second
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Computing log-likelihood of 98 initial trees ... 6.942 seconds
Current best score: -58558.000

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -58487.179
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -58510.975 / Time: 0h:0m:54s
Finish initializing candidate tree set (20)
Current best tree score: -58477.013 / CPU time: 45.973
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -58473.873
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 47: -58446.667
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 49: -58446.005
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WARNING: Log-likelihood -107361 of FLU+I+R10 worse than FLU+I+R9 -107356
1122  FLU+I+R10     107360.879   554 215829.758   830769.758   218060.088
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1143  FLU+F+I+R9    106817.807   571 214777.615   868001.615   217076.384
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BETTER TREE FOUND at iteration 65: -58444.777
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BETTER TREE FOUND at iteration 104: -58444.698
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Iteration 110 / LogL: -58501.805 / Time: 0h:3m:33s (0h:3m:4s left)
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WARNING: Log-likelihood -106821 of FLU+F+I+R10 worse than FLU+F+I+R9 -106818
1144  FLU+F+I+R10   106821.220   573 214788.440   872592.440   217095.261
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1165  rtREV+I+R9    107026.598   552 215157.197   825669.197   217379.475
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Iteration 190 / LogL: -58459.008 / Time: 0h:5m:44s (0h:0m:25s left)
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1166  rtREV+I+R10   107024.912   554 215157.824   830097.824   217388.153
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Iteration 200 / LogL: -58445.797 / Time: 0h:6m:1s (0h:0m:7s left)
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1187  rtREV+F+I+R9  106609.301   571 214360.601   867584.601   216659.371
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TREE SEARCH COMPLETED AFTER 205 ITERATIONS / Time: 0h:6m:9s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58444.698
Optimal log-likelihood: -58444.696
Site proportion and rates:  (0.118,0.067) (0.125,0.218) (0.100,0.406) (0.097,0.465) (0.173,0.758) (0.190,1.212) (0.166,2.234) (0.029,4.958)
Parameters optimization took 1 rounds (0.428 sec)
BEST SCORE FOUND : -58444.696
Total tree length: 42.432

Total number of iterations: 205
CPU time used for tree search: 1069.613 sec (0h:17m:49s)
Wall-clock time used for tree search: 360.844 sec (0h:6m:0s)
Total CPU time used: 1096.198 sec (0h:18m:16s)
Total wall-clock time used: 369.680 sec (0h:6m:9s)

===> START BOOTSTRAP REPLICATE NUMBER 9

Creating bootstrap alignment (seed: 956258)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.052 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -62049.702
2. Current log-likelihood: -61424.358
Optimizing NNI: done in 6.48799 secs using 398.4% CPU
Iteration 440 / LogL: -192330.102 / Time: 0h:50m:20s (0h:8m:8s left)
3. Current log-likelihood: -61420.080
4. Current log-likelihood: -61418.317
5. Current log-likelihood: -61415.074
6. Current log-likelihood: -61409.952
7. Current log-likelihood: -61402.748
Optimizing NNI: done in 5.73932 secs using 398.2% CPU
8. Current log-likelihood: -61393.512
9. Current log-likelihood: -61392.723
Optimal log-likelihood: -61392.627
Site proportion and rates:  (0.097,0.053) (0.103,0.177) (0.110,0.367) (0.063,0.389) (0.230,0.643) (0.182,1.123) (0.191,2.225) (0.023,5.883)
Parameters optimization took 9 rounds (9.452 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.48922 secs using 299.9% CPU
Computing ML distances took 1.489437 sec (of wall-clock time) 4.466268 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000469208 secs using 148.5% CPU
Constructing RapidNJ tree: done in 0.00389504 secs using 209.8% CPU
Computing RapidNJ tree took 0.004451 sec (of wall-clock time) 0.009383 sec (of CPU time)
Log-likelihood of RapidNJ tree: -61392.473
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 6.34097 secs using 398.6% CPU
4.967 second
Optimizing NNI: done in 6.04031 secs using 398.5% CPU
Computing log-likelihood of 98 initial trees ... 6.924 seconds
Current best score: -61372.209

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -61133.629
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -61080.943
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 8: -61072.084
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Iteration 10 / LogL: -61086.502 / Time: 0h:0m:47s
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Iteration 450 / LogL: -192283.475 / Time: 0h:51m:23s (0h:6m:58s left)
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Iteration 20 / LogL: -61090.153 / Time: 0h:1m:5s
Finish initializing candidate tree set (20)
Current best tree score: -61072.084 / CPU time: 54.143
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -61060.455
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -61044.087
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Iteration 30 / LogL: -61087.083 / Time: 0h:1m:27s (0h:4m:53s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -61024.920
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -61014.051
Iteration 40 / LogL: -61014.051 / Time: 0h:1m:50s (0h:4m:43s left)
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Optimizing NNI: done in 1.74508 secs using 299.2% CPU
Optimizing NNI: done in 1.48879 secs using 299.6% CPU
1188  rtREV+F+I+R10 106601.272   573 214348.544   872152.544   216655.366
Optimizing NNI: done in 2.03117 secs using 299.2% CPU
Optimizing NNI: done in 5.78079 secs using 398.3% CPU
Iteration 460 / LogL: -192785.696 / Time: 0h:52m:24s (0h:5m:49s left)
Optimizing NNI: done in 1.82793 secs using 299.3% CPU
Optimizing NNI: done in 2.30194 secs using 299.2% CPU
Iteration 50 / LogL: -61024.988 / Time: 0h:2m:9s (0h:3m:57s left)
Optimizing NNI: done in 1.76445 secs using 299.3% CPU
1209  cpREV+I+R9    106274.024   552 213652.047   824164.047   215874.325
Optimizing NNI: done in 5.67009 secs using 398.1% CPU
Optimizing NNI: done in 1.88886 secs using 299.5% CPU
Optimizing NNI: done in 1.82438 secs using 299% CPU
Optimizing NNI: done in 1.69625 secs using 299.2% CPU
Optimizing NNI: done in 5.63286 secs using 398.3% CPU
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Optimizing NNI: done in 5.32635 secs using 398.5% CPU
Optimizing NNI: done in 2.11777 secs using 299.6% CPU
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Optimizing NNI: done in 1.77319 secs using 299.4% CPU
Optimizing NNI: done in 1.84014 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 6.02597 secs using 398.3% CPU
Optimizing NNI: done in 5.80297 secs using 398.7% CPU
BETTER TREE FOUND at iteration 60: -61000.376
Iteration 60 / LogL: -61000.376 / Time: 0h:2m:39s (0h:4m:29s left)
Optimizing NNI: done in 5.8129 secs using 398% CPU
Optimizing NNI: done in 1.86669 secs using 299.1% CPU
Optimizing NNI: done in 1.91758 secs using 299.5% CPU
Optimizing NNI: done in 1.81609 secs using 298.6% CPU
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Optimizing NNI: done in 6.60099 secs using 398.5% CPU
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Optimizing NNI: done in 6.82585 secs using 398.7% CPU
Optimizing NNI: done in 1.74803 secs using 299.6% CPU
Optimizing NNI: done in 1.97745 secs using 299.3% CPU
Optimizing NNI: done in 1.49003 secs using 299.4% CPU
Iteration 70 / LogL: -61044.303 / Time: 0h:2m:57s (0h:3m:51s left)
Optimizing NNI: done in 1.42801 secs using 299.6% CPU
Optimizing NNI: done in 5.90211 secs using 398.8% CPU
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Optimizing NNI: done in 1.66948 secs using 299.3% CPU
Optimizing NNI: done in 5.68242 secs using 398.2% CPU
Iteration 470 / LogL: -192281.037 / Time: 0h:53m:24s (0h:4m:40s left)
Optimizing NNI: done in 1.76218 secs using 299.3% CPU
Optimizing NNI: done in 1.71818 secs using 299% CPU
Optimizing NNI: done in 1.95506 secs using 299.3% CPU
Optimizing NNI: done in 6.17034 secs using 398.6% CPU
Optimizing NNI: done in 1.86026 secs using 298.9% CPU
Optimizing NNI: done in 1.87572 secs using 299.4% CPU
Optimizing NNI: done in 1.73124 secs using 299.4% CPU
Iteration 80 / LogL: -61003.863 / Time: 0h:3m:16s (0h:3m:18s left)
Optimizing NNI: done in 6.04767 secs using 398.7% CPU
Optimizing NNI: done in 2.1778 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 81: -61000.055
Optimizing NNI: done in 2.15969 secs using 299.5% CPU
Optimizing NNI: done in 1.66866 secs using 299.5% CPU
Optimizing NNI: done in 6.85457 secs using 398.6% CPU
Optimizing NNI: done in 2.1086 secs using 299.5% CPU
Optimizing NNI: done in 2.12354 secs using 299.4% CPU
BETTER TREE FOUND at iteration 85: -61000.048
Optimizing NNI: done in 2.21341 secs using 299.3% CPU
Optimizing NNI: done in 6.05346 secs using 398.3% CPU
Optimizing NNI: done in 1.98035 secs using 299.6% CPU
Optimizing NNI: done in 1.80874 secs using 299% CPU
Optimizing NNI: done in 2.05211 secs using 299.4% CPU
Optimizing NNI: done in 1.93735 secs using 299.5% CPU
Iteration 90 / LogL: -61004.512 / Time: 0h:3m:37s (0h:3m:52s left)
Optimizing NNI: done in 6.56076 secs using 398.6% CPU
Optimizing NNI: done in 1.89719 secs using 299.3% CPU
Optimizing NNI: done in 2.18875 secs using 298.8% CPU
Optimizing NNI: done in 2.02523 secs using 299.5% CPU
Optimizing NNI: done in 5.90767 secs using 398.4% CPU
Optimizing NNI: done in 1.57278 secs using 299.1% CPU
Optimizing NNI: done in 1.79927 secs using 299% CPU
Optimizing NNI: done in 1.82716 secs using 299.6% CPU
Optimizing NNI: done in 6.65529 secs using 398.6% CPU
Optimizing NNI: done in 1.64561 secs using 299.6% CPU
Optimizing NNI: done in 2.07501 secs using 299.4% CPU
1210  cpREV+I+R10   106265.456   554 213638.913   828578.913   215869.243
Optimizing NNI: done in 1.5515 secs using 299.5% CPU
Optimizing NNI: done in 1.91461 secs using 299.4% CPU
Iteration 100 / LogL: -61004.368 / Time: 0h:3m:56s (0h:3m:22s left)
Optimizing NNI: done in 6.38584 secs using 398.6% CPU
Optimizing NNI: done in 2.20095 secs using 299.1% CPU
Optimizing NNI: done in 1.95341 secs using 299.2% CPU
BETTER TREE FOUND at iteration 102: -61000.047
Optimizing NNI: done in 1.80356 secs using 299.5% CPU
1231  cpREV+F+I+R9  106393.320   571 213928.639   867152.639   216227.409
Optimizing NNI: done in 6.5439 secs using 398.5% CPU
Optimizing NNI: done in 2.37184 secs using 299.1% CPU
Optimizing NNI: done in 1.95526 secs using 299.4% CPU
Optimizing NNI: done in 1.94106 secs using 299.8% CPU
Optimizing NNI: done in 6.53862 secs using 398.4% CPU
Iteration 480 / LogL: -192305.829 / Time: 0h:54m:28s (0h:3m:31s left)
Optimizing NNI: done in 2.13894 secs using 299.4% CPU
Optimizing NNI: done in 1.75658 secs using 299.3% CPU
Optimizing NNI: done in 1.85271 secs using 299.2% CPU
Optimizing NNI: done in 1.71196 secs using 299.4% CPU
Iteration 110 / LogL: -61007.432 / Time: 0h:4m:16s (0h:3m:36s left)
Optimizing NNI: done in 7.40963 secs using 398.6% CPU
Optimizing NNI: done in 1.95208 secs using 299.4% CPU
Optimizing NNI: done in 1.69579 secs using 299.2% CPU
Optimizing NNI: done in 2.08157 secs using 299.3% CPU
Optimizing NNI: done in 1.67703 secs using 299.5% CPU
Optimizing NNI: done in 6.33796 secs using 398.6% CPU
Optimizing NNI: done in 1.5744 secs using 299.4% CPU
Optimizing NNI: done in 1.875 secs using 299% CPU
Optimizing NNI: done in 2.22556 secs using 299.4% CPU
Optimizing NNI: done in 5.75821 secs using 398.7% CPU
Optimizing NNI: done in 2.10028 secs using 299.1% CPU
Optimizing NNI: done in 1.90717 secs using 299.3% CPU
Optimizing NNI: done in 1.99056 secs using 299.3% CPU
Iteration 120 / LogL: -61017.044 / Time: 0h:4m:35s (0h:3m:9s left)
Optimizing NNI: done in 6.83685 secs using 398.1% CPU
Optimizing NNI: done in 2.30461 secs using 299.5% CPU
Optimizing NNI: done in 1.83939 secs using 299.5% CPU
Optimizing NNI: done in 2.04097 secs using 299.4% CPU
Optimizing NNI: done in 6.19538 secs using 398.7% CPU
Optimizing NNI: done in 2.36631 secs using 299.3% CPU
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Optimizing NNI: done in 5.96386 secs using 398.4% CPU
Optimizing NNI: done in 1.7846 secs using 299.5% CPU
Optimizing NNI: done in 1.8306 secs using 299.4% CPU
Optimizing NNI: done in 1.85396 secs using 299.3% CPU
Optimizing NNI: done in 5.43709 secs using 398.8% CPU
Optimizing NNI: done in 1.79991 secs using 299.5% CPU
Iteration 130 / LogL: -61000.051 / Time: 0h:4m:54s (0h:2m:44s left)
Optimizing NNI: done in 1.73505 secs using 299.6% CPU
Optimizing NNI: done in 1.89375 secs using 299.3% CPU
Optimizing NNI: done in 1.94148 secs using 299.4% CPU
Optimizing NNI: done in 6.62537 secs using 398.6% CPU
Optimizing NNI: done in 1.86726 secs using 299.2% CPU
Optimizing NNI: done in 2.04117 secs using 299.5% CPU
Optimizing NNI: done in 2.23834 secs using 299.5% CPU
Optimizing NNI: done in 5.74963 secs using 398.5% CPU
Optimizing NNI: done in 1.71225 secs using 299.4% CPU
Optimizing NNI: done in 2.18559 secs using 299.2% CPU
Optimizing NNI: done in 1.73793 secs using 299.4% CPU
Optimizing NNI: done in 5.83677 secs using 398.5% CPU
Iteration 490 / LogL: -192289.650 / Time: 0h:55m:31s (0h:2m:23s left)
Optimizing NNI: done in 1.84871 secs using 299.3% CPU
Iteration 140 / LogL: -61027.877 / Time: 0h:5m:14s (0h:2m:20s left)
Optimizing NNI: done in 1.52625 secs using 299.3% CPU
Optimizing NNI: done in 2.11106 secs using 299.4% CPU
Optimizing NNI: done in 6.08847 secs using 398.5% CPU
Optimizing NNI: done in 2.03004 secs using 299.3% CPU
Optimizing NNI: done in 2.16232 secs using 299.3% CPU
Optimizing NNI: done in 1.84631 secs using 298.9% CPU
Optimizing NNI: done in 6.36721 secs using 398.7% CPU
Optimizing NNI: done in 1.97981 secs using 299.3% CPU
Optimizing NNI: done in 1.74468 secs using 299.1% CPU
Optimizing NNI: done in 1.93443 secs using 299.3% CPU
Optimizing NNI: done in 2.04846 secs using 298.6% CPU
Optimizing NNI: done in 6.19219 secs using 398.5% CPU
Optimizing NNI: done in 1.67324 secs using 299.2% CPU
Iteration 150 / LogL: -61000.052 / Time: 0h:5m:33s (0h:1m:56s left)
Optimizing NNI: done in 1.67318 secs using 298.9% CPU
Optimizing NNI: done in 1.9519 secs using 299.4% CPU
Optimizing NNI: done in 6.59487 secs using 398.7% CPU
Optimizing NNI: done in 1.74511 secs using 298.9% CPU
Optimizing NNI: done in 1.74375 secs using 299.3% CPU
Optimizing NNI: done in 1.80175 secs using 299.1% CPU
Optimizing NNI: done in 1.74212 secs using 298.8% CPU
Optimizing NNI: done in 5.80371 secs using 398.8% CPU
Optimizing NNI: done in 2.1148 secs using 299.4% CPU
Optimizing NNI: done in 1.75742 secs using 299% CPU
Optimizing NNI: done in 1.85331 secs using 299.6% CPU
Optimizing NNI: done in 6.14849 secs using 398.4% CPU
Optimizing NNI: done in 2.11726 secs using 299.3% CPU
Iteration 160 / LogL: -61000.049 / Time: 0h:5m:52s (0h:1m:33s left)
Optimizing NNI: done in 1.83507 secs using 299.6% CPU
Optimizing NNI: done in 1.8949 secs using 299.7% CPU
Optimizing NNI: done in 6.44041 secs using 398.2% CPU
Optimizing NNI: done in 1.86554 secs using 299.4% CPU
1232  cpREV+F+I+R10 106392.025   573 213930.050   871734.050   216236.871
Akaike Information Criterion:           Q.plant+I+R10
Corrected Akaike Information Criterion: LG+G4
Bayesian Information Criterion:         Q.plant+I+R9
Best-fit model: Q.plant+I+R9 chosen according to BIC

All model information printed to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.model.gz
CPU time for ModelFinder: 27122.919 seconds (7h:32m:2s)
Wall-clock time for ModelFinder: 9104.626 seconds (2h:31m:44s)

===> START BOOTSTRAP REPLICATE NUMBER 1

Creating bootstrap alignment (seed: 957372)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.119 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106205.545
Optimizing NNI: done in 1.83311 secs using 299.4% CPU
2. Current log-likelihood: -104392.648
Optimizing NNI: done in 1.63588 secs using 299.5% CPU
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  

******************************************************
CHECKPOINT: Resuming analysis from /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.ckp.gz

IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/biosynthesis.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis
Seed:    680532 (Using SPRNG - Scalable Parallel Random Number Generator)
******************************************************
CHECKPOINT: Resuming analysis from /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.ckp.gz

IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport
Seed:    682847 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Mon Jul  7 16:01:04 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Time:    Mon Jul  7 16:01:04 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/biosynthesis.fasta ... Fasta format detected
Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta ... Fasta format detected
Reading fasta file: done in 0.00202489 secs using 98.77% CPU
Reading fasta file: done in 0.00423384 secs using 91.41% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.00860786 secs using 1544% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.00559211 secs using 5323% CPU
Alignment has 153 sequences with 492 columns, 492 distinct patterns
459 parsimony-informative, 24 singleton sites, 9 constant sites
            Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.000282049 secs using 5415% CPU
Alignment has 495 sequences with 575 columns, 575 distinct patterns
575 parsimony-informative, 0 singleton sites, 0 constant sites
   1  NsewqfDnSs    3.46%    passed     97.60%
   2  658EaRrivK    2.64%    passed     23.03%
   3  tKsE6g1a0S    4.07%    passed     54.20%
   4  aQNZilE2JJ    0.41%    passed     92.98%
   5  UwrRLjbq3B    3.86%    passed     74.56%
   6  TV90ozJidG    3.86%    passed     25.51%
   7  c3HM96fVqq    5.28%    passed     20.38%
   8  xxTGRlTa7K    4.67%    passed      9.52%
   9  Jvz3UnpNYR    4.88%    failed      3.89%
  10  mdN0ObKfmv    4.67%    failed      2.52%
  11  qum1IQqgRL    4.47%    passed     28.80%
  12  ucpMvNZqY4   50.61%    passed     58.99%
  13  Dwmf0ZcWVI    3.86%    passed     95.81%
  14  7ahTE2wEe5    5.49%    passed     89.63%
  15  tCzrpKtpcF    2.64%    passed     80.54%
  16  J0P8Xwv2Bh    6.10%    passed     96.97%
  17  vjnC2m0pnm   34.15%    passed     13.88%
  18  BhMleetcPb    0.61%    passed     88.14%
  19  83HNImqlFJ    4.27%    passed     97.08%
  20  9fh7iXeyTa    2.44%    passed     78.96%
  21  RCuQu9oGZY    2.85%    passed     96.58%
  22  W6nHCI2Wsy    0.81%    passed      5.62%
  23  S1A8zUjUKT    1.22%    passed     22.40%
  24  LcCM4OUpmU    4.47%    failed      0.40%
  25  Q2DajquNQZ    3.05%    passed     87.23%
  26  PmpEdiT477    4.88%    failed      3.14%
  27  F21or9tcNh    5.08%    failed      0.00%
  28  AsTKtmGBgC    1.42%    passed     74.54%
  29  bXEBREFYJ7    1.42%    passed     84.71%
  30  oyPE5XbvlM    7.32%    passed     98.65%
  31  rMwSb8FeWI    0.61%    passed     93.96%
  32  AveHckggo7    9.76%    passed     91.63%
  33  8Yqrasn3bU    0.61%    passed     97.00%
  34  3oJexyoj51    2.64%    passed     97.79%
  35  I8haDcxmGF   18.50%    passed     68.65%
  36  AqcNj4ozIg   10.37%    passed     87.07%
  37  RA52wdQzM0   21.54%    passed     84.92%
  38  INof63Zg1b   12.40%    passed     95.27%
  39  xIGuGjnQck    0.61%    passed     99.65%
  40  B9HWzepxl3    0.41%    passed     99.98%
  41  oWBZGcpKdf    2.44%    passed     97.48%
  42  jMq4G1hugD   18.29%    passed     76.03%
  43  CRHzNcE7hH   10.16%    passed     87.13%
  44  npLJ3gBI7w   21.34%    passed     94.19%
  45  CBxBTRkg8F   12.20%    passed     99.39%
  46  6AmSNES3Yt    0.41%    passed     98.49%
  47  W9sWvMxXl8    2.44%    passed     98.39%
  48  dPbJJzuHAw    0.61%    passed     97.60%
  49  NUP3Qg7UKZ    1.63%    passed     99.28%
  50  KSpoqshUGd    0.41%    passed     99.94%
  51  y6RinBeWkh   12.20%    passed     99.94%
  52  2aqY9Y5XOA   10.16%    passed     98.19%
  53  9uej6gprBY    2.44%    passed     99.12%
  54  kbAupxTeXc    2.44%    passed     92.38%
  55  jH3L6ZyOSg    2.44%    passed     88.23%
  56  o43in6b1l6    0.41%    passed     94.88%
  57  sSXbGZ4LtJ    9.96%    passed     93.06%
  58  pEm28yHrqJ    0.41%    passed     99.73%
  59  B8avP7St1b    1.63%    passed     99.42%
  60  MU8hXHYjfg    0.61%    passed     99.12%
  61  Q62u69DgSU    1.42%    passed     99.16%
  62  aA4U3jpPBM    2.44%    passed     99.66%
  63  SJOWQe9Pls   16.87%    failed      1.88%
  64  vJMp8Q8WIF    2.64%    failed      2.52%
  65  V4d7bLFWj5    0.20%    failed      0.46%
  66  AMAF22mqG6    0.61%    failed      2.30%
  67  wjzmloRyhK    0.61%    failed      4.77%
  68  91p63ULeyU    0.41%    failed      1.14%
  69  gud5XcZSky    2.85%    failed      0.78%
  70  p5Vp0bEK1M   19.92%    failed      0.64%
  71  oziMBoUfTw    0.61%    passed     14.68%
  72  9wLRCRFTWk    0.61%    passed     11.43%
  73  v7XgG9Q2Mu    0.61%    passed     14.68%
  74  YvUlv8Ajlj   28.25%    passed      9.64%
  75  hkFgAfCQMe   43.70%    failed      0.08%
  76  vFYRvvYw5q    1.83%    passed     67.23%
  77  MDZgl64OFf    2.24%    passed     99.18%
  78  dARK0kAImG    4.27%    passed     95.59%
  79  XTMxyDh5Jp   34.55%    passed     78.07%
  80  hGUbtT0sPx   27.03%    passed     67.25%
  81  4MEg44jcgn    4.27%    passed     95.59%
  82  xMQtzFnFjY    3.86%    passed     94.85%
  83  vSUoiw4nAv    3.86%    passed     94.85%
  84  zd4NP5bgCn    3.86%    passed     94.85%
  85  SrcTR9TVTe    4.88%    passed     78.14%
  86  LUOTpsMW9Z   10.37%    passed     73.84%
  87  lS9cRq1wDg    3.25%    passed     81.37%
  88  ibzyhlVeLd    1.02%    passed     99.99%
  89  PrzRBbweDr    0.41%    passed     88.33%
  90  UgrgpQ3Re3    3.05%    passed     11.72%
  91  uo1wFa9kTY    3.66%    passed     32.55%
  92  04evyV0x2J    1.02%    passed    100.00%
  93  VQOYTWEXRd    1.02%    passed     35.73%
  94  nGZxWJfnLq   10.57%    passed     99.36%
  95  VrFNoG8CSK    3.05%    passed     98.20%
  96  qAnI4od5wb    3.05%    passed     98.53%
  97  1Nf8MNh0qe    5.28%    passed     95.57%
  98  v1DX3Octxe    2.24%    passed     99.87%
  99  GBB9rjdLAe    3.46%    passed     65.29%
 100  xAnABV48FP   23.78%    passed      9.80%
 101  WBN81pJk9d   41.46%    passed     16.12%
 102  ukj88OiCCs    0.61%    passed     99.96%
 103  7HVBf2lN5X    3.86%    passed     85.96%
 104  fW6nXZ4jo9    0.61%    passed     99.35%
 105  gD9lJD4Soc    0.81%    passed     73.95%
 106  VSLI0QFCNE    0.81%    passed     37.23%
 107  NpXX0H6JOz    5.28%    passed     99.78%
 108  4Co497GPZv    0.81%    passed     99.21%
 109  d35px4TEeG    3.05%    passed     16.82%
 110  MarWtGvQwP    2.85%    passed     67.22%
 111  AGwsEagGat    3.05%    passed     69.04%
 112  Mfjn35Y7sd    3.86%    passed     90.71%
 113  zw0LKEkItm    3.86%    passed     90.71%
 114  LfDxwAh7Vj    4.67%    passed     94.69%
 115  2tKIrteaC9   29.07%    passed     96.69%
 116  7ek5ox6dTM    3.86%    passed     96.21%
 117  J9yhwttCKv    3.86%    passed     95.92%
 118  Ms0jxML186    3.05%    passed     92.93%
 119  2LhvyAjgLE    1.02%    passed     97.44%
 120  hcgITnpCwJ    0.81%    passed     97.28%
 121  Spa2PmhvTm    0.81%    passed     47.00%
 122  kxrQDICQMY    0.81%    passed     47.00%
 123  lHBAun0J0R   17.68%    passed     99.94%
 124  LR9r4dhR2l    2.24%    passed     56.33%
 125  p2YgBHtdE6    3.46%    passed     96.80%
 126  ZFU9VNJsz8    3.46%    passed     99.94%
 127  UY2QKYWPGB    1.22%    passed    100.00%
 128  bYmVEY2Ndb    0.41%    passed     99.08%
 129  JA7h40jhHP    0.61%    passed     89.33%
 130  R9Kzaow2zy    1.02%    passed     92.82%
 131  9sNaZtxabc    1.22%    passed     92.85%
 132  rJgjpUVrep    0.61%    passed     77.37%
 133  ilhlAyWtMf    1.22%    passed     97.90%
 134  JI55JkIpoJ    0.61%    passed     97.27%
 135  BwOn3B9Qlp    7.32%    passed     97.58%
 136  EqQL1uIwj2    1.22%    passed     99.72%
 137  QxgvHLRTMH    2.64%    passed     99.86%
 138  69uQAcSijv   12.40%    passed     99.88%
 139  fB3H4TdUAh   12.40%    passed     97.83%
 140  JEz9kz3nnP    4.27%    passed     99.85%
 141  AaUKTvI6pt   27.44%    passed     69.34%
 142  MiIKhPn35C    1.02%    passed     87.28%
 143  sqzWAXE12K    4.88%    passed     77.67%
 144  wKc1R5h9ZW    4.27%    passed     72.88%
 145  6bnym5iDFB    0.61%    passed     75.18%
 146  AmfA6Wj4Um    0.81%    passed     97.64%
 147  Lcs5teD2mW    0.41%    passed     74.06%
 148  jwiftTw4qK    7.11%    passed     10.75%
 149  jq2abWHxsF    3.86%    passed     85.06%
 150  F6xcUciw9j    0.41%    passed     97.31%
 151  0GIcC3M4B0    3.66%    passed     83.11%
 152  qCyccTtF6Y    3.66%    passed     86.68%
 153  3fRiMt57tm    2.24%    passed     32.43%
WARNING: 1 sequences contain more than 50% gaps/ambiguity
****  TOTAL         5.99%  14 sequences failed composition chi2 test (p-value<5%; df=19)
CHECKPOINT: 8 bootstrap analyses restored
            Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.000967979 secs using 2958% CPU
   1  8nJh6NUzJV   12.00%    passed     10.27%
   2  z0YCu0xtFo   11.30%    passed     15.88%
   3  1JN1q1h7Jh    8.35%    passed      9.02%
   4  E2n5Y5UQiG    8.52%    passed     43.28%
   5  cMoC1WsTO6    8.17%    failed      2.01%
   6  ys0DcEs0US    8.35%    passed     77.31%
   7  1s9qnaxMSp    9.04%    failed      2.14%
   8  FtHEpsU1vB    9.04%    failed      2.61%
   9  oeJuwbyE7Q    9.91%    passed      8.44%
  10  qCgVEYLhzI   17.39%    passed      9.43%
  11  zyhovbZkFP    9.91%    passed      8.44%
  12  jOk4aex96C   19.65%    passed      9.17%
  13  AR0npWZQ83    8.17%    passed     22.96%
  14  F5Si2gBtZe   21.91%    passed     13.69%
  15  FG021XCxMA   18.09%    passed     68.58%
  16  MCX7xygB2V    8.70%    passed     73.82%
  17  iVpOwiZzba    9.04%    passed     21.82%
  18  iPjBM3iYZR   80.35%    failed      2.62%
  19  qbFBJDOQUO    9.39%    passed     92.00%
  20  x5jv5lpB2O    9.22%    passed     43.94%
  21  y5M7y721WQ   11.30%    passed     52.45%
  22  MwDLYKIKBx   16.70%    passed     52.35%
  23  EsTTc2nPxQ    8.00%    passed     56.73%
  24  vnhywKRkFl   13.91%    passed     61.80%
  25  7JZdwvMv24   10.09%    passed     62.94%
  26  dQjyx7OIYV   27.30%    passed     66.63%
  27  irBovt5bLa    8.17%    passed     37.03%
  28  Ewm24Mlvnq    8.17%    failed      0.91%
  29  XDJ4JoLzyH   17.22%    passed     87.03%
  30  4kC0x0kjdn    7.65%    passed     35.61%
  31  RARcF60S6a    8.00%    passed     18.15%
  32  WlelCJO26H   12.17%    passed     15.31%
  33  mhk5OTojgz    7.83%    passed     22.72%
  34  pTM2DvE1xM    7.83%    passed     23.80%
  35  tlXXT5aWqu    8.35%    passed     25.18%
  36  TC8Xnd4iFa    8.35%    passed     68.65%
  37  02HhJs6pa3   11.13%    passed     51.90%
  38  NEeqpPtHg5    9.91%    passed     53.60%
  39  qbTDasygHV    8.00%    failed      4.34%
  40  7Yh1YhvFVC    9.04%    passed     82.42%
  41  VvE6sMyCv8    9.22%    passed     82.98%
  42  WjMMQYeUC2    9.74%    passed     28.42%
  43  W7Mh0FRDU6    9.57%    passed     47.24%
  44  2nrE64urGV    7.83%    failed      0.05%
  45  UzprTJ7K6d    7.83%    failed      0.07%
  46  UlwuxTyGoO    8.17%    passed     35.83%
  47  iaXjDyTif3    9.91%    passed     26.12%
  48  B6M0EvUDsT    8.17%    passed     57.64%
  49  1G5hXRghEG    7.83%    passed     46.06%
  50  gTvhxQmbWZ    7.83%    passed     59.90%
  51  8l37MLA1ms    7.83%    passed     66.42%
  52  vLizyHtRBL    6.96%    passed     45.67%
  53  S5ByYpGeqY    7.30%    passed     14.75%
  54  Fedl6T4xon    7.83%    passed     26.99%
  55  4BymctPkH6    9.22%    passed     90.46%
  56  s5wLZ9vWaO   22.96%    passed     14.42%
  57  awKrv6hUok    8.00%    failed      0.00%
  58  kWFqKgyYB3   18.61%    failed      0.35%
  59  DcYLS8gvW9    8.17%    passed     14.76%
  60  McRlo7Hy0B    8.35%    failed      1.15%
  61  tf71jZDs7S   14.78%    failed      0.00%
  62  vMqsZO8YaG   12.00%    passed     25.19%
  63  5AMYxNwgiK   14.26%    passed     72.77%
  64  wxoZBV0PHy    7.65%    passed     28.65%
  65  KeSH8I0Fea   10.96%    passed     34.97%
  66  KCrIGLQ7Q1    8.87%    passed     28.42%
  67  4LT0U0c0Do    8.17%    passed     45.98%
  68  CGeXrJPsGL    7.30%    passed     26.80%
  69  xxKiyIW1gr    8.35%    passed     42.35%
  70  xs9ieaVe53   24.17%    passed      5.89%
  71  NQWmJIpRFE    8.17%    passed     36.46%
  72  nkfchBpcgh    9.91%    passed     49.94%
  73  jdOhfl36g8    9.91%    passed     49.94%
  74  KVoy4GxdpT    8.70%    passed     30.77%
  75  WUIEff6ikU    9.74%    failed      3.44%
  76  coeQ6zHZ24    8.52%    passed     15.26%
  77  HWG7P94Eio    7.65%    passed     33.53%
  78  9Vw494DXPc    9.74%    passed     30.82%
  79  g6PJxKZvcf    8.17%    passed     67.92%
  80  AvvCKxHYp4    8.87%    passed     94.08%
  81  CemxIJafw8    8.87%    passed     94.94%
  82  dsBdLHptXN    7.30%    passed     26.31%
  83  4MVqW0qAIi    8.17%    passed      7.58%
  84  LcWgRv0iB6    8.17%    passed      6.57%
  85  fd8RtQX78T    8.35%    passed     67.99%
  86  D9LASQ998i    7.13%    passed     64.85%
  87  Uz7TnODNGf    8.17%    passed     61.10%
  88  Sp3Vq6QoAR   12.00%    passed     25.06%
  89  gtPloLimDb   14.61%    passed     16.69%
  90  GFnS6AyinZ   13.74%    passed     62.22%
  91  U9Eib0qR6X    9.39%    passed     80.44%
  92  dZ9ze414KZ    8.52%    passed     34.81%
  93  ydHAIeuwbW    9.04%    passed     24.32%
  94  e67HigPrjf    8.70%    passed     10.03%
  95  U5KrYXobqi    7.83%    passed     28.30%
  96  rqX0m8aZs1    8.52%    passed     74.68%
  97  JTOoSRn6ib    8.52%    passed     63.83%
  98  X4XbPR7Rfa    9.91%    passed     88.47%
  99  etCZH2Htco   11.30%    passed     96.50%
 100  7kS1ZU0pFM    9.74%    passed     63.62%
 101  rUnfYSLNJJ    8.35%    passed     25.59%
 102  YjqMqBCaiv    7.13%    passed     35.60%
 103  YXN7x6IbOx    8.35%    passed     52.18%
 104  bN8jt2Atwp   10.43%    passed     56.67%
 105  hgeyXdJgqq    9.22%    passed     56.85%
 106  1horVoEi3u    7.13%    failed      1.07%
 107  EDGqQf981n   10.09%    passed     86.16%
 108  3nDVNG9sKr   10.61%    passed     15.44%
 109  fFDoKaygf0    8.00%    passed     43.10%
 110  cRRsJgsBlZ    8.70%    passed     85.09%
 111  BI3jho3ECe    9.22%    passed     51.11%
 112  TIeppwLKSz    9.57%    passed     34.47%
 113  a8nt9ktZTC   24.35%    passed     70.98%
 114  GtfO72MtR2   22.26%    passed     65.46%
 115  xKzEmKT1dB   21.39%    passed     47.26%
 116  cTDPKciopP   11.83%    passed     67.98%
 117  xdNOUh7eMp    8.00%    passed     86.96%
 118  k3bzPFly41    8.17%    failed      0.00%
 119  ukUu00fP6L    9.39%    failed      0.29%
 120  up1UWJJzNf    9.22%    failed      3.36%
 121  GZASsy6wnT    8.17%    failed      0.00%
 122  PbkNCoK5ix   10.96%    passed     34.06%
 123  GfLEAInBd6   10.26%    passed     45.24%
 124  7OOuM97Qkr    8.70%    passed     42.00%
 125  d9kVhxwUcH    9.22%    passed     36.90%
 126  pn3nIof2qW    8.70%    passed     82.33%
 127  jYBcxGIen7   19.30%    passed     48.83%
 128  Y2YJcqt3IL   27.30%    passed     72.36%
 129  DQnwdMJsVl    9.39%    passed     17.77%
 130  Gvb4AsKEVi    8.35%    failed      0.00%
 131  d5E6EHDpwi    7.65%    passed     78.94%
 132  yA69Aemq0C    9.57%    passed     51.08%
 133  9f7AMvazZf    8.70%    passed     87.18%
 134  tD3ewCYOQG    9.22%    passed     39.14%
 135  yHwEtbE4JZ    8.87%    passed     51.50%
 136  HZpFQAW00k   12.87%    passed     16.94%
 137  FCPk6mdvI6    8.35%    passed     85.41%
 138  C50stY8CeY    9.22%    passed     15.26%
 139  WQOxpzhoLN    8.17%    passed     95.19%
 140  lU6fN5cAZQ   16.87%    passed     26.00%
 141  w34zJrGIvJ   13.04%    passed     46.23%
 142  R4SazYxajJ   13.22%    passed     24.74%
 143  oyLJTIsT1Z   12.00%    passed     35.61%
 144  95FTGjmRiw   16.87%    passed     10.92%
 145  MVSYHU9DCt   12.17%    passed     83.71%
 146  RhS1O12ekg    8.52%    passed     98.08%
 147  sthKhyT8fy    9.04%    passed     79.34%
 148  O2gQ2myCZn   11.30%    passed     66.29%
 149  B7PVgc3v8q    8.52%    passed     67.20%
 150  FlAHhYz62Q    6.96%    passed     92.12%
 151  PZqL2meUHi    8.35%    passed     89.55%
 152  XJTzBvD6pQ    8.70%    passed     73.32%
 153  FtEYGIUfBM   10.78%    passed     55.74%
 154  NUAWacASLt   10.26%    passed     81.70%
 155  3FdA2TKbHR   10.26%    passed     77.97%
 156  TCgaJethwm    9.74%    passed     51.49%
 157  V8Ort0OUIV    9.39%    passed     75.80%
 158  gKxOBa9lC3   80.35%    failed      4.37%
 159  ZJBcyycwk4   21.91%    passed     83.00%
 160  BXOEqGyzK2    9.04%    passed     82.96%
 161  5yy8DKtZ5c   12.35%    passed     70.92%
 162  cY7oeSnppq    9.74%    passed     78.00%
 163  vUEx5gqasN    9.74%    passed     22.71%
 164  2jCJDig3v9   17.39%    passed     45.79%
 165  lzBWRCtyx0   17.39%    passed     45.79%
 166  DBMxujRgHK   10.43%    passed     76.44%
 167  x3ZrH0XGfQ   13.04%    passed     40.57%
 168  SgWCfVzTG4    9.39%    passed     23.64%
 169  f62ksK5UEj   33.39%    passed     48.62%
 170  hkIztfSCD1   10.09%    passed     60.28%
 171  iRnB4M1GLD   11.30%    passed     35.88%
 172  CU0XuCnsFL   42.61%    failed      1.05%
 173  42tdKq8PSX   12.87%    passed     50.93%
 174  gXeZ52LCvM   12.87%    passed     50.93%
 175  u8cLLIfWEX   12.87%    passed     50.93%
 176  dmOh7r7eKT   12.52%    passed     43.59%
 177  3c6hZoOqvP   12.87%    passed     51.70%
 178  bu2UDzewiZ   16.35%    passed     97.52%
 179  SYc4eSftSt    7.30%    passed     55.76%
 180  zlSzVB3W0P    9.91%    passed     23.47%
 181  3C2pM8OlsA   16.00%    passed     44.07%
 182  Pxcz4xw4KG    8.52%    passed     89.90%
 183  UcghE30qVq   10.26%    passed     98.72%
 184  qIB6gS9bgA   10.26%    passed     99.50%
 185  UDehzYJL1w    9.91%    passed     84.08%
 186  BB4241mZBL    9.74%    passed     18.51%
 187  c6c8r06RzT   14.09%    passed     51.46%
 188  XQT9xr4ybf   14.09%    passed     51.46%
 189  SCnTy3bpY1   12.00%    passed     52.85%
 190  jev8yDUHvc   37.22%    passed     46.96%
 191  bK3G4lRT3G    9.74%    passed     18.84%
 192  Z5XH3L582l    9.39%    passed     64.30%
 193  dhUTnrRr7d    9.04%    passed     17.65%
 194  2ifGWJmasz   13.39%    passed     53.39%
 195  WB36HQui6V   13.22%    passed     13.09%
 196  QNNkPiHWnJ   13.57%    passed     15.99%
 197  WHGNQkrc10   16.70%    passed     15.42%
 198  h5LGHiiOXm   13.04%    passed      8.14%
 199  3zhlkwsAL6   11.65%    passed     68.02%
 200  i2Lb0rchl2   17.74%    passed     40.76%
 201  yMqx9t1LVd   11.83%    passed     95.23%
 202  2W3WY0vBww   18.09%    passed     31.19%
 203  wTTqfzkYo6   12.35%    passed     65.69%
 204  0vKBWD6wpY   19.83%    passed     72.14%
 205  SJgohIdqev   13.04%    passed     56.62%
 206  9DPLpYQWNv    8.35%    passed     79.37%
 207  8uUTsKFjlb    9.74%    passed     57.77%
 208  xVujdvY6Nr   15.65%    passed     86.08%
 209  NImtrhZGKE   18.61%    passed     29.08%
 210  YugOzGk8Ov    8.00%    passed     61.92%
 211  DeWEtikGbq    9.39%    passed     58.48%
 212  x0olbpog9B   10.78%    failed      3.15%
 213  pAhidh8xBZ    9.22%    passed     20.39%
 214  PlPvNaQDzl   78.26%    failed      2.70%
 215  NPvXCeLNmx    9.22%    passed     19.23%
 216  yVup7G0SEF    9.39%    passed      5.94%
 217  vPQhR8sENE    9.22%    passed     25.50%
 218  nU2WbHAcGl    8.00%    passed     38.25%
 219  5LDURAlPH2   18.96%    passed     93.03%
 220  BWFcvfZnO3   19.83%    passed     80.72%
 221  pygYFVFfpx   18.96%    passed     64.25%
 222  SHqN6p0dYV   11.65%    passed     77.47%
 223  qsVXrYaG9q   16.52%    passed     62.49%
 224  3cAaekWMpW   17.57%    passed     67.41%
 225  N40B32hpg1   12.00%    passed     79.79%
 226  JPT5lhIP82   16.17%    passed     61.51%
 227  ZLXDnoVm6b    8.87%    passed     65.21%
 228  X85YtZdfkf    9.04%    passed     76.50%
 229  8UiTG47Ec2    9.04%    passed     76.50%
 230  rIeH6RocN2   11.13%    passed     16.99%
 231  JEeirH12E1   31.48%    passed     21.21%
 232  UzAtwShlJN   15.48%    failed      0.00%
 233  2pVvPoBi2c   15.65%    failed      0.00%
 234  scQ10Wo461   39.13%    passed     23.66%
 235  Nb1rJKftmp   17.91%    failed      0.00%
 236  nhoqJOOPX2   17.04%    passed     88.57%
 237  39gkmZTScW   18.26%    passed     91.96%
 238  BGkr4JUYAf   13.39%    passed     93.93%
 239  DulbVCzsEt   24.35%    passed     66.60%
 240  cSruxLJuyQ   26.96%    passed     10.64%
 241  1XfSwqn4ef   25.04%    passed     39.48%
 242  96xj01KeXJ   68.17%    passed     84.97%
 243  eq1zGc6rtT   29.04%    passed     18.35%
 244  VfUM5i9jsn   41.91%    failed      4.66%
 245  20sicocoSo   23.83%    failed      0.74%
 246  RLpJhYeIPE   25.91%    passed     47.76%
 247  C8YPeCC1NI   28.87%    passed     14.80%
 248  xxnHHiKI8Z   28.52%    passed      5.76%
 249  3Je7M7o4rZ   33.39%    passed     11.10%
 250  47EKfQlPcw   28.35%    passed     38.14%
 251  9C0byE309K   34.43%    passed     22.05%
 252  TsIfWQzrph   28.35%    passed     38.14%
 253  hTPGiqrFV4   42.09%    passed     88.30%
 254  aFMglfB8eH   24.52%    passed     15.36%
 255  JQcRFbokY2   28.35%    passed     32.19%
 256  jFdaAxFg6n   23.13%    passed     47.94%
 257  KRYbednenZ   23.13%    passed     42.60%
 258  FyIDyqrLwr   23.13%    passed     47.94%
 259  8XGfcNsQ09   23.83%    passed     62.09%
 260  QyNf0mVNlz   23.83%    passed     10.54%
 261  f9oKgpE1wE   23.48%    passed     56.82%
 262  REBVZFiPEf   23.30%    passed     27.01%
 263  ItesG8T6sN   23.83%    passed     47.79%
 264  TSGS90hx1G   23.30%    passed     24.55%
 265  ZRAzqCtrNA   24.17%    passed     57.76%
 266  eeM5JHuVuf   24.35%    passed     50.06%
 267  oe9Vawfrxg   24.35%    passed     26.16%
 268  rgglFfiKnC   28.00%    passed     45.26%
 269  bCjdcpAF4v   24.00%    passed     70.09%
 270  OmcerY3zVm   64.35%    passed     66.28%
 271  zcG6I9U7zt   43.13%    passed     73.90%
 272  QKniumy84t   24.00%    passed     71.91%
 273  158IGk2w8A   24.00%    passed     40.59%
 274  kI8iG2U2gQ   23.30%    passed     85.81%
 275  fPZNEk39Af   26.78%    passed     15.99%
 276  hrBvV4AmlN   24.17%    passed     20.25%
 277  myGUzZ8LDH   24.00%    passed     24.24%
 278  sHkv5UU91e   23.65%    passed     10.45%
 279  GNzRUX9ddm   23.65%    passed     13.36%
 280  zsnvwGvGgv   24.00%    passed     30.90%
 281  9OoygEJxNJ   23.13%    passed     19.47%
 282  IjtzwwEpZt   24.70%    passed     32.04%
 283  nSDhHtKOaz   76.87%    passed     72.40%
 284  A0R7Dl6WnL   24.00%    passed     27.63%
 285  CvviaWP5QG   24.17%    passed     57.70%
 286  pPSEGFgq5j   79.13%    passed     12.51%
 287  UdG6KQNIp6   24.52%    passed      9.66%
 288  8EVSPtaAhX   24.35%    passed     42.22%
 289  uiafGbGfwA   27.30%    passed     85.86%
 290  XZFyxFJmTO   24.70%    passed     34.27%
 291  H6HkWi4jLJ   26.26%    passed     57.81%
 292  uALm9y36Bq   28.70%    passed     22.86%
 293  EUEmaNv0jU   23.30%    passed     16.64%
 294  miFIpMQUO8   25.04%    passed      5.34%
 295  qsWsb5TOjf   26.09%    passed     11.23%
 296  WLDkRifOr1   25.74%    passed     31.25%
 297  u7RGaLBmh5   25.74%    passed     85.68%
 298  n4n2Sa9hou   25.39%    passed     53.48%
 299  gZV6bt6UCn   24.17%    passed     46.31%
 300  PortTSlpTI   41.74%    passed     26.87%
 301  2Nn52BMVGD   28.00%    passed     32.50%
 302  sQl8vIYhWL   27.30%    passed     24.87%
 303  nlyynuwvAY   27.13%    passed     84.06%
 304  iM9z6TKAcr   41.39%    passed     18.69%
 305  pVpmbqWKfw   36.70%    failed      1.72%
 306  r4JpMWXYFJ   26.09%    passed     11.04%
 307  CcX8oiPHcg   27.83%    passed     27.83%
 308  G2BVFEVILA   25.04%    passed     61.18%
 309  BNYVmW4TYG   25.91%    passed     54.90%
 310  ExQ8uNPj7h   34.26%    passed     66.82%
 311  whmj06xoF5   28.17%    failed      0.02%
 312  VqFVtnHfVy   25.22%    passed     79.18%
 313  Mqy8imXZ6G   25.91%    failed      0.02%
 314  s0NXcs97L3   25.91%    failed      0.02%
 315  Iqt8ZiOu6k   25.74%    failed      0.00%
 316  XsWTxkH1p7   25.57%    passed     19.64%
 317  zoRaGfFB7U   24.52%    passed     48.77%
 318  qqN1dh1OOy   24.35%    passed     14.36%
 319  T1wQDvF98B   24.35%    passed      7.77%
 320  lkTsXyry76   26.43%    passed     26.11%
 321  hSqg5YYyOm   27.48%    failed      0.44%
 322  puRVWMvppN   28.35%    passed     22.55%
 323  1LbFAdgLuC   25.74%    passed     11.73%
 324  y5MmiioIHk   25.91%    failed      1.83%
 325  BnR8odZPBs   25.91%    passed     15.58%
 326  ajGvkpi5As   25.91%    passed      8.73%
 327  qbTJcwpdwP   26.61%    passed     13.99%
 328  vCxAIjCqNl   24.87%    passed     46.42%
 329  mPlwp1JlUK   27.30%    passed     36.54%
 330  rYWDHuLHvt   29.91%    failed      1.32%
 331  C0RnyRzFMX   71.65%    passed     45.95%
 332  7Aa2sW2uFn   28.00%    failed      3.36%
 333  0djEp2FhF9   28.00%    failed      3.36%
 334  l1pN6WjG1N   80.17%    passed     21.40%
 335  XLgmciWSgo   46.09%    passed     14.00%
 336  D8WaLv1pNN   30.78%    passed     27.06%
 337  12VY0qcAbu   29.39%    passed     74.33%
 338  JNoGNci0kO   28.87%    passed     95.56%
 339  VGEALS8WvR   40.70%    passed     16.49%
 340  D7iWRjKQ8X   25.74%    passed     47.65%
 341  upEmmPcbTB   27.48%    passed     22.48%
 342  UpKcpH8xp2   26.78%    passed      7.74%
 343  hreWbDAWDh   23.65%    passed      8.09%
 344  5oPFYbGk9x   24.52%    passed     66.68%
 345  bKMx8usLZf   35.83%    passed      9.39%
 346  9waTHuOjG2   43.48%    passed     27.73%
 347  y13PUGF6fd   29.39%    passed     50.29%
 348  MCxeCrj6og   25.22%    passed     77.92%
 349  JqQlZRu8jp   25.91%    passed     38.60%
 350  ZrMp8mhVn3   56.35%    passed      9.73%
 351  PVum0t8D9w   48.52%    failed      3.01%
 352  mA0FIy0SqW   24.70%    passed      5.42%
 353  EacivjsFt1   26.61%    passed     43.72%
 354  FKAuFXjrK2   29.57%    failed      2.12%
 355  eOn8Fw1qPv   27.48%    failed      3.53%
 356  D0XDiTOIfD   34.78%    passed      9.81%
 357  910hgdbBRd   28.00%    passed     51.49%
 358  ijUTPEstS6   33.39%    passed     28.87%
 359  bUU4czn7NG   27.83%    passed     60.40%
 360  INEhHLWnmb   37.04%    failed      1.97%
 361  LMA81zzKSe   37.04%    failed      0.01%
 362  TUCOIK4ZQn   33.91%    failed      0.52%
 363  yvso4goGdQ   34.96%    failed      4.00%
 364  YWPX00OZwF   36.00%    failed      3.54%
 365  qKqJ6yzKtT   34.61%    passed     10.13%
 366  49Qin0CHkb   34.61%    passed      9.62%
 367  63Q15egMZA   34.26%    passed      6.18%
 368  nWYlGrbPPc   34.61%    failed      4.67%
 369  JvcE4PBExA   33.74%    passed      7.73%
 370  LUlT7ehgwb   36.00%    passed     26.12%
 371  pVpykOHqYZ   39.48%    failed      0.85%
 372  v2K68153zf   38.26%    failed      0.55%
 373  qYhA4tEOW1   34.78%    failed      0.03%
 374  grGtjFUUTt   34.43%    failed      0.23%
 375  qWhSnx7aMf   44.87%    passed      5.50%
 376  v1oAyLSJtz   50.96%    passed     28.72%
 377  BadtzwpMMs   38.43%    passed      9.62%
 378  6DLNJCEk13   34.61%    passed      8.29%
 379  w2DOMr7ED6   41.39%    failed      3.23%
 380  JK0CadwxtV   33.74%    failed      1.62%
 381  thXzqzsTWd   33.04%    failed      4.58%
 382  cza9cyArKR   33.04%    failed      3.45%
 383  64i2bPRqyf   38.09%    failed      1.24%
 384  Tu05kR9iNy   35.30%    failed      2.13%
 385  ryyuwN9EeF   35.83%    failed      3.08%
 386  9i9iYEz14b   36.87%    passed     43.29%
 387  e5Z7VURlcd   56.00%    failed      0.95%
 388  ndIdlcACpn   34.61%    failed      0.11%
 389  miylOtOHke   36.00%    passed      5.91%
 390  jGxqmOPSFz   33.91%    failed      1.22%
 391  UpRnjomc4O   36.17%    passed     26.63%
 392  ebCUnMXr2f   38.43%    passed     15.56%
 393  21yjS1P784   34.43%    failed      0.27%
 394  XU8ct59Imq   34.26%    failed      0.70%
 395  mWu9nYUMB2   34.26%    passed      5.63%
 396  6N8VC2LDv6   34.26%    passed      5.63%
 397  Tp4oCldie4   38.09%    failed      4.42%
 398  LdahhT5atZ   34.26%    passed      5.63%
 399  ohdNT1wCFZ   34.26%    passed      7.14%
 400  QY3dkiwN48   41.57%    failed      3.72%
 401  Ip06mTdO2e   35.65%    failed      2.00%
 402  P5RXO2szhK   29.57%    passed     33.39%
 403  offjx75l6X   85.22%    passed     26.57%
 404  EdOuOhohBn   33.91%    passed     23.13%
 405  ZjYUAXvbUC   34.26%    passed      8.29%
 406  lpxtOw9xf3   36.52%    passed     12.71%
 407  4bSmqRgfRI   34.09%    passed     12.39%
 408  gminDyGtcG   34.78%    failed      2.44%
 409  lDQWwcBkMU   34.78%    passed     33.99%
 410  CUTMeJuwSv   33.74%    passed     78.03%
 411  OI80q3iM3F   33.74%    passed     81.17%
 412  xnKco929hT   37.57%    passed      8.65%
 413  RPfcmWXHCA   37.57%    passed     20.91%
 414  6mj1jZTKcU   36.17%    failed      4.67%
 415  Gr87dxYVyz   43.83%    failed      4.55%
 416  VGvhdii6IX   73.22%    passed     54.33%
 417  wJTuSg6Gc6   35.65%    passed     75.44%
 418  K3Flz6km5g   35.65%    passed     71.14%
 419  Tu0u89fzoU   35.48%    passed     16.33%
 420  IpceOBVrBQ   35.48%    passed     13.04%
 421  JAjUuwFnV7   36.35%    passed     34.52%
 422  wSnvqYXqTg   32.00%    passed     24.03%
 423  keWKiDv5J1   36.35%    passed     23.38%
 424  r5NSp8dbtM   37.39%    passed     32.60%
 425  wxLKLb6SMC   35.13%    passed     25.74%
 426  qw6gF6ZapY   35.13%    passed     25.74%
 427  ZGvDd4xvwy   37.91%    passed     30.11%
 428  8lXCZuvq8q   34.26%    passed     25.11%
 429  qvg1my8Wlp   48.70%    failed      3.30%
 430  ZdWaANa0Et   32.87%    passed      6.04%
 431  Onz2iyjxH3   42.96%    failed      0.02%
 432  AJImOJUang   66.09%    passed      8.67%
 433  rbo3OKIe4x   36.52%    failed      0.54%
 434  pGufZSTMNB   36.52%    passed     12.14%
 435  FLjy3W79tg   36.52%    passed     17.85%
 436  jYaSjXdhUR   34.78%    passed     22.31%
 437  HGW1EoyaVz   49.22%    passed     75.08%
 438  HQpmvbcKV0   36.35%    passed     71.28%
 439  Us22uQdloc   73.22%    passed     88.61%
 440  Nczi5Cos47   34.96%    passed     68.86%
 441  IV8TgD1mQj   36.52%    passed     65.05%
 442  QKsY8kV1rB   34.43%    passed     49.51%
 443  TrIc96BqkG   34.96%    passed      7.64%
 444  pnjqLcOivm   34.61%    passed      9.34%
 445  SY2alUymun   36.00%    passed     31.87%
 446  GXBps2FgSH   37.57%    failed      4.23%
 447  ZldeYJmzLx   39.48%    failed      0.13%
 448  8biR24Gazc   33.91%    passed     22.85%
 449  NBJ6cvHYoU   34.43%    passed     22.55%
 450  egq7pHRqeL   38.78%    passed     36.06%
 451  y0r2SVxwqI   35.30%    passed     55.80%
 452  evUBWmPjS2   35.30%    passed     23.87%
 453  ikh1qtxydC   36.00%    failed      2.62%
 454  BRdJ9RHZQj   35.65%    passed      8.09%
 455  l25CgIsmfn   35.65%    passed      8.09%
 456  XPdvjShyOo   37.57%    passed      7.82%
 457  M144qciIKM   34.96%    passed     30.15%
 458  BnE96TDyk8   35.48%    passed     26.42%
 459  jeohLZ0eYF   36.87%    failed      0.20%
 460  YvoxlQmxl7   36.87%    failed      0.20%
 461  R0wuUn8J0h   33.57%    passed     30.51%
 462  oeFPRaQBYZ   33.39%    passed     26.87%
 463  xqlhblg6dL   33.91%    passed     25.42%
 464  6Qs9p4Rx4f   34.09%    passed     25.71%
 465  QPlyWfEtzz   34.43%    passed     29.56%
 466  Yo6roMcRLy   35.30%    passed     25.15%
 467  PwuAxgsPD6   42.78%    passed     42.46%
 468  vaFUdeGB10   33.91%    failed      2.49%
 469  8GM1psnK6y   36.87%    failed      0.09%
 470  E6RVlyXu6C   33.74%    passed     45.21%
 471  SuF6hGymBQ   36.00%    failed      2.74%
 472  cgJCegWwAr   70.96%    passed     99.24%
 473  i10ONbBPRV   34.96%    passed     50.77%
 474  FaaaR0oHe4   35.13%    passed     47.29%
 475  RrNP3l8SS7   36.52%    failed      0.47%
 476  BuFyz2PMN4   34.43%    passed     49.11%
 477  Y10Qa1Da4V   38.78%    passed     65.87%
 478  8zkzdNvfM0   34.43%    passed     49.11%
 479  rA4KjQCVx3   32.00%    passed     90.85%
 480  au044S3YHW   35.30%    passed     43.12%
 481  cIR66o13VD   35.65%    passed     81.03%
 482  fkB1xaD3I7   35.83%    passed     66.46%
 483  CwGGcZADEn   35.30%    passed     25.37%
 484  fNHflelF6b   34.61%    passed     14.83%
 485  8zGWBmbKDs   83.65%    passed     77.32%
 486  LC2TsjjWfV   35.65%    passed     44.42%
 487  rsgxiUIZDl   41.74%    passed     41.79%
 488  Srvt2UziZu   34.43%    passed     97.83%
 489  zPT9rylEFV   34.43%    passed     97.83%
 490  rXls0PgjJv   35.48%    passed      5.47%
 491  TcLIjpisFo   51.83%    passed     29.28%
 492  RMfRwwtcqL   32.17%    passed      5.11%
 493  zzJMOnIGaE   34.09%    failed      0.02%
 494  bkj6PiDj99   34.78%    passed     36.79%
 495  QPtDeO8Fse   34.61%    passed     64.43%
WARNING: 19 sequences contain more than 50% gaps/ambiguity
****  TOTAL        23.94%  82 sequences failed composition chi2 test (p-value<5%; df=19)

NOTE: Restoring information from model checkpoint file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz

NOTE: Restoring information from model checkpoint file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.model.gz

CHECKPOINT: Initial tree restored
Measuring multi-threading efficiency up to 96 CPU cores

CHECKPOINT: Initial tree restored
Measuring multi-threading efficiency up to 96 CPU cores
Increase to 10 rounds for branch lengths
Increase to 10 rounds for branch lengths
IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/cdhit_phobius_tm_RECEPTORS.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS
Seed:    68183 (Using SPRNG - Scalable Parallel Random Number Generator)

******************************************************
CHECKPOINT: Resuming analysis from /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.ckp.gz

IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/biosynthesis.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis
Seed:    67463 (Using SPRNG - Scalable Parallel Random Number Generator)

******************************************************
CHECKPOINT: Resuming analysis from /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.ckp.gz

IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport
Seed:    70464 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Mon Jul  7 16:03:14 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Time:    Mon Jul  7 16:03:14 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/biosynthesis.fasta ... Fasta format detected
Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/cdhit_phobius_tm_RECEPTORS.fasta ... Fasta format detected
Time:    Mon Jul  7 16:03:14 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta ... Fasta format detected
Reading fasta file: done in 0.00301313 secs using 98.97% CPU
Reading fasta file: done in 0.00333405 secs using 68.87% CPU
Reading fasta file: done in 0.00566697 secs using 99.75% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.00508308 secs using 1209% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.00844884 secs using 1845% CPU
Alignment has 153 sequences with 492 columns, 492 distinct patterns
459 parsimony-informative, 24 singleton sites, 9 constant sites
            Gap/Ambiguity  Composition  p-value
Alignment has 495 sequences with 575 columns, 575 distinct patterns
575 parsimony-informative, 0 singleton sites, 0 constant sites
Analyzing sequences: done in 0.00726318 secs using 1693% CPU
Alignment most likely contains protein sequences
            Gap/Ambiguity  Composition  p-value
   1  NsewqfDnSs    3.46%    passed     97.60%
   2  658EaRrivK    2.64%    passed     23.03%
   3  tKsE6g1a0S    4.07%    passed     54.20%
   4  aQNZilE2JJ    0.41%    passed     92.98%
   5  UwrRLjbq3B    3.86%    passed     74.56%
   6  TV90ozJidG    3.86%    passed     25.51%
   7  c3HM96fVqq    5.28%    passed     20.38%
   8  xxTGRlTa7K    4.67%    passed      9.52%
   9  Jvz3UnpNYR    4.88%    failed      3.89%
  10  mdN0ObKfmv    4.67%    failed      2.52%
  11  qum1IQqgRL    4.47%    passed     28.80%
  12  ucpMvNZqY4   50.61%    passed     58.99%
  13  Dwmf0ZcWVI    3.86%    passed     95.81%
  14  7ahTE2wEe5    5.49%    passed     89.63%
  15  tCzrpKtpcF    2.64%    passed     80.54%
  16  J0P8Xwv2Bh    6.10%    passed     96.97%
  17  vjnC2m0pnm   34.15%    passed     13.88%
  18  BhMleetcPb    0.61%    passed     88.14%
  19  83HNImqlFJ    4.27%    passed     97.08%
  20  9fh7iXeyTa    2.44%    passed     78.96%
  21  RCuQu9oGZY    2.85%    passed     96.58%
  22  W6nHCI2Wsy    0.81%    passed      5.62%
  23  S1A8zUjUKT    1.22%    passed     22.40%
  24  LcCM4OUpmU    4.47%    failed      0.40%
  25  Q2DajquNQZ    3.05%    passed     87.23%
  26  PmpEdiT477    4.88%    failed      3.14%
  27  F21or9tcNh    5.08%    failed      0.00%
  28  AsTKtmGBgC    1.42%    passed     74.54%
  29  bXEBREFYJ7    1.42%    passed     84.71%
  30  oyPE5XbvlM    7.32%    passed     98.65%
  31  rMwSb8FeWI    0.61%    passed     93.96%
  32  AveHckggo7    9.76%    passed     91.63%
  33  8Yqrasn3bU    0.61%    passed     97.00%
  34  3oJexyoj51    2.64%    passed     97.79%
  35  I8haDcxmGF   18.50%    passed     68.65%
  36  AqcNj4ozIg   10.37%    passed     87.07%
  37  RA52wdQzM0   21.54%    passed     84.92%
  38  INof63Zg1b   12.40%    passed     95.27%
  39  xIGuGjnQck    0.61%    passed     99.65%
  40  B9HWzepxl3    0.41%    passed     99.98%
  41  oWBZGcpKdf    2.44%    passed     97.48%
  42  jMq4G1hugD   18.29%    passed     76.03%
  43  CRHzNcE7hH   10.16%    passed     87.13%
  44  npLJ3gBI7w   21.34%    passed     94.19%
  45  CBxBTRkg8F   12.20%    passed     99.39%
  46  6AmSNES3Yt    0.41%    passed     98.49%
  47  W9sWvMxXl8    2.44%    passed     98.39%
  48  dPbJJzuHAw    0.61%    passed     97.60%
  49  NUP3Qg7UKZ    1.63%    passed     99.28%
  50  KSpoqshUGd    0.41%    passed     99.94%
  51  y6RinBeWkh   12.20%    passed     99.94%
  52  2aqY9Y5XOA   10.16%    passed     98.19%
  53  9uej6gprBY    2.44%    passed     99.12%
  54  kbAupxTeXc    2.44%    passed     92.38%
  55  jH3L6ZyOSg    2.44%    passed     88.23%
  56  o43in6b1l6    0.41%    passed     94.88%
  57  sSXbGZ4LtJ    9.96%    passed     93.06%
  58  pEm28yHrqJ    0.41%    passed     99.73%
  59  B8avP7St1b    1.63%    passed     99.42%
  60  MU8hXHYjfg    0.61%    passed     99.12%
  61  Q62u69DgSU    1.42%    passed     99.16%
  62  aA4U3jpPBM    2.44%    passed     99.66%
  63  SJOWQe9Pls   16.87%    failed      1.88%
  64  vJMp8Q8WIF    2.64%    failed      2.52%
  65  V4d7bLFWj5    0.20%    failed      0.46%
  66  AMAF22mqG6    0.61%    failed      2.30%
  67  wjzmloRyhK    0.61%    failed      4.77%
  68  91p63ULeyU    0.41%    failed      1.14%
  69  gud5XcZSky    2.85%    failed      0.78%
  70  p5Vp0bEK1M   19.92%    failed      0.64%
  71  oziMBoUfTw    0.61%    passed     14.68%
  72  9wLRCRFTWk    0.61%    passed     11.43%
  73  v7XgG9Q2Mu    0.61%    passed     14.68%
  74  YvUlv8Ajlj   28.25%    passed      9.64%
  75  hkFgAfCQMe   43.70%    failed      0.08%
  76  vFYRvvYw5q    1.83%    passed     67.23%
  77  MDZgl64OFf    2.24%    passed     99.18%
  78  dARK0kAImG    4.27%    passed     95.59%
  79  XTMxyDh5Jp   34.55%    passed     78.07%
  80  hGUbtT0sPx   27.03%    passed     67.25%
  81  4MEg44jcgn    4.27%    passed     95.59%
  82  xMQtzFnFjY    3.86%    passed     94.85%
  83  vSUoiw4nAv    3.86%    passed     94.85%
  84  zd4NP5bgCn    3.86%    passed     94.85%
  85  SrcTR9TVTe    4.88%    passed     78.14%
  86  LUOTpsMW9Z   10.37%    passed     73.84%
  87  lS9cRq1wDg    3.25%    passed     81.37%
  88  ibzyhlVeLd    1.02%    passed     99.99%
  89  PrzRBbweDr    0.41%    passed     88.33%
  90  UgrgpQ3Re3    3.05%    passed     11.72%
  91  uo1wFa9kTY    3.66%    passed     32.55%
  92  04evyV0x2J    1.02%    passed    100.00%
  93  VQOYTWEXRd    1.02%    passed     35.73%
  94  nGZxWJfnLq   10.57%    passed     99.36%
  95  VrFNoG8CSK    3.05%    passed     98.20%
  96  qAnI4od5wb    3.05%    passed     98.53%
  97  1Nf8MNh0qe    5.28%    passed     95.57%
  98  v1DX3Octxe    2.24%    passed     99.87%
  99  GBB9rjdLAe    3.46%    passed     65.29%
 100  xAnABV48FP   23.78%    passed      9.80%
 101  WBN81pJk9d   41.46%    passed     16.12%
 102  ukj88OiCCs    0.61%    passed     99.96%
 103  7HVBf2lN5X    3.86%    passed     85.96%
 104  fW6nXZ4jo9    0.61%    passed     99.35%
 105  gD9lJD4Soc    0.81%    passed     73.95%
 106  VSLI0QFCNE    0.81%    passed     37.23%
 107  NpXX0H6JOz    5.28%    passed     99.78%
 108  4Co497GPZv    0.81%    passed     99.21%
 109  d35px4TEeG    3.05%    passed     16.82%
 110  MarWtGvQwP    2.85%    passed     67.22%
 111  AGwsEagGat    3.05%    passed     69.04%
 112  Mfjn35Y7sd    3.86%    passed     90.71%
 113  zw0LKEkItm    3.86%    passed     90.71%
 114  LfDxwAh7Vj    4.67%    passed     94.69%
 115  2tKIrteaC9   29.07%    passed     96.69%
 116  7ek5ox6dTM    3.86%    passed     96.21%
 117  J9yhwttCKv    3.86%    passed     95.92%
 118  Ms0jxML186    3.05%    passed     92.93%
 119  2LhvyAjgLE    1.02%    passed     97.44%
 120  hcgITnpCwJ    0.81%    passed     97.28%
 121  Spa2PmhvTm    0.81%    passed     47.00%
 122  kxrQDICQMY    0.81%    passed     47.00%
 123  lHBAun0J0R   17.68%    passed     99.94%
 124  LR9r4dhR2l    2.24%    passed     56.33%
 125  p2YgBHtdE6    3.46%    passed     96.80%
 126  ZFU9VNJsz8    3.46%    passed     99.94%
 127  UY2QKYWPGB    1.22%    passed    100.00%
 128  bYmVEY2Ndb    0.41%    passed     99.08%
 129  JA7h40jhHP    0.61%    passed     89.33%
 130  R9Kzaow2zy    1.02%    passed     92.82%
 131  9sNaZtxabc    1.22%    passed     92.85%
 132  rJgjpUVrep    0.61%    passed     77.37%
 133  ilhlAyWtMf    1.22%    passed     97.90%
 134  JI55JkIpoJ    0.61%    passed     97.27%
 135  BwOn3B9Qlp    7.32%    passed     97.58%
 136  EqQL1uIwj2    1.22%    passed     99.72%
 137  QxgvHLRTMH    2.64%    passed     99.86%
 138  69uQAcSijv   12.40%    passed     99.88%
 139  fB3H4TdUAh   12.40%    passed     97.83%
 140  JEz9kz3nnP    4.27%    passed     99.85%
 141  AaUKTvI6pt   27.44%    passed     69.34%
 142  MiIKhPn35C    1.02%    passed     87.28%
 143  sqzWAXE12K    4.88%    passed     77.67%
 144  wKc1R5h9ZW    4.27%    passed     72.88%
 145  6bnym5iDFB    0.61%    passed     75.18%
 146  AmfA6Wj4Um    0.81%    passed     97.64%
 147  Lcs5teD2mW    0.41%    passed     74.06%
 148  jwiftTw4qK    7.11%    passed     10.75%
 149  jq2abWHxsF    3.86%    passed     85.06%
 150  F6xcUciw9j    0.41%    passed     97.31%
 151  0GIcC3M4B0    3.66%    passed     83.11%
 152  qCyccTtF6Y    3.66%    passed     86.68%
 153  3fRiMt57tm    2.24%    passed     32.43%
WARNING: 1 sequences contain more than 50% gaps/ambiguity
****  TOTAL         5.99%  14 sequences failed composition chi2 test (p-value<5%; df=19)
CHECKPOINT: 8 bootstrap analyses restored
Analyzing sequences: done in 0.000581026 secs using 2174% CPU
Constructing alignment: done in 0.0161481 secs using 3512% CPU

NOTE: Restoring information from model checkpoint file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.model.gz
Alignment has 269 sequences with 414 columns, 410 distinct patterns
397 parsimony-informative, 5 singleton sites, 12 constant sites
            Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.000566959 secs using 4106% CPU
   1  c2nvJkfrfN   14.49%    passed     16.79%
   2  6v71cA4wPA   17.39%    passed     61.71%
   3  KoMzCAq4js   18.60%    passed     93.43%
   4  lxlM6A3JbT   10.87%    failed      0.28%
   5  E4wkUUcW9k   14.25%    passed     88.60%
   6  zNKTwqlwI7   17.15%    passed     64.10%
   7  xJCaoYe6x7   20.77%    passed     61.31%
   8  hRN1Wy69Ah   19.08%    passed     92.85%
   9  ZvBC32nrED   19.08%    failed      0.12%
  10  RaObTYvjqb    8.45%    passed     89.43%
  11  lHRXTHlK1w   16.43%    failed      0.00%
  12  XEbJPCtGac   15.22%    passed     25.66%
  13  5cKSP1mz8P   14.73%    failed      1.15%
  14  XEMbna5PTc   16.91%    passed     42.05%
  15  7nQDPMneN2   14.01%    passed     27.59%
  16  e40qziD7i7   17.15%    passed     95.87%
  17  ZG3Jmo6e7V   19.57%    passed     40.97%
  18  wHZy5Q8IJI    8.45%    passed     71.01%
  19  b74PatoLe4    8.21%    passed     39.31%
  20  XGas1ggnUa   11.11%    passed     19.19%
  21  IVTbt8Udzq   11.84%    passed     95.94%
  22  Pfn5zv9XX5    9.18%    passed     30.82%
  23  YCsFSoRXqE    8.21%    failed      2.84%
  24  ot7OqrLzX5   22.22%    passed     18.48%
  25  PWjd4lRbiM   16.18%    passed     62.94%
  26  AICC2u7c3U   12.08%    failed      0.00%
  27  IZ5hNTt2vT   17.39%    failed      0.00%
  28  Z51fe4z5fd   14.01%    passed     85.03%
  29  Tkqfc0SeOG   20.77%    passed     20.69%
  30  iiIa5izPqm   22.22%    passed     12.87%
  31  v4fUVbAyCP   16.43%    passed     87.63%
  32  6Uoim418Lz   22.71%    passed     86.96%
  33  fm80Plhz7F   12.08%    failed      4.29%
  34  onW0cY5h5o   10.39%    passed     81.72%
  35  N9pESfrjq2   14.25%    passed     33.04%
  36  5rjVc8vWLK   12.32%    passed     90.02%
  37  ipy3Nr1Y7C   14.01%    passed     34.00%
  38  Yrr4ZSKKC9   20.29%    passed     68.26%
  39  AuJ54E1C8c   21.01%    passed     53.09%
  40  jva1qkj7r3    9.42%    passed      7.23%
  41  tPS4ZlQpLO   20.53%    passed     93.70%
  42  ZuL1ZJlBoc   14.25%    passed     98.78%
  43  6smEYSMtgB   13.77%    passed     50.25%
  44  OmEFZmh9Xk   19.32%    passed     59.86%
  45  HPGR8QqxLN   14.49%    passed     89.86%
  46  BhNqusWZNJ   19.08%    passed     58.02%
  47  UW8C8HS7IW   14.49%    passed     23.66%
  48  IXVYbhEiFa    8.21%    failed      0.01%
  49  AjttkrIBDE   16.91%    passed     76.47%
  50  o4DTptAEa7   16.67%    passed     92.22%
  51  3569NNqeHr   10.63%    passed     16.11%
  52  VbeUA5Lmv1   11.35%    passed     10.81%
  53  s438BUrIld   12.08%    passed     97.72%
  54  kZxa6ms4fT   12.32%    passed     35.70%
  55  yKB0rmTTAd   13.53%    passed     99.88%
  56  R3rYagRgkA   21.74%    passed      9.58%
  57  LbAfNvLG0L   15.22%    passed     85.99%
  58  VyRxiwg9OH   16.91%    passed     55.88%
  59  Ih0FYSZPuQ   11.84%    passed     98.11%
  60  lhDnsli570   13.04%    passed     96.03%
  61  oxTFCHgUrH   14.98%    passed     93.85%
  62  lxbMM8cWpP   16.43%    passed     36.26%
  63  Uw4WAsVs2V   12.80%    passed     55.06%
  64  lyrWZMVXT3   13.77%    passed     70.12%
  65  OyaeKE1frb   16.43%    passed     86.38%
  66  d1JUougmwO   13.29%    passed     88.72%
  67  n3cpwW2FHB   13.29%    passed     65.82%
  68  AlrwQSS6wg   14.25%    passed     17.97%
  69  UuXrZQLZFl   16.67%    passed     25.64%
  70  4erBqEBFMP   19.81%    passed     10.98%
  71  jxhNFGngrh   21.01%    passed     84.69%
  72  Wm098GODX1   22.95%    passed     22.93%
  73  9yBRcXGPW3    9.42%    passed     95.14%
  74  XdXJPD1B99   14.98%    passed     74.55%
  75  36Z3LxBjPl   17.63%    passed     63.50%
  76  kvpaBQTK2F   17.15%    passed     22.83%
  77  OPtLNHMxEK   13.77%    passed     38.90%
  78  FNavqnaurn   15.70%    passed     43.86%
  79  U9atOteYMr   18.84%    passed     76.67%
  80  jW1iHKeXfb   25.36%    passed     27.48%
  81  yQ6RZhmbOA   14.73%    passed     99.94%
  82  i0aI5XCRaQ   18.60%    passed     99.75%
  83  Emh5GVVBM7   11.59%    passed     59.87%
  84  seCpqYzobh   17.39%    failed      2.12%
  85  Yild6PEkHw   17.87%    passed     30.32%
  86  kbUXzYwyJT   18.12%    passed     64.46%
  87  BnaGpooeOd   11.84%    failed      2.60%
  88  ObxFZPrSW5   18.84%    passed     29.19%
  89  SuSbie4gj4   23.19%    passed     34.58%
  90  4bfvNf8AFQ   13.77%    passed     74.75%
  91  IDqCgXNOAR   21.74%    passed     72.57%
  92  ylLkHnrsg4   12.08%    passed     90.58%
  93  6CsniPjxAT   20.29%    passed     11.78%
  94  EbHYNkVDGh   15.22%    passed     10.10%
  95  ClUKTDfvJI   23.19%    passed     80.74%
  96  mHWkgELohz   17.15%    passed     97.96%
  97  YwLM4N6m6Z   19.81%    passed     17.28%
  98  YH2jvsJ8dY   24.40%    passed     86.48%
  99  G9b28gN5VH   13.77%    passed     80.92%
 100  3kndjxAPF9   23.43%    passed     60.78%
 101  fSOOhYALAC   10.63%    passed     18.24%
 102  MYEUikYcJB   22.22%    passed     59.06%
 103  ihdDnmX2iD   11.11%    passed     14.19%
 104  gYvledWOAb   19.08%    passed     44.03%
 105  Ez9ZtxssKH    9.66%    passed     56.14%
 106  Yu2cfILHmc   21.26%    passed     99.19%
 107  sXb4pc8vkJ   17.63%    passed     99.18%
 108  OPaiUWVYAg   19.32%    passed     16.86%
 109  0oe9qWxWgC   12.08%    passed     43.62%
 110  QQ58S3chME   20.53%    passed     53.70%
 111  GsNfFnNm9k   12.56%    passed     77.57%
 112  Nvc3tne6MO   18.60%    passed     66.88%
 113  9NFHCOJ3mt   15.94%    passed     96.43%
 114  7abZLMDRv5   11.84%    passed     90.56%
 115  A9MeIBAjV9   22.46%    passed     27.72%
 116  tFq6SZ4duR   13.29%    failed      3.67%
 117  hsGr8UQtI6   14.49%    passed     72.12%
 118  PsaQsrOOic   21.26%    passed     92.40%
 119  b3rYWyuQhm   25.12%    passed     21.71%
 120  D2Ut2I6kRR   16.43%    passed     99.88%
 121  oZNYuBDmJR   19.32%    passed     99.83%
 122  oHJYtIofr8   13.04%    passed     54.36%
 123  2VQ2kdTDs8   16.67%    passed     97.28%
 124  0BEqzqGTzo   13.29%    passed     37.44%
 125  V7UFl5t0og   12.56%    passed     82.75%
 126  yWWKXX0tOb   18.12%    passed     81.89%
 127  BEwYUowpIl   19.57%    passed     94.20%
 128  6RP65KbJuF   21.50%    failed      0.39%
 129  eCQKmw2pOP   15.22%    passed    100.00%
 130  SHrMCYIrqF   21.98%    passed     83.59%
 131  SuTPtZY9fG   13.04%    passed     34.72%
 132  ywcAduJMee   16.67%    failed      0.00%
 133  ZsVb4os2cb   12.80%    passed     45.91%
 134  UP6HfeKfau   15.22%    passed     95.40%
 135  98pkxfYHE6   20.53%    passed     69.80%
 136  dScYTJASy3   13.29%    passed     17.91%
 137  A83Zj7fGiH   21.74%    passed     98.02%
 138  aegE8u72ZI   14.01%    passed     52.74%
 139  Uj66wqobxX   21.50%    passed     86.94%
 140  ZKBdy0qp0c   21.74%    passed     67.74%
 141  setTvQyVfa   21.26%    passed     68.97%
 142  6YcyVMi9HU   19.08%    passed     72.90%
 143  bKXtRZnILM   18.84%    passed     93.87%
 144  9zCo3T9kHs   13.77%    passed     80.09%
 145  FM3U96ERbZ   12.32%    passed     28.38%
 146  vtxKriXTJb   14.01%    passed     16.96%
 147  mHAx5tEew1   11.11%    passed     27.92%
 148  tK9Y1h0vmG   19.32%    failed      0.83%
 149  rddJIJqTyp   14.25%    passed     75.77%
 150  iLQ3EX95bZ   13.29%    passed     67.27%
 151  clTHPO2kTP   15.46%    passed     79.49%
 152  srLFcibeWN   10.63%    passed     54.55%
 153  HMsATDtoEZ   19.81%    passed     65.15%
 154  rTOE0myIj1   16.43%    failed      0.74%
 155  Kj5hAn4v6q   19.81%    passed     79.07%
 156  LsoOtPQfJ5   13.53%    passed     60.22%
 157  ECanJJ4ncI   12.08%    passed     93.08%
 158  COqJyjUzEG   19.57%    passed     98.63%
 159  Z6xloI3oDo   11.84%    passed     93.32%
 160  vpMwgz3vLP    9.66%    passed     88.22%
 161  BAxjMqLOrV   14.49%    passed      7.89%
 162  tWLDJkeSf6   12.80%    failed      0.40%
 163  Ogxj4OyvD7   13.04%    passed     94.62%
 164  bSuFG152uE   14.01%    passed     96.44%
 165  HdLYk2vd7J   22.22%    passed     44.48%
 166  ahsba9i3Ki   13.29%    passed      7.71%
 167  J9JRrc39aH   12.56%    passed     49.24%
 168  9X41ZUX7sk   14.01%    passed     76.04%
 169  2lLPbY3bIA   17.39%    passed     80.34%
 170  fsCKb933p1   15.46%    passed     61.43%
 171  HR9CNTg3nN   15.46%    passed    100.00%
 172  ej0NOsAKz0   14.49%    passed     20.03%
 173  3JBHsIlGYM   14.73%    passed     89.02%
 174  cIJDI1ElWX    9.90%    passed     71.92%
 175  rDwRatbDPi   13.04%    passed     64.87%
 176  eTS75PP6iB   22.46%    failed      1.84%
 177  aHVp2cBgGN   21.26%    passed     89.22%
 178  htw6R69tCN   15.94%    passed     82.97%
 179  Y6nMrUpOQy   20.05%    failed      1.71%
 180  gZEsHkbcuV   17.15%    passed     53.80%
 181  r36YE0G9qX   14.01%    passed     62.04%
 182  Nq94vUXx6J   12.56%    passed     52.75%
 183  UrVDM79A7d   19.81%    passed     94.40%
 184  RrHy6Wx7gZ   16.43%    passed     42.62%
 185  jr16YVdriy   17.63%    passed     84.57%
 186  LmkMEQF4DR   21.01%    failed      0.01%
 187  zJFuHTnbRq   19.57%    passed     87.77%
 188  YI1L8xHuuM   18.12%    failed      0.02%
 189  zlKlE9DMy9   17.87%    passed     63.67%
 190  XIKdpG1v5e   27.78%    failed      1.44%
 191  y26Opks9vx   16.67%    passed     61.80%
 192  HpehaSDGPK   14.73%    passed      9.89%
 193  RX5cDS5ygC   22.71%    passed     67.07%
 194  aJXccw9WVd   14.01%    passed     67.55%
 195  CFlZ3Yynoy   11.35%    passed      5.35%
 196  1PKgVKI1on   14.49%    passed     45.97%
 197  BfAlPFZr1B   19.81%    passed     97.14%
 198  HzW9kYfmiG   11.35%    passed     29.13%
 199  jf8HZslfsd   13.77%    passed     96.06%
 200  1gjVsly7ZT   29.71%    passed     81.90%
 201  yTN3HKtHgW   12.56%    passed     96.72%
 202  DzXQl3ixjn   24.15%    passed     45.97%
 203  H8w47ZcyKP   10.39%    passed     21.67%
 204  50AYMHqNK0   29.47%    passed     48.69%
 205  52ZDhjNETE   21.01%    passed     75.42%
 206  EG8X1IG6EU   18.12%    passed     27.36%
 207  hHDQviDuXc   17.39%    passed     99.16%
 208  lbOxXnN8b7   24.15%    passed     36.55%
 209  lSJwJYUL1Y   19.08%    passed     95.92%
 210  PMbKXaBN6F    9.90%    passed     84.87%
 211  bSHRAKMHsK   14.49%    passed     99.44%
 212  LGe5jQhMVY   21.50%    passed     78.65%
 213  xCao0DuYt0   14.73%    passed     64.52%
 214  xarXCvI4gY   14.73%    passed     83.15%
 215  GN9LlBOOkT   14.25%    passed     20.02%
 216  oEPBj45bmy   21.50%    failed      0.00%
 217  fP4fRY7tjS   14.98%    passed      8.93%
 218  a5QvoSesca   10.39%    passed     20.43%
 219  5DU1LU9aZ2   11.11%    passed     60.11%
 220  ioXzsSSnhq   21.01%    passed      7.39%
 221  VuLMFqp5mG   16.43%    passed     40.09%
 222  aPdY5V1uOS   13.04%    passed     21.85%
 223  iVLIgog8ZD   23.67%    passed     96.25%
 224  ZcjF0aDH2l   12.56%    passed     92.81%
 225  rBn0zuuQO5   10.63%    passed     86.81%
 226  WYxLjs2S65   21.50%    passed     50.01%
 227  1tOEEBFDV2   21.26%    passed     91.36%
 228  4AQGhYYqZd   22.95%    passed     95.25%
 229  fuPQWxprqQ   14.98%    passed     93.04%
 230  MQ9V4Zj61g   20.53%    passed     96.80%
 231  t6dNTk9ubs   25.85%    failed      3.36%
 232  79Py93EM0n   13.53%    passed     95.10%
 233  RVJDDAJe6D    9.90%    passed     85.58%
 234  yAtKAqFh3f   13.29%    passed     98.59%
 235  3qTi4z1Qys   11.35%    passed      9.95%
 236  AsEACEZyje   15.22%    passed     76.91%
 237  14Cv16S4pA   21.50%    passed     70.32%
 238  09y9SNapkT   25.85%    passed     65.76%
 239  uM6QBwh65Q   20.29%    passed     68.80%
 240  CKvs8jeInU   16.43%    passed     95.25%
 241  s1HvKHReky   15.46%    passed     89.91%
 242  AEVEctaMi5   13.77%    passed     41.83%
 243  fFkKaIm0M3   18.36%    passed     64.11%
 244  2WeFoqGNAI   24.64%    passed     99.23%
 245  DH1HoFGqtF   21.98%    failed      4.28%
 246  E01291uRl2   15.22%    passed     19.71%
 247  RMNeZ2LTKq   14.01%    passed     24.64%
 248  t5BNkjMP5g   14.98%    passed     97.68%
 249  wuqkcc1DBy   18.60%    passed     45.97%
 250  oBOfif9LBJ   13.29%    passed     57.86%
 251  lWYIhCDZyl   18.84%    passed     15.77%
 252  WH8Pi4c3UY   14.98%    passed     98.40%
 253  HWHIYqt9D2   21.74%    passed      6.30%
 254  o5Gb2AX50s   15.22%    passed     66.91%
 255  vyxoQRA4cI   14.49%    passed     87.89%
 256  cOF5xGJ8FX   15.94%    passed     77.56%
 257  BCOck7IwQD   15.22%    passed     45.92%
 258  VYWJtTRjIz   13.77%    passed     97.90%
 259  QP7Akm5rRv   14.73%    passed     95.10%
 260  p5bEB7zEbb   18.36%    passed     54.85%
 261  n1WIkGjHMl   18.36%    passed     87.38%
 262  WSkvfJAjT0   17.63%    passed     52.24%
 263  pNNoFuexDA   12.08%    failed      3.92%
 264  WQ1lDIUS8r   13.53%    passed     15.84%
 265  1R3SzgebA4   10.14%    failed      3.69%
 266  vZS2mZsiyg   15.46%    failed      2.93%
 267  TUCHbMHBCQ   16.67%    failed      0.94%
 268  5StJ1ELBQ5   14.01%    passed     95.29%
 269  W0kYhrEL8O   14.01%    passed     68.31%
****  TOTAL        16.37%  29 sequences failed composition chi2 test (p-value<5%; df=19)
   1  8nJh6NUzJV   12.00%    passed     10.27%
   2  z0YCu0xtFo   11.30%    passed     15.88%
   3  1JN1q1h7Jh    8.35%    passed      9.02%
   4  E2n5Y5UQiG    8.52%    passed     43.28%
   5  cMoC1WsTO6    8.17%    failed      2.01%
   6  ys0DcEs0US    8.35%    passed     77.31%
   7  1s9qnaxMSp    9.04%    failed      2.14%
   8  FtHEpsU1vB    9.04%    failed      2.61%
   9  oeJuwbyE7Q    9.91%    passed      8.44%
  10  qCgVEYLhzI   17.39%    passed      9.43%
  11  zyhovbZkFP    9.91%    passed      8.44%
  12  jOk4aex96C   19.65%    passed      9.17%
  13  AR0npWZQ83    8.17%    passed     22.96%
  14  F5Si2gBtZe   21.91%    passed     13.69%
  15  FG021XCxMA   18.09%    passed     68.58%
  16  MCX7xygB2V    8.70%    passed     73.82%
  17  iVpOwiZzba    9.04%    passed     21.82%
  18  iPjBM3iYZR   80.35%    failed      2.62%
  19  qbFBJDOQUO    9.39%    passed     92.00%
  20  x5jv5lpB2O    9.22%    passed     43.94%
  21  y5M7y721WQ   11.30%    passed     52.45%
  22  MwDLYKIKBx   16.70%    passed     52.35%
  23  EsTTc2nPxQ    8.00%    passed     56.73%
  24  vnhywKRkFl   13.91%    passed     61.80%
  25  7JZdwvMv24   10.09%    passed     62.94%
  26  dQjyx7OIYV   27.30%    passed     66.63%
  27  irBovt5bLa    8.17%    passed     37.03%
  28  Ewm24Mlvnq    8.17%    failed      0.91%
  29  XDJ4JoLzyH   17.22%    passed     87.03%
  30  4kC0x0kjdn    7.65%    passed     35.61%
  31  RARcF60S6a    8.00%    passed     18.15%
  32  WlelCJO26H   12.17%    passed     15.31%
  33  mhk5OTojgz    7.83%    passed     22.72%
  34  pTM2DvE1xM    7.83%    passed     23.80%
  35  tlXXT5aWqu    8.35%    passed     25.18%
  36  TC8Xnd4iFa    8.35%    passed     68.65%
  37  02HhJs6pa3   11.13%    passed     51.90%
  38  NEeqpPtHg5    9.91%    passed     53.60%
  39  qbTDasygHV    8.00%    failed      4.34%
  40  7Yh1YhvFVC    9.04%    passed     82.42%
  41  VvE6sMyCv8    9.22%    passed     82.98%
  42  WjMMQYeUC2    9.74%    passed     28.42%
  43  W7Mh0FRDU6    9.57%    passed     47.24%
  44  2nrE64urGV    7.83%    failed      0.05%
  45  UzprTJ7K6d    7.83%    failed      0.07%
  46  UlwuxTyGoO    8.17%    passed     35.83%
  47  iaXjDyTif3    9.91%    passed     26.12%
  48  B6M0EvUDsT    8.17%    passed     57.64%
  49  1G5hXRghEG    7.83%    passed     46.06%
  50  gTvhxQmbWZ    7.83%    passed     59.90%
  51  8l37MLA1ms    7.83%    passed     66.42%
  52  vLizyHtRBL    6.96%    passed     45.67%
  53  S5ByYpGeqY    7.30%    passed     14.75%
  54  Fedl6T4xon    7.83%    passed     26.99%
  55  4BymctPkH6    9.22%    passed     90.46%
  56  s5wLZ9vWaO   22.96%    passed     14.42%
  57  awKrv6hUok    8.00%    failed      0.00%
  58  kWFqKgyYB3   18.61%    failed      0.35%
  59  DcYLS8gvW9    8.17%    passed     14.76%
  60  McRlo7Hy0B    8.35%    failed      1.15%
  61  tf71jZDs7S   14.78%    failed      0.00%
  62  vMqsZO8YaG   12.00%    passed     25.19%
  63  5AMYxNwgiK   14.26%    passed     72.77%
  64  wxoZBV0PHy    7.65%    passed     28.65%
  65  KeSH8I0Fea   10.96%    passed     34.97%
  66  KCrIGLQ7Q1    8.87%    passed     28.42%
  67  4LT0U0c0Do    8.17%    passed     45.98%
  68  CGeXrJPsGL    7.30%    passed     26.80%
  69  xxKiyIW1gr    8.35%    passed     42.35%
  70  xs9ieaVe53   24.17%    passed      5.89%
  71  NQWmJIpRFE    8.17%    passed     36.46%
  72  nkfchBpcgh    9.91%    passed     49.94%
  73  jdOhfl36g8    9.91%    passed     49.94%
  74  KVoy4GxdpT    8.70%    passed     30.77%
  75  WUIEff6ikU    9.74%    failed      3.44%
  76  coeQ6zHZ24    8.52%    passed     15.26%
  77  HWG7P94Eio    7.65%    passed     33.53%
  78  9Vw494DXPc    9.74%    passed     30.82%
  79  g6PJxKZvcf    8.17%    passed     67.92%
  80  AvvCKxHYp4    8.87%    passed     94.08%
  81  CemxIJafw8    8.87%    passed     94.94%
  82  dsBdLHptXN    7.30%    passed     26.31%
  83  4MVqW0qAIi    8.17%    passed      7.58%
  84  LcWgRv0iB6    8.17%    passed      6.57%
  85  fd8RtQX78T    8.35%    passed     67.99%
  86  D9LASQ998i    7.13%    passed     64.85%
  87  Uz7TnODNGf    8.17%    passed     61.10%
  88  Sp3Vq6QoAR   12.00%    passed     25.06%
  89  gtPloLimDb   14.61%    passed     16.69%
  90  GFnS6AyinZ   13.74%    passed     62.22%
  91  U9Eib0qR6X    9.39%    passed     80.44%
  92  dZ9ze414KZ    8.52%    passed     34.81%
  93  ydHAIeuwbW    9.04%    passed     24.32%
  94  e67HigPrjf    8.70%    passed     10.03%
  95  U5KrYXobqi    7.83%    passed     28.30%
  96  rqX0m8aZs1    8.52%    passed     74.68%
  97  JTOoSRn6ib    8.52%    passed     63.83%
  98  X4XbPR7Rfa    9.91%    passed     88.47%
  99  etCZH2Htco   11.30%    passed     96.50%
 100  7kS1ZU0pFM    9.74%    passed     63.62%
 101  rUnfYSLNJJ    8.35%    passed     25.59%
 102  YjqMqBCaiv    7.13%    passed     35.60%
 103  YXN7x6IbOx    8.35%    passed     52.18%
 104  bN8jt2Atwp   10.43%    passed     56.67%
 105  hgeyXdJgqq    9.22%    passed     56.85%
 106  1horVoEi3u    7.13%    failed      1.07%
 107  EDGqQf981n   10.09%    passed     86.16%
 108  3nDVNG9sKr   10.61%    passed     15.44%
 109  fFDoKaygf0    8.00%    passed     43.10%
 110  cRRsJgsBlZ    8.70%    passed     85.09%
 111  BI3jho3ECe    9.22%    passed     51.11%
 112  TIeppwLKSz    9.57%    passed     34.47%
 113  a8nt9ktZTC   24.35%    passed     70.98%
 114  GtfO72MtR2   22.26%    passed     65.46%
 115  xKzEmKT1dB   21.39%    passed     47.26%
 116  cTDPKciopP   11.83%    passed     67.98%
 117  xdNOUh7eMp    8.00%    passed     86.96%
 118  k3bzPFly41    8.17%    failed      0.00%
 119  ukUu00fP6L    9.39%    failed      0.29%
 120  up1UWJJzNf    9.22%    failed      3.36%
 121  GZASsy6wnT    8.17%    failed      0.00%
 122  PbkNCoK5ix   10.96%    passed     34.06%
 123  GfLEAInBd6   10.26%    passed     45.24%
 124  7OOuM97Qkr    8.70%    passed     42.00%
 125  d9kVhxwUcH    9.22%    passed     36.90%
 126  pn3nIof2qW    8.70%    passed     82.33%
 127  jYBcxGIen7   19.30%    passed     48.83%
 128  Y2YJcqt3IL   27.30%    passed     72.36%
 129  DQnwdMJsVl    9.39%    passed     17.77%
 130  Gvb4AsKEVi    8.35%    failed      0.00%
 131  d5E6EHDpwi    7.65%    passed     78.94%
 132  yA69Aemq0C    9.57%    passed     51.08%
 133  9f7AMvazZf    8.70%    passed     87.18%
 134  tD3ewCYOQG    9.22%    passed     39.14%
 135  yHwEtbE4JZ    8.87%    passed     51.50%
 136  HZpFQAW00k   12.87%    passed     16.94%
 137  FCPk6mdvI6    8.35%    passed     85.41%
 138  C50stY8CeY    9.22%    passed     15.26%
 139  WQOxpzhoLN    8.17%    passed     95.19%
 140  lU6fN5cAZQ   16.87%    passed     26.00%
 141  w34zJrGIvJ   13.04%    passed     46.23%
 142  R4SazYxajJ   13.22%    passed     24.74%
 143  oyLJTIsT1Z   12.00%    passed     35.61%
 144  95FTGjmRiw   16.87%    passed     10.92%
 145  MVSYHU9DCt   12.17%    passed     83.71%
 146  RhS1O12ekg    8.52%    passed     98.08%
 147  sthKhyT8fy    9.04%    passed     79.34%
 148  O2gQ2myCZn   11.30%    passed     66.29%
 149  B7PVgc3v8q    8.52%    passed     67.20%
 150  FlAHhYz62Q    6.96%    passed     92.12%
 151  PZqL2meUHi    8.35%    passed     89.55%
 152  XJTzBvD6pQ    8.70%    passed     73.32%
 153  FtEYGIUfBM   10.78%    passed     55.74%
 154  NUAWacASLt   10.26%    passed     81.70%
 155  3FdA2TKbHR   10.26%    passed     77.97%
 156  TCgaJethwm    9.74%    passed     51.49%
 157  V8Ort0OUIV    9.39%    passed     75.80%
 158  gKxOBa9lC3   80.35%    failed      4.37%
 159  ZJBcyycwk4   21.91%    passed     83.00%
 160  BXOEqGyzK2    9.04%    passed     82.96%
 161  5yy8DKtZ5c   12.35%    passed     70.92%
 162  cY7oeSnppq    9.74%    passed     78.00%
 163  vUEx5gqasN    9.74%    passed     22.71%
 164  2jCJDig3v9   17.39%    passed     45.79%
 165  lzBWRCtyx0   17.39%    passed     45.79%
 166  DBMxujRgHK   10.43%    passed     76.44%
 167  x3ZrH0XGfQ   13.04%    passed     40.57%
 168  SgWCfVzTG4    9.39%    passed     23.64%
 169  f62ksK5UEj   33.39%    passed     48.62%
 170  hkIztfSCD1   10.09%    passed     60.28%
 171  iRnB4M1GLD   11.30%    passed     35.88%
 172  CU0XuCnsFL   42.61%    failed      1.05%
 173  42tdKq8PSX   12.87%    passed     50.93%
 174  gXeZ52LCvM   12.87%    passed     50.93%
 175  u8cLLIfWEX   12.87%    passed     50.93%
 176  dmOh7r7eKT   12.52%    passed     43.59%
 177  3c6hZoOqvP   12.87%    passed     51.70%
 178  bu2UDzewiZ   16.35%    passed     97.52%
 179  SYc4eSftSt    7.30%    passed     55.76%
 180  zlSzVB3W0P    9.91%    passed     23.47%
 181  3C2pM8OlsA   16.00%    passed     44.07%
 182  Pxcz4xw4KG    8.52%    passed     89.90%
 183  UcghE30qVq   10.26%    passed     98.72%
 184  qIB6gS9bgA   10.26%    passed     99.50%
 185  UDehzYJL1w    9.91%    passed     84.08%
 186  BB4241mZBL    9.74%    passed     18.51%
 187  c6c8r06RzT   14.09%    passed     51.46%
 188  XQT9xr4ybf   14.09%    passed     51.46%
 189  SCnTy3bpY1   12.00%    passed     52.85%
 190  jev8yDUHvc   37.22%    passed     46.96%
 191  bK3G4lRT3G    9.74%    passed     18.84%
 192  Z5XH3L582l    9.39%    passed     64.30%
 193  dhUTnrRr7d    9.04%    passed     17.65%
 194  2ifGWJmasz   13.39%    passed     53.39%
 195  WB36HQui6V   13.22%    passed     13.09%
 196  QNNkPiHWnJ   13.57%    passed     15.99%
 197  WHGNQkrc10   16.70%    passed     15.42%
 198  h5LGHiiOXm   13.04%    passed      8.14%
 199  3zhlkwsAL6   11.65%    passed     68.02%
 200  i2Lb0rchl2   17.74%    passed     40.76%
 201  yMqx9t1LVd   11.83%    passed     95.23%
 202  2W3WY0vBww   18.09%    passed     31.19%
 203  wTTqfzkYo6   12.35%    passed     65.69%
 204  0vKBWD6wpY   19.83%    passed     72.14%
 205  SJgohIdqev   13.04%    passed     56.62%
 206  9DPLpYQWNv    8.35%    passed     79.37%
 207  8uUTsKFjlb    9.74%    passed     57.77%
 208  xVujdvY6Nr   15.65%    passed     86.08%
 209  NImtrhZGKE   18.61%    passed     29.08%
 210  YugOzGk8Ov    8.00%    passed     61.92%
 211  DeWEtikGbq    9.39%    passed     58.48%
 212  x0olbpog9B   10.78%    failed      3.15%
 213  pAhidh8xBZ    9.22%    passed     20.39%
 214  PlPvNaQDzl   78.26%    failed      2.70%
 215  NPvXCeLNmx    9.22%    passed     19.23%
 216  yVup7G0SEF    9.39%    passed      5.94%
 217  vPQhR8sENE    9.22%    passed     25.50%
 218  nU2WbHAcGl    8.00%    passed     38.25%
 219  5LDURAlPH2   18.96%    passed     93.03%
 220  BWFcvfZnO3   19.83%    passed     80.72%
 221  pygYFVFfpx   18.96%    passed     64.25%
 222  SHqN6p0dYV   11.65%    passed     77.47%
 223  qsVXrYaG9q   16.52%    passed     62.49%
 224  3cAaekWMpW   17.57%    passed     67.41%
 225  N40B32hpg1   12.00%    passed     79.79%
 226  JPT5lhIP82   16.17%    passed     61.51%
 227  ZLXDnoVm6b    8.87%    passed     65.21%
 228  X85YtZdfkf    9.04%    passed     76.50%
 229  8UiTG47Ec2    9.04%    passed     76.50%
 230  rIeH6RocN2   11.13%    passed     16.99%
 231  JEeirH12E1   31.48%    passed     21.21%
 232  UzAtwShlJN   15.48%    failed      0.00%
 233  2pVvPoBi2c   15.65%    failed      0.00%
 234  scQ10Wo461   39.13%    passed     23.66%
 235  Nb1rJKftmp   17.91%    failed      0.00%
 236  nhoqJOOPX2   17.04%    passed     88.57%
 237  39gkmZTScW   18.26%    passed     91.96%
 238  BGkr4JUYAf   13.39%    passed     93.93%
 239  DulbVCzsEt   24.35%    passed     66.60%
 240  cSruxLJuyQ   26.96%    passed     10.64%
 241  1XfSwqn4ef   25.04%    passed     39.48%
 242  96xj01KeXJ   68.17%    passed     84.97%
 243  eq1zGc6rtT   29.04%    passed     18.35%
 244  VfUM5i9jsn   41.91%    failed      4.66%
 245  20sicocoSo   23.83%    failed      0.74%
 246  RLpJhYeIPE   25.91%    passed     47.76%
 247  C8YPeCC1NI   28.87%    passed     14.80%
 248  xxnHHiKI8Z   28.52%    passed      5.76%
 249  3Je7M7o4rZ   33.39%    passed     11.10%
 250  47EKfQlPcw   28.35%    passed     38.14%
 251  9C0byE309K   34.43%    passed     22.05%
 252  TsIfWQzrph   28.35%    passed     38.14%
 253  hTPGiqrFV4   42.09%    passed     88.30%
 254  aFMglfB8eH   24.52%    passed     15.36%
 255  JQcRFbokY2   28.35%    passed     32.19%
 256  jFdaAxFg6n   23.13%    passed     47.94%
 257  KRYbednenZ   23.13%    passed     42.60%
 258  FyIDyqrLwr   23.13%    passed     47.94%
 259  8XGfcNsQ09   23.83%    passed     62.09%
 260  QyNf0mVNlz   23.83%    passed     10.54%
 261  f9oKgpE1wE   23.48%    passed     56.82%
 262  REBVZFiPEf   23.30%    passed     27.01%
 263  ItesG8T6sN   23.83%    passed     47.79%
 264  TSGS90hx1G   23.30%    passed     24.55%
 265  ZRAzqCtrNA   24.17%    passed     57.76%
 266  eeM5JHuVuf   24.35%    passed     50.06%
 267  oe9Vawfrxg   24.35%    passed     26.16%
 268  rgglFfiKnC   28.00%    passed     45.26%
 269  bCjdcpAF4v   24.00%    passed     70.09%
 270  OmcerY3zVm   64.35%    passed     66.28%
 271  zcG6I9U7zt   43.13%    passed     73.90%
 272  QKniumy84t   24.00%    passed     71.91%
 273  158IGk2w8A   24.00%    passed     40.59%
 274  kI8iG2U2gQ   23.30%    passed     85.81%
 275  fPZNEk39Af   26.78%    passed     15.99%
 276  hrBvV4AmlN   24.17%    passed     20.25%
 277  myGUzZ8LDH   24.00%    passed     24.24%
 278  sHkv5UU91e   23.65%    passed     10.45%
 279  GNzRUX9ddm   23.65%    passed     13.36%
 280  zsnvwGvGgv   24.00%    passed     30.90%
 281  9OoygEJxNJ   23.13%    passed     19.47%
 282  IjtzwwEpZt   24.70%    passed     32.04%
 283  nSDhHtKOaz   76.87%    passed     72.40%
 284  A0R7Dl6WnL   24.00%    passed     27.63%
 285  CvviaWP5QG   24.17%    passed     57.70%
 286  pPSEGFgq5j   79.13%    passed     12.51%
 287  UdG6KQNIp6   24.52%    passed      9.66%
 288  8EVSPtaAhX   24.35%    passed     42.22%
 289  uiafGbGfwA   27.30%    passed     85.86%
 290  XZFyxFJmTO   24.70%    passed     34.27%
 291  H6HkWi4jLJ   26.26%    passed     57.81%
 292  uALm9y36Bq   28.70%    passed     22.86%
 293  EUEmaNv0jU   23.30%    passed     16.64%
 294  miFIpMQUO8   25.04%    passed      5.34%
 295  qsWsb5TOjf   26.09%    passed     11.23%
 296  WLDkRifOr1   25.74%    passed     31.25%
 297  u7RGaLBmh5   25.74%    passed     85.68%
 298  n4n2Sa9hou   25.39%    passed     53.48%
 299  gZV6bt6UCn   24.17%    passed     46.31%
 300  PortTSlpTI   41.74%    passed     26.87%
 301  2Nn52BMVGD   28.00%    passed     32.50%
 302  sQl8vIYhWL   27.30%    passed     24.87%
 303  nlyynuwvAY   27.13%    passed     84.06%
 304  iM9z6TKAcr   41.39%    passed     18.69%
 305  pVpmbqWKfw   36.70%    failed      1.72%
 306  r4JpMWXYFJ   26.09%    passed     11.04%
 307  CcX8oiPHcg   27.83%    passed     27.83%
 308  G2BVFEVILA   25.04%    passed     61.18%
 309  BNYVmW4TYG   25.91%    passed     54.90%
 310  ExQ8uNPj7h   34.26%    passed     66.82%
 311  whmj06xoF5   28.17%    failed      0.02%
 312  VqFVtnHfVy   25.22%    passed     79.18%
 313  Mqy8imXZ6G   25.91%    failed      0.02%
 314  s0NXcs97L3   25.91%    failed      0.02%
 315  Iqt8ZiOu6k   25.74%    failed      0.00%
 316  XsWTxkH1p7   25.57%    passed     19.64%
 317  zoRaGfFB7U   24.52%    passed     48.77%
 318  qqN1dh1OOy   24.35%    passed     14.36%
 319  T1wQDvF98B   24.35%    passed      7.77%
 320  lkTsXyry76   26.43%    passed     26.11%
 321  hSqg5YYyOm   27.48%    failed      0.44%
 322  puRVWMvppN   28.35%    passed     22.55%
 323  1LbFAdgLuC   25.74%    passed     11.73%
 324  y5MmiioIHk   25.91%    failed      1.83%
 325  BnR8odZPBs   25.91%    passed     15.58%
 326  ajGvkpi5As   25.91%    passed      8.73%
 327  qbTJcwpdwP   26.61%    passed     13.99%
 328  vCxAIjCqNl   24.87%    passed     46.42%
 329  mPlwp1JlUK   27.30%    passed     36.54%
 330  rYWDHuLHvt   29.91%    failed      1.32%
 331  C0RnyRzFMX   71.65%    passed     45.95%
 332  7Aa2sW2uFn   28.00%    failed      3.36%
 333  0djEp2FhF9   28.00%    failed      3.36%
 334  l1pN6WjG1N   80.17%    passed     21.40%
 335  XLgmciWSgo   46.09%    passed     14.00%
 336  D8WaLv1pNN   30.78%    passed     27.06%
 337  12VY0qcAbu   29.39%    passed     74.33%
 338  JNoGNci0kO   28.87%    passed     95.56%
 339  VGEALS8WvR   40.70%    passed     16.49%
 340  D7iWRjKQ8X   25.74%    passed     47.65%
 341  upEmmPcbTB   27.48%    passed     22.48%
 342  UpKcpH8xp2   26.78%    passed      7.74%
 343  hreWbDAWDh   23.65%    passed      8.09%
 344  5oPFYbGk9x   24.52%    passed     66.68%
 345  bKMx8usLZf   35.83%    passed      9.39%
 346  9waTHuOjG2   43.48%    passed     27.73%
 347  y13PUGF6fd   29.39%    passed     50.29%
 348  MCxeCrj6og   25.22%    passed     77.92%
 349  JqQlZRu8jp   25.91%    passed     38.60%
 350  ZrMp8mhVn3   56.35%    passed      9.73%
 351  PVum0t8D9w   48.52%    failed      3.01%
 352  mA0FIy0SqW   24.70%    passed      5.42%
 353  EacivjsFt1   26.61%    passed     43.72%
 354  FKAuFXjrK2   29.57%    failed      2.12%
 355  eOn8Fw1qPv   27.48%    failed      3.53%
 356  D0XDiTOIfD   34.78%    passed      9.81%
 357  910hgdbBRd   28.00%    passed     51.49%
 358  ijUTPEstS6   33.39%    passed     28.87%
 359  bUU4czn7NG   27.83%    passed     60.40%
 360  INEhHLWnmb   37.04%    failed      1.97%
 361  LMA81zzKSe   37.04%    failed      0.01%
 362  TUCOIK4ZQn   33.91%    failed      0.52%
 363  yvso4goGdQ   34.96%    failed      4.00%
 364  YWPX00OZwF   36.00%    failed      3.54%
 365  qKqJ6yzKtT   34.61%    passed     10.13%
 366  49Qin0CHkb   34.61%    passed      9.62%
 367  63Q15egMZA   34.26%    passed      6.18%
 368  nWYlGrbPPc   34.61%    failed      4.67%
 369  JvcE4PBExA   33.74%    passed      7.73%
 370  LUlT7ehgwb   36.00%    passed     26.12%
 371  pVpykOHqYZ   39.48%    failed      0.85%
 372  v2K68153zf   38.26%    failed      0.55%
 373  qYhA4tEOW1   34.78%    failed      0.03%
 374  grGtjFUUTt   34.43%    failed      0.23%
 375  qWhSnx7aMf   44.87%    passed      5.50%
 376  v1oAyLSJtz   50.96%    passed     28.72%
 377  BadtzwpMMs   38.43%    passed      9.62%
 378  6DLNJCEk13   34.61%    passed      8.29%
 379  w2DOMr7ED6   41.39%    failed      3.23%
 380  JK0CadwxtV   33.74%    failed      1.62%
 381  thXzqzsTWd   33.04%    failed      4.58%
 382  cza9cyArKR   33.04%    failed      3.45%
 383  64i2bPRqyf   38.09%    failed      1.24%
 384  Tu05kR9iNy   35.30%    failed      2.13%
 385  ryyuwN9EeF   35.83%    failed      3.08%
 386  9i9iYEz14b   36.87%    passed     43.29%
 387  e5Z7VURlcd   56.00%    failed      0.95%
 388  ndIdlcACpn   34.61%    failed      0.11%
 389  miylOtOHke   36.00%    passed      5.91%
 390  jGxqmOPSFz   33.91%    failed      1.22%
 391  UpRnjomc4O   36.17%    passed     26.63%
 392  ebCUnMXr2f   38.43%    passed     15.56%
 393  21yjS1P784   34.43%    failed      0.27%
 394  XU8ct59Imq   34.26%    failed      0.70%
 395  mWu9nYUMB2   34.26%    passed      5.63%
 396  6N8VC2LDv6   34.26%    passed      5.63%
 397  Tp4oCldie4   38.09%    failed      4.42%
 398  LdahhT5atZ   34.26%    passed      5.63%
 399  ohdNT1wCFZ   34.26%    passed      7.14%
 400  QY3dkiwN48   41.57%    failed      3.72%
 401  Ip06mTdO2e   35.65%    failed      2.00%
 402  P5RXO2szhK   29.57%    passed     33.39%
 403  offjx75l6X   85.22%    passed     26.57%
 404  EdOuOhohBn   33.91%    passed     23.13%
 405  ZjYUAXvbUC   34.26%    passed      8.29%
 406  lpxtOw9xf3   36.52%    passed     12.71%
 407  4bSmqRgfRI   34.09%    passed     12.39%
 408  gminDyGtcG   34.78%    failed      2.44%
 409  lDQWwcBkMU   34.78%    passed     33.99%
 410  CUTMeJuwSv   33.74%    passed     78.03%
 411  OI80q3iM3F   33.74%    passed     81.17%
 412  xnKco929hT   37.57%    passed      8.65%
 413  RPfcmWXHCA   37.57%    passed     20.91%
 414  6mj1jZTKcU   36.17%    failed      4.67%
 415  Gr87dxYVyz   43.83%    failed      4.55%
 416  VGvhdii6IX   73.22%    passed     54.33%
 417  wJTuSg6Gc6   35.65%    passed     75.44%
 418  K3Flz6km5g   35.65%    passed     71.14%
 419  Tu0u89fzoU   35.48%    passed     16.33%
 420  IpceOBVrBQ   35.48%    passed     13.04%
 421  JAjUuwFnV7   36.35%    passed     34.52%
 422  wSnvqYXqTg   32.00%    passed     24.03%
 423  keWKiDv5J1   36.35%    passed     23.38%
 424  r5NSp8dbtM   37.39%    passed     32.60%
 425  wxLKLb6SMC   35.13%    passed     25.74%
 426  qw6gF6ZapY   35.13%    passed     25.74%
 427  ZGvDd4xvwy   37.91%    passed     30.11%
 428  8lXCZuvq8q   34.26%    passed     25.11%
 429  qvg1my8Wlp   48.70%    failed      3.30%
 430  ZdWaANa0Et   32.87%    passed      6.04%
 431  Onz2iyjxH3   42.96%    failed      0.02%
 432  AJImOJUang   66.09%    passed      8.67%
 433  rbo3OKIe4x   36.52%    failed      0.54%
 434  pGufZSTMNB   36.52%    passed     12.14%
 435  FLjy3W79tg   36.52%    passed     17.85%
 436  jYaSjXdhUR   34.78%    passed     22.31%
 437  HGW1EoyaVz   49.22%    passed     75.08%
 438  HQpmvbcKV0   36.35%    passed     71.28%
 439  Us22uQdloc   73.22%    passed     88.61%
 440  Nczi5Cos47   34.96%    passed     68.86%
 441  IV8TgD1mQj   36.52%    passed     65.05%
 442  QKsY8kV1rB   34.43%    passed     49.51%
 443  TrIc96BqkG   34.96%    passed      7.64%
 444  pnjqLcOivm   34.61%    passed      9.34%
 445  SY2alUymun   36.00%    passed     31.87%
 446  GXBps2FgSH   37.57%    failed      4.23%
 447  ZldeYJmzLx   39.48%    failed      0.13%
 448  8biR24Gazc   33.91%    passed     22.85%
 449  NBJ6cvHYoU   34.43%    passed     22.55%
 450  egq7pHRqeL   38.78%    passed     36.06%
 451  y0r2SVxwqI   35.30%    passed     55.80%
 452  evUBWmPjS2   35.30%    passed     23.87%
 453  ikh1qtxydC   36.00%    failed      2.62%
 454  BRdJ9RHZQj   35.65%    passed      8.09%
 455  l25CgIsmfn   35.65%    passed      8.09%
 456  XPdvjShyOo   37.57%    passed      7.82%
 457  M144qciIKM   34.96%    passed     30.15%
 458  BnE96TDyk8   35.48%    passed     26.42%
 459  jeohLZ0eYF   36.87%    failed      0.20%
 460  YvoxlQmxl7   36.87%    failed      0.20%
 461  R0wuUn8J0h   33.57%    passed     30.51%
 462  oeFPRaQBYZ   33.39%    passed     26.87%
 463  xqlhblg6dL   33.91%    passed     25.42%
 464  6Qs9p4Rx4f   34.09%    passed     25.71%
 465  QPlyWfEtzz   34.43%    passed     29.56%
 466  Yo6roMcRLy   35.30%    passed     25.15%
 467  PwuAxgsPD6   42.78%    passed     42.46%
 468  vaFUdeGB10   33.91%    failed      2.49%
 469  8GM1psnK6y   36.87%    failed      0.09%
 470  E6RVlyXu6C   33.74%    passed     45.21%
 471  SuF6hGymBQ   36.00%    failed      2.74%
 472  cgJCegWwAr   70.96%    passed     99.24%
 473  i10ONbBPRV   34.96%    passed     50.77%
 474  FaaaR0oHe4   35.13%    passed     47.29%
 475  RrNP3l8SS7   36.52%    failed      0.47%
 476  BuFyz2PMN4   34.43%    passed     49.11%
 477  Y10Qa1Da4V   38.78%    passed     65.87%
 478  8zkzdNvfM0   34.43%    passed     49.11%
 479  rA4KjQCVx3   32.00%    passed     90.85%
 480  au044S3YHW   35.30%    passed     43.12%
 481  cIR66o13VD   35.65%    passed     81.03%
 482  fkB1xaD3I7   35.83%    passed     66.46%
 483  CwGGcZADEn   35.30%    passed     25.37%
 484  fNHflelF6b   34.61%    passed     14.83%
 485  8zGWBmbKDs   83.65%    passed     77.32%
 486  LC2TsjjWfV   35.65%    passed     44.42%
 487  rsgxiUIZDl   41.74%    passed     41.79%
 488  Srvt2UziZu   34.43%    passed     97.83%
 489  zPT9rylEFV   34.43%    passed     97.83%
 490  rXls0PgjJv   35.48%    passed      5.47%
 491  TcLIjpisFo   51.83%    passed     29.28%
 492  RMfRwwtcqL   32.17%    passed      5.11%
 493  zzJMOnIGaE   34.09%    failed      0.02%
 494  bkj6PiDj99   34.78%    passed     36.79%
 495  QPtDeO8Fse   34.61%    passed     64.43%
WARNING: 19 sequences contain more than 50% gaps/ambiguity
****  TOTAL        23.94%  82 sequences failed composition chi2 test (p-value<5%; df=19)


NOTE: Restoring information from model checkpoint file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz


CHECKPOINT: Initial tree restored
Measuring multi-threading efficiency up to 96 CPU cores

CHECKPOINT: Initial tree restored
Measuring multi-threading efficiency up to 96 CPU cores
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.262 seconds
Measuring multi-threading efficiency up to 96 CPU cores
Increase to 10 rounds for branch lengths
Increase to 10 rounds for branch lengths
Increase to 10 rounds for branch lengths
92 trees examined
Threads: 1 / Time: 96.254 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -101173
22 trees examined
Threads: 1 / Time: 97.549 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -471723
61 trees examined
Threads: 1 / Time: 97.419 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -175449
Threads: 2 / Time: 53.688 sec / Speedup: 1.817 / Efficiency: 91% / LogL: -471723
Threads: 2 / Time: 54.530 sec / Speedup: 1.787 / Efficiency: 89% / LogL: -175449
Threads: 2 / Time: 68.082 sec / Speedup: 1.414 / Efficiency: 71% / LogL: -101173
Threads: 3 / Time: 40.079 sec / Speedup: 2.434 / Efficiency: 81% / LogL: -471723
Threads: 3 / Time: 48.086 sec / Speedup: 2.026 / Efficiency: 68% / LogL: -175449
Threads: 3 / Time: 48.624 sec / Speedup: 1.980 / Efficiency: 66% / LogL: -101173
Threads: 4 / Time: 33.701 sec / Speedup: 2.895 / Efficiency: 72% / LogL: -471723
Threads: 4 / Time: 39.649 sec / Speedup: 2.457 / Efficiency: 61% / LogL: -175449
Threads: 4 / Time: 36.375 sec / Speedup: 2.646 / Efficiency: 66% / LogL: -101173
Threads: 5 / Time: 28.392 sec / Speedup: 3.436 / Efficiency: 69% / LogL: -471723
Threads: 6 / Time: 26.111 sec / Speedup: 3.736 / Efficiency: 62% / LogL: -471723
Threads: 5 / Time: 44.114 sec / Speedup: 2.208 / Efficiency: 44% / LogL: -175449
Determining AUTO threadcount: done in 283.818 secs using 256.4% CPU
BEST NUMBER OF THREADS: 4

Perform fast likelihood tree search using LG+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 1.42876 secs using 399% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -105993.124
Optimal log-likelihood: -105992.443
Proportion of invariable sites: 0.029
Gamma shape alpha: 0.847
Parameters optimization took 1 rounds (0.251 sec)
Time for fast ML tree search: 2.759 seconds

NOTE: ModelFinder requires 179 MB RAM!
ModelFinder will test up to 1232 protein models (sample size: 414) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  LG            114651.506   535 230373.013   803893.013   232526.851
  2  LG+I          113901.703   536 228875.406   804539.406   231033.270
  3  LG+G4         106077.366   536 213226.732   788890.732   215384.597
  4  LG+I+G4       105992.371   537 213058.741   790870.741   215220.631
  5  LG+R2         108150.057   537 217374.113   795186.113   219536.003
Threads: 5 / Time: 41.377 sec / Speedup: 2.326 / Efficiency: 47% / LogL: -101173
Determining AUTO threadcount: done in 290.76 secs using 251.1% CPU
BEST NUMBER OF THREADS: 4

Perform fast likelihood tree search using LG+I+G model...
CHECKPOINT: Tree restored, LogL: -59524.228
NOTE: ModelFinder requires 121 MB RAM!
ModelFinder will test up to 1232 protein models (sample size: 492) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  LG            62877.656    303 126361.312   127341.227   127633.451
  2  LG+I          62746.902    304 126101.805   127093.462   127378.142
  3  LG+G4         59525.217    304 119658.433   120650.091   120934.771
  4  LG+I+G4       59520.759    305 119651.519   120655.067   120932.055
  5  LG+R2         60281.148    305 121172.296   122175.844   122452.832
  6  LG+R3         59673.480    307 119960.960   120988.742   121249.893
  7  LG+R4         59517.015    309 119652.030   120704.667   120949.360
  8  LG+R5         59458.290    311 119538.580   120616.713   120844.306
  9  LG+R6         59413.228    313 119452.455   120556.748   120766.579
 10  LG+R7         59406.451    315 119442.902   120574.039   120765.423
 11  LG+R8         59398.958    317 119431.915   120590.605   120762.833
 12  LG+R9         59397.375    319 119432.749   120619.726   120772.064
 14  LG+I+R2       60231.507    306 121075.014   122090.603   122359.748
 15  LG+I+R3       59658.571    308 119933.141   120973.272   121226.273
 16  LG+I+R4       59512.518    310 119645.036   120710.340   120946.564
 17  LG+I+R5       59456.780    312 119537.561   120628.689   120847.486
 18  LG+I+R6       59412.217    314 119452.434   120570.062   120770.757
 19  LG+I+R7       59406.446    316 119444.893   120589.716   120771.612
 31  LG+F+R6       59437.121    332 119538.243   120928.884   120932.138
 32  LG+F+R7       59430.407    334 119528.813   120954.163   120931.105
 33  LG+F+R8       59421.458    336 119514.916   120975.974   120925.605
 34  LG+F+R9       59420.206    338 119516.412   121014.216   120935.498
 40  LG+F+I+R6     59436.464    333 119538.929   120946.802   120937.022
 41  LG+F+I+R7     59430.640    335 119531.280   120974.357   120937.770
 53  WAG+R6        59804.889    313 120235.778   121340.071   121549.902
 54  WAG+R7        59796.966    315 120223.932   121355.068   121546.453
 55  WAG+R8        59792.254    317 120218.509   121377.199   121549.427
 62  WAG+I+R6      59804.263    314 120236.525   121354.152   121554.848
 63  WAG+I+R7      59796.876    316 120225.753   121370.576   121552.472
 75  WAG+F+R6      59751.895    332 120167.790   121558.431   121561.685
 76  WAG+F+R7      59743.193    334 120154.385   121579.736   121556.677
 77  WAG+F+R8      59737.298    336 120146.595   121607.653   121557.284
 84  WAG+F+I+R6    59750.194    333 120166.387   121574.260   121564.480
 85  WAG+F+I+R7    59743.566    335 120157.133   121600.209   121563.623
 97  JTT+R6        60074.266    313 120774.532   121878.824   122088.656
 98  JTT+R7        60060.733    315 120751.466   121882.603   122073.987
 99  JTT+R8        60055.294    317 120744.588   121903.277   122075.505
106  JTT+I+R6      60070.838    314 120769.676   121887.303   122087.998
107  JTT+I+R7      60059.283    316 120750.566   121895.389   122077.286
119  JTT+F+R6      60066.585    332 120797.169   122187.811   122191.064
120  JTT+F+R7      60056.320    334 120780.640   122205.990   122182.932
121  JTT+F+R8      60049.742    336 120771.484   122232.542   122182.173
122  JTT+F+R9      60048.136    338 120772.273   122270.077   122191.359
128  JTT+F+I+R6    60063.360    333 120792.720   122200.594   122190.814
129  JTT+F+I+R7    60054.636    335 120779.271   122222.348   122185.762
WARNING: Normalizing state frequencies so that sum of them equals to 1
141  Q.pfam+R6     59479.017    313 119584.035   120688.327   120898.159
WARNING: Normalizing state frequencies so that sum of them equals to 1
142  Q.pfam+R7     59473.613    315 119577.227   120708.363   120899.747
WARNING: Normalizing state frequencies so that sum of them equals to 1
150  Q.pfam+I+R6   59478.275    314 119584.550   120702.177   120902.872
WARNING: Normalizing state frequencies so that sum of them equals to 1
151  Q.pfam+I+R7   59473.897    316 119579.795   120724.617   120906.514
WARNING: Normalizing state frequencies so that sum of them equals to 1
163  Q.pfam+F+R6   59490.640    332 119645.281   121035.922   121039.176
WARNING: Normalizing state frequencies so that sum of them equals to 1
164  Q.pfam+F+R7   59486.230    334 119640.460   121065.810   121042.752
WARNING: Normalizing state frequencies so that sum of them equals to 1
172  Q.pfam+F+I+R6 59490.182    333 119646.364   121054.237   121044.457
WARNING: Normalizing state frequencies so that sum of them equals to 1
173  Q.pfam+F+I+R7 59486.432    335 119642.864   121085.941   121049.354
WARNING: Normalizing state frequencies so that sum of them equals to 1
185  Q.bird+R6     61133.071    313 122892.142   123996.434   124206.266
WARNING: Normalizing state frequencies so that sum of them equals to 1
186  Q.bird+R7     61117.291    315 122864.582   123995.719   124187.103
WARNING: Normalizing state frequencies so that sum of them equals to 1
187  Q.bird+R8     61111.896    317 122857.793   124016.483   124188.711
WARNING: Normalizing state frequencies so that sum of them equals to 1
194  Q.bird+I+R6   61131.985    314 122891.970   124009.597   124210.292
WARNING: Normalizing state frequencies so that sum of them equals to 1
195  Q.bird+I+R7   61116.198    316 122864.396   124009.219   124191.115
WARNING: Normalizing state frequencies so that sum of them equals to 1
207  Q.bird+F+R6   61244.582    332 123153.164   124543.806   124547.059
WARNING: Normalizing state frequencies so that sum of them equals to 1
208  Q.bird+F+R7   61227.499    334 123122.999   124548.349   124525.291
WARNING: Normalizing state frequencies so that sum of them equals to 1
209  Q.bird+F+R8   61224.264    336 123120.529   124581.587   124531.218
WARNING: Normalizing state frequencies so that sum of them equals to 1
216  Q.bird+F+I+R6 61244.077    333 123154.154   124562.027   124552.247
WARNING: Normalizing state frequencies so that sum of them equals to 1
217  Q.bird+F+I+R7 61226.730    335 123123.459   124566.536   124529.950
WARNING: Normalizing state frequencies so that sum of them equals to 1
229  Q.mammal+R6   60679.748    313 121985.496   123089.788   123299.619
WARNING: Normalizing state frequencies so that sum of them equals to 1
230  Q.mammal+R7   60672.349    315 121974.698   123105.835   123297.219
WARNING: Normalizing state frequencies so that sum of them equals to 1
231  Q.mammal+R8   60660.688    317 121955.377   123114.066   123286.294
WARNING: Normalizing state frequencies so that sum of them equals to 1
232  Q.mammal+R9   60658.391    319 121954.782   123141.759   123294.097
WARNING: Normalizing state frequencies so that sum of them equals to 1
238  Q.mammal+I+R6 60677.423    314 121982.846   123100.473   123301.168
WARNING: Normalizing state frequencies so that sum of them equals to 1
239  Q.mammal+I+R7 60670.841    316 121973.683   123118.505   123300.402
WARNING: Normalizing state frequencies so that sum of them equals to 1
251  Q.mammal+F+R6 60769.205    332 122202.410   123593.051   123596.305
WARNING: Normalizing state frequencies so that sum of them equals to 1
252  Q.mammal+F+R7 60756.768    334 122181.537   123606.887   123583.829
WARNING: Normalizing state frequencies so that sum of them equals to 1
253  Q.mammal+F+R8 60753.074    336 122178.148   123639.207   123588.837
WARNING: Normalizing state frequencies so that sum of them equals to 1
260  Q.mammal+F+I+R6 60767.982    333 122201.963   123609.837   123600.057
WARNING: Normalizing state frequencies so that sum of them equals to 1
261  Q.mammal+F+I+R7 60755.456    335 122180.913   123623.990   123587.403
273  Q.insect+R6   59495.703    313 119617.406   120721.698   120931.530
274  Q.insect+R7   59486.836    315 119603.673   120734.809   120926.194
275  Q.insect+R8   59477.039    317 119588.079   120746.768   120918.996
276  Q.insect+R9   59475.145    319 119588.290   120775.266   120927.604
282  Q.insect+I+R6 59492.203    314 119612.407   120730.034   120930.729
283  Q.insect+I+R7 59485.174    316 119602.348   120747.171   120929.067
295  Q.insect+F+R6 59769.062    332 120202.125   121592.766   121596.020
296  Q.insect+F+R7 59752.577    334 120173.154   121598.505   121575.446
297  Q.insect+F+R8 59745.192    336 120162.385   121623.443   121573.073
298  Q.insect+F+R9 59743.208    338 120162.416   121660.220   121581.502
304  Q.insect+F+I+R6 59768.715    333 120203.430   121611.303   121601.523
305  Q.insect+F+I+R7 59751.169    335 120172.337   121615.414   121578.828
WARNING: Normalizing state frequencies so that sum of them equals to 1
317  Q.plant+R6    60006.620    313 120639.241   121743.533   121953.364
WARNING: Normalizing state frequencies so that sum of them equals to 1
318  Q.plant+R7    59991.276    315 120612.551   121743.687   121935.072
WARNING: Normalizing state frequencies so that sum of them equals to 1
319  Q.plant+R8    59987.162    317 120608.323   121767.013   121939.241
WARNING: Normalizing state frequencies so that sum of them equals to 1
326  Q.plant+I+R6  60005.327    314 120638.655   121756.282   121956.977
WARNING: Normalizing state frequencies so that sum of them equals to 1
327  Q.plant+I+R7  59990.384    316 120612.768   121757.590   121939.487
WARNING: Normalizing state frequencies so that sum of them equals to 1
339  Q.plant+F+R6  60121.458    332 120906.916   122297.557   122300.811
WARNING: Normalizing state frequencies so that sum of them equals to 1
340  Q.plant+F+R7  60115.627    334 120899.253   122324.604   122301.545
WARNING: Normalizing state frequencies so that sum of them equals to 1
348  Q.plant+F+I+R6 60120.118    333 120906.237   122314.110   122304.330
WARNING: Normalizing state frequencies so that sum of them equals to 1
349  Q.plant+F+I+R7 60115.178    335 120900.356   122343.433   122306.846
WARNING: Normalizing state frequencies so that sum of them equals to 1
361  Q.yeast+R6    59532.562    313 119691.124   120795.417   121005.248
WARNING: Normalizing state frequencies so that sum of them equals to 1
362  Q.yeast+R7    59522.381    315 119674.763   120805.899   120997.283
WARNING: Normalizing state frequencies so that sum of them equals to 1
363  Q.yeast+R8    59515.869    317 119665.738   120824.428   120996.656
WARNING: Normalizing state frequencies so that sum of them equals to 1
364  Q.yeast+R9    59514.866    319 119667.732   120854.708   121007.046
WARNING: Normalizing state frequencies so that sum of them equals to 1
370  Q.yeast+I+R6  59530.703    314 119689.406   120807.033   121007.728
WARNING: Normalizing state frequencies so that sum of them equals to 1
371  Q.yeast+I+R7  59521.895    316 119675.790   120820.613   121002.510
WARNING: Normalizing state frequencies so that sum of them equals to 1
383  Q.yeast+F+R6  59600.416    332 119864.832   121255.474   121258.727
WARNING: Normalizing state frequencies so that sum of them equals to 1
384  Q.yeast+F+R7  59583.663    334 119835.327   121260.677   121237.619
WARNING: Normalizing state frequencies so that sum of them equals to 1
385  Q.yeast+F+R8  59576.754    336 119825.507   121286.565   121236.196
WARNING: Normalizing state frequencies so that sum of them equals to 1
386  Q.yeast+F+R9  59576.014    338 119828.027   121325.831   121247.113
WARNING: Normalizing state frequencies so that sum of them equals to 1
392  Q.yeast+F+I+R6 59601.742    333 119869.483   121277.357   121267.577
WARNING: Normalizing state frequencies so that sum of them equals to 1
393  Q.yeast+F+I+R7 59583.173    335 119836.346   121279.423   121242.836
405  JTTDCMut+R6   60065.179    313 120756.357   121860.649   122070.481
406  JTTDCMut+R7   60051.419    315 120732.838   121863.974   122055.359
407  JTTDCMut+R8   60045.997    317 120725.994   121884.683   122056.911
414  JTTDCMut+I+R6 60061.676    314 120751.351   121868.978   122069.673
415  JTTDCMut+I+R7 60049.755    316 120731.509   121876.332   122058.228
427  JTTDCMut+F+R6 60058.397    332 120780.793   122171.435   122174.688
428  JTTDCMut+F+R7 60047.984    334 120763.969   122189.319   122166.261
429  JTTDCMut+F+R8 60041.317    336 120754.634   122215.692   122165.323
430  JTTDCMut+F+R9 60039.752    338 120755.505   122253.309   122174.590
436  JTTDCMut+F+I+R6 60055.030    333 120776.060   122183.933   122174.153
437  JTTDCMut+F+I+R7 60046.210    335 120762.419   122205.496   122168.910
449  DCMut+R6      60668.488    313 121962.975   123067.268   123277.099
450  DCMut+R7      60652.813    315 121935.626   123066.762   123258.147
451  DCMut+R8      60648.578    317 121931.156   123089.845   123262.074
458  DCMut+I+R6    60665.033    314 121958.067   123075.694   123276.389
459  DCMut+I+R7    60649.047    316 121930.094   123074.917   123256.813
471  DCMut+F+R6    60593.102    332 121850.204   123240.846   123244.099
472  DCMut+F+R7    60580.254    334 121828.509   123253.859   123230.801
473  DCMut+F+R8    60574.694    336 121821.387   123282.445   123232.076
480  DCMut+F+I+R6  60586.513    333 121839.025   123246.899   123237.119
481  DCMut+F+I+R7  60579.937    335 121829.875   123272.951   123236.365
493  VT+R6         59991.693    313 120609.386   121713.678   121923.510
494  VT+R7         59983.961    315 120597.921   121729.058   121920.442
495  VT+R8         59977.569    317 120589.139   121747.828   121920.057
496  VT+R9         59976.356    319 120590.712   121777.689   121930.027
502  VT+I+R6       59989.999    314 120607.998   121725.625   121926.321
503  VT+I+R7       59983.952    316 120599.903   121744.726   121926.623
515  VT+F+R6       60006.991    332 120677.982   122068.623   122071.877
516  VT+F+R7       60000.049    334 120668.098   122093.448   122070.390
517  VT+F+R8       59993.844    336 120659.688   122120.746   122070.377
518  VT+F+R9       59992.313    338 120660.625   122158.429   122079.711
524  VT+F+I+R6     60005.611    333 120677.222   122085.095   122075.315
525  VT+F+I+R7     60000.235    335 120670.470   122113.547   122076.960
537  PMB+R6        60396.277    313 121418.554   122522.846   122732.678
538  PMB+R7        60390.118    315 121410.236   122541.372   122732.757
546  PMB+I+R6      60395.163    314 121418.327   122535.954   122736.649
547  PMB+I+R7      60390.809    316 121413.618   122558.441   122740.338
559  PMB+F+R6      60473.358    332 121610.716   123001.357   123004.611
560  PMB+F+R7      60466.670    334 121601.340   123026.690   123003.632
561  PMB+F+R8      60460.735    336 121593.470   123054.528   123004.159
568  PMB+F+I+R6    60471.900    333 121609.800   123017.674   123007.894
569  PMB+F+I+R7    60467.163    335 121604.326   123047.403   123010.817
581  Blosum62+R6   60277.331    313 121180.661   122284.953   122494.785
582  Blosum62+R7   60270.511    315 121171.022   122302.159   122493.543
583  Blosum62+R8   60263.582    317 121161.163   122319.853   122492.081
584  Blosum62+R9   60262.225    319 121162.450   122349.427   122501.765
590  Blosum62+I+R6 60277.217    314 121182.434   122300.061   122500.757
591  Blosum62+I+R7 60271.055    316 121174.111   122318.933   122500.830
603  Blosum62+F+R6 60372.862    332 121409.723   122800.365   122803.618
604  Blosum62+F+R7 60365.124    334 121398.248   122823.598   122800.540
605  Blosum62+F+R8 60358.971    336 121389.941   122850.999   122800.630
612  Blosum62+F+I+R6 60372.554    333 121411.108   122818.982   122809.202
613  Blosum62+F+I+R7 60365.655    335 121401.310   122844.387   122807.800
625  Dayhoff+R6    60665.533    313 121957.066   123061.358   123271.189
626  Dayhoff+R7    60649.782    315 121929.564   123060.700   123252.085
627  Dayhoff+R8    60645.551    317 121925.102   123083.791   123256.019
634  Dayhoff+I+R6  60662.272    314 121952.544   123070.171   123270.866
635  Dayhoff+I+R7  60646.014    316 121924.028   123068.851   123250.747
647  Dayhoff+F+R6  60590.639    332 121845.279   123235.920   123239.174
648  Dayhoff+F+R7  60577.726    334 121823.452   123248.802   123225.744
649  Dayhoff+F+R8  60572.198    336 121816.396   123277.454   123227.085
656  Dayhoff+F+I+R6 60584.026    333 121834.052   123241.926   123232.146
657  Dayhoff+F+I+R7 60572.635    335 121815.269   123258.346   123221.760
669  mtREV+R6      62499.837    313 125625.675   126729.967   126939.798
670  mtREV+R7      62487.330    315 125604.660   126735.796   126927.181
671  mtREV+R8      62485.980    317 125605.961   126764.650   126936.878
678  mtREV+I+R6    62500.369    314 125628.737   126746.364   126947.059
679  mtREV+I+R7    62487.692    316 125607.385   126752.208   126934.104
691  mtREV+F+R6    60468.631    332 121601.263   122991.904   122995.158
692  mtREV+F+R7    60454.479    334 121576.958   123002.308   122979.250
693  mtREV+F+R8    60448.613    336 121569.227   123030.285   122979.915
700  mtREV+F+I+R6  60467.056    333 121600.111   123007.985   122998.205
701  mtREV+F+I+R7  60454.408    335 121578.815   123021.892   122985.306
713  mtART+R6      62852.803    313 126331.607   127435.899   127645.731
714  mtART+R7      62831.608    315 126293.216   127424.352   127615.737
715  mtART+R8      62826.466    317 126286.932   127445.622   127617.850
722  mtART+I+R6    62854.881    314 126337.762   127455.389   127656.085
723  mtART+I+R7    62832.267    316 126296.533   127441.356   127623.252
735  mtART+F+R6    61003.545    332 122671.091   124061.732   124064.986
736  mtART+F+R7    60985.523    334 122639.045   124064.396   124041.337
737  mtART+F+R8    60983.078    336 122638.155   124099.213   124048.844
744  mtART+F+I+R6  61003.257    333 122672.514   124080.387   124070.607
745  mtART+F+I+R7  60985.504    335 122641.009   124084.086   124047.499
757  mtZOA+R6      61377.869    313 123381.738   124486.030   124695.861
758  mtZOA+R7      61368.510    315 123367.020   124498.156   124689.541
759  mtZOA+R8      61356.530    317 123347.060   124505.750   124677.978
760  mtZOA+R9      61356.212    319 123350.424   124537.401   124689.739
766  mtZOA+I+R6    61377.854    314 123383.708   124501.336   124702.031
767  mtZOA+I+R7    61363.311    316 123358.623   124503.446   124685.342
779  mtZOA+F+R6    60214.531    332 121093.062   122483.703   122486.956
780  mtZOA+F+R7    60195.212    334 121058.424   122483.774   122460.715
781  mtZOA+F+R8    60191.888    336 121055.776   122516.834   122466.465
788  mtZOA+F+I+R6  60213.763    333 121093.525   122501.399   122491.619
789  mtZOA+F+I+R7  60194.708    335 121059.417   122502.494   122465.907
801  mtMet+R6      62101.921    313 124829.842   125934.134   126143.966
802  mtMet+R7      62093.666    315 124817.332   125948.469   126139.853
803  mtMet+R8      62081.311    317 124796.622   125955.311   126127.540
804  mtMet+R9      62081.351    319 124800.702   125987.679   126140.017
810  mtMet+I+R6    62101.693    314 124831.386   125949.013   126149.708
811  mtMet+I+R7    62094.240    316 124820.481   125965.304   126147.200
823  mtMet+F+R6    60455.726    332 121575.452   122966.093   122969.347
824  mtMet+F+R7    60437.393    334 121542.787   122968.137   122945.078
825  mtMet+F+R8    60433.088    336 121538.177   122999.235   122948.866
832  mtMet+F+I+R6  60453.915    333 121573.829   122981.703   122971.923
833  mtMet+F+I+R7  60435.792    335 121541.585   122984.662   122948.075
845  mtVer+R6      62797.259    313 126220.519   127324.811   127534.642
846  mtVer+R7      62780.850    315 126191.700   127322.836   127514.221
847  mtVer+R8      62768.302    317 126170.604   127329.294   127501.522
848  mtVer+R9      62764.125    319 126166.251   127353.228   127505.566
854  mtVer+I+R6    62797.426    314 126222.852   127340.479   127541.174
855  mtVer+I+R7    62781.330    316 126194.660   127339.483   127521.379
867  mtVer+F+R6    61347.538    332 123359.076   124749.718   124752.971
868  mtVer+F+R7    61329.959    334 123327.919   124753.269   124730.211
869  mtVer+F+R8    61323.177    336 123318.354   124779.412   124729.043
870  mtVer+F+R9    61321.918    338 123319.836   124817.640   124738.922
876  mtVer+F+I+R6  61343.147    333 123352.293   124760.166   124750.386
877  mtVer+F+I+R7  61326.325    335 123322.650   124765.727   124729.140
889  mtInv+R6      62323.205    313 125272.410   126376.702   126586.534
890  mtInv+R7      62309.931    315 125249.862   126380.998   126572.383
891  mtInv+R8      62308.746    317 125251.492   126410.182   126582.410
898  mtInv+I+R6    62323.080    314 125274.161   126391.788   126592.483
899  mtInv+I+R7    62310.234    316 125252.469   126397.292   126579.188
911  mtInv+F+R6    60145.705    332 120955.411   122346.052   122349.306
912  mtInv+F+R7    60130.008    334 120928.016   122353.366   122330.308
913  mtInv+F+R8    60128.022    336 120928.044   122389.102   122338.733
920  mtInv+F+I+R6  60143.730    333 120953.460   122361.333   122351.553
921  mtInv+F+I+R7  60128.152    335 120926.304   122369.381   122332.794
933  mtMAM+R6      63712.112    313 128050.224   129154.516   129364.347
934  mtMAM+R7      63684.089    315 127998.178   129129.314   129320.698
935  mtMAM+R8      63668.492    317 127970.984   129129.674   129301.902
936  mtMAM+R9      63668.264    319 127974.528   129161.505   129313.843
942  mtMAM+I+R6    63712.305    314 128052.611   129170.238   129370.933
943  mtMAM+I+R7    63684.235    316 128000.470   129145.293   129327.190
955  mtMAM+F+R6    61878.116    332 124420.231   125810.873   125814.126
956  mtMAM+F+R7    61854.633    334 124377.266   125802.616   125779.558
957  mtMAM+F+R8    61844.924    336 124361.848   125822.906   125772.537
958  mtMAM+F+R9    61843.394    338 124362.788   125860.592   125781.874
964  mtMAM+F+I+R6  61877.208    333 124420.417   125828.290   125818.510
965  mtMAM+F+I+R7  61854.353    335 124378.706   125821.783   125785.197
WARNING: Normalizing state frequencies so that sum of them equals to 1
977  FLAVI+R6      62815.374    313 126256.748   127361.040   127570.872
WARNING: Normalizing state frequencies so that sum of them equals to 1
978  FLAVI+R7      62789.908    315 126209.816   127340.952   127532.337
WARNING: Normalizing state frequencies so that sum of them equals to 1
979  FLAVI+R8      62785.192    317 126204.383   127363.073   127535.301
WARNING: Normalizing state frequencies so that sum of them equals to 1
986  FLAVI+I+R6    62815.031    314 126258.062   127375.689   127576.385
WARNING: Normalizing state frequencies so that sum of them equals to 1
987  FLAVI+I+R7    62789.557    316 126211.114   127355.937   127537.833
WARNING: Normalizing state frequencies so that sum of them equals to 1
999  FLAVI+F+R6    62636.840    332 125937.679   127328.321   127331.574
WARNING: Normalizing state frequencies so that sum of them equals to 1
1000  FLAVI+F+R7    62615.110    334 125898.220   127323.570   127300.512
WARNING: Normalizing state frequencies so that sum of them equals to 1
1001  FLAVI+F+R8    62610.598    336 125893.196   127354.254   127303.885
WARNING: Normalizing state frequencies so that sum of them equals to 1
1008  FLAVI+F+I+R6  62636.276    333 125938.552   127346.426   127336.646
WARNING: Normalizing state frequencies so that sum of them equals to 1
1009  FLAVI+F+I+R7  62614.816    335 125899.631   127342.708   127306.122
1021  HIVb+R6       61602.342    313 123830.684   124934.976   125144.808
1022  HIVb+R7       61598.334    315 123826.667   124957.804   125149.188
1030  HIVb+I+R6     61601.684    314 123831.369   124948.996   125149.691
1031  HIVb+I+R7     61598.003    316 123828.006   124972.828   125154.725
1043  HIVb+F+R6     61283.289    332 123230.577   124621.219   124624.472
1044  HIVb+F+R7     61279.972    334 123227.944   124653.294   124630.236
1052  HIVb+F+I+R6   61283.115    333 123232.229   124640.103   124630.323
1053  HIVb+F+I+R7   61280.040    335 123230.079   124673.156   124636.570
1065  HIVw+R6       64522.959    313 129671.919   130776.211   130986.043
1066  HIVw+R7       64494.595    315 129619.189   130750.326   130941.710
1067  HIVw+R8       64490.582    317 129615.163   130773.853   130946.081
1074  HIVw+I+R6     64521.854    314 129671.708   130789.335   130990.030
1075  HIVw+I+R7     64493.543    316 129619.086   130763.909   130945.805
1087  HIVw+F+R6     63532.197    332 127728.394   129119.035   129122.289
1088  HIVw+F+R7     63515.599    334 127699.197   129124.548   129101.489
1089  HIVw+F+R8     63509.986    336 127691.972   129153.030   129102.661
1096  HIVw+F+I+R6   63531.944    333 127729.888   129137.762   129127.982
1097  HIVw+F+I+R7   63515.653    335 127701.306   129144.383   129107.796
1109  FLU+R6        61371.791    313 123369.583   124473.875   124683.706
1110  FLU+R7        61363.433    315 123356.866   124488.002   124679.387
1111  FLU+R8        61354.945    317 123343.891   124502.580   124674.808
1112  FLU+R9        61352.112    319 123342.224   124529.201   124681.539
1118  FLU+I+R6      61367.705    314 123363.411   124481.038   124681.733
1119  FLU+I+R7      61361.082    316 123354.164   124498.987   124680.883
1131  FLU+F+R6      61080.692    332 122825.383   124216.025   124219.278
1132  FLU+F+R7      61074.901    334 122817.802   124243.152   124220.094
1140  FLU+F+I+R6    61079.005    333 122824.009   124231.883   124222.103
1141  FLU+F+I+R7    61074.340    335 122818.679   124261.756   124225.169
1153  rtREV+R6      60257.949    313 121141.898   122246.191   122456.022
1154  rtREV+R7      60251.101    315 121132.202   122263.338   122454.723
1155  rtREV+R8      60244.011    317 121122.022   122280.712   122452.940
1156  rtREV+R9      60243.349    319 121124.699   122311.675   122464.013
1162  rtREV+I+R6    60257.784    314 121143.568   122261.195   122461.890
1163  rtREV+I+R7    60251.370    316 121134.740   122279.563   122461.460
1175  rtREV+F+R6    59892.087    332 120448.174   121838.816   121842.069
1176  rtREV+F+R7    59885.038    334 120438.076   121863.426   121840.368
1177  rtREV+F+R8    59876.997    336 120425.993   121887.051   121836.682
1178  rtREV+F+R9    59876.123    338 120428.246   121926.050   121847.332
1184  rtREV+F+I+R6  59891.586    333 120449.172   121857.045   121847.265
1185  rtREV+F+I+R7  59884.896    335 120439.792   121882.869   121846.282
1197  cpREV+R6      60125.526    313 120877.052   121981.344   122191.176
1198  cpREV+R7      60114.354    315 120858.707   121989.843   122181.228
1199  cpREV+R8      60110.898    317 120855.795   122014.485   122186.713
1206  cpREV+I+R6    60123.873    314 120875.747   121993.374   122194.069
1207  cpREV+I+R7    60114.273    316 120860.546   122005.369   122187.266
1219  cpREV+F+R6    59920.197    332 120504.394   121895.036   121898.289
1220  cpREV+F+R7    59900.106    334 120468.213   121893.563   121870.505
1221  cpREV+F+R8    59898.397    336 120468.794   121929.852   121879.483
1228  cpREV+F+I+R6  59916.314    333 120498.627   121906.501   121896.721
1229  cpREV+F+I+R7  59900.315    335 120470.631   121913.708   121877.121
Akaike Information Criterion:           LG+R8
Corrected Akaike Information Criterion: LG+R6
Bayesian Information Criterion:         LG+R8
Best-fit model: LG+R8 chosen according to BIC

All model information printed to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.model.gz
CPU time for ModelFinder: 733.153 seconds (0h:12m:13s)
Wall-clock time for ModelFinder: 291.013 seconds (0h:4m:51s)

===> START BOOTSTRAP REPLICATE NUMBER 9

Creating bootstrap alignment (seed: 67471)...

CHECKPOINT: Initial tree restored

NOTE: 62 MB RAM (0 GB) is required!
CHECKPOINT: Model parameters restored, LogL: -62513.162
Wrote distance file to... 
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
CHECKPOINT: Candidate tree set restored, best LogL: -61000.047
Finish initializing candidate tree set (20)
Current best tree score: -61000.047 / CPU time: 0.000
Number of iterations: 107
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.9273 secs using 398.8% CPU
  6  LG+R3         106585.962   539 214249.924   796369.924   216419.866
Optimizing NNI: done in 2.48626 secs using 398.5% CPU
Optimizing NNI: done in 2.72455 secs using 398.5% CPU
Iteration 110 / LogL: -62149.641 / Time: 0h:0m:8s (0h:0m:6s left)
Optimizing NNI: done in 2.76516 secs using 399.1% CPU
Optimizing NNI: done in 2.93515 secs using 398.6% CPU
Optimizing NNI: done in 2.54732 secs using 399.1% CPU
  7  LG+R4         106054.268   541 213190.536   799634.536   215368.529
Optimizing NNI: done in 2.78878 secs using 398.4% CPU
Optimizing NNI: done in 2.08686 secs using 397.6% CPU
Threads: 7 / Time: 33.753 sec / Speedup: 2.890 / Efficiency: 41% / LogL: -471723
Determining AUTO threadcount: done in 313.356 secs using 316.7% CPU
BEST NUMBER OF THREADS: 6

Perform fast likelihood tree search using LG+G model...
CHECKPOINT: Tree restored, LogL: -195489.756
NOTE: ModelFinder requires 455 MB RAM!
ModelFinder will test up to 616 protein models (sample size: 575) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  LG            200322.611   987 402619.222   2352931.222  406916.985
  2  LG+G4         195470.344   988 392916.688   2347180.688  397218.805
  3  LG+R2         196589.598   989 395157.196   2353377.196  399463.668
  4  LG+R3         195780.340   991 393542.681   2359686.681  397857.862
  5  LG+R4         195429.122   993 392844.244   2366928.244  397168.133
  6  LG+R5         195312.276   995 392614.553   2374654.553  396947.151
  7  LG+R6         195240.929   997 392475.859   2382487.859  396817.166
  8  LG+R7         195209.395   999 392416.790   2390416.790  396766.806
  9  LG+R8         195184.144   1001 392370.288   2398374.288  396729.013
 10  LG+R9         195175.348   1003 392356.697   2406380.697  396724.130
 11  LG+R10        195171.997   1005 392353.994   2414413.994  396730.135
 20  LG+F+R8       194402.294   1020 390844.587   2473684.587  395286.045
 21  LG+F+R9       194396.917   1022 390837.834   2481849.834  395288.000
 31  WAG+R8        196252.507   1001 394507.014   2400511.014  398865.738
 32  WAG+R9        196242.300   1003 394490.599   2408514.599  398858.033
 33  WAG+R10       196241.628   1005 394493.256   2416553.256  398869.398
 42  WAG+F+R8      194842.645   1020 391725.291   2474565.291  396166.748
 43  WAG+F+R9      194839.005   1022 391722.011   2482734.011  396172.177
 53  JTT+R8        195608.757   1001 393219.514   2399223.514  397578.238
 54  JTT+R9        195593.125   1003 393192.250   2407216.250  397559.683
 55  JTT+R10       195590.207   1005 393190.414   2415250.414  397566.556
 64  JTT+F+R8      194695.864   1020 391431.729   2474271.729  395873.186
 65  JTT+F+R9      194690.743   1022 391425.486   2482437.486  395875.652
WARNING: Normalizing state frequencies so that sum of them equals to 1
 75  Q.pfam+R8     194892.568   1001 391787.135   2397791.135  396145.860
WARNING: Normalizing state frequencies so that sum of them equals to 1
 76  Q.pfam+R9     194887.665   1003 391781.330   2405805.330  396148.763
WARNING: Normalizing state frequencies so that sum of them equals to 1
 86  Q.pfam+F+R8   194521.401   1020 391082.801   2473922.801  395524.259
WARNING: Normalizing state frequencies so that sum of them equals to 1
 87  Q.pfam+F+R9   194515.431   1022 391074.862   2482086.862  395525.029
WARNING: Normalizing state frequencies so that sum of them equals to 1
 97  Q.bird+R8     197829.393   1001 397660.786   2403664.786  402019.511
WARNING: Normalizing state frequencies so that sum of them equals to 1
 98  Q.bird+R9     197820.275   1003 397646.550   2411670.550  402013.983
WARNING: Normalizing state frequencies so that sum of them equals to 1
 99  Q.bird+R10    197814.318   1005 397638.636   2419698.636  402014.778
WARNING: Normalizing state frequencies so that sum of them equals to 1
108  Q.bird+F+R8   198079.035   1020 398198.069   2481038.069  402639.527
WARNING: Normalizing state frequencies so that sum of them equals to 1
109  Q.bird+F+R9   198072.616   1022 398189.232   2489201.232  402639.398
WARNING: Normalizing state frequencies so that sum of them equals to 1
110  Q.bird+F+R10  198068.569   1024 398185.139   2497385.139  402644.014
WARNING: Normalizing state frequencies so that sum of them equals to 1
119  Q.mammal+R8   196715.407   1001 395432.814   2401436.814  399791.538
WARNING: Normalizing state frequencies so that sum of them equals to 1
120  Q.mammal+R9   196707.402   1003 395420.804   2409444.804  399788.237
WARNING: Normalizing state frequencies so that sum of them equals to 1
121  Q.mammal+R10  196703.479   1005 395416.958   2417476.958  399793.100
WARNING: Normalizing state frequencies so that sum of them equals to 1
130  Q.mammal+F+R8 196877.834   1020 395795.669   2478635.669  400237.126
WARNING: Normalizing state frequencies so that sum of them equals to 1
131  Q.mammal+F+R9 196872.663   1022 395789.327   2486801.327  400239.493
141  Q.insect+R8   195081.318   1001 392164.635   2398168.635  396523.360
142  Q.insect+R9   195076.551   1003 392159.102   2406183.102  396526.535
152  Q.insect+F+R8 194860.269   1020 391760.539   2474600.539  396201.996
153  Q.insect+F+R9 194858.288   1022 391760.576   2482772.576  396210.742
WARNING: Normalizing state frequencies so that sum of them equals to 1
163  Q.plant+R8    194919.373   1001 391840.745   2397844.745  396199.470
WARNING: Normalizing state frequencies so that sum of them equals to 1
164  Q.plant+R9    194913.090   1003 391832.180   2405856.180  396199.613
WARNING: Normalizing state frequencies so that sum of them equals to 1
174  Q.plant+F+R8  194822.604   1020 391685.208   2474525.208  396126.665
WARNING: Normalizing state frequencies so that sum of them equals to 1
175  Q.plant+F+R9  194819.592   1022 391683.184   2482695.184  396133.350
WARNING: Normalizing state frequencies so that sum of them equals to 1
185  Q.yeast+R8    195446.700   1001 392895.400   2398899.400  397254.125
WARNING: Normalizing state frequencies so that sum of them equals to 1
186  Q.yeast+R9    195439.881   1003 392885.762   2406909.762  397253.195
WARNING: Normalizing state frequencies so that sum of them equals to 1
187  Q.yeast+R10   195435.549   1005 392881.097   2414941.097  397257.239
WARNING: Normalizing state frequencies so that sum of them equals to 1
196  Q.yeast+F+R8  194579.068   1020 391198.136   2474038.136  395639.593
WARNING: Normalizing state frequencies so that sum of them equals to 1
197  Q.yeast+F+R9  194573.538   1022 391191.077   2482203.077  395641.243
207  JTTDCMut+R8   195684.064   1001 393370.127   2399374.127  397728.852
208  JTTDCMut+R9   195667.689   1003 393341.377   2407365.377  397708.810
209  JTTDCMut+R10  195664.727   1005 393339.454   2415399.454  397715.596
218  JTTDCMut+F+R8 194737.502   1020 391515.003   2474355.003  395956.461
219  JTTDCMut+F+R9 194732.541   1022 391509.083   2482521.083  395959.249
229  DCMut+R8      198858.399   1001 399718.798   2405722.798  404077.523
230  DCMut+R9      198850.908   1003 399707.816   2413731.816  404075.249
231  DCMut+R10     198848.803   1005 399707.606   2421767.606  404083.748
240  DCMut+F+R8    196826.536   1020 395693.071   2478533.071  400134.529
241  DCMut+F+R9    196816.360   1022 395676.721   2486688.721  400126.887
242  DCMut+F+R10   196813.450   1024 395674.901   2494874.901  400133.776
251  VT+R8         196235.054   1001 394472.109   2400476.109  398830.833
252  VT+R9         196229.175   1003 394464.350   2408488.350  398831.783
262  VT+F+R8       195084.460   1020 392208.920   2475048.920  396650.377
263  VT+F+R9       195080.573   1022 392205.145   2483217.145  396655.311
273  PMB+R8        197315.374   1001 396632.748   2402636.748  400991.472
274  PMB+R9        197308.918   1003 396623.836   2410647.836  400991.269
275  PMB+R10       197306.392   1005 396622.785   2418682.785  400998.926
284  PMB+F+R8      197173.282   1020 396386.563   2479226.563  400828.020
285  PMB+F+R9      197172.042   1022 396388.084   2487400.084  400838.251
295  Blosum62+R8   197539.412   1001 397080.824   2403084.824  401439.549
296  Blosum62+R9   197530.232   1003 397066.464   2411090.464  401433.897
297  Blosum62+R10  197526.017   1005 397062.034   2419122.034  401438.175
306  Blosum62+F+R8 196901.090   1020 395842.180   2478682.180  400283.637
307  Blosum62+F+R9 196899.776   1022 395843.552   2486855.552  400293.718
317  Dayhoff+R8    198852.273   1001 399706.545   2405710.545  404065.270
318  Dayhoff+R9    198844.881   1003 399695.761   2413719.761  404063.195
319  Dayhoff+R10   198842.886   1005 399695.772   2421755.772  404071.914
328  Dayhoff+F+R8  196817.472   1020 395674.945   2478514.945  400116.402
329  Dayhoff+F+R9  196807.436   1022 395658.873   2486670.873  400109.039
330  Dayhoff+F+R10 196804.462   1024 395656.923   2494856.923  400115.798
339  mtREV+R8      202211.703   1001 406425.405   2412429.405  410784.129
340  mtREV+R9      202203.018   1003 406412.035   2420436.035  410779.468
341  mtREV+R10     202198.737   1005 406407.475   2428467.475  410783.617
350  mtREV+F+R8    197257.838   1020 396555.675   2479395.675  400997.133
351  mtREV+F+R9    197248.935   1022 396541.871   2487553.871  400992.037
352  mtREV+F+R10   197245.156   1024 396538.312   2495738.312  400997.187
361  mtART+R8      203583.239   1001 409168.478   2415172.478  413527.203
362  mtART+R9      203529.654   1003 409065.309   2423089.309  413432.742
363  mtART+R10     203525.582   1005 409061.164   2431121.164  413437.306
372  mtART+F+R8    200433.253   1020 402906.506   2485746.506  407347.963
373  mtART+F+R9    200385.741   1022 402815.481   2493827.481  407265.647
374  mtART+F+R10   200379.364   1024 402806.728   2502006.728  407265.603
383  mtZOA+R8      198366.129   1001 398734.257   2404738.257  403092.982
384  mtZOA+R9      198360.117   1003 398726.235   2412750.235  403093.668
394  mtZOA+F+R8    196919.533   1020 395879.066   2478719.066  400320.523
395  mtZOA+F+R9    196898.434   1022 395840.867   2486852.867  400291.033
396  mtZOA+F+R10   196891.474   1024 395830.948   2495030.948  400289.823
405  mtMet+R8      200042.427   1001 402086.853   2408090.853  406445.578
406  mtMet+R9      200019.941   1003 402045.882   2416069.882  406413.316
407  mtMet+R10     200049.839   1005 402109.679   2424169.679  406485.821
416  mtMet+F+R8    196455.394   1020 394950.789   2477790.789  399392.246
417  mtMet+F+R9    196440.614   1022 394925.229   2485937.229  399375.395
418  mtMet+F+R10   196431.320   1024 394910.641   2494110.641  399369.516
427  mtVer+R8      203014.713   1001 408031.426   2414035.426  412390.150
428  mtVer+R9      203008.014   1003 408022.029   2422046.029  412389.462
429  mtVer+R10     202969.843   1005 407949.685   2430009.685  412325.827
438  mtVer+F+R8    198883.127   1020 399806.254   2482646.254  404247.711
439  mtVer+F+R9    198874.584   1022 399793.168   2490805.168  404243.334
440  mtVer+F+R10   198869.999   1024 399787.998   2498987.998  404246.873
449  mtInv+R8      200418.426   1001 402838.852   2408842.852  407197.577
450  mtInv+R9      200410.477   1003 402826.954   2416850.954  407194.387
451  mtInv+R10     200408.596   1005 402827.192   2424887.192  407203.334
460  mtInv+F+R8    195221.172   1020 392482.344   2475322.344  396923.802
461  mtInv+F+R9    195216.016   1022 392476.033   2483488.033  396926.199
471  mtMAM+R8      207137.637   1001 416277.273   2422281.273  420635.998
472  mtMAM+R9      207095.777   1003 416197.555   2430221.555  420564.988
473  mtMAM+R10     207079.072   1005 416168.143   2438228.143  420544.285
482  mtMAM+F+R8    202259.202   1020 406558.403   2489398.403  410999.861
483  mtMAM+F+R9    202225.832   1022 406495.663   2497507.663  410945.830
484  mtMAM+F+R10   202217.624   1024 406483.248   2505683.248  410942.123
WARNING: Normalizing state frequencies so that sum of them equals to 1
493  FLAVI+R8      202777.540   1001 407557.080   2413561.080  411915.804
WARNING: Normalizing state frequencies so that sum of them equals to 1
494  FLAVI+R9      202768.495   1003 407542.991   2421566.991  411910.424
WARNING: Normalizing state frequencies so that sum of them equals to 1
495  FLAVI+R10     202753.049   1005 407516.099   2429576.099  411892.240
WARNING: Normalizing state frequencies so that sum of them equals to 1
504  FLAVI+F+R8    202442.661   1020 406925.322   2489765.322  411366.780
WARNING: Normalizing state frequencies so that sum of them equals to 1
505  FLAVI+F+R9    202434.692   1022 406913.384   2497925.384  411363.551
WARNING: Normalizing state frequencies so that sum of them equals to 1
506  FLAVI+F+R10   202428.582   1024 406905.164   2506105.164  411364.039
515  HIVb+R8       200393.670   1001 402789.341   2408793.341  407148.065
516  HIVb+R9       200381.791   1003 402769.582   2416793.582  407137.016
517  HIVb+R10      200371.459   1005 402752.918   2424812.918  407129.060
526  HIVb+F+R8     198771.236   1020 399582.473   2482422.473  404023.930
527  HIVb+F+R9     198764.928   1022 399573.855   2490585.855  404024.021
537  HIVw+R8       209399.096   1001 420800.192   2426804.192  425158.916
538  HIVw+R9       209380.617   1003 420767.234   2434791.234  425134.668
539  HIVw+R10      209376.097   1005 420762.193   2442822.193  425138.335
548  HIVw+F+R8     204961.158   1020 411962.315   2494802.315  416403.773
549  HIVw+F+R9     204951.516   1022 411947.031   2502959.031  416397.198
550  HIVw+F+R10    204945.555   1024 411939.109   2511139.109  416397.984
559  FLU+R8        200582.056   1001 403166.112   2409170.112  407524.836
560  FLU+R9        200563.618   1003 403133.235   2417157.235  407500.668
561  FLU+R10       200558.394   1005 403126.789   2425186.789  407502.931
570  FLU+F+R8      199008.285   1020 400056.570   2482896.570  404498.027
571  FLU+F+R9      198994.223   1022 400032.445   2491044.445  404482.611
572  FLU+F+R10     198990.836   1024 400029.672   2499229.672  404488.547
581  rtREV+R8      198734.452   1001 399470.904   2405474.904  403829.628
582  rtREV+R9      198720.690   1003 399447.380   2413471.380  403814.813
583  rtREV+R10     198718.347   1005 399446.693   2421506.693  403822.835
592  rtREV+F+R8    196515.045   1020 395070.090   2477910.090  399511.547
593  rtREV+F+R9    196508.638   1022 395061.277   2486073.277  399511.443
594  rtREV+F+R10   196506.672   1024 395061.344   2494261.344  399520.219
603  cpREV+R8      196528.431   1001 395058.861   2401062.861  399417.586
604  cpREV+R9      196515.402   1003 395036.804   2409060.804  399404.237
605  cpREV+R10     196510.888   1005 395031.776   2417091.776  399407.918
614  cpREV+F+R8    195115.409   1020 392270.817   2475110.817  396712.275
615  cpREV+F+R9    195110.263   1022 392264.525   2483276.525  396714.691
Akaike Information Criterion:           LG+F+R9
Corrected Akaike Information Criterion: LG+G4
Bayesian Information Criterion:         LG+F+R8
Best-fit model: LG+F+R8 chosen according to BIC

All model information printed to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz
CPU time for ModelFinder: 995.666 seconds (0h:16m:35s)
Wall-clock time for ModelFinder: 313.661 seconds (0h:5m:13s)

===> START BOOTSTRAP REPLICATE NUMBER 1

Creating bootstrap alignment (seed: 70464)...

CHECKPOINT: Initial tree restored

NOTE: 232 MB RAM (0 GB) is required!
CHECKPOINT: Model parameters restored, LogL: -194001.081
Wrote distance file to... 
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
CHECKPOINT: Candidate tree set restored, best LogL: -192267.667
Finish initializing candidate tree set (20)
Current best tree score: -192267.667 / CPU time: 0.000
Number of iterations: 479
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.84759 secs using 399% CPU
Optimizing NNI: done in 1.78818 secs using 398.2% CPU
Optimizing NNI: done in 1.6646 secs using 399.2% CPU
Optimizing NNI: done in 1.68814 secs using 398.9% CPU
Optimizing NNI: done in 1.58823 secs using 398.9% CPU
Iteration 120 / LogL: -62135.010 / Time: 0h:0m:30s (0h:0m:20s left)
Optimizing NNI: done in 7.68704 secs using 597.4% CPU
Iteration 480 / LogL: -192673.453 / Time: 0h:0m:7s (0h:0m:0s left)
Optimizing NNI: done in 1.52715 secs using 398.7% CPU
Optimizing NNI: done in 1.84848 secs using 398.6% CPU
Optimizing NNI: done in 1.75098 secs using 398.7% CPU
Optimizing NNI: done in 1.63821 secs using 398.8% CPU
Optimizing NNI: done in 7.5224 secs using 597.2% CPU
Optimizing NNI: done in 1.57828 secs using 399.4% CPU
Optimizing NNI: done in 1.95266 secs using 399.3% CPU
Optimizing NNI: done in 1.8394 secs using 399.4% CPU
Optimizing NNI: done in 5.31468 secs using 595.3% CPU
Optimizing NNI: done in 1.93607 secs using 399% CPU
Optimizing NNI: done in 1.71815 secs using 399% CPU
Optimizing NNI: done in 1.93097 secs using 399% CPU
Iteration 130 / LogL: -62141.829 / Time: 0h:0m:47s (0h:0m:26s left)
Optimizing NNI: done in 5.59452 secs using 596.5% CPU
Optimizing NNI: done in 1.8776 secs using 399.2% CPU
Optimizing NNI: done in 1.78599 secs using 398.8% CPU
  8  LG+R5         105754.826   543 212595.653   803379.653   214781.698
Optimizing NNI: done in 1.9499 secs using 398.9% CPU
Optimizing NNI: done in 4.85523 secs using 597.8% CPU
Optimizing NNI: done in 1.70309 secs using 399% CPU
Optimizing NNI: done in 1.81511 secs using 399.1% CPU
Optimizing NNI: done in 1.66351 secs using 399.3% CPU
Optimizing NNI: done in 5.76385 secs using 597.3% CPU
Optimizing NNI: done in 2.14911 secs using 398.7% CPU
Optimizing NNI: done in 2.17413 secs using 399.1% CPU
Optimizing NNI: done in 1.85311 secs using 399% CPU
Optimizing NNI: done in 5.73534 secs using 597.1% CPU
Optimizing NNI: done in 1.84278 secs using 399.5% CPU
Iteration 140 / LogL: -63092.737 / Time: 0h:1m:6s (0h:0m:29s left)
Optimizing NNI: done in 2.21105 secs using 399% CPU
Optimizing NNI: done in 4.84026 secs using 597.7% CPU
Optimizing NNI: done in 1.88939 secs using 398.7% CPU
Optimizing NNI: done in 2.13927 secs using 398.8% CPU
Optimizing NNI: done in 2.30689 secs using 399.2% CPU
Optimizing NNI: done in 5.49774 secs using 597.2% CPU
Optimizing NNI: done in 1.83465 secs using 399.1% CPU
Optimizing NNI: done in 1.98735 secs using 399.1% CPU
Optimizing NNI: done in 4.74788 secs using 597.5% CPU
Optimizing NNI: done in 1.60505 secs using 399.2% CPU
Optimizing NNI: done in 1.91424 secs using 399.1% CPU
Optimizing NNI: done in 1.98255 secs using 399.1% CPU
Optimizing NNI: done in 5.6163 secs using 597.4% CPU
Iteration 490 / LogL: -192760.468 / Time: 0h:1m:3s (0h:0m:2s left)
Optimizing NNI: done in 1.82122 secs using 398.8% CPU
Iteration 150 / LogL: -62081.142 / Time: 0h:1m:26s (0h:0m:30s left)
Optimizing NNI: done in 1.91593 secs using 398.8% CPU
Optimizing NNI: done in 2.08004 secs using 399% CPU
  9  LG+R6         105626.270   545 212342.539   807482.539   214536.636
Optimizing NNI: done in 1.83343 secs using 399% CPU
Optimizing NNI: done in 5.94874 secs using 598% CPU
Optimizing NNI: done in 1.57505 secs using 398.9% CPU
Optimizing NNI: done in 1.99173 secs using 398.8% CPU
Optimizing NNI: done in 1.70348 secs using 399.7% CPU
Optimizing NNI: done in 6.17085 secs using 597.8% CPU
Optimizing NNI: done in 1.80842 secs using 397.7% CPU
Optimizing NNI: done in 1.74396 secs using 399.6% CPU
Optimizing NNI: done in 1.63925 secs using 398.6% CPU
Optimizing NNI: done in 5.41577 secs using 597.2% CPU
Optimizing NNI: done in 2.16268 secs using 398.6% CPU
Iteration 160 / LogL: -62089.158 / Time: 0h:1m:45s (0h:0m:27s left)
Optimizing NNI: done in 1.69836 secs using 398.7% CPU
Optimizing NNI: done in 1.96874 secs using 398.7% CPU
Optimizing NNI: done in 5.32316 secs using 597.5% CPU
Optimizing NNI: done in 1.51179 secs using 398.2% CPU
Optimizing NNI: done in 1.85646 secs using 399.4% CPU
Optimizing NNI: done in 1.75398 secs using 398.8% CPU
Optimizing NNI: done in 5.51719 secs using 597.9% CPU
Optimizing NNI: done in 2.09895 secs using 398.8% CPU
Optimizing NNI: done in 2.1741 secs using 399% CPU
Optimizing NNI: done in 4.12249 secs using 598.1% CPU
Optimizing NNI: done in 1.83925 secs using 399.1% CPU
Optimizing NNI: done in 2.02245 secs using 399.4% CPU
Optimizing NNI: done in 1.85535 secs using 398.9% CPU
Iteration 170 / LogL: -62093.604 / Time: 0h:2m:4s (0h:0m:23s left)
Optimizing NNI: done in 1.76473 secs using 398.7% CPU
Optimizing NNI: done in 7.14929 secs using 597.4% CPU
Optimizing NNI: done in 2.20358 secs using 398.9% CPU
Optimizing NNI: done in 1.57143 secs using 398.8% CPU
Optimizing NNI: done in 1.70039 secs using 398.5% CPU
Optimizing NNI: done in 1.62739 secs using 399% CPU
Optimizing NNI: done in 7.63625 secs using 597.6% CPU
Optimizing NNI: done in 1.49891 secs using 398.6% CPU
Optimizing NNI: done in 1.59397 secs using 398.7% CPU
Optimizing NNI: done in 1.61928 secs using 399.3% CPU
Optimizing NNI: done in 1.77336 secs using 398.9% CPU
Optimizing NNI: done in 5.69443 secs using 597.2% CPU
Optimizing NNI: done in 1.63446 secs using 399.3% CPU
Iteration 180 / LogL: -62151.646 / Time: 0h:2m:21s (0h:0m:17s left)
Optimizing NNI: done in 1.66367 secs using 399.2% CPU
Optimizing NNI: done in 2.13677 secs using 399.2% CPU
 10  LG+R7         105558.674   547 212211.348   811723.348   214413.497
Optimizing NNI: done in 1.86063 secs using 399.5% CPU
Optimizing NNI: done in 8.07008 secs using 597.5% CPU
Iteration 500 / LogL: -192704.076 / Time: 0h:2m:5s (0h:0m:2s left)
Optimizing NNI: done in 1.69537 secs using 399.1% CPU
Optimizing NNI: done in 2.06427 secs using 398.4% CPU
Optimizing NNI: done in 1.41296 secs using 398.7% CPU
Optimizing NNI: done in 1.96219 secs using 399% CPU
Optimizing NNI: done in 6.08404 secs using 597.6% CPU
Optimizing NNI: done in 1.95238 secs using 398.3% CPU
Optimizing NNI: done in 2.30583 secs using 399% CPU
Optimizing NNI: done in 5.34279 secs using 597.7% CPU
Optimizing NNI: done in 1.74047 secs using 399.3% CPU
Iteration 190 / LogL: -62148.100 / Time: 0h:2m:40s (0h:0m:10s left)
Optimizing NNI: done in 1.63135 secs using 399.2% CPU
Optimizing NNI: done in 1.57333 secs using 398.9% CPU
Optimizing NNI: done in 4.64789 secs using 597.4% CPU
Optimizing NNI: done in 1.82415 secs using 399.3% CPU
Optimizing NNI: done in 1.57031 secs using 398.9% CPU
Optimizing NNI: done in 1.83282 secs using 398.5% CPU
Optimizing NNI: done in 4.44137 secs using 597.7% CPU
Optimizing NNI: done in 1.90781 secs using 399% CPU
Optimizing NNI: done in 1.90794 secs using 398.7% CPU
Optimizing NNI: done in 5.12227 secs using 597.2% CPU
Optimizing NNI: done in 1.75736 secs using 399.4% CPU
Optimizing NNI: done in 1.72074 secs using 398.2% CPU
Optimizing NNI: done in 1.60161 secs using 399.1% CPU
Iteration 200 / LogL: -62116.572 / Time: 0h:2m:57s (0h:0m:1s left)
Optimizing NNI: done in 5.09965 secs using 597.9% CPU
Optimizing NNI: done in 2.07345 secs using 399% CPU
Optimizing NNI: done in 1.63753 secs using 399.3% CPU
Optimizing NNI: done in 1.59261 secs using 399.2% CPU
TREE SEARCH COMPLETED AFTER 203 ITERATIONS / Time: 0h:3m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -62513.162
2. Current log-likelihood: -62236.797
3. Current log-likelihood: -62236.119
4. Current log-likelihood: -62236.048
Optimizing NNI: done in 6.24186 secs using 597.8% CPU
5. Current log-likelihood: -62236.026
Optimal log-likelihood: -62236.016
Site proportion and rates:  (0.081,0.054) (0.122,0.168) (0.135,0.359) (0.205,0.595) (0.190,0.969) (0.100,1.612) (0.138,2.251) (0.028,5.222)
Parameters optimization took 5 rounds (3.512 sec)
BEST SCORE FOUND : -62236.016
Total tree length: 48.447

Total number of iterations: 203
CPU time used for tree search: 730.038 sec (0h:12m:10s)
Wall-clock time used for tree search: 183.030 sec (0h:3m:3s)
Total CPU time used: 744.209 sec (0h:12m:24s)
Total wall-clock time used: 186.594 sec (0h:3m:6s)

===> START BOOTSTRAP REPLICATE NUMBER 10

Creating bootstrap alignment (seed: 67472)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.057 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61313.942
2. Current log-likelihood: -60675.358
3. Current log-likelihood: -60662.092
4. Current log-likelihood: -60656.998
5. Current log-likelihood: -60651.817
6. Current log-likelihood: -60643.084
Optimizing NNI: done in 5.63419 secs using 597.4% CPU
7. Current log-likelihood: -60641.866
8. Current log-likelihood: -60641.530
9. Current log-likelihood: -60641.305
10. Current log-likelihood: -60641.148
11. Current log-likelihood: -60641.005
12. Current log-likelihood: -60640.846
13. Current log-likelihood: -60640.648
14. Current log-likelihood: -60640.376
15. Current log-likelihood: -60639.974
Optimizing NNI: done in 6.14848 secs using 597.6% CPU
16. Current log-likelihood: -60639.406
17. Current log-likelihood: -60638.808
18. Current log-likelihood: -60638.322
19. Current log-likelihood: -60637.944
20. Current log-likelihood: -60637.635
21. Current log-likelihood: -60637.375
22. Current log-likelihood: -60637.160
23. Current log-likelihood: -60636.985
Optimizing NNI: done in 5.50851 secs using 597.3% CPU
Iteration 510 / LogL: -192738.213 / Time: 0h:3m:0s (0h:0m:0s left)
24. Current log-likelihood: -60636.845
25. Current log-likelihood: -60636.730
Optimal log-likelihood: -60636.639
Site proportion and rates:  (0.109,0.058) (0.088,0.195) (0.198,0.359) (0.200,0.679) (0.141,0.972) (0.127,1.609) (0.105,2.396) (0.033,5.356)
Parameters optimization took 25 rounds (17.899 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.13746 secs using 399.8% CPU
Computing ML distances took 1.137642 sec (of wall-clock time) 4.548517 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000420094 secs using 399.9% CPU
Constructing RapidNJ tree: done in 0.00433397 secs using 367.1% CPU
Computing RapidNJ tree took 0.004817 sec (of wall-clock time) 0.018241 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60858.007
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 6.38547 secs using 597.7% CPU
4.962 second
 11  LG+R8         105542.681   549 212183.362   816083.362   214393.563
Computing log-likelihood of 98 initial trees ... 5.347 seconds
Current best score: -60622.994

Do NNI search on 20 best initial trees
Optimizing NNI: done in 7.02444 secs using 597.5% CPU
TREE SEARCH COMPLETED AFTER 512 ITERATIONS / Time: 0h:3m:13s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -194001.081
Optimizing NNI: done in 1.51468 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
2. Current log-likelihood: -193112.227
BETTER TREE FOUND at iteration 1: -60409.586
3. Current log-likelihood: -193107.504
Optimizing NNI: done in 1.11617 secs using 398.7% CPU
4. Current log-likelihood: -193106.937
Optimizing NNI: done in 1.42433 secs using 399.5% CPU
Optimizing NNI: done in 1.57901 secs using 399.2% CPU
5. Current log-likelihood: -193106.828
6. Current log-likelihood: -193106.810
Optimal log-likelihood: -193106.802
Site proportion and rates:  (0.014,0.118) (0.060,0.238) (0.126,0.383) (0.258,0.566) (0.147,0.808) (0.135,1.089) (0.151,1.621) (0.109,2.555)
Parameters optimization took 6 rounds (10.816 sec)
BEST SCORE FOUND : -193106.802
Total tree length: 153.000

Total number of iterations: 512
CPU time used for tree search: 1157.375 sec (0h:19m:17s)
Wall-clock time used for tree search: 193.754 sec (0h:3m:13s)
Total CPU time used: 1222.482 sec (0h:20m:22s)
Total wall-clock time used: 204.698 sec (0h:3m:24s)

===> START BOOTSTRAP REPLICATE NUMBER 2

Creating bootstrap alignment (seed: 70465)...

Optimizing NNI: done in 1.76266 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.317 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194388.944
2. Current log-likelihood: -191844.094
3. Current log-likelihood: -191803.416
BETTER TREE FOUND at iteration 5: -60387.193
4. Current log-likelihood: -191802.516
Optimizing NNI: done in 1.76033 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -60370.904
5. Current log-likelihood: -191802.372
Optimizing NNI: done in 2.0168 secs using 398.9% CPU
6. Current log-likelihood: -191802.268
Optimizing NNI: done in 1.38477 secs using 399.5% CPU
Optimal log-likelihood: -191802.206
Site proportion and rates:  (0.011,0.094) (0.027,0.225) (0.021,0.242) (0.163,0.397) (0.267,0.598) (0.271,0.986) (0.114,1.593) (0.125,2.515)
Parameters optimization took 6 rounds (13.782 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.66715 secs using 399.6% CPU
Optimizing NNI: done in 1.43068 secs using 398.7% CPU
Iteration 10 / LogL: -60440.103 / Time: 0h:0m:57s
Optimizing NNI: done in 1.49629 secs using 398.6% CPU
Optimizing NNI: done in 1.80567 secs using 399.1% CPU
Optimizing NNI: done in 1.50659 secs using 399% CPU
Optimizing NNI: done in 1.64443 secs using 398.4% CPU
Calculating distance matrix: done in 10.2467 secs using 599.8% CPU
Computing ML distances took 10.247275 sec (of wall-clock time) 61.464225 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00145292 secs using 324.2% CPU
Constructing RapidNJ tree: done in 0.0230119 secs using 648.3% CPU
Computing RapidNJ tree took 0.024552 sec (of wall-clock time) 0.153969 sec (of CPU time)
Optimizing NNI: done in 1.74836 secs using 398.7% CPU
Log-likelihood of RapidNJ tree: -196616.101
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.54742 secs using 398.9% CPU
Optimizing NNI: done in 1.7736 secs using 398.7% CPU
Optimizing NNI: done in 1.64703 secs using 399.2% CPU
Optimizing NNI: done in 1.56829 secs using 399.4% CPU
Optimizing NNI: done in 1.53332 secs using 398.4% CPU
Iteration 20 / LogL: -60393.431 / Time: 0h:1m:13s
Finish initializing candidate tree set (20)
Current best tree score: -60370.904 / CPU time: 54.079
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.4207 secs using 399.1% CPU
Optimizing NNI: done in 1.31428 secs using 398.7% CPU
Optimizing NNI: done in 1.59015 secs using 399% CPU
Optimizing NNI: done in 1.2009 secs using 399.6% CPU
Optimizing NNI: done in 1.86093 secs using 398.9% CPU
Optimizing NNI: done in 1.25342 secs using 399.1% CPU
Optimizing NNI: done in 1.55101 secs using 399.1% CPU
Optimizing NNI: done in 1.27738 secs using 399.2% CPU
Optimizing NNI: done in 1.55617 secs using 398.8% CPU
Optimizing NNI: done in 1.64126 secs using 398.9% CPU
Iteration 30 / LogL: -60377.536 / Time: 0h:1m:28s (0h:3m:51s left)
Optimizing NNI: done in 1.51722 secs using 399.2% CPU
Optimizing NNI: done in 1.03136 secs using 399.2% CPU
Optimizing NNI: done in 1.24791 secs using 399.5% CPU
Optimizing NNI: done in 1.36968 secs using 399.1% CPU
Optimizing NNI: done in 1.44874 secs using 399.1% CPU
Optimizing NNI: done in 1.42271 secs using 399.4% CPU
30.322 second
Optimizing NNI: done in 1.53985 secs using 398.5% CPU
Optimizing NNI: done in 1.58037 secs using 399.1% CPU
Optimizing NNI: done in 1.42992 secs using 399.4% CPU
Optimizing NNI: done in 1.56604 secs using 399.2% CPU
Iteration 40 / LogL: -60380.403 / Time: 0h:1m:42s (0h:2m:53s left)
Optimizing NNI: done in 1.15089 secs using 399.1% CPU
Optimizing NNI: done in 1.66514 secs using 398.4% CPU
Optimizing NNI: done in 1.55066 secs using 398.8% CPU
Optimizing NNI: done in 1.27217 secs using 398.9% CPU
Optimizing NNI: done in 1.65452 secs using 399.3% CPU
Optimizing NNI: done in 1.68917 secs using 398.3% CPU
Optimizing NNI: done in 1.08203 secs using 398.8% CPU
Computing log-likelihood of 98 initial trees ... 17.006 seconds
Current best score: -191802.206

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.40124 secs using 398.9% CPU
Optimizing NNI: done in 1.43886 secs using 398.9% CPU
Optimizing NNI: done in 2.84631 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.25384 secs using 399.5% CPU
Iteration 50 / LogL: -60388.463 / Time: 0h:1m:56s (0h:2m:13s left)
Optimizing NNI: done in 1.32056 secs using 398.8% CPU
Optimizing NNI: done in 1.287 secs using 397.5% CPU
BETTER TREE FOUND at iteration 1: -191316.488
Optimizing NNI: done in 1.10165 secs using 399.2% CPU
Optimizing NNI: done in 1.5602 secs using 399% CPU
Optimizing NNI: done in 3.54245 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 56: -60369.386
BETTER TREE FOUND at iteration 2: -191223.406
Optimizing NNI: done in 1.52536 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.72601 secs using 399.3% CPU
Optimizing NNI: done in 1.62721 secs using 398.6% CPU
Iteration 60 / LogL: -60372.184 / Time: 0h:2m:13s (0h:3m:36s left)
Optimizing NNI: done in 1.80177 secs using 398.5% CPU
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Iteration 70 / LogL: -60380.240 / Time: 0h:2m:29s (0h:3m:6s left)
 12  LG+R9         105467.498   551 212036.997   820340.997   214255.249
Optimizing NNI: done in 1.65176 secs using 399.3% CPU
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BETTER TREE FOUND at iteration 3: -191198.530
Optimizing NNI: done in 1.70212 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 80: -60368.318
Iteration 80 / LogL: -60368.318 / Time: 0h:2m:47s (0h:3m:32s left)
Optimizing NNI: done in 4.00724 secs using 596.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.34147 secs using 399.2% CPU
Optimizing NNI: done in 1.35515 secs using 399.1% CPU
BETTER TREE FOUND at iteration 6: -191124.806
Optimizing NNI: done in 1.18003 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.32774 secs using 399.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -191122.169
BETTER TREE FOUND at iteration 87: -60368.072
Optimizing NNI: done in 1.75111 secs using 398.7% CPU
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Iteration 90 / LogL: -60388.043 / Time: 0h:3m:2s (0h:3m:18s left)
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Iteration 10 / LogL: -191257.514 / Time: 0h:2m:28s
Optimizing NNI: done in 1.43281 secs using 398.8% CPU
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Iteration 100 / LogL: -60372.255 / Time: 0h:3m:16s (0h:2m:52s left)
Optimizing NNI: done in 4.08401 secs using 597% CPU
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Iteration 110 / LogL: -60371.457 / Time: 0h:3m:30s (0h:2m:28s left)
Optimizing NNI: done in 1.46412 secs using 398.8% CPU
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Iteration 120 / LogL: -60385.032 / Time: 0h:3m:44s (0h:2m:6s left)
Optimizing NNI: done in 4.03161 secs using 598% CPU
Optimizing NNI: done in 1.72848 secs using 399.1% CPU
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Optimizing NNI: done in 3.38587 secs using 598% CPU
Iteration 20 / LogL: -191325.377 / Time: 0h:3m:7s
Finish initializing candidate tree set (20)
Current best tree score: -191122.169 / CPU time: 161.392
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.41776 secs using 398.8% CPU
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Iteration 130 / LogL: -60385.596 / Time: 0h:3m:58s (0h:1m:45s left)
Optimizing NNI: done in 4.90006 secs using 597.5% CPU
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Iteration 140 / LogL: -60368.755 / Time: 0h:4m:13s (0h:1m:25s left)
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Iteration 150 / LogL: -60369.996 / Time: 0h:4m:27s (0h:1m:6s left)
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Iteration 30 / LogL: -191351.136 / Time: 0h:3m:53s (0h:10m:19s left)
Optimizing NNI: done in 1.82604 secs using 399% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.48947 secs using 399.3% CPU
BETTER TREE FOUND at iteration 31: -191116.156
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Optimizing NNI: done in 1.45633 secs using 399% CPU
Iteration 160 / LogL: -60446.844 / Time: 0h:4m:43s (0h:0m:48s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 33: -191113.217
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Iteration 170 / LogL: -60375.767 / Time: 0h:4m:57s (0h:0m:29s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.48283 secs using 398.5% CPU
BETTER TREE FOUND at iteration 34: -191099.119
Optimizing NNI: done in 1.41299 secs using 398.9% CPU
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Optimizing NNI: done in 1.84304 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
 13  LG+R10        105460.453   553 212026.906   824750.906   214253.210
 14  LG+I+R2       107873.486   538 216822.972   796786.972   218988.888
BETTER TREE FOUND at iteration 176: -60358.815
Optimizing NNI: done in 1.15702 secs using 398.8% CPU
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Iteration 180 / LogL: -60376.128 / Time: 0h:5m:14s (0h:2m:48s left)
 15  LG+I+R3       106444.458   540 213968.917   798248.917   216142.884
Optimizing NNI: done in 4.79182 secs using 597.4% CPU
Optimizing NNI: done in 1.63396 secs using 398.5% CPU
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BETTER TREE FOUND at iteration 184: -60358.810
Optimizing NNI: done in 4.58312 secs using 597.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 186: -60358.698
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 189: -60358.443
Optimizing NNI: done in 4.74306 secs using 597.5% CPU
Iteration 40 / LogL: -191157.872 / Time: 0h:4m:48s (0h:11m:34s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 190: -60344.525
Iteration 190 / LogL: -60344.525 / Time: 0h:5m:30s (0h:2m:55s left)
 16  LG+I+R4       105974.767   542 213033.535   801645.535   215215.554
Optimizing NNI: done in 1.19367 secs using 399.1% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.41986 secs using 399.2% CPU
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BETTER TREE FOUND at iteration 41: -191096.418
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 197: -60342.684
Optimizing NNI: done in 4.41641 secs using 598% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.21263 secs using 597.1% CPU
BETTER TREE FOUND at iteration 200: -60341.936
Iteration 200 / LogL: -60341.936 / Time: 0h:5m:46s (0h:2m:54s left)
Optimizing NNI: done in 1.62056 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.20796 secs using 399.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 204: -60337.134
BETTER TREE FOUND at iteration 44: -191088.768
Optimizing NNI: done in 1.38177 secs using 399.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 208: -60336.901
Optimizing NNI: done in 1.50873 secs using 398.8% CPU
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Iteration 210 / LogL: -60340.763 / Time: 0h:6m:2s (0h:2m:49s left)
Optimizing NNI: done in 5.20848 secs using 597.3% CPU
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 17  LG+I+R5       105697.274   544 212482.548   805442.548   214672.620
Optimizing NNI: done in 4.51089 secs using 597.5% CPU
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Iteration 220 / LogL: -60340.770 / Time: 0h:6m:16s (0h:2m:31s left)
Optimizing NNI: done in 5.44839 secs using 597.3% CPU
Optimizing NNI: done in 1.76113 secs using 399.1% CPU
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Iteration 50 / LogL: -191102.219 / Time: 0h:5m:42s (0h:10m:56s left)
Optimizing NNI: done in 1.45971 secs using 399.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.38663 secs using 398.7% CPU
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BETTER TREE FOUND at iteration 51: -191074.034
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Iteration 230 / LogL: -60359.078 / Time: 0h:6m:31s (0h:2m:13s left)
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 18  LG+I+R6       105569.455   546 212230.910   809554.910   214429.033
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Iteration 240 / LogL: -60336.978 / Time: 0h:6m:45s (0h:1m:55s left)
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Iteration 250 / LogL: -60353.220 / Time: 0h:7m:0s (0h:1m:37s left)
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Iteration 60 / LogL: -191087.862 / Time: 0h:6m:31s (0h:10m:2s left)
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Iteration 260 / LogL: -60355.551 / Time: 0h:7m:15s (0h:1m:20s left)
 19  LG+I+R7       105508.376   548 212112.752   813816.752   214318.926
Optimizing NNI: done in 1.39472 secs using 399.3% CPU
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Iteration 270 / LogL: -60383.643 / Time: 0h:7m:29s (0h:1m:3s left)
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Iteration 280 / LogL: -60393.850 / Time: 0h:7m:44s (0h:0m:46s left)
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 20  LG+I+R8       105493.060   550 212086.120   818186.120   214300.347
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Iteration 290 / LogL: -60348.078 / Time: 0h:7m:59s (0h:0m:29s left)
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Iteration 70 / LogL: -191117.875 / Time: 0h:7m:18s (0h:8m:34s left)
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Iteration 300 / LogL: -60338.530 / Time: 0h:8m:14s (0h:0m:13s left)
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TREE SEARCH COMPLETED AFTER 309 ITERATIONS / Time: 0h:8m:27s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60336.901
2. Current log-likelihood: -60336.889
Optimal log-likelihood: -60336.872
Site proportion and rates:  (0.108,0.057) (0.097,0.192) (0.219,0.380) (0.245,0.749) (0.116,1.192) (0.138,1.946) (0.047,2.721) (0.029,5.889)
Parameters optimization took 2 rounds (0.963 sec)
BEST SCORE FOUND : -60336.872
Total tree length: 48.220

Total number of iterations: 309
CPU time used for tree search: 1930.744 sec (0h:32m:10s)
Wall-clock time used for tree search: 487.627 sec (0h:8m:7s)
Total CPU time used: 2012.480 sec (0h:33m:32s)
Total wall-clock time used: 508.109 sec (0h:8m:28s)

===> START BOOTSTRAP REPLICATE NUMBER 11

Creating bootstrap alignment (seed: 67473)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59003.543
2. Current log-likelihood: -58498.655
3. Current log-likelihood: -58493.374
Optimizing NNI: done in 4.20567 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
4. Current log-likelihood: -58488.106
5. Current log-likelihood: -58483.899
6. Current log-likelihood: -58480.338
7. Current log-likelihood: -58473.448
BETTER TREE FOUND at iteration 77: -191062.056
8. Current log-likelihood: -58467.042
9. Current log-likelihood: -58466.772
Optimal log-likelihood: -58466.757
Site proportion and rates:  (0.124,0.070) (0.072,0.184) (0.124,0.369) (0.139,0.484) (0.203,0.781) (0.126,1.305) (0.194,2.284) (0.017,5.803)
Parameters optimization took 9 rounds (8.455 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09551 secs using 399.6% CPU
Computing ML distances took 1.095701 sec (of wall-clock time) 4.377928 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000371218 secs using 387.1% CPU
Constructing RapidNJ tree: done in 0.00460887 secs using 454.3% CPU
Computing RapidNJ tree took 0.005049 sec (of wall-clock time) 0.023145 sec (of CPU time)
Log-likelihood of RapidNJ tree: -58534.030
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.88421 secs using 597.1% CPU
4.950 second
Optimizing NNI: done in 5.67608 secs using 597.3% CPU
Computing log-likelihood of 98 initial trees ... 5.476 seconds
Current best score: -58397.298

Do NNI search on 20 best initial trees
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Iteration 80 / LogL: -191132.238 / Time: 0h:8m:8s (0h:9m:59s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -58182.450
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 4: -58177.577
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Iteration 10 / LogL: -58213.579 / Time: 0h:0m:43s
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 21  LG+I+R9       105445.525   552 211995.050   822507.050   214217.328
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 18: -58172.046
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Iteration 20 / LogL: -58232.195 / Time: 0h:0m:57s
Finish initializing candidate tree set (20)
Current best tree score: -58172.046 / CPU time: 47.388
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -58160.741
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Iteration 90 / LogL: -191108.766 / Time: 0h:8m:55s (0h:8m:43s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -58151.017
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -58132.456
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Iteration 30 / LogL: -58168.055 / Time: 0h:1m:16s (0h:4m:19s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -58128.248
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Iteration 40 / LogL: -58131.921 / Time: 0h:1m:31s (0h:3m:35s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 42: -58118.004
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 45: -58116.492
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Iteration 50 / LogL: -58127.731 / Time: 0h:1m:47s (0h:3m:29s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 100 / LogL: -191071.247 / Time: 0h:9m:49s (0h:7m:38s left)
BETTER TREE FOUND at iteration 60: -58115.424
Iteration 60 / LogL: -58115.424 / Time: 0h:2m:3s (0h:3m:28s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 70: -58114.017
Iteration 70 / LogL: -58114.017 / Time: 0h:2m:17s (0h:3m:18s left)
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 22  LG+I+R10      105441.190   554 211990.381   826930.381   214220.710
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Iteration 80 / LogL: -58158.317 / Time: 0h:2m:30s (0h:2m:51s left)
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Iteration 90 / LogL: -58118.495 / Time: 0h:2m:43s (0h:2m:27s left)
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UPDATE BEST LOG-LIKELIHOOD: -58114.014
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 43  LG+F+I+R9     105592.352   571 212326.704   865550.704   214625.473
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Iteration 100 / LogL: -58117.276 / Time: 0h:2m:56s (0h:2m:4s left)
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Iteration 120 / LogL: -58121.238 / Time: 0h:3m:22s (0h:1m:25s left)
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Iteration 160 / LogL: -58121.184 / Time: 0h:4m:13s (0h:0m:15s left)
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 44  LG+F+I+R10    105585.680   573 212317.360   870121.360   214624.181
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Optimizing NNI: done in 1.35584 secs using 398.3% CPU
Iteration 170 / LogL: -58129.100 / Time: 0h:4m:27s (0h:0m:0s left)
Optimizing NNI: done in 1.20171 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 171 ITERATIONS / Time: 0h:4m:28s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58114.014
Optimal log-likelihood: -58114.011
Site proportion and rates:  (0.129,0.073) (0.069,0.186) (0.212,0.389) (0.202,0.699) (0.131,1.076) (0.088,1.691) (0.153,2.408) (0.017,5.737)
Parameters optimization took 1 rounds (0.354 sec)
BEST SCORE FOUND : -58114.011
Total tree length: 42.078

Total number of iterations: 171
CPU time used for tree search: 1015.740 sec (0h:16m:55s)
Wall-clock time used for tree search: 258.280 sec (0h:4m:18s)
Total CPU time used: 1057.592 sec (0h:17m:37s)
Total wall-clock time used: 268.761 sec (0h:4m:28s)

===> START BOOTSTRAP REPLICATE NUMBER 12

Creating bootstrap alignment (seed: 67474)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.057 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58695.466
2. Current log-likelihood: -58037.444
Optimizing NNI: done in 4.41807 secs using 597.6% CPU
Iteration 130 / LogL: -191076.599 / Time: 0h:12m:17s (0h:4m:28s left)
3. Current log-likelihood: -58019.751
4. Current log-likelihood: -58009.545
 65  WAG+I+R9      105825.714   552 212755.427   823267.427   214977.705
5. Current log-likelihood: -58003.374
6. Current log-likelihood: -58002.944
Optimal log-likelihood: -58002.860
Site proportion and rates:  (0.094,0.053) (0.102,0.173) (0.127,0.348) (0.096,0.350) (0.238,0.705) (0.135,1.250) (0.166,2.061) (0.044,5.096)
Parameters optimization took 6 rounds (5.527 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.26387 secs using 596.9% CPU
Estimate model parameters (epsilon = 0.100)
Calculating distance matrix: done in 1.10309 secs using 399.9% CPU
Computing ML distances took 1.103297 sec (of wall-clock time) 4.411320 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000344038 secs using 125% CPU
Constructing RapidNJ tree: done in 0.00440478 secs using 287.7% CPU
Computing RapidNJ tree took 0.004823 sec (of wall-clock time) 0.015388 sec (of CPU time)
BETTER TREE FOUND at iteration 131: -191048.592
Log-likelihood of RapidNJ tree: -58108.815
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.10558 secs using 597.7% CPU
5.067 second
Optimizing NNI: done in 4.39379 secs using 597.6% CPU
Computing log-likelihood of 98 initial trees ... 5.600 seconds
Current best score: -57976.640

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.30213 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.42919 secs using 597.3% CPU
BETTER TREE FOUND at iteration 1: -57776.283
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.21831 secs using 597.9% CPU
BETTER TREE FOUND at iteration 9: -57772.295
Optimizing NNI: done in 1.48792 secs using 399.2% CPU
Iteration 10 / LogL: -57801.417 / Time: 0h:0m:34s
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Iteration 140 / LogL: -191077.348 / Time: 0h:13m:1s (0h:8m:31s left)
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Iteration 20 / LogL: -57858.246 / Time: 0h:0m:49s
Finish initializing candidate tree set (20)
Current best tree score: -57772.295 / CPU time: 42.018
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -57770.377
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -57754.823
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -57753.576
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Iteration 30 / LogL: -57816.089 / Time: 0h:1m:9s (0h:3m:55s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.37836 secs using 597.2% CPU
BETTER TREE FOUND at iteration 31: -57747.437
 66  WAG+I+R10     105818.713   554 212745.426   827685.426   214975.756
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 87  WAG+F+I+R9    105739.658   571 212621.315   865845.315   214920.085
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Iteration 40 / LogL: -58625.780 / Time: 0h:1m:27s (0h:3m:23s left)
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Iteration 150 / LogL: -191153.791 / Time: 0h:13m:45s (0h:7m:28s left)
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Iteration 50 / LogL: -57757.346 / Time: 0h:1m:43s (0h:2m:51s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 57: -57747.376
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Iteration 60 / LogL: -57748.230 / Time: 0h:2m:0s (0h:3m:18s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 61: -57737.037
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Iteration 160 / LogL: -191159.183 / Time: 0h:14m:29s (0h:6m:27s left)
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 88  WAG+F+I+R10   105738.445   573 212622.890   870426.890   214929.712
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 89: -57735.366
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109  JTT+I+R9      105305.437   552 211714.874   822226.874   213937.152
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Iteration 170 / LogL: -191088.218 / Time: 0h:15m:13s (0h:5m:29s left)
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BETTER TREE FOUND at iteration 96: -57735.366
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Iteration 100 / LogL: -57814.574 / Time: 0h:3m:7s (0h:3m:1s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 136: -57735.011
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 150: -57733.393
Iteration 150 / LogL: -57733.393 / Time: 0h:4m:37s (0h:3m:6s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 151: -57732.953
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110  JTT+I+R10     105305.462   554 211718.924   826658.924   213949.254
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Optimizing NNI: done in 1.67711 secs using 399.1% CPU
Optimizing NNI: done in 1.81265 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.20377 secs using 597.3% CPU
131  JTT+F+I+R9    105431.332   571 212004.663   865228.663   214303.432
BETTER TREE FOUND at iteration 174: -57732.370
Optimizing NNI: done in 1.58896 secs using 399.5% CPU
Optimizing NNI: done in 1.63657 secs using 399.2% CPU
Optimizing NNI: done in 4.15724 secs using 597% CPU
Optimizing NNI: done in 1.47526 secs using 399.3% CPU
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Optimizing NNI: done in 4.45808 secs using 597.5% CPU
Optimizing NNI: done in 1.70664 secs using 398.9% CPU
Optimizing NNI: done in 1.87964 secs using 399% CPU
Iteration 180 / LogL: -57742.920 / Time: 0h:5m:29s (0h:2m:52s left)
Optimizing NNI: done in 1.67036 secs using 399% CPU
Optimizing NNI: done in 4.45638 secs using 597.9% CPU
Optimizing NNI: done in 1.49643 secs using 398.6% CPU
Optimizing NNI: done in 1.2045 secs using 399.2% CPU
Optimizing NNI: done in 1.64898 secs using 399.3% CPU
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Optimizing NNI: done in 1.92537 secs using 398.6% CPU
Optimizing NNI: done in 4.12385 secs using 597.7% CPU
Optimizing NNI: done in 1.48528 secs using 399.3% CPU
Optimizing NNI: done in 1.59486 secs using 399.1% CPU
Optimizing NNI: done in 1.31106 secs using 398.8% CPU
Optimizing NNI: done in 3.95836 secs using 597.2% CPU
Optimizing NNI: done in 1.68063 secs using 398.9% CPU
Iteration 190 / LogL: -57734.026 / Time: 0h:5m:44s (0h:2m:33s left)
Optimizing NNI: done in 1.78298 secs using 398.7% CPU
Optimizing NNI: done in 1.68313 secs using 398.8% CPU
Optimizing NNI: done in 4.41472 secs using 596.6% CPU
Optimizing NNI: done in 1.80198 secs using 398.8% CPU
Optimizing NNI: done in 1.91024 secs using 399.6% CPU
Optimizing NNI: done in 4.17832 secs using 597.9% CPU
Iteration 210 / LogL: -191220.926 / Time: 0h:18m:8s (0h:1m:49s left)
Optimizing NNI: done in 1.63686 secs using 399.1% CPU
Optimizing NNI: done in 1.7214 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 196: -57732.090
Optimizing NNI: done in 4.79651 secs using 597.7% CPU
Optimizing NNI: done in 1.79349 secs using 398.9% CPU
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Optimizing NNI: done in 4.08017 secs using 597.8% CPU
Optimizing NNI: done in 1.93835 secs using 399.3% CPU
Optimizing NNI: done in 1.62376 secs using 398.7% CPU
Iteration 200 / LogL: -57750.126 / Time: 0h:6m:3s (0h:2m:55s left)
Optimizing NNI: done in 3.93754 secs using 597.2% CPU
Optimizing NNI: done in 1.82813 secs using 399% CPU
Optimizing NNI: done in 1.67126 secs using 399.4% CPU
Optimizing NNI: done in 1.8617 secs using 398.8% CPU
Optimizing NNI: done in 4.35908 secs using 596.9% CPU
Optimizing NNI: done in 1.59652 secs using 398.9% CPU
Optimizing NNI: done in 1.70693 secs using 399% CPU
Optimizing NNI: done in 1.52349 secs using 399.3% CPU
Optimizing NNI: done in 4.38598 secs using 597.2% CPU
Optimizing NNI: done in 1.49335 secs using 398.9% CPU
Optimizing NNI: done in 1.83612 secs using 399.1% CPU
Optimizing NNI: done in 1.20618 secs using 398.8% CPU
Optimizing NNI: done in 4.37452 secs using 597.3% CPU
Optimizing NNI: done in 1.72265 secs using 398.6% CPU
Iteration 210 / LogL: -57751.075 / Time: 0h:6m:20s (0h:2m:36s left)
Optimizing NNI: done in 1.53342 secs using 398.8% CPU
Optimizing NNI: done in 4.35529 secs using 597.3% CPU
Optimizing NNI: done in 1.39007 secs using 398.7% CPU
Optimizing NNI: done in 1.52403 secs using 399% CPU
Optimizing NNI: done in 1.70006 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -57732.088
Optimizing NNI: done in 3.99266 secs using 597.5% CPU
Optimizing NNI: done in 1.73979 secs using 398.8% CPU
Optimizing NNI: done in 1.97628 secs using 398.7% CPU
Optimizing NNI: done in 1.48819 secs using 399.1% CPU
Optimizing NNI: done in 4.75684 secs using 596.6% CPU
Optimizing NNI: done in 1.97354 secs using 399% CPU
Optimizing NNI: done in 1.66359 secs using 398.9% CPU
Optimizing NNI: done in 4.07881 secs using 596.7% CPU
Iteration 220 / LogL: -191192.268 / Time: 0h:18m:52s (0h:0m:56s left)
Optimizing NNI: done in 1.61356 secs using 397.9% CPU
Iteration 220 / LogL: -57738.917 / Time: 0h:6m:37s (0h:2m:17s left)
Optimizing NNI: done in 1.88979 secs using 399.5% CPU
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Optimizing NNI: done in 1.51636 secs using 398.5% CPU
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Optimizing NNI: done in 1.66757 secs using 399.1% CPU
132  JTT+F+I+R10   105424.396   573 211994.792   869798.792   214301.613
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 3.91152 secs using 597.5% CPU
Optimizing NNI: done in 1.71959 secs using 399.1% CPU
Iteration 230 / LogL: -57784.778 / Time: 0h:6m:54s (0h:1m:59s left)
Optimizing NNI: done in 1.75791 secs using 399% CPU
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Optimizing NNI: done in 2.03836 secs using 398.9% CPU
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Optimizing NNI: done in 1.48454 secs using 399.5% CPU
Optimizing NNI: done in 1.64132 secs using 399.2% CPU
153  Q.pfam+I+R9   105274.451   552 211652.902   822164.902   213875.180
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 1.72175 secs using 399.2% CPU
Optimizing NNI: done in 4.69147 secs using 596.5% CPU
Optimizing NNI: done in 1.50919 secs using 399% CPU
Optimizing NNI: done in 1.51767 secs using 398.6% CPU
Optimizing NNI: done in 1.64465 secs using 398.5% CPU
Iteration 240 / LogL: -57896.383 / Time: 0h:7m:10s (0h:1m:40s left)
Optimizing NNI: done in 4.3695 secs using 596.2% CPU
Optimizing NNI: done in 1.6821 secs using 398.7% CPU
Optimizing NNI: done in 1.92413 secs using 399.2% CPU
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Optimizing NNI: done in 1.72118 secs using 398.8% CPU
Optimizing NNI: done in 1.57548 secs using 399.1% CPU
Optimizing NNI: done in 1.897 secs using 398.7% CPU
Optimizing NNI: done in 4.73607 secs using 597.3% CPU
Iteration 230 / LogL: -191066.148 / Time: 0h:19m:36s (0h:0m:5s left)
Optimizing NNI: done in 1.8582 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 246: -57732.070
Optimizing NNI: done in 1.54555 secs using 399.2% CPU
Optimizing NNI: done in 1.53947 secs using 398.5% CPU
Optimizing NNI: done in 4.50978 secs using 597.1% CPU
Optimizing NNI: done in 1.67779 secs using 398.9% CPU
Optimizing NNI: done in 1.7337 secs using 398.7% CPU
Iteration 250 / LogL: -57738.551 / Time: 0h:7m:28s (0h:2m:52s left)
Optimizing NNI: done in 4.22983 secs using 598.3% CPU
TREE SEARCH COMPLETED AFTER 232 ITERATIONS / Time: 0h:19m:45s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -191048.592
Optimizing NNI: done in 1.66487 secs using 398.6% CPU
Optimal log-likelihood: -191048.582
Site proportion and rates:  (0.013,0.103) (0.046,0.238) (0.136,0.379) (0.255,0.564) (0.108,0.804) (0.211,1.046) (0.113,1.639) (0.118,2.545)
Parameters optimization took 1 rounds (1.296 sec)
BEST SCORE FOUND : -191048.582
Total tree length: 157.164

Total number of iterations: 232
CPU time used for tree search: 6776.757 sec (1h:52m:56s)
Wall-clock time used for tree search: 1159.727 sec (0h:19m:19s)
Total CPU time used: 6938.810 sec (1h:55m:38s)
Total wall-clock time used: 1186.929 sec (0h:19m:46s)

===> START BOOTSTRAP REPLICATE NUMBER 3

Creating bootstrap alignment (seed: 70466)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.287 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -195236.309
Optimizing NNI: done in 1.52729 secs using 398.7% CPU
Optimizing NNI: done in 1.39012 secs using 399.4% CPU
2. Current log-likelihood: -192586.016
Optimizing NNI: done in 1.77976 secs using 398.8% CPU
3. Current log-likelihood: -192560.273
Optimizing NNI: done in 1.6332 secs using 399.1% CPU
4. Current log-likelihood: -192554.126
Optimizing NNI: done in 1.83585 secs using 398.7% CPU
Optimizing NNI: done in 1.73722 secs using 398.7% CPU
5. Current log-likelihood: -192544.748
Optimizing NNI: done in 1.41341 secs using 398.8% CPU
6. Current log-likelihood: -192537.008
Optimizing NNI: done in 1.88184 secs using 399.2% CPU
7. Current log-likelihood: -192535.134
Optimizing NNI: done in 1.64415 secs using 398.5% CPU
Iteration 260 / LogL: -57740.590 / Time: 0h:7m:45s (0h:2m:34s left)
Optimizing NNI: done in 1.65804 secs using 398.8% CPU
8. Current log-likelihood: -192534.809
Optimizing NNI: done in 1.57316 secs using 399% CPU
Optimal log-likelihood: -192534.768
Site proportion and rates:  (0.024,0.097) (0.059,0.239) (0.123,0.369) (0.208,0.564) (0.197,0.777) (0.147,1.068) (0.116,1.670) (0.126,2.510)
Parameters optimization took 8 rounds (18.227 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.2225 secs using 398.5% CPU
Optimizing NNI: done in 1.8329 secs using 399% CPU
Optimizing NNI: done in 1.51127 secs using 398.8% CPU
Optimizing NNI: done in 1.71515 secs using 398.9% CPU
Optimizing NNI: done in 1.71409 secs using 398.9% CPU
Optimizing NNI: done in 1.69297 secs using 398.3% CPU
Calculating distance matrix: done in 10.044 secs using 599.6% CPU
Computing ML distances took 10.044524 sec (of wall-clock time) 60.222371 sec (of CPU time)
Optimizing NNI: done in 1.23332 secs using 399.4% CPU
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00130677 secs using 430.1% CPU
Constructing RapidNJ tree: done in 0.0227132 secs using 678.7% CPU
Computing RapidNJ tree took 0.024111 sec (of wall-clock time) 0.161472 sec (of CPU time)
Optimizing NNI: done in 1.51271 secs using 399% CPU
Iteration 270 / LogL: -57735.509 / Time: 0h:8m:1s (0h:2m:15s left)
Log-likelihood of RapidNJ tree: -197016.300
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.25789 secs using 399.1% CPU
Optimizing NNI: done in 1.24955 secs using 399.6% CPU
Optimizing NNI: done in 1.54832 secs using 399% CPU
Optimizing NNI: done in 1.35164 secs using 398.8% CPU
Optimizing NNI: done in 1.43068 secs using 398.6% CPU
Optimizing NNI: done in 1.5065 secs using 398.8% CPU
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Optimizing NNI: done in 2.06861 secs using 398.4% CPU
Optimizing NNI: done in 2.7009 secs using 398.5% CPU
Iteration 280 / LogL: -57809.109 / Time: 0h:8m:18s (0h:1m:57s left)
Optimizing NNI: done in 2.24327 secs using 398.4% CPU
154  Q.pfam+I+R10  105272.708   554 211653.416   826593.416   213883.746
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 2.35926 secs using 398% CPU
Optimizing NNI: done in 2.00559 secs using 398.2% CPU
Optimizing NNI: done in 2.00794 secs using 397.9% CPU
Optimizing NNI: done in 1.55099 secs using 399.2% CPU
Optimizing NNI: done in 1.70222 secs using 398.7% CPU
29.448 second
Optimizing NNI: done in 1.99021 secs using 398.5% CPU
Optimizing NNI: done in 1.79725 secs using 399.1% CPU
175  Q.pfam+F+I+R9 105612.280   571 212366.559   865590.559   214665.329
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 1.48612 secs using 398.8% CPU
Optimizing NNI: done in 1.4704 secs using 398.5% CPU
Iteration 290 / LogL: -57738.720 / Time: 0h:8m:37s (0h:1m:40s left)
Optimizing NNI: done in 1.45599 secs using 398.2% CPU
Optimizing NNI: done in 1.80317 secs using 399% CPU
Optimizing NNI: done in 1.572 secs using 399% CPU
Optimizing NNI: done in 1.98061 secs using 398.8% CPU
Optimizing NNI: done in 1.66546 secs using 398.7% CPU
Optimizing NNI: done in 1.37346 secs using 398.9% CPU
Computing log-likelihood of 98 initial trees ... 17.257 seconds
Current best score: -192534.768

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.59925 secs using 398.4% CPU
Optimizing NNI: done in 1.70793 secs using 398.9% CPU
Optimizing NNI: done in 3.43826 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.61234 secs using 399.3% CPU
Optimizing NNI: done in 1.62688 secs using 399% CPU
Iteration 300 / LogL: -57739.418 / Time: 0h:8m:53s (0h:1m:22s left)
BETTER TREE FOUND at iteration 1: -191769.044
Optimizing NNI: done in 1.76889 secs using 398.9% CPU
Optimizing NNI: done in 1.43713 secs using 398.7% CPU
Optimizing NNI: done in 3.8833 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.59686 secs using 399.2% CPU
Optimizing NNI: done in 1.78903 secs using 398.8% CPU
BETTER TREE FOUND at iteration 2: -191541.098
Optimizing NNI: done in 1.78811 secs using 399% CPU
Optimizing NNI: done in 1.59278 secs using 399% CPU
Optimizing NNI: done in 3.92487 secs using 597.4% CPU
Optimizing NNI: done in 1.94798 secs using 398.8% CPU
Optimizing NNI: done in 1.79486 secs using 399% CPU
Optimizing NNI: done in 3.67501 secs using 596.8% CPU
Optimizing NNI: done in 1.58392 secs using 399.3% CPU
Optimizing NNI: done in 1.46502 secs using 398.6% CPU
Iteration 310 / LogL: -57737.478 / Time: 0h:9m:10s (0h:1m:4s left)
Optimizing NNI: done in 1.6561 secs using 398.6% CPU
Optimizing NNI: done in 3.99876 secs using 597.8% CPU
Optimizing NNI: done in 1.92985 secs using 399% CPU
Optimizing NNI: done in 1.55989 secs using 399% CPU
Optimizing NNI: done in 4.37091 secs using 596.3% CPU
Optimizing NNI: done in 1.4757 secs using 399.2% CPU
Optimizing NNI: done in 1.59704 secs using 398.7% CPU
Optimizing NNI: done in 1.45463 secs using 398.8% CPU
Optimizing NNI: done in 4.24854 secs using 596.3% CPU
Optimizing NNI: done in 1.44845 secs using 399.1% CPU
Optimizing NNI: done in 1.82591 secs using 398.5% CPU
Optimizing NNI: done in 1.70893 secs using 398.9% CPU
Optimizing NNI: done in 3.98636 secs using 596.4% CPU
Optimizing NNI: done in 2.31294 secs using 399% CPU
Iteration 320 / LogL: -57736.749 / Time: 0h:9m:27s (0h:0m:46s left)
Optimizing NNI: done in 3.82981 secs using 597.2% CPU
Optimizing NNI: done in 1.6852 secs using 398.8% CPU
Optimizing NNI: done in 1.82617 secs using 399.2% CPU
Optimizing NNI: done in 3.91031 secs using 596.7% CPU
Iteration 10 / LogL: -191614.706 / Time: 0h:2m:2s
Optimizing NNI: done in 2.31857 secs using 399.1% CPU
UPDATE BEST LOG-LIKELIHOOD: -57732.070
Optimizing NNI: done in 1.78392 secs using 398.8% CPU
Optimizing NNI: done in 1.65361 secs using 399.3% CPU
Optimizing NNI: done in 4.37997 secs using 597.4% CPU
Optimizing NNI: done in 1.87481 secs using 398.8% CPU
Optimizing NNI: done in 1.9754 secs using 398.7% CPU
Optimizing NNI: done in 4.03965 secs using 597.2% CPU
Optimizing NNI: done in 1.73075 secs using 399.3% CPU
Optimizing NNI: done in 1.78689 secs using 398.7% CPU
Optimizing NNI: done in 4.08545 secs using 595.4% CPU
Optimizing NNI: done in 1.48234 secs using 398.3% CPU
Iteration 330 / LogL: -57744.627 / Time: 0h:9m:45s (0h:0m:28s left)
Optimizing NNI: done in 1.6841 secs using 399.3% CPU
Optimizing NNI: done in 1.62656 secs using 399.4% CPU
Optimizing NNI: done in 4.15023 secs using 597% CPU
Optimizing NNI: done in 1.70121 secs using 399.1% CPU
Optimizing NNI: done in 1.5714 secs using 398.9% CPU
Optimizing NNI: done in 1.45748 secs using 399% CPU
Optimizing NNI: done in 4.60655 secs using 596.9% CPU
Optimizing NNI: done in 1.45662 secs using 398.9% CPU
Optimizing NNI: done in 1.49022 secs using 399.2% CPU
Optimizing NNI: done in 1.79488 secs using 398.6% CPU
Optimizing NNI: done in 4.21718 secs using 596.9% CPU
Optimizing NNI: done in 1.84051 secs using 399% CPU
Optimizing NNI: done in 1.46445 secs using 399.2% CPU
Iteration 340 / LogL: -57740.909 / Time: 0h:10m:2s (0h:0m:10s left)
Optimizing NNI: done in 4.06294 secs using 597.7% CPU
Optimizing NNI: done in 1.67495 secs using 399.3% CPU
Optimizing NNI: done in 1.4793 secs using 399.4% CPU
Optimizing NNI: done in 1.49528 secs using 398.9% CPU
Optimizing NNI: done in 4.43399 secs using 596.6% CPU
Optimizing NNI: done in 1.77036 secs using 399.1% CPU
Optimizing NNI: done in 1.83333 secs using 398.6% CPU
Optimizing NNI: done in 1.35257 secs using 399% CPU
Optimizing NNI: done in 4.46044 secs using 597.1% CPU
Optimizing NNI: done in 1.68617 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 347 ITERATIONS / Time: 0h:10m:13s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57732.070
Optimal log-likelihood: -57732.068
Site proportion and rates:  (0.106,0.060) (0.094,0.171) (0.126,0.362) (0.095,0.362) (0.236,0.706) (0.128,1.235) (0.169,2.046) (0.045,4.997)
Parameters optimization took 1 rounds (0.393 sec)
BEST SCORE FOUND : -57732.068
Total tree length: 46.141

Total number of iterations: 347
CPU time used for tree search: 2403.520 sec (0h:40m:3s)
Wall-clock time used for tree search: 606.324 sec (0h:10m:6s)
Total CPU time used: 2433.806 sec (0h:40m:33s)
Total wall-clock time used: 613.890 sec (0h:10m:13s)

===> START BOOTSTRAP REPLICATE NUMBER 13

Creating bootstrap alignment (seed: 67475)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.035 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58173.158
2. Current log-likelihood: -57606.011
3. Current log-likelihood: -57598.393
Optimizing NNI: done in 4.41691 secs using 597% CPU
Iteration 20 / LogL: -191576.996 / Time: 0h:2m:45s
Finish initializing candidate tree set (20)
Current best tree score: -191541.098 / CPU time: 135.170
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
4. Current log-likelihood: -57594.430
5. Current log-likelihood: -57584.094
6. Current log-likelihood: -57564.290
7. Current log-likelihood: -57560.052
8. Current log-likelihood: -57559.662
Optimizing NNI: done in 4.17162 secs using 597.6% CPU
9. Current log-likelihood: -57559.549
10. Current log-likelihood: -57559.437
11. Current log-likelihood: -57559.327
12. Current log-likelihood: -57559.219
13. Current log-likelihood: -57559.115
14. Current log-likelihood: -57559.012
Optimizing NNI: done in 4.71371 secs using 596.1% CPU
15. Current log-likelihood: -57558.912
Optimal log-likelihood: -57558.748
Site proportion and rates:  (0.099,0.052) (0.139,0.166) (0.095,0.392) (0.076,0.392) (0.262,0.734) (0.139,1.220) (0.154,2.291) (0.035,5.374)
Parameters optimization took 15 rounds (12.354 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.08768 secs using 399.7% CPU
Computing ML distances took 1.087872 sec (of wall-clock time) 4.347659 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000338078 secs using 392.2% CPU
Constructing RapidNJ tree: done in 0.00437593 secs using 367.2% CPU
Computing RapidNJ tree took 0.004785 sec (of wall-clock time) 0.018182 sec (of CPU time)
Log-likelihood of RapidNJ tree: -57516.207
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 5.26554 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
5.004 second
BETTER TREE FOUND at iteration 23: -191537.093
Computing log-likelihood of 98 initial trees ... 5.420 seconds
Current best score: -57480.378

Do NNI search on 20 best initial trees
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BETTER TREE FOUND at iteration 1: -57296.915
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176  Q.pfam+F+I+R10 105607.860   573 212361.720   870165.720   214668.542
WARNING: Normalizing state frequencies so that sum of them equals to 1
BETTER TREE FOUND at iteration 2: -57289.192
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BETTER TREE FOUND at iteration 26: -191520.581
BETTER TREE FOUND at iteration 6: -57258.364
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BETTER TREE FOUND at iteration 8: -57240.543
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Iteration 10 / LogL: -57266.654 / Time: 0h:0m:46s
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Iteration 30 / LogL: -191623.425 / Time: 0h:3m:41s (0h:12m:13s left)
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Iteration 20 / LogL: -57273.758 / Time: 0h:0m:59s
Finish initializing candidate tree set (20)
Current best tree score: -57240.543 / CPU time: 45.334
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 31: -191513.879
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BETTER TREE FOUND at iteration 30: -57229.303
Iteration 30 / LogL: -57229.303 / Time: 0h:1m:15s (0h:4m:20s left)
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BETTER TREE FOUND at iteration 33: -57212.177
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197  Q.bird+I+R9   105987.526   552 213079.051   823591.051   215301.329
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BETTER TREE FOUND at iteration 40: -57198.328
Iteration 40 / LogL: -57198.328 / Time: 0h:1m:34s (0h:4m:1s left)
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BETTER TREE FOUND at iteration 53: -57197.529
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BETTER TREE FOUND at iteration 59: -57194.670
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BETTER TREE FOUND at iteration 71: -57192.204
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Iteration 90 / LogL: -57208.692 / Time: 0h:2m:47s (0h:2m:32s left)
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BETTER TREE FOUND at iteration 91: -57191.588
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BETTER TREE FOUND at iteration 126: -57191.315
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198  Q.bird+I+R10  105983.580   554 213075.160   828015.160   215305.490
WARNING: Normalizing state frequencies so that sum of them equals to 1
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219  Q.bird+F+I+R9 106716.456   571 214574.911   867798.911   216873.681
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Iteration 150 / LogL: -57196.040 / Time: 0h:4m:13s (0h:2m:9s left)
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UPDATE BEST LOG-LIKELIHOOD: -57191.311
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Iteration 160 / LogL: -57232.105 / Time: 0h:4m:26s (0h:1m:50s left)
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BETTER TREE FOUND at iteration 191: -57191.311
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220  Q.bird+F+I+R10 106708.808   573 214563.616   872367.616   216870.437
WARNING: Normalizing state frequencies so that sum of them equals to 1
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241  Q.mammal+I+R9 105506.060   552 212116.121   822628.121   214338.399
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Iteration 250 / LogL: -57197.120 / Time: 0h:6m:29s (0h:1m:4s left)
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BETTER TREE FOUND at iteration 256: -57191.310
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Iteration 260 / LogL: -57192.321 / Time: 0h:6m:44s (0h:2m:29s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 97: -191483.339
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Iteration 280 / LogL: -57202.840 / Time: 0h:7m:12s (0h:1m:57s left)
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242  Q.mammal+I+R10 105503.127   554 212114.253   827054.253   214344.583
WARNING: Normalizing state frequencies so that sum of them equals to 1
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Iteration 290 / LogL: -57207.227 / Time: 0h:7m:26s (0h:1m:41s left)
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263  Q.mammal+F+I+R9 106250.996   571 213643.993   866867.993   215942.762
WARNING: Normalizing state frequencies so that sum of them equals to 1
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Iteration 340 / LogL: -57191.316 / Time: 0h:8m:36s (0h:0m:24s left)
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Iteration 120 / LogL: -191594.936 / Time: 0h:11m:23s (0h:7m:21s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.44079 secs using 398.8% CPU
Iteration 350 / LogL: -57207.695 / Time: 0h:8m:50s (0h:0m:9s left)
Optimizing NNI: done in 1.38613 secs using 399.3% CPU
Optimizing NNI: done in 1.47393 secs using 398.7% CPU
BETTER TREE FOUND at iteration 122: -191470.990
Optimizing NNI: done in 1.54748 secs using 399% CPU
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Optimizing NNI: done in 5.68458 secs using 597.1% CPU
Optimizing NNI: done in 1.35636 secs using 398.5% CPU
TREE SEARCH COMPLETED AFTER 357 ITERATIONS / Time: 0h:9m:0s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57191.310
2. Current log-likelihood: -57191.291
3. Current log-likelihood: -57191.275
4. Current log-likelihood: -57191.260
5. Current log-likelihood: -57191.244
6. Current log-likelihood: -57191.227
7. Current log-likelihood: -57191.212
8. Current log-likelihood: -57191.198
9. Current log-likelihood: -57191.183
10. Current log-likelihood: -57191.166
Optimizing NNI: done in 5.66351 secs using 596.9% CPU
11. Current log-likelihood: -57191.152
12. Current log-likelihood: -57191.137
13. Current log-likelihood: -57191.123
14. Current log-likelihood: -57191.106
15. Current log-likelihood: -57191.092
16. Current log-likelihood: -57191.078
17. Current log-likelihood: -57191.061
18. Current log-likelihood: -57191.045
19. Current log-likelihood: -57191.030
20. Current log-likelihood: -57191.016
21. Current log-likelihood: -57191.002
Optimizing NNI: done in 4.73299 secs using 597% CPU
22. Current log-likelihood: -57190.988
23. Current log-likelihood: -57190.974
24. Current log-likelihood: -57190.958
25. Current log-likelihood: -57190.944
26. Current log-likelihood: -57190.928
27. Current log-likelihood: -57190.914
28. Current log-likelihood: -57190.898
29. Current log-likelihood: -57190.884
30. Current log-likelihood: -57190.871
31. Current log-likelihood: -57190.857
32. Current log-likelihood: -57190.843
Optimizing NNI: done in 4.69272 secs using 598.4% CPU
264  Q.mammal+F+I+R10 106245.505   573 213637.011   871441.011   215943.832
33. Current log-likelihood: -57190.827
34. Current log-likelihood: -57190.814
35. Current log-likelihood: -57190.801
36. Current log-likelihood: -57190.787
37. Current log-likelihood: -57190.774
38. Current log-likelihood: -57190.759
39. Current log-likelihood: -57190.746
40. Current log-likelihood: -57190.732
41. Current log-likelihood: -57190.719
42. Current log-likelihood: -57190.707
43. Current log-likelihood: -57190.691
44. Current log-likelihood: -57190.678
Optimizing NNI: done in 4.967 secs using 596.7% CPU
45. Current log-likelihood: -57190.665
46. Current log-likelihood: -57190.653
47. Current log-likelihood: -57190.638
48. Current log-likelihood: -57190.625
49. Current log-likelihood: -57190.610
50. Current log-likelihood: -57190.597
51. Current log-likelihood: -57190.584
52. Current log-likelihood: -57190.571
53. Current log-likelihood: -57190.559
54. Current log-likelihood: -57190.546
55. Current log-likelihood: -57190.531
56. Current log-likelihood: -57190.519
Optimizing NNI: done in 4.98476 secs using 597% CPU
57. Current log-likelihood: -57190.507
58. Current log-likelihood: -57190.492
59. Current log-likelihood: -57190.479
60. Current log-likelihood: -57190.465
61. Current log-likelihood: -57190.452
62. Current log-likelihood: -57190.440
285  Q.insect+I+R9 105385.524   552 211875.048   822387.048   214097.326
63. Current log-likelihood: -57190.427
64. Current log-likelihood: -57190.415
65. Current log-likelihood: -57190.403
66. Current log-likelihood: -57190.391
67. Current log-likelihood: -57190.377
Optimizing NNI: done in 4.66141 secs using 597.6% CPU
68. Current log-likelihood: -57190.365
69. Current log-likelihood: -57190.353
70. Current log-likelihood: -57190.341
71. Current log-likelihood: -57190.329
72. Current log-likelihood: -57190.318
73. Current log-likelihood: -57190.306
74. Current log-likelihood: -57190.292
75. Current log-likelihood: -57190.280
76. Current log-likelihood: -57190.269
77. Current log-likelihood: -57190.257
78. Current log-likelihood: -57190.246
Optimizing NNI: done in 4.59509 secs using 597.7% CPU
Iteration 130 / LogL: -191646.559 / Time: 0h:12m:17s (0h:8m:45s left)
79. Current log-likelihood: -57190.232
80. Current log-likelihood: -57190.221
81. Current log-likelihood: -57190.207
82. Current log-likelihood: -57190.195
83. Current log-likelihood: -57190.184
84. Current log-likelihood: -57190.172
85. Current log-likelihood: -57190.161
86. Current log-likelihood: -57190.150
87. Current log-likelihood: -57190.136
88. Current log-likelihood: -57190.125
Optimizing NNI: done in 4.56156 secs using 596.9% CPU
89. Current log-likelihood: -57190.112
90. Current log-likelihood: -57190.101
91. Current log-likelihood: -57190.089
92. Current log-likelihood: -57190.078
93. Current log-likelihood: -57190.067
94. Current log-likelihood: -57190.056
95. Current log-likelihood: -57190.043
96. Current log-likelihood: -57190.032
97. Current log-likelihood: -57190.021
98. Current log-likelihood: -57190.008
Optimizing NNI: done in 4.55112 secs using 596.9% CPU
99. Current log-likelihood: -57189.997
Optimal log-likelihood: -57189.997
Site proportion and rates:  (0.081,0.041) (0.164,0.157) (0.103,0.415) (0.082,0.415) (0.251,0.749) (0.123,1.189) (0.159,2.267) (0.037,5.362)
Parameters optimization took 99 rounds (43.000 sec)
BEST SCORE FOUND : -57189.997
Total tree length: 44.065

Total number of iterations: 357
CPU time used for tree search: 2086.907 sec (0h:34m:46s)
Wall-clock time used for tree search: 526.770 sec (0h:8m:46s)
Total CPU time used: 2313.284 sec (0h:38m:33s)
Total wall-clock time used: 583.618 sec (0h:9m:43s)

===> START BOOTSTRAP REPLICATE NUMBER 14

Creating bootstrap alignment (seed: 67476)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59299.678
2. Current log-likelihood: -58763.894
3. Current log-likelihood: -58746.464
4. Current log-likelihood: -58732.015
5. Current log-likelihood: -58729.365
6. Current log-likelihood: -58728.918
Optimizing NNI: done in 4.99359 secs using 597.4% CPU
Optimal log-likelihood: -58728.856
Site proportion and rates:  (0.102,0.057) (0.126,0.188) (0.074,0.403) (0.092,0.405) (0.231,0.736) (0.159,1.201) (0.179,2.177) (0.038,4.074)
Parameters optimization took 6 rounds (5.612 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.07589 secs using 399.8% CPU
Computing ML distances took 1.076113 sec (of wall-clock time) 4.302243 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000404119 secs using 403.3% CPU
Constructing RapidNJ tree: done in 0.00433707 secs using 297.7% CPU
Computing RapidNJ tree took 0.004817 sec (of wall-clock time) 0.017273 sec (of CPU time)
Log-likelihood of RapidNJ tree: -58930.645
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.43843 secs using 597.3% CPU
5.104 second
Optimizing NNI: done in 6.50027 secs using 597% CPU
Computing log-likelihood of 98 initial trees ... 5.482 seconds
Current best score: -58728.856

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.745388 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -58614.320
Optimizing NNI: done in 1.13285 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.01231 secs using 597.9% CPU
BETTER TREE FOUND at iteration 2: -58598.798
Optimizing NNI: done in 1.04508 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -58569.993
Optimizing NNI: done in 1.22581 secs using 398.9% CPU
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Iteration 10 / LogL: -58597.332 / Time: 0h:0m:34s
Optimizing NNI: done in 1.3087 secs using 399.1% CPU
Optimizing NNI: done in 1.09597 secs using 398.4% CPU
Optimizing NNI: done in 5.2824 secs using 597.3% CPU
Optimizing NNI: done in 1.49099 secs using 399% CPU
Optimizing NNI: done in 1.46228 secs using 398.7% CPU
Optimizing NNI: done in 1.1427 secs using 399.4% CPU
Optimizing NNI: done in 1.5442 secs using 399.4% CPU
Optimizing NNI: done in 1.37978 secs using 398.5% CPU
Optimizing NNI: done in 6.35901 secs using 596.8% CPU
Iteration 140 / LogL: -191556.978 / Time: 0h:13m:10s (0h:7m:46s left)
Optimizing NNI: done in 1.29347 secs using 399.2% CPU
Optimizing NNI: done in 1.20544 secs using 399% CPU
Optimizing NNI: done in 1.29202 secs using 399.1% CPU
Iteration 20 / LogL: -58643.074 / Time: 0h:0m:47s
Finish initializing candidate tree set (20)
Current best tree score: -58569.993 / CPU time: 40.411
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.41892 secs using 399.2% CPU
Optimizing NNI: done in 5.19827 secs using 596.4% CPU
Optimizing NNI: done in 1.59977 secs using 398.7% CPU
Optimizing NNI: done in 1.5981 secs using 398.8% CPU
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Optimizing NNI: done in 4.75213 secs using 597.2% CPU
Optimizing NNI: done in 1.68531 secs using 398.9% CPU
Optimizing NNI: done in 1.87396 secs using 398.8% CPU
Optimizing NNI: done in 1.51896 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.78656 secs using 597.5% CPU
BETTER TREE FOUND at iteration 27: -58560.595
Optimizing NNI: done in 1.53677 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -58554.366
Optimizing NNI: done in 5.26371 secs using 597.1% CPU
Optimizing NNI: done in 1.7641 secs using 398.9% CPU
Optimizing NNI: done in 1.60174 secs using 398.9% CPU
Iteration 30 / LogL: -58616.671 / Time: 0h:1m:6s (0h:3m:44s left)
Optimizing NNI: done in 1.3205 secs using 398.3% CPU
Optimizing NNI: done in 4.36785 secs using 596.5% CPU
Optimizing NNI: done in 1.20749 secs using 398.9% CPU
Optimizing NNI: done in 1.44914 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
286  Q.insect+I+R10 105381.528   554 211871.057   826811.057   214101.387
BETTER TREE FOUND at iteration 33: -58550.419
Optimizing NNI: done in 1.4106 secs using 399.1% CPU
Optimizing NNI: done in 4.73576 secs using 597.4% CPU
Optimizing NNI: done in 1.74693 secs using 398.9% CPU
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Optimizing NNI: done in 1.40995 secs using 399.3% CPU
Optimizing NNI: done in 1.39607 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 39: -58540.277
Optimizing NNI: done in 1.36644 secs using 399.3% CPU
Iteration 40 / LogL: -58578.800 / Time: 0h:1m:22s (0h:3m:30s left)
Optimizing NNI: done in 4.85733 secs using 597.7% CPU
Optimizing NNI: done in 1.47855 secs using 398.6% CPU
Optimizing NNI: done in 1.17583 secs using 398.5% CPU
Optimizing NNI: done in 1.44064 secs using 398.7% CPU
Optimizing NNI: done in 4.9315 secs using 597% CPU
307  Q.insect+F+I+R9 105553.950   571 212249.900   865473.900   214548.670
Optimizing NNI: done in 1.53171 secs using 398.7% CPU
Optimizing NNI: done in 1.26556 secs using 399.1% CPU
Optimizing NNI: done in 1.47077 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 46: -58529.236
Optimizing NNI: done in 4.7216 secs using 596.5% CPU
Iteration 150 / LogL: -191535.828 / Time: 0h:13m:59s (0h:6m:45s left)
Optimizing NNI: done in 1.58685 secs using 398.7% CPU
Optimizing NNI: done in 1.72531 secs using 398.9% CPU
Optimizing NNI: done in 1.5221 secs using 398.6% CPU
Optimizing NNI: done in 4.59752 secs using 597.8% CPU
Optimizing NNI: done in 1.45035 secs using 398.8% CPU
Iteration 50 / LogL: -58530.870 / Time: 0h:1m:38s (0h:3m:13s left)
Optimizing NNI: done in 1.27789 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -58529.004
Optimizing NNI: done in 4.70558 secs using 597.4% CPU
Optimizing NNI: done in 1.61527 secs using 399.2% CPU
Optimizing NNI: done in 1.37739 secs using 399% CPU
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Optimizing NNI: done in 1.38286 secs using 398.8% CPU
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Optimizing NNI: done in 1.41641 secs using 399.1% CPU
Optimizing NNI: done in 1.51586 secs using 399.4% CPU
Iteration 60 / LogL: -58543.215 / Time: 0h:1m:54s (0h:2m:55s left)
Optimizing NNI: done in 1.6242 secs using 399.1% CPU
Optimizing NNI: done in 1.43032 secs using 399% CPU
Optimizing NNI: done in 4.92827 secs using 596.7% CPU
Optimizing NNI: done in 1.40032 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 63: -58528.653
Optimizing NNI: done in 1.35935 secs using 398.9% CPU
Optimizing NNI: done in 4.44069 secs using 596.7% CPU
Optimizing NNI: done in 1.2957 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -58527.957
Optimizing NNI: done in 1.38821 secs using 399.3% CPU
Optimizing NNI: done in 4.53513 secs using 597.2% CPU
Optimizing NNI: done in 1.74884 secs using 399.1% CPU
Optimizing NNI: done in 1.49753 secs using 398.9% CPU
Optimizing NNI: done in 1.34653 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 69: -58527.118
Optimizing NNI: done in 4.45447 secs using 598.1% CPU
Optimizing NNI: done in 1.35685 secs using 398.9% CPU
Iteration 70 / LogL: -58530.874 / Time: 0h:2m:11s (0h:3m:8s left)
Optimizing NNI: done in 1.52669 secs using 399.1% CPU
Optimizing NNI: done in 1.1885 secs using 399% CPU
Optimizing NNI: done in 4.60024 secs using 596.9% CPU
Optimizing NNI: done in 1.32146 secs using 398.6% CPU
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Optimizing NNI: done in 1.48688 secs using 399.2% CPU
Optimizing NNI: done in 1.3623 secs using 398.9% CPU
Optimizing NNI: done in 4.84076 secs using 597% CPU
Iteration 160 / LogL: -191506.942 / Time: 0h:14m:46s (0h:5m:45s left)
Optimizing NNI: done in 1.3978 secs using 398.7% CPU
Optimizing NNI: done in 1.77127 secs using 399.2% CPU
Optimizing NNI: done in 1.43297 secs using 399.5% CPU
Optimizing NNI: done in 4.81524 secs using 597.8% CPU
Optimizing NNI: done in 1.51364 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 80: -58522.638
Iteration 80 / LogL: -58522.638 / Time: 0h:2m:26s (0h:3m:5s left)
Optimizing NNI: done in 1.57276 secs using 399.2% CPU
Optimizing NNI: done in 4.58347 secs using 597.8% CPU
Optimizing NNI: done in 1.49469 secs using 399.2% CPU
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Optimizing NNI: done in 1.37389 secs using 398.5% CPU
Optimizing NNI: done in 1.40463 secs using 398.6% CPU
Optimizing NNI: done in 4.83445 secs using 597.4% CPU
Optimizing NNI: done in 1.66139 secs using 399% CPU
Optimizing NNI: done in 1.55592 secs using 398.7% CPU
Optimizing NNI: done in 1.36224 secs using 399.4% CPU
Optimizing NNI: done in 4.68436 secs using 597.2% CPU
Optimizing NNI: done in 1.24396 secs using 398.3% CPU
Optimizing NNI: done in 1.23756 secs using 398.9% CPU
Iteration 90 / LogL: -58550.999 / Time: 0h:2m:41s (0h:2m:43s left)
Optimizing NNI: done in 1.24269 secs using 399.1% CPU
Optimizing NNI: done in 1.35323 secs using 398.6% CPU
Optimizing NNI: done in 5.02557 secs using 597.9% CPU
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Optimizing NNI: done in 1.37855 secs using 398.7% CPU
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Optimizing NNI: done in 4.54388 secs using 597.9% CPU
Optimizing NNI: done in 1.24152 secs using 399.3% CPU
Optimizing NNI: done in 1.32166 secs using 398.6% CPU
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Optimizing NNI: done in 1.24007 secs using 399.7% CPU
Optimizing NNI: done in 5.14186 secs using 597.5% CPU
Optimizing NNI: done in 1.24516 secs using 398.7% CPU
Iteration 100 / LogL: -58527.535 / Time: 0h:2m:54s (0h:2m:21s left)
Optimizing NNI: done in 1.4073 secs using 398.7% CPU
Optimizing NNI: done in 1.50646 secs using 398.7% CPU
Optimizing NNI: done in 4.50962 secs using 597.9% CPU
Optimizing NNI: done in 1.46844 secs using 399% CPU
Optimizing NNI: done in 1.29367 secs using 398.9% CPU
Optimizing NNI: done in 1.49043 secs using 398.8% CPU
Optimizing NNI: done in 1.31658 secs using 399.1% CPU
Optimizing NNI: done in 4.70374 secs using 596.8% CPU
Optimizing NNI: done in 1.50852 secs using 398.9% CPU
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Optimizing NNI: done in 1.29276 secs using 398.5% CPU
Optimizing NNI: done in 4.6503 secs using 598% CPU
Iteration 170 / LogL: -191522.686 / Time: 0h:15m:34s (0h:4m:47s left)
Optimizing NNI: done in 1.46155 secs using 398.4% CPU
Iteration 110 / LogL: -58572.941 / Time: 0h:3m:9s (0h:2m:1s left)
Optimizing NNI: done in 1.41902 secs using 398.9% CPU
Optimizing NNI: done in 1.30941 secs using 398.5% CPU
Optimizing NNI: done in 4.93444 secs using 597.1% CPU
Optimizing NNI: done in 1.49753 secs using 399.2% CPU
Optimizing NNI: done in 1.42923 secs using 398.8% CPU
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Optimizing NNI: done in 4.60875 secs using 596.8% CPU
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Optimizing NNI: done in 1.43495 secs using 398.6% CPU
Optimizing NNI: done in 1.23507 secs using 399.1% CPU
Optimizing NNI: done in 1.74522 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.62148 secs using 596.7% CPU
BETTER TREE FOUND at iteration 119: -58521.515
Optimizing NNI: done in 1.39369 secs using 399.2% CPU
BETTER TREE FOUND at iteration 120: -58521.514
Iteration 120 / LogL: -58521.514 / Time: 0h:3m:24s (0h:2m:51s left)
Optimizing NNI: done in 1.31941 secs using 398.7% CPU
308  Q.insect+F+I+R10 105544.760   573 212235.519   870039.519   214542.340
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 1.23592 secs using 399.4% CPU
Optimizing NNI: done in 4.74116 secs using 596.8% CPU
Optimizing NNI: done in 1.23511 secs using 398.9% CPU
Optimizing NNI: done in 1.23049 secs using 398.9% CPU
Optimizing NNI: done in 1.34653 secs using 399.2% CPU
Optimizing NNI: done in 4.09027 secs using 598% CPU
Optimizing NNI: done in 1.39613 secs using 399.1% CPU
Optimizing NNI: done in 1.56889 secs using 399.1% CPU
Optimizing NNI: done in 1.53512 secs using 397.9% CPU
329  Q.plant+I+R9  105148.611   552 211401.223   821913.223   213623.501
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 4.70514 secs using 597.4% CPU
Optimizing NNI: done in 1.4588 secs using 399.2% CPU
Optimizing NNI: done in 1.46729 secs using 399.1% CPU
Iteration 130 / LogL: -58524.090 / Time: 0h:3m:38s (0h:2m:32s left)
Optimizing NNI: done in 1.33176 secs using 398.8% CPU
Optimizing NNI: done in 4.94424 secs using 597.8% CPU
Optimizing NNI: done in 1.66813 secs using 399.1% CPU
Optimizing NNI: done in 1.1823 secs using 399% CPU
Optimizing NNI: done in 1.55963 secs using 398.7% CPU
Optimizing NNI: done in 1.35499 secs using 399% CPU
Optimizing NNI: done in 4.84475 secs using 597.2% CPU
Optimizing NNI: done in 1.51171 secs using 399% CPU
Optimizing NNI: done in 1.52307 secs using 398.6% CPU
Optimizing NNI: done in 1.39635 secs using 398.7% CPU
Optimizing NNI: done in 4.57733 secs using 597.5% CPU
Optimizing NNI: done in 1.52311 secs using 398.9% CPU
Optimizing NNI: done in 1.49288 secs using 399.4% CPU
Iteration 140 / LogL: -58538.377 / Time: 0h:3m:53s (0h:2m:14s left)
Optimizing NNI: done in 1.37987 secs using 399.1% CPU
Optimizing NNI: done in 4.90226 secs using 597.6% CPU
Iteration 180 / LogL: -191568.294 / Time: 0h:16m:22s (0h:3m:50s left)
Optimizing NNI: done in 1.59809 secs using 398.6% CPU
Optimizing NNI: done in 1.19741 secs using 398.9% CPU
BETTER TREE FOUND at iteration 143: -58521.514
Optimizing NNI: done in 1.38117 secs using 399.2% CPU
Optimizing NNI: done in 1.5716 secs using 398.8% CPU
Optimizing NNI: done in 5.96543 secs using 597.1% CPU
Optimizing NNI: done in 1.48272 secs using 399.1% CPU
Optimizing NNI: done in 1.21255 secs using 399.6% CPU
Optimizing NNI: done in 1.14143 secs using 398.7% CPU
Optimizing NNI: done in 1.43971 secs using 399% CPU
Optimizing NNI: done in 5.29444 secs using 597.6% CPU
Optimizing NNI: done in 1.64254 secs using 399% CPU
Iteration 150 / LogL: -58561.619 / Time: 0h:4m:7s (0h:2m:34s left)
Optimizing NNI: done in 1.53656 secs using 398.9% CPU
Optimizing NNI: done in 1.35592 secs using 398.8% CPU
Optimizing NNI: done in 1.46935 secs using 398.9% CPU
Optimizing NNI: done in 5.01194 secs using 597.1% CPU
Optimizing NNI: done in 1.44442 secs using 398.8% CPU
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Optimizing NNI: done in 5.23731 secs using 597.4% CPU
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Optimizing NNI: done in 1.4502 secs using 399.5% CPU
Optimizing NNI: done in 1.67233 secs using 399.1% CPU
Iteration 160 / LogL: -58534.100 / Time: 0h:4m:21s (0h:2m:16s left)
Optimizing NNI: done in 4.54097 secs using 596.5% CPU
Optimizing NNI: done in 1.3031 secs using 399% CPU
Optimizing NNI: done in 1.41238 secs using 398.9% CPU
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Optimizing NNI: done in 4.89727 secs using 597.9% CPU
Optimizing NNI: done in 1.67749 secs using 399.2% CPU
Optimizing NNI: done in 1.68288 secs using 399.1% CPU
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Optimizing NNI: done in 1.48209 secs using 399.1% CPU
Optimizing NNI: done in 1.31524 secs using 399.3% CPU
Iteration 170 / LogL: -58539.276 / Time: 0h:4m:36s (0h:1m:59s left)
Optimizing NNI: done in 4.73355 secs using 598% CPU
Optimizing NNI: done in 1.08276 secs using 399.1% CPU
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Optimizing NNI: done in 1.46665 secs using 399.1% CPU
Optimizing NNI: done in 1.57386 secs using 398.7% CPU
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Optimizing NNI: done in 4.95221 secs using 596.7% CPU
Iteration 190 / LogL: -191558.979 / Time: 0h:17m:13s (0h:2m:54s left)
Optimizing NNI: done in 1.3511 secs using 399.6% CPU
Optimizing NNI: done in 1.52285 secs using 399.1% CPU
Optimizing NNI: done in 1.52745 secs using 399% CPU
Iteration 180 / LogL: -58540.807 / Time: 0h:4m:50s (0h:1m:42s left)
Optimizing NNI: done in 4.41744 secs using 597.8% CPU
Optimizing NNI: done in 1.54143 secs using 398.7% CPU
Optimizing NNI: done in 1.50189 secs using 399% CPU
Optimizing NNI: done in 1.45534 secs using 398.9% CPU
Optimizing NNI: done in 4.41255 secs using 597.4% CPU
Optimizing NNI: done in 1.41444 secs using 399.3% CPU
Optimizing NNI: done in 1.44271 secs using 398.3% CPU
Optimizing NNI: done in 1.15386 secs using 399.2% CPU
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Optimizing NNI: done in 4.9065 secs using 597.5% CPU
Optimizing NNI: done in 1.20223 secs using 399% CPU
Optimizing NNI: done in 1.55466 secs using 399.3% CPU
Optimizing NNI: done in 1.11189 secs using 399.2% CPU
Iteration 190 / LogL: -58696.728 / Time: 0h:5m:4s (0h:1m:25s left)
Optimizing NNI: done in 4.83742 secs using 596.7% CPU
Optimizing NNI: done in 1.66576 secs using 398.3% CPU
Optimizing NNI: done in 1.64401 secs using 398.9% CPU
Optimizing NNI: done in 1.63721 secs using 399.2% CPU
Optimizing NNI: done in 4.58395 secs using 597.8% CPU
Optimizing NNI: done in 1.19959 secs using 399.1% CPU
Optimizing NNI: done in 1.24964 secs using 399.1% CPU
Optimizing NNI: done in 1.21994 secs using 399.2% CPU
Optimizing NNI: done in 1.28944 secs using 399.4% CPU
Optimizing NNI: done in 4.41979 secs using 597.4% CPU
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Optimizing NNI: done in 1.58701 secs using 398.7% CPU
Optimizing NNI: done in 1.40849 secs using 398.9% CPU
Iteration 200 / LogL: -58521.514 / Time: 0h:5m:18s (0h:1m:8s left)
Optimizing NNI: done in 4.48103 secs using 597.2% CPU
Optimizing NNI: done in 1.26525 secs using 399.1% CPU
Optimizing NNI: done in 1.44072 secs using 398.4% CPU
Optimizing NNI: done in 1.48334 secs using 399% CPU
Optimizing NNI: done in 1.5979 secs using 398.7% CPU
Optimizing NNI: done in 5.48788 secs using 597.2% CPU
Optimizing NNI: done in 1.37552 secs using 399% CPU
Optimizing NNI: done in 1.38643 secs using 398.5% CPU
330  Q.plant+I+R10 105146.066   554 211400.131   826340.131   213630.461
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 1.49558 secs using 399.2% CPU
Optimizing NNI: done in 4.41709 secs using 597.5% CPU
Optimizing NNI: done in 1.48888 secs using 398.8% CPU
Optimizing NNI: done in 1.13268 secs using 399.4% CPU
Optimizing NNI: done in 1.18251 secs using 398.9% CPU
Iteration 210 / LogL: -58523.910 / Time: 0h:5m:32s (0h:0m:52s left)
Optimizing NNI: done in 1.56574 secs using 398.9% CPU
Optimizing NNI: done in 5.65469 secs using 597.6% CPU
Iteration 200 / LogL: -191596.408 / Time: 0h:18m:1s (0h:1m:59s left)
Optimizing NNI: done in 1.23303 secs using 398.7% CPU
Optimizing NNI: done in 1.53674 secs using 399.1% CPU
Optimizing NNI: done in 1.4844 secs using 399.3% CPU
Optimizing NNI: done in 4.69815 secs using 596.9% CPU
Optimizing NNI: done in 1.27711 secs using 398.9% CPU
Optimizing NNI: done in 1.46329 secs using 398.9% CPU
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Optimizing NNI: done in 1.48283 secs using 399.1% CPU
Optimizing NNI: done in 4.61229 secs using 598% CPU
Optimizing NNI: done in 1.36453 secs using 399% CPU
Optimizing NNI: done in 1.4195 secs using 399.2% CPU
Iteration 220 / LogL: -58535.849 / Time: 0h:5m:47s (0h:0m:36s left)
Optimizing NNI: done in 1.26422 secs using 399.1% CPU
Optimizing NNI: done in 4.5682 secs using 597.3% CPU
Optimizing NNI: done in 1.64387 secs using 399% CPU
Optimizing NNI: done in 1.4708 secs using 398.5% CPU
Optimizing NNI: done in 1.39221 secs using 398.7% CPU
351  Q.plant+F+I+R9 105686.149   571 212514.298   865738.298   214813.068
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 4.84197 secs using 596.7% CPU
Optimizing NNI: done in 1.2125 secs using 398.9% CPU
Optimizing NNI: done in 1.24588 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -58521.514
Optimizing NNI: done in 1.58605 secs using 398.6% CPU
Optimizing NNI: done in 1.19993 secs using 399.3% CPU
Optimizing NNI: done in 4.91894 secs using 597.4% CPU
Optimizing NNI: done in 1.21843 secs using 398.5% CPU
Optimizing NNI: done in 1.41173 secs using 398.7% CPU
Iteration 230 / LogL: -58534.071 / Time: 0h:6m:1s (0h:0m:20s left)
Optimizing NNI: done in 1.47637 secs using 398.5% CPU
Optimizing NNI: done in 1.228 secs using 399.2% CPU
Optimizing NNI: done in 5.09307 secs using 597.1% CPU
Optimizing NNI: done in 1.56622 secs using 399.3% CPU
Optimizing NNI: done in 1.34737 secs using 399.5% CPU
Optimizing NNI: done in 1.62957 secs using 399.3% CPU
Optimizing NNI: done in 4.97617 secs using 597.1% CPU
Optimizing NNI: done in 1.69346 secs using 399.1% CPU
Optimizing NNI: done in 1.20231 secs using 399.7% CPU
Optimizing NNI: done in 1.43298 secs using 398.7% CPU
Optimizing NNI: done in 1.51663 secs using 398.7% CPU
Optimizing NNI: done in 5.14552 secs using 597.7% CPU
Optimizing NNI: done in 1.56538 secs using 398.8% CPU
Iteration 240 / LogL: -58521.515 / Time: 0h:6m:15s (0h:0m:4s left)
Optimizing NNI: done in 1.57438 secs using 398.4% CPU
Optimizing NNI: done in 1.28372 secs using 399.2% CPU
Optimizing NNI: done in 4.39463 secs using 596.4% CPU
Optimizing NNI: done in 1.44169 secs using 399.1% CPU
Optimizing NNI: done in 1.42957 secs using 398.4% CPU
TREE SEARCH COMPLETED AFTER 244 ITERATIONS / Time: 0h:6m:21s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58521.514
Optimal log-likelihood: -58521.511
Site proportion and rates:  (0.105,0.058) (0.126,0.190) (0.077,0.411) (0.096,0.411) (0.260,0.785) (0.145,1.310) (0.161,2.294) (0.030,4.506)
Parameters optimization took 1 rounds (0.448 sec)
BEST SCORE FOUND : -58521.511
Total tree length: 42.546

Total number of iterations: 244
CPU time used for tree search: 1479.392 sec (0h:24m:39s)
Wall-clock time used for tree search: 374.557 sec (0h:6m:14s)
Total CPU time used: 1509.745 sec (0h:25m:9s)
Total wall-clock time used: 382.149 sec (0h:6m:22s)

===> START BOOTSTRAP REPLICATE NUMBER 15

Creating bootstrap alignment (seed: 67477)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59981.478
2. Current log-likelihood: -59421.244
Optimizing NNI: done in 4.12876 secs using 597.9% CPU
Iteration 210 / LogL: -191570.879 / Time: 0h:18m:49s (0h:1m:4s left)
3. Current log-likelihood: -59357.733
4. Current log-likelihood: -59348.265
5. Current log-likelihood: -59347.700
6. Current log-likelihood: -59347.593
Optimal log-likelihood: -59347.534
Site proportion and rates:  (0.106,0.055) (0.105,0.187) (0.092,0.396) (0.118,0.433) (0.204,0.728) (0.182,1.151) (0.158,2.039) (0.035,6.002)
Parameters optimization took 6 rounds (5.319 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.8943 secs using 598% CPU
Calculating distance matrix: done in 1.09843 secs using 400% CPU
Computing ML distances took 1.098604 sec (of wall-clock time) 4.393719 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000352859 secs using 397.9% CPU
Constructing RapidNJ tree: done in 0.0044322 secs using 297.9% CPU
Computing RapidNJ tree took 0.004850 sec (of wall-clock time) 0.017398 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59476.738
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 5.103 second
Optimizing NNI: done in 6.33299 secs using 597.2% CPU
Optimizing NNI: done in 4.83718 secs using 597.5% CPU
Computing log-likelihood of 98 initial trees ... 5.813 seconds
Current best score: -59347.534

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.00566 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -59187.424
Optimizing NNI: done in 1.34612 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.92755 secs using 597.5% CPU
BETTER TREE FOUND at iteration 2: -59149.666
Optimizing NNI: done in 1.43924 secs using 399.1% CPU
Optimizing NNI: done in 1.44553 secs using 398.8% CPU
Optimizing NNI: done in 1.23324 secs using 398.7% CPU
Optimizing NNI: done in 5.35491 secs using 597.3% CPU
Optimizing NNI: done in 1.29095 secs using 398.5% CPU
Optimizing NNI: done in 1.37655 secs using 399% CPU
Optimizing NNI: done in 1.35098 secs using 399.3% CPU
Optimizing NNI: done in 4.77608 secs using 598% CPU
Optimizing NNI: done in 1.38973 secs using 398.7% CPU
Optimizing NNI: done in 1.40399 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 10: -59146.246
Iteration 10 / LogL: -59146.246 / Time: 0h:0m:35s
Optimizing NNI: done in 1.24812 secs using 398.5% CPU
Optimizing NNI: done in 5.0597 secs using 597.4% CPU
Optimizing NNI: done in 1.4244 secs using 398.7% CPU
Optimizing NNI: done in 1.26869 secs using 399.2% CPU
Optimizing NNI: done in 1.37107 secs using 398.5% CPU
Optimizing NNI: done in 4.66748 secs using 597.4% CPU
Optimizing NNI: done in 1.37498 secs using 399% CPU
Optimizing NNI: done in 1.34107 secs using 398.7% CPU
Optimizing NNI: done in 1.30423 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 17: -59143.589
Optimizing NNI: done in 4.80138 secs using 597.5% CPU
Optimizing NNI: done in 1.33329 secs using 399.2% CPU
Optimizing NNI: done in 1.3295 secs using 398.9% CPU
Optimizing NNI: done in 1.42534 secs using 398.6% CPU
Iteration 20 / LogL: -59197.017 / Time: 0h:0m:50s
Finish initializing candidate tree set (20)
Current best tree score: -59143.589 / CPU time: 43.715
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.29356 secs using 597.2% CPU
Iteration 220 / LogL: -191471.971 / Time: 0h:19m:40s (0h:0m:10s left)
Optimizing NNI: done in 1.72748 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 6.35568 secs using 596.9% CPU
Optimizing NNI: done in 4.87928 secs using 597.3% CPU
Optimizing NNI: done in 4.37504 secs using 597.7% CPU
TREE SEARCH COMPLETED AFTER 223 ITERATIONS / Time: 0h:19m:56s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -191470.990
BETTER TREE FOUND at iteration 21: -59136.779
Optimal log-likelihood: -191470.981
Site proportion and rates:  (0.025,0.097) (0.057,0.248) (0.121,0.361) (0.219,0.565) (0.194,0.775) (0.151,1.098) (0.120,1.711) (0.114,2.586)
Parameters optimization took 1 rounds (1.272 sec)
BEST SCORE FOUND : -191470.981
Total tree length: 146.688

Total number of iterations: 223
CPU time used for tree search: 6816.156 sec (1h:53m:36s)
Wall-clock time used for tree search: 1165.822 sec (0h:19m:25s)
Total CPU time used: 7004.736 sec (1h:56m:44s)
Total wall-clock time used: 1197.460 sec (0h:19m:57s)

===> START BOOTSTRAP REPLICATE NUMBER 4

Creating bootstrap alignment (seed: 70467)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.346 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -200118.947
Optimizing NNI: done in 1.70437 secs using 398.8% CPU
Optimizing NNI: done in 1.5715 secs using 398.7% CPU
2. Current log-likelihood: -197299.157
Optimizing NNI: done in 1.40883 secs using 399.1% CPU
3. Current log-likelihood: -197265.585
Optimizing NNI: done in 1.54885 secs using 399.2% CPU
Optimizing NNI: done in 1.61102 secs using 398.3% CPU
352  Q.plant+F+I+R10 105684.349   573 212514.699   870318.699   214821.520
WARNING: Normalizing state frequencies so that sum of them equals to 1
4. Current log-likelihood: -197262.739
Optimizing NNI: done in 1.82111 secs using 399.1% CPU
5. Current log-likelihood: -197259.035
Optimizing NNI: done in 1.68555 secs using 399% CPU
Optimizing NNI: done in 1.69177 secs using 399.1% CPU
6. Current log-likelihood: -197254.012
Optimizing NNI: done in 1.42008 secs using 399% CPU
Iteration 30 / LogL: -59145.532 / Time: 0h:1m:23s (0h:4m:20s left)
Optimizing NNI: done in 1.25 secs using 398.3% CPU
7. Current log-likelihood: -197252.951
Optimizing NNI: done in 1.65413 secs using 398.8% CPU
8. Current log-likelihood: -197252.702
Optimizing NNI: done in 1.65102 secs using 398.8% CPU
Optimal log-likelihood: -197252.605
Site proportion and rates:  (0.015,0.124) (0.067,0.249) (0.102,0.377) (0.183,0.536) (0.176,0.725) (0.238,1.008) (0.176,1.806) (0.043,3.684)
Parameters optimization took 8 rounds (20.027 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.64468 secs using 398.7% CPU
Optimizing NNI: done in 1.44845 secs using 397.9% CPU
373  Q.yeast+I+R9  105710.175   552 212524.349   823036.349   214746.627
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 1.71097 secs using 398.6% CPU
Optimizing NNI: done in 1.63992 secs using 398.9% CPU
Optimizing NNI: done in 1.58817 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -59130.712
Calculating distance matrix: done in 9.40263 secs using 599.9% CPU
Computing ML distances took 9.403178 sec (of wall-clock time) 56.406742 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00132513 secs using 291.1% CPU
Constructing RapidNJ tree: done in 0.02354 secs using 683.9% CPU
Computing RapidNJ tree took 0.024949 sec (of wall-clock time) 0.166486 sec (of CPU time)
Optimizing NNI: done in 1.4385 secs using 397.9% CPU
BETTER TREE FOUND at iteration 39: -59130.707
Log-likelihood of RapidNJ tree: -200570.097
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.51996 secs using 399.1% CPU
Iteration 40 / LogL: -59135.752 / Time: 0h:1m:41s (0h:4m:17s left)
Optimizing NNI: done in 1.37548 secs using 399.3% CPU
Optimizing NNI: done in 1.72711 secs using 398.2% CPU
Optimizing NNI: done in 1.49413 secs using 399.1% CPU
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Optimizing NNI: done in 1.4621 secs using 398.6% CPU
Optimizing NNI: done in 1.61024 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 49: -59129.868
Optimizing NNI: done in 1.53753 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 50: -59128.110
Iteration 50 / LogL: -59128.110 / Time: 0h:1m:58s (0h:4m:2s left)
Optimizing NNI: done in 1.63843 secs using 399.4% CPU
Optimizing NNI: done in 1.21296 secs using 399.1% CPU
Optimizing NNI: done in 1.32148 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 53: -59126.648
Optimizing NNI: done in 1.46746 secs using 399.1% CPU
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Optimizing NNI: done in 1.28022 secs using 399% CPU
Optimizing NNI: done in 1.63089 secs using 398.7% CPU
30.475 second
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Optimizing NNI: done in 1.55687 secs using 398.3% CPU
Optimizing NNI: done in 1.47218 secs using 399% CPU
Iteration 60 / LogL: -59168.427 / Time: 0h:2m:14s (0h:3m:31s left)
Optimizing NNI: done in 1.66951 secs using 399% CPU
Optimizing NNI: done in 1.64433 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 62: -59125.455
Optimizing NNI: done in 1.16222 secs using 398.5% CPU
Optimizing NNI: done in 1.75267 secs using 398.5% CPU
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Optimizing NNI: done in 1.68106 secs using 399% CPU
Optimizing NNI: done in 1.77396 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 67: -59118.727
Computing log-likelihood of 98 initial trees ... 17.386 seconds
Current best score: -197252.605

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.64518 secs using 398.5% CPU
Optimizing NNI: done in 1.59122 secs using 399% CPU
Optimizing NNI: done in 3.39166 secs using 598.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.8063 secs using 398.8% CPU
Iteration 70 / LogL: -59128.406 / Time: 0h:2m:32s (0h:3m:34s left)
Optimizing NNI: done in 1.61843 secs using 399.1% CPU
Optimizing NNI: done in 1.79919 secs using 398.8% CPU
Optimizing NNI: done in 1.4507 secs using 398.4% CPU
Optimizing NNI: done in 1.76963 secs using 398.8% CPU
BETTER TREE FOUND at iteration 1: -196620.963
Optimizing NNI: done in 1.49243 secs using 399.4% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.41283 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 78: -59118.232
Optimizing NNI: done in 1.85278 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -196609.374
BETTER TREE FOUND at iteration 79: -59116.756
Optimizing NNI: done in 1.536 secs using 398.6% CPU
Iteration 80 / LogL: -59132.673 / Time: 0h:2m:51s (0h:3m:34s left)
Optimizing NNI: done in 1.78694 secs using 399.2% CPU
Optimizing NNI: done in 4.95852 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.30812 secs using 398.9% CPU
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Optimizing NNI: done in 1.55999 secs using 398.7% CPU
Optimizing NNI: done in 1.41572 secs using 399% CPU
BETTER TREE FOUND at iteration 3: -196587.730
Optimizing NNI: done in 1.26948 secs using 399% CPU
Optimizing NNI: done in 1.6003 secs using 399% CPU
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Optimizing NNI: done in 4.95513 secs using 597.7% CPU
Optimizing NNI: done in 1.59327 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 90: -59114.271
Iteration 90 / LogL: -59114.271 / Time: 0h:3m:8s (0h:3m:31s left)
374  Q.yeast+I+R10 105708.908   554 212525.816   827465.816   214756.146
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 1.59319 secs using 398.9% CPU
Optimizing NNI: done in 5.35602 secs using 596.9% CPU
Optimizing NNI: done in 1.71079 secs using 398.6% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 93: -59112.724
Optimizing NNI: done in 1.69316 secs using 398.9% CPU
Optimizing NNI: done in 1.64128 secs using 399.3% CPU
Optimizing NNI: done in 5.61813 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.56394 secs using 399% CPU
Optimizing NNI: done in 1.52687 secs using 399.4% CPU
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Optimizing NNI: done in 1.66584 secs using 398.9% CPU
Iteration 100 / LogL: -59117.266 / Time: 0h:3m:24s (0h:3m:12s left)
Optimizing NNI: done in 1.49747 secs using 399% CPU
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BETTER TREE FOUND at iteration 6: -196484.068
Optimizing NNI: done in 1.74522 secs using 399% CPU
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Optimizing NNI: done in 1.62171 secs using 399% CPU
Iteration 110 / LogL: -59113.593 / Time: 0h:3m:40s (0h:2m:47s left)
Optimizing NNI: done in 1.40587 secs using 398.9% CPU
395  Q.yeast+F+I+R9 105585.204   571 212312.408   865536.408   214611.177
WARNING: Normalizing state frequencies so that sum of them equals to 1
Optimizing NNI: done in 1.55505 secs using 398.9% CPU
Optimizing NNI: done in 5.51528 secs using 596.5% CPU
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Optimizing NNI: done in 5.42161 secs using 596.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.60609 secs using 399% CPU
Iteration 120 / LogL: -59122.020 / Time: 0h:3m:56s (0h:2m:24s left)
Optimizing NNI: done in 1.50142 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 10: -196463.834
Iteration 10 / LogL: -196463.834 / Time: 0h:2m:49s
BETTER TREE FOUND at iteration 121: -59112.435
Optimizing NNI: done in 1.51526 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.26491 secs using 597.5% CPU
BETTER TREE FOUND at iteration 124: -59111.576
Optimizing NNI: done in 1.68992 secs using 399.1% CPU
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Optimizing NNI: done in 1.62027 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 128: -59111.324
Optimizing NNI: done in 1.60284 secs using 398.6% CPU
Optimizing NNI: done in 1.30127 secs using 399.5% CPU
Iteration 130 / LogL: -59117.478 / Time: 0h:4m:14s (0h:3m:13s left)
Optimizing NNI: done in 5.56113 secs using 597.7% CPU
Optimizing NNI: done in 1.45766 secs using 398.9% CPU
Optimizing NNI: done in 1.57791 secs using 398.7% CPU
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Iteration 140 / LogL: -59114.133 / Time: 0h:4m:30s (0h:2m:50s left)
Optimizing NNI: done in 1.60362 secs using 399.2% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 142: -59108.331
Optimizing NNI: done in 4.53188 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.46462 secs using 399% CPU
Optimizing NNI: done in 1.60378 secs using 399.5% CPU
BETTER TREE FOUND at iteration 17: -196446.355
Optimizing NNI: done in 1.60192 secs using 398.5% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 146: -59108.256
Optimizing NNI: done in 1.51552 secs using 398.5% CPU
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Iteration 150 / LogL: -59137.459 / Time: 0h:4m:46s (0h:3m:4s left)
Optimizing NNI: done in 1.28982 secs using 399.2% CPU
Optimizing NNI: done in 5.3887 secs using 597.2% CPU
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BETTER TREE FOUND at iteration 154: -59108.255
Optimizing NNI: done in 1.52751 secs using 398.6% CPU
Optimizing NNI: done in 5.83964 secs using 596.8% CPU
Iteration 20 / LogL: -196515.225 / Time: 0h:3m:45s
Finish initializing candidate tree set (20)
Current best tree score: -196446.355 / CPU time: 193.924
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.66866 secs using 399.2% CPU
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BETTER TREE FOUND at iteration 160: -59108.254
Iteration 160 / LogL: -59108.254 / Time: 0h:5m:2s (0h:3m:10s left)
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BETTER TREE FOUND at iteration 177: -59108.252
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Iteration 180 / LogL: -59115.543 / Time: 0h:5m:32s (0h:3m:0s left)
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BETTER TREE FOUND at iteration 30: -196432.306
Iteration 30 / LogL: -196432.306 / Time: 0h:4m:37s (0h:15m:55s left)
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396  Q.yeast+F+I+R10 105576.960   573 212299.920   870103.920   214606.741
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417  JTTDCMut+I+R9 105350.942   552 211805.885   822317.885   214028.163
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Iteration 270 / LogL: -59119.284 / Time: 0h:7m:51s (0h:0m:12s left)
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TREE SEARCH COMPLETED AFTER 278 ITERATIONS / Time: 0h:8m:4s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59108.252
2. Current log-likelihood: -59108.232
Optimizing NNI: done in 4.74805 secs using 598.1% CPU
Optimal log-likelihood: -59108.216
Site proportion and rates:  (0.100,0.051) (0.115,0.180) (0.192,0.404) (0.168,0.660) (0.162,0.987) (0.098,1.411) (0.131,2.135) (0.034,6.083)
Parameters optimization took 2 rounds (1.414 sec)
BEST SCORE FOUND : -59108.216
Total tree length: 46.408

Total number of iterations: 278
CPU time used for tree search: 1888.446 sec (0h:31m:28s)
Wall-clock time used for tree search: 477.186 sec (0h:7m:57s)
Total CPU time used: 1922.244 sec (0h:32m:2s)
Total wall-clock time used: 485.623 sec (0h:8m:5s)

===> START BOOTSTRAP REPLICATE NUMBER 16

Creating bootstrap alignment (seed: 67478)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.072 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59914.758
2. Current log-likelihood: -59294.934
3. Current log-likelihood: -59245.421
4. Current log-likelihood: -59213.018
5. Current log-likelihood: -59211.325
Optimizing NNI: done in 4.8237 secs using 597.9% CPU
Optimal log-likelihood: -59211.251
Site proportion and rates:  (0.107,0.054) (0.091,0.173) (0.130,0.343) (0.131,0.494) (0.171,0.668) (0.160,1.130) (0.170,2.032) (0.039,5.819)
Parameters optimization took 5 rounds (4.487 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10273 secs using 400% CPU
Computing ML distances took 1.102945 sec (of wall-clock time) 4.411113 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000365019 secs using 317.5% CPU
Constructing RapidNJ tree: done in 0.00460792 secs using 276.4% CPU
Computing RapidNJ tree took 0.005044 sec (of wall-clock time) 0.016214 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59240.194
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.98584 secs using 597.3% CPU
5.102 second
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Estimate model parameters (epsilon = 0.100)
418  JTTDCMut+I+R10 105350.747   554 211809.495   826749.495   214039.825
BETTER TREE FOUND at iteration 60: -196400.357
Iteration 60 / LogL: -196400.357 / Time: 0h:7m:13s (0h:12m:13s left)
Computing log-likelihood of 98 initial trees ... 5.382 seconds
Current best score: -59175.089

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -58892.810
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439  JTTDCMut+F+I+R9 105467.294   571 212076.588   865300.588   214375.357
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -58865.338
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Iteration 10 / LogL: -58895.482 / Time: 0h:0m:36s
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Iteration 20 / LogL: -58928.960 / Time: 0h:0m:48s
Finish initializing candidate tree set (20)
Current best tree score: -58865.338 / CPU time: 42.366
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -58848.074
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 73: -196387.812
BETTER TREE FOUND at iteration 45: -58846.117
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -58825.478
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Optimizing NNI: done in 4.406 secs using 597.4% CPU
Optimizing NNI: done in 1.30781 secs using 398.8% CPU
Optimizing NNI: done in 1.40972 secs using 399.2% CPU
Iteration 80 / LogL: -58846.972 / Time: 0h:2m:23s (0h:2m:33s left)
Optimizing NNI: done in 1.56034 secs using 399.2% CPU
Optimizing NNI: done in 4.82574 secs using 597.7% CPU
Optimizing NNI: done in 1.49005 secs using 399.1% CPU
Optimizing NNI: done in 1.24588 secs using 399% CPU
Optimizing NNI: done in 1.299 secs using 399.3% CPU
Optimizing NNI: done in 1.2595 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
440  JTTDCMut+F+I+R10 105460.146   573 212066.292   869870.292   214373.114
BETTER TREE FOUND at iteration 85: -58825.386
Optimizing NNI: done in 5.42525 secs using 598% CPU
Optimizing NNI: done in 1.23504 secs using 398.7% CPU
Optimizing NNI: done in 1.37596 secs using 398.6% CPU
Optimizing NNI: done in 1.50478 secs using 399.1% CPU
Optimizing NNI: done in 5.20087 secs using 598% CPU
Optimizing NNI: done in 1.5146 secs using 399.2% CPU
Optimizing NNI: done in 1.41047 secs using 399% CPU
Iteration 90 / LogL: -58825.553 / Time: 0h:2m:37s (0h:2m:48s left)
Optimizing NNI: done in 1.4485 secs using 398.9% CPU
Optimizing NNI: done in 1.33849 secs using 399.2% CPU
Optimizing NNI: done in 4.49535 secs using 597.9% CPU
Optimizing NNI: done in 1.25786 secs using 399.1% CPU
Optimizing NNI: done in 1.46557 secs using 398.6% CPU
Optimizing NNI: done in 1.47099 secs using 398.7% CPU
Optimizing NNI: done in 4.54818 secs using 598% CPU
Optimizing NNI: done in 1.38459 secs using 398.9% CPU
Optimizing NNI: done in 1.19638 secs using 398.8% CPU
Optimizing NNI: done in 1.38673 secs using 399.6% CPU
Optimizing NNI: done in 1.53455 secs using 399.1% CPU
Optimizing NNI: done in 5.0825 secs using 597.5% CPU
Iteration 90 / LogL: -196425.280 / Time: 0h:9m:47s (0h:9m:7s left)
Optimizing NNI: done in 1.46828 secs using 399% CPU
Iteration 100 / LogL: -58831.854 / Time: 0h:2m:51s (0h:2m:27s left)
Optimizing NNI: done in 1.53914 secs using 399.1% CPU
Optimizing NNI: done in 1.50689 secs using 398.9% CPU
Optimizing NNI: done in 5.01173 secs using 597.3% CPU
Optimizing NNI: done in 1.57287 secs using 398.7% CPU
Optimizing NNI: done in 1.59436 secs using 399.1% CPU
Optimizing NNI: done in 1.2195 secs using 398.7% CPU
Optimizing NNI: done in 4.41845 secs using 598% CPU
Optimizing NNI: done in 1.38261 secs using 399% CPU
Optimizing NNI: done in 1.52037 secs using 399.1% CPU
Optimizing NNI: done in 1.50664 secs using 399% CPU
Optimizing NNI: done in 5.22887 secs using 597.8% CPU
Optimizing NNI: done in 1.59262 secs using 399% CPU
Optimizing NNI: done in 1.25959 secs using 398.8% CPU
Iteration 110 / LogL: -58838.280 / Time: 0h:3m:6s (0h:2m:8s left)
Optimizing NNI: done in 1.27228 secs using 399.4% CPU
Optimizing NNI: done in 1.29306 secs using 399.2% CPU
Optimizing NNI: done in 4.95243 secs using 597% CPU
Optimizing NNI: done in 1.52671 secs using 399.1% CPU
461  DCMut+I+R9    106802.652   552 214709.304   825221.304   216931.582
Optimizing NNI: done in 1.31861 secs using 399.2% CPU
Optimizing NNI: done in 1.45167 secs using 398.8% CPU
Optimizing NNI: done in 1.15785 secs using 398.7% CPU
Optimizing NNI: done in 4.90961 secs using 597.4% CPU
Optimizing NNI: done in 1.3673 secs using 398.7% CPU
Optimizing NNI: done in 1.36447 secs using 398.9% CPU
Optimizing NNI: done in 1.55506 secs using 399.2% CPU
Optimizing NNI: done in 4.96966 secs using 597% CPU
Optimizing NNI: done in 1.27082 secs using 398.7% CPU
Iteration 120 / LogL: -58834.780 / Time: 0h:3m:20s (0h:1m:49s left)
Optimizing NNI: done in 1.46134 secs using 399.2% CPU
Optimizing NNI: done in 1.3066 secs using 398.1% CPU
Optimizing NNI: done in 1.60068 secs using 398.9% CPU
Optimizing NNI: done in 5.02548 secs using 597.9% CPU
Optimizing NNI: done in 1.41339 secs using 398.6% CPU
Optimizing NNI: done in 1.34001 secs using 398.5% CPU
Optimizing NNI: done in 1.43804 secs using 399.2% CPU
Optimizing NNI: done in 4.05844 secs using 598.1% CPU
Optimizing NNI: done in 1.25708 secs using 398.9% CPU
Optimizing NNI: done in 1.64865 secs using 399.1% CPU
Optimizing NNI: done in 1.18674 secs using 398.8% CPU
Optimizing NNI: done in 4.73321 secs using 597.7% CPU
Optimizing NNI: done in 1.66248 secs using 399.1% CPU
Iteration 130 / LogL: -58844.523 / Time: 0h:3m:34s (0h:1m:31s left)
Optimizing NNI: done in 1.39208 secs using 399.1% CPU
Optimizing NNI: done in 1.42011 secs using 399.4% CPU
Optimizing NNI: done in 1.36709 secs using 399.4% CPU
Optimizing NNI: done in 4.78935 secs using 597.9% CPU
Iteration 100 / LogL: -196389.573 / Time: 0h:10m:36s (0h:7m:48s left)
Optimizing NNI: done in 1.38476 secs using 398.5% CPU
Optimizing NNI: done in 1.34942 secs using 399.3% CPU
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Optimizing NNI: done in 4.97151 secs using 597.4% CPU
Optimizing NNI: done in 1.57178 secs using 398.8% CPU
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Optimizing NNI: done in 1.30075 secs using 399.6% CPU
Optimizing NNI: done in 1.3462 secs using 399.2% CPU
Iteration 140 / LogL: -58826.421 / Time: 0h:3m:49s (0h:1m:14s left)
Optimizing NNI: done in 5.1455 secs using 597.6% CPU
Optimizing NNI: done in 1.33098 secs using 399.2% CPU
Optimizing NNI: done in 1.22417 secs using 398.9% CPU
Optimizing NNI: done in 1.25268 secs using 398.7% CPU
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Optimizing NNI: done in 5.35679 secs using 596.7% CPU
Optimizing NNI: done in 1.37986 secs using 398.9% CPU
Optimizing NNI: done in 1.40502 secs using 398.6% CPU
Optimizing NNI: done in 1.41757 secs using 398.9% CPU
Optimizing NNI: done in 1.17639 secs using 398.9% CPU
Optimizing NNI: done in 5.12106 secs using 597.2% CPU
Optimizing NNI: done in 1.24493 secs using 399.3% CPU
Optimizing NNI: done in 1.58258 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.75005 secs using 597.5% CPU
BETTER TREE FOUND at iteration 150: -58820.063
Iteration 150 / LogL: -58820.063 / Time: 0h:4m:4s (0h:2m:44s left)
Optimizing NNI: done in 1.69165 secs using 398.9% CPU
Optimizing NNI: done in 1.46968 secs using 399.1% CPU
Optimizing NNI: done in 4.58302 secs using 596.8% CPU
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Optimizing NNI: done in 4.42485 secs using 597.6% CPU
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Optimizing NNI: done in 4.56258 secs using 597.4% CPU
Optimizing NNI: done in 1.32049 secs using 398.8% CPU
Iteration 160 / LogL: -58829.931 / Time: 0h:4m:19s (0h:2m:27s left)
Optimizing NNI: done in 1.36444 secs using 398.9% CPU
Optimizing NNI: done in 1.3368 secs using 399% CPU
Optimizing NNI: done in 1.45271 secs using 398.9% CPU
Optimizing NNI: done in 5.47849 secs using 597.5% CPU
Optimizing NNI: done in 1.19123 secs using 399% CPU
Optimizing NNI: done in 1.34173 secs using 398.9% CPU
Optimizing NNI: done in 1.47531 secs using 398.7% CPU
Optimizing NNI: done in 4.4791 secs using 597.5% CPU
Iteration 110 / LogL: -196415.659 / Time: 0h:11m:25s (0h:6m:36s left)
Optimizing NNI: done in 1.78041 secs using 398.7% CPU
Optimizing NNI: done in 1.50818 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 168: -58819.308
Optimizing NNI: done in 4.77766 secs using 597.7% CPU
Optimizing NNI: done in 1.44004 secs using 398.7% CPU
Optimizing NNI: done in 1.3447 secs using 399.2% CPU
Iteration 170 / LogL: -58844.859 / Time: 0h:4m:35s (0h:2m:39s left)
Optimizing NNI: done in 1.43683 secs using 399.1% CPU
Optimizing NNI: done in 5.13001 secs using 597.5% CPU
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Optimizing NNI: done in 1.22043 secs using 398.6% CPU
Iteration 180 / LogL: -58831.515 / Time: 0h:4m:49s (0h:2m:22s left)
Optimizing NNI: done in 1.3502 secs using 398.8% CPU
Optimizing NNI: done in 1.34845 secs using 399.5% CPU
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Optimizing NNI: done in 5.30125 secs using 597% CPU
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Optimizing NNI: done in 1.49865 secs using 399.4% CPU
Iteration 190 / LogL: -58915.290 / Time: 0h:5m:3s (0h:2m:5s left)
Optimizing NNI: done in 4.92496 secs using 597.9% CPU
Optimizing NNI: done in 1.25454 secs using 398.9% CPU
Optimizing NNI: done in 1.34455 secs using 398.9% CPU
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Optimizing NNI: done in 5.12046 secs using 597.5% CPU
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Optimizing NNI: done in 1.4051 secs using 398.8% CPU
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Optimizing NNI: done in 4.86235 secs using 597.4% CPU
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Optimizing NNI: done in 1.46332 secs using 398.8% CPU
Optimizing NNI: done in 1.65051 secs using 397.6% CPU
Iteration 200 / LogL: -58856.345 / Time: 0h:5m:18s (0h:1m:48s left)
Optimizing NNI: done in 4.70485 secs using 598% CPU
Iteration 120 / LogL: -196457.618 / Time: 0h:12m:15s (0h:5m:27s left)
Optimizing NNI: done in 1.48927 secs using 398.5% CPU
Optimizing NNI: done in 1.45619 secs using 399.6% CPU
Optimizing NNI: done in 1.25705 secs using 399.4% CPU
Optimizing NNI: done in 4.84064 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.4084 secs using 399.3% CPU
Optimizing NNI: done in 1.46585 secs using 399.2% CPU
Optimizing NNI: done in 1.37534 secs using 398.9% CPU
BETTER TREE FOUND at iteration 121: -196378.019
Optimizing NNI: done in 1.58466 secs using 399% CPU
Optimizing NNI: done in 1.58942 secs using 398.8% CPU
Optimizing NNI: done in 1.31256 secs using 398.5% CPU
Optimizing NNI: done in 4.82806 secs using 598% CPU
Optimizing NNI: done in 1.38328 secs using 399% CPU
Iteration 210 / LogL: -58835.981 / Time: 0h:5m:32s (0h:1m:32s left)
Optimizing NNI: done in 1.36023 secs using 398.9% CPU
Optimizing NNI: done in 1.31434 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 212: -58804.702
Optimizing NNI: done in 5.29129 secs using 596.9% CPU
Optimizing NNI: done in 1.47461 secs using 399.1% CPU
Optimizing NNI: done in 1.49078 secs using 398.7% CPU
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Optimizing NNI: done in 4.65299 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.41371 secs using 399.1% CPU
Iteration 220 / LogL: -58834.000 / Time: 0h:5m:49s (0h:2m:26s left)
Optimizing NNI: done in 1.43454 secs using 398% CPU
BETTER TREE FOUND at iteration 125: -196372.493
Optimizing NNI: done in 1.43131 secs using 399.3% CPU
Optimizing NNI: done in 1.56115 secs using 399.2% CPU
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Iteration 230 / LogL: -58807.851 / Time: 0h:6m:3s (0h:2m:10s left)
Optimizing NNI: done in 3.75949 secs using 597.2% CPU
Optimizing NNI: done in 1.42059 secs using 398.8% CPU
Optimizing NNI: done in 1.386 secs using 399.4% CPU
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Optimizing NNI: done in 4.87665 secs using 597% CPU
Iteration 130 / LogL: -196455.778 / Time: 0h:13m:11s (0h:9m:42s left)
Optimizing NNI: done in 1.30606 secs using 398.7% CPU
Optimizing NNI: done in 1.47444 secs using 399% CPU
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Iteration 240 / LogL: -58807.936 / Time: 0h:6m:18s (0h:1m:53s left)
Optimizing NNI: done in 4.66284 secs using 597.1% CPU
Optimizing NNI: done in 1.6293 secs using 399.3% CPU
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Optimizing NNI: done in 4.06202 secs using 598% CPU
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Iteration 250 / LogL: -58846.724 / Time: 0h:6m:33s (0h:1m:38s left)
Optimizing NNI: done in 1.70268 secs using 399.2% CPU
Optimizing NNI: done in 1.35488 secs using 399.7% CPU
Optimizing NNI: done in 5.0442 secs using 597% CPU
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Optimizing NNI: done in 1.4286 secs using 398.5% CPU
Optimizing NNI: done in 1.50571 secs using 399% CPU
Optimizing NNI: done in 1.39296 secs using 399.1% CPU
Optimizing NNI: done in 4.6671 secs using 597.1% CPU
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Optimizing NNI: done in 4.48339 secs using 596.8% CPU
Optimizing NNI: done in 1.39278 secs using 398.9% CPU
Iteration 260 / LogL: -58811.774 / Time: 0h:6m:48s (0h:1m:21s left)
Optimizing NNI: done in 1.59883 secs using 399% CPU
Optimizing NNI: done in 1.24434 secs using 399.4% CPU
Optimizing NNI: done in 5.17734 secs using 596.8% CPU
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Optimizing NNI: done in 1.47108 secs using 398.8% CPU
Optimizing NNI: done in 1.44037 secs using 399.1% CPU
462  DCMut+I+R10   106798.331   554 214704.661   829644.661   216934.991
Optimizing NNI: done in 4.41941 secs using 597% CPU
Optimizing NNI: done in 1.41346 secs using 399% CPU
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Optimizing NNI: done in 1.40288 secs using 398.9% CPU
Optimizing NNI: done in 1.566 secs using 399% CPU
Optimizing NNI: done in 5.34041 secs using 597.7% CPU
Iteration 140 / LogL: -196380.794 / Time: 0h:13m:59s (0h:8m:32s left)
Optimizing NNI: done in 1.38269 secs using 398.6% CPU
Iteration 270 / LogL: -58809.806 / Time: 0h:7m:2s (0h:1m:5s left)
Optimizing NNI: done in 1.32612 secs using 398.5% CPU
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Optimizing NNI: done in 4.43447 secs using 597.4% CPU
Optimizing NNI: done in 1.45409 secs using 398.9% CPU
483  DCMut+F+I+R9  106301.554   571 213745.107   866969.107   216043.877
Optimizing NNI: done in 1.17422 secs using 399.2% CPU
Optimizing NNI: done in 1.4305 secs using 399.1% CPU
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Optimizing NNI: done in 4.9628 secs using 597.4% CPU
Optimizing NNI: done in 1.41425 secs using 398.9% CPU
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Optimizing NNI: done in 1.37671 secs using 399.2% CPU
Iteration 280 / LogL: -58814.263 / Time: 0h:7m:16s (0h:0m:50s left)
Optimizing NNI: done in 1.69685 secs using 399.1% CPU
Optimizing NNI: done in 1.44464 secs using 398.5% CPU
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Optimizing NNI: done in 4.89697 secs using 597.6% CPU
Optimizing NNI: done in 1.50025 secs using 398.8% CPU
Iteration 290 / LogL: -58869.828 / Time: 0h:7m:32s (0h:0m:34s left)
Optimizing NNI: done in 1.38933 secs using 399.3% CPU
Optimizing NNI: done in 1.49347 secs using 398.9% CPU
Optimizing NNI: done in 4.81057 secs using 597.9% CPU
Optimizing NNI: done in 1.45288 secs using 398.4% CPU
Optimizing NNI: done in 1.37269 secs using 399% CPU
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Optimizing NNI: done in 4.69282 secs using 597.2% CPU
Optimizing NNI: done in 1.43436 secs using 398.9% CPU
Iteration 300 / LogL: -58805.528 / Time: 0h:7m:46s (0h:0m:18s left)
Optimizing NNI: done in 1.33155 secs using 398.8% CPU
Optimizing NNI: done in 1.26858 secs using 399.3% CPU
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Optimizing NNI: done in 4.65599 secs using 597.6% CPU
Iteration 150 / LogL: -196466.042 / Time: 0h:14m:47s (0h:7m:26s left)
Optimizing NNI: done in 1.45216 secs using 399.6% CPU
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Iteration 310 / LogL: -58844.643 / Time: 0h:8m:0s (0h:0m:3s left)
Optimizing NNI: done in 1.44594 secs using 399.4% CPU
Optimizing NNI: done in 1.42826 secs using 399.1% CPU
Optimizing NNI: done in 5.06729 secs using 597.4% CPU
Optimizing NNI: done in 1.66373 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 313 ITERATIONS / Time: 0h:8m:5s

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|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58804.702
2. Current log-likelihood: -58804.678
3. Current log-likelihood: -58804.657
4. Current log-likelihood: -58804.628
5. Current log-likelihood: -58804.611
6. Current log-likelihood: -58804.591
7. Current log-likelihood: -58804.564
Optimizing NNI: done in 4.50454 secs using 597.5% CPU
8. Current log-likelihood: -58804.548
9. Current log-likelihood: -58804.531
10. Current log-likelihood: -58804.513
11. Current log-likelihood: -58804.497
12. Current log-likelihood: -58804.480
13. Current log-likelihood: -58804.464
14. Current log-likelihood: -58804.447
15. Current log-likelihood: -58804.430
16. Current log-likelihood: -58804.414
17. Current log-likelihood: -58804.399
Optimizing NNI: done in 4.45309 secs using 598.4% CPU
18. Current log-likelihood: -58804.382
19. Current log-likelihood: -58804.367
20. Current log-likelihood: -58804.351
21. Current log-likelihood: -58804.336
22. Current log-likelihood: -58804.320
23. Current log-likelihood: -58804.305
24. Current log-likelihood: -58804.290
25. Current log-likelihood: -58804.275
26. Current log-likelihood: -58804.259
27. Current log-likelihood: -58804.244
28. Current log-likelihood: -58804.229
Optimizing NNI: done in 4.44178 secs using 597.4% CPU
29. Current log-likelihood: -58804.215
30. Current log-likelihood: -58804.199
31. Current log-likelihood: -58804.185
32. Current log-likelihood: -58804.170
33. Current log-likelihood: -58804.156
34. Current log-likelihood: -58804.141
35. Current log-likelihood: -58804.127
36. Current log-likelihood: -58804.113
37. Current log-likelihood: -58804.099
Optimizing NNI: done in 4.21917 secs using 597.9% CPU
38. Current log-likelihood: -58804.085
39. Current log-likelihood: -58804.071
40. Current log-likelihood: -58804.057
41. Current log-likelihood: -58804.044
42. Current log-likelihood: -58804.031
43. Current log-likelihood: -58804.018
44. Current log-likelihood: -58804.003
45. Current log-likelihood: -58803.991
46. Current log-likelihood: -58803.977
47. Current log-likelihood: -58803.965
Optimizing NNI: done in 4.45089 secs using 597.1% CPU
48. Current log-likelihood: -58803.952
49. Current log-likelihood: -58803.940
50. Current log-likelihood: -58803.926
51. Current log-likelihood: -58803.914
52. Current log-likelihood: -58803.901
53. Current log-likelihood: -58803.889
54. Current log-likelihood: -58803.877
55. Current log-likelihood: -58803.865
56. Current log-likelihood: -58803.852
57. Current log-likelihood: -58803.840
58. Current log-likelihood: -58803.828
Optimizing NNI: done in 4.57366 secs using 597.5% CPU
59. Current log-likelihood: -58803.816
60. Current log-likelihood: -58803.805
61. Current log-likelihood: -58803.793
62. Current log-likelihood: -58803.782
63. Current log-likelihood: -58803.771
64. Current log-likelihood: -58803.760
65. Current log-likelihood: -58803.750
66. Current log-likelihood: -58803.739
67. Current log-likelihood: -58803.728
68. Current log-likelihood: -58803.718
69. Current log-likelihood: -58803.707
70. Current log-likelihood: -58803.697
71. Current log-likelihood: -58803.687
Optimizing NNI: done in 4.97037 secs using 597.1% CPU
Iteration 160 / LogL: -196410.299 / Time: 0h:15m:33s (0h:6m:21s left)
72. Current log-likelihood: -58803.677
73. Current log-likelihood: -58803.666
74. Current log-likelihood: -58803.656
Optimal log-likelihood: -58803.641
Site proportion and rates:  (0.090,0.049) (0.096,0.148) (0.184,0.348) (0.064,0.620) (0.189,0.620) (0.168,1.116) (0.168,2.073) (0.041,5.460)
Parameters optimization took 74 rounds (33.255 sec)
BEST SCORE FOUND : -58803.641
Total tree length: 47.218

Total number of iterations: 313
CPU time used for tree search: 1894.627 sec (0h:31m:34s)
Wall-clock time used for tree search: 478.641 sec (0h:7m:58s)
Total CPU time used: 2053.649 sec (0h:34m:13s)
Total wall-clock time used: 518.533 sec (0h:8m:38s)

===> START BOOTSTRAP REPLICATE NUMBER 17

Creating bootstrap alignment (seed: 67479)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60311.830
2. Current log-likelihood: -59665.871
3. Current log-likelihood: -59633.333
4. Current log-likelihood: -59619.926
Optimizing NNI: done in 4.60376 secs using 596.8% CPU
5. Current log-likelihood: -59618.511
6. Current log-likelihood: -59617.972
7. Current log-likelihood: -59617.005
8. Current log-likelihood: -59615.376
9. Current log-likelihood: -59613.616
10. Current log-likelihood: -59612.482
11. Current log-likelihood: -59611.882
Optimizing NNI: done in 4.78298 secs using 597.8% CPU
12. Current log-likelihood: -59611.550
13. Current log-likelihood: -59611.352
14. Current log-likelihood: -59611.222
Optimal log-likelihood: -59611.111
Site proportion and rates:  (0.108,0.057) (0.071,0.186) (0.198,0.331) (0.216,0.603) (0.170,0.998) (0.099,1.610) (0.102,2.368) (0.036,5.901)
Parameters optimization took 14 rounds (10.710 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.11899 secs using 399.9% CPU
Computing ML distances took 1.119327 sec (of wall-clock time) 4.475636 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00035882 secs using 391.6% CPU
Constructing RapidNJ tree: done in 0.00460196 secs using 365.7% CPU
Computing RapidNJ tree took 0.005032 sec (of wall-clock time) 0.019167 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59774.316
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.81048 secs using 597.4% CPU
4.978 second
Optimizing NNI: done in 5.75866 secs using 597.3% CPU
Computing log-likelihood of 98 initial trees ... 5.403 seconds
Current best score: -59600.119

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.86299 secs using 598.2% CPU
Optimizing NNI: done in 1.54878 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -59413.971
Optimizing NNI: done in 0.997828 secs using 399.5% CPU
Optimizing NNI: done in 4.46999 secs using 598.2% CPU
Optimizing NNI: done in 1.42454 secs using 398.8% CPU
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Optimizing NNI: done in 1.87073 secs using 399.2% CPU
Optimizing NNI: done in 1.56264 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -59407.106
Optimizing NNI: done in 4.87059 secs using 597.7% CPU
Optimizing NNI: done in 1.49113 secs using 399.4% CPU
Optimizing NNI: done in 1.45392 secs using 398.4% CPU
Optimizing NNI: done in 1.35639 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 10: -59401.636
Iteration 10 / LogL: -59401.636 / Time: 0h:0m:42s
Optimizing NNI: done in 4.79935 secs using 597.9% CPU
Optimizing NNI: done in 1.56482 secs using 398.7% CPU
Optimizing NNI: done in 1.39308 secs using 399% CPU
Optimizing NNI: done in 1.82933 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.5637 secs using 597.6% CPU
Iteration 170 / LogL: -196382.188 / Time: 0h:16m:23s (0h:5m:19s left)
BETTER TREE FOUND at iteration 13: -59392.919
Optimizing NNI: done in 1.53711 secs using 398.7% CPU
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Optimizing NNI: done in 1.62425 secs using 399.1% CPU
Optimizing NNI: done in 1.68629 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 19: -59391.541
Optimizing NNI: done in 4.76198 secs using 597.6% CPU
Optimizing NNI: done in 1.77673 secs using 399.2% CPU
Iteration 20 / LogL: -59437.602 / Time: 0h:1m:3s
Finish initializing candidate tree set (20)
Current best tree score: -59391.541 / CPU time: 51.082
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.65365 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -59386.917
Optimizing NNI: done in 4.82542 secs using 596.7% CPU
Optimizing NNI: done in 1.36636 secs using 398.6% CPU
Optimizing NNI: done in 1.61288 secs using 398.4% CPU
Iteration 30 / LogL: -59389.385 / Time: 0h:1m:20s (0h:4m:30s left)
484  DCMut+F+I+R10 106299.210   573 213744.420   871548.420   216051.241
Optimizing NNI: done in 4.65753 secs using 597.3% CPU
Optimizing NNI: done in 1.85251 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -59376.746
Optimizing NNI: done in 1.3724 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -59366.582
Optimizing NNI: done in 4.40968 secs using 597.5% CPU
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505  VT+I+R9       105832.975   552 212769.950   823281.950   214992.228
Optimizing NNI: done in 1.70936 secs using 399% CPU
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Iteration 180 / LogL: -196388.728 / Time: 0h:17m:11s (0h:4m:19s left)
Optimizing NNI: done in 1.60571 secs using 398.9% CPU
Optimizing NNI: done in 1.67115 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -59360.800
Iteration 40 / LogL: -59360.800 / Time: 0h:1m:40s (0h:4m:16s left)
Optimizing NNI: done in 4.61336 secs using 597% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 47: -59360.481
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Iteration 50 / LogL: -59365.350 / Time: 0h:1m:56s (0h:3m:50s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.44536 secs using 597.5% CPU
BETTER TREE FOUND at iteration 58: -59358.912
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Iteration 60 / LogL: -59364.116 / Time: 0h:2m:13s (0h:3m:41s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 61: -59358.494
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Iteration 190 / LogL: -196379.343 / Time: 0h:17m:58s (0h:3m:19s left)
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Iteration 70 / LogL: -59373.411 / Time: 0h:2m:31s (0h:3m:20s left)
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Iteration 80 / LogL: -59403.677 / Time: 0h:2m:47s (0h:2m:51s left)
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Iteration 90 / LogL: -59385.192 / Time: 0h:3m:4s (0h:2m:26s left)
Optimizing NNI: done in 1.85622 secs using 399% CPU
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506  VT+I+R10      105826.286   554 212760.573   827700.573   214990.903
Optimizing NNI: done in 1.20479 secs using 398.8% CPU
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Iteration 200 / LogL: -196382.035 / Time: 0h:18m:48s (0h:2m:21s left)
Optimizing NNI: done in 1.78993 secs using 398.5% CPU
Optimizing NNI: done in 1.46663 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 97: -59358.000
Optimizing NNI: done in 4.53893 secs using 597.9% CPU
Optimizing NNI: done in 1.72066 secs using 399.1% CPU
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Iteration 100 / LogL: -59375.177 / Time: 0h:3m:21s (0h:3m:17s left)
Optimizing NNI: done in 5.22977 secs using 596.6% CPU
Optimizing NNI: done in 1.22458 secs using 399.2% CPU
527  VT+F+I+R9     105884.164   571 212910.329   866134.329   215209.098
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Iteration 110 / LogL: -59380.814 / Time: 0h:3m:36s (0h:2m:52s left)
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Iteration 120 / LogL: -59377.885 / Time: 0h:3m:52s (0h:2m:30s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 122: -59355.623
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Iteration 210 / LogL: -196586.847 / Time: 0h:19m:36s (0h:1m:24s left)
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Iteration 130 / LogL: -59383.678 / Time: 0h:4m:11s (0h:2m:59s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 138: -59353.170
Optimizing NNI: done in 4.53681 secs using 597.6% CPU
Optimizing NNI: done in 1.85552 secs using 398.8% CPU
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Iteration 140 / LogL: -59357.908 / Time: 0h:4m:28s (0h:3m:8s left)
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Optimizing NNI: done in 1.50921 secs using 398.9% CPU
Optimizing NNI: done in 1.63153 secs using 399% CPU
Optimizing NNI: done in 1.94096 secs using 398.6% CPU
Iteration 150 / LogL: -59360.392 / Time: 0h:4m:44s (0h:2m:47s left)
Optimizing NNI: done in 5.39018 secs using 597.2% CPU
Optimizing NNI: done in 1.45917 secs using 399.3% CPU
Optimizing NNI: done in 1.47893 secs using 398.6% CPU
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Optimizing NNI: done in 1.57356 secs using 399.2% CPU
Optimizing NNI: done in 4.56048 secs using 597.2% CPU
Iteration 220 / LogL: -196555.065 / Time: 0h:20m:25s (0h:0m:27s left)
Optimizing NNI: done in 1.80601 secs using 398.6% CPU
Optimizing NNI: done in 1.07112 secs using 398.8% CPU
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Optimizing NNI: done in 4.75685 secs using 597.6% CPU
Optimizing NNI: done in 1.52876 secs using 398.8% CPU
Optimizing NNI: done in 1.64789 secs using 399.4% CPU
528  VT+F+I+R10    105882.614   573 212911.228   870715.228   215218.049
Optimizing NNI: done in 1.5252 secs using 398.6% CPU
Iteration 160 / LogL: -59370.855 / Time: 0h:4m:59s (0h:2m:26s left)
Optimizing NNI: done in 4.62117 secs using 597.4% CPU
Optimizing NNI: done in 1.44403 secs using 398.6% CPU
Optimizing NNI: done in 1.44724 secs using 398.7% CPU
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Optimizing NNI: done in 1.57251 secs using 399.3% CPU
Optimizing NNI: done in 5.59836 secs using 597.9% CPU
Optimizing NNI: done in 1.52325 secs using 398.8% CPU
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Optimizing NNI: done in 4.36062 secs using 598% CPU
Optimizing NNI: done in 1.58265 secs using 399.3% CPU
Optimizing NNI: done in 1.76491 secs using 399.4% CPU
549  PMB+I+R9      106509.202   552 214122.404   824634.404   216344.682
Optimizing NNI: done in 1.69624 secs using 398.4% CPU
Optimizing NNI: done in 4.41098 secs using 597.4% CPU
Optimizing NNI: done in 1.70644 secs using 398.8% CPU
Iteration 170 / LogL: -59372.426 / Time: 0h:5m:15s (0h:2m:6s left)
Optimizing NNI: done in 1.57561 secs using 398.9% CPU
Optimizing NNI: done in 1.79721 secs using 398.9% CPU
Optimizing NNI: done in 5.04245 secs using 597.2% CPU
TREE SEARCH COMPLETED AFTER 226 ITERATIONS / Time: 0h:20m:54s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -196372.493
Optimal log-likelihood: -196372.493
Site proportion and rates:  (0.018,0.132) (0.095,0.281) (0.156,0.440) (0.233,0.642) (0.257,0.950) (0.119,1.509) (0.093,2.229) (0.031,4.003)
Parameters optimization took 1 rounds (0.520 sec)
BEST SCORE FOUND : -196372.493
Total tree length: 156.829

Total number of iterations: 226
CPU time used for tree search: 7154.105 sec (1h:59m:14s)
Wall-clock time used for tree search: 1222.906 sec (0h:20m:22s)
Total CPU time used: 7346.187 sec (2h:2m:26s)
Total wall-clock time used: 1255.193 sec (0h:20m:55s)

===> START BOOTSTRAP REPLICATE NUMBER 5

Creating bootstrap alignment (seed: 70468)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.291 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -203873.310
Optimizing NNI: done in 1.57139 secs using 398.6% CPU
Optimizing NNI: done in 1.51307 secs using 399% CPU
2. Current log-likelihood: -201112.690
Optimizing NNI: done in 1.19486 secs using 399.2% CPU
Optimizing NNI: done in 1.66325 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
3. Current log-likelihood: -201091.022
BETTER TREE FOUND at iteration 176: -59351.987
Optimizing NNI: done in 1.44748 secs using 398.4% CPU
4. Current log-likelihood: -201090.719
Optimizing NNI: done in 1.6492 secs using 399.3% CPU
Optimal log-likelihood: -201090.665
Site proportion and rates:  (0.019,0.095) (0.001,0.199) (0.104,0.296) (0.153,0.460) (0.198,0.621) (0.271,0.945) (0.146,1.633) (0.107,2.602)
Parameters optimization took 4 rounds (9.331 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.29876 secs using 398.4% CPU
Optimizing NNI: done in 1.38521 secs using 399.1% CPU
Iteration 180 / LogL: -59406.751 / Time: 0h:5m:31s (0h:2m:57s left)
Optimizing NNI: done in 1.57979 secs using 399.2% CPU
Optimizing NNI: done in 1.93363 secs using 399% CPU
Optimizing NNI: done in 1.59207 secs using 398.8% CPU
Optimizing NNI: done in 1.58434 secs using 399.1% CPU
Optimizing NNI: done in 1.22001 secs using 398.5% CPU
Calculating distance matrix: done in 10.7598 secs using 599.9% CPU
Computing ML distances took 10.760331 sec (of wall-clock time) 64.547185 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00133491 secs using 425.9% CPU
Constructing RapidNJ tree: done in 0.0230849 secs using 675.6% CPU
Computing RapidNJ tree took 0.024507 sec (of wall-clock time) 0.163630 sec (of CPU time)
Optimizing NNI: done in 1.56582 secs using 398.9% CPU
Log-likelihood of RapidNJ tree: -205047.209
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.60061 secs using 398.5% CPU
Optimizing NNI: done in 1.21452 secs using 398.2% CPU
Optimizing NNI: done in 2.20403 secs using 398.7% CPU
Optimizing NNI: done in 2.03609 secs using 399% CPU
Iteration 190 / LogL: -59372.622 / Time: 0h:5m:47s (0h:2m:38s left)
Optimizing NNI: done in 2.32833 secs using 398.9% CPU
Optimizing NNI: done in 2.00308 secs using 398.6% CPU
Optimizing NNI: done in 1.78258 secs using 399.1% CPU
Optimizing NNI: done in 2.25496 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 194: -59351.246
Optimizing NNI: done in 1.74868 secs using 399.4% CPU
Optimizing NNI: done in 1.40395 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -59351.245
Optimizing NNI: done in 1.37009 secs using 398.6% CPU
Optimizing NNI: done in 1.32237 secs using 399.4% CPU
Optimizing NNI: done in 1.34401 secs using 399.2% CPU
Optimizing NNI: done in 1.50177 secs using 398.8% CPU
Iteration 200 / LogL: -59368.504 / Time: 0h:6m:5s (0h:2m:52s left)
Optimizing NNI: done in 1.6889 secs using 399.1% CPU
Optimizing NNI: done in 1.46928 secs using 398.3% CPU
Optimizing NNI: done in 1.55873 secs using 399% CPU
Optimizing NNI: done in 1.52114 secs using 399% CPU
30.595 second
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Optimizing NNI: done in 1.54502 secs using 399% CPU
Optimizing NNI: done in 1.31335 secs using 398.6% CPU
Optimizing NNI: done in 1.29548 secs using 398.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -59351.239
Optimizing NNI: done in 1.74556 secs using 399.5% CPU
Iteration 210 / LogL: -59358.239 / Time: 0h:6m:21s (0h:2m:33s left)
Optimizing NNI: done in 1.16884 secs using 398.9% CPU
Optimizing NNI: done in 1.41892 secs using 398.9% CPU
Optimizing NNI: done in 1.44307 secs using 398.6% CPU
Optimizing NNI: done in 1.49129 secs using 398.3% CPU
Optimizing NNI: done in 1.73866 secs using 398.6% CPU
Computing log-likelihood of 98 initial trees ... 17.056 seconds
Current best score: -201090.665

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.46538 secs using 399% CPU
Optimizing NNI: done in 1.39273 secs using 398.7% CPU
Optimizing NNI: done in 2.70759 secs using 598.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.3964 secs using 398.5% CPU
Optimizing NNI: done in 1.59905 secs using 398.9% CPU
Optimizing NNI: done in 1.23182 secs using 399% CPU
Iteration 220 / LogL: -59362.721 / Time: 0h:6m:35s (0h:2m:13s left)
BETTER TREE FOUND at iteration 1: -200443.999
Optimizing NNI: done in 1.64602 secs using 398.3% CPU
Optimizing NNI: done in 1.41512 secs using 398.8% CPU
Optimizing NNI: done in 1.61928 secs using 399.1% CPU
Optimizing NNI: done in 3.71522 secs using 598.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.49143 secs using 398.8% CPU
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Optimizing NNI: done in 1.42472 secs using 399.3% CPU
Optimizing NNI: done in 1.85844 secs using 398.9% CPU
550  PMB+I+R10     106508.782   554 214125.565   829065.565   216355.895
Optimizing NNI: done in 1.50587 secs using 398.9% CPU
Optimizing NNI: done in 1.58419 secs using 398.9% CPU
Iteration 230 / LogL: -59354.424 / Time: 0h:6m:51s (0h:1m:55s left)
Optimizing NNI: done in 1.33188 secs using 398.8% CPU
Optimizing NNI: done in 1.16102 secs using 399.1% CPU
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Optimizing NNI: done in 2.01639 secs using 398.7% CPU
571  PMB+F+I+R9    106866.946   571 214875.892   868099.892   217174.662
Optimizing NNI: done in 1.54797 secs using 399.2% CPU
Optimizing NNI: done in 1.76253 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 236: -59349.634
Optimizing NNI: done in 1.36802 secs using 398.4% CPU
Optimizing NNI: done in 1.53747 secs using 399.1% CPU
Optimizing NNI: done in 1.53803 secs using 399% CPU
Optimizing NNI: done in 1.39136 secs using 399.2% CPU
Iteration 240 / LogL: -59378.510 / Time: 0h:7m:7s (0h:2m:51s left)
Optimizing NNI: done in 1.35088 secs using 398.4% CPU
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Optimizing NNI: done in 1.29691 secs using 398.7% CPU
BETTER TREE FOUND at iteration 2: -200357.105
Optimizing NNI: done in 1.88079 secs using 398.5% CPU
Optimizing NNI: done in 1.47667 secs using 398.5% CPU
Optimizing NNI: done in 3.69726 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.5511 secs using 399% CPU
Optimizing NNI: done in 1.54421 secs using 398.4% CPU
Optimizing NNI: done in 1.25547 secs using 398.8% CPU
Iteration 250 / LogL: -59395.469 / Time: 0h:7m:22s (0h:2m:32s left)
BETTER TREE FOUND at iteration 3: -200326.309
Optimizing NNI: done in 1.58909 secs using 399.2% CPU
Optimizing NNI: done in 1.71983 secs using 399% CPU
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Iteration 260 / LogL: -59370.056 / Time: 0h:7m:39s (0h:2m:14s left)
Optimizing NNI: done in 4.19409 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.40991 secs using 398.6% CPU
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Optimizing NNI: done in 1.29691 secs using 398.6% CPU
BETTER TREE FOUND at iteration 7: -200316.936
Optimizing NNI: done in 1.3336 secs using 398.8% CPU
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Iteration 270 / LogL: -59356.109 / Time: 0h:7m:54s (0h:1m:56s left)
Optimizing NNI: done in 1.59736 secs using 398.4% CPU
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Optimizing NNI: done in 3.68629 secs using 597.3% CPU
Iteration 10 / LogL: -200434.121 / Time: 0h:2m:41s
Optimizing NNI: done in 1.29523 secs using 399.1% CPU
Optimizing NNI: done in 1.55594 secs using 398.6% CPU
Optimizing NNI: done in 1.62094 secs using 398.7% CPU
Optimizing NNI: done in 3.91551 secs using 598.6% CPU
Optimizing NNI: done in 1.56686 secs using 398.8% CPU
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Optimizing NNI: done in 3.40111 secs using 597.8% CPU
Optimizing NNI: done in 1.88516 secs using 399.3% CPU
Iteration 280 / LogL: -59356.976 / Time: 0h:8m:9s (0h:1m:38s left)
Optimizing NNI: done in 1.39896 secs using 399% CPU
Optimizing NNI: done in 4.15322 secs using 598% CPU
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Optimizing NNI: done in 1.42134 secs using 398.8% CPU
Optimizing NNI: done in 1.302 secs using 398.2% CPU
Optimizing NNI: done in 4.26653 secs using 597.2% CPU
Optimizing NNI: done in 1.87884 secs using 398.9% CPU
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Optimizing NNI: done in 1.51782 secs using 399.1% CPU
Optimizing NNI: done in 4.17293 secs using 597.6% CPU
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Optimizing NNI: done in 4.07825 secs using 597.4% CPU
Optimizing NNI: done in 1.38205 secs using 398.7% CPU
Iteration 290 / LogL: -59385.610 / Time: 0h:8m:25s (0h:1m:20s left)
Optimizing NNI: done in 1.61992 secs using 399.1% CPU
UPDATE BEST LOG-LIKELIHOOD: -59349.626
Optimizing NNI: done in 1.4043 secs using 399.2% CPU
Optimizing NNI: done in 4.17503 secs using 598% CPU
Optimizing NNI: done in 1.51067 secs using 398.7% CPU
Optimizing NNI: done in 1.26256 secs using 399% CPU
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Optimizing NNI: done in 3.75391 secs using 597.2% CPU
Optimizing NNI: done in 1.65849 secs using 398.7% CPU
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Optimizing NNI: done in 1.6829 secs using 399.1% CPU
Optimizing NNI: done in 1.36919 secs using 398.8% CPU
Iteration 300 / LogL: -59421.020 / Time: 0h:8m:40s (0h:1m:2s left)
Optimizing NNI: done in 4.0218 secs using 596.9% CPU
Iteration 20 / LogL: -200351.912 / Time: 0h:3m:21s
Finish initializing candidate tree set (20)
Current best tree score: -200316.936 / CPU time: 178.512
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.25205 secs using 399.3% CPU
Optimizing NNI: done in 1.4712 secs using 399% CPU
Optimizing NNI: done in 1.38715 secs using 398.9% CPU
Optimizing NNI: done in 4.41993 secs using 596.9% CPU
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Optimizing NNI: done in 2.12419 secs using 398.5% CPU
Optimizing NNI: done in 4.07807 secs using 596.9% CPU
Optimizing NNI: done in 1.66057 secs using 398.6% CPU
Optimizing NNI: done in 1.67815 secs using 398.5% CPU
Optimizing NNI: done in 1.6944 secs using 398.3% CPU
Optimizing NNI: done in 4.50601 secs using 597.9% CPU
Optimizing NNI: done in 1.65187 secs using 399% CPU
Optimizing NNI: done in 1.39996 secs using 399.1% CPU
Iteration 310 / LogL: -59369.793 / Time: 0h:8m:56s (0h:0m:45s left)
Optimizing NNI: done in 1.79712 secs using 398.8% CPU
Optimizing NNI: done in 4.59789 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.74394 secs using 399.1% CPU
Optimizing NNI: done in 1.48148 secs using 398.6% CPU
Optimizing NNI: done in 1.41927 secs using 398.6% CPU
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Optimizing NNI: done in 1.38168 secs using 399.1% CPU
Optimizing NNI: done in 1.57123 secs using 398.5% CPU
Iteration 320 / LogL: -59352.340 / Time: 0h:9m:11s (0h:0m:27s left)
BETTER TREE FOUND at iteration 24: -200302.391
Optimizing NNI: done in 1.48034 secs using 398.3% CPU
Optimizing NNI: done in 1.73727 secs using 398.8% CPU
Optimizing NNI: done in 1.79005 secs using 399% CPU
Optimizing NNI: done in 4.64484 secs using 598.2% CPU
Optimizing NNI: done in 1.67278 secs using 398.7% CPU
Optimizing NNI: done in 1.6226 secs using 398.7% CPU
Optimizing NNI: done in 1.5297 secs using 399.2% CPU
Optimizing NNI: done in 4.28933 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.5242 secs using 399.2% CPU
Optimizing NNI: done in 1.4118 secs using 398.8% CPU
Optimizing NNI: done in 1.49758 secs using 399.2% CPU
Optimizing NNI: done in 1.45804 secs using 399.1% CPU
Iteration 330 / LogL: -59373.326 / Time: 0h:9m:27s (0h:0m:10s left)
Optimizing NNI: done in 1.68531 secs using 399.2% CPU
BETTER TREE FOUND at iteration 26: -200230.310
Optimizing NNI: done in 1.62442 secs using 399.1% CPU
Optimizing NNI: done in 1.44627 secs using 399.1% CPU
Optimizing NNI: done in 1.41566 secs using 398.7% CPU
Optimizing NNI: done in 4.42834 secs using 597.7% CPU
Optimizing NNI: done in 1.68313 secs using 399.1% CPU
Optimizing NNI: done in 1.55547 secs using 398.8% CPU
Optimizing NNI: done in 1.23825 secs using 398.4% CPU
TREE SEARCH COMPLETED AFTER 337 ITERATIONS / Time: 0h:9m:37s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59349.626
Optimizing NNI: done in 4.16275 secs using 598.1% CPU
2. Current log-likelihood: -59349.610
WARNING: Log-likelihood -106869 of PMB+F+I+R10 worse than PMB+F+I+R9 -106867
572  PMB+F+I+R10   106868.985   573 214883.970   872687.970   217190.791
3. Current log-likelihood: -59349.600
4. Current log-likelihood: -59349.589
5. Current log-likelihood: -59349.579
Optimal log-likelihood: -59349.565
Site proportion and rates:  (0.093,0.049) (0.085,0.165) (0.202,0.342) (0.205,0.604) (0.174,0.968) (0.134,1.693) (0.071,2.560) (0.036,5.872)
Parameters optimization took 5 rounds (2.471 sec)
BEST SCORE FOUND : -59349.565
Total tree length: 48.055

Total number of iterations: 337
CPU time used for tree search: 2241.844 sec (0h:37m:21s)
Wall-clock time used for tree search: 565.721 sec (0h:9m:25s)
Total CPU time used: 2300.445 sec (0h:38m:20s)
Total wall-clock time used: 580.392 sec (0h:9m:40s)

===> START BOOTSTRAP REPLICATE NUMBER 18

Creating bootstrap alignment (seed: 67480)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.035 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59005.616
2. Current log-likelihood: -58467.324
3. Current log-likelihood: -58447.378
Optimizing NNI: done in 4.55742 secs using 597.4% CPU
4. Current log-likelihood: -58425.871
5. Current log-likelihood: -58422.022
6. Current log-likelihood: -58421.671
7. Current log-likelihood: -58421.410
8. Current log-likelihood: -58421.109
9. Current log-likelihood: -58420.724
Optimizing NNI: done in 4.23922 secs using 598.3% CPU
Iteration 30 / LogL: -200265.484 / Time: 0h:4m:27s (0h:14m:45s left)
10. Current log-likelihood: -58420.225
11. Current log-likelihood: -58419.596
12. Current log-likelihood: -58418.855
13. Current log-likelihood: -58418.079
14. Current log-likelihood: -58417.449
15. Current log-likelihood: -58417.074
Optimizing NNI: done in 4.72386 secs using 597.1% CPU
16. Current log-likelihood: -58416.899
Optimal log-likelihood: -58416.822
Site proportion and rates:  (0.110,0.073) (0.047,0.200) (0.178,0.309) (0.244,0.596) (0.194,1.013) (0.078,1.570) (0.117,2.406) (0.031,5.790)
Parameters optimization took 16 rounds (12.973 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
593  Blosum62+I+R9 106739.865   552 214583.730   825095.730   216806.008
Calculating distance matrix: done in 1.0868 secs using 399.8% CPU
Computing ML distances took 1.087007 sec (of wall-clock time) 4.345183 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000369072 secs using 394% CPU
Constructing RapidNJ tree: done in 0.00438809 secs using 369.2% CPU
Computing RapidNJ tree took 0.004828 sec (of wall-clock time) 0.018354 sec (of CPU time)
Log-likelihood of RapidNJ tree: -58730.925
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 4.11914 secs using 597.9% CPU
5.129 second
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Computing log-likelihood of 98 initial trees ... 5.376 seconds
Current best score: -58381.023

Do NNI search on 20 best initial trees
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BETTER TREE FOUND at iteration 4: -58215.665
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Iteration 40 / LogL: -200216.762 / Time: 0h:5m:19s (0h:13m:13s left)
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Iteration 20 / LogL: -58239.485 / Time: 0h:1m:2s
Finish initializing candidate tree set (20)
Current best tree score: -58208.587 / CPU time: 47.634
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 30 / LogL: -58197.217 / Time: 0h:1m:21s (0h:4m:41s left)
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594  Blosum62+I+R10 106740.069   554 214588.139   829528.139   216818.468
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615  Blosum62+F+I+R9 106808.088   571 214758.176   867982.176   217056.945
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Iteration 190 / LogL: -58253.270 / Time: 0h:5m:22s (0h:1m:45s left)
WARNING: Log-likelihood -106809 of Blosum62+F+I+R10 worse than Blosum62+F+I+R9 -106808
616  Blosum62+F+I+R10 106809.183   573 214764.366   872568.366   217071.187
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Optimizing NNI: done in 1.57856 secs using 398.8% CPU
Iteration 210 / LogL: -58203.644 / Time: 0h:5m:52s (0h:1m:10s left)
Optimizing NNI: done in 1.50963 secs using 398.4% CPU
Optimizing NNI: done in 4.38009 secs using 596.6% CPU
Optimizing NNI: done in 1.4416 secs using 398.5% CPU
Optimizing NNI: done in 1.60374 secs using 398.8% CPU
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Optimizing NNI: done in 4.66868 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
637  Dayhoff+I+R9  106797.567   552 214699.134   825211.134   216921.412
Optimizing NNI: done in 1.63043 secs using 399% CPU
BETTER TREE FOUND at iteration 107: -200164.011
Optimizing NNI: done in 1.69654 secs using 399% CPU
Optimizing NNI: done in 1.45389 secs using 398.9% CPU
Iteration 220 / LogL: -58203.580 / Time: 0h:6m:6s (0h:0m:53s left)
Optimizing NNI: done in 1.5152 secs using 399.1% CPU
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Iteration 110 / LogL: -200201.584 / Time: 0h:10m:38s (0h:9m:28s left)
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Iteration 230 / LogL: -58335.614 / Time: 0h:6m:21s (0h:0m:36s left)
Optimizing NNI: done in 4.48816 secs using 597.3% CPU
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Optimizing NNI: done in 1.66108 secs using 398.8% CPU
Iteration 240 / LogL: -58201.543 / Time: 0h:6m:36s (0h:0m:19s left)
Optimizing NNI: done in 1.47808 secs using 398.8% CPU
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Optimizing NNI: done in 1.4984 secs using 398.7% CPU
Iteration 250 / LogL: -58200.908 / Time: 0h:6m:51s (0h:0m:3s left)
Optimizing NNI: done in 1.61257 secs using 398.5% CPU
Optimizing NNI: done in 4.53912 secs using 597.1% CPU
Optimizing NNI: done in 1.28885 secs using 399.5% CPU
Optimizing NNI: done in 1.44036 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 253 ITERATIONS / Time: 0h:6m:55s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58196.158
2. Current log-likelihood: -58196.148
Optimal log-likelihood: -58196.144
Site proportion and rates:  (0.112,0.074) (0.056,0.213) (0.179,0.317) (0.246,0.612) (0.209,1.064) (0.064,1.758) (0.102,2.490) (0.032,5.761)
Parameters optimization took 2 rounds (1.666 sec)
BEST SCORE FOUND : -58196.144
Total tree length: 43.632

Total number of iterations: 253
CPU time used for tree search: 1584.200 sec (0h:26m:24s)
Wall-clock time used for tree search: 400.937 sec (0h:6m:40s)
Total CPU time used: 1649.235 sec (0h:27m:29s)
Total wall-clock time used: 417.230 sec (0h:6m:57s)

===> START BOOTSTRAP REPLICATE NUMBER 19

Creating bootstrap alignment (seed: 67481)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.074 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -63061.594
Optimizing NNI: done in 4.26772 secs using 596.5% CPU
2. Current log-likelihood: -62502.000
3. Current log-likelihood: -62495.531
4. Current log-likelihood: -62492.557
5. Current log-likelihood: -62488.463
Optimizing NNI: done in 4.21056 secs using 597% CPU
Iteration 120 / LogL: -200198.584 / Time: 0h:11m:22s (0h:8m:18s left)
6. Current log-likelihood: -62473.490
7. Current log-likelihood: -62467.737
8. Current log-likelihood: -62467.082
9. Current log-likelihood: -62466.827
10. Current log-likelihood: -62466.649
11. Current log-likelihood: -62466.515
Optimizing NNI: done in 4.4096 secs using 597.5% CPU
12. Current log-likelihood: -62466.403
Optimal log-likelihood: -62466.312
Site proportion and rates:  (0.099,0.057) (0.073,0.184) (0.137,0.314) (0.156,0.548) (0.224,0.864) (0.132,1.381) (0.153,2.192) (0.026,5.359)
Parameters optimization took 12 rounds (10.462 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.0982 secs using 399.7% CPU
Computing ML distances took 1.098396 sec (of wall-clock time) 4.389839 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000394106 secs using 659.5% CPU
Constructing RapidNJ tree: done in 0.00430012 secs using 500.9% CPU
Computing RapidNJ tree took 0.004760 sec (of wall-clock time) 0.024202 sec (of CPU time)
Log-likelihood of RapidNJ tree: -62655.450
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.01553 secs using 598.5% CPU
5.141 second
Optimizing NNI: done in 4.29586 secs using 597.4% CPU
Optimizing NNI: done in 4.15752 secs using 597.4% CPU
Computing log-likelihood of 98 initial trees ... 5.422 seconds
Current best score: -62456.220

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.18016 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -62206.208
Optimizing NNI: done in 4.26687 secs using 597.1% CPU
Optimizing NNI: done in 0.781037 secs using 398.9% CPU
Optimizing NNI: done in 1.28563 secs using 398.5% CPU
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Iteration 10 / LogL: -62241.898 / Time: 0h:0m:36s
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Optimizing NNI: done in 3.7939 secs using 597.8% CPU
Iteration 130 / LogL: -200278.056 / Time: 0h:12m:4s (0h:7m:12s left)
Optimizing NNI: done in 1.49875 secs using 399% CPU
Optimizing NNI: done in 1.4007 secs using 398.5% CPU
Iteration 20 / LogL: -62265.655 / Time: 0h:0m:49s
Finish initializing candidate tree set (20)
Current best tree score: -62206.208 / CPU time: 36.940
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.23021 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -62204.561
Optimizing NNI: done in 3.99511 secs using 597.9% CPU
Optimizing NNI: done in 1.46061 secs using 398.7% CPU
Optimizing NNI: done in 1.46616 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -62204.093
Optimizing NNI: done in 4.10886 secs using 597.2% CPU
Optimizing NNI: done in 1.15211 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -62202.817
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Iteration 30 / LogL: -62214.783 / Time: 0h:1m:5s (0h:3m:32s left)
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Iteration 40 / LogL: -62217.292 / Time: 0h:1m:19s (0h:2m:51s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -62197.816
Optimizing NNI: done in 1.34719 secs using 399.2% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.9826 secs using 597.1% CPU
Iteration 140 / LogL: -200164.173 / Time: 0h:12m:48s (0h:6m:10s left)
BETTER TREE FOUND at iteration 46: -62191.080
Optimizing NNI: done in 1.37208 secs using 399.1% CPU
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Iteration 50 / LogL: -62214.312 / Time: 0h:1m:36s (0h:3m:8s left)
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Iteration 60 / LogL: -62223.875 / Time: 0h:1m:49s (0h:2m:39s left)
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Iteration 70 / LogL: -62197.590 / Time: 0h:2m:4s (0h:2m:16s left)
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Iteration 150 / LogL: -200208.697 / Time: 0h:13m:33s (0h:5m:10s left)
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Iteration 80 / LogL: -62222.598 / Time: 0h:2m:17s (0h:1m:55s left)
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Iteration 90 / LogL: -62251.894 / Time: 0h:2m:31s (0h:1m:35s left)
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Optimizing NNI: done in 1.51592 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 98: -62190.323
638  Dayhoff+I+R10 106793.149   554 214694.298   829634.298   216924.628
Optimizing NNI: done in 4.03107 secs using 597.8% CPU
Optimizing NNI: done in 1.30784 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 99: -62186.998
Optimizing NNI: done in 1.44537 secs using 399.1% CPU
Iteration 100 / LogL: -62192.365 / Time: 0h:2m:47s (0h:2m:47s left)
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Estimate model parameters (epsilon = 0.100)
659  Dayhoff+F+I+R9 106295.615   571 213733.231   866957.231   216032.000
BETTER TREE FOUND at iteration 106: -62185.032
Optimizing NNI: done in 1.28947 secs using 399% CPU
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Iteration 160 / LogL: -200213.653 / Time: 0h:14m:16s (0h:4m:12s left)
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Iteration 110 / LogL: -62205.780 / Time: 0h:3m:2s (0h:2m:40s left)
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Iteration 120 / LogL: -62197.965 / Time: 0h:3m:16s (0h:2m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 125: -62184.259
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Iteration 130 / LogL: -62193.261 / Time: 0h:3m:30s (0h:2m:34s left)
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Iteration 170 / LogL: -200333.670 / Time: 0h:14m:59s (0h:3m:16s left)
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Iteration 140 / LogL: -62219.837 / Time: 0h:3m:45s (0h:2m:17s left)
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Iteration 150 / LogL: -62185.040 / Time: 0h:3m:58s (0h:2m:0s left)
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Iteration 160 / LogL: -62280.611 / Time: 0h:4m:12s (0h:1m:43s left)
Optimizing NNI: done in 4.01893 secs using 597% CPU
Optimizing NNI: done in 1.291 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 161: -62183.062
Optimizing NNI: done in 1.64311 secs using 399.2% CPU
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Iteration 180 / LogL: -200178.489 / Time: 0h:15m:43s (0h:2m:22s left)
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BETTER TREE FOUND at iteration 169: -62181.925
Optimizing NNI: done in 1.3882 secs using 399.3% CPU
Iteration 170 / LogL: -62264.215 / Time: 0h:4m:28s (0h:2m:37s left)
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Iteration 180 / LogL: -62181.986 / Time: 0h:4m:42s (0h:2m:20s left)
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Iteration 190 / LogL: -62187.485 / Time: 0h:4m:55s (0h:2m:3s left)
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BETTER TREE FOUND at iteration 187: -200156.458
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BETTER TREE FOUND at iteration 197: -62181.917
Optimizing NNI: done in 1.54088 secs using 398.7% CPU
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Iteration 200 / LogL: -62188.938 / Time: 0h:5m:9s (0h:2m:30s left)
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Iteration 190 / LogL: -200281.896 / Time: 0h:16m:30s (0h:8m:27s left)
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BETTER TREE FOUND at iteration 205: -62181.915
Optimizing NNI: done in 1.28641 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 208: -62181.262
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Iteration 210 / LogL: -62243.498 / Time: 0h:5m:23s (0h:2m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 218: -62181.168
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Iteration 220 / LogL: -62184.147 / Time: 0h:5m:37s (0h:2m:31s left)
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Iteration 230 / LogL: -62192.569 / Time: 0h:5m:51s (0h:2m:14s left)
660  Dayhoff+F+I+R10 106293.137   573 213732.274   871536.274   216039.095
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Iteration 200 / LogL: -200707.090 / Time: 0h:17m:11s (0h:7m:30s left)
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Iteration 240 / LogL: -62191.198 / Time: 0h:6m:5s (0h:1m:59s left)
681  mtREV+I+R9    110319.856   552 221743.713   832255.713   223965.991
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 203: -200155.203
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Iteration 250 / LogL: -62184.554 / Time: 0h:6m:19s (0h:1m:43s left)
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Iteration 260 / LogL: -62188.559 / Time: 0h:6m:33s (0h:1m:28s left)
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Iteration 210 / LogL: -200199.098 / Time: 0h:17m:58s (0h:7m:59s left)
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Iteration 270 / LogL: -62199.477 / Time: 0h:6m:47s (0h:1m:12s left)
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Iteration 280 / LogL: -62181.292 / Time: 0h:7m:1s (0h:0m:57s left)
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Iteration 290 / LogL: -62185.567 / Time: 0h:7m:15s (0h:0m:42s left)
Optimizing NNI: done in 1.44956 secs using 399.5% CPU
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Iteration 220 / LogL: -200212.477 / Time: 0h:18m:41s (0h:7m:4s left)
Optimizing NNI: done in 1.62477 secs using 399% CPU
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BETTER TREE FOUND at iteration 298: -62181.167
Optimizing NNI: done in 1.25292 secs using 399.1% CPU
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Iteration 300 / LogL: -62189.831 / Time: 0h:7m:29s (0h:2m:27s left)
Optimizing NNI: done in 1.47722 secs using 399% CPU
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WARNING: Log-likelihood -110326 of mtREV+I+R10 worse than mtREV+I+R9 -110320
682  mtREV+I+R10   110326.415   554 221760.831   836700.831   223991.160
Optimizing NNI: done in 4.61325 secs using 598.3% CPU
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Optimizing NNI: done in 1.45755 secs using 398.8% CPU
BETTER TREE FOUND at iteration 310: -62181.164
Iteration 310 / LogL: -62181.164 / Time: 0h:7m:42s (0h:2m:29s left)
Optimizing NNI: done in 1.15283 secs using 399% CPU
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Iteration 320 / LogL: -62197.690 / Time: 0h:7m:56s (0h:2m:14s left)
703  mtREV+F+I+R9  107406.853   571 215955.705   869179.705   218254.475
Optimizing NNI: done in 1.28079 secs using 399% CPU
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Iteration 230 / LogL: -200228.000 / Time: 0h:19m:24s (0h:6m:11s left)
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Iteration 330 / LogL: -62181.166 / Time: 0h:8m:9s (0h:1m:59s left)
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Iteration 340 / LogL: -62186.432 / Time: 0h:8m:22s (0h:1m:43s left)
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Iteration 350 / LogL: -62187.488 / Time: 0h:8m:36s (0h:1m:28s left)
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Iteration 240 / LogL: -200212.037 / Time: 0h:20m:7s (0h:5m:18s left)
Optimizing NNI: done in 1.30405 secs using 398.5% CPU
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Iteration 360 / LogL: -62188.441 / Time: 0h:8m:50s (0h:1m:13s left)
704  mtREV+F+I+R10 107402.753   573 215951.506   873755.506   218258.327
Optimizing NNI: done in 1.38861 secs using 399% CPU
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Iteration 370 / LogL: -62186.261 / Time: 0h:9m:4s (0h:0m:59s left)
725  mtART+I+R9    111278.032   552 223660.063   834172.063   225882.341
Optimizing NNI: done in 1.31631 secs using 398.2% CPU
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Iteration 380 / LogL: -62185.434 / Time: 0h:9m:17s (0h:0m:44s left)
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Iteration 390 / LogL: -62190.733 / Time: 0h:9m:30s (0h:0m:29s left)
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Iteration 250 / LogL: -200244.882 / Time: 0h:20m:50s (0h:4m:26s left)
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Iteration 400 / LogL: -62185.827 / Time: 0h:9m:44s (0h:0m:14s left)
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Iteration 410 / LogL: -62236.134 / Time: 0h:9m:58s (0h:0m:0s left)
Optimizing NNI: done in 1.44173 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 411 ITERATIONS / Time: 0h:9m:59s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -62181.164
Optimal log-likelihood: -62181.154
Site proportion and rates:  (0.094,0.055) (0.078,0.179) (0.143,0.310) (0.163,0.573) (0.214,0.860) (0.129,1.392) (0.154,2.222) (0.025,5.447)
Parameters optimization took 1 rounds (0.511 sec)
BEST SCORE FOUND : -62181.154
Total tree length: 47.469

Total number of iterations: 411
CPU time used for tree search: 2329.901 sec (0h:38m:49s)
Wall-clock time used for tree search: 587.837 sec (0h:9m:47s)
Total CPU time used: 2380.366 sec (0h:39m:40s)
Total wall-clock time used: 600.462 sec (0h:10m:0s)

===> START BOOTSTRAP REPLICATE NUMBER 20

Creating bootstrap alignment (seed: 67482)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.055 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -62997.704
2. Current log-likelihood: -62419.841
Optimizing NNI: done in 4.07249 secs using 597.2% CPU
3. Current log-likelihood: -62415.118
4. Current log-likelihood: -62414.918
5. Current log-likelihood: -62414.785
6. Current log-likelihood: -62414.602
7. Current log-likelihood: -62414.278
Optimizing NNI: done in 4.10332 secs using 597.3% CPU
8. Current log-likelihood: -62413.671
9. Current log-likelihood: -62412.582
10. Current log-likelihood: -62410.964
11. Current log-likelihood: -62409.802
12. Current log-likelihood: -62409.351
Optimizing NNI: done in 4.2705 secs using 597.5% CPU
13. Current log-likelihood: -62409.170
Optimal log-likelihood: -62409.096
Site proportion and rates:  (0.101,0.058) (0.093,0.183) (0.094,0.365) (0.191,0.548) (0.184,0.882) (0.141,1.392) (0.122,2.068) (0.073,3.079)
Parameters optimization took 13 rounds (11.712 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.08282 secs using 399.7% CPU
Computing ML distances took 1.082993 sec (of wall-clock time) 4.328436 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000355005 secs using 395.2% CPU
Constructing RapidNJ tree: done in 0.00431299 secs using 393.1% CPU
Computing RapidNJ tree took 0.004732 sec (of wall-clock time) 0.018974 sec (of CPU time)
Log-likelihood of RapidNJ tree: -62376.444
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.55635 secs using 597.7% CPU
Iteration 260 / LogL: -200243.295 / Time: 0h:21m:33s (0h:3m:34s left)
5.072 second
WARNING: Log-likelihood -111288 of mtART+I+R10 worse than mtART+I+R9 -111278
726  mtART+I+R10   111287.501   554 223683.001   838623.001   225913.331
Optimizing NNI: done in 5.58636 secs using 596.8% CPU
Computing log-likelihood of 98 initial trees ... 5.583 seconds
Current best score: -62234.720

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -62059.830
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 264: -200152.116
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747  mtART+F+I+R9  108938.989   571 219019.978   872243.978   221318.747
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Iteration 10 / LogL: -62119.000 / Time: 0h:0m:44s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 17: -62057.441
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Iteration 270 / LogL: -200189.498 / Time: 0h:22m:18s (0h:7m:47s left)
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Iteration 20 / LogL: -62142.523 / Time: 0h:1m:6s
Finish initializing candidate tree set (20)
Current best tree score: -62057.441 / CPU time: 53.131
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -62052.788
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BETTER TREE FOUND at iteration 29: -62050.031
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Iteration 30 / LogL: -62055.107 / Time: 0h:1m:29s (0h:5m:4s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 32: -62048.940
748  mtART+F+I+R10 108901.689   573 218949.377   876753.377   221256.198
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -62046.692
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Iteration 280 / LogL: -200217.359 / Time: 0h:23m:1s (0h:6m:55s left)
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769  mtZOA+I+R9    108385.444   552 217874.887   828386.887   220097.165
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Iteration 40 / LogL: -62049.037 / Time: 0h:1m:50s (0h:4m:29s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 50 / LogL: -62050.063 / Time: 0h:2m:9s (0h:3m:43s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 57: -62045.480
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 69: -62044.446
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Iteration 300 / LogL: -200327.076 / Time: 0h:24m:33s (0h:6m:58s left)
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Iteration 90 / LogL: -62046.425 / Time: 0h:3m:29s (0h:3m:5s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 91: -62040.370
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Iteration 100 / LogL: -62065.908 / Time: 0h:3m:47s (0h:3m:29s left)
770  mtZOA+I+R10   108374.764   554 217857.528   832797.528   220087.858
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791  mtZOA+F+I+R9  107160.174   571 215462.348   868686.348   217761.117
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UPDATE BEST LOG-LIKELIHOOD: -62040.360
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Iteration 120 / LogL: -62040.476 / Time: 0h:4m:24s (0h:2m:37s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 316: -200142.796
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Iteration 140 / LogL: -62050.305 / Time: 0h:5m:2s (0h:1m:50s left)
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792  mtZOA+F+I+R10 107154.253   573 215454.506   873258.506   217761.327
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813  mtMet+I+R9    109377.894   552 219859.788   830371.788   222082.066
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Iteration 150 / LogL: -62045.525 / Time: 0h:5m:20s (0h:1m:28s left)
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Iteration 330 / LogL: -200192.736 / Time: 0h:26m:48s (0h:7m:0s left)
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Iteration 160 / LogL: -62060.053 / Time: 0h:5m:39s (0h:1m:6s left)
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Iteration 340 / LogL: -200160.102 / Time: 0h:27m:30s (0h:6m:10s left)
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Iteration 180 / LogL: -62042.115 / Time: 0h:6m:17s (0h:0m:23s left)
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Iteration 190 / LogL: -62048.765 / Time: 0h:6m:36s (0h:0m:2s left)
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TREE SEARCH COMPLETED AFTER 192 ITERATIONS / Time: 0h:6m:40s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -62040.360
2. Current log-likelihood: -62040.349
Optimal log-likelihood: -62040.341
Site proportion and rates:  (0.103,0.061) (0.093,0.186) (0.130,0.397) (0.165,0.580) (0.179,0.891) (0.152,1.420) (0.136,2.255) (0.042,3.545)
Parameters optimization took 2 rounds (1.226 sec)
BEST SCORE FOUND : -62040.341
Total tree length: 44.730

Total number of iterations: 192
CPU time used for tree search: 1527.755 sec (0h:25m:27s)
Wall-clock time used for tree search: 386.723 sec (0h:6m:26s)
Total CPU time used: 1585.766 sec (0h:26m:25s)
Total wall-clock time used: 401.251 sec (0h:6m:41s)

===> START BOOTSTRAP REPLICATE NUMBER 21

Creating bootstrap alignment (seed: 67483)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.060 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59623.772
2. Current log-likelihood: -59103.353
Optimizing NNI: done in 4.81893 secs using 597.6% CPU
3. Current log-likelihood: -59098.664
4. Current log-likelihood: -59090.466
5. Current log-likelihood: -59084.273
6. Current log-likelihood: -59081.169
7. Current log-likelihood: -59075.821
8. Current log-likelihood: -59074.780
Optimizing NNI: done in 4.75992 secs using 597.9% CPU
Optimal log-likelihood: -59074.720
Site proportion and rates:  (0.101,0.069) (0.118,0.204) (0.084,0.413) (0.106,0.429) (0.236,0.749) (0.167,1.285) (0.163,2.272) (0.025,5.125)
Parameters optimization took 8 rounds (7.106 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.08578 secs using 399.6% CPU
Computing ML distances took 1.085963 sec (of wall-clock time) 4.339131 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000360966 secs using 420% CPU
Constructing RapidNJ tree: done in 0.00430202 secs using 334.3% CPU
Computing RapidNJ tree took 0.004724 sec (of wall-clock time) 0.017969 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59158.719
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 3.88973 secs using 596.6% CPU
5.356 second
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Iteration 350 / LogL: -200216.974 / Time: 0h:28m:14s (0h:5m:20s left)
Optimizing NNI: done in 4.40236 secs using 597.2% CPU
Computing log-likelihood of 98 initial trees ... 5.501 seconds
Current best score: -58998.862

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -58806.223
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -58796.945
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -58771.665
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Iteration 10 / LogL: -58826.466 / Time: 0h:0m:37s
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814  mtMet+I+R10   109375.680   554 219859.360   834799.360   222089.690
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Iteration 20 / LogL: -58818.089 / Time: 0h:0m:50s
Finish initializing candidate tree set (20)
Current best tree score: -58771.665 / CPU time: 41.413
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -58759.317
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835  mtMet+F+I+R9  106622.393   571 214386.786   867610.786   216685.556
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Iteration 360 / LogL: -200296.676 / Time: 0h:28m:58s (0h:4m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -58756.647
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -58754.479
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Iteration 40 / LogL: -58763.573 / Time: 0h:1m:23s (0h:3m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -58754.103
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -58752.876
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Iteration 380 / LogL: -200303.048 / Time: 0h:30m:26s (0h:2m:53s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 82: -58747.489
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Iteration 90 / LogL: -58747.557 / Time: 0h:2m:40s (0h:2m:45s left)
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BETTER TREE FOUND at iteration 96: -58747.488
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Iteration 100 / LogL: -58750.758 / Time: 0h:2m:55s (0h:2m:49s left)
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WARNING: Log-likelihood -106624 of mtMet+F+I+R10 worse than mtMet+F+I+R9 -106622
836  mtMet+F+I+R10 106624.494   573 214394.988   872198.988   216701.809
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Iteration 110 / LogL: -58798.892 / Time: 0h:3m:9s (0h:2m:29s left)
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BETTER TREE FOUND at iteration 119: -58747.488
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Iteration 120 / LogL: -58747.490 / Time: 0h:3m:25s (0h:2m:50s left)
857  mtVer+I+R9    110551.891   552 222207.782   832719.782   224430.060
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Iteration 130 / LogL: -58747.488 / Time: 0h:3m:40s (0h:2m:31s left)
Optimizing NNI: done in 1.52812 secs using 399% CPU
Optimizing NNI: done in 1.58967 secs using 398.8% CPU
Optimizing NNI: done in 4.28234 secs using 598% CPU
Optimizing NNI: done in 1.04733 secs using 399% CPU
Optimizing NNI: done in 1.53012 secs using 399.3% CPU
Optimizing NNI: done in 1.48866 secs using 398.8% CPU
Optimizing NNI: done in 4.42108 secs using 597.7% CPU
Optimizing NNI: done in 1.41368 secs using 399.4% CPU
Optimizing NNI: done in 1.43459 secs using 398.8% CPU
Optimizing NNI: done in 1.65998 secs using 399% CPU
Optimizing NNI: done in 3.75656 secs using 598% CPU
Iteration 400 / LogL: -200174.786 / Time: 0h:31m:52s (0h:1m:16s left)
Optimizing NNI: done in 1.47996 secs using 398.4% CPU
Optimizing NNI: done in 1.63042 secs using 399% CPU
Iteration 140 / LogL: -58763.424 / Time: 0h:3m:54s (0h:2m:13s left)
Optimizing NNI: done in 1.20681 secs using 399.5% CPU
Optimizing NNI: done in 4.42427 secs using 597.5% CPU
Optimizing NNI: done in 1.36361 secs using 399.1% CPU
Optimizing NNI: done in 1.32861 secs using 398.9% CPU
Optimizing NNI: done in 1.67996 secs using 399.2% CPU
Optimizing NNI: done in 3.9782 secs using 597.9% CPU
Optimizing NNI: done in 1.41675 secs using 399% CPU
Optimizing NNI: done in 1.49981 secs using 399.4% CPU
Optimizing NNI: done in 1.5593 secs using 399.4% CPU
Optimizing NNI: done in 4.56842 secs using 597.1% CPU
Optimizing NNI: done in 1.59294 secs using 399.1% CPU
Optimizing NNI: done in 1.60417 secs using 399.1% CPU
Optimizing NNI: done in 1.4628 secs using 399.2% CPU
Iteration 150 / LogL: -58747.552 / Time: 0h:4m:9s (0h:1m:55s left)
Optimizing NNI: done in 4.37858 secs using 597% CPU
Optimizing NNI: done in 1.22843 secs using 399% CPU
Optimizing NNI: done in 1.53453 secs using 399.1% CPU
Optimizing NNI: done in 3.79938 secs using 597.7% CPU
Optimizing NNI: done in 1.46144 secs using 398.9% CPU
Optimizing NNI: done in 1.25784 secs using 399.4% CPU
Optimizing NNI: done in 1.60425 secs using 399.3% CPU
Optimizing NNI: done in 4.19495 secs using 598% CPU
Optimizing NNI: done in 1.54658 secs using 399.2% CPU
Optimizing NNI: done in 1.60088 secs using 399.4% CPU
Optimizing NNI: done in 1.5538 secs using 399.2% CPU
Optimizing NNI: done in 3.91403 secs using 598.6% CPU
Optimizing NNI: done in 1.4827 secs using 399.1% CPU
Optimizing NNI: done in 1.37796 secs using 399.1% CPU
Iteration 160 / LogL: -58754.829 / Time: 0h:4m:24s (0h:1m:38s left)
WARNING: Log-likelihood -110569 of mtVer+I+R10 worse than mtVer+I+R9 -110552
858  mtVer+I+R10   110568.998   554 222245.996   837185.996   224476.326
Optimizing NNI: done in 1.11587 secs using 399.2% CPU
Optimizing NNI: done in 4.22254 secs using 597.2% CPU
Optimizing NNI: done in 1.61739 secs using 398.6% CPU
Optimizing NNI: done in 1.36993 secs using 398.8% CPU
Optimizing NNI: done in 3.78495 secs using 597.7% CPU
Optimizing NNI: done in 1.67667 secs using 399.1% CPU
Optimizing NNI: done in 1.64675 secs using 399.1% CPU
Optimizing NNI: done in 1.38611 secs using 399% CPU
Optimizing NNI: done in 4.02346 secs using 597.7% CPU
Iteration 410 / LogL: -200162.272 / Time: 0h:32m:33s (0h:0m:28s left)
Optimizing NNI: done in 1.26909 secs using 399.2% CPU
Optimizing NNI: done in 1.33433 secs using 399.1% CPU
Optimizing NNI: done in 1.38711 secs using 399.1% CPU
Optimizing NNI: done in 4.11823 secs using 597.5% CPU
Optimizing NNI: done in 1.30652 secs using 399.1% CPU
Iteration 170 / LogL: -58809.250 / Time: 0h:4m:38s (0h:1m:20s left)
Optimizing NNI: done in 1.27134 secs using 399.6% CPU
879  mtVer+F+I+R9  107889.284   571 216920.568   870144.568   219219.337
Optimizing NNI: done in 1.16486 secs using 399.2% CPU
Optimizing NNI: done in 1.55393 secs using 399.1% CPU
Optimizing NNI: done in 4.44616 secs using 597.4% CPU
Optimizing NNI: done in 1.11212 secs using 399.3% CPU
Optimizing NNI: done in 1.57919 secs using 398.6% CPU
Optimizing NNI: done in 1.37423 secs using 399.2% CPU
Optimizing NNI: done in 4.15776 secs using 597.5% CPU
Optimizing NNI: done in 1.63 secs using 399.1% CPU
Optimizing NNI: done in 1.48654 secs using 398.8% CPU
Optimizing NNI: done in 4.01077 secs using 598.2% CPU
Optimizing NNI: done in 1.41151 secs using 398.6% CPU
Optimizing NNI: done in 1.71727 secs using 399.1% CPU
Iteration 180 / LogL: -58747.553 / Time: 0h:4m:53s (0h:1m:3s left)
Optimizing NNI: done in 1.17606 secs using 398.8% CPU
Optimizing NNI: done in 4.28062 secs using 597.2% CPU
Optimizing NNI: done in 1.25806 secs using 399.1% CPU
Optimizing NNI: done in 1.11895 secs using 399.2% CPU
Optimizing NNI: done in 1.34309 secs using 398.7% CPU
Optimizing NNI: done in 1.2467 secs using 399% CPU
Optimizing NNI: done in 4.18076 secs using 597.6% CPU
Optimizing NNI: done in 1.52431 secs using 399% CPU
Optimizing NNI: done in 1.3525 secs using 399.2% CPU
Optimizing NNI: done in 1.38867 secs using 398.8% CPU
Optimizing NNI: done in 4.25582 secs using 597.6% CPU
TREE SEARCH COMPLETED AFTER 417 ITERATIONS / Time: 0h:33m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -200142.796
Optimizing NNI: done in 1.3801 secs using 398.9% CPU
2. Current log-likelihood: -200142.786
Optimizing NNI: done in 1.36743 secs using 399% CPU
Iteration 190 / LogL: -58753.899 / Time: 0h:5m:6s (0h:0m:47s left)
Optimal log-likelihood: -200142.780
Site proportion and rates:  (0.019,0.100) (0.105,0.294) (0.121,0.455) (0.204,0.595) (0.117,0.826) (0.184,0.994) (0.149,1.651) (0.101,2.629)
Parameters optimization took 2 rounds (2.576 sec)
BEST SCORE FOUND : -200142.780
Total tree length: 157.270

Total number of iterations: 417
CPU time used for tree search: 11563.693 sec (3h:12m:43s)
Wall-clock time used for tree search: 1961.198 sec (0h:32m:41s)
Total CPU time used: 11713.962 sec (3h:15m:13s)
Total wall-clock time used: 1986.415 sec (0h:33m:6s)

===> START BOOTSTRAP REPLICATE NUMBER 6

Creating bootstrap alignment (seed: 70469)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.287 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194892.684
Optimizing NNI: done in 1.84089 secs using 399.2% CPU
Optimizing NNI: done in 1.53108 secs using 399% CPU
2. Current log-likelihood: -192376.222
Optimizing NNI: done in 1.50102 secs using 399.3% CPU
3. Current log-likelihood: -192324.837
Optimizing NNI: done in 1.45437 secs using 399.1% CPU
Optimizing NNI: done in 1.34799 secs using 398.6% CPU
4. Current log-likelihood: -192322.162
Optimizing NNI: done in 1.75327 secs using 399.6% CPU
5. Current log-likelihood: -192319.757
Optimizing NNI: done in 1.5452 secs using 399.1% CPU
6. Current log-likelihood: -192315.856
Optimizing NNI: done in 1.4513 secs using 399.4% CPU
Optimizing NNI: done in 1.42519 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -58747.488
7. Current log-likelihood: -192311.393
Optimizing NNI: done in 1.56811 secs using 398.6% CPU
Iteration 200 / LogL: -58754.940 / Time: 0h:5m:22s (0h:0m:30s left)
8. Current log-likelihood: -192309.997
Optimizing NNI: done in 1.7579 secs using 399.2% CPU
Optimizing NNI: done in 1.47662 secs using 399.4% CPU
9. Current log-likelihood: -192309.802
Optimizing NNI: done in 1.64834 secs using 398.8% CPU
Optimal log-likelihood: -192309.774
Site proportion and rates:  (0.012,0.087) (0.068,0.223) (0.108,0.362) (0.260,0.544) (0.125,0.782) (0.169,1.063) (0.154,1.624) (0.104,2.644)
Parameters optimization took 9 rounds (20.796 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.63429 secs using 399.1% CPU
Optimizing NNI: done in 1.51364 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -58747.488
Optimizing NNI: done in 1.54886 secs using 399.1% CPU
Optimizing NNI: done in 1.63445 secs using 399.2% CPU
Optimizing NNI: done in 1.34956 secs using 399% CPU
Optimizing NNI: done in 1.61961 secs using 398.9% CPU
Optimizing NNI: done in 1.40829 secs using 398.8% CPU
Iteration 210 / LogL: -58747.489 / Time: 0h:5m:37s (0h:0m:14s left)
Calculating distance matrix: done in 10.1839 secs using 599.9% CPU
Computing ML distances took 10.184413 sec (of wall-clock time) 61.090859 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.001333 secs using 588.2% CPU
Constructing RapidNJ tree: done in 0.0232 secs using 680% CPU
Computing RapidNJ tree took 0.024633 sec (of wall-clock time) 0.166486 sec (of CPU time)
Optimizing NNI: done in 1.43864 secs using 399.2% CPU
Log-likelihood of RapidNJ tree: -195441.841
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.53093 secs using 399% CPU
Optimizing NNI: done in 1.67707 secs using 399.3% CPU
Optimizing NNI: done in 1.26411 secs using 399% CPU
Optimizing NNI: done in 1.34952 secs using 398.5% CPU
Optimizing NNI: done in 1.32343 secs using 399.3% CPU
Optimizing NNI: done in 1.27954 secs using 398.8% CPU
Optimizing NNI: done in 1.35886 secs using 399.1% CPU
Optimizing NNI: done in 1.19032 secs using 399% CPU
Optimizing NNI: done in 1.46304 secs using 399% CPU
Iteration 220 / LogL: -58755.661 / Time: 0h:5m:51s (0h:0m:-2s left)
TREE SEARCH COMPLETED AFTER 220 ITERATIONS / Time: 0h:5m:51s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58747.488
Optimal log-likelihood: -58747.485
Site proportion and rates:  (0.100,0.068) (0.128,0.207) (0.073,0.420) (0.093,0.420) (0.242,0.715) (0.171,1.246) (0.170,2.305) (0.023,5.186)
Parameters optimization took 1 rounds (0.634 sec)
BEST SCORE FOUND : -58747.485
Total tree length: 43.012

Total number of iterations: 220
CPU time used for tree search: 1353.803 sec (0h:22m:33s)
Wall-clock time used for tree search: 343.227 sec (0h:5m:43s)
Total CPU time used: 1390.978 sec (0h:23m:10s)
Total wall-clock time used: 352.519 sec (0h:5m:52s)

===> START BOOTSTRAP REPLICATE NUMBER 22

Creating bootstrap alignment (seed: 67484)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.068 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59836.832
2. Current log-likelihood: -59279.064
3. Current log-likelihood: -59272.761
4. Current log-likelihood: -59267.876
5. Current log-likelihood: -59260.713
6. Current log-likelihood: -59240.598
WARNING: Log-likelihood -107907 of mtVer+F+I+R10 worse than mtVer+F+I+R9 -107889
880  mtVer+F+I+R10 107907.498   573 216960.996   874764.996   219267.817
7. Current log-likelihood: -59239.102
8. Current log-likelihood: -59238.939
9. Current log-likelihood: -59238.793
10. Current log-likelihood: -59238.626
11. Current log-likelihood: -59238.413
12. Current log-likelihood: -59238.137
13. Current log-likelihood: -59237.799
14. Current log-likelihood: -59237.409
15. Current log-likelihood: -59236.993
16. Current log-likelihood: -59236.573
17. Current log-likelihood: -59236.195
18. Current log-likelihood: -59235.907
19. Current log-likelihood: -59235.721
20. Current log-likelihood: -59235.618
Optimal log-likelihood: -59235.563
Site proportion and rates:  (0.133,0.074) (0.091,0.243) (0.147,0.396) (0.213,0.669) (0.139,1.007) (0.111,1.519) (0.139,2.305) (0.026,5.210)
Parameters optimization took 20 rounds (16.559 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.08186 secs using 399.8% CPU
Computing ML distances took 1.082051 sec (of wall-clock time) 4.325539 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00037694 secs using 420.2% CPU
Constructing RapidNJ tree: done in 0.00418615 secs using 332.6% CPU
Computing RapidNJ tree took 0.004617 sec (of wall-clock time) 0.018530 sec (of CPU time)
30.514 second
Log-likelihood of RapidNJ tree: -59443.615
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 901  mtInv+I+R9    109939.125   552 220982.250   831494.250   223204.528
5.239 second
Computing log-likelihood of 98 initial trees ... 5.385 seconds
Current best score: -59217.710

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.3854 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -59031.878
Optimizing NNI: done in 1.07952 secs using 398.7% CPU
Optimizing NNI: done in 1.59534 secs using 399.3% CPU
Computing log-likelihood of 98 initial trees ... 17.102 seconds
Current best score: -192309.774

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.43976 secs using 398.9% CPU
Optimizing NNI: done in 1.13708 secs using 399.1% CPU
Optimizing NNI: done in 3.13144 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.52785 secs using 399.3% CPU
Optimizing NNI: done in 1.45211 secs using 398.6% CPU
BETTER TREE FOUND at iteration 1: -191634.199
Optimizing NNI: done in 1.65729 secs using 398.8% CPU
Optimizing NNI: done in 1.41536 secs using 398.5% CPU
Optimizing NNI: done in 1.73912 secs using 398.7% CPU
Iteration 10 / LogL: -59120.266 / Time: 0h:0m:44s
Optimizing NNI: done in 1.69114 secs using 399.2% CPU
Optimizing NNI: done in 5.1452 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.72819 secs using 399.1% CPU
Optimizing NNI: done in 1.48775 secs using 398.6% CPU
BETTER TREE FOUND at iteration 2: -191484.965
Optimizing NNI: done in 1.38939 secs using 399.1% CPU
Optimizing NNI: done in 1.62826 secs using 398.7% CPU
Optimizing NNI: done in 1.24812 secs using 399.1% CPU
Optimizing NNI: done in 4.32828 secs using 596.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.69065 secs using 399% CPU
Optimizing NNI: done in 1.43405 secs using 398.5% CPU
BETTER TREE FOUND at iteration 3: -191476.798
Optimizing NNI: done in 1.78545 secs using 398.6% CPU
Optimizing NNI: done in 1.41878 secs using 399% CPU
Iteration 20 / LogL: -59077.087 / Time: 0h:1m:0s
Finish initializing candidate tree set (20)
Current best tree score: -59031.878 / CPU time: 42.316
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.31102 secs using 398.7% CPU
Optimizing NNI: done in 4.26951 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.49448 secs using 398.8% CPU
BETTER TREE FOUND at iteration 4: -191473.029
Optimizing NNI: done in 1.58113 secs using 398.8% CPU
Optimizing NNI: done in 1.47645 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -59029.306
Optimizing NNI: done in 4.50592 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.85573 secs using 399.2% CPU
Optimizing NNI: done in 1.55478 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -191414.460
BETTER TREE FOUND at iteration 26: -59024.956
Optimizing NNI: done in 1.57228 secs using 399.3% CPU
Optimizing NNI: done in 1.44701 secs using 399.3% CPU
Optimizing NNI: done in 4.18868 secs using 597.9% CPU
Optimizing NNI: done in 1.51784 secs using 399.3% CPU
Optimizing NNI: done in 1.76119 secs using 399.4% CPU
Iteration 30 / LogL: -59041.065 / Time: 0h:1m:19s (0h:4m:22s left)
Optimizing NNI: done in 1.40684 secs using 399.3% CPU
Optimizing NNI: done in 4.52694 secs using 597.2% CPU
Optimizing NNI: done in 1.649 secs using 399.1% CPU
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Optimizing NNI: done in 4.02214 secs using 597% CPU
Optimizing NNI: done in 1.51742 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 34: -59022.627
Optimizing NNI: done in 1.99786 secs using 399.1% CPU
Optimizing NNI: done in 4.35246 secs using 597.5% CPU
Optimizing NNI: done in 1.72257 secs using 399.3% CPU
Optimizing NNI: done in 1.55343 secs using 398.8% CPU
Optimizing NNI: done in 1.5391 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.27449 secs using 596.8% CPU
Iteration 10 / LogL: -191536.797 / Time: 0h:2m:19s
BETTER TREE FOUND at iteration 38: -59018.813
Optimizing NNI: done in 1.74684 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 39: -59006.136
Optimizing NNI: done in 4.03439 secs using 597.3% CPU
Optimizing NNI: done in 1.6827 secs using 399.4% CPU
Iteration 40 / LogL: -59033.521 / Time: 0h:1m:39s (0h:4m:11s left)
Optimizing NNI: done in 1.61824 secs using 398.7% CPU
Optimizing NNI: done in 4.05905 secs using 597.3% CPU
Optimizing NNI: done in 1.90706 secs using 398.9% CPU
Optimizing NNI: done in 1.64294 secs using 399% CPU
Optimizing NNI: done in 1.58437 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.0554 secs using 597.5% CPU
BETTER TREE FOUND at iteration 44: -59000.668
Optimizing NNI: done in 1.72482 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 45: -58997.674
Optimizing NNI: done in 4.07773 secs using 598% CPU
Optimizing NNI: done in 1.98447 secs using 399.3% CPU
Optimizing NNI: done in 1.59549 secs using 399% CPU
Optimizing NNI: done in 4.14301 secs using 597.6% CPU
Optimizing NNI: done in 1.51977 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 48: -58996.061
Optimizing NNI: done in 1.53452 secs using 399.1% CPU
Optimizing NNI: done in 4.20614 secs using 597% CPU
Optimizing NNI: done in 1.786 secs using 399.1% CPU
Iteration 50 / LogL: -59006.039 / Time: 0h:1m:59s (0h:3m:58s left)
Optimizing NNI: done in 1.55173 secs using 398.9% CPU
Optimizing NNI: done in 3.69884 secs using 597.6% CPU
Optimizing NNI: done in 1.66857 secs using 399.2% CPU
Optimizing NNI: done in 1.56536 secs using 398.7% CPU
Optimizing NNI: done in 1.35286 secs using 398.9% CPU
Optimizing NNI: done in 4.08816 secs using 596.7% CPU
Optimizing NNI: done in 1.61239 secs using 399% CPU
Optimizing NNI: done in 1.38904 secs using 399% CPU
Optimizing NNI: done in 3.45867 secs using 597% CPU
Optimizing NNI: done in 1.55488 secs using 398.7% CPU
Optimizing NNI: done in 1.87336 secs using 399% CPU
Optimizing NNI: done in 1.66368 secs using 398.6% CPU
Optimizing NNI: done in 4.7601 secs using 597.7% CPU
Iteration 20 / LogL: -191474.727 / Time: 0h:3m:0s
Finish initializing candidate tree set (20)
Current best tree score: -191414.460 / CPU time: 147.512
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.82508 secs using 399.1% CPU
Iteration 60 / LogL: -59002.347 / Time: 0h:2m:15s (0h:3m:22s left)
Optimizing NNI: done in 1.58166 secs using 399.2% CPU
Optimizing NNI: done in 1.67537 secs using 398.7% CPU
Optimizing NNI: done in 5.04475 secs using 597.2% CPU
Optimizing NNI: done in 1.64077 secs using 398.6% CPU
BETTER TREE FOUND at iteration 63: -58996.061
Optimizing NNI: done in 1.47435 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 64: -58995.197
Optimizing NNI: done in 5.11664 secs using 598.1% CPU
Optimizing NNI: done in 1.50072 secs using 398.8% CPU
Optimizing NNI: done in 1.68602 secs using 399.3% CPU
Optimizing NNI: done in 1.92223 secs using 398.8% CPU
Optimizing NNI: done in 5.22569 secs using 597.5% CPU
Optimizing NNI: done in 1.91987 secs using 399.2% CPU
Optimizing NNI: done in 1.85115 secs using 398.8% CPU
Optimizing NNI: done in 1.68931 secs using 399.1% CPU
Iteration 70 / LogL: -59012.230 / Time: 0h:2m:34s (0h:3m:30s left)
Optimizing NNI: done in 5.37697 secs using 597.9% CPU
Optimizing NNI: done in 1.58139 secs using 399.3% CPU
Optimizing NNI: done in 1.67294 secs using 398.7% CPU
BETTER TREE FOUND at iteration 72: -58995.188
Optimizing NNI: done in 1.2767 secs using 398.9% CPU
Optimizing NNI: done in 1.33428 secs using 399.4% CPU
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Estimate model parameters (epsilon = 0.100)
902  mtInv+I+R10   109936.058   554 220980.115   835920.115   223210.445
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Iteration 80 / LogL: -59000.897 / Time: 0h:2m:50s (0h:3m:31s left)
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BETTER TREE FOUND at iteration 100: -58995.070
Iteration 100 / LogL: -58995.070 / Time: 0h:3m:22s (0h:3m:24s left)
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923  mtInv+F+I+R9  106061.263   571 213264.526   866488.526   215563.295
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UPDATE BEST LOG-LIKELIHOOD: -58995.070
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BETTER TREE FOUND at iteration 40: -191362.951
Iteration 40 / LogL: -191362.951 / Time: 0h:4m:51s (0h:12m:26s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 160 / LogL: -58995.196 / Time: 0h:5m:0s (0h:1m:15s left)
BETTER TREE FOUND at iteration 51: -191333.781
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 63: -191324.860
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Estimate model parameters (epsilon = 0.100)
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Iteration 200 / LogL: -58995.198 / Time: 0h:6m:5s (0h:0m:0s left)
BETTER TREE FOUND at iteration 64: -191313.838
Optimizing NNI: done in 1.45193 secs using 399.2% CPU
TREE SEARCH COMPLETED AFTER 201 ITERATIONS / Time: 0h:6m:6s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58995.070
Optimal log-likelihood: -58995.070
Site proportion and rates:  (0.138,0.074) (0.068,0.238) (0.160,0.375) (0.195,0.653) (0.166,0.980) (0.120,1.539) (0.126,2.363) (0.027,5.188)
Parameters optimization took 1 rounds (0.175 sec)
BEST SCORE FOUND : -58995.070
Total tree length: 43.568

Total number of iterations: 201
CPU time used for tree search: 1375.479 sec (0h:22m:55s)
Wall-clock time used for tree search: 348.604 sec (0h:5m:48s)
Total CPU time used: 1449.083 sec (0h:24m:9s)
Total wall-clock time used: 367.063 sec (0h:6m:7s)

===> START BOOTSTRAP REPLICATE NUMBER 23

Creating bootstrap alignment (seed: 67485)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60615.721
2. Current log-likelihood: -60116.514
3. Current log-likelihood: -60114.068
4. Current log-likelihood: -60113.596
5. Current log-likelihood: -60113.133
6. Current log-likelihood: -60112.649
Optimizing NNI: done in 4.84356 secs using 597.2% CPU
7. Current log-likelihood: -60112.119
8. Current log-likelihood: -60111.550
9. Current log-likelihood: -60110.918
10. Current log-likelihood: -60109.772
11. Current log-likelihood: -60106.554
12. Current log-likelihood: -60097.601
13. Current log-likelihood: -60086.702
14. Current log-likelihood: -60084.924
Optimizing NNI: done in 5.6957 secs using 596.6% CPU
Optimal log-likelihood: -60084.845
Site proportion and rates:  (0.074,0.055) (0.105,0.189) (0.081,0.421) (0.137,0.428) (0.221,0.745) (0.201,1.198) (0.166,2.318) (0.015,6.221)
Parameters optimization took 14 rounds (10.445 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.07443 secs using 399.9% CPU
Computing ML distances took 1.074634 sec (of wall-clock time) 4.297049 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000365973 secs using 386.1% CPU
Constructing RapidNJ tree: done in 0.00431204 secs using 349.8% CPU
Computing RapidNJ tree took 0.004759 sec (of wall-clock time) 0.017061 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60089.647
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.94572 secs using 597.4% CPU
5.377 second
Optimizing NNI: done in 6.56971 secs using 597.3% CPU
Computing log-likelihood of 98 initial trees ... 5.224 seconds
Current best score: -59975.482

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -59843.522
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -59814.885
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Iteration 70 / LogL: -191427.532 / Time: 0h:7m:24s (0h:10m:5s left)
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Iteration 10 / LogL: -59920.493 / Time: 0h:0m:37s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 12: -59806.598
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Iteration 20 / LogL: -59852.722 / Time: 0h:0m:51s
Finish initializing candidate tree set (20)
Current best tree score: -59806.598 / CPU time: 39.769
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 30 / LogL: -59813.613 / Time: 0h:1m:6s (0h:3m:8s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -59804.456
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Iteration 80 / LogL: -191375.899 / Time: 0h:8m:10s (0h:8m:41s left)
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924  mtInv+F+I+R10 106055.691   573 213257.381   871061.381   215564.203
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Iteration 50 / LogL: -59806.199 / Time: 0h:1m:38s (0h:2m:50s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 52: -59803.294
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 54: -59801.384
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 56: -59800.223
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Estimate model parameters (epsilon = 0.100)
945  mtMAM+I+R9    112612.520   552 226329.041   836841.041   228551.319
BETTER TREE FOUND at iteration 57: -59796.959
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946  mtMAM+I+R10   112569.310   554 226246.620   841186.620   228476.950
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967  mtMAM+F+I+R9  109649.437   571 220440.875   873664.875   222739.644
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968  mtMAM+F+I+R10 109601.566   573 220349.133   878153.133   222655.954
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989  FLAVI+I+R9    108205.101   552 217514.202   828026.202   219736.480
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WARNING: Log-likelihood -108227 of FLAVI+I+R10 worse than FLAVI+I+R9 -108205
990  FLAVI+I+R10   108226.733   554 217561.466   832501.466   219791.796
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Iteration 210 / LogL: -59779.671 / Time: 0h:5m:52s (0h:0m:1s left)
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TREE SEARCH COMPLETED AFTER 212 ITERATIONS / Time: 0h:5m:55s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59779.611
Optimal log-likelihood: -59779.601
Site proportion and rates:  (0.071,0.053) (0.101,0.184) (0.090,0.429) (0.152,0.429) (0.249,0.801) (0.160,1.269) (0.163,2.320) (0.014,6.543)
Parameters optimization took 1 rounds (0.677 sec)
BEST SCORE FOUND : -59779.601
Total tree length: 42.053

Total number of iterations: 212
CPU time used for tree search: 1355.441 sec (0h:22m:35s)
Wall-clock time used for tree search: 343.740 sec (0h:5m:43s)
Total CPU time used: 1405.896 sec (0h:23m:25s)
Total wall-clock time used: 356.373 sec (0h:5m:56s)

===> START BOOTSTRAP REPLICATE NUMBER 24

Creating bootstrap alignment (seed: 67486)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.058 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59090.505
2. Current log-likelihood: -58534.654
3. Current log-likelihood: -58516.585
4. Current log-likelihood: -58512.225
Optimizing NNI: done in 4.4705 secs using 598.1% CPU
5. Current log-likelihood: -58504.525
6. Current log-likelihood: -58499.129
7. Current log-likelihood: -58498.755
Optimal log-likelihood: -58498.705
Site proportion and rates:  (0.105,0.057) (0.136,0.182) (0.144,0.366) (0.079,0.585) (0.178,0.710) (0.147,1.241) (0.185,2.282) (0.025,5.445)
Parameters optimization took 7 rounds (5.872 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10636 secs using 399.6% CPU
Computing ML distances took 1.106561 sec (of wall-clock time) 4.421835 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000340939 secs using 183.9% CPU
Constructing RapidNJ tree: done in 0.00433993 secs using 363% CPU
Computing RapidNJ tree took 0.004746 sec (of wall-clock time) 0.018262 sec (of CPU time)
Log-likelihood of RapidNJ tree: -58386.611
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.22793 secs using 596.9% CPU
Iteration 140 / LogL: -191349.603 / Time: 0h:12m:57s (0h:4m:45s left)
1011  FLAVI+F+I+R9  108334.673   571 217811.347   871035.347   220110.116
WARNING: Normalizing state frequencies so that sum of them equals to 1
4.953 second
Optimizing NNI: done in 6.32925 secs using 597.2% CPU
Computing log-likelihood of 98 initial trees ... 5.338 seconds
Current best score: -58330.661

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -58121.272
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -58116.856
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 5: -58107.094
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 7: -58095.722
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Iteration 10 / LogL: -58168.052 / Time: 0h:0m:37s
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WARNING: Log-likelihood -108374 of FLAVI+F+I+R10 worse than FLAVI+F+I+R9 -108335
1012  FLAVI+F+I+R10 108374.064   573 217894.129   875698.129   220200.950
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Iteration 20 / LogL: -58149.046 / Time: 0h:0m:49s
Finish initializing candidate tree set (20)
Current best tree score: -58095.722 / CPU time: 42.555
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.59289 secs using 597.9% CPU
Iteration 150 / LogL: -191354.865 / Time: 0h:13m:46s (0h:3m:47s left)
BETTER TREE FOUND at iteration 25: -58089.118
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1033  HIVb+I+R9     107334.486   552 215772.972   826284.972   217995.250
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Iteration 30 / LogL: -58122.507 / Time: 0h:1m:5s (0h:3m:32s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -58072.627
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BETTER TREE FOUND at iteration 39: -58068.399
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Iteration 40 / LogL: -58088.162 / Time: 0h:1m:21s (0h:3m:26s left)
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BETTER TREE FOUND at iteration 43: -58067.402
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BETTER TREE FOUND at iteration 49: -58063.765
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Iteration 50 / LogL: -58080.680 / Time: 0h:1m:36s (0h:3m:15s left)
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Iteration 160 / LogL: -191320.670 / Time: 0h:14m:33s (0h:2m:50s left)
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BETTER TREE FOUND at iteration 57: -58056.631
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Iteration 60 / LogL: -58072.680 / Time: 0h:1m:51s (0h:3m:2s left)
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Iteration 70 / LogL: -58062.910 / Time: 0h:2m:5s (0h:2m:38s left)
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Iteration 80 / LogL: -58107.850 / Time: 0h:2m:19s (0h:2m:15s left)
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Iteration 170 / LogL: -191358.328 / Time: 0h:15m:21s (0h:1m:54s left)
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BETTER TREE FOUND at iteration 98: -58056.628
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Iteration 100 / LogL: -58065.005 / Time: 0h:2m:46s (0h:2m:44s left)
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Iteration 110 / LogL: -58064.407 / Time: 0h:3m:0s (0h:2m:25s left)
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1034  HIVb+I+R10    107328.320   554 215764.640   830704.640   217994.970
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BETTER TREE FOUND at iteration 178: -191310.316
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UPDATE BEST LOG-LIKELIHOOD: -58056.627
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BETTER TREE FOUND at iteration 125: -58056.535
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Iteration 180 / LogL: -191316.327 / Time: 0h:16m:11s (0h:8m:51s left)
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Iteration 130 / LogL: -58058.040 / Time: 0h:3m:28s (0h:2m:33s left)
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BETTER TREE FOUND at iteration 131: -58056.531
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1055  HIVb+F+I+R9   107154.395   571 215450.791   868674.791   217749.560
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Iteration 140 / LogL: -58062.560 / Time: 0h:3m:41s (0h:2m:24s left)
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BETTER TREE FOUND at iteration 149: -58056.384
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Iteration 150 / LogL: -58068.654 / Time: 0h:3m:55s (0h:2m:36s left)
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BETTER TREE FOUND at iteration 155: -58056.381
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Iteration 160 / LogL: -58060.891 / Time: 0h:4m:10s (0h:2m:29s left)
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Iteration 190 / LogL: -191372.678 / Time: 0h:17m:2s (0h:8m:50s left)
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Iteration 170 / LogL: -58063.567 / Time: 0h:4m:23s (0h:2m:12s left)
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Iteration 180 / LogL: -58058.555 / Time: 0h:4m:38s (0h:1m:56s left)
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Iteration 190 / LogL: -58071.163 / Time: 0h:4m:52s (0h:1m:40s left)
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UPDATE BEST LOG-LIKELIHOOD: -58056.381
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Iteration 200 / LogL: -191323.134 / Time: 0h:17m:52s (0h:7m:54s left)
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Iteration 200 / LogL: -58062.602 / Time: 0h:5m:5s (0h:1m:24s left)
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Iteration 210 / LogL: -58081.054 / Time: 0h:5m:19s (0h:1m:8s left)
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Iteration 220 / LogL: -58056.746 / Time: 0h:5m:33s (0h:0m:53s left)
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Iteration 230 / LogL: -58062.007 / Time: 0h:5m:47s (0h:0m:37s left)
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Iteration 210 / LogL: -191412.125 / Time: 0h:18m:37s (0h:6m:56s left)
Optimizing NNI: done in 1.24858 secs using 398.8% CPU
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WARNING: Log-likelihood -107162 of HIVb+F+I+R10 worse than HIVb+F+I+R9 -107154
1056  HIVb+F+I+R10  107161.691   573 215469.383   873273.383   217776.204
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Iteration 240 / LogL: -58063.891 / Time: 0h:6m:0s (0h:0m:22s left)
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1077  HIVw+I+R9     111393.496   552 223890.992   834402.992   226113.270
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Iteration 250 / LogL: -58065.656 / Time: 0h:6m:14s (0h:0m:7s left)
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BETTER TREE FOUND at iteration 256: -58056.379
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Iteration 260 / LogL: -58130.907 / Time: 0h:6m:28s (0h:2m:23s left)
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Iteration 350 / LogL: -58065.246 / Time: 0h:8m:31s (0h:0m:8s left)
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TREE SEARCH COMPLETED AFTER 357 ITERATIONS / Time: 0h:8m:41s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58056.379
2. Current log-likelihood: -58056.358
3. Current log-likelihood: -58056.330
4. Current log-likelihood: -58056.314
5. Current log-likelihood: -58056.296
Optimizing NNI: done in 4.14484 secs using 598.1% CPU
6. Current log-likelihood: -58056.280
7. Current log-likelihood: -58056.264
8. Current log-likelihood: -58056.249
9. Current log-likelihood: -58056.233
10. Current log-likelihood: -58056.219
11. Current log-likelihood: -58056.204
12. Current log-likelihood: -58056.190
13. Current log-likelihood: -58056.177
14. Current log-likelihood: -58056.164
15. Current log-likelihood: -58056.152
16. Current log-likelihood: -58056.140
Optimizing NNI: done in 4.65227 secs using 598.3% CPU
17. Current log-likelihood: -58056.128
18. Current log-likelihood: -58056.117
19. Current log-likelihood: -58056.106
20. Current log-likelihood: -58056.095
21. Current log-likelihood: -58056.085
Optimal log-likelihood: -58056.070
Site proportion and rates:  (0.094,0.053) (0.143,0.168) (0.169,0.380) (0.170,0.677) (0.064,0.677) (0.156,1.234) (0.179,2.322) (0.025,5.509)
Parameters optimization took 21 rounds (8.792 sec)
BEST SCORE FOUND : -58056.070
Total tree length: 43.784

Total number of iterations: 357
CPU time used for tree search: 2034.638 sec (0h:33m:54s)
Wall-clock time used for tree search: 513.759 sec (0h:8m:33s)
Total CPU time used: 2099.158 sec (0h:34m:59s)
Total wall-clock time used: 529.934 sec (0h:8m:49s)

===> START BOOTSTRAP REPLICATE NUMBER 25

Creating bootstrap alignment (seed: 67487)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.074 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61931.701
2. Current log-likelihood: -61312.321
3. Current log-likelihood: -61255.619
Optimizing NNI: done in 4.53588 secs using 597.1% CPU
4. Current log-likelihood: -61246.957
5. Current log-likelihood: -61246.456
6. Current log-likelihood: -61246.272
7. Current log-likelihood: -61246.103
8. Current log-likelihood: -61245.958
Optimal log-likelihood: -61245.851
Site proportion and rates:  (0.086,0.067) (0.102,0.175) (0.117,0.368) (0.051,0.398) (0.237,0.659) (0.211,1.086) (0.160,2.046) (0.036,5.618)
Parameters optimization took 8 rounds (6.574 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.83038 secs using 597.1% CPU
Calculating distance matrix: done in 1.10237 secs using 399.9% CPU
Computing ML distances took 1.102555 sec (of wall-clock time) 4.408518 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000349045 secs using 350.1% CPU
Constructing RapidNJ tree: done in 0.004246 secs using 314.3% CPU
Computing RapidNJ tree took 0.004668 sec (of wall-clock time) 0.015738 sec (of CPU time)
Log-likelihood of RapidNJ tree: -61258.357
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.5565 secs using 597.2% CPU
Iteration 250 / LogL: -191320.447 / Time: 0h:21m:51s (0h:3m:20s left)
4.961 second
Optimizing NNI: done in 4.87174 secs using 597.4% CPU
Computing log-likelihood of 98 initial trees ... 5.476 seconds
Current best score: -61216.644

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -60928.657
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -60895.209
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Iteration 10 / LogL: -61050.576 / Time: 0h:0m:35s
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Iteration 20 / LogL: -61034.866 / Time: 0h:0m:49s
Finish initializing candidate tree set (20)
Current best tree score: -60895.209 / CPU time: 41.416
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 21: -60895.015
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1078  HIVw+I+R10    111393.399   554 223894.798   838834.798   226125.128
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -60891.928
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Iteration 30 / LogL: -60892.435 / Time: 0h:1m:5s (0h:3m:31s left)
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BETTER TREE FOUND at iteration 36: -60891.789
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 38: -60890.707
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Iteration 40 / LogL: -60894.726 / Time: 0h:1m:22s (0h:3m:28s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 41: -60888.805
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1099  HIVw+F+I+R9   109130.874   571 219403.748   872627.748   221702.517
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 47: -60887.944
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Iteration 50 / LogL: -60894.553 / Time: 0h:1m:39s (0h:3m:17s left)
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Iteration 60 / LogL: -60890.696 / Time: 0h:1m:54s (0h:2m:48s left)
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Iteration 80 / LogL: -60900.995 / Time: 0h:2m:23s (0h:2m:1s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 280: -191300.848
Iteration 280 / LogL: -191300.848 / Time: 0h:24m:16s (0h:8m:41s left)
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Iteration 90 / LogL: -60889.785 / Time: 0h:2m:38s (0h:1m:41s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 95: -60887.773
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 96: -60884.274
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Iteration 100 / LogL: -60891.693 / Time: 0h:2m:55s (0h:2m:49s left)
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Iteration 110 / LogL: -60889.297 / Time: 0h:3m:10s (0h:2m:30s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 117: -60883.699
Optimizing NNI: done in 1.37919 secs using 398.9% CPU
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Iteration 290 / LogL: -191326.296 / Time: 0h:25m:4s (0h:7m:48s left)
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Iteration 120 / LogL: -60936.113 / Time: 0h:3m:26s (0h:2m:48s left)
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BETTER TREE FOUND at iteration 125: -60883.698
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Iteration 130 / LogL: -60888.380 / Time: 0h:3m:40s (0h:2m:42s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 134: -60882.589
Optimizing NNI: done in 4.74137 secs using 598.2% CPU
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Iteration 140 / LogL: -60883.559 / Time: 0h:3m:55s (0h:2m:38s left)
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Iteration 150 / LogL: -60891.814 / Time: 0h:4m:9s (0h:2m:20s left)
Optimizing NNI: done in 1.38656 secs using 398.8% CPU
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Optimizing NNI: done in 5.23419 secs using 597.4% CPU
Iteration 300 / LogL: -191380.186 / Time: 0h:25m:52s (0h:6m:55s left)
Optimizing NNI: done in 1.37836 secs using 399.5% CPU
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Optimizing NNI: done in 1.32504 secs using 398.7% CPU
WARNING: Log-likelihood -109134 of HIVw+F+I+R10 worse than HIVw+F+I+R9 -109131
1100  HIVw+F+I+R10  109133.519   573 219413.038   877217.038   221719.859
Optimizing NNI: done in 1.41223 secs using 398.8% CPU
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Iteration 160 / LogL: -60894.248 / Time: 0h:4m:23s (0h:2m:2s left)
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Optimizing NNI: done in 1.32578 secs using 398.7% CPU
1121  FLU+I+R9      107360.021   552 215824.042   826336.042   218046.320
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Iteration 170 / LogL: -60883.902 / Time: 0h:4m:38s (0h:1m:45s left)
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Iteration 180 / LogL: -60892.881 / Time: 0h:4m:53s (0h:1m:28s left)
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Iteration 310 / LogL: -191370.116 / Time: 0h:26m:40s (0h:6m:2s left)
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Iteration 190 / LogL: -60892.788 / Time: 0h:5m:7s (0h:1m:11s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 197: -60882.227
Optimizing NNI: done in 1.30911 secs using 398.8% CPU
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Iteration 200 / LogL: -60920.888 / Time: 0h:5m:22s (0h:2m:37s left)
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Iteration 210 / LogL: -60882.637 / Time: 0h:5m:37s (0h:2m:20s left)
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Iteration 320 / LogL: -191306.305 / Time: 0h:27m:28s (0h:5m:10s left)
Optimizing NNI: done in 1.20921 secs using 399% CPU
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Iteration 220 / LogL: -60897.711 / Time: 0h:5m:52s (0h:2m:3s left)
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Iteration 230 / LogL: -60905.258 / Time: 0h:6m:7s (0h:1m:47s left)
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Iteration 240 / LogL: -60884.011 / Time: 0h:6m:21s (0h:1m:30s left)
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Iteration 250 / LogL: -60897.024 / Time: 0h:6m:34s (0h:1m:14s left)
Optimizing NNI: done in 1.47089 secs using 398.9% CPU
WARNING: Log-likelihood -107363 of FLU+I+R10 worse than FLU+I+R9 -107360
1122  FLU+I+R10     107362.686   554 215833.372   830773.372   218063.702
Optimizing NNI: done in 1.26822 secs using 399% CPU
Optimizing NNI: done in 4.94553 secs using 597.9% CPU
Iteration 330 / LogL: -191336.617 / Time: 0h:28m:16s (0h:4m:17s left)
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1143  FLU+F+I+R9    106825.546   571 214793.092   868017.092   217091.861
Optimizing NNI: done in 5.00064 secs using 598% CPU
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Iteration 260 / LogL: -60895.102 / Time: 0h:6m:48s (0h:0m:58s left)
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Optimizing NNI: done in 1.45199 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.34308 secs using 598.4% CPU
BETTER TREE FOUND at iteration 262: -60882.084
Optimizing NNI: done in 1.34367 secs using 399.1% CPU
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Iteration 270 / LogL: -60934.819 / Time: 0h:7m:3s (0h:2m:24s left)
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Iteration 280 / LogL: -60882.858 / Time: 0h:7m:17s (0h:2m:8s left)
Optimizing NNI: done in 1.3511 secs using 398.7% CPU
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Iteration 340 / LogL: -191368.313 / Time: 0h:29m:3s (0h:3m:25s left)
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Iteration 290 / LogL: -60917.872 / Time: 0h:7m:32s (0h:1m:52s left)
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Iteration 300 / LogL: -60882.240 / Time: 0h:7m:47s (0h:1m:36s left)
Optimizing NNI: done in 1.48765 secs using 399.1% CPU
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Optimizing NNI: done in 1.47746 secs using 398.7% CPU
WARNING: Log-likelihood -106829 of FLU+F+I+R10 worse than FLU+F+I+R9 -106826
1144  FLU+F+I+R10   106829.207   573 214804.415   872608.415   217111.236
Optimizing NNI: done in 1.32451 secs using 398.7% CPU
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BETTER TREE FOUND at iteration 309: -60882.084
1165  rtREV+I+R9    107034.588   552 215173.177   825685.177   217395.455
Optimizing NNI: done in 1.50387 secs using 398.8% CPU
Iteration 310 / LogL: -61119.658 / Time: 0h:8m:1s (0h:2m:34s left)
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Iteration 350 / LogL: -191401.947 / Time: 0h:29m:53s (0h:2m:34s left)
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Iteration 320 / LogL: -60904.172 / Time: 0h:8m:16s (0h:2m:18s left)
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Optimizing NNI: done in 4.5962 secs using 597.4% CPU
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Optimizing NNI: done in 1.05378 secs using 399.7% CPU
Optimizing NNI: done in 1.29949 secs using 399.1% CPU
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Optimizing NNI: done in 4.93284 secs using 597.4% CPU
Optimizing NNI: done in 1.43689 secs using 398.7% CPU
Iteration 330 / LogL: -60892.175 / Time: 0h:8m:29s (0h:2m:2s left)
Optimizing NNI: done in 1.59386 secs using 398.6% CPU
Optimizing NNI: done in 1.52749 secs using 398.9% CPU
Optimizing NNI: done in 1.4362 secs using 399% CPU
Optimizing NNI: done in 5.12013 secs using 597.7% CPU
Optimizing NNI: done in 1.22917 secs using 399.2% CPU
Optimizing NNI: done in 1.55259 secs using 399% CPU
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Optimizing NNI: done in 5.02133 secs using 597% CPU
Optimizing NNI: done in 1.83464 secs using 398.7% CPU
Optimizing NNI: done in 1.31828 secs using 398.2% CPU
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Optimizing NNI: done in 4.78466 secs using 597.2% CPU
Optimizing NNI: done in 1.46002 secs using 398.8% CPU
Iteration 340 / LogL: -60935.295 / Time: 0h:8m:44s (0h:1m:46s left)
Optimizing NNI: done in 1.30688 secs using 398.6% CPU
Optimizing NNI: done in 1.20875 secs using 398.9% CPU
Optimizing NNI: done in 1.28625 secs using 398.3% CPU
Optimizing NNI: done in 4.46141 secs using 597.5% CPU
Optimizing NNI: done in 1.4018 secs using 399.2% CPU
Optimizing NNI: done in 1.65816 secs using 399.3% CPU
Optimizing NNI: done in 1.59678 secs using 398.5% CPU
Optimizing NNI: done in 4.59658 secs using 597.8% CPU
Optimizing NNI: done in 1.24523 secs using 399.1% CPU
Optimizing NNI: done in 1.73798 secs using 398.6% CPU
Optimizing NNI: done in 1.5829 secs using 398.5% CPU
Optimizing NNI: done in 4.54975 secs using 597.2% CPU
Optimizing NNI: done in 1.60204 secs using 398.3% CPU
Iteration 350 / LogL: -60888.624 / Time: 0h:8m:59s (0h:1m:31s left)
Optimizing NNI: done in 1.15765 secs using 398.6% CPU
Optimizing NNI: done in 1.39829 secs using 398.7% CPU
Optimizing NNI: done in 4.5767 secs using 597.4% CPU
Iteration 360 / LogL: -191416.327 / Time: 0h:30m:41s (0h:1m:42s left)
Optimizing NNI: done in 1.4416 secs using 399.3% CPU
Optimizing NNI: done in 1.69368 secs using 399.3% CPU
Optimizing NNI: done in 1.47496 secs using 398.9% CPU
Optimizing NNI: done in 4.72714 secs using 597.8% CPU
Optimizing NNI: done in 1.35431 secs using 398.9% CPU
Optimizing NNI: done in 1.17817 secs using 399.1% CPU
Optimizing NNI: done in 1.42344 secs using 399% CPU
Optimizing NNI: done in 1.18368 secs using 399.4% CPU
Optimizing NNI: done in 4.7108 secs using 598.4% CPU
Optimizing NNI: done in 1.47827 secs using 398.5% CPU
Iteration 360 / LogL: -60883.082 / Time: 0h:9m:13s (0h:1m:15s left)
Optimizing NNI: done in 1.6685 secs using 399% CPU
Optimizing NNI: done in 1.58575 secs using 399% CPU
Optimizing NNI: done in 4.85996 secs using 597.2% CPU
Optimizing NNI: done in 1.40549 secs using 399% CPU
Optimizing NNI: done in 1.13124 secs using 398.9% CPU
Optimizing NNI: done in 1.63373 secs using 399% CPU
Optimizing NNI: done in 4.59409 secs using 596.8% CPU
Optimizing NNI: done in 1.5872 secs using 398.8% CPU
1166  rtREV+I+R10   107033.337   554 215174.674   830114.674   217405.003
Optimizing NNI: done in 1.57462 secs using 398.8% CPU
Optimizing NNI: done in 1.69182 secs using 398.7% CPU
Optimizing NNI: done in 4.39698 secs using 597.8% CPU
Optimizing NNI: done in 1.40931 secs using 399% CPU
Optimizing NNI: done in 1.39941 secs using 398.9% CPU
Iteration 370 / LogL: -60885.161 / Time: 0h:9m:28s (0h:1m:0s left)
Optimizing NNI: done in 1.48533 secs using 399.4% CPU
Optimizing NNI: done in 4.56902 secs using 597.9% CPU
Optimizing NNI: done in 1.4478 secs using 399.1% CPU
Optimizing NNI: done in 1.4213 secs using 398.2% CPU
Optimizing NNI: done in 1.33369 secs using 398.9% CPU
Optimizing NNI: done in 4.74405 secs using 597.9% CPU
Optimizing NNI: done in 1.44708 secs using 399.5% CPU
Optimizing NNI: done in 1.4731 secs using 398.5% CPU
Optimizing NNI: done in 1.27093 secs using 398.7% CPU
Optimizing NNI: done in 1.34122 secs using 399.3% CPU
Optimizing NNI: done in 4.80592 secs using 597.5% CPU
Optimizing NNI: done in 1.63925 secs using 399.4% CPU
1187  rtREV+F+I+R9  106619.441   571 214380.882   867604.882   216679.651
Optimizing NNI: done in 1.27324 secs using 398.5% CPU
Iteration 380 / LogL: -60883.023 / Time: 0h:9m:42s (0h:0m:44s left)
Optimizing NNI: done in 1.50445 secs using 398.4% CPU
Optimizing NNI: done in 4.14693 secs using 597.5% CPU
Optimizing NNI: done in 1.35067 secs using 398.8% CPU
Optimizing NNI: done in 1.40415 secs using 398.9% CPU
Optimizing NNI: done in 1.46213 secs using 399.4% CPU
Optimizing NNI: done in 4.85456 secs using 596.9% CPU
Iteration 370 / LogL: -191330.298 / Time: 0h:31m:28s (0h:0m:51s left)
Optimizing NNI: done in 1.54761 secs using 398.7% CPU
Optimizing NNI: done in 1.47699 secs using 398.9% CPU
Optimizing NNI: done in 1.42363 secs using 398.2% CPU
Optimizing NNI: done in 1.35282 secs using 399% CPU
Optimizing NNI: done in 5.0533 secs using 597.3% CPU
Optimizing NNI: done in 1.64991 secs using 398.9% CPU
Optimizing NNI: done in 1.20127 secs using 399% CPU
Iteration 390 / LogL: -60883.082 / Time: 0h:9m:57s (0h:0m:29s left)
Optimizing NNI: done in 1.62094 secs using 398.5% CPU
Optimizing NNI: done in 4.78011 secs using 597.6% CPU
Optimizing NNI: done in 1.34068 secs using 398.6% CPU
Optimizing NNI: done in 1.56597 secs using 399.2% CPU
Optimizing NNI: done in 1.3232 secs using 399.5% CPU
Optimizing NNI: done in 4.28233 secs using 597.9% CPU
Optimizing NNI: done in 1.2088 secs using 398.9% CPU
Optimizing NNI: done in 1.53431 secs using 399.1% CPU
Optimizing NNI: done in 1.26469 secs using 399.6% CPU
Optimizing NNI: done in 4.5837 secs using 597.5% CPU
Optimizing NNI: done in 1.30584 secs using 398.8% CPU
Optimizing NNI: done in 1.45062 secs using 399.3% CPU
Optimizing NNI: done in 1.53039 secs using 398.7% CPU
Iteration 400 / LogL: -60901.082 / Time: 0h:10m:11s (0h:0m:13s left)
Optimizing NNI: done in 1.61366 secs using 398.9% CPU
Optimizing NNI: done in 5.1404 secs using 597.6% CPU
Optimizing NNI: done in 1.52436 secs using 399% CPU
Optimizing NNI: done in 1.36668 secs using 399.1% CPU
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Optimizing NNI: done in 4.66917 secs using 597.6% CPU
Optimizing NNI: done in 1.60207 secs using 399.4% CPU
Optimizing NNI: done in 1.72212 secs using 399.1% CPU
Optimizing NNI: done in 1.49046 secs using 399.3% CPU
Optimizing NNI: done in 4.43107 secs using 597.9% CPU
Optimizing NNI: done in 1.22094 secs using 399.3% CPU
Optimizing NNI: done in 1.49498 secs using 399.4% CPU
Optimizing NNI: done in 1.20444 secs using 398.7% CPU
Iteration 410 / LogL: -60905.155 / Time: 0h:10m:26s (0h:0m:-2s left)
TREE SEARCH COMPLETED AFTER 410 ITERATIONS / Time: 0h:10m:26s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60882.084
Optimal log-likelihood: -60882.078
Site proportion and rates:  (0.092,0.070) (0.096,0.176) (0.125,0.379) (0.054,0.379) (0.258,0.697) (0.204,1.164) (0.135,2.163) (0.035,5.704)
Parameters optimization took 1 rounds (0.348 sec)
BEST SCORE FOUND : -60882.078
Total tree length: 47.033

Total number of iterations: 410
CPU time used for tree search: 2451.355 sec (0h:40m:51s)
Wall-clock time used for tree search: 618.104 sec (0h:10m:18s)
Total CPU time used: 2485.572 sec (0h:41m:25s)
Total wall-clock time used: 626.654 sec (0h:10m:26s)

===> START BOOTSTRAP REPLICATE NUMBER 26

Creating bootstrap alignment (seed: 67488)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.036 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -63079.993
Optimizing NNI: done in 4.6626 secs using 598% CPU
2. Current log-likelihood: -62478.878
3. Current log-likelihood: -62469.508
4. Current log-likelihood: -62462.092
5. Current log-likelihood: -62458.487
6. Current log-likelihood: -62455.360
7. Current log-likelihood: -62454.116
Optimizing NNI: done in 4.74565 secs using 596.8% CPU
8. Current log-likelihood: -62453.811
9. Current log-likelihood: -62453.648
10. Current log-likelihood: -62453.535
Optimal log-likelihood: -62453.446
Site proportion and rates:  (0.115,0.077) (0.055,0.193) (0.148,0.366) (0.161,0.569) (0.194,0.864) (0.135,1.346) (0.163,2.196) (0.029,4.424)
Parameters optimization took 10 rounds (8.246 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09272 secs using 400% CPU
Computing ML distances took 1.092901 sec (of wall-clock time) 4.371057 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000340939 secs using 393.3% CPU
Constructing RapidNJ tree: done in 0.00446105 secs using 399.2% CPU
Computing RapidNJ tree took 0.004874 sec (of wall-clock time) 0.019560 sec (of CPU time)
Log-likelihood of RapidNJ tree: -62426.877
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.76147 secs using 598% CPU
Iteration 380 / LogL: -191336.953 / Time: 0h:32m:16s (0h:0m:0s left)
5.124 second
Optimizing NNI: done in 4.87081 secs using 597.9% CPU
TREE SEARCH COMPLETED AFTER 381 ITERATIONS / Time: 0h:32m:20s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -191300.848
Optimal log-likelihood: -191300.847
Site proportion and rates:  (0.012,0.087) (0.078,0.228) (0.106,0.367) (0.257,0.548) (0.135,0.795) (0.155,1.075) (0.156,1.639) (0.101,2.684)
Parameters optimization took 1 rounds (0.492 sec)
BEST SCORE FOUND : -191300.847
Total tree length: 153.053

Total number of iterations: 381
CPU time used for tree search: 11244.879 sec (3h:7m:24s)
Wall-clock time used for tree search: 1907.790 sec (0h:31m:47s)
Total CPU time used: 11445.836 sec (3h:10m:45s)
Total wall-clock time used: 1941.488 sec (0h:32m:21s)

===> START BOOTSTRAP REPLICATE NUMBER 7

Creating bootstrap alignment (seed: 70470)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.289 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -204166.456
2. Current log-likelihood: -201367.547
Computing log-likelihood of 98 initial trees ... 5.471 seconds
Current best score: -62290.178

Do NNI search on 20 best initial trees
3. Current log-likelihood: -201348.211
Optimizing NNI: done in 1.361 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -62092.339
4. Current log-likelihood: -201346.630
Optimizing NNI: done in 1.02926 secs using 398.8% CPU
5. Current log-likelihood: -201346.104
Optimizing NNI: done in 1.89655 secs using 398.9% CPU
Optimizing NNI: done in 1.49537 secs using 399.4% CPU
6. Current log-likelihood: -201345.848
Optimizing NNI: done in 1.663 secs using 399% CPU
7. Current log-likelihood: -201345.710
Optimizing NNI: done in 1.49185 secs using 399.2% CPU
Optimal log-likelihood: -201345.627
Site proportion and rates:  (0.015,0.097) (0.047,0.217) (0.083,0.337) (0.187,0.497) (0.154,0.656) (0.239,0.945) (0.159,1.541) (0.116,2.545)
Parameters optimization took 7 rounds (16.047 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.57144 secs using 398.9% CPU
Optimizing NNI: done in 1.35966 secs using 398.8% CPU
Optimizing NNI: done in 1.44279 secs using 399.2% CPU
Optimizing NNI: done in 1.61107 secs using 399.1% CPU
Iteration 10 / LogL: -62216.092 / Time: 0h:0m:37s
Optimizing NNI: done in 1.51465 secs using 399.1% CPU
Optimizing NNI: done in 1.73646 secs using 398.8% CPU
Calculating distance matrix: done in 9.92267 secs using 599.9% CPU
Computing ML distances took 9.923240 sec (of wall-clock time) 59.524640 sec (of CPU time)
Optimizing NNI: done in 1.59294 secs using 398.4% CPU
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00135994 secs using 424.1% CPU
Constructing RapidNJ tree: done in 0.022521 secs using 684% CPU
Computing RapidNJ tree took 0.023974 sec (of wall-clock time) 0.161333 sec (of CPU time)
Optimizing NNI: done in 1.07342 secs using 398.8% CPU
Optimizing NNI: done in 1.15984 secs using 399.6% CPU
Optimizing NNI: done in 1.3162 secs using 399% CPU
Log-likelihood of RapidNJ tree: -205491.900
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.69471 secs using 399.2% CPU
Optimizing NNI: done in 1.66092 secs using 399.2% CPU
Optimizing NNI: done in 1.52781 secs using 399.1% CPU
Optimizing NNI: done in 1.94069 secs using 398.8% CPU
Iteration 20 / LogL: -62220.946 / Time: 0h:0m:52s
Finish initializing candidate tree set (20)
Current best tree score: -62092.339 / CPU time: 42.625
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.23554 secs using 399.3% CPU
1188  rtREV+F+I+R10 106612.750   573 214371.500   872175.500   216678.322
Optimizing NNI: done in 1.81569 secs using 399% CPU
Optimizing NNI: done in 1.51248 secs using 399% CPU
Optimizing NNI: done in 1.62664 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -62078.916
1209  cpREV+I+R9    106265.403   552 213634.806   824146.806   215857.084
Optimizing NNI: done in 1.36946 secs using 399.5% CPU
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Optimizing NNI: done in 1.42443 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -62075.592
Optimizing NNI: done in 1.6673 secs using 399.2% CPU
Optimizing NNI: done in 1.38177 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -62073.690
Iteration 30 / LogL: -62073.690 / Time: 0h:1m:11s (0h:4m:4s left)
Optimizing NNI: done in 1.46252 secs using 398.9% CPU
Optimizing NNI: done in 1.58101 secs using 399.2% CPU
Optimizing NNI: done in 1.6371 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
30.026 second
BETTER TREE FOUND at iteration 33: -62069.254
Optimizing NNI: done in 1.60756 secs using 399.1% CPU
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Optimizing NNI: done in 1.22733 secs using 398.9% CPU
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Optimizing NNI: done in 1.37693 secs using 399% CPU
Iteration 40 / LogL: -62076.418 / Time: 0h:1m:27s (0h:3m:27s left)
Optimizing NNI: done in 1.37067 secs using 398.7% CPU
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Optimizing NNI: done in 1.08883 secs using 399.4% CPU
Optimizing NNI: done in 1.51236 secs using 399.4% CPU
Computing log-likelihood of 98 initial trees ... 17.209 seconds
Current best score: -201345.627

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.54975 secs using 399.3% CPU
Optimizing NNI: done in 1.58625 secs using 399.1% CPU
Optimizing NNI: done in 2.96959 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.38986 secs using 398.7% CPU
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Optimizing NNI: done in 1.3302 secs using 399.5% CPU
BETTER TREE FOUND at iteration 1: -200752.047
Optimizing NNI: done in 1.61302 secs using 399% CPU
Iteration 50 / LogL: -62110.505 / Time: 0h:1m:41s (0h:2m:51s left)
Optimizing NNI: done in 1.47993 secs using 398.8% CPU
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Optimizing NNI: done in 3.99198 secs using 596.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.499 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 53: -62064.061
Optimizing NNI: done in 1.36655 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 58: -62054.113
Optimizing NNI: done in 1.31262 secs using 398.8% CPU
Optimizing NNI: done in 1.38145 secs using 399.1% CPU
Iteration 60 / LogL: -62071.240 / Time: 0h:1m:58s (0h:3m:16s left)
Optimizing NNI: done in 1.4764 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -200631.412
BETTER TREE FOUND at iteration 61: -62051.636
Optimizing NNI: done in 1.41641 secs using 399.2% CPU
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Optimizing NNI: done in 1.44283 secs using 398.4% CPU
Iteration 70 / LogL: -62061.410 / Time: 0h:2m:14s (0h:2m:57s left)
Optimizing NNI: done in 5.25068 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.40262 secs using 399% CPU
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BETTER TREE FOUND at iteration 5: -200605.381
Optimizing NNI: done in 1.5838 secs using 398.9% CPU
Optimizing NNI: done in 1.57047 secs using 398.6% CPU
Optimizing NNI: done in 1.5232 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.52877 secs using 597.4% CPU
BETTER TREE FOUND at iteration 77: -62050.816
1210  cpREV+I+R10   106257.429   554 213622.859   828562.859   215853.189
Optimizing NNI: done in 1.47254 secs using 398.7% CPU
Optimizing NNI: done in 1.51893 secs using 399.1% CPU
Optimizing NNI: done in 1.44147 secs using 399.2% CPU
Iteration 80 / LogL: -62059.858 / Time: 0h:2m:31s (0h:3m:5s left)
Optimizing NNI: done in 5.59709 secs using 597.8% CPU
Optimizing NNI: done in 1.46015 secs using 398.8% CPU
1231  cpREV+F+I+R9  106389.059   571 213920.119   867144.119   216218.888
Optimizing NNI: done in 1.61006 secs using 399.2% CPU
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Optimizing NNI: done in 4.51822 secs using 598% CPU
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Optimizing NNI: done in 1.16238 secs using 399% CPU
Iteration 90 / LogL: -62051.738 / Time: 0h:2m:45s (0h:2m:41s left)
Optimizing NNI: done in 1.69205 secs using 398.5% CPU
Optimizing NNI: done in 5.79804 secs using 596.6% CPU
Iteration 10 / LogL: -200651.893 / Time: 0h:2m:31s
Optimizing NNI: done in 1.16693 secs using 398.6% CPU
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Optimizing NNI: done in 4.67177 secs using 597.1% CPU
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Iteration 100 / LogL: -62051.735 / Time: 0h:2m:59s (0h:2m:19s left)
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Iteration 110 / LogL: -62063.308 / Time: 0h:3m:14s (0h:1m:59s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 118: -62050.439
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Iteration 120 / LogL: -62158.979 / Time: 0h:3m:28s (0h:2m:51s left)
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Iteration 20 / LogL: -200714.436 / Time: 0h:3m:18s
Finish initializing candidate tree set (20)
Current best tree score: -200605.381 / CPU time: 167.532
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 130 / LogL: -62065.826 / Time: 0h:3m:43s (0h:2m:32s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 140 / LogL: -62060.371 / Time: 0h:3m:57s (0h:2m:13s left)
BETTER TREE FOUND at iteration 23: -200561.480
Optimizing NNI: done in 1.27573 secs using 398.5% CPU
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Optimizing NNI: done in 1.42771 secs using 398.2% CPU
1232  cpREV+F+I+R10 106386.986   573 213919.971   871723.971   216226.793
Akaike Information Criterion:           Q.plant+I+R10
Corrected Akaike Information Criterion: LG+G4
Bayesian Information Criterion:         Q.plant+I+R9
Best-fit model: Q.plant+I+R9 chosen according to BIC

All model information printed to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.model.gz
CPU time for ModelFinder: 32705.750 seconds (9h:5m:5s)
Wall-clock time for ModelFinder: 8318.593 seconds (2h:18m:38s)

===> START BOOTSTRAP REPLICATE NUMBER 1

Creating bootstrap alignment (seed: 68183)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.101 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106253.260
Optimizing NNI: done in 1.52827 secs using 399.2% CPU
2. Current log-likelihood: -104384.932
Optimizing NNI: done in 1.75926 secs using 399.1% CPU
3. Current log-likelihood: -104301.566
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Optimizing NNI: done in 1.56319 secs using 398.9% CPU
Iteration 150 / LogL: -62060.341 / Time: 0h:4m:12s (0h:1m:55s left)
4. Current log-likelihood: -104294.418
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5. Current log-likelihood: -104293.278
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6. Current log-likelihood: -104292.668
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7. Current log-likelihood: -104292.216
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8. Current log-likelihood: -104291.889
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9. Current log-likelihood: -104291.647
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10. Current log-likelihood: -104291.522
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 157: -62050.219
11. Current log-likelihood: -104291.417
Optimizing NNI: done in 7.42528 secs using 597.1% CPU
Optimizing NNI: done in 1.58444 secs using 398.8% CPU
Optimal log-likelihood: -104291.291
Proportion of invariable sites: 0.017
Site proportion and rates:  (0.089,0.031) (0.088,0.091) (0.013,0.175) (0.088,0.205) (0.172,0.380) (0.123,0.667) (0.155,1.107) (0.176,1.828) (0.079,4.165)
Parameters optimization took 11 rounds (17.801 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.36234 secs using 398.6% CPU
Optimizing NNI: done in 1.55237 secs using 399% CPU
Iteration 160 / LogL: -62059.902 / Time: 0h:4m:28s (0h:2m:43s left)
Optimizing NNI: done in 1.82026 secs using 398.9% CPU
Calculating distance matrix: done in 4.71078 secs using 399.8% CPU
Computing ML distances took 4.711079 sec (of wall-clock time) 18.836911 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000801802 secs using 397.4% CPU
Constructing RapidNJ tree: done in 0.00893593 secs using 487.8% CPU
Computing RapidNJ tree took 0.009815 sec (of wall-clock time) 0.047336 sec (of CPU time)
Log-likelihood of RapidNJ tree: -104015.276
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.74674 secs using 398.6% CPU
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10.507 second
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Iteration 170 / LogL: -62050.924 / Time: 0h:4m:44s (0h:2m:26s left)
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Iteration 30 / LogL: -200585.191 / Time: 0h:4m:29s (0h:14m:23s left)
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Optimizing NNI: done in 7.13946 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
Computing log-likelihood of 98 initial trees ... 10.310 seconds
Current best score: -104015.276

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 31: -200555.315
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Iteration 180 / LogL: -62051.526 / Time: 0h:4m:58s (0h:2m:8s left)
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Iteration 190 / LogL: -62060.843 / Time: 0h:5m:13s (0h:1m:51s left)
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Iteration 10 / LogL: -103415.747 / Time: 0h:1m:16s
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Estimate model parameters (epsilon = 0.100)
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Iteration 210 / LogL: -62055.291 / Time: 0h:5m:43s (0h:1m:17s left)
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Iteration 40 / LogL: -200555.530 / Time: 0h:5m:33s (0h:12m:56s left)
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Iteration 20 / LogL: -103407.032 / Time: 0h:1m:42s
Finish initializing candidate tree set (20)
Current best tree score: -103365.199 / CPU time: 79.307
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Iteration 220 / LogL: -62107.808 / Time: 0h:5m:58s (0h:1m:0s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -103361.835
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 28: -103355.462
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Iteration 230 / LogL: -62057.792 / Time: 0h:6m:14s (0h:0m:44s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 240 / LogL: -62061.731 / Time: 0h:6m:29s (0h:0m:27s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 40 / LogL: -103352.741 / Time: 0h:2m:35s (0h:6m:34s left)
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Iteration 250 / LogL: -62129.121 / Time: 0h:6m:44s (0h:0m:11s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 44: -103344.554
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Iteration 50 / LogL: -200513.423 / Time: 0h:6m:39s (0h:12m:54s left)
Optimizing NNI: done in 1.4276 secs using 399.2% CPU
TREE SEARCH COMPLETED AFTER 258 ITERATIONS / Time: 0h:6m:55s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -62050.219
Optimal log-likelihood: -62050.218
Site proportion and rates:  (0.115,0.077) (0.058,0.192) (0.178,0.378) (0.154,0.619) (0.177,0.893) (0.127,1.373) (0.161,2.195) (0.031,4.246)
Parameters optimization took 1 rounds (0.280 sec)
BEST SCORE FOUND : -62050.218
Total tree length: 46.450

Total number of iterations: 258
CPU time used for tree search: 1603.298 sec (0h:26m:43s)
Wall-clock time used for tree search: 405.647 sec (0h:6m:45s)
Total CPU time used: 1644.009 sec (0h:27m:24s)
Total wall-clock time used: 415.828 sec (0h:6m:55s)

===> START BOOTSTRAP REPLICATE NUMBER 27

Creating bootstrap alignment (seed: 67489)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -63382.691
Optimizing NNI: done in 2.24358 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
2. Current log-likelihood: -62760.160
3. Current log-likelihood: -62752.157
BETTER TREE FOUND at iteration 45: -103341.995
4. Current log-likelihood: -62749.292
5. Current log-likelihood: -62748.122
6. Current log-likelihood: -62747.508
Optimizing NNI: done in 1.9493 secs using 398.8% CPU
7. Current log-likelihood: -62746.883
Optimizing NNI: done in 5.40142 secs using 597.5% CPU
8. Current log-likelihood: -62745.579
9. Current log-likelihood: -62742.948
Optimizing NNI: done in 2.1061 secs using 398.6% CPU
10. Current log-likelihood: -62742.491
Optimal log-likelihood: -62742.417
Site proportion and rates:  (0.085,0.054) (0.103,0.172) (0.106,0.329) (0.118,0.506) (0.193,0.716) (0.158,1.163) (0.208,2.073) (0.029,4.494)
Parameters optimization took 10 rounds (7.738 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.08987 secs using 399.8% CPU
Computing ML distances took 1.090071 sec (of wall-clock time) 4.357527 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000334978 secs using 149.9% CPU
Constructing RapidNJ tree: done in 0.00428486 secs using 268.8% CPU
Computing RapidNJ tree took 0.004679 sec (of wall-clock time) 0.013761 sec (of CPU time)
Log-likelihood of RapidNJ tree: -62756.052
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.96296 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 52: -200493.276
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Iteration 50 / LogL: -103354.661 / Time: 0h:3m:0s (0h:5m:49s left)
5.269 second
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BETTER TREE FOUND at iteration 51: -103336.936
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Estimate model parameters (epsilon = 0.100)
Computing log-likelihood of 98 initial trees ... 5.504 seconds
Current best score: -62642.249

Do NNI search on 20 best initial trees
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Iteration 20 / LogL: -62442.018 / Time: 0h:0m:58s
Finish initializing candidate tree set (20)
Current best tree score: -62371.713 / CPU time: 48.788
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 90: -200487.654
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Iteration 150 / LogL: -62362.142 / Time: 0h:4m:12s (0h:0m:27s left)
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Iteration 160 / LogL: -62345.369 / Time: 0h:4m:27s (0h:0m:10s left)
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Iteration 100 / LogL: -200703.546 / Time: 0h:11m:10s (0h:10m:8s left)
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TREE SEARCH COMPLETED AFTER 167 ITERATIONS / Time: 0h:4m:38s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -62344.885
Optimizing NNI: done in 2.20057 secs using 398.2% CPU
Iteration 170 / LogL: -103353.910 / Time: 0h:7m:26s (0h:1m:35s left)
2. Current log-likelihood: -62344.867
Optimizing NNI: done in 5.23438 secs using 597.3% CPU
3. Current log-likelihood: -62344.854
4. Current log-likelihood: -62344.843
Optimal log-likelihood: -62344.833
Site proportion and rates:  (0.088,0.055) (0.115,0.181) (0.129,0.366) (0.208,0.620) (0.178,0.976) (0.128,1.667) (0.127,2.258) (0.027,4.561)
Parameters optimization took 4 rounds (2.825 sec)
BEST SCORE FOUND : -62344.833
Total tree length: 47.278

Total number of iterations: 167
CPU time used for tree search: 1057.347 sec (0h:17m:37s)
Wall-clock time used for tree search: 268.865 sec (0h:4m:28s)
Total CPU time used: 1106.165 sec (0h:18m:26s)
Total wall-clock time used: 281.093 sec (0h:4m:41s)

===> START BOOTSTRAP REPLICATE NUMBER 28

Creating bootstrap alignment (seed: 67490)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.060 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59600.755
Optimizing NNI: done in 2.52238 secs using 398.5% CPU
2. Current log-likelihood: -59088.863
3. Current log-likelihood: -59086.007
Optimizing NNI: done in 1.989 secs using 398.8% CPU
4. Current log-likelihood: -59085.906
Optimal log-likelihood: -59085.833
Site proportion and rates:  (0.092,0.056) (0.098,0.183) (0.111,0.352) (0.160,0.516) (0.126,0.776) (0.131,0.959) (0.118,1.533) (0.163,2.754)
Parameters optimization took 4 rounds (3.217 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.06991 secs using 399.8% CPU
Computing ML distances took 1.070101 sec (of wall-clock time) 4.277705 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000338078 secs using 345.2% CPU
Constructing RapidNJ tree: done in 0.00444794 secs using 281.7% CPU
Computing RapidNJ tree took 0.004852 sec (of wall-clock time) 0.015455 sec (of CPU time)
Log-likelihood of RapidNJ tree: -58949.248
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.23789 secs using 398.6% CPU
Optimizing NNI: done in 2.3207 secs using 398.8% CPU
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4.997 second
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Optimizing NNI: done in 4.4398 secs using 597.9% CPU
Computing log-likelihood of 98 initial trees ... 5.424 seconds
Current best score: -58892.622

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 180 / LogL: -103606.429 / Time: 0h:7m:48s (0h:1m:8s left)
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BETTER TREE FOUND at iteration 1: -58662.661
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 185: -103328.938
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Iteration 110 / LogL: -200518.144 / Time: 0h:12m:0s (0h:8m:48s left)
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Iteration 20 / LogL: -58730.481 / Time: 0h:0m:48s
Finish initializing candidate tree set (20)
Current best tree score: -58662.661 / CPU time: 43.841
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 196: -103327.809
BETTER TREE FOUND at iteration 25: -58657.806
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Iteration 40 / LogL: -58761.803 / Time: 0h:1m:22s (0h:3m:26s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 50: -58653.166
Iteration 50 / LogL: -58653.166 / Time: 0h:1m:38s (0h:3m:20s left)
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Iteration 70 / LogL: -58650.429 / Time: 0h:2m:8s (0h:3m:5s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 90: -58648.657
Iteration 90 / LogL: -58648.657 / Time: 0h:2m:40s (0h:2m:59s left)
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Iteration 110 / LogL: -58653.622 / Time: 0h:3m:10s (0h:2m:19s left)
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Iteration 260 / LogL: -103340.991 / Time: 0h:10m:46s (0h:1m:29s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 116: -58643.102
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Iteration 140 / LogL: -200519.060 / Time: 0h:14m:45s (0h:9m:58s left)
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Iteration 120 / LogL: -58650.194 / Time: 0h:3m:27s (0h:2m:47s left)
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Iteration 270 / LogL: -103343.968 / Time: 0h:11m:8s (0h:1m:4s left)
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Iteration 130 / LogL: -58649.671 / Time: 0h:3m:42s (0h:2m:28s left)
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Iteration 140 / LogL: -58766.006 / Time: 0h:3m:57s (0h:2m:9s left)
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Iteration 280 / LogL: -103341.591 / Time: 0h:11m:30s (0h:0m:39s left)
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Iteration 150 / LogL: -58651.255 / Time: 0h:4m:13s (0h:1m:52s left)
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Iteration 150 / LogL: -200595.724 / Time: 0h:15m:41s (0h:8m:50s left)
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Iteration 290 / LogL: -103395.256 / Time: 0h:11m:53s (0h:0m:14s left)
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Iteration 160 / LogL: -58649.332 / Time: 0h:4m:28s (0h:1m:34s left)
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TREE SEARCH COMPLETED AFTER 297 ITERATIONS / Time: 0h:12m:8s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -103327.809
Optimal log-likelihood: -103327.806
Proportion of invariable sites: 0.017
Site proportion and rates:  (0.090,0.030) (0.087,0.085) (0.060,0.190) (0.036,0.191) (0.175,0.368) (0.118,0.647) (0.159,1.091) (0.185,1.822) (0.074,4.350)
Parameters optimization took 1 rounds (0.624 sec)
BEST SCORE FOUND : -103327.806
Total tree length: 170.469

Total number of iterations: 297
CPU time used for tree search: 2778.073 sec (0h:46m:18s)
Wall-clock time used for tree search: 704.837 sec (0h:11m:44s)
Total CPU time used: 2875.068 sec (0h:47m:55s)
Total wall-clock time used: 729.138 sec (0h:12m:9s)

===> START BOOTSTRAP REPLICATE NUMBER 2

Creating bootstrap alignment (seed: 68184)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.104 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105419.236
Optimizing NNI: done in 1.49016 secs using 398.7% CPU
Optimizing NNI: done in 5.13192 secs using 596.9% CPU
2. Current log-likelihood: -103509.085
Optimizing NNI: done in 1.65879 secs using 398.6% CPU
Iteration 170 / LogL: -58670.645 / Time: 0h:4m:42s (0h:1m:16s left)
3. Current log-likelihood: -103438.360
Optimizing NNI: done in 1.70775 secs using 398.4% CPU
Optimizing NNI: done in 4.01037 secs using 598.3% CPU
Optimizing NNI: done in 1.62707 secs using 398.6% CPU
4. Current log-likelihood: -103435.071
Optimizing NNI: done in 1.18559 secs using 399% CPU
5. Current log-likelihood: -103432.540
Optimizing NNI: done in 1.66303 secs using 399% CPU
6. Current log-likelihood: -103429.342
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7. Current log-likelihood: -103428.004
Optimizing NNI: done in 5.38344 secs using 597% CPU
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8. Current log-likelihood: -103426.824
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9. Current log-likelihood: -103426.069
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10. Current log-likelihood: -103425.571
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11. Current log-likelihood: -103425.187
Optimizing NNI: done in 1.58554 secs using 398.7% CPU
Iteration 180 / LogL: -58643.870 / Time: 0h:4m:57s (0h:0m:59s left)
12. Current log-likelihood: -103424.938
Optimizing NNI: done in 1.52082 secs using 399.4% CPU
13. Current log-likelihood: -103424.716
Optimizing NNI: done in 1.48896 secs using 399% CPU
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14. Current log-likelihood: -103424.525
Optimizing NNI: done in 1.8083 secs using 398.8% CPU
15. Current log-likelihood: -103424.365
Optimizing NNI: done in 1.68026 secs using 399.1% CPU
16. Current log-likelihood: -103424.238
Optimizing NNI: done in 1.41481 secs using 398.7% CPU
Optimizing NNI: done in 4.8377 secs using 596.4% CPU
17. Current log-likelihood: -103424.137
Optimizing NNI: done in 1.61881 secs using 398.6% CPU
Optimal log-likelihood: -103424.000
Proportion of invariable sites: 0.028
Site proportion and rates:  (0.103,0.037) (0.104,0.120) (0.098,0.238) (0.117,0.372) (0.089,0.597) (0.072,0.930) (0.146,1.282) (0.185,2.033) (0.057,4.100)
Parameters optimization took 17 rounds (27.568 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.68746 secs using 398.6% CPU
Optimizing NNI: done in 1.19021 secs using 399.1% CPU
Optimizing NNI: done in 1.4657 secs using 398.7% CPU
Optimizing NNI: done in 5.86957 secs using 597.4% CPU
Iteration 160 / LogL: -200522.382 / Time: 0h:16m:33s (0h:7m:42s left)
Calculating distance matrix: done in 4.70555 secs using 399.9% CPU
Computing ML distances took 4.705940 sec (of wall-clock time) 18.816369 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000699997 secs using 325.3% CPU
Constructing RapidNJ tree: done in 0.00867105 secs using 331.7% CPU
Computing RapidNJ tree took 0.009440 sec (of wall-clock time) 0.033732 sec (of CPU time)
Optimizing NNI: done in 1.39247 secs using 399.4% CPU
Iteration 190 / LogL: -58645.997 / Time: 0h:5m:13s (0h:0m:43s left)
Log-likelihood of RapidNJ tree: -103743.425
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.77947 secs using 399.1% CPU
Optimizing NNI: done in 1.37768 secs using 399.1% CPU
Optimizing NNI: done in 4.85772 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.52192 secs using 399.1% CPU
BETTER TREE FOUND at iteration 161: -200483.094
Optimizing NNI: done in 1.71951 secs using 399% CPU
Optimizing NNI: done in 1.62437 secs using 398.9% CPU
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10.740 second
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Optimizing NNI: done in 1.30947 secs using 398.8% CPU
Iteration 200 / LogL: -59392.503 / Time: 0h:5m:28s (0h:0m:26s left)
Optimizing NNI: done in 1.58186 secs using 398.5% CPU
Optimizing NNI: done in 1.74059 secs using 398.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -58643.100
Optimizing NNI: done in 1.77611 secs using 399.1% CPU
Optimizing NNI: done in 5.60992 secs using 597.1% CPU
Optimizing NNI: done in 1.4723 secs using 399.1% CPU
Computing log-likelihood of 98 initial trees ... 10.561 seconds
Current best score: -103424.000

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.47978 secs using 398.9% CPU
Optimizing NNI: done in 2.20664 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.63308 secs using 398.8% CPU
Optimizing NNI: done in 4.66656 secs using 597.4% CPU
Optimizing NNI: done in 1.50738 secs using 399% CPU
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Optimizing NNI: done in 1.278 secs using 398.9% CPU
Optimizing NNI: done in 4.47713 secs using 597.5% CPU
BETTER TREE FOUND at iteration 1: -102913.868
Optimizing NNI: done in 1.3984 secs using 399.3% CPU
Iteration 210 / LogL: -58767.710 / Time: 0h:5m:43s (0h:0m:9s left)
Optimizing NNI: done in 2.33786 secs using 398.1% CPU
Optimizing NNI: done in 2.93402 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.93055 secs using 597.3% CPU
Optimizing NNI: done in 2.286 secs using 398.1% CPU
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Optimizing NNI: done in 5.50935 secs using 597.8% CPU
Optimizing NNI: done in 2.31043 secs using 398.6% CPU
TREE SEARCH COMPLETED AFTER 217 ITERATIONS / Time: 0h:5m:59s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58643.100
Optimal log-likelihood: -58643.089
Site proportion and rates:  (0.103,0.060) (0.104,0.197) (0.131,0.365) (0.127,0.519) (0.249,0.815) (0.112,1.416) (0.138,2.355) (0.036,4.813)
Parameters optimization took 1 rounds (1.035 sec)
BEST SCORE FOUND : -58643.089
Total tree length: 43.696

Total number of iterations: 217
CPU time used for tree search: 1398.690 sec (0h:23m:18s)
Wall-clock time used for tree search: 354.322 sec (0h:5m:54s)
Total CPU time used: 1422.796 sec (0h:23m:42s)
Total wall-clock time used: 360.340 sec (0h:6m:0s)

===> START BOOTSTRAP REPLICATE NUMBER 29

Creating bootstrap alignment (seed: 67491)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.065 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -62778.316
2. Current log-likelihood: -62169.623
BETTER TREE FOUND at iteration 2: -102784.554
3. Current log-likelihood: -62139.436
Optimizing NNI: done in 4.91635 secs using 598.1% CPU
Iteration 170 / LogL: -200507.950 / Time: 0h:17m:23s (0h:9m:21s left)
4. Current log-likelihood: -62125.121
5. Current log-likelihood: -62122.750
Optimizing NNI: done in 3.1463 secs using 398.4% CPU
6. Current log-likelihood: -62122.578
Optimal log-likelihood: -62122.562
Site proportion and rates:  (0.117,0.069) (0.079,0.167) (0.118,0.323) (0.088,0.475) (0.190,0.674) (0.160,1.060) (0.203,2.004) (0.047,4.160)
Parameters optimization took 6 rounds (4.870 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10755 secs using 399.8% CPU
Computing ML distances took 1.107738 sec (of wall-clock time) 4.428444 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000359058 secs using 393.3% CPU
Constructing RapidNJ tree: done in 0.00446701 secs using 375.6% CPU
Computing RapidNJ tree took 0.004887 sec (of wall-clock time) 0.018603 sec (of CPU time)
Log-likelihood of RapidNJ tree: -62102.777
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.94496 secs using 597.7% CPU
Optimizing NNI: done in 3.05352 secs using 398.5% CPU
Optimizing NNI: done in 3.1065 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
4.978 second
BETTER TREE FOUND at iteration 5: -102775.597
Optimizing NNI: done in 5.22183 secs using 598% CPU
Optimizing NNI: done in 2.07536 secs using 398.6% CPU
Computing log-likelihood of 98 initial trees ... 5.029 seconds
Current best score: -62017.193

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.86489 secs using 398.8% CPU
Optimizing NNI: done in 1.28422 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.45898 secs using 597.2% CPU
BETTER TREE FOUND at iteration 1: -61750.541
Optimizing NNI: done in 2.9814 secs using 398.4% CPU
Optimizing NNI: done in 1.26668 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.81503 secs using 398.5% CPU
BETTER TREE FOUND at iteration 2: -61744.878
Optimizing NNI: done in 5.06015 secs using 595.5% CPU
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Optimizing NNI: done in 1.34859 secs using 398.4% CPU
Optimizing NNI: done in 3.62421 secs using 398.5% CPU
Iteration 10 / LogL: -102832.473 / Time: 0h:1m:45s
Optimizing NNI: done in 0.998705 secs using 399.1% CPU
Optimizing NNI: done in 4.40435 secs using 597.7% CPU
Optimizing NNI: done in 1.66304 secs using 399.1% CPU
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Optimizing NNI: done in 1.22331 secs using 399.7% CPU
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Optimizing NNI: done in 3.09781 secs using 398.3% CPU
Optimizing NNI: done in 1.64521 secs using 398.5% CPU
Optimizing NNI: done in 1.25833 secs using 398.5% CPU
Iteration 10 / LogL: -61846.031 / Time: 0h:0m:34s
Optimizing NNI: done in 1.20316 secs using 398.8% CPU
Optimizing NNI: done in 3.29895 secs using 398.2% CPU
Optimizing NNI: done in 4.12122 secs using 597.8% CPU
Optimizing NNI: done in 0.941258 secs using 399% CPU
Optimizing NNI: done in 1.41857 secs using 398.9% CPU
Optimizing NNI: done in 3.0281 secs using 398.4% CPU
Optimizing NNI: done in 1.32448 secs using 398.9% CPU
Optimizing NNI: done in 1.46331 secs using 399.2% CPU
Optimizing NNI: done in 5.71696 secs using 597.4% CPU
Optimizing NNI: done in 3.01139 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.3951 secs using 399.2% CPU
Optimizing NNI: done in 1.26713 secs using 399% CPU
BETTER TREE FOUND at iteration 15: -102764.146
Optimizing NNI: done in 1.25732 secs using 398.5% CPU
Optimizing NNI: done in 3.82628 secs using 598.1% CPU
Optimizing NNI: done in 1.37781 secs using 399.3% CPU
Optimizing NNI: done in 1.37769 secs using 398.9% CPU
Iteration 20 / LogL: -61837.186 / Time: 0h:0m:47s
Finish initializing candidate tree set (20)
Current best tree score: -61744.878 / CPU time: 40.723
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 3.27525 secs using 398.5% CPU
Optimizing NNI: done in 1.31712 secs using 399.5% CPU
Optimizing NNI: done in 1.71693 secs using 399.3% CPU
Optimizing NNI: done in 4.84978 secs using 597.3% CPU
Iteration 180 / LogL: -200504.805 / Time: 0h:18m:11s (0h:8m:13s left)
Optimizing NNI: done in 2.81434 secs using 398.1% CPU
Optimizing NNI: done in 1.20542 secs using 399.3% CPU
Optimizing NNI: done in 1.50549 secs using 399.1% CPU
Optimizing NNI: done in 3.15331 secs using 398.8% CPU
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Optimizing NNI: done in 4.51935 secs using 597.9% CPU
Optimizing NNI: done in 1.26716 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.33057 secs using 398.4% CPU
BETTER TREE FOUND at iteration 26: -61743.297
Optimizing NNI: done in 1.37078 secs using 399.2% CPU
Optimizing NNI: done in 4.94466 secs using 597.5% CPU
Optimizing NNI: done in 1.24326 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.14702 secs using 398.2% CPU
Iteration 20 / LogL: -102791.269 / Time: 0h:2m:20s
Finish initializing candidate tree set (20)
Current best tree score: -102764.146 / CPU time: 106.173
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
BETTER TREE FOUND at iteration 28: -61741.688
Optimizing NNI: done in 1.16943 secs using 398.5% CPU
Optimizing NNI: done in 2.33498 secs using 398.5% CPU
Optimizing NNI: done in 1.62822 secs using 398.8% CPU
Iteration 30 / LogL: -61763.267 / Time: 0h:1m:3s (0h:3m:34s left)
Optimizing NNI: done in 1.2553 secs using 399.2% CPU
Optimizing NNI: done in 2.39871 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.07873 secs using 398.7% CPU
Optimizing NNI: done in 1.43993 secs using 399.2% CPU
Optimizing NNI: done in 8.17713 secs using 597.1% CPU
Optimizing NNI: done in 1.3175 secs using 399.7% CPU
Optimizing NNI: done in 1.4077 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -102760.145
BETTER TREE FOUND at iteration 35: -61735.574
Optimizing NNI: done in 1.40822 secs using 399% CPU
Optimizing NNI: done in 3.55961 secs using 397.4% CPU
Optimizing NNI: done in 1.37599 secs using 398.7% CPU
Optimizing NNI: done in 7.16829 secs using 597.3% CPU
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Optimizing NNI: done in 2.83224 secs using 398% CPU
Optimizing NNI: done in 1.36491 secs using 398.8% CPU
Optimizing NNI: done in 1.69943 secs using 399.1% CPU
Iteration 40 / LogL: -61762.678 / Time: 0h:1m:18s (0h:3m:12s left)
Optimizing NNI: done in 2.91383 secs using 398.2% CPU
Optimizing NNI: done in 1.33852 secs using 398.9% CPU
Optimizing NNI: done in 6.01531 secs using 596.2% CPU
Optimizing NNI: done in 1.33275 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.36428 secs using 399.2% CPU
Optimizing NNI: done in 1.69932 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.01768 secs using 596.8% CPU
BETTER TREE FOUND at iteration 26: -102758.787
BETTER TREE FOUND at iteration 45: -61734.933
Optimizing NNI: done in 1.06444 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.33819 secs using 398.8% CPU
BETTER TREE FOUND at iteration 46: -61731.365
Optimizing NNI: done in 1.37183 secs using 399.4% CPU
Optimizing NNI: done in 2.33826 secs using 397.9% CPU
Optimizing NNI: done in 1.43234 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.68232 secs using 597.5% CPU
BETTER TREE FOUND at iteration 48: -61728.722
Optimizing NNI: done in 2.84182 secs using 397.9% CPU
Optimizing NNI: done in 1.46573 secs using 399.3% CPU
Optimizing NNI: done in 1.34162 secs using 399.2% CPU
Iteration 50 / LogL: -61898.933 / Time: 0h:1m:35s (0h:3m:11s left)
Optimizing NNI: done in 2.50342 secs using 398.6% CPU
Iteration 30 / LogL: -102760.270 / Time: 0h:2m:56s (0h:9m:44s left)
Optimizing NNI: done in 1.41566 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.61624 secs using 597.6% CPU
BETTER TREE FOUND at iteration 51: -61728.214
Optimizing NNI: done in 2.37451 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.19974 secs using 399.4% CPU
Optimizing NNI: done in 1.34294 secs using 399.4% CPU
BETTER TREE FOUND at iteration 31: -102755.139
Optimizing NNI: done in 1.27772 secs using 399.4% CPU
Optimizing NNI: done in 5.32081 secs using 597.1% CPU
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Optimizing NNI: done in 4.96495 secs using 597.2% CPU
Iteration 190 / LogL: -200568.484 / Time: 0h:19m:9s (0h:7m:11s left)
Optimizing NNI: done in 1.3809 secs using 399.1% CPU
Optimizing NNI: done in 2.18207 secs using 398% CPU
Optimizing NNI: done in 1.2528 secs using 399.4% CPU
Iteration 60 / LogL: -61731.103 / Time: 0h:1m:50s (0h:2m:49s left)
Optimizing NNI: done in 1.3453 secs using 399.3% CPU
Optimizing NNI: done in 2.73391 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.18125 secs using 596.3% CPU
Optimizing NNI: done in 1.308 secs using 398.5% CPU
BETTER TREE FOUND at iteration 35: -102753.638
Optimizing NNI: done in 1.35471 secs using 399.1% CPU
Optimizing NNI: done in 1.43081 secs using 399.2% CPU
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Optimizing NNI: done in 5.6244 secs using 597% CPU
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Optimizing NNI: done in 2.17292 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.11132 secs using 597.8% CPU
Optimizing NNI: done in 1.5388 secs using 399.4% CPU
Iteration 70 / LogL: -61749.681 / Time: 0h:2m:3s (0h:2m:25s left)
Optimizing NNI: done in 1.2417 secs using 399.3% CPU
BETTER TREE FOUND at iteration 39: -102746.128
Optimizing NNI: done in 1.13219 secs using 398.8% CPU
Optimizing NNI: done in 1.26454 secs using 398.7% CPU
Optimizing NNI: done in 2.77161 secs using 398% CPU
Iteration 40 / LogL: -102821.589 / Time: 0h:3m:28s (0h:8m:48s left)
Optimizing NNI: done in 5.25752 secs using 597.4% CPU
Optimizing NNI: done in 1.21892 secs using 399% CPU
Optimizing NNI: done in 1.19343 secs using 399.4% CPU
Optimizing NNI: done in 1.13329 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.88339 secs using 397.8% CPU
BETTER TREE FOUND at iteration 76: -61727.898
Optimizing NNI: done in 4.10816 secs using 597.3% CPU
Optimizing NNI: done in 1.22372 secs using 399% CPU
Optimizing NNI: done in 2.68218 secs using 397.6% CPU
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Optimizing NNI: done in 1.11826 secs using 399% CPU
Optimizing NNI: done in 2.24726 secs using 398.4% CPU
Optimizing NNI: done in 1.06332 secs using 399.6% CPU
Iteration 80 / LogL: -61730.204 / Time: 0h:2m:16s (0h:2m:45s left)
Optimizing NNI: done in 4.27575 secs using 597.2% CPU
Optimizing NNI: done in 1.36643 secs using 398.9% CPU
Optimizing NNI: done in 2.23285 secs using 398.2% CPU
Optimizing NNI: done in 1.29596 secs using 399.1% CPU
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Optimizing NNI: done in 1.11557 secs using 399.3% CPU
Optimizing NNI: done in 3.34264 secs using 397.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.23783 secs using 597.4% CPU
Optimizing NNI: done in 1.30202 secs using 399.5% CPU
Optimizing NNI: done in 1.35679 secs using 399.2% CPU
Optimizing NNI: done in 1.36541 secs using 398.7% CPU
BETTER TREE FOUND at iteration 45: -102743.963
Optimizing NNI: done in 1.46284 secs using 398.8% CPU
Optimizing NNI: done in 4.85895 secs using 597.6% CPU
Optimizing NNI: done in 2.45219 secs using 398.8% CPU
Optimizing NNI: done in 1.41791 secs using 399.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -61727.896
Optimizing NNI: done in 1.38195 secs using 399.3% CPU
Iteration 90 / LogL: -61744.032 / Time: 0h:2m:29s (0h:2m:24s left)
Optimizing NNI: done in 2.13861 secs using 398.7% CPU
Optimizing NNI: done in 1.1602 secs using 399.1% CPU
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Optimizing NNI: done in 1.84615 secs using 399.5% CPU
Iteration 50 / LogL: -102754.313 / Time: 0h:3m:57s (0h:7m:39s left)
Optimizing NNI: done in 1.32415 secs using 398.8% CPU
Optimizing NNI: done in 5.62132 secs using 597% CPU
Iteration 200 / LogL: -200492.657 / Time: 0h:20m:0s (0h:6m:7s left)
Optimizing NNI: done in 1.09382 secs using 398.4% CPU
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Optimizing NNI: done in 2.28744 secs using 399% CPU
Optimizing NNI: done in 1.23495 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -61727.896
Iteration 100 / LogL: -61727.896 / Time: 0h:2m:42s (0h:2m:5s left)
Optimizing NNI: done in 5.00656 secs using 597.6% CPU
Optimizing NNI: done in 2.1171 secs using 398.7% CPU
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Optimizing NNI: done in 1.40677 secs using 398.9% CPU
Iteration 110 / LogL: -61729.184 / Time: 0h:2m:56s (0h:1m:47s left)
Optimizing NNI: done in 5.07651 secs using 597.1% CPU
Optimizing NNI: done in 1.49077 secs using 398.5% CPU
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Iteration 60 / LogL: -102761.629 / Time: 0h:4m:21s (0h:6m:15s left)
Optimizing NNI: done in 1.47562 secs using 398.9% CPU
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Optimizing NNI: done in 1.32881 secs using 399.2% CPU
Iteration 120 / LogL: -61728.740 / Time: 0h:3m:10s (0h:1m:29s left)
Optimizing NNI: done in 1.26132 secs using 399.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -61727.896
Optimizing NNI: done in 2.14903 secs using 398.7% CPU
Optimizing NNI: done in 1.08182 secs using 399.6% CPU
Optimizing NNI: done in 4.80559 secs using 598.1% CPU
Optimizing NNI: done in 1.31808 secs using 398.9% CPU
Optimizing NNI: done in 2.11231 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.36419 secs using 399.3% CPU
Optimizing NNI: done in 1.29856 secs using 399.4% CPU
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BETTER TREE FOUND at iteration 66: -102742.332
Optimizing NNI: done in 4.00115 secs using 597.5% CPU
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Optimizing NNI: done in 1.09621 secs using 399.3% CPU
Iteration 130 / LogL: -61829.496 / Time: 0h:3m:23s (0h:1m:12s left)
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Iteration 210 / LogL: -200633.553 / Time: 0h:20m:48s (0h:5m:4s left)
Optimizing NNI: done in 1.33945 secs using 398.9% CPU
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Iteration 70 / LogL: -102818.860 / Time: 0h:4m:51s (0h:6m:45s left)
Optimizing NNI: done in 4.92953 secs using 597% CPU
Optimizing NNI: done in 1.18683 secs using 399% CPU
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Optimizing NNI: done in 1.29131 secs using 399% CPU
Optimizing NNI: done in 1.36714 secs using 399% CPU
Iteration 140 / LogL: -61728.243 / Time: 0h:3m:36s (0h:0m:56s left)
Optimizing NNI: done in 5.04763 secs using 597.6% CPU
Optimizing NNI: done in 2.70222 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.2221 secs using 398.6% CPU
Optimizing NNI: done in 1.24551 secs using 399.3% CPU
BETTER TREE FOUND at iteration 72: -102739.010
Optimizing NNI: done in 1.40628 secs using 399.5% CPU
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Iteration 150 / LogL: -61728.983 / Time: 0h:3m:50s (0h:0m:40s left)
Optimizing NNI: done in 2.89517 secs using 398.1% CPU
Optimizing NNI: done in 1.16216 secs using 398.8% CPU
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Iteration 80 / LogL: -102746.546 / Time: 0h:5m:20s (0h:6m:13s left)
Optimizing NNI: done in 1.5877 secs using 399.1% CPU
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Iteration 160 / LogL: -61741.395 / Time: 0h:4m:3s (0h:0m:24s left)
Optimizing NNI: done in 1.23644 secs using 399.3% CPU
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Iteration 220 / LogL: -200661.938 / Time: 0h:21m:39s (0h:4m:3s left)
Optimizing NNI: done in 1.2925 secs using 398.9% CPU
Iteration 170 / LogL: -61780.404 / Time: 0h:4m:17s (0h:0m:9s left)
Optimizing NNI: done in 2.71471 secs using 398.2% CPU
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Optimizing NNI: done in 1.33597 secs using 399.1% CPU
Optimizing NNI: done in 1.13457 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 177 ITERATIONS / Time: 0h:4m:26s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -61727.896
Optimal log-likelihood: -61727.893
Site proportion and rates:  (0.138,0.074) (0.046,0.172) (0.142,0.319) (0.087,0.487) (0.211,0.713) (0.134,1.093) (0.196,2.039) (0.047,4.255)
Parameters optimization took 1 rounds (0.324 sec)
BEST SCORE FOUND : -61727.893
Total tree length: 48.657

Total number of iterations: 177
CPU time used for tree search: 1022.850 sec (0h:17m:2s)
Wall-clock time used for tree search: 259.971 sec (0h:4m:19s)
Total CPU time used: 1050.212 sec (0h:17m:30s)
Total wall-clock time used: 266.810 sec (0h:4m:26s)

===> START BOOTSTRAP REPLICATE NUMBER 30

Creating bootstrap alignment (seed: 67492)...

Optimizing NNI: done in 2.95772 secs using 398.2% CPU
Iteration 90 / LogL: -102763.943 / Time: 0h:5m:46s (0h:5m:19s left)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 64 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58483.415
Optimizing NNI: done in 5.00764 secs using 597.8% CPU
2. Current log-likelihood: -57955.739
3. Current log-likelihood: -57950.418
Optimizing NNI: done in 2.50068 secs using 398.4% CPU
4. Current log-likelihood: -57943.105
5. Current log-likelihood: -57930.265
6. Current log-likelihood: -57914.555
Optimizing NNI: done in 2.66038 secs using 398.4% CPU
7. Current log-likelihood: -57913.189
Optimizing NNI: done in 6.02637 secs using 597.5% CPU
Optimal log-likelihood: -57913.144
Site proportion and rates:  (0.130,0.068) (0.116,0.186) (0.090,0.402) (0.101,0.412) (0.229,0.779) (0.136,1.348) (0.171,2.263) (0.029,5.070)
Parameters optimization took 7 rounds (6.282 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09596 secs using 399.8% CPU
Computing ML distances took 1.096141 sec (of wall-clock time) 4.381772 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000369072 secs using 192.1% CPU
Constructing RapidNJ tree: done in 0.00440001 secs using 264.8% CPU
Computing RapidNJ tree took 0.004826 sec (of wall-clock time) 0.014401 sec (of CPU time)
Log-likelihood of RapidNJ tree: -57948.666
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.61745 secs using 398% CPU
Optimizing NNI: done in 2.62606 secs using 397.9% CPU
5.157 second
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Computing log-likelihood of 98 initial trees ... 5.243 seconds
Current best score: -57903.516

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -57665.937
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -57643.481
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Iteration 100 / LogL: -102746.752 / Time: 0h:6m:12s (0h:4m:30s left)
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Iteration 10 / LogL: -57702.558 / Time: 0h:0m:34s
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BETTER TREE FOUND at iteration 105: -102737.839
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Iteration 230 / LogL: -200531.277 / Time: 0h:22m:31s (0h:3m:2s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 17: -57635.903
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Iteration 20 / LogL: -57685.392 / Time: 0h:0m:49s
Finish initializing candidate tree set (20)
Current best tree score: -57635.903 / CPU time: 41.857
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 40 / LogL: -57596.587 / Time: 0h:1m:22s (0h:3m:31s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 91: -57594.728
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BETTER TREE FOUND at iteration 110: -57594.728
Iteration 110 / LogL: -57594.728 / Time: 0h:3m:5s (0h:2m:50s left)
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TREE SEARCH COMPLETED AFTER 262 ITERATIONS / Time: 0h:25m:5s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -200483.094
Optimal log-likelihood: -200483.086
Site proportion and rates:  (0.020,0.107) (0.069,0.255) (0.128,0.405) (0.214,0.570) (0.150,0.799) (0.158,1.037) (0.156,1.602) (0.105,2.600)
Parameters optimization took 1 rounds (1.029 sec)
BEST SCORE FOUND : -200483.086
Total tree length: 161.516

Total number of iterations: 262
CPU time used for tree search: 8658.666 sec (2h:24m:18s)
Wall-clock time used for tree search: 1474.674 sec (0h:24m:34s)
Total CPU time used: 8846.972 sec (2h:27m:26s)
Total wall-clock time used: 1506.263 sec (0h:25m:6s)

===> START BOOTSTRAP REPLICATE NUMBER 8

Creating bootstrap alignment (seed: 70471)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.310 seconds

NOTE: 242 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.47811 secs using 398.6% CPU
1. Initial log-likelihood: -199020.872
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Iteration 120 / LogL: -57598.626 / Time: 0h:3m:21s (0h:2m:32s left)
2. Current log-likelihood: -196469.504
Optimizing NNI: done in 1.36696 secs using 398.4% CPU
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3. Current log-likelihood: -196449.385
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4. Current log-likelihood: -196447.807
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5. Current log-likelihood: -196445.678
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6. Current log-likelihood: -196443.269
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7. Current log-likelihood: -196441.602
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8. Current log-likelihood: -196440.574
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Iteration 180 / LogL: -102736.526 / Time: 0h:9m:22s (0h:3m:17s left)
9. Current log-likelihood: -196439.997
Optimizing NNI: done in 1.6545 secs using 398.8% CPU
Iteration 130 / LogL: -57599.066 / Time: 0h:3m:36s (0h:2m:14s left)
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Optimizing NNI: done in 1.66024 secs using 399% CPU
10. Current log-likelihood: -196439.697
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11. Current log-likelihood: -196439.562
Optimizing NNI: done in 1.60514 secs using 399.2% CPU
Optimal log-likelihood: -196439.512
Site proportion and rates:  (0.018,0.109) (0.057,0.250) (0.104,0.368) (0.200,0.540) (0.168,0.715) (0.193,0.989) (0.148,1.612) (0.112,2.572)
Parameters optimization took 11 rounds (24.079 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 10.1272 secs using 599.9% CPU
Computing ML distances took 10.127840 sec (of wall-clock time) 60.756478 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00131989 secs using 514.6% CPU
Constructing RapidNJ tree: done in 0.022428 secs using 673.3% CPU
Computing RapidNJ tree took 0.023836 sec (of wall-clock time) 0.158778 sec (of CPU time)
Optimizing NNI: done in 1.52232 secs using 398.9% CPU
Iteration 140 / LogL: -57597.232 / Time: 0h:3m:52s (0h:1m:57s left)
Optimizing NNI: done in 2.14137 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.61487 secs using 398.9% CPU
Log-likelihood of RapidNJ tree: -201408.063
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... BETTER TREE FOUND at iteration 188: -102734.988
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 146: -57593.889
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Computing log-likelihood of 98 initial trees ... 16.708 seconds
Current best score: -196439.512

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -195908.964
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -195808.499 / Time: 0h:2m:52s
Finish initializing candidate tree set (20)
Current best tree score: -195749.810 / CPU time: 135.188
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 250 / LogL: -102758.887 / Time: 0h:12m:6s (0h:1m:50s left)
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Iteration 240 / LogL: -57594.750 / Time: 0h:6m:22s (0h:0m:9s left)
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Optimizing NNI: done in 1.74886 secs using 398.4% CPU
TREE SEARCH COMPLETED AFTER 247 ITERATIONS / Time: 0h:6m:33s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57593.889
2. Current log-likelihood: -57593.871
Optimal log-likelihood: -57593.864
Site proportion and rates:  (0.127,0.067) (0.129,0.188) (0.091,0.418) (0.104,0.436) (0.205,0.780) (0.139,1.325) (0.176,2.231) (0.030,4.934)
Parameters optimization took 2 rounds (1.312 sec)
BEST SCORE FOUND : -57593.864
Total tree length: 42.776

Total number of iterations: 247
CPU time used for tree search: 1523.951 sec (0h:25m:23s)
Wall-clock time used for tree search: 385.746 sec (0h:6m:25s)
Total CPU time used: 1560.283 sec (0h:26m:0s)
Total wall-clock time used: 394.831 sec (0h:6m:34s)

===> START BOOTSTRAP REPLICATE NUMBER 31

Creating bootstrap alignment (seed: 67493)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58187.125
Optimizing NNI: done in 2.2296 secs using 399% CPU
2. Current log-likelihood: -57593.969
3. Current log-likelihood: -57575.562
Optimizing NNI: done in 2.40738 secs using 398.7% CPU
Optimizing NNI: done in 4.25841 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
4. Current log-likelihood: -57548.786
5. Current log-likelihood: -57543.975
6. Current log-likelihood: -57543.782
Optimizing NNI: done in 2.09257 secs using 398.6% CPU
Optimal log-likelihood: -57543.768
Site proportion and rates:  (0.112,0.071) (0.089,0.185) (0.156,0.336) (0.055,0.472) (0.256,0.734) (0.153,1.314) (0.144,2.237) (0.035,5.334)
Parameters optimization took 6 rounds (5.456 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
BETTER TREE FOUND at iteration 26: -195723.655
Calculating distance matrix: done in 1.09379 secs using 399.8% CPU
Computing ML distances took 1.093966 sec (of wall-clock time) 4.373175 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000338793 secs using 415.6% CPU
Constructing RapidNJ tree: done in 0.00452685 secs using 440.7% CPU
Computing RapidNJ tree took 0.004918 sec (of wall-clock time) 0.022318 sec (of CPU time)
Optimizing NNI: done in 2.08131 secs using 398.9% CPU
Iteration 260 / LogL: -102773.354 / Time: 0h:12m:28s (0h:1m:20s left)
Log-likelihood of RapidNJ tree: -57717.230
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.13816 secs using 399% CPU
Optimizing NNI: done in 2.47129 secs using 398.9% CPU
Optimizing NNI: done in 5.61381 secs using 596.8% CPU
5.110 second
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Optimizing NNI: done in 4.71084 secs using 597% CPU
Computing log-likelihood of 98 initial trees ... 5.141 seconds
Current best score: -57513.870

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 30 / LogL: -195809.897 / Time: 0h:3m:42s (0h:12m:15s left)
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Iteration 270 / LogL: -102789.076 / Time: 0h:12m:50s (0h:0m:51s left)
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BETTER TREE FOUND at iteration 1: -57303.045
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Estimate model parameters (epsilon = 0.100)
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Iteration 10 / LogL: -57328.249 / Time: 0h:0m:43s
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BETTER TREE FOUND at iteration 34: -195717.597
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Iteration 280 / LogL: -102764.437 / Time: 0h:13m:12s (0h:0m:22s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -57368.392 / Time: 0h:0m:57s
Finish initializing candidate tree set (20)
Current best tree score: -57303.045 / CPU time: 50.236
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 36: -195714.412
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BETTER TREE FOUND at iteration 24: -57301.514
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 2.14958 secs using 398.6% CPU
TREE SEARCH COMPLETED AFTER 289 ITERATIONS / Time: 0h:13m:31s

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|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102734.988
Optimizing NNI: done in 1.47914 secs using 399.1% CPU
Optimal log-likelihood: -102734.983
Proportion of invariable sites: 0.028
Site proportion and rates:  (0.104,0.037) (0.119,0.126) (0.131,0.271) (0.101,0.442) (0.076,0.681) (0.154,1.120) (0.149,1.698) (0.097,2.454) (0.040,4.610)
Parameters optimization took 1 rounds (0.856 sec)
BEST SCORE FOUND : -102734.983
Total tree length: 156.739

Total number of iterations: 289
CPU time used for tree search: 3066.374 sec (0h:51m:6s)
Wall-clock time used for tree search: 777.504 sec (0h:12m:57s)
Total CPU time used: 3204.852 sec (0h:53m:24s)
Total wall-clock time used: 812.234 sec (0h:13m:32s)

===> START BOOTSTRAP REPLICATE NUMBER 3

Creating bootstrap alignment (seed: 68185)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106179.171
BETTER TREE FOUND at iteration 38: -195686.354
Optimizing NNI: done in 1.31158 secs using 399.2% CPU
2. Current log-likelihood: -104429.524
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3. Current log-likelihood: -104318.552
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Iteration 30 / LogL: -57311.037 / Time: 0h:1m:15s (0h:4m:5s left)
4. Current log-likelihood: -104310.912
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5. Current log-likelihood: -104310.451
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6. Current log-likelihood: -104310.080
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Iteration 40 / LogL: -195724.813 / Time: 0h:4m:36s (0h:11m:34s left)
7. Current log-likelihood: -104309.752
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8. Current log-likelihood: -104309.465
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Estimate model parameters (epsilon = 0.100)
9. Current log-likelihood: -104309.210
BETTER TREE FOUND at iteration 35: -57295.892
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10. Current log-likelihood: -104309.066
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11. Current log-likelihood: -104308.923
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12. Current log-likelihood: -104308.790
13. Current log-likelihood: -104308.671
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14. Current log-likelihood: -104308.561
15. Current log-likelihood: -104308.459
Optimizing NNI: done in 1.73005 secs using 399% CPU
Iteration 40 / LogL: -57337.406 / Time: 0h:1m:31s (0h:3m:43s left)
Optimal log-likelihood: -104308.312
Proportion of invariable sites: 0.015
Site proportion and rates:  (0.086,0.038) (0.105,0.121) (0.059,0.207) (0.121,0.336) (0.121,0.480) (0.086,0.761) (0.147,1.167) (0.195,1.911) (0.065,4.039)
Parameters optimization took 15 rounds (21.418 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 41: -57290.260
Calculating distance matrix: done in 4.6551 secs using 399.9% CPU
Computing ML distances took 4.655492 sec (of wall-clock time) 18.613871 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000696182 secs using 236% CPU
Constructing RapidNJ tree: done in 0.00847006 secs using 360.5% CPU
Computing RapidNJ tree took 0.009234 sec (of wall-clock time) 0.034784 sec (of CPU time)
Optimizing NNI: done in 1.82367 secs using 399.3% CPU
Log-likelihood of RapidNJ tree: -104594.009
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.1672 secs using 598.2% CPU
Optimizing NNI: done in 1.38902 secs using 399.2% CPU
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10.675 second
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Iteration 50 / LogL: -57311.321 / Time: 0h:1m:49s (0h:3m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -57289.547
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Computing log-likelihood of 98 initial trees ... 9.654 seconds
Current best score: -104308.312

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -103825.073
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 60: -57286.080
Iteration 60 / LogL: -57286.080 / Time: 0h:2m:6s (0h:3m:34s left)
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Iteration 50 / LogL: -195739.308 / Time: 0h:5m:24s (0h:9m:42s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 10 / LogL: -104089.383 / Time: 0h:1m:11s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 76: -57281.851
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Iteration 80 / LogL: -57281.927 / Time: 0h:2m:39s (0h:3m:13s left)
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Iteration 20 / LogL: -103880.388 / Time: 0h:1m:31s
Finish initializing candidate tree set (20)
Current best tree score: -103790.788 / CPU time: 64.638
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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UPDATE BEST LOG-LIKELIHOOD: -57279.944
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BETTER TREE FOUND at iteration 30: -103780.208
Iteration 30 / LogL: -103780.208 / Time: 0h:1m:56s (0h:6m:40s left)
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BETTER TREE FOUND at iteration 100: -57276.591
Iteration 100 / LogL: -57276.591 / Time: 0h:3m:13s (0h:3m:15s left)
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UPDATE BEST LOG-LIKELIHOOD: -57276.586
Iteration 190 / LogL: -57276.586 / Time: 0h:5m:30s (0h:1m:2s left)
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BETTER TREE FOUND at iteration 100: -195651.536
Iteration 100 / LogL: -195651.536 / Time: 0h:9m:23s (0h:9m:28s left)
BETTER TREE FOUND at iteration 112: -103750.840
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BETTER TREE FOUND at iteration 117: -103748.424
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TREE SEARCH COMPLETED AFTER 227 ITERATIONS / Time: 0h:6m:28s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57276.586
Optimizing NNI: done in 1.95682 secs using 399.1% CPU
2. Current log-likelihood: -57276.575
Optimal log-likelihood: -57276.566
Site proportion and rates:  (0.109,0.072) (0.129,0.201) (0.167,0.387) (0.217,0.699) (0.137,1.046) (0.117,1.732) (0.089,2.430) (0.035,5.400)
Parameters optimization took 2 rounds (1.029 sec)
BEST SCORE FOUND : -57276.566
Total tree length: 43.864

Total number of iterations: 227
CPU time used for tree search: 1502.416 sec (0h:25m:2s)
Wall-clock time used for tree search: 380.318 sec (0h:6m:20s)
Total CPU time used: 1537.369 sec (0h:25m:37s)
Total wall-clock time used: 389.057 sec (0h:6m:29s)

===> START BOOTSTRAP REPLICATE NUMBER 32

Creating bootstrap alignment (seed: 67494)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61027.075
2. Current log-likelihood: -60469.516
Optimizing NNI: done in 1.98567 secs using 398.7% CPU
3. Current log-likelihood: -60456.610
4. Current log-likelihood: -60442.685
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5. Current log-likelihood: -60413.719
Optimizing NNI: done in 2.00945 secs using 398.7% CPU
6. Current log-likelihood: -60412.016
Optimal log-likelihood: -60411.973
Site proportion and rates:  (0.093,0.061) (0.101,0.177) (0.122,0.378) (0.123,0.385) (0.174,0.721) (0.181,1.137) (0.183,2.168) (0.023,6.800)
Parameters optimization took 6 rounds (4.965 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.19322 secs using 398.3% CPU
Calculating distance matrix: done in 1.09618 secs using 400% CPU
Computing ML distances took 1.096362 sec (of wall-clock time) 4.384783 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000334024 secs using 392.5% CPU
Constructing RapidNJ tree: done in 0.004457 secs using 330.7% CPU
Computing RapidNJ tree took 0.004847 sec (of wall-clock time) 0.017443 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60384.930
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 4.42351 secs using 597.4% CPU
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4.921 second
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Iteration 130 / LogL: -103778.015 / Time: 0h:5m:33s (0h:3m:44s left)
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Computing log-likelihood of 98 initial trees ... 5.173 seconds
Current best score: -60329.201

Do NNI search on 20 best initial trees
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BETTER TREE FOUND at iteration 1: -60129.750
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Iteration 10 / LogL: -60166.488 / Time: 0h:0m:38s
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Iteration 20 / LogL: -60199.591 / Time: 0h:0m:51s
Finish initializing candidate tree set (20)
Current best tree score: -60106.427 / CPU time: 44.582
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Iteration 150 / LogL: -103757.666 / Time: 0h:6m:12s (0h:2m:47s left)
BETTER TREE FOUND at iteration 21: -60099.006
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -60096.741
BETTER TREE FOUND at iteration 119: -195626.632
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Iteration 30 / LogL: -60099.693 / Time: 0h:1m:7s (0h:3m:51s left)
BETTER TREE FOUND at iteration 157: -103747.843
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BETTER TREE FOUND at iteration 31: -60093.627
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Iteration 120 / LogL: -195690.169 / Time: 0h:10m:57s (0h:9m:6s left)
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Iteration 160 / LogL: -103750.449 / Time: 0h:6m:32s (0h:3m:59s left)
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BETTER TREE FOUND at iteration 37: -60085.668
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Iteration 40 / LogL: -60088.763 / Time: 0h:1m:24s (0h:3m:31s left)
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BETTER TREE FOUND at iteration 42: -60084.723
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Iteration 170 / LogL: -103770.267 / Time: 0h:6m:51s (0h:3m:31s left)
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Iteration 50 / LogL: -60679.864 / Time: 0h:1m:43s (0h:3m:14s left)
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BETTER TREE FOUND at iteration 53: -60084.643
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Iteration 180 / LogL: -103772.143 / Time: 0h:7m:10s (0h:3m:5s left)
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Iteration 130 / LogL: -195667.076 / Time: 0h:11m:41s (0h:8m:3s left)
BETTER TREE FOUND at iteration 57: -60084.185
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Iteration 60 / LogL: -60084.637 / Time: 0h:1m:59s (0h:3m:15s left)
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BETTER TREE FOUND at iteration 65: -60083.817
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Iteration 190 / LogL: -103759.550 / Time: 0h:7m:30s (0h:2m:39s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 70: -60082.626
Iteration 70 / LogL: -60082.626 / Time: 0h:2m:14s (0h:3m:15s left)
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UPDATE BEST LOG-LIKELIHOOD: -60082.620
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 79: -60076.714
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Iteration 80 / LogL: -60085.202 / Time: 0h:2m:31s (0h:3m:9s left)
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Iteration 200 / LogL: -103768.461 / Time: 0h:7m:50s (0h:2m:14s left)
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Iteration 140 / LogL: -195712.132 / Time: 0h:12m:24s (0h:7m:2s left)
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Iteration 90 / LogL: -60082.308 / Time: 0h:2m:45s (0h:2m:45s left)
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Iteration 210 / LogL: -103771.911 / Time: 0h:8m:9s (0h:1m:50s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 95: -60070.106
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Iteration 100 / LogL: -60127.949 / Time: 0h:3m:1s (0h:2m:53s left)
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Iteration 220 / LogL: -103749.153 / Time: 0h:8m:29s (0h:1m:26s left)
BETTER TREE FOUND at iteration 106: -60067.645
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Iteration 110 / LogL: -60090.702 / Time: 0h:3m:16s (0h:2m:53s left)
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BETTER TREE FOUND at iteration 113: -60062.751
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Iteration 150 / LogL: -195629.419 / Time: 0h:13m:8s (0h:6m:4s left)
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BETTER TREE FOUND at iteration 229: -103747.291
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Iteration 130 / LogL: -60078.831 / Time: 0h:3m:45s (0h:2m:25s left)
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BETTER TREE FOUND at iteration 134: -60062.748
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Iteration 240 / LogL: -103967.332 / Time: 0h:9m:10s (0h:3m:24s left)
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BETTER TREE FOUND at iteration 159: -195623.075
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BETTER TREE FOUND at iteration 143: -60062.187
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Iteration 160 / LogL: -195650.804 / Time: 0h:13m:52s (0h:8m:38s left)
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BETTER TREE FOUND at iteration 250: -103746.082
Iteration 250 / LogL: -103746.082 / Time: 0h:9m:31s (0h:3m:49s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 168: -60060.567
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Iteration 170 / LogL: -60084.896 / Time: 0h:4m:44s (0h:2m:44s left)
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Iteration 170 / LogL: -195904.781 / Time: 0h:14m:37s (0h:7m:41s left)
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Iteration 270 / LogL: -103759.521 / Time: 0h:10m:10s (0h:3m:1s left)
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Iteration 180 / LogL: -60064.866 / Time: 0h:4m:59s (0h:2m:27s left)
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Iteration 280 / LogL: -103792.280 / Time: 0h:10m:29s (0h:2m:37s left)
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Iteration 190 / LogL: -60061.772 / Time: 0h:5m:13s (0h:2m:9s left)
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Optimizing NNI: done in 4.17593 secs using 597.3% CPU
BETTER TREE FOUND at iteration 282: -103745.650
BETTER TREE FOUND at iteration 191: -60055.421
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BETTER TREE FOUND at iteration 196: -60054.014
Optimizing NNI: done in 1.98086 secs using 399% CPU
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BETTER TREE FOUND at iteration 287: -103744.875
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Iteration 200 / LogL: -60066.905 / Time: 0h:5m:30s (0h:2m:39s left)
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Iteration 290 / LogL: -103873.525 / Time: 0h:10m:52s (0h:3m:39s left)
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Iteration 180 / LogL: -195671.591 / Time: 0h:15m:20s (0h:6m:46s left)
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BETTER TREE FOUND at iteration 293: -103742.228
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Iteration 210 / LogL: -60055.190 / Time: 0h:5m:44s (0h:2m:21s left)
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Iteration 300 / LogL: -103794.356 / Time: 0h:11m:14s (0h:3m:29s left)
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Iteration 220 / LogL: -60116.412 / Time: 0h:5m:58s (0h:2m:4s left)
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Iteration 230 / LogL: -60055.190 / Time: 0h:6m:13s (0h:1m:47s left)
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BETTER TREE FOUND at iteration 309: -103740.551
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Iteration 190 / LogL: -195650.477 / Time: 0h:16m:2s (0h:5m:51s left)
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Iteration 310 / LogL: -103801.529 / Time: 0h:11m:36s (0h:3m:43s left)
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BETTER TREE FOUND at iteration 311: -103739.162
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BETTER TREE FOUND at iteration 237: -60053.830
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Iteration 240 / LogL: -60066.918 / Time: 0h:6m:28s (0h:2m:37s left)
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Iteration 320 / LogL: -103739.513 / Time: 0h:11m:57s (0h:3m:24s left)
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Iteration 250 / LogL: -60067.955 / Time: 0h:6m:43s (0h:2m:20s left)
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Iteration 260 / LogL: -60060.177 / Time: 0h:6m:58s (0h:2m:4s left)
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Iteration 200 / LogL: -195750.885 / Time: 0h:16m:45s (0h:4m:57s left)
BETTER TREE FOUND at iteration 329: -103730.290
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Iteration 330 / LogL: -103741.303 / Time: 0h:12m:19s (0h:3m:42s left)
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Iteration 270 / LogL: -60060.858 / Time: 0h:7m:13s (0h:1m:47s left)
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Iteration 340 / LogL: -103742.153 / Time: 0h:12m:38s (0h:3m:19s left)
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Iteration 280 / LogL: -60054.182 / Time: 0h:7m:27s (0h:1m:31s left)
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Iteration 350 / LogL: -103740.816 / Time: 0h:12m:58s (0h:2m:56s left)
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Iteration 210 / LogL: -195625.540 / Time: 0h:17m:27s (0h:4m:5s left)
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Iteration 290 / LogL: -60057.671 / Time: 0h:7m:43s (0h:1m:15s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 353: -103729.690
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Iteration 300 / LogL: -60054.661 / Time: 0h:7m:57s (0h:0m:59s left)
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Iteration 360 / LogL: -103735.219 / Time: 0h:13m:20s (0h:3m:27s left)
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Iteration 310 / LogL: -60070.205 / Time: 0h:8m:12s (0h:0m:43s left)
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Iteration 370 / LogL: -103735.343 / Time: 0h:13m:39s (0h:3m:4s left)
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BETTER TREE FOUND at iteration 317: -60053.830
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Iteration 400 / LogL: -103732.189 / Time: 0h:14m:35s (0h:1m:56s left)
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Iteration 360 / LogL: -60066.066 / Time: 0h:9m:24s (0h:1m:29s left)
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Iteration 410 / LogL: -103748.825 / Time: 0h:14m:54s (0h:1m:34s left)
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Iteration 370 / LogL: -60058.366 / Time: 0h:9m:38s (0h:1m:13s left)
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Iteration 240 / LogL: -195660.795 / Time: 0h:19m:38s (0h:1m:33s left)
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Iteration 380 / LogL: -60072.312 / Time: 0h:9m:53s (0h:0m:57s left)
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Iteration 420 / LogL: -103742.444 / Time: 0h:15m:13s (0h:1m:11s left)
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Iteration 390 / LogL: -60053.831 / Time: 0h:10m:8s (0h:0m:42s left)
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Iteration 430 / LogL: -103741.150 / Time: 0h:15m:32s (0h:0m:50s left)
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Iteration 400 / LogL: -60077.689 / Time: 0h:10m:22s (0h:0m:26s left)
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Iteration 440 / LogL: -103749.783 / Time: 0h:15m:52s (0h:0m:28s left)
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Optimizing NNI: done in 4.3309 secs using 597.3% CPU
Iteration 250 / LogL: -195635.862 / Time: 0h:20m:22s (0h:0m:44s left)
Optimizing NNI: done in 1.43965 secs using 399.3% CPU
Iteration 410 / LogL: -60118.929 / Time: 0h:10m:37s (0h:0m:10s left)
Optimizing NNI: done in 2.38358 secs using 398.6% CPU
Optimizing NNI: done in 1.26013 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.10854 secs using 398.5% CPU
BETTER TREE FOUND at iteration 411: -60052.421
Optimizing NNI: done in 5.02647 secs using 596.8% CPU
Optimizing NNI: done in 1.68397 secs using 399.3% CPU
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Iteration 450 / LogL: -103736.820 / Time: 0h:16m:11s (0h:0m:6s left)
Optimizing NNI: done in 1.70402 secs using 399.2% CPU
Iteration 420 / LogL: -60061.212 / Time: 0h:10m:53s (0h:2m:22s left)
Optimizing NNI: done in 4.3793 secs using 597% CPU
Optimizing NNI: done in 1.14696 secs using 399.1% CPU
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Optimizing NNI: done in 1.31322 secs using 398.9% CPU
Optimizing NNI: done in 1.82535 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 454 ITERATIONS / Time: 0h:16m:19s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -103729.690
Optimizing NNI: done in 1.63595 secs using 398.6% CPU
Optimal log-likelihood: -103729.681
Proportion of invariable sites: 0.015
Site proportion and rates:  (0.086,0.035) (0.119,0.121) (0.042,0.211) (0.084,0.308) (0.158,0.444) (0.095,0.763) (0.142,1.188) (0.194,1.932) (0.067,3.938)
Parameters optimization took 1 rounds (0.757 sec)
BEST SCORE FOUND : -103729.681
Total tree length: 154.234

Total number of iterations: 454
CPU time used for tree search: 3766.005 sec (1h:2m:46s)
Wall-clock time used for tree search: 952.368 sec (0h:15m:52s)
Total CPU time used: 3877.666 sec (1h:4m:37s)
Total wall-clock time used: 980.362 sec (0h:16m:20s)

===> START BOOTSTRAP REPLICATE NUMBER 4

Creating bootstrap alignment (seed: 68186)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.145 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -108031.258
Optimizing NNI: done in 3.54258 secs using 597.3% CPU
Optimizing NNI: done in 1.21446 secs using 399% CPU
2. Current log-likelihood: -106012.025
Optimizing NNI: done in 1.41878 secs using 399.2% CPU
3. Current log-likelihood: -105875.395
Optimizing NNI: done in 1.32369 secs using 398.6% CPU
Optimizing NNI: done in 1.26376 secs using 398.9% CPU
Iteration 430 / LogL: -60079.723 / Time: 0h:11m:7s (0h:2m:5s left)
Optimizing NNI: done in 4.8443 secs using 596.7% CPU
4. Current log-likelihood: -105869.732
Optimizing NNI: done in 1.32002 secs using 398.9% CPU
5. Current log-likelihood: -105869.047
Optimizing NNI: done in 1.19431 secs using 399.4% CPU
6. Current log-likelihood: -105868.790
Optimizing NNI: done in 1.58339 secs using 398.8% CPU
Optimizing NNI: done in 4.39044 secs using 597.9% CPU
Optimal log-likelihood: -105868.683
Proportion of invariable sites: 0.035
Site proportion and rates:  (0.107,0.047) (0.082,0.133) (0.066,0.225) (0.125,0.355) (0.122,0.578) (0.086,0.811) (0.143,1.189) (0.166,1.922) (0.068,4.317)
Parameters optimization took 6 rounds (9.843 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.36146 secs using 399.5% CPU
Optimizing NNI: done in 1.13017 secs using 399% CPU
Optimizing NNI: done in 1.68605 secs using 399% CPU
Optimizing NNI: done in 4.56858 secs using 597.6% CPU
Calculating distance matrix: done in 4.64808 secs using 399.9% CPU
Computing ML distances took 4.648456 sec (of wall-clock time) 18.589615 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000735044 secs using 420.4% CPU
Constructing RapidNJ tree: done in 0.00860095 secs using 388.7% CPU
Computing RapidNJ tree took 0.009399 sec (of wall-clock time) 0.036579 sec (of CPU time)
Optimizing NNI: done in 1.65827 secs using 399.2% CPU
Log-likelihood of RapidNJ tree: -106092.836
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.31401 secs using 399.3% CPU
Optimizing NNI: done in 1.30166 secs using 399.3% CPU
Optimizing NNI: done in 1.37926 secs using 398.7% CPU
Iteration 440 / LogL: -60053.168 / Time: 0h:11m:21s (0h:1m:50s left)
Optimizing NNI: done in 4.70755 secs using 597.2% CPU
Iteration 260 / LogL: -195762.595 / Time: 0h:21m:7s (0h:0m:-5s left)
TREE SEARCH COMPLETED AFTER 260 ITERATIONS / Time: 0h:21m:7s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -195623.075
Optimizing NNI: done in 1.54051 secs using 399% CPU
2. Current log-likelihood: -195623.062
Optimal log-likelihood: -195623.062
Site proportion and rates:  (0.020,0.120) (0.062,0.258) (0.110,0.380) (0.217,0.557) (0.146,0.735) (0.185,0.998) (0.151,1.606) (0.109,2.605)
Parameters optimization took 2 rounds (2.600 sec)
BEST SCORE FOUND : -195623.062
Total tree length: 153.161

Total number of iterations: 260
CPU time used for tree search: 7199.045 sec (1h:59m:59s)
Wall-clock time used for tree search: 1230.103 sec (0h:20m:30s)
Total CPU time used: 7436.767 sec (2h:3m:56s)
Total wall-clock time used: 1269.998 sec (0h:21m:9s)

===> START BOOTSTRAP REPLICATE NUMBER 9

Creating bootstrap alignment (seed: 70472)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.282 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.50625 secs using 398.8% CPU
1. Initial log-likelihood: -201940.924
Optimizing NNI: done in 1.43237 secs using 399.3% CPU
Optimizing NNI: done in 1.29506 secs using 398.5% CPU
BETTER TREE FOUND at iteration 444: -60052.417
2. Current log-likelihood: -199351.071
Optimizing NNI: done in 1.30125 secs using 399.2% CPU
10.922 second
Optimizing NNI: done in 1.31974 secs using 398.9% CPU
3. Current log-likelihood: -199332.563
Optimizing NNI: done in 1.54227 secs using 398.5% CPU
Optimizing NNI: done in 1.34896 secs using 399.1% CPU
4. Current log-likelihood: -199331.904
Optimizing NNI: done in 1.57603 secs using 398.8% CPU
Optimizing NNI: done in 1.4517 secs using 398.9% CPU
Iteration 450 / LogL: -60058.833 / Time: 0h:11m:35s (0h:2m:25s left)
5. Current log-likelihood: -199331.472
Optimizing NNI: done in 1.42277 secs using 399.2% CPU
Optimizing NNI: done in 1.45575 secs using 398.8% CPU
6. Current log-likelihood: -199331.351
Computing log-likelihood of 98 initial trees ... 9.893 seconds
Current best score: -105868.683

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.4375 secs using 399.2% CPU
Optimizing NNI: done in 2.34824 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimal log-likelihood: -199331.319
Site proportion and rates:  (0.011,0.095) (0.033,0.222) (0.034,0.344) (0.121,0.387) (0.251,0.590) (0.279,0.920) (0.179,1.579) (0.092,2.673)
Parameters optimization took 6 rounds (16.977 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.50195 secs using 398.8% CPU
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BETTER TREE FOUND at iteration 457: -60052.417
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Iteration 460 / LogL: -60061.159 / Time: 0h:11m:50s (0h:2m:30s left)
Calculating distance matrix: done in 10.104 secs using 599.7% CPU
Computing ML distances took 10.104619 sec (of wall-clock time) 60.600305 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00167489 secs using 411.1% CPU
Constructing RapidNJ tree: done in 0.034703 secs using 691.4% CPU
Computing RapidNJ tree took 0.036457 sec (of wall-clock time) 0.247472 sec (of CPU time)
Optimizing NNI: done in 1.67355 secs using 399.2% CPU
Log-likelihood of RapidNJ tree: -202820.806
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.65248 secs using 399.1% CPU
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Iteration 470 / LogL: -60089.439 / Time: 0h:12m:5s (0h:2m:14s left)
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BETTER TREE FOUND at iteration 1: -105306.977
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Iteration 480 / LogL: -60060.909 / Time: 0h:12m:20s (0h:1m:58s left)
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29.901 second
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Estimate model parameters (epsilon = 0.100)
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Iteration 490 / LogL: -60112.207 / Time: 0h:12m:35s (0h:1m:43s left)
BETTER TREE FOUND at iteration 5: -105297.274
Optimizing NNI: done in 1.46631 secs using 399.4% CPU
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Computing log-likelihood of 98 initial trees ... 23.022 seconds
Current best score: -199331.319

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.4679 secs using 399.3% CPU
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Estimate model parameters (epsilon = 0.100)
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Iteration 500 / LogL: -60054.177 / Time: 0h:12m:49s (0h:1m:27s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 10: -105292.331
Iteration 10 / LogL: -105292.331 / Time: 0h:1m:50s
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Iteration 510 / LogL: -60058.903 / Time: 0h:13m:4s (0h:1m:12s left)
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BETTER TREE FOUND at iteration 1: -198556.463
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Iteration 20 / LogL: -105334.799 / Time: 0h:2m:15s
Finish initializing candidate tree set (20)
Current best tree score: -105292.331 / CPU time: 119.735
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 3.80381 secs using 597.3% CPU
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Iteration 520 / LogL: -60052.418 / Time: 0h:13m:18s (0h:0m:56s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 550 / LogL: -60077.374 / Time: 0h:14m:2s (0h:0m:10s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 38: -105231.345
Optimizing NNI: done in 1.58522 secs using 398.7% CPU
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Optimizing NNI: done in 1.4599 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 558 ITERATIONS / Time: 0h:14m:13s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60052.417
Optimal log-likelihood: -60052.411
Site proportion and rates:  (0.082,0.059) (0.110,0.166) (0.134,0.389) (0.133,0.390) (0.251,0.841) (0.113,1.432) (0.154,2.233) (0.024,6.476)
Parameters optimization took 1 rounds (0.539 sec)
BEST SCORE FOUND : -60052.411
Total tree length: 45.455

Total number of iterations: 558
CPU time used for tree search: 3365.411 sec (0h:56m:5s)
Wall-clock time used for tree search: 847.114 sec (0h:14m:7s)
Total CPU time used: 3393.794 sec (0h:56m:33s)
Total wall-clock time used: 854.196 sec (0h:14m:14s)

===> START BOOTSTRAP REPLICATE NUMBER 33

Creating bootstrap alignment (seed: 67495)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.049 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61259.783
Optimizing NNI: done in 2.45474 secs using 398% CPU
Iteration 40 / LogL: -105239.658 / Time: 0h:3m:12s (0h:8m:2s left)
2. Current log-likelihood: -60713.830
3. Current log-likelihood: -60700.426
Optimizing NNI: done in 2.25421 secs using 398.6% CPU
4. Current log-likelihood: -60696.364
Optimizing NNI: done in 3.97308 secs using 597.3% CPU
5. Current log-likelihood: -60689.129
6. Current log-likelihood: -60674.006
Optimizing NNI: done in 2.28904 secs using 397.9% CPU
7. Current log-likelihood: -60672.966
Optimal log-likelihood: -60672.925
Site proportion and rates:  (0.108,0.064) (0.088,0.180) (0.115,0.370) (0.085,0.429) (0.210,0.708) (0.211,1.177) (0.160,2.258) (0.022,6.342)
Parameters optimization took 7 rounds (6.119 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 3.88779 secs using 596.9% CPU
Optimizing NNI: done in 2.3295 secs using 397.4% CPU
Calculating distance matrix: done in 1.09861 secs using 399.8% CPU
Computing ML distances took 1.098788 sec (of wall-clock time) 4.392513 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000379086 secs using 123.2% CPU
Constructing RapidNJ tree: done in 0.00437784 secs using 361.1% CPU
Computing RapidNJ tree took 0.004812 sec (of wall-clock time) 0.018415 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60690.901
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.64609 secs using 398.3% CPU
Optimizing NNI: done in 2.21465 secs using 398.1% CPU
5.055 second
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 20: -198537.529
Iteration 20 / LogL: -198537.529 / Time: 0h:3m:6s
Finish initializing candidate tree set (20)
Current best tree score: -198537.529 / CPU time: 157.080
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 2.41181 secs using 398.4% CPU
Computing log-likelihood of 98 initial trees ... 5.106 seconds
Current best score: -60486.036

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -198515.975
BETTER TREE FOUND at iteration 49: -105229.241
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Iteration 50 / LogL: -105254.868 / Time: 0h:3m:37s (0h:7m:19s left)
BETTER TREE FOUND at iteration 1: -60251.062
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -60232.903
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 23: -198481.858
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Iteration 10 / LogL: -60260.825 / Time: 0h:0m:40s
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Iteration 20 / LogL: -60264.339 / Time: 0h:0m:52s
Finish initializing candidate tree set (20)
Current best tree score: -60232.903 / CPU time: 45.026
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 60: -105218.855
Iteration 60 / LogL: -105218.855 / Time: 0h:4m:7s (0h:6m:58s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -60232.089
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Iteration 30 / LogL: -198570.965 / Time: 0h:3m:54s (0h:12m:30s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -60228.914
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Iteration 30 / LogL: -60240.544 / Time: 0h:1m:7s (0h:3m:50s left)
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Estimate model parameters (epsilon = 0.100)
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UPDATE BEST LOG-LIKELIHOOD: -60222.933
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 73: -198461.406
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BETTER TREE FOUND at iteration 77: -198458.383
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Iteration 180 / LogL: -60226.149 / Time: 0h:4m:32s (0h:0m:4s left)
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Estimate model parameters (epsilon = 0.100)
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TREE SEARCH COMPLETED AFTER 184 ITERATIONS / Time: 0h:4m:37s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60222.933
Optimizing NNI: done in 2.23462 secs using 397.3% CPU
Iteration 150 / LogL: -105232.047 / Time: 0h:7m:50s (0h:3m:2s left)
Optimal log-likelihood: -60222.925
Site proportion and rates:  (0.111,0.067) (0.086,0.188) (0.193,0.392) (0.162,0.657) (0.204,1.001) (0.119,1.628) (0.103,2.470) (0.021,6.603)
Parameters optimization took 1 rounds (0.399 sec)
BEST SCORE FOUND : -60222.925
Total tree length: 44.633

Total number of iterations: 184
CPU time used for tree search: 1063.237 sec (0h:17m:43s)
Wall-clock time used for tree search: 270.219 sec (0h:4m:30s)
Total CPU time used: 1095.725 sec (0h:18m:15s)
Total wall-clock time used: 278.333 sec (0h:4m:38s)

===> START BOOTSTRAP REPLICATE NUMBER 34

Creating bootstrap alignment (seed: 67496)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.057 seconds

NOTE: 64 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60945.974
2. Current log-likelihood: -60366.053
BETTER TREE FOUND at iteration 79: -198456.728
3. Current log-likelihood: -60357.840
Optimizing NNI: done in 2.35221 secs using 398.2% CPU
4. Current log-likelihood: -60344.985
5. Current log-likelihood: -60324.489
6. Current log-likelihood: -60323.095
Optimizing NNI: done in 2.39389 secs using 398.2% CPU
Optimal log-likelihood: -60323.064
Site proportion and rates:  (0.099,0.065) (0.117,0.178) (0.121,0.346) (0.080,0.472) (0.207,0.731) (0.168,1.212) (0.174,2.138) (0.034,4.912)
Parameters optimization took 6 rounds (4.888 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 3.98705 secs using 597.7% CPU
Iteration 80 / LogL: -198566.339 / Time: 0h:7m:34s (0h:9m:28s left)
Calculating distance matrix: done in 1.10297 secs using 399.9% CPU
Computing ML distances took 1.103153 sec (of wall-clock time) 4.410859 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000343084 secs using 752.3% CPU
Constructing RapidNJ tree: done in 0.00442386 secs using 283.9% CPU
Computing RapidNJ tree took 0.004822 sec (of wall-clock time) 0.015168 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60439.327
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.36505 secs using 398.1% CPU
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5.055 second
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Computing log-likelihood of 98 initial trees ... 6.202 seconds
Current best score: -60274.837

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Iteration 20 / LogL: -60177.422 / Time: 0h:0m:46s
Finish initializing candidate tree set (20)
Current best tree score: -60064.797 / CPU time: 40.597
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 130 / LogL: -198495.121 / Time: 0h:11m:15s (0h:6m:48s left)
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TREE SEARCH COMPLETED AFTER 155 ITERATIONS / Time: 0h:3m:52s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60014.667
Optimizing NNI: done in 2.09659 secs using 397.7% CPU
2. Current log-likelihood: -60014.647
3. Current log-likelihood: -60014.630
4. Current log-likelihood: -60014.617
Optimizing NNI: done in 4.00813 secs using 597.2% CPU
Optimizing NNI: done in 2.485 secs using 398.1% CPU
Optimal log-likelihood: -60014.605
Site proportion and rates:  (0.098,0.064) (0.122,0.178) (0.168,0.367) (0.075,0.604) (0.149,0.745) (0.173,1.159) (0.179,2.132) (0.036,4.811)
Parameters optimization took 4 rounds (3.178 sec)
BEST SCORE FOUND : -60014.605
Total tree length: 46.169

Total number of iterations: 155
CPU time used for tree search: 888.622 sec (0h:14m:48s)
Wall-clock time used for tree search: 226.390 sec (0h:3m:46s)
Total CPU time used: 926.886 sec (0h:15m:26s)
Total wall-clock time used: 235.957 sec (0h:3m:55s)

===> START BOOTSTRAP REPLICATE NUMBER 35

Creating bootstrap alignment (seed: 67497)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61616.827
2. Current log-likelihood: -61032.659
3. Current log-likelihood: -61025.787
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4. Current log-likelihood: -61023.919
5. Current log-likelihood: -61022.220
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6. Current log-likelihood: -61019.273
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7. Current log-likelihood: -61009.245
8. Current log-likelihood: -61002.243
9. Current log-likelihood: -61001.800
Optimizing NNI: done in 2.63157 secs using 398.1% CPU
Optimal log-likelihood: -61001.782
Site proportion and rates:  (0.126,0.059) (0.048,0.181) (0.161,0.338) (0.054,0.358) (0.252,0.705) (0.171,1.298) (0.149,2.268) (0.040,4.379)
Parameters optimization took 9 rounds (6.780 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.10263 secs using 399.8% CPU
Computing ML distances took 1.102801 sec (of wall-clock time) 4.408374 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000339985 secs using 685% CPU
Constructing RapidNJ tree: done in 0.004318 secs using 314.2% CPU
Computing RapidNJ tree took 0.004724 sec (of wall-clock time) 0.015932 sec (of CPU time)
Log-likelihood of RapidNJ tree: -61080.201
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.32935 secs using 397.8% CPU
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Iteration 250 / LogL: -105261.068 / Time: 0h:11m:57s (0h:4m:13s left)
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5.045 second
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Computing log-likelihood of 98 initial trees ... 5.031 seconds
Current best score: -60967.331

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 140 / LogL: -198458.983 / Time: 0h:11m:58s (0h:5m:51s left)
BETTER TREE FOUND at iteration 9: -60754.587
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Iteration 20 / LogL: -60760.853 / Time: 0h:0m:54s
Finish initializing candidate tree set (20)
Current best tree score: -60712.555 / CPU time: 46.377
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Iteration 50 / LogL: -60695.042 / Time: 0h:1m:39s (0h:3m:22s left)
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Optimizing NNI: done in 1.24082 secs using 398.9% CPU
Optimizing NNI: done in 1.13581 secs using 399% CPU
Optimizing NNI: done in 4.04008 secs using 598% CPU
Optimizing NNI: done in 2.36144 secs using 398.6% CPU
Iteration 330 / LogL: -105229.434 / Time: 0h:15m:5s (0h:0m:22s left)
Optimizing NNI: done in 1.44247 secs using 399.2% CPU
Optimizing NNI: done in 1.4442 secs using 399.4% CPU
Optimizing NNI: done in 2.52928 secs using 398.1% CPU
Optimizing NNI: done in 3.59424 secs using 597.8% CPU
Optimizing NNI: done in 1.22742 secs using 399.4% CPU
Iteration 130 / LogL: -60700.127 / Time: 0h:3m:22s (0h:2m:18s left)
Optimizing NNI: done in 0.991808 secs using 399% CPU
Optimizing NNI: done in 2.05025 secs using 398.4% CPU
Optimizing NNI: done in 1.32885 secs using 398.7% CPU
Optimizing NNI: done in 1.00877 secs using 399.5% CPU
Optimizing NNI: done in 3.89644 secs using 597.9% CPU
Iteration 180 / LogL: -198465.693 / Time: 0h:14m:50s (0h:2m:19s left)
Optimizing NNI: done in 2.54624 secs using 398.1% CPU
Optimizing NNI: done in 1.31954 secs using 399% CPU
Optimizing NNI: done in 1.1556 secs using 398.7% CPU
Optimizing NNI: done in 2.84216 secs using 398.1% CPU
Optimizing NNI: done in 1.16077 secs using 399.8% CPU
Optimizing NNI: done in 4.04124 secs using 597.1% CPU
Optimizing NNI: done in 1.10931 secs using 399.3% CPU
Optimizing NNI: done in 2.20164 secs using 398% CPU
Optimizing NNI: done in 1.25497 secs using 399.1% CPU
Optimizing NNI: done in 1.13444 secs using 399.1% CPU
Optimizing NNI: done in 2.20289 secs using 398.3% CPU
Optimizing NNI: done in 1.31105 secs using 399.1% CPU
Iteration 140 / LogL: -60724.074 / Time: 0h:3m:34s (0h:2m:0s left)
Optimizing NNI: done in 4.66622 secs using 598% CPU
Optimizing NNI: done in 1.10675 secs using 399% CPU
Optimizing NNI: done in 2.56342 secs using 397.9% CPU
Optimizing NNI: done in 1.31904 secs using 399.1% CPU
UPDATE BEST LOG-LIKELIHOOD: -60687.395
Optimizing NNI: done in 1.40521 secs using 399% CPU
Optimizing NNI: done in 2.23997 secs using 397.6% CPU
Optimizing NNI: done in 3.92074 secs using 597.9% CPU
Optimizing NNI: done in 1.22569 secs using 399% CPU
Optimizing NNI: done in 0.96945 secs using 399.4% CPU
Optimizing NNI: done in 2.66622 secs using 398.2% CPU
TREE SEARCH COMPLETED AFTER 339 ITERATIONS / Time: 0h:15m:28s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -105207.234
Optimizing NNI: done in 1.12089 secs using 399.3% CPU
2. Current log-likelihood: -105207.224
Optimal log-likelihood: -105207.209
Proportion of invariable sites: 0.034
Site proportion and rates:  (0.086,0.034) (0.085,0.096) (0.088,0.202) (0.119,0.351) (0.133,0.568) (0.081,0.828) (0.141,1.170) (0.166,1.891) (0.067,4.620)
Parameters optimization took 2 rounds (1.346 sec)
BEST SCORE FOUND : -105207.209
Total tree length: 175.297

Total number of iterations: 339
CPU time used for tree search: 3597.368 sec (0h:59m:57s)
Wall-clock time used for tree search: 911.967 sec (0h:15m:11s)
Total CPU time used: 3666.899 sec (1h:1m:6s)
Total wall-clock time used: 929.370 sec (0h:15m:29s)

===> START BOOTSTRAP REPLICATE NUMBER 5

Creating bootstrap alignment (seed: 68187)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.104 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -109909.963
Optimizing NNI: done in 4.13502 secs using 597.8% CPU
Optimizing NNI: done in 1.48296 secs using 398.5% CPU
Optimizing NNI: done in 1.29901 secs using 399.6% CPU
2. Current log-likelihood: -107997.544
Optimizing NNI: done in 1.07689 secs using 399.4% CPU
3. Current log-likelihood: -107909.015
Optimizing NNI: done in 1.07573 secs using 399.5% CPU
Iteration 150 / LogL: -60689.962 / Time: 0h:3m:46s (0h:1m:43s left)
Optimizing NNI: done in 4.10689 secs using 597.4% CPU
Optimizing NNI: done in 1.16602 secs using 399.3% CPU
4. Current log-likelihood: -107901.374
Optimizing NNI: done in 1.11309 secs using 399.3% CPU
5. Current log-likelihood: -107899.956
Optimizing NNI: done in 1.20842 secs using 399.3% CPU
Optimizing NNI: done in 3.68003 secs using 597.4% CPU
Optimizing NNI: done in 1.15456 secs using 399.2% CPU
6. Current log-likelihood: -107898.581
Optimizing NNI: done in 1.15457 secs using 399.2% CPU
7. Current log-likelihood: -107895.606
Optimizing NNI: done in 1.22512 secs using 399.2% CPU
Optimizing NNI: done in 1.09075 secs using 399.4% CPU
8. Current log-likelihood: -107888.244
Optimizing NNI: done in 4.58983 secs using 597.8% CPU
Optimizing NNI: done in 1.31414 secs using 399% CPU
9. Current log-likelihood: -107885.958
Optimizing NNI: done in 1.307 secs using 399.5% CPU
10. Current log-likelihood: -107885.457
Optimizing NNI: done in 1.32789 secs using 399.1% CPU
Iteration 160 / LogL: -60689.755 / Time: 0h:3m:59s (0h:1m:27s left)
11. Current log-likelihood: -107885.076
Optimizing NNI: done in 4.26537 secs using 598.2% CPU
Optimizing NNI: done in 1.26644 secs using 399.1% CPU
12. Current log-likelihood: -107884.718
Optimizing NNI: done in 1.233 secs using 399.3% CPU
13. Current log-likelihood: -107884.394
Optimizing NNI: done in 1.24578 secs using 398.9% CPU
Optimizing NNI: done in 1.12847 secs using 399% CPU
14. Current log-likelihood: -107884.259
Optimizing NNI: done in 4.37617 secs using 597.9% CPU
Optimizing NNI: done in 1.06667 secs using 398.7% CPU
15. Current log-likelihood: -107884.052
16. Current log-likelihood: -107883.939
Optimizing NNI: done in 1.45181 secs using 399% CPU
17. Current log-likelihood: -107883.765
Optimizing NNI: done in 1.26292 secs using 398.5% CPU
Optimal log-likelihood: -107883.633
Proportion of invariable sites: 0.021
Site proportion and rates:  (0.080,0.035) (0.060,0.110) (0.111,0.209) (0.153,0.370) (0.125,0.568) (0.090,0.883) (0.128,1.221) (0.160,1.930) (0.072,4.101)
Parameters optimization took 17 rounds (25.560 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.07325 secs using 399.6% CPU
Optimizing NNI: done in 4.99128 secs using 597.3% CPU
Iteration 190 / LogL: -198582.717 / Time: 0h:15m:34s (0h:1m:28s left)
Optimizing NNI: done in 1.19471 secs using 398.4% CPU
Optimizing NNI: done in 1.19288 secs using 399.4% CPU
Iteration 170 / LogL: -60701.215 / Time: 0h:4m:11s (0h:1m:11s left)
Optimizing NNI: done in 1.27761 secs using 399.1% CPU
Calculating distance matrix: done in 4.76499 secs using 399.8% CPU
Computing ML distances took 4.765260 sec (of wall-clock time) 19.053464 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000684023 secs using 364.5% CPU
Constructing RapidNJ tree: done in 0.00848508 secs using 359.7% CPU
Computing RapidNJ tree took 0.009238 sec (of wall-clock time) 0.034919 sec (of CPU time)
Optimizing NNI: done in 3.96425 secs using 597.8% CPU
Optimizing NNI: done in 1.27099 secs using 399.4% CPU
Log-likelihood of RapidNJ tree: -108133.860
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.32184 secs using 398.9% CPU
Optimizing NNI: done in 1.07397 secs using 399.3% CPU
Optimizing NNI: done in 1.43818 secs using 399.1% CPU
Optimizing NNI: done in 1.08045 secs using 399.6% CPU
Optimizing NNI: done in 5.94608 secs using 597.3% CPU
Optimizing NNI: done in 1.12743 secs using 399.4% CPU
Optimizing NNI: done in 1.17779 secs using 398.3% CPU
Optimizing NNI: done in 1.15169 secs using 399.6% CPU
Optimizing NNI: done in 1.12566 secs using 399% CPU
Iteration 180 / LogL: -60688.201 / Time: 0h:4m:23s (0h:0m:55s left)
Optimizing NNI: done in 1.12896 secs using 398.9% CPU
Optimizing NNI: done in 5.65728 secs using 598% CPU
10.709 second
Optimizing NNI: done in 1.19048 secs using 399.4% CPU
Optimizing NNI: done in 1.17912 secs using 399.3% CPU
Optimizing NNI: done in 1.22439 secs using 399% CPU
Optimizing NNI: done in 4.08206 secs using 598% CPU
Optimizing NNI: done in 1.24481 secs using 398.9% CPU
Optimizing NNI: done in 1.09815 secs using 399.4% CPU
Optimizing NNI: done in 1.21738 secs using 398.9% CPU
Optimizing NNI: done in 1.28069 secs using 399.2% CPU
Optimizing NNI: done in 1.44495 secs using 399.1% CPU
Optimizing NNI: done in 5.22307 secs using 597.1% CPU
Computing log-likelihood of 98 initial trees ... 10.220 seconds
Current best score: -107883.633

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.1342 secs using 398.8% CPU
Iteration 190 / LogL: -60688.216 / Time: 0h:4m:35s (0h:0m:40s left)
Optimizing NNI: done in 1.32794 secs using 399.1% CPU
Optimizing NNI: done in 1.7814 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.05841 secs using 399.5% CPU
Optimizing NNI: done in 3.98789 secs using 598.4% CPU
Optimizing NNI: done in 1.16308 secs using 399.1% CPU
Optimizing NNI: done in 0.925744 secs using 398.7% CPU
Optimizing NNI: done in 0.90055 secs using 398.9% CPU
Optimizing NNI: done in 1.08993 secs using 399% CPU
Optimizing NNI: done in 4.62197 secs using 597% CPU
Optimizing NNI: done in 1.11435 secs using 399.2% CPU
Optimizing NNI: done in 1.02964 secs using 399% CPU
Optimizing NNI: done in 1.21456 secs using 398.8% CPU
Optimizing NNI: done in 1.23688 secs using 399% CPU
Iteration 200 / LogL: -60687.403 / Time: 0h:4m:47s (0h:0m:25s left)
Optimizing NNI: done in 3.80785 secs using 597.8% CPU
Optimizing NNI: done in 1.20491 secs using 399.4% CPU
Optimizing NNI: done in 1.00312 secs using 398.9% CPU
Optimizing NNI: done in 1.01356 secs using 399.4% CPU
Optimizing NNI: done in 3.77887 secs using 597.7% CPU
Optimizing NNI: done in 1.1248 secs using 398.4% CPU
Optimizing NNI: done in 1.13811 secs using 399.4% CPU
Optimizing NNI: done in 1.2422 secs using 399.4% CPU
BETTER TREE FOUND at iteration 1: -107384.341
Optimizing NNI: done in 1.05434 secs using 399.2% CPU
Optimizing NNI: done in 1.31105 secs using 399% CPU
Optimizing NNI: done in 5.1137 secs using 597.7% CPU
Iteration 200 / LogL: -198443.637 / Time: 0h:16m:20s (0h:0m:39s left)
Optimizing NNI: done in 3.08682 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.15099 secs using 399.6% CPU
Optimizing NNI: done in 1.32556 secs using 398.8% CPU
Iteration 210 / LogL: -60688.341 / Time: 0h:4m:58s (0h:0m:11s left)
Optimizing NNI: done in 1.08642 secs using 398.7% CPU
Optimizing NNI: done in 1.06159 secs using 399.2% CPU
BETTER TREE FOUND at iteration 2: -107184.734
Optimizing NNI: done in 0.927993 secs using 398.8% CPU
Optimizing NNI: done in 6.11089 secs using 597.9% CPU
Optimizing NNI: done in 1.21184 secs using 399.2% CPU
Optimizing NNI: done in 1.89397 secs using 398.4% CPU
Optimizing NNI: done in 1.32306 secs using 398.9% CPU
Optimizing NNI: done in 1.87503 secs using 398.7% CPU
Optimizing NNI: done in 1.37162 secs using 399.3% CPU
Optimizing NNI: done in 1.72841 secs using 398.5% CPU
Optimizing NNI: done in 1.31237 secs using 399.2% CPU
Optimizing NNI: done in 1.24587 secs using 399.3% CPU
Optimizing NNI: done in 5.98147 secs using 598% CPU
Optimizing NNI: done in 1.38405 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 219 ITERATIONS / Time: 0h:5m:9s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60687.395
Optimizing NNI: done in 2.72594 secs using 398.5% CPU
Optimal log-likelihood: -60687.388
Site proportion and rates:  (0.137,0.064) (0.082,0.241) (0.122,0.357) (0.054,0.400) (0.246,0.705) (0.168,1.299) (0.153,2.260) (0.037,4.518)
Parameters optimization took 1 rounds (0.701 sec)
BEST SCORE FOUND : -60687.388
Total tree length: 47.266

Total number of iterations: 219
CPU time used for tree search: 1188.097 sec (0h:19m:48s)
Wall-clock time used for tree search: 301.399 sec (0h:5m:1s)
Total CPU time used: 1224.323 sec (0h:20m:24s)
Total wall-clock time used: 310.459 sec (0h:5m:10s)

===> START BOOTSTRAP REPLICATE NUMBER 36

Creating bootstrap alignment (seed: 67498)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.051 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60977.823
Optimizing NNI: done in 1.58413 secs using 398.6% CPU
2. Current log-likelihood: -60384.187
3. Current log-likelihood: -60381.153
4. Current log-likelihood: -60380.084
Optimizing NNI: done in 1.76351 secs using 398.4% CPU
5. Current log-likelihood: -60378.868
Optimizing NNI: done in 5.49065 secs using 597.7% CPU
6. Current log-likelihood: -60375.767
7. Current log-likelihood: -60353.521
Optimizing NNI: done in 2.66971 secs using 398.4% CPU
8. Current log-likelihood: -60339.303
9. Current log-likelihood: -60338.824
Optimizing NNI: done in 2.05847 secs using 397.8% CPU
Iteration 10 / LogL: -107272.292 / Time: 0h:1m:35s
Optimal log-likelihood: -60338.811
Site proportion and rates:  (0.109,0.057) (0.128,0.182) (0.118,0.340) (0.069,0.501) (0.204,0.749) (0.170,1.228) (0.174,2.216) (0.029,5.220)
Parameters optimization took 9 rounds (7.455 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10038 secs using 399.9% CPU
Computing ML distances took 1.100547 sec (of wall-clock time) 4.400558 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00036478 secs using 569.9% CPU
Constructing RapidNJ tree: done in 0.00429392 secs using 311.6% CPU
Computing RapidNJ tree took 0.004712 sec (of wall-clock time) 0.015510 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60251.350
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.68433 secs using 596.3% CPU
Optimizing NNI: done in 3.03177 secs using 398.6% CPU
Optimizing NNI: done in 1.85706 secs using 398.8% CPU
5.193 second
Optimizing NNI: done in 2.73484 secs using 398.3% CPU
Optimizing NNI: done in 5.82568 secs using 598.2% CPU
Optimizing NNI: done in 2.35406 secs using 398.7% CPU
Computing log-likelihood of 98 initial trees ... 5.243 seconds
Current best score: -60201.106

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.36322 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.3325 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 6.14499 secs using 595.1% CPU
BETTER TREE FOUND at iteration 15: -107168.374
Optimizing NNI: done in 2.49015 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -59962.206
Optimizing NNI: done in 6.73431 secs using 595.9% CPU
Optimizing NNI: done in 1.33454 secs using 399.4% CPU
Optimizing NNI: done in 1.48101 secs using 399% CPU
BETTER TREE FOUND at iteration 16: -107166.534
Optimizing NNI: done in 1.27239 secs using 399% CPU
Optimizing NNI: done in 2.05979 secs using 399% CPU
Optimizing NNI: done in 1.28173 secs using 399.2% CPU
Optimizing NNI: done in 1.01433 secs using 398.9% CPU
Optimizing NNI: done in 6.4947 secs using 598.1% CPU
Optimizing NNI: done in 1.51903 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.89864 secs using 398.4% CPU
BETTER TREE FOUND at iteration 7: -59944.085
Optimizing NNI: done in 1.32876 secs using 398.9% CPU
Optimizing NNI: done in 2.34082 secs using 399% CPU
Optimizing NNI: done in 1.00037 secs using 398.7% CPU
Optimizing NNI: done in 1.39585 secs using 399.1% CPU
Iteration 10 / LogL: -59954.614 / Time: 0h:0m:39s
Optimizing NNI: done in 2.37242 secs using 398.7% CPU
Iteration 20 / LogL: -107211.017 / Time: 0h:2m:7s
Finish initializing candidate tree set (20)
Current best tree score: -107166.534 / CPU time: 95.964
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 5.77456 secs using 597.8% CPU
TREE SEARCH COMPLETED AFTER 209 ITERATIONS / Time: 0h:17m:15s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -198439.333
Optimizing NNI: done in 1.19967 secs using 399% CPU
Optimal log-likelihood: -198439.330
Site proportion and rates:  (0.013,0.105) (0.027,0.230) (0.132,0.354) (0.223,0.543) (0.173,0.767) (0.173,1.017) (0.169,1.621) (0.090,2.699)
Parameters optimization took 1 rounds (1.198 sec)
BEST SCORE FOUND : -198439.330
Total tree length: 154.366

Total number of iterations: 209
CPU time used for tree search: 5863.614 sec (1h:37m:43s)
Wall-clock time used for tree search: 1006.314 sec (0h:16m:46s)
Total CPU time used: 6045.138 sec (1h:40m:45s)
Total wall-clock time used: 1036.806 sec (0h:17m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 10

Creating bootstrap alignment (seed: 70473)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.255 seconds

NOTE: 242 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199715.278
Optimizing NNI: done in 2.12434 secs using 398.5% CPU
Optimizing NNI: done in 1.35062 secs using 399.2% CPU
Optimizing NNI: done in 1.20714 secs using 399% CPU
Optimizing NNI: done in 0.998163 secs using 398.7% CPU
Optimizing NNI: done in 2.3993 secs using 398.6% CPU
2. Current log-likelihood: -197314.404
Optimizing NNI: done in 1.37247 secs using 399.3% CPU
Optimizing NNI: done in 2.16083 secs using 399.1% CPU
Optimizing NNI: done in 1.5542 secs using 399% CPU
3. Current log-likelihood: -197235.113
Optimizing NNI: done in 1.19591 secs using 398.6% CPU
Optimizing NNI: done in 2.20666 secs using 399.1% CPU
Optimizing NNI: done in 1.39795 secs using 398.8% CPU
4. Current log-likelihood: -197232.708
Optimizing NNI: done in 2.19713 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.40909 secs using 398.8% CPU
Optimizing NNI: done in 1.3076 secs using 398.5% CPU
Iteration 20 / LogL: -60040.743 / Time: 0h:0m:52s
Finish initializing candidate tree set (20)
Current best tree score: -59944.085 / CPU time: 43.861
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
BETTER TREE FOUND at iteration 25: -107162.828
5. Current log-likelihood: -197232.473
Optimizing NNI: done in 1.72889 secs using 399% CPU
Optimizing NNI: done in 2.242 secs using 398.8% CPU
Optimizing NNI: done in 1.56835 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
6. Current log-likelihood: -197232.269
BETTER TREE FOUND at iteration 22: -59916.332
Optimizing NNI: done in 2.0996 secs using 398.7% CPU
7. Current log-likelihood: -197232.083
Optimizing NNI: done in 1.6235 secs using 399.3% CPU
Optimizing NNI: done in 1.9612 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.23347 secs using 399% CPU
8. Current log-likelihood: -197231.881
Optimizing NNI: done in 1.65855 secs using 399% CPU
Optimizing NNI: done in 1.5484 secs using 399.2% CPU
9. Current log-likelihood: -197231.640
Optimizing NNI: done in 1.07749 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -59910.572
10. Current log-likelihood: -197231.272
Optimizing NNI: done in 1.58051 secs using 399.3% CPU
11. Current log-likelihood: -197230.664
Optimizing NNI: done in 1.3738 secs using 398.8% CPU
Optimizing NNI: done in 1.18309 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -59909.241
Iteration 30 / LogL: -59909.241 / Time: 0h:1m:11s (0h:4m:6s left)
12. Current log-likelihood: -197229.574
Optimizing NNI: done in 1.62153 secs using 399.2% CPU
Optimizing NNI: done in 1.39804 secs using 398.8% CPU
13. Current log-likelihood: -197227.642
Optimizing NNI: done in 1.28622 secs using 398.9% CPU
Optimizing NNI: done in 1.34742 secs using 398.8% CPU
14. Current log-likelihood: -197224.599
Optimizing NNI: done in 1.27018 secs using 398.4% CPU
BETTER TREE FOUND at iteration 28: -107132.074
15. Current log-likelihood: -197222.009
Optimizing NNI: done in 1.58888 secs using 399% CPU
Optimizing NNI: done in 1.23498 secs using 399.1% CPU
Optimizing NNI: done in 2.28694 secs using 398.7% CPU
16. Current log-likelihood: -197221.037
Optimizing NNI: done in 1.2274 secs using 398.9% CPU
Optimizing NNI: done in 1.32357 secs using 399.4% CPU
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Iteration 30 / LogL: -107143.374 / Time: 0h:2m:51s (0h:9m:40s left)
17. Current log-likelihood: -197220.840
Optimizing NNI: done in 1.39785 secs using 399.2% CPU
Iteration 40 / LogL: -59909.457 / Time: 0h:1m:25s (0h:3m:16s left)
Optimizing NNI: done in 1.9454 secs using 398.1% CPU
Optimizing NNI: done in 1.59162 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimal log-likelihood: -197220.804
Site proportion and rates:  (0.015,0.108) (0.058,0.254) (0.133,0.393) (0.230,0.594) (0.132,0.831) (0.204,1.087) (0.138,1.669) (0.090,2.594)
Parameters optimization took 17 rounds (45.322 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.02597 secs using 398.8% CPU
BETTER TREE FOUND at iteration 41: -59906.103
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Estimate model parameters (epsilon = 0.100)
Calculating distance matrix: done in 9.8879 secs using 599.8% CPU
Computing ML distances took 9.888670 sec (of wall-clock time) 59.314546 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00175118 secs using 595.7% CPU
Constructing RapidNJ tree: done in 0.0317609 secs using 693.5% CPU
Computing RapidNJ tree took 0.033588 sec (of wall-clock time) 0.231391 sec (of CPU time)
BETTER TREE FOUND at iteration 47: -59905.768
Optimizing NNI: done in 2.0988 secs using 398.5% CPU
Log-likelihood of RapidNJ tree: -201805.467
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.44291 secs using 399.2% CPU
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Iteration 40 / LogL: -107142.989 / Time: 0h:3m:12s (0h:7m:14s left)
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Estimate model parameters (epsilon = 0.100)
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30.295 second
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Iteration 80 / LogL: -59905.770 / Time: 0h:2m:23s (0h:2m:1s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 57: -107120.988
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Computing log-likelihood of 98 initial trees ... 21.574 seconds
Current best score: -197220.804

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 60 / LogL: -107134.045 / Time: 0h:4m:3s (0h:6m:39s left)
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BETTER TREE FOUND at iteration 1: -196654.118
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Estimate model parameters (epsilon = 0.100)
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Iteration 100 / LogL: -59922.615 / Time: 0h:2m:50s (0h:1m:21s left)
BETTER TREE FOUND at iteration 2: -196559.892
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 10 / LogL: -196716.633 / Time: 0h:2m:50s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 87: -107108.782
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Iteration 140 / LogL: -59924.161 / Time: 0h:3m:45s (0h:0m:11s left)
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Iteration 90 / LogL: -107122.770 / Time: 0h:5m:15s (0h:5m:43s left)
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TREE SEARCH COMPLETED AFTER 148 ITERATIONS / Time: 0h:3m:56s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59905.768
Optimizing NNI: done in 1.99068 secs using 398.7% CPU
Optimal log-likelihood: -59905.759
Site proportion and rates:  (0.114,0.059) (0.128,0.187) (0.117,0.336) (0.167,0.589) (0.184,0.930) (0.108,1.417) (0.157,2.318) (0.026,5.631)
Parameters optimization took 1 rounds (0.829 sec)
BEST SCORE FOUND : -59905.759
Total tree length: 44.843

Total number of iterations: 148
CPU time used for tree search: 892.174 sec (0h:14m:52s)
Wall-clock time used for tree search: 227.370 sec (0h:3m:47s)
Total CPU time used: 931.638 sec (0h:15m:31s)
Total wall-clock time used: 237.231 sec (0h:3m:57s)

===> START BOOTSTRAP REPLICATE NUMBER 37

Creating bootstrap alignment (seed: 67499)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.034 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60197.762
2. Current log-likelihood: -59524.715
3. Current log-likelihood: -59478.813
Optimizing NNI: done in 2.42269 secs using 398.1% CPU
4. Current log-likelihood: -59470.493
5. Current log-likelihood: -59468.871
Optimizing NNI: done in 4.88619 secs using 597.7% CPU
6. Current log-likelihood: -59468.746
Optimizing NNI: done in 2.03576 secs using 398.3% CPU
Optimal log-likelihood: -59468.681
Site proportion and rates:  (0.109,0.053) (0.093,0.180) (0.119,0.325) (0.098,0.425) (0.189,0.663) (0.152,1.077) (0.198,2.042) (0.041,4.898)
Parameters optimization took 6 rounds (4.796 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10645 secs using 399.9% CPU
Computing ML distances took 1.106634 sec (of wall-clock time) 4.424906 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000375032 secs using 417.6% CPU
Constructing RapidNJ tree: done in 0.00432611 secs using 339.2% CPU
Computing RapidNJ tree took 0.004761 sec (of wall-clock time) 0.019099 sec (of CPU time)
Optimizing NNI: done in 2.01427 secs using 397.9% CPU
Log-likelihood of RapidNJ tree: -59444.231
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.89617 secs using 398.5% CPU
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Optimizing NNI: done in 2.16772 secs using 398.3% CPU
5.005 second
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Iteration 100 / LogL: -107119.701 / Time: 0h:5m:36s (0h:4m:56s left)
Optimizing NNI: done in 5.04798 secs using 595.4% CPU
Optimizing NNI: done in 2.01358 secs using 398.1% CPU
Computing log-likelihood of 98 initial trees ... 5.037 seconds
Current best score: -59436.685

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 4.87852 secs using 597.5% CPU
BETTER TREE FOUND at iteration 1: -59192.664
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Iteration 20 / LogL: -196645.125 / Time: 0h:3m:39s
Finish initializing candidate tree set (20)
Current best tree score: -196559.892 / CPU time: 162.167
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 106: -107105.788
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Iteration 10 / LogL: -59257.895 / Time: 0h:0m:30s
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Iteration 110 / LogL: -107233.511 / Time: 0h:5m:59s (0h:5m:16s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -196524.554
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Iteration 20 / LogL: -59240.625 / Time: 0h:0m:42s
Finish initializing candidate tree set (20)
Current best tree score: -59192.664 / CPU time: 36.211
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 21: -59179.270
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 24: -59178.518
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Iteration 120 / LogL: -107108.890 / Time: 0h:6m:20s (0h:4m:35s left)
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Optimizing NNI: done in 5.94915 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.18992 secs using 398.4% CPU
Optimizing NNI: done in 1.3092 secs using 399.2% CPU
Iteration 30 / LogL: -59192.510 / Time: 0h:0m:58s (0h:3m:9s left)
BETTER TREE FOUND at iteration 25: -196521.019
Optimizing NNI: done in 1.54954 secs using 399% CPU
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BETTER TREE FOUND at iteration 36: -59178.263
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Iteration 40 / LogL: -59184.655 / Time: 0h:1m:14s (0h:3m:2s left)
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Optimizing NNI: done in 2.23495 secs using 398.2% CPU
Iteration 130 / LogL: -107157.219 / Time: 0h:6m:42s (0h:3m:57s left)
BETTER TREE FOUND at iteration 42: -59168.540
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BETTER TREE FOUND at iteration 133: -107103.589
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Iteration 50 / LogL: -59175.883 / Time: 0h:1m:29s (0h:2m:47s left)
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BETTER TREE FOUND at iteration 134: -107102.879
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Iteration 30 / LogL: -196610.818 / Time: 0h:4m:46s (0h:15m:39s left)
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BETTER TREE FOUND at iteration 52: -59167.778
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Optimizing NNI: done in 5.99569 secs using 597.4% CPU
BETTER TREE FOUND at iteration 60: -59158.213
Iteration 60 / LogL: -59158.213 / Time: 0h:1m:43s (0h:2m:54s left)
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Iteration 140 / LogL: -107106.965 / Time: 0h:7m:8s (0h:4m:49s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 33: -196497.234
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Iteration 70 / LogL: -59170.933 / Time: 0h:1m:55s (0h:2m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 72: -59153.395
Optimizing NNI: done in 2.23272 secs using 398.3% CPU
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Iteration 150 / LogL: -107114.818 / Time: 0h:7m:29s (0h:4m:13s left)
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Iteration 80 / LogL: -59159.265 / Time: 0h:2m:11s (0h:2m:32s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 87: -59152.952
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.34503 secs using 399% CPU
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Iteration 90 / LogL: -59159.211 / Time: 0h:2m:25s (0h:2m:38s left)
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Iteration 160 / LogL: -107111.184 / Time: 0h:7m:51s (0h:3m:39s left)
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UPDATE BEST LOG-LIKELIHOOD: -59152.947
BETTER TREE FOUND at iteration 38: -196488.014
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Iteration 100 / LogL: -59165.179 / Time: 0h:2m:37s (0h:2m:18s left)
Optimizing NNI: done in 5.38284 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.14364 secs using 399.2% CPU
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BETTER TREE FOUND at iteration 40: -196484.821
Iteration 40 / LogL: -196484.821 / Time: 0h:5m:56s (0h:15m:13s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 170: -107101.686
Iteration 170 / LogL: -107101.686 / Time: 0h:8m:13s (0h:4m:52s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 109: -59152.802
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Iteration 110 / LogL: -59153.608 / Time: 0h:2m:51s (0h:2m:35s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.23355 secs using 398.3% CPU
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BETTER TREE FOUND at iteration 42: -196484.041
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.03611 secs using 399% CPU
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Iteration 120 / LogL: -59191.888 / Time: 0h:3m:4s (0h:2m:17s left)
BETTER TREE FOUND at iteration 43: -196469.886
Optimizing NNI: done in 1.2626 secs using 398.8% CPU
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Iteration 180 / LogL: -107108.737 / Time: 0h:8m:34s (0h:4m:18s left)
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Iteration 130 / LogL: -59154.765 / Time: 0h:3m:17s (0h:2m:0s left)
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Iteration 140 / LogL: -59175.496 / Time: 0h:3m:29s (0h:1m:44s left)
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Iteration 190 / LogL: -107112.861 / Time: 0h:8m:56s (0h:3m:46s left)
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Iteration 50 / LogL: -196690.728 / Time: 0h:6m:57s (0h:13m:12s left)
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Iteration 150 / LogL: -59153.313 / Time: 0h:3m:42s (0h:1m:28s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 200: -107101.124
Iteration 200 / LogL: -107101.124 / Time: 0h:9m:19s (0h:4m:41s left)
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Iteration 160 / LogL: -59155.825 / Time: 0h:3m:55s (0h:1m:12s left)
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UPDATE BEST LOG-LIKELIHOOD: -59152.795
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Estimate model parameters (epsilon = 0.100)
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Iteration 170 / LogL: -59157.579 / Time: 0h:4m:8s (0h:0m:57s left)
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BETTER TREE FOUND at iteration 54: -196461.033
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Iteration 210 / LogL: -107117.068 / Time: 0h:9m:39s (0h:4m:9s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 177: -59152.669
Optimizing NNI: done in 1.96129 secs using 398.5% CPU
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Iteration 180 / LogL: -59161.427 / Time: 0h:4m:21s (0h:2m:21s left)
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BETTER TREE FOUND at iteration 182: -59152.664
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 57: -196457.887
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Iteration 190 / LogL: -59153.269 / Time: 0h:4m:33s (0h:2m:13s left)
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Iteration 220 / LogL: -107109.510 / Time: 0h:10m:0s (0h:3m:39s left)
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Iteration 200 / LogL: -59153.184 / Time: 0h:4m:47s (0h:1m:58s left)
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Iteration 60 / LogL: -196472.650 / Time: 0h:8m:3s (0h:13m:14s left)
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Iteration 230 / LogL: -107116.881 / Time: 0h:10m:21s (0h:3m:9s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 210 / LogL: -59180.553 / Time: 0h:5m:0s (0h:1m:43s left)
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BETTER TREE FOUND at iteration 62: -196452.517
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Iteration 220 / LogL: -59226.622 / Time: 0h:5m:13s (0h:1m:28s left)
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Iteration 240 / LogL: -107103.895 / Time: 0h:10m:42s (0h:2m:41s left)
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Iteration 230 / LogL: -59172.221 / Time: 0h:5m:25s (0h:1m:13s left)
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Iteration 70 / LogL: -196558.080 / Time: 0h:8m:51s (0h:11m:48s left)
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Iteration 240 / LogL: -59153.181 / Time: 0h:5m:38s (0h:0m:59s left)
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Iteration 250 / LogL: -107108.099 / Time: 0h:11m:4s (0h:2m:13s left)
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Iteration 250 / LogL: -59153.656 / Time: 0h:5m:50s (0h:0m:45s left)
Optimizing NNI: done in 5.32161 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.79649 secs using 397.8% CPU
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Optimizing NNI: done in 1.81521 secs using 398.6% CPU
BETTER TREE FOUND at iteration 73: -196451.384
Optimizing NNI: done in 1.42714 secs using 399.1% CPU
Optimizing NNI: done in 1.95537 secs using 398.3% CPU
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Iteration 260 / LogL: -107106.612 / Time: 0h:11m:24s (0h:1m:45s left)
Optimizing NNI: done in 1.39395 secs using 399% CPU
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Iteration 260 / LogL: -59156.705 / Time: 0h:6m:4s (0h:0m:30s left)
Optimizing NNI: done in 2.26089 secs using 398.1% CPU
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Optimizing NNI: done in 4.23616 secs using 597.6% CPU
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Optimizing NNI: done in 1.24905 secs using 399.2% CPU
Iteration 270 / LogL: -59153.296 / Time: 0h:6m:17s (0h:0m:16s left)
Optimizing NNI: done in 2.17719 secs using 397.8% CPU
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Iteration 270 / LogL: -107108.702 / Time: 0h:11m:46s (0h:1m:18s left)
Optimizing NNI: done in 4.72587 secs using 597.2% CPU
Optimizing NNI: done in 1.25182 secs using 399.4% CPU
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Optimizing NNI: done in 4.76719 secs using 597.3% CPU
Iteration 80 / LogL: -196470.596 / Time: 0h:9m:41s (0h:11m:24s left)
Optimizing NNI: done in 1.31323 secs using 399.4% CPU
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Optimizing NNI: done in 1.27692 secs using 399% CPU
Optimizing NNI: done in 1.79087 secs using 398.1% CPU
Optimizing NNI: done in 1.43215 secs using 399.4% CPU
Iteration 280 / LogL: -59156.078 / Time: 0h:6m:29s (0h:0m:2s left)
Optimizing NNI: done in 1.3682 secs using 399.6% CPU
Optimizing NNI: done in 2.13102 secs using 398% CPU
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Optimizing NNI: done in 5.86956 secs using 597.3% CPU
Optimizing NNI: done in 1.32001 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 283 ITERATIONS / Time: 0h:6m:33s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59152.664
Optimizing NNI: done in 2.44294 secs using 398.1% CPU
2. Current log-likelihood: -59152.634
3. Current log-likelihood: -59152.595
Optimizing NNI: done in 1.83074 secs using 398.1% CPU
4. Current log-likelihood: -59152.559
5. Current log-likelihood: -59152.523
Optimizing NNI: done in 4.62295 secs using 597.6% CPU
6. Current log-likelihood: -59152.487
Optimizing NNI: done in 1.97603 secs using 398.1% CPU
7. Current log-likelihood: -59152.457
8. Current log-likelihood: -59152.440
9. Current log-likelihood: -59152.408
10. Current log-likelihood: -59152.376
Optimizing NNI: done in 2.1198 secs using 397.8% CPU
11. Current log-likelihood: -59152.348
12. Current log-likelihood: -59152.332
Optimizing NNI: done in 1.71427 secs using 398.1% CPU
Iteration 280 / LogL: -107202.667 / Time: 0h:12m:6s (0h:0m:52s left)
13. Current log-likelihood: -59152.316
Optimizing NNI: done in 5.03363 secs using 597.6% CPU
14. Current log-likelihood: -59152.301
15. Current log-likelihood: -59152.286
16. Current log-likelihood: -59152.271
17. Current log-likelihood: -59152.253
Optimizing NNI: done in 2.56253 secs using 398.3% CPU
18. Current log-likelihood: -59152.239
19. Current log-likelihood: -59152.224
20. Current log-likelihood: -59152.210
21. Current log-likelihood: -59152.196
Optimizing NNI: done in 1.80562 secs using 398.4% CPU
22. Current log-likelihood: -59152.181
Optimizing NNI: done in 4.43946 secs using 597.2% CPU
23. Current log-likelihood: -59152.168
24. Current log-likelihood: -59152.155
25. Current log-likelihood: -59152.142
Optimizing NNI: done in 1.9702 secs using 398.4% CPU
26. Current log-likelihood: -59152.129
27. Current log-likelihood: -59152.117
28. Current log-likelihood: -59152.104
29. Current log-likelihood: -59152.091
Optimizing NNI: done in 1.90646 secs using 398% CPU
30. Current log-likelihood: -59152.079
31. Current log-likelihood: -59152.067
32. Current log-likelihood: -59152.055
Optimizing NNI: done in 4.26917 secs using 597.5% CPU
33. Current log-likelihood: -59152.044
34. Current log-likelihood: -59152.033
35. Current log-likelihood: -59152.022
36. Current log-likelihood: -59152.012
37. Current log-likelihood: -59152.001
Optimizing NNI: done in 2.88689 secs using 398.2% CPU
38. Current log-likelihood: -59151.991
39. Current log-likelihood: -59151.981
Optimal log-likelihood: -59151.966
Site proportion and rates:  (0.100,0.048) (0.102,0.170) (0.123,0.373) (0.096,0.373) (0.209,0.683) (0.146,1.150) (0.182,2.110) (0.041,4.898)
Parameters optimization took 39 rounds (20.632 sec)
BEST SCORE FOUND : -59151.966
Total tree length: 47.251

Total number of iterations: 283
CPU time used for tree search: 1531.721 sec (0h:25m:31s)
Wall-clock time used for tree search: 387.492 sec (0h:6m:27s)
Total CPU time used: 1639.022 sec (0h:27m:19s)
Total wall-clock time used: 414.392 sec (0h:6m:54s)

===> START BOOTSTRAP REPLICATE NUMBER 38

Creating bootstrap alignment (seed: 67500)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.042 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60918.615
Optimizing NNI: done in 1.88358 secs using 398.6% CPU
Optimizing NNI: done in 4.13594 secs using 597.6% CPU
2. Current log-likelihood: -60386.754
3. Current log-likelihood: -60375.270
4. Current log-likelihood: -60373.285
Optimizing NNI: done in 2.12271 secs using 398.2% CPU
5. Current log-likelihood: -60368.969
6. Current log-likelihood: -60355.729
7. Current log-likelihood: -60353.641
Optimizing NNI: done in 2.19333 secs using 397.9% CPU
8. Current log-likelihood: -60352.382
Optimizing NNI: done in 4.9864 secs using 597.6% CPU
9. Current log-likelihood: -60351.028
Optimizing NNI: done in 1.8948 secs using 398.1% CPU
10. Current log-likelihood: -60349.744
11. Current log-likelihood: -60348.536
12. Current log-likelihood: -60347.451
13. Current log-likelihood: -60346.666
Optimizing NNI: done in 2.18394 secs using 398.2% CPU
Iteration 290 / LogL: -107107.915 / Time: 0h:12m:28s (0h:0m:25s left)
14. Current log-likelihood: -60346.286
Optimizing NNI: done in 4.42962 secs using 597.5% CPU
15. Current log-likelihood: -60346.157
Optimizing NNI: done in 1.90657 secs using 398.6% CPU
Optimal log-likelihood: -60346.120
Site proportion and rates:  (0.093,0.062) (0.125,0.193) (0.150,0.379) (0.184,0.557) (0.204,0.998) (0.099,1.676) (0.115,2.442) (0.028,5.610)
Parameters optimization took 15 rounds (11.021 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09624 secs using 399.8% CPU
Computing ML distances took 1.096420 sec (of wall-clock time) 4.382963 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000344038 secs using 416.5% CPU
Constructing RapidNJ tree: done in 0.00424814 secs using 349.8% CPU
Computing RapidNJ tree took 0.004643 sec (of wall-clock time) 0.018623 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60318.296
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.10507 secs using 398.4% CPU
Optimizing NNI: done in 2.10921 secs using 398.4% CPU
Optimizing NNI: done in 5.51077 secs using 597.1% CPU
5.218 second
Optimizing NNI: done in 2.40135 secs using 398.3% CPU
Optimizing NNI: done in 2.35194 secs using 398.6% CPU
Optimizing NNI: done in 5.88177 secs using 596.7% CPU
Iteration 90 / LogL: -196456.895 / Time: 0h:10m:31s (0h:9m:48s left)
Optimizing NNI: done in 2.11642 secs using 398.3% CPU
Computing log-likelihood of 98 initial trees ... 5.235 seconds
Current best score: -60226.190

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.37045 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.04899 secs using 398.4% CPU
Optimizing NNI: done in 2.147 secs using 398.1% CPU
Optimizing NNI: done in 4.70419 secs using 597.8% CPU
BETTER TREE FOUND at iteration 1: -59969.225
Optimizing NNI: done in 1.11794 secs using 398.7% CPU
Optimizing NNI: done in 2.43432 secs using 398.6% CPU
Optimizing NNI: done in 1.42639 secs using 399.1% CPU
Optimizing NNI: done in 1.46789 secs using 399.2% CPU
Optimizing NNI: done in 1.93157 secs using 398.5% CPU
Iteration 300 / LogL: -107109.910 / Time: 0h:12m:50s (0h:0m:0s left)
Optimizing NNI: done in 5.00308 secs using 597.4% CPU
Optimizing NNI: done in 1.16368 secs using 399.2% CPU
Optimizing NNI: done in 2.11461 secs using 398.1% CPU
TREE SEARCH COMPLETED AFTER 301 ITERATIONS / Time: 0h:12m:52s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -107101.124
Optimizing NNI: done in 1.46224 secs using 398.8% CPU
Optimal log-likelihood: -107101.114
Proportion of invariable sites: 0.020
Site proportion and rates:  (0.079,0.030) (0.057,0.096) (0.121,0.207) (0.153,0.370) (0.129,0.580) (0.143,0.961) (0.143,1.499) (0.101,2.250) (0.054,4.783)
Parameters optimization took 1 rounds (0.953 sec)
BEST SCORE FOUND : -107101.114
Total tree length: 171.734

Total number of iterations: 301
CPU time used for tree search: 2917.846 sec (0h:48m:37s)
Wall-clock time used for tree search: 740.454 sec (0h:12m:20s)
Total CPU time used: 3048.320 sec (0h:50m:48s)
Total wall-clock time used: 773.173 sec (0h:12m:53s)

===> START BOOTSTRAP REPLICATE NUMBER 6

Creating bootstrap alignment (seed: 68188)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.127 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -109687.528
Optimizing NNI: done in 1.65731 secs using 398.6% CPU
2. Current log-likelihood: -107318.702
Optimizing NNI: done in 4.6831 secs using 597% CPU
Optimizing NNI: done in 1.47874 secs using 398.8% CPU
3. Current log-likelihood: -107256.789
Optimizing NNI: done in 1.40929 secs using 399.1% CPU
4. Current log-likelihood: -107256.264
Optimizing NNI: done in 1.47557 secs using 399.5% CPU
Iteration 10 / LogL: -60040.214 / Time: 0h:0m:39s
Optimizing NNI: done in 1.13518 secs using 398.8% CPU
5. Current log-likelihood: -107255.941
Optimizing NNI: done in 4.34947 secs using 597.8% CPU
6. Current log-likelihood: -107255.707
Optimizing NNI: done in 1.76746 secs using 398.9% CPU
7. Current log-likelihood: -107255.590
Optimizing NNI: done in 1.4222 secs using 399.3% CPU
8. Current log-likelihood: -107255.487
Optimizing NNI: done in 1.38982 secs using 398.7% CPU
Optimizing NNI: done in 4.89248 secs using 597% CPU
Optimal log-likelihood: -107255.354
Proportion of invariable sites: 0.016
Site proportion and rates:  (0.123,0.039) (0.093,0.122) (0.062,0.208) (0.071,0.293) (0.084,0.408) (0.136,0.618) (0.153,0.985) (0.176,1.867) (0.086,4.106)
Parameters optimization took 8 rounds (11.989 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.52849 secs using 399.2% CPU
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Calculating distance matrix: done in 4.91266 secs using 399.9% CPU
Computing ML distances took 4.912896 sec (of wall-clock time) 19.644533 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000713825 secs using 416.8% CPU
Constructing RapidNJ tree: done in 0.00877404 secs using 378.2% CPU
Computing RapidNJ tree took 0.009553 sec (of wall-clock time) 0.038439 sec (of CPU time)
Optimizing NNI: done in 1.46214 secs using 398.4% CPU
Log-likelihood of RapidNJ tree: -107543.933
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.60168 secs using 399.2% CPU
Optimizing NNI: done in 1.53411 secs using 398.8% CPU
Iteration 20 / LogL: -60032.312 / Time: 0h:0m:54s
Finish initializing candidate tree set (20)
Current best tree score: -59969.225 / CPU time: 41.838
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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10.930 second
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Iteration 30 / LogL: -60082.954 / Time: 0h:1m:11s (0h:4m:4s left)
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Iteration 100 / LogL: -196574.764 / Time: 0h:11m:22s (0h:11m:7s left)
Computing log-likelihood of 98 initial trees ... 10.021 seconds
Current best score: -107255.354

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Iteration 40 / LogL: -59970.727 / Time: 0h:1m:29s (0h:3m:39s left)
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UPDATE BEST LOG-LIKELIHOOD: -59937.259
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Iteration 20 / LogL: -106767.379 / Time: 0h:1m:46s
Finish initializing candidate tree set (20)
Current best tree score: -106705.654 / CPU time: 88.533
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 52: -106688.757
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 60: -106688.006
Iteration 60 / LogL: -106688.006 / Time: 0h:3m:35s (0h:6m:4s left)
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Iteration 140 / LogL: -196468.082 / Time: 0h:14m:27s (0h:5m:55s left)
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Iteration 150 / LogL: -59939.595 / Time: 0h:4m:19s (0h:0m:-2s left)
TREE SEARCH COMPLETED AFTER 150 ITERATIONS / Time: 0h:4m:19s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59937.259
2. Current log-likelihood: -59937.235
Optimizing NNI: done in 2.57626 secs using 398.7% CPU
3. Current log-likelihood: -59937.224
4. Current log-likelihood: -59937.214
5. Current log-likelihood: -59937.203
Optimal log-likelihood: -59937.188
Site proportion and rates:  (0.090,0.061) (0.136,0.190) (0.165,0.389) (0.173,0.590) (0.193,1.009) (0.107,1.679) (0.111,2.513) (0.026,5.764)
Parameters optimization took 5 rounds (2.351 sec)
BEST SCORE FOUND : -59937.188
Total tree length: 45.627

Total number of iterations: 150
CPU time used for tree search: 972.099 sec (0h:16m:12s)
Wall-clock time used for tree search: 247.428 sec (0h:4m:7s)
Total CPU time used: 1031.285 sec (0h:17m:11s)
Total wall-clock time used: 262.245 sec (0h:4m:22s)
Optimizing NNI: done in 4.56466 secs using 597.7% CPU

===> START BOOTSTRAP REPLICATE NUMBER 39

Creating bootstrap alignment (seed: 67501)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.075 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59857.382
2. Current log-likelihood: -59282.518
Optimizing NNI: done in 2.59873 secs using 398.5% CPU
3. Current log-likelihood: -59265.489
4. Current log-likelihood: -59263.427
5. Current log-likelihood: -59262.227
Optimizing NNI: done in 2.09206 secs using 398.2% CPU
6. Current log-likelihood: -59261.137
Optimizing NNI: done in 4.45549 secs using 597.9% CPU
7. Current log-likelihood: -59260.308
8. Current log-likelihood: -59260.113
Optimizing NNI: done in 2.44614 secs using 398.7% CPU
Optimal log-likelihood: -59260.077
Site proportion and rates:  (0.138,0.074) (0.084,0.178) (0.110,0.366) (0.057,0.396) (0.233,0.710) (0.165,1.188) (0.171,2.128) (0.042,4.490)
Parameters optimization took 8 rounds (6.040 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09543 secs using 399.4% CPU
Computing ML distances took 1.095622 sec (of wall-clock time) 4.376351 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000351191 secs using 415.4% CPU
Constructing RapidNJ tree: done in 0.00430799 secs using 344.5% CPU
Computing RapidNJ tree took 0.004714 sec (of wall-clock time) 0.016924 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59288.112
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.30967 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 69: -106685.865
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Iteration 70 / LogL: -106701.591 / Time: 0h:4m:0s (0h:5m:45s left)
5.204 second
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Computing log-likelihood of 98 initial trees ... 7.112 seconds
Current best score: -59174.450

Do NNI search on 20 best initial trees
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BETTER TREE FOUND at iteration 75: -106678.911
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Iteration 20 / LogL: -59027.656 / Time: 0h:1m:5s
Finish initializing candidate tree set (20)
Current best tree score: -58904.665 / CPU time: 57.470
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 2.7971 secs using 398.1% CPU
Optimizing NNI: done in 1.39626 secs using 398.3% CPU
Optimizing NNI: done in 2.22841 secs using 398.6% CPU
Optimizing NNI: done in 1.43885 secs using 399% CPU
Optimizing NNI: done in 5.12646 secs using 597.7% CPU
Optimizing NNI: done in 1.25398 secs using 399.3% CPU
Optimizing NNI: done in 2.42037 secs using 398.3% CPU
Optimizing NNI: done in 1.15705 secs using 399.5% CPU
Optimizing NNI: done in 1.69231 secs using 399.1% CPU
Iteration 150 / LogL: -58975.176 / Time: 0h:4m:14s (0h:2m:16s left)
Optimizing NNI: done in 2.28541 secs using 398.6% CPU
Optimizing NNI: done in 4.46067 secs using 597.5% CPU
Optimizing NNI: done in 1.57758 secs using 399.2% CPU
Optimizing NNI: done in 1.39947 secs using 398.9% CPU
Optimizing NNI: done in 2.67547 secs using 398.5% CPU
Optimizing NNI: done in 1.32916 secs using 398.9% CPU
Optimizing NNI: done in 4.12632 secs using 598.1% CPU
Optimizing NNI: done in 2.33236 secs using 397.9% CPU
Iteration 170 / LogL: -106767.974 / Time: 0h:8m:8s (0h:0m:14s left)
Optimizing NNI: done in 1.24233 secs using 399.3% CPU
Optimizing NNI: done in 1.31205 secs using 399.4% CPU
Optimizing NNI: done in 2.26553 secs using 398.7% CPU
Optimizing NNI: done in 1.18277 secs using 398.8% CPU
Optimizing NNI: done in 1.49715 secs using 399.4% CPU
Optimizing NNI: done in 4.14704 secs using 597.7% CPU
Optimizing NNI: done in 2.39577 secs using 398.2% CPU
Optimizing NNI: done in 1.54364 secs using 399% CPU
Optimizing NNI: done in 1.21093 secs using 399.4% CPU
Optimizing NNI: done in 2.25431 secs using 397.9% CPU
Optimizing NNI: done in 1.5924 secs using 399.3% CPU
Iteration 160 / LogL: -58918.593 / Time: 0h:4m:28s (0h:1m:58s left)
Optimizing NNI: done in 4.37618 secs using 597.6% CPU
Optimizing NNI: done in 2.44918 secs using 397.8% CPU
Optimizing NNI: done in 1.3446 secs using 398.7% CPU
Optimizing NNI: done in 1.45257 secs using 399.3% CPU
Optimizing NNI: done in 2.23076 secs using 398.6% CPU
Optimizing NNI: done in 1.24513 secs using 399% CPU
Optimizing NNI: done in 4.27605 secs using 597.6% CPU
Optimizing NNI: done in 1.84092 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 176 ITERATIONS / Time: 0h:8m:22s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106678.911
Optimizing NNI: done in 1.47099 secs using 399.2% CPU
Optimal log-likelihood: -106678.907
Proportion of invariable sites: 0.015
Site proportion and rates:  (0.119,0.036) (0.089,0.114) (0.075,0.194) (0.073,0.305) (0.081,0.415) (0.118,0.593) (0.166,0.953) (0.185,1.868) (0.078,4.384)
Parameters optimization took 1 rounds (0.493 sec)
BEST SCORE FOUND : -106678.907
Total tree length: 190.284

Total number of iterations: 176
CPU time used for tree search: 1895.754 sec (0h:31m:35s)
Wall-clock time used for tree search: 483.972 sec (0h:8m:3s)
Total CPU time used: 1969.852 sec (0h:32m:49s)
Total wall-clock time used: 502.530 sec (0h:8m:22s)

===> START BOOTSTRAP REPLICATE NUMBER 7

Creating bootstrap alignment (seed: 68189)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -112054.344
Optimizing NNI: done in 1.24808 secs using 399.2% CPU
2. Current log-likelihood: -109911.329
Optimizing NNI: done in 1.49742 secs using 399.3% CPU
Optimizing NNI: done in 3.98481 secs using 597.3% CPU
Iteration 200 / LogL: -196447.991 / Time: 0h:19m:9s (0h:7m:24s left)
3. Current log-likelihood: -109827.228
Optimizing NNI: done in 1.4188 secs using 399% CPU
4. Current log-likelihood: -109823.865
Optimizing NNI: done in 1.54071 secs using 398.9% CPU
5. Current log-likelihood: -109823.359
Optimizing NNI: done in 3.94841 secs using 596.9% CPU
Optimizing NNI: done in 1.26196 secs using 399.5% CPU
6. Current log-likelihood: -109822.961
Optimizing NNI: done in 1.31092 secs using 398.8% CPU
Iteration 170 / LogL: -58895.045 / Time: 0h:4m:42s (0h:1m:40s left)
Optimizing NNI: done in 1.07658 secs using 398.4% CPU
7. Current log-likelihood: -109822.612
Optimizing NNI: done in 1.26928 secs using 399.8% CPU
Optimizing NNI: done in 4.25422 secs using 597% CPU
8. Current log-likelihood: -109822.299
Optimizing NNI: done in 1.52727 secs using 398.7% CPU
9. Current log-likelihood: -109822.021
Optimizing NNI: done in 1.29619 secs using 398.8% CPU
10. Current log-likelihood: -109821.866
Optimizing NNI: done in 1.46902 secs using 398.9% CPU
11. Current log-likelihood: -109821.633
Optimizing NNI: done in 4.61783 secs using 596.2% CPU
Optimizing NNI: done in 1.67143 secs using 398.8% CPU
12. Current log-likelihood: -109821.507
Optimizing NNI: done in 1.38764 secs using 398.6% CPU
13. Current log-likelihood: -109821.384
14. Current log-likelihood: -109821.267
Optimizing NNI: done in 1.2996 secs using 398.9% CPU
Optimizing NNI: done in 4.61946 secs using 597.5% CPU
15. Current log-likelihood: -109821.153
Optimizing NNI: done in 1.31281 secs using 399% CPU
16. Current log-likelihood: -109821.050
Optimizing NNI: done in 1.57458 secs using 398.9% CPU
Iteration 180 / LogL: -59078.483 / Time: 0h:4m:56s (0h:1m:22s left)
Optimal log-likelihood: -109820.899
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.084,0.036) (0.073,0.112) (0.041,0.192) (0.126,0.310) (0.079,0.430) (0.132,0.639) (0.166,1.063) (0.197,1.780) (0.077,3.852)
Parameters optimization took 16 rounds (23.642 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.58341 secs using 398.9% CPU
Optimizing NNI: done in 4.53242 secs using 597.3% CPU
Optimizing NNI: done in 1.28933 secs using 399.4% CPU
Optimizing NNI: done in 1.4278 secs using 399.4% CPU
Optimizing NNI: done in 1.47894 secs using 399% CPU
Calculating distance matrix: done in 4.65793 secs using 399.9% CPU
Computing ML distances took 4.658318 sec (of wall-clock time) 18.630179 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000741005 secs using 264.8% CPU
Constructing RapidNJ tree: done in 0.00869012 secs using 378.5% CPU
Computing RapidNJ tree took 0.009485 sec (of wall-clock time) 0.036728 sec (of CPU time)
Optimizing NNI: done in 4.16624 secs using 597.4% CPU
Optimizing NNI: done in 1.27557 secs using 398.6% CPU
Log-likelihood of RapidNJ tree: -110013.901
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.80024 secs using 398.9% CPU
Optimizing NNI: done in 1.08553 secs using 399.7% CPU
Optimizing NNI: done in 4.14654 secs using 597.9% CPU
Optimizing NNI: done in 1.24181 secs using 399.3% CPU
Optimizing NNI: done in 1.19302 secs using 398.5% CPU
Optimizing NNI: done in 1.38606 secs using 399% CPU
Iteration 190 / LogL: -58893.368 / Time: 0h:5m:10s (0h:1m:5s left)
Optimizing NNI: done in 1.57944 secs using 399.1% CPU
Optimizing NNI: done in 4.43393 secs using 598.1% CPU
Optimizing NNI: done in 1.26643 secs using 398.7% CPU
Optimizing NNI: done in 1.50335 secs using 399.2% CPU
10.919 second
Optimizing NNI: done in 1.44671 secs using 398.7% CPU
Optimizing NNI: done in 5.07035 secs using 596.9% CPU
Optimizing NNI: done in 2.09972 secs using 398.5% CPU
Optimizing NNI: done in 2.33459 secs using 398.6% CPU
Optimizing NNI: done in 4.77788 secs using 596.8% CPU
Iteration 210 / LogL: -196516.367 / Time: 0h:19m:54s (0h:6m:22s left)
Optimizing NNI: done in 1.51215 secs using 399.4% CPU
Optimizing NNI: done in 1.53453 secs using 398.9% CPU
Computing log-likelihood of 98 initial trees ... 10.066 seconds
Current best score: -109820.899

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.20722 secs using 399.5% CPU
Optimizing NNI: done in 1.13959 secs using 399.8% CPU
Iteration 200 / LogL: -58899.692 / Time: 0h:5m:26s (0h:0m:49s left)
Optimizing NNI: done in 4.68812 secs using 597.6% CPU
Optimizing NNI: done in 2.13513 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.37458 secs using 399.3% CPU
Optimizing NNI: done in 1.33618 secs using 399.1% CPU
Optimizing NNI: done in 1.22851 secs using 398.8% CPU
BETTER TREE FOUND at iteration 1: -109273.448
Optimizing NNI: done in 1.2207 secs using 399.3% CPU
Optimizing NNI: done in 4.54463 secs using 597.2% CPU
Optimizing NNI: done in 1.64129 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.38511 secs using 398.8% CPU
Optimizing NNI: done in 1.32625 secs using 399% CPU
Optimizing NNI: done in 1.36408 secs using 398.7% CPU
Optimizing NNI: done in 4.47976 secs using 597.2% CPU
Optimizing NNI: done in 1.57034 secs using 399.2% CPU
Optimizing NNI: done in 1.59705 secs using 399.2% CPU
BETTER TREE FOUND at iteration 2: -109115.547
Optimizing NNI: done in 1.16172 secs using 399.5% CPU
Iteration 210 / LogL: -59031.250 / Time: 0h:5m:39s (0h:0m:32s left)
Optimizing NNI: done in 1.56747 secs using 398.5% CPU
Optimizing NNI: done in 4.44667 secs using 597.8% CPU
Optimizing NNI: done in 1.40097 secs using 398.8% CPU
Optimizing NNI: done in 1.77804 secs using 398.5% CPU
Optimizing NNI: done in 1.28001 secs using 398.8% CPU
Optimizing NNI: done in 1.66343 secs using 398.5% CPU
Optimizing NNI: done in 1.74761 secs using 399.2% CPU
Optimizing NNI: done in 4.22941 secs using 597.5% CPU
Optimizing NNI: done in 1.29362 secs using 399.1% CPU
Optimizing NNI: done in 2.10186 secs using 398.3% CPU
Optimizing NNI: done in 1.15837 secs using 397.7% CPU
Optimizing NNI: done in 1.16722 secs using 398.8% CPU
Optimizing NNI: done in 2.74901 secs using 397.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.45016 secs using 597.6% CPU
Optimizing NNI: done in 1.48118 secs using 399.2% CPU
Optimizing NNI: done in 1.54603 secs using 397.9% CPU
Optimizing NNI: done in 1.60897 secs using 399% CPU
BETTER TREE FOUND at iteration 7: -109080.582
Optimizing NNI: done in 1.41912 secs using 398.4% CPU
Iteration 220 / LogL: -58902.247 / Time: 0h:5m:54s (0h:0m:16s left)
Optimizing NNI: done in 4.93213 secs using 597.8% CPU
Optimizing NNI: done in 2.05233 secs using 398.5% CPU
Optimizing NNI: done in 1.40448 secs using 399.1% CPU
Optimizing NNI: done in 1.29703 secs using 399.4% CPU
Optimizing NNI: done in 1.10122 secs using 399.1% CPU
Optimizing NNI: done in 2.7101 secs using 398.7% CPU
Optimizing NNI: done in 4.63749 secs using 597.6% CPU
Optimizing NNI: done in 1.17948 secs using 398.6% CPU
Optimizing NNI: done in 1.84053 secs using 398.6% CPU
Iteration 10 / LogL: -109154.765 / Time: 0h:1m:25s
Optimizing NNI: done in 1.15073 secs using 399.7% CPU
Optimizing NNI: done in 1.75067 secs using 397.9% CPU
Optimizing NNI: done in 1.66565 secs using 399% CPU
Optimizing NNI: done in 1.42008 secs using 399% CPU
Optimizing NNI: done in 4.44438 secs using 597.7% CPU
Optimizing NNI: done in 2.251 secs using 398.5% CPU
Optimizing NNI: done in 1.13857 secs using 399.1% CPU
Optimizing NNI: done in 1.93678 secs using 398.8% CPU
Optimizing NNI: done in 1.77025 secs using 399.1% CPU
Optimizing NNI: done in 1.12615 secs using 398.6% CPU
Iteration 230 / LogL: -58978.310 / Time: 0h:6m:7s (0h:0m:0s left)
Optimizing NNI: done in 2.05912 secs using 398.7% CPU
Optimizing NNI: done in 4.58354 secs using 597.5% CPU
Iteration 220 / LogL: -196443.080 / Time: 0h:20m:40s (0h:5m:22s left)
Optimizing NNI: done in 1.40135 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 231 ITERATIONS / Time: 0h:6m:8s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58891.207
2. Current log-likelihood: -58891.192
Optimizing NNI: done in 1.83293 secs using 398% CPU
3. Current log-likelihood: -58891.181
Optimal log-likelihood: -58891.170
Site proportion and rates:  (0.150,0.078) (0.101,0.211) (0.123,0.384) (0.171,0.621) (0.175,0.935) (0.154,1.672) (0.098,2.519) (0.028,5.250)
Parameters optimization took 3 rounds (1.914 sec)
BEST SCORE FOUND : -58891.170
Total tree length: 46.085

Total number of iterations: 231
CPU time used for tree search: 1425.696 sec (0h:23m:45s)
Wall-clock time used for tree search: 361.154 sec (0h:6m:1s)
Total CPU time used: 1464.582 sec (0h:24m:24s)
Total wall-clock time used: 370.884 sec (0h:6m:10s)

===> START BOOTSTRAP REPLICATE NUMBER 40

Creating bootstrap alignment (seed: 67502)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.041 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60447.874
2. Current log-likelihood: -59861.317
Optimizing NNI: done in 2.1519 secs using 398.4% CPU
3. Current log-likelihood: -59857.258
Optimizing NNI: done in 4.92767 secs using 597.2% CPU
4. Current log-likelihood: -59856.786
Optimizing NNI: done in 1.56677 secs using 398.7% CPU
5. Current log-likelihood: -59856.480
6. Current log-likelihood: -59856.298
7. Current log-likelihood: -59856.192
Optimizing NNI: done in 2.53785 secs using 398.1% CPU
Optimal log-likelihood: -59856.111
Site proportion and rates:  (0.075,0.055) (0.117,0.175) (0.114,0.396) (0.101,0.400) (0.205,0.732) (0.104,1.097) (0.136,1.627) (0.147,2.744)
Parameters optimization took 7 rounds (5.236 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.06623 secs using 399.9% CPU
Computing ML distances took 1.066398 sec (of wall-clock time) 4.264864 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000349998 secs using 424.6% CPU
Constructing RapidNJ tree: done in 0.00437403 secs using 352.1% CPU
Computing RapidNJ tree took 0.004775 sec (of wall-clock time) 0.018197 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59809.560
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.74766 secs using 597.8% CPU
Optimizing NNI: done in 2.67659 secs using 398.4% CPU
Optimizing NNI: done in 2.69566 secs using 398.2% CPU
Iteration 20 / LogL: -109105.695 / Time: 0h:1m:47s
Finish initializing candidate tree set (20)
Current best tree score: -109080.582 / CPU time: 77.426
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
4.830 second
Optimizing NNI: done in 2.18437 secs using 398.5% CPU
Optimizing NNI: done in 6.16326 secs using 597.5% CPU
Optimizing NNI: done in 2.10817 secs using 399.2% CPU
Computing log-likelihood of 98 initial trees ... 5.140 seconds
Current best score: -59712.195

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.28294 secs using 398.4% CPU
Optimizing NNI: done in 4.50617 secs using 598.1% CPU
Optimizing NNI: done in 1.3832 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.17455 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -109079.785
Optimizing NNI: done in 4.5685 secs using 596.8% CPU
BETTER TREE FOUND at iteration 1: -59524.368
Optimizing NNI: done in 1.22868 secs using 399% CPU
Optimizing NNI: done in 2.12625 secs using 398.4% CPU
Optimizing NNI: done in 1.44197 secs using 398% CPU
Optimizing NNI: done in 1.67898 secs using 398.1% CPU
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Optimizing NNI: done in 2.01371 secs using 398.8% CPU
Optimizing NNI: done in 1.43648 secs using 398.8% CPU
Optimizing NNI: done in 1.60225 secs using 398.6% CPU
Optimizing NNI: done in 2.37107 secs using 398.8% CPU
Optimizing NNI: done in 1.52377 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.56416 secs using 598.2% CPU
Optimizing NNI: done in 1.7798 secs using 398.8% CPU
Optimizing NNI: done in 2.2705 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -109060.628
Iteration 30 / LogL: -109060.628 / Time: 0h:2m:12s (0h:7m:35s left)
Optimizing NNI: done in 4.35993 secs using 597.3% CPU
Optimizing NNI: done in 2.02465 secs using 399.1% CPU
BETTER TREE FOUND at iteration 7: -59512.426
Optimizing NNI: done in 2.39951 secs using 398.5% CPU
Optimizing NNI: done in 4.39264 secs using 597.7% CPU
Optimizing NNI: done in 1.09578 secs using 398.8% CPU
Optimizing NNI: done in 1.14264 secs using 399.3% CPU
Optimizing NNI: done in 1.92705 secs using 398.8% CPU
Optimizing NNI: done in 1.21768 secs using 399% CPU
Iteration 10 / LogL: -59524.969 / Time: 0h:0m:43s
Optimizing NNI: done in 1.12437 secs using 398.6% CPU
Optimizing NNI: done in 2.32369 secs using 398.6% CPU
Optimizing NNI: done in 4.70639 secs using 597.1% CPU
Iteration 230 / LogL: -196555.536 / Time: 0h:21m:28s (0h:4m:24s left)
Optimizing NNI: done in 1.30154 secs using 398.9% CPU
Optimizing NNI: done in 2.07368 secs using 398.6% CPU
Optimizing NNI: done in 1.23398 secs using 398.8% CPU
Optimizing NNI: done in 1.15229 secs using 399% CPU
Optimizing NNI: done in 1.75325 secs using 398.5% CPU
Optimizing NNI: done in 1.14008 secs using 399.3% CPU
Optimizing NNI: done in 4.8503 secs using 597.3% CPU
Optimizing NNI: done in 1.34385 secs using 399.1% CPU
Optimizing NNI: done in 2.19212 secs using 398.9% CPU
Optimizing NNI: done in 1.17533 secs using 399.4% CPU
Optimizing NNI: done in 1.96187 secs using 398.4% CPU
Optimizing NNI: done in 1.04696 secs using 398.6% CPU
Optimizing NNI: done in 1.17855 secs using 399% CPU
Optimizing NNI: done in 2.00234 secs using 398.8% CPU
Optimizing NNI: done in 4.90205 secs using 597.2% CPU
Optimizing NNI: done in 1.08797 secs using 399.3% CPU
Iteration 20 / LogL: -59555.863 / Time: 0h:0m:54s
Finish initializing candidate tree set (20)
Current best tree score: -59512.426 / CPU time: 48.297
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.29586 secs using 398.8% CPU
Optimizing NNI: done in 1.8748 secs using 398.3% CPU
Iteration 40 / LogL: -109131.651 / Time: 0h:2m:33s (0h:5m:53s left)
Optimizing NNI: done in 1.50444 secs using 399.2% CPU
Optimizing NNI: done in 1.86926 secs using 398.8% CPU
Optimizing NNI: done in 1.25735 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -59505.430
Optimizing NNI: done in 5.19229 secs using 597.4% CPU
Optimizing NNI: done in 2.26175 secs using 398.8% CPU
Optimizing NNI: done in 1.54214 secs using 399.2% CPU
Optimizing NNI: done in 2.10178 secs using 399% CPU
Optimizing NNI: done in 1.43208 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -59503.885
Optimizing NNI: done in 2.00121 secs using 398.7% CPU
Optimizing NNI: done in 4.81478 secs using 597.2% CPU
Optimizing NNI: done in 1.31356 secs using 399.2% CPU
Optimizing NNI: done in 1.38949 secs using 399.1% CPU
Optimizing NNI: done in 2.37721 secs using 398.8% CPU
Optimizing NNI: done in 1.52336 secs using 399% CPU
Optimizing NNI: done in 1.8492 secs using 398.9% CPU
Optimizing NNI: done in 4.60356 secs using 598.1% CPU
Optimizing NNI: done in 1.31699 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.76514 secs using 399.2% CPU
BETTER TREE FOUND at iteration 29: -59498.772
Optimizing NNI: done in 1.42578 secs using 399.4% CPU
Iteration 30 / LogL: -59502.020 / Time: 0h:1m:12s (0h:4m:7s left)
Optimizing NNI: done in 2.22768 secs using 399.3% CPU
Optimizing NNI: done in 1.38856 secs using 398.5% CPU
Optimizing NNI: done in 4.65218 secs using 597.8% CPU
Optimizing NNI: done in 1.77616 secs using 398.8% CPU
Optimizing NNI: done in 1.40979 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -59493.662
Optimizing NNI: done in 2.27089 secs using 398.8% CPU
Iteration 50 / LogL: -109093.943 / Time: 0h:2m:53s (0h:4m:43s left)
Optimizing NNI: done in 1.53242 secs using 399.2% CPU
Optimizing NNI: done in 4.25665 secs using 598% CPU
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Iteration 40 / LogL: -59493.770 / Time: 0h:1m:27s (0h:3m:26s left)
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Iteration 240 / LogL: -196476.810 / Time: 0h:22m:14s (0h:3m:26s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 44: -59486.268
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Iteration 60 / LogL: -109063.352 / Time: 0h:3m:14s (0h:3m:50s left)
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Iteration 50 / LogL: -59501.533 / Time: 0h:1m:42s (0h:3m:16s left)
BETTER TREE FOUND at iteration 61: -109056.880
Optimizing NNI: done in 1.2119 secs using 399.5% CPU
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BETTER TREE FOUND at iteration 64: -109054.631
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Iteration 60 / LogL: -59498.884 / Time: 0h:1m:55s (0h:2m:44s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 66: -59482.925
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Iteration 70 / LogL: -109078.731 / Time: 0h:3m:41s (0h:5m:2s left)
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Iteration 250 / LogL: -196606.680 / Time: 0h:22m:59s (0h:2m:29s left)
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BETTER TREE FOUND at iteration 77: -109047.145
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Iteration 80 / LogL: -59491.035 / Time: 0h:2m:24s (0h:2m:37s left)
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Iteration 80 / LogL: -109065.444 / Time: 0h:4m:5s (0h:5m:0s left)
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BETTER TREE FOUND at iteration 89: -59481.213
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Iteration 90 / LogL: -59487.135 / Time: 0h:2m:38s (0h:2m:56s left)
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Iteration 90 / LogL: -109055.226 / Time: 0h:4m:26s (0h:4m:20s left)
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Iteration 100 / LogL: -59490.464 / Time: 0h:2m:53s (0h:2m:35s left)
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Iteration 260 / LogL: -196464.092 / Time: 0h:23m:44s (0h:1m:33s left)
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BETTER TREE FOUND at iteration 120: -59481.204
Iteration 120 / LogL: -59481.204 / Time: 0h:3m:20s (0h:2m:48s left)
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Iteration 110 / LogL: -109088.126 / Time: 0h:5m:7s (0h:3m:9s left)
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Iteration 270 / LogL: -196513.357 / Time: 0h:24m:29s (0h:0m:38s left)
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Iteration 120 / LogL: -109331.158 / Time: 0h:5m:27s (0h:2m:36s left)
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Iteration 150 / LogL: -59503.384 / Time: 0h:4m:0s (0h:1m:52s left)
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Iteration 130 / LogL: -109056.836 / Time: 0h:5m:47s (0h:2m:6s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.49296 secs using 399.1% CPU
Iteration 160 / LogL: -59489.121 / Time: 0h:4m:14s (0h:1m:36s left)
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BETTER TREE FOUND at iteration 132: -109045.396
Optimizing NNI: done in 4.09971 secs using 598.2% CPU
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Optimizing NNI: done in 2.40239 secs using 398.1% CPU
Optimizing NNI: done in 4.41997 secs using 597.5% CPU
TREE SEARCH COMPLETED AFTER 278 ITERATIONS / Time: 0h:25m:5s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -196435.295
Optimizing NNI: done in 1.43407 secs using 399% CPU
2. Current log-likelihood: -196435.278
Optimizing NNI: done in 1.90319 secs using 398.9% CPU
Optimizing NNI: done in 1.31936 secs using 399.1% CPU
Optimal log-likelihood: -196435.268
Site proportion and rates:  (0.016,0.112) (0.051,0.252) (0.127,0.375) (0.221,0.569) (0.135,0.789) (0.221,1.074) (0.141,1.671) (0.089,2.616)
Parameters optimization took 2 rounds (1.940 sec)
BEST SCORE FOUND : -196435.268
Total tree length: 150.590

Total number of iterations: 278
CPU time used for tree search: 8499.679 sec (2h:21m:39s)
Wall-clock time used for tree search: 1448.053 sec (0h:24m:8s)
Total CPU time used: 8853.620 sec (2h:27m:33s)
Total wall-clock time used: 1507.461 sec (0h:25m:7s)

===> START BOOTSTRAP REPLICATE NUMBER 11

Creating bootstrap alignment (seed: 70474)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.318 seconds

NOTE: 230 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -193486.207
Optimizing NNI: done in 1.46128 secs using 399.3% CPU
Optimizing NNI: done in 2.63363 secs using 398.3% CPU
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2. Current log-likelihood: -190702.696
Optimizing NNI: done in 1.09632 secs using 399.1% CPU
Iteration 170 / LogL: -59481.209 / Time: 0h:4m:27s (0h:1m:19s left)
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Optimizing NNI: done in 1.14218 secs using 398.9% CPU
3. Current log-likelihood: -190680.361
Optimizing NNI: done in 1.41981 secs using 399% CPU
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4. Current log-likelihood: -190675.244
Optimizing NNI: done in 2.23387 secs using 398.6% CPU
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Iteration 140 / LogL: -109079.704 / Time: 0h:6m:11s (0h:4m:5s left)
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5. Current log-likelihood: -190665.660
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6. Current log-likelihood: -190661.078
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7. Current log-likelihood: -190659.952
Optimizing NNI: done in 1.56781 secs using 398.8% CPU
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8. Current log-likelihood: -190659.680
Optimizing NNI: done in 1.36584 secs using 399.1% CPU
Iteration 180 / LogL: -59489.792 / Time: 0h:4m:42s (0h:1m:3s left)
Optimizing NNI: done in 1.93394 secs using 398.4% CPU
Optimizing NNI: done in 1.44895 secs using 398.6% CPU
Optimal log-likelihood: -190659.610
Site proportion and rates:  (0.013,0.093) (0.070,0.231) (0.138,0.382) (0.192,0.539) (0.173,0.765) (0.134,1.052) (0.168,1.586) (0.113,2.543)
Parameters optimization took 8 rounds (19.538 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 150 / LogL: -109049.040 / Time: 0h:6m:30s (0h:3m:34s left)
Calculating distance matrix: done in 9.75369 secs using 599.9% CPU
Computing ML distances took 9.754242 sec (of wall-clock time) 58.512831 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00151706 secs using 399.5% CPU
Constructing RapidNJ tree: done in 0.022718 secs using 639.9% CPU
Computing RapidNJ tree took 0.024314 sec (of wall-clock time) 0.151849 sec (of CPU time)
Optimizing NNI: done in 1.35863 secs using 398.8% CPU
Log-likelihood of RapidNJ tree: -194872.382
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.94234 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 195: -59480.806
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29.313 second
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Computing log-likelihood of 98 initial trees ... 16.272 seconds
Current best score: -190617.319

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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UPDATE BEST LOG-LIKELIHOOD: -59477.950
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Iteration 10 / LogL: -189680.958 / Time: 0h:1m:59s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 246: -59477.553
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 263: -59475.899
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 19: -189647.909
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Iteration 20 / LogL: -189712.102 / Time: 0h:2m:44s
Finish initializing candidate tree set (20)
Current best tree score: -189647.909 / CPU time: 133.238
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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UPDATE BEST LOG-LIKELIHOOD: -59475.440
Iteration 290 / LogL: -59475.440 / Time: 0h:7m:25s (0h:2m:26s left)
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BETTER TREE FOUND at iteration 23: -189600.873
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UPDATE BEST LOG-LIKELIHOOD: -59475.438
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Iteration 230 / LogL: -109068.742 / Time: 0h:9m:9s (0h:0m:4s left)
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TREE SEARCH COMPLETED AFTER 233 ITERATIONS / Time: 0h:9m:15s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -109045.396
Optimizing NNI: done in 1.2943 secs using 399.1% CPU
Iteration 300 / LogL: -59584.928 / Time: 0h:7m:39s (0h:2m:10s left)
2. Current log-likelihood: -109045.357
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3. Current log-likelihood: -109045.324
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4. Current log-likelihood: -109045.288
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Estimate model parameters (epsilon = 0.100)
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5. Current log-likelihood: -109045.255
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BETTER TREE FOUND at iteration 26: -189576.171
6. Current log-likelihood: -109045.222
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7. Current log-likelihood: -109045.187
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8. Current log-likelihood: -109045.147
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9. Current log-likelihood: -109045.099
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Estimate model parameters (epsilon = 0.100)
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10. Current log-likelihood: -109045.037
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11. Current log-likelihood: -109044.940
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Iteration 310 / LogL: -59482.027 / Time: 0h:7m:53s (0h:1m:55s left)
BETTER TREE FOUND at iteration 27: -189571.906
12. Current log-likelihood: -109044.759
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13. Current log-likelihood: -109044.263
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14. Current log-likelihood: -109042.533
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15. Current log-likelihood: -109035.943
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16. Current log-likelihood: -109026.766
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17. Current log-likelihood: -109026.232
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18. Current log-likelihood: -109026.135
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19. Current log-likelihood: -109026.076
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20. Current log-likelihood: -109026.022
21. Current log-likelihood: -109025.975
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Iteration 320 / LogL: -59484.022 / Time: 0h:8m:7s (0h:1m:39s left)
Optimizing NNI: done in 4.42402 secs using 597.4% CPU
Iteration 30 / LogL: -190301.676 / Time: 0h:3m:42s (0h:12m:24s left)
22. Current log-likelihood: -109025.936
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23. Current log-likelihood: -109025.903
24. Current log-likelihood: -109025.886
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25. Current log-likelihood: -109025.869
26. Current log-likelihood: -109025.857
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27. Current log-likelihood: -109025.844
28. Current log-likelihood: -109025.832
Optimizing NNI: done in 1.43966 secs using 399.4% CPU
29. Current log-likelihood: -109025.820
Optimizing NNI: done in 5.65633 secs using 597.1% CPU
Optimal log-likelihood: -109025.808
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.088,0.037) (0.062,0.103) (0.085,0.212) (0.154,0.361) (0.124,0.586) (0.117,0.927) (0.145,1.362) (0.126,1.957) (0.075,3.898)
Parameters optimization took 29 rounds (35.281 sec)
BEST SCORE FOUND : -109025.808
Total tree length: 180.301

Total number of iterations: 233
CPU time used for tree search: 2061.276 sec (0h:34m:21s)
Wall-clock time used for tree search: 525.218 sec (0h:8m:45s)
Total CPU time used: 2320.638 sec (0h:38m:40s)
Total wall-clock time used: 590.301 sec (0h:9m:50s)

===> START BOOTSTRAP REPLICATE NUMBER 8

Creating bootstrap alignment (seed: 68190)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.090 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -110023.326
Optimizing NNI: done in 1.50792 secs using 399.2% CPU
2. Current log-likelihood: -107899.819
Optimizing NNI: done in 1.30593 secs using 398.9% CPU
Optimizing NNI: done in 1.19158 secs using 398.5% CPU
3. Current log-likelihood: -107822.671
Optimizing NNI: done in 5.1076 secs using 596.7% CPU
Optimizing NNI: done in 1.38443 secs using 398.9% CPU
4. Current log-likelihood: -107816.827
Optimizing NNI: done in 1.42305 secs using 398.6% CPU
5. Current log-likelihood: -107813.591
Optimizing NNI: done in 1.0903 secs using 398.8% CPU
Iteration 330 / LogL: -59484.015 / Time: 0h:8m:20s (0h:1m:23s left)
Optimizing NNI: done in 1.34364 secs using 399.5% CPU
6. Current log-likelihood: -107811.683
Optimizing NNI: done in 4.51902 secs using 597.4% CPU
Optimizing NNI: done in 1.37305 secs using 399.3% CPU
7. Current log-likelihood: -107811.042
Optimizing NNI: done in 1.28118 secs using 398.7% CPU
8. Current log-likelihood: -107810.280
Optimizing NNI: done in 1.23814 secs using 399.4% CPU
9. Current log-likelihood: -107809.868
Optimizing NNI: done in 1.37467 secs using 399.3% CPU
Optimizing NNI: done in 4.76491 secs using 597.3% CPU
10. Current log-likelihood: -107809.290
Optimizing NNI: done in 1.45652 secs using 398.8% CPU
Optimizing NNI: done in 1.1092 secs using 399.2% CPU
11. Current log-likelihood: -107809.031
Optimizing NNI: done in 1.29024 secs using 399.1% CPU
12. Current log-likelihood: -107808.818
Optimizing NNI: done in 4.80098 secs using 597.6% CPU
13. Current log-likelihood: -107808.661
Optimizing NNI: done in 1.26009 secs using 398.7% CPU
Optimizing NNI: done in 1.10234 secs using 398.7% CPU
Iteration 340 / LogL: -59477.015 / Time: 0h:8m:33s (0h:1m:8s left)
14. Current log-likelihood: -107808.459
Optimizing NNI: done in 1.27295 secs using 399.1% CPU
Optimal log-likelihood: -107808.320
Proportion of invariable sites: 0.016
Site proportion and rates:  (0.070,0.035) (0.101,0.111) (0.064,0.194) (0.122,0.321) (0.163,0.497) (0.107,0.791) (0.138,1.270) (0.139,1.896) (0.079,4.166)
Parameters optimization took 14 rounds (21.502 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.35994 secs using 398.9% CPU
Optimizing NNI: done in 4.04024 secs using 597.4% CPU
Optimizing NNI: done in 1.12393 secs using 399.3% CPU
Optimizing NNI: done in 1.24061 secs using 399.5% CPU
Calculating distance matrix: done in 4.7409 secs using 399.9% CPU
Computing ML distances took 4.741285 sec (of wall-clock time) 18.959226 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000884056 secs using 246.7% CPU
Constructing RapidNJ tree: done in 0.00869417 secs using 413.3% CPU
Computing RapidNJ tree took 0.009638 sec (of wall-clock time) 0.038520 sec (of CPU time)
Optimizing NNI: done in 1.32679 secs using 399.1% CPU
Optimizing NNI: done in 4.30666 secs using 597% CPU
Log-likelihood of RapidNJ tree: -108115.134
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.23626 secs using 399.4% CPU
Optimizing NNI: done in 1.30778 secs using 399.1% CPU
Optimizing NNI: done in 1.36991 secs using 398.8% CPU
Optimizing NNI: done in 1.47753 secs using 399% CPU
Optimizing NNI: done in 1.5561 secs using 398.4% CPU
Iteration 350 / LogL: -59515.836 / Time: 0h:8m:47s (0h:0m:52s left)
Optimizing NNI: done in 6.37368 secs using 597.8% CPU
Optimizing NNI: done in 1.26979 secs using 399.2% CPU
Optimizing NNI: done in 1.35335 secs using 398.4% CPU
Optimizing NNI: done in 1.24799 secs using 399.4% CPU
10.744 second
Optimizing NNI: done in 1.52336 secs using 398.8% CPU
Optimizing NNI: done in 6.15963 secs using 597.8% CPU
Optimizing NNI: done in 1.59891 secs using 398.3% CPU
Optimizing NNI: done in 2.24244 secs using 398% CPU
Optimizing NNI: done in 2.24646 secs using 398.2% CPU
Optimizing NNI: done in 6.33225 secs using 597.7% CPU
Iteration 40 / LogL: -189599.332 / Time: 0h:4m:35s (0h:10m:13s left)
Optimizing NNI: done in 1.93624 secs using 398.8% CPU
Computing log-likelihood of 98 initial trees ... 9.978 seconds
Current best score: -107808.320

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.21857 secs using 398.6% CPU
Optimizing NNI: done in 1.92562 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.65861 secs using 398.6% CPU
Iteration 360 / LogL: -59477.142 / Time: 0h:9m:4s (0h:0m:37s left)
Optimizing NNI: done in 5.75175 secs using 598% CPU
Optimizing NNI: done in 1.38292 secs using 398.4% CPU
Optimizing NNI: done in 1.53804 secs using 399.3% CPU
Optimizing NNI: done in 1.37427 secs using 398.7% CPU
Optimizing NNI: done in 1.25557 secs using 398.9% CPU
Optimizing NNI: done in 4.58382 secs using 597.9% CPU
Optimizing NNI: done in 1.42037 secs using 399.6% CPU
Optimizing NNI: done in 1.37127 secs using 399% CPU
Optimizing NNI: done in 1.32095 secs using 398.6% CPU
Optimizing NNI: done in 4.2674 secs using 596.7% CPU
Optimizing NNI: done in 1.35153 secs using 398.8% CPU
Optimizing NNI: done in 1.21093 secs using 398.9% CPU
Optimizing NNI: done in 1.35461 secs using 399.4% CPU
Iteration 370 / LogL: -59759.130 / Time: 0h:9m:18s (0h:0m:22s left)
Optimizing NNI: done in 4.46648 secs using 597.5% CPU
Optimizing NNI: done in 1.4877 secs using 399.2% CPU
Optimizing NNI: done in 1.39103 secs using 398.8% CPU
Optimizing NNI: done in 1.42669 secs using 399.3% CPU
Optimizing NNI: done in 4.25861 secs using 597% CPU
Optimizing NNI: done in 1.21405 secs using 399.3% CPU
Optimizing NNI: done in 1.33872 secs using 398.5% CPU
Optimizing NNI: done in 1.63506 secs using 398.9% CPU
Optimizing NNI: done in 4.4726 secs using 596.6% CPU
Optimizing NNI: done in 1.38284 secs using 399.1% CPU
Optimizing NNI: done in 1.49378 secs using 399.1% CPU
Optimizing NNI: done in 1.08725 secs using 399.6% CPU
Optimizing NNI: done in 1.38023 secs using 399% CPU
Iteration 380 / LogL: -59554.897 / Time: 0h:9m:32s (0h:0m:7s left)
Optimizing NNI: done in 4.41244 secs using 597.6% CPU
BETTER TREE FOUND at iteration 1: -107243.943
Optimizing NNI: done in 1.17526 secs using 399.6% CPU
Optimizing NNI: done in 1.39054 secs using 399.1% CPU
Optimizing NNI: done in 1.94258 secs using 399.3% CPU
Optimizing NNI: done in 1.44007 secs using 398.7% CPU
Optimizing NNI: done in 4.21805 secs using 597.4% CPU
Optimizing NNI: done in 1.47518 secs using 398.7% CPU
Optimizing NNI: done in 3.23605 secs using 398.9% CPU
Optimizing NNI: done in 1.62435 secs using 399.2% CPU
Optimizing NNI: done in 1.49665 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 386 ITERATIONS / Time: 0h:9m:41s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59475.438
Optimizing NNI: done in 2.90611 secs using 398.9% CPU
Optimal log-likelihood: -59475.427
Site proportion and rates:  (0.069,0.053) (0.122,0.166) (0.103,0.400) (0.117,0.400) (0.253,0.762) (0.168,1.452) (0.157,2.464) (0.012,5.543)
Parameters optimization took 1 rounds (0.502 sec)
BEST SCORE FOUND : -59475.427
Total tree length: 41.061

Total number of iterations: 386
CPU time used for tree search: 2276.952 sec (0h:37m:56s)
Wall-clock time used for tree search: 574.353 sec (0h:9m:34s)
Total CPU time used: 2305.711 sec (0h:38m:25s)
Total wall-clock time used: 581.534 sec (0h:9m:41s)

===> START BOOTSTRAP REPLICATE NUMBER 41

Creating bootstrap alignment (seed: 67503)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.049 seconds

NOTE: 64 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -57874.763
2. Current log-likelihood: -57319.980
Optimizing NNI: done in 5.9246 secs using 596.9% CPU
3. Current log-likelihood: -57284.742
Optimizing NNI: done in 2.30233 secs using 398.3% CPU
4. Current log-likelihood: -57262.034
5. Current log-likelihood: -57260.234
6. Current log-likelihood: -57260.118
Optimizing NNI: done in 2.74062 secs using 398.5% CPU
7. Current log-likelihood: -57260.000
8. Current log-likelihood: -57259.869
Optimizing NNI: done in 4.45647 secs using 597.9% CPU
Iteration 50 / LogL: -189612.529 / Time: 0h:5m:22s (0h:8m:26s left)
9. Current log-likelihood: -57259.725
10. Current log-likelihood: -57259.566
Optimizing NNI: done in 2.90244 secs using 398.2% CPU
11. Current log-likelihood: -57259.391
12. Current log-likelihood: -57259.187
13. Current log-likelihood: -57258.944
14. Current log-likelihood: -57258.656
Optimizing NNI: done in 4.57527 secs using 597.4% CPU
Optimizing NNI: done in 3.00419 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
15. Current log-likelihood: -57258.322
16. Current log-likelihood: -57257.984
17. Current log-likelihood: -57257.698
18. Current log-likelihood: -57257.496
19. Current log-likelihood: -57257.369
Optimizing NNI: done in 4.00676 secs using 597.8% CPU
Optimal log-likelihood: -57257.294
Site proportion and rates:  (0.129,0.074) (0.076,0.191) (0.213,0.356) (0.197,0.649) (0.136,0.984) (0.095,1.541) (0.112,2.256) (0.042,5.705)
Parameters optimization took 19 rounds (14.564 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10802 secs using 399.6% CPU
Computing ML distances took 1.108203 sec (of wall-clock time) 4.428498 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000357866 secs using 764% CPU
Constructing RapidNJ tree: done in 0.00440001 secs using 283.8% CPU
Computing RapidNJ tree took 0.004828 sec (of wall-clock time) 0.015258 sec (of CPU time)
Log-likelihood of RapidNJ tree: -57280.413
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 5.23162 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
5.203 second
BETTER TREE FOUND at iteration 8: -107241.020
BETTER TREE FOUND at iteration 53: -189555.468
Optimizing NNI: done in 2.50056 secs using 398.6% CPU
Computing log-likelihood of 98 initial trees ... 7.333 seconds
Current best score: -57257.294

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.68125 secs using 398.5% CPU
Iteration 10 / LogL: -107358.112 / Time: 0h:1m:57s
Optimizing NNI: done in 1.46063 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.28661 secs using 598% CPU
Optimizing NNI: done in 3.06981 secs using 398.5% CPU
Optimizing NNI: done in 4.51281 secs using 597.4% CPU
Optimizing NNI: done in 2.76818 secs using 398.8% CPU
BETTER TREE FOUND at iteration 1: -57102.445
Optimizing NNI: done in 1.28103 secs using 397.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.32744 secs using 398.4% CPU
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Optimizing NNI: done in 2.17833 secs using 398.5% CPU
BETTER TREE FOUND at iteration 2: -57025.911
Optimizing NNI: done in 3.09897 secs using 398.6% CPU
Optimizing NNI: done in 2.28085 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.8808 secs using 598% CPU
Optimizing NNI: done in 2.78173 secs using 398.5% CPU
BETTER TREE FOUND at iteration 3: -57023.125
Optimizing NNI: done in 4.0267 secs using 597.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.69036 secs using 398.2% CPU
Optimizing NNI: done in 4.08448 secs using 597.4% CPU
BETTER TREE FOUND at iteration 5: -56999.247
Optimizing NNI: done in 2.77277 secs using 398.3% CPU
Optimizing NNI: done in 2.30632 secs using 398.5% CPU
Optimizing NNI: done in 4.73574 secs using 597.8% CPU
Iteration 60 / LogL: -189602.708 / Time: 0h:6m:14s (0h:9m:49s left)
Optimizing NNI: done in 2.78234 secs using 398.6% CPU
Iteration 20 / LogL: -107323.628 / Time: 0h:2m:25s
Finish initializing candidate tree set (20)
Current best tree score: -107241.020 / CPU time: 117.638
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 2.6247 secs using 398% CPU
Optimizing NNI: done in 2.33422 secs using 399% CPU
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Optimizing NNI: done in 2.14196 secs using 398.1% CPU
Iteration 10 / LogL: -57067.603 / Time: 0h:1m:5s
Optimizing NNI: done in 2.25607 secs using 399% CPU
Optimizing NNI: done in 4.67641 secs using 597.4% CPU
Optimizing NNI: done in 1.76176 secs using 397.3% CPU
Optimizing NNI: done in 2.28593 secs using 398.7% CPU
Optimizing NNI: done in 1.66121 secs using 399.3% CPU
Optimizing NNI: done in 1.41674 secs using 398.9% CPU
Optimizing NNI: done in 3.11151 secs using 398.7% CPU
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Optimizing NNI: done in 1.98878 secs using 398.2% CPU
Optimizing NNI: done in 7.26325 secs using 597.5% CPU
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Optimizing NNI: done in 1.68074 secs using 399% CPU
Optimizing NNI: done in 1.80452 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.36757 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 17: -56970.700
Optimizing NNI: done in 5.64257 secs using 597.3% CPU
Optimizing NNI: done in 1.44643 secs using 399.1% CPU
BETTER TREE FOUND at iteration 29: -107219.278
Optimizing NNI: done in 1.78183 secs using 398.8% CPU
Optimizing NNI: done in 1.51554 secs using 399.7% CPU
Iteration 20 / LogL: -56978.283 / Time: 0h:1m:23s
Finish initializing candidate tree set (20)
Current best tree score: -56970.700 / CPU time: 67.205
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.70667 secs using 399.3% CPU
Iteration 30 / LogL: -107244.695 / Time: 0h:2m:51s (0h:9m:44s left)
Optimizing NNI: done in 4.62545 secs using 597.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.62291 secs using 596.9% CPU
Optimizing NNI: done in 1.95445 secs using 399.4% CPU
BETTER TREE FOUND at iteration 26: -56967.483
Optimizing NNI: done in 2.07513 secs using 399% CPU
Optimizing NNI: done in 1.37148 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -56965.493
Optimizing NNI: done in 1.90897 secs using 398.6% CPU
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Optimizing NNI: done in 2.19337 secs using 398.7% CPU
Optimizing NNI: done in 1.37646 secs using 399.5% CPU
Iteration 30 / LogL: -57011.318 / Time: 0h:1m:41s (0h:5m:39s left)
Optimizing NNI: done in 2.22944 secs using 398.9% CPU
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Optimizing NNI: done in 1.68438 secs using 399% CPU
Optimizing NNI: done in 2.21616 secs using 398.5% CPU
Iteration 40 / LogL: -107235.619 / Time: 0h:3m:12s (0h:7m:19s left)
Optimizing NNI: done in 1.76704 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.55863 secs using 399.4% CPU
Optimizing NNI: done in 5.45325 secs using 597.8% CPU
Iteration 70 / LogL: -189689.861 / Time: 0h:7m:5s (0h:8m:31s left)
Optimizing NNI: done in 1.12626 secs using 399.7% CPU
BETTER TREE FOUND at iteration 41: -107216.348
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Optimizing NNI: done in 2.23397 secs using 398.6% CPU
Optimizing NNI: done in 1.36815 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 37: -56965.403
Optimizing NNI: done in 4.20713 secs using 597.7% CPU
Optimizing NNI: done in 1.91605 secs using 399% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.36828 secs using 399.3% CPU
Optimizing NNI: done in 4.41247 secs using 597.6% CPU
Optimizing NNI: done in 1.59395 secs using 399.1% CPU
Iteration 40 / LogL: -56970.502 / Time: 0h:1m:57s (0h:4m:52s left)
BETTER TREE FOUND at iteration 44: -107212.493
Optimizing NNI: done in 1.26368 secs using 399.5% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.62616 secs using 399% CPU
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BETTER TREE FOUND at iteration 73: -189553.691
Optimizing NNI: done in 1.7667 secs using 399.1% CPU
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Iteration 50 / LogL: -107240.278 / Time: 0h:3m:39s (0h:7m:1s left)
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Iteration 50 / LogL: -56967.962 / Time: 0h:2m:12s (0h:3m:55s left)
Optimizing NNI: done in 1.35147 secs using 399.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.76437 secs using 598% CPU
BETTER TREE FOUND at iteration 54: -56963.286
Optimizing NNI: done in 2.10586 secs using 398.5% CPU
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 77: -189550.486
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Iteration 60 / LogL: -56976.069 / Time: 0h:2m:29s (0h:3m:57s left)
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BETTER TREE FOUND at iteration 62: -56962.924
Optimizing NNI: done in 2.20892 secs using 399.3% CPU
Iteration 60 / LogL: -107236.058 / Time: 0h:4m:1s (0h:5m:44s left)
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Iteration 80 / LogL: -189579.251 / Time: 0h:7m:56s (0h:9m:44s left)
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BETTER TREE FOUND at iteration 61: -107209.996
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Iteration 70 / LogL: -57009.240 / Time: 0h:2m:46s (0h:3m:41s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 78: -56961.383
Optimizing NNI: done in 6.65004 secs using 597.3% CPU
Optimizing NNI: done in 1.96715 secs using 399.1% CPU
Iteration 70 / LogL: -107239.084 / Time: 0h:4m:27s (0h:5m:52s left)
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Iteration 80 / LogL: -56961.387 / Time: 0h:3m:1s (0h:3m:45s left)
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Optimizing NNI: done in 2.34076 secs using 398.9% CPU
BETTER TREE FOUND at iteration 81: -56952.656
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Iteration 90 / LogL: -56964.791 / Time: 0h:3m:17s (0h:3m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 92: -56951.869
Optimizing NNI: done in 2.21643 secs using 399% CPU
Iteration 80 / LogL: -107239.637 / Time: 0h:4m:49s (0h:4m:56s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.45297 secs using 399.1% CPU
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Iteration 90 / LogL: -189578.343 / Time: 0h:8m:43s (0h:8m:31s left)
BETTER TREE FOUND at iteration 95: -56950.630
Optimizing NNI: done in 2.15014 secs using 398.5% CPU
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BETTER TREE FOUND at iteration 98: -56950.625
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Iteration 100 / LogL: -56966.028 / Time: 0h:3m:35s (0h:3m:33s left)
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Optimizing NNI: done in 2.03163 secs using 398.8% CPU
BETTER TREE FOUND at iteration 101: -56950.289
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BETTER TREE FOUND at iteration 103: -56950.284
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Iteration 90 / LogL: -107237.943 / Time: 0h:5m:11s (0h:4m:8s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 109: -56949.133
Optimizing NNI: done in 1.85578 secs using 399% CPU
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Iteration 110 / LogL: -56959.532 / Time: 0h:3m:53s (0h:3m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 114: -56944.263
Optimizing NNI: done in 2.03455 secs using 398.7% CPU
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Iteration 100 / LogL: -107229.631 / Time: 0h:5m:32s (0h:3m:24s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.23732 secs using 398.9% CPU
BETTER TREE FOUND at iteration 120: -56944.100
Iteration 120 / LogL: -56944.100 / Time: 0h:4m:10s (0h:3m:30s left)
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Iteration 100 / LogL: -189619.948 / Time: 0h:9m:28s (0h:7m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 127: -56943.959
Optimizing NNI: done in 2.37738 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 128: -56942.089
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Iteration 130 / LogL: -56946.310 / Time: 0h:4m:26s (0h:3m:22s left)
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Iteration 110 / LogL: -107230.248 / Time: 0h:5m:55s (0h:2m:46s left)
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Iteration 140 / LogL: -56942.578 / Time: 0h:4m:41s (0h:2m:58s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.99317 secs using 399.4% CPU
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BETTER TREE FOUND at iteration 119: -107208.249
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Iteration 120 / LogL: -107212.323 / Time: 0h:6m:20s (0h:5m:16s left)
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Iteration 150 / LogL: -56945.133 / Time: 0h:4m:56s (0h:2m:35s left)
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Iteration 110 / LogL: -189746.498 / Time: 0h:10m:14s (0h:6m:17s left)
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Iteration 160 / LogL: -56971.842 / Time: 0h:5m:9s (0h:2m:12s left)
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Iteration 130 / LogL: -107225.926 / Time: 0h:6m:42s (0h:4m:37s left)
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Iteration 170 / LogL: -56960.147 / Time: 0h:5m:25s (0h:1m:51s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.02082 secs using 399% CPU
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BETTER TREE FOUND at iteration 117: -189549.715
Optimizing NNI: done in 2.24672 secs using 398.7% CPU
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Iteration 140 / LogL: -107212.516 / Time: 0h:7m:5s (0h:4m:1s left)
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Iteration 180 / LogL: -56969.416 / Time: 0h:5m:38s (0h:1m:30s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.47826 secs using 399% CPU
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BETTER TREE FOUND at iteration 119: -189530.030
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Iteration 120 / LogL: -189541.321 / Time: 0h:11m:5s (0h:9m:13s left)
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Iteration 190 / LogL: -56961.139 / Time: 0h:5m:54s (0h:1m:11s left)
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Iteration 150 / LogL: -107213.365 / Time: 0h:7m:26s (0h:3m:26s left)
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Iteration 200 / LogL: -56942.990 / Time: 0h:6m:8s (0h:0m:51s left)
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Iteration 160 / LogL: -107218.568 / Time: 0h:7m:48s (0h:2m:53s left)
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Optimizing NNI: done in 1.40927 secs using 398.1% CPU
Iteration 210 / LogL: -56954.173 / Time: 0h:6m:21s (0h:0m:32s left)
Optimizing NNI: done in 2.0224 secs using 398.9% CPU
Optimizing NNI: done in 1.22063 secs using 399% CPU
Optimizing NNI: done in 1.34855 secs using 399% CPU
Optimizing NNI: done in 2.28387 secs using 398.9% CPU
Optimizing NNI: done in 4.17139 secs using 597% CPU
Optimizing NNI: done in 1.41784 secs using 399% CPU
Optimizing NNI: done in 2.11005 secs using 399% CPU
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Optimizing NNI: done in 1.7266 secs using 399.3% CPU
Optimizing NNI: done in 1.88095 secs using 398.8% CPU
Optimizing NNI: done in 1.42595 secs using 398.9% CPU
Optimizing NNI: done in 2.0826 secs using 398.9% CPU
Optimizing NNI: done in 1.30632 secs using 398.8% CPU
Optimizing NNI: done in 1.9307 secs using 399% CPU
Optimizing NNI: done in 1.55921 secs using 398.9% CPU
Optimizing NNI: done in 4.72575 secs using 596.8% CPU
Iteration 130 / LogL: -189542.147 / Time: 0h:11m:52s (0h:8m:11s left)
Optimizing NNI: done in 1.51881 secs using 399.3% CPU
Iteration 220 / LogL: -56942.092 / Time: 0h:6m:36s (0h:0m:14s left)
Optimizing NNI: done in 2.31331 secs using 398.9% CPU
Optimizing NNI: done in 1.57365 secs using 399.2% CPU
Optimizing NNI: done in 2.04948 secs using 399.1% CPU
Optimizing NNI: done in 1.42817 secs using 398.7% CPU
Optimizing NNI: done in 4.80579 secs using 597.5% CPU
Optimizing NNI: done in 1.26275 secs using 399.5% CPU
Optimizing NNI: done in 2.25834 secs using 398.7% CPU
Iteration 170 / LogL: -107250.050 / Time: 0h:8m:9s (0h:2m:21s left)
Optimizing NNI: done in 1.40707 secs using 399% CPU
Optimizing NNI: done in 1.97581 secs using 398.8% CPU
Optimizing NNI: done in 1.36513 secs using 399.2% CPU
Optimizing NNI: done in 4.13684 secs using 597.7% CPU
Optimizing NNI: done in 1.34523 secs using 399% CPU
Optimizing NNI: done in 2.24914 secs using 398.9% CPU
Optimizing NNI: done in 1.62267 secs using 399.4% CPU
Optimizing NNI: done in 1.14384 secs using 399.6% CPU
Optimizing NNI: done in 2.04277 secs using 399% CPU
Optimizing NNI: done in 3.71665 secs using 597.1% CPU
Optimizing NNI: done in 1.59471 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 229 ITERATIONS / Time: 0h:6m:49s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -56942.089
Optimizing NNI: done in 2.0168 secs using 398.3% CPU
Optimal log-likelihood: -56942.085
Site proportion and rates:  (0.134,0.073) (0.062,0.187) (0.225,0.358) (0.227,0.665) (0.147,1.143) (0.109,1.853) (0.057,2.461) (0.040,5.940)
Parameters optimization took 1 rounds (0.838 sec)
BEST SCORE FOUND : -56942.085
Total tree length: 45.715

Total number of iterations: 229
CPU time used for tree search: 1553.301 sec (0h:25m:53s)
Wall-clock time used for tree search: 393.205 sec (0h:6m:33s)
Total CPU time used: 1621.412 sec (0h:27m:1s)
Total wall-clock time used: 410.273 sec (0h:6m:50s)

===> START BOOTSTRAP REPLICATE NUMBER 42

Creating bootstrap alignment (seed: 67504)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.042 seconds

NOTE: 60 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61145.196
2. Current log-likelihood: -60537.014
Optimizing NNI: done in 1.72893 secs using 398.9% CPU
3. Current log-likelihood: -60528.873
4. Current log-likelihood: -60521.233
Optimizing NNI: done in 4.84413 secs using 597% CPU
5. Current log-likelihood: -60511.344
Optimizing NNI: done in 1.92699 secs using 398.8% CPU
6. Current log-likelihood: -60501.270
7. Current log-likelihood: -60500.276
Optimal log-likelihood: -60500.229
Site proportion and rates:  (0.143,0.089) (0.017,0.186) (0.136,0.352) (0.087,0.352) (0.240,0.716) (0.186,1.239) (0.162,2.256) (0.029,4.844)
Parameters optimization took 7 rounds (5.661 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.57817 secs using 398.9% CPU
Calculating distance matrix: done in 1.06785 secs using 399.8% CPU
Computing ML distances took 1.068037 sec (of wall-clock time) 4.269562 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000374079 secs using 245.7% CPU
Constructing RapidNJ tree: done in 0.00450897 secs using 326% CPU
Computing RapidNJ tree took 0.004940 sec (of wall-clock time) 0.017820 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60586.454
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.6915 secs using 598.1% CPU
Optimizing NNI: done in 2.20744 secs using 398.9% CPU
Optimizing NNI: done in 1.98755 secs using 398.9% CPU
4.987 second
Optimizing NNI: done in 1.9731 secs using 398.6% CPU
Iteration 180 / LogL: -107236.095 / Time: 0h:8m:30s (0h:1m:51s left)
Optimizing NNI: done in 4.8211 secs using 597.9% CPU
Optimizing NNI: done in 1.98984 secs using 399% CPU
Optimizing NNI: done in 2.23148 secs using 399.1% CPU
Computing log-likelihood of 98 initial trees ... 4.999 seconds
Current best score: -60391.921

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.13954 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.81703 secs using 597.1% CPU
Optimizing NNI: done in 2.38481 secs using 398.8% CPU
BETTER TREE FOUND at iteration 1: -60203.498
Optimizing NNI: done in 0.88462 secs using 398.8% CPU
Optimizing NNI: done in 2.01443 secs using 398.7% CPU
Optimizing NNI: done in 1.11491 secs using 399.1% CPU
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Optimizing NNI: done in 2.67385 secs using 398.7% CPU
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Optimizing NNI: done in 1.11055 secs using 398.9% CPU
Optimizing NNI: done in 1.81356 secs using 399.2% CPU
Optimizing NNI: done in 0.955835 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -60164.829
Optimizing NNI: done in 2.26927 secs using 398.7% CPU
Optimizing NNI: done in 1.1292 secs using 398.8% CPU
Optimizing NNI: done in 1.05151 secs using 399.5% CPU
Optimizing NNI: done in 2.09601 secs using 398.9% CPU
Optimizing NNI: done in 6.13625 secs using 597.5% CPU
Optimizing NNI: done in 1.19118 secs using 399.2% CPU
Iteration 10 / LogL: -60270.249 / Time: 0h:0m:30s
Optimizing NNI: done in 1.19122 secs using 399.5% CPU
Optimizing NNI: done in 2.09942 secs using 398.4% CPU
Optimizing NNI: done in 1.15888 secs using 398.9% CPU
Optimizing NNI: done in 0.9815 secs using 399% CPU
Optimizing NNI: done in 2.31636 secs using 399% CPU
Iteration 190 / LogL: -107224.868 / Time: 0h:8m:52s (0h:1m:21s left)
Optimizing NNI: done in 1.15123 secs using 398.8% CPU
Optimizing NNI: done in 1.12381 secs using 398.9% CPU
Optimizing NNI: done in 2.5245 secs using 399.1% CPU
Optimizing NNI: done in 6.85385 secs using 597.6% CPU
Iteration 140 / LogL: -189631.935 / Time: 0h:12m:44s (0h:7m:14s left)
Optimizing NNI: done in 1.33947 secs using 398.6% CPU
Optimizing NNI: done in 1.26699 secs using 398.6% CPU
Optimizing NNI: done in 2.1728 secs using 398.5% CPU
Optimizing NNI: done in 1.07523 secs using 399.4% CPU
Optimizing NNI: done in 2.20304 secs using 398.8% CPU
Optimizing NNI: done in 1.24737 secs using 399.3% CPU
Optimizing NNI: done in 1.18536 secs using 398.6% CPU
Iteration 20 / LogL: -60303.407 / Time: 0h:0m:42s
Finish initializing candidate tree set (20)
Current best tree score: -60164.829 / CPU time: 35.545
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.82934 secs using 398.1% CPU
Optimizing NNI: done in 6.03731 secs using 596.9% CPU
Optimizing NNI: done in 1.36325 secs using 399% CPU
Optimizing NNI: done in 2.09915 secs using 398.8% CPU
Optimizing NNI: done in 1.4618 secs using 398.8% CPU
Optimizing NNI: done in 1.56128 secs using 398.9% CPU
Optimizing NNI: done in 2.23499 secs using 398.2% CPU
Optimizing NNI: done in 1.56448 secs using 399.3% CPU
Optimizing NNI: done in 1.29739 secs using 398.8% CPU
Optimizing NNI: done in 2.3225 secs using 398.9% CPU
Optimizing NNI: done in 1.36928 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 7.87192 secs using 597.8% CPU
Optimizing NNI: done in 2.34431 secs using 399% CPU
BETTER TREE FOUND at iteration 26: -60155.344
Optimizing NNI: done in 1.28146 secs using 399.2% CPU
Optimizing NNI: done in 2.09368 secs using 399.1% CPU
Optimizing NNI: done in 1.72994 secs using 399.2% CPU
Optimizing NNI: done in 2.39262 secs using 398.6% CPU
Iteration 200 / LogL: -107235.266 / Time: 0h:9m:14s (0h:0m:52s left)
Optimizing NNI: done in 1.06033 secs using 399.1% CPU
Optimizing NNI: done in 1.53847 secs using 399.1% CPU
Iteration 30 / LogL: -60163.398 / Time: 0h:0m:58s (0h:3m:13s left)
Optimizing NNI: done in 7.11325 secs using 597.3% CPU
Optimizing NNI: done in 2.12823 secs using 398.7% CPU
Optimizing NNI: done in 1.50712 secs using 398.6% CPU
Optimizing NNI: done in 2.31844 secs using 398.7% CPU
Optimizing NNI: done in 1.33937 secs using 398.6% CPU
Optimizing NNI: done in 1.32314 secs using 398.8% CPU
Optimizing NNI: done in 2.25741 secs using 398.6% CPU
Optimizing NNI: done in 1.32696 secs using 399.4% CPU
Optimizing NNI: done in 1.17238 secs using 398.7% CPU
Optimizing NNI: done in 6.88715 secs using 597.4% CPU
Optimizing NNI: done in 2.7556 secs using 398.8% CPU
Optimizing NNI: done in 1.37398 secs using 399.3% CPU
Optimizing NNI: done in 1.1829 secs using 398.8% CPU
Optimizing NNI: done in 1.89756 secs using 398.6% CPU
Optimizing NNI: done in 1.47696 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -60154.849
Optimizing NNI: done in 2.27345 secs using 398.6% CPU
Optimizing NNI: done in 6.13195 secs using 596.9% CPU
Optimizing NNI: done in 1.53365 secs using 399.3% CPU
Optimizing NNI: done in 2.29422 secs using 399.2% CPU
Optimizing NNI: done in 1.26632 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -60151.899
Iteration 40 / LogL: -60151.899 / Time: 0h:1m:13s (0h:3m:9s left)
Optimizing NNI: done in 1.99329 secs using 398.7% CPU
Optimizing NNI: done in 1.35743 secs using 398.8% CPU
Optimizing NNI: done in 4.83836 secs using 597.5% CPU
Optimizing NNI: done in 1.33718 secs using 399.4% CPU
Optimizing NNI: done in 2.03813 secs using 398.8% CPU
Optimizing NNI: done in 1.3191 secs using 399.3% CPU
Optimizing NNI: done in 1.93189 secs using 398.6% CPU
Iteration 210 / LogL: -107221.172 / Time: 0h:9m:37s (0h:0m:24s left)
Optimizing NNI: done in 1.48298 secs using 397.9% CPU
Optimizing NNI: done in 4.05912 secs using 597.4% CPU
Optimizing NNI: done in 1.28819 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.3585 secs using 398.6% CPU
BETTER TREE FOUND at iteration 45: -60148.202
Optimizing NNI: done in 1.1959 secs using 399.1% CPU
Optimizing NNI: done in 2.26286 secs using 398.9% CPU
Optimizing NNI: done in 1.31112 secs using 398.6% CPU
Optimizing NNI: done in 2.37632 secs using 398.8% CPU
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Optimizing NNI: done in 6.44623 secs using 596.1% CPU
Optimizing NNI: done in 1.39633 secs using 398.8% CPU
Optimizing NNI: done in 2.16912 secs using 398.8% CPU
Optimizing NNI: done in 1.29224 secs using 398.8% CPU
Iteration 50 / LogL: -60163.432 / Time: 0h:1m:28s (0h:2m:52s left)
Optimizing NNI: done in 1.25341 secs using 399.2% CPU
Optimizing NNI: done in 2.11976 secs using 399% CPU
Optimizing NNI: done in 1.31162 secs using 398.5% CPU
Optimizing NNI: done in 4.84727 secs using 597.4% CPU
Optimizing NNI: done in 2.01418 secs using 398.6% CPU
Optimizing NNI: done in 1.40216 secs using 399.3% CPU
Optimizing NNI: done in 1.24287 secs using 398.7% CPU
Optimizing NNI: done in 1.85567 secs using 399.1% CPU
Optimizing NNI: done in 1.47245 secs using 399.6% CPU
Optimizing NNI: done in 2.23516 secs using 398.9% CPU
Optimizing NNI: done in 1.17393 secs using 399.7% CPU
Optimizing NNI: done in 1.25276 secs using 399.3% CPU
Optimizing NNI: done in 6.56964 secs using 597.9% CPU
Iteration 150 / LogL: -189548.409 / Time: 0h:13m:45s (0h:6m:22s left)
Optimizing NNI: done in 2.17861 secs using 398.7% CPU
Optimizing NNI: done in 1.27342 secs using 398.4% CPU
Optimizing NNI: done in 1.35291 secs using 398.9% CPU
Optimizing NNI: done in 2.37351 secs using 398.9% CPU
Iteration 220 / LogL: -107249.738 / Time: 0h:9m:59s (0h:0m:-3s left)
TREE SEARCH COMPLETED AFTER 220 ITERATIONS / Time: 0h:9m:59s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -107208.249
Optimizing NNI: done in 1.26479 secs using 399% CPU
Iteration 60 / LogL: -60148.327 / Time: 0h:1m:42s (0h:2m:26s left)
2. Current log-likelihood: -107208.216
3. Current log-likelihood: -107208.192
Optimizing NNI: done in 1.12196 secs using 399.2% CPU
4. Current log-likelihood: -107208.182
5. Current log-likelihood: -107208.170
Optimizing NNI: done in 5.60348 secs using 597.9% CPU
Optimizing NNI: done in 1.2683 secs using 398.9% CPU
6. Current log-likelihood: -107208.160
7. Current log-likelihood: -107208.149
Optimizing NNI: done in 1.19078 secs using 399.2% CPU
Optimal log-likelihood: -107208.138
Proportion of invariable sites: 0.015
Site proportion and rates:  (0.061,0.030) (0.099,0.089) (0.078,0.182) (0.131,0.316) (0.170,0.506) (0.092,0.815) (0.147,1.285) (0.130,1.899) (0.075,4.463)
Parameters optimization took 7 rounds (5.140 sec)
BEST SCORE FOUND : -107208.138
Total tree length: 179.414

Total number of iterations: 220
CPU time used for tree search: 2247.759 sec (0h:37m:27s)
Wall-clock time used for tree search: 571.778 sec (0h:9m:31s)
Total CPU time used: 2378.138 sec (0h:39m:38s)
Total wall-clock time used: 604.470 sec (0h:10m:4s)

===> START BOOTSTRAP REPLICATE NUMBER 9

Creating bootstrap alignment (seed: 68191)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.143 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -108685.887
Optimizing NNI: done in 1.43574 secs using 399.4% CPU
2. Current log-likelihood: -106687.213
Optimizing NNI: done in 1.40865 secs using 399.1% CPU
Optimizing NNI: done in 4.28958 secs using 597.8% CPU
Optimizing NNI: done in 1.3115 secs using 398.9% CPU
3. Current log-likelihood: -106584.165
Optimizing NNI: done in 1.27281 secs using 399.7% CPU
4. Current log-likelihood: -106576.332
Optimizing NNI: done in 1.25922 secs using 399.1% CPU
5. Current log-likelihood: -106575.312
Optimizing NNI: done in 5.0965 secs using 597.3% CPU
Optimizing NNI: done in 1.4321 secs using 398.9% CPU
6. Current log-likelihood: -106574.208
Optimizing NNI: done in 1.50253 secs using 399% CPU
Iteration 70 / LogL: -60165.540 / Time: 0h:1m:55s (0h:2m:5s left)
7. Current log-likelihood: -106573.053
Optimizing NNI: done in 1.27833 secs using 399.4% CPU
8. Current log-likelihood: -106572.324
Optimizing NNI: done in 1.48231 secs using 398.7% CPU
Optimizing NNI: done in 1.22566 secs using 398.9% CPU
9. Current log-likelihood: -106571.983
Optimizing NNI: done in 6.39868 secs using 598.1% CPU
Optimizing NNI: done in 1.19256 secs using 399.4% CPU
10. Current log-likelihood: -106571.773
Optimizing NNI: done in 1.11296 secs using 398.5% CPU
11. Current log-likelihood: -106571.555
Optimizing NNI: done in 1.38384 secs using 398.9% CPU
12. Current log-likelihood: -106571.417
Optimizing NNI: done in 1.39466 secs using 399.3% CPU
13. Current log-likelihood: -106571.277
Optimizing NNI: done in 5.02917 secs using 597.4% CPU
14. Current log-likelihood: -106571.104
Optimizing NNI: done in 1.26344 secs using 399.1% CPU
Optimizing NNI: done in 1.35363 secs using 398.9% CPU
Optimal log-likelihood: -106570.993
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.106,0.037) (0.066,0.118) (0.072,0.202) (0.139,0.348) (0.102,0.549) (0.091,0.819) (0.128,1.142) (0.195,1.822) (0.073,3.998)
Parameters optimization took 14 rounds (20.815 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.26934 secs using 398.9% CPU
Iteration 80 / LogL: -60155.255 / Time: 0h:2m:8s (0h:1m:45s left)
Optimizing NNI: done in 4.03505 secs using 597.8% CPU
Optimizing NNI: done in 1.35598 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 81: -60145.934
Optimizing NNI: done in 1.36968 secs using 398.7% CPU
Calculating distance matrix: done in 4.71176 secs using 399.9% CPU
Computing ML distances took 4.712158 sec (of wall-clock time) 18.843212 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000741005 secs using 397.6% CPU
Constructing RapidNJ tree: done in 0.00845385 secs using 369.1% CPU
Computing RapidNJ tree took 0.009257 sec (of wall-clock time) 0.035243 sec (of CPU time)
Optimizing NNI: done in 1.21061 secs using 399% CPU
Optimizing NNI: done in 4.36106 secs using 597.7% CPU
Log-likelihood of RapidNJ tree: -107037.302
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.11274 secs using 398.8% CPU
Optimizing NNI: done in 1.11431 secs using 399.7% CPU
Optimizing NNI: done in 1.14548 secs using 398.5% CPU
Optimizing NNI: done in 1.19914 secs using 399.1% CPU
Optimizing NNI: done in 1.22276 secs using 398.7% CPU
Optimizing NNI: done in 5.62916 secs using 597.5% CPU
Optimizing NNI: done in 1.11723 secs using 399.5% CPU
Optimizing NNI: done in 1.20196 secs using 399.4% CPU
Iteration 90 / LogL: -60148.478 / Time: 0h:2m:21s (0h:2m:24s left)
Optimizing NNI: done in 1.13093 secs using 398.9% CPU
Optimizing NNI: done in 1.10908 secs using 399% CPU
10.748 second
Optimizing NNI: done in 1.20864 secs using 399% CPU
Optimizing NNI: done in 1.18311 secs using 398.8% CPU
Optimizing NNI: done in 6.54955 secs using 597.5% CPU
Optimizing NNI: done in 1.33003 secs using 398% CPU
Optimizing NNI: done in 1.20916 secs using 398.7% CPU
Optimizing NNI: done in 1.30269 secs using 399.2% CPU
Optimizing NNI: done in 1.36629 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 98: -60144.191
Optimizing NNI: done in 6.35962 secs using 597.6% CPU
Iteration 160 / LogL: -189562.745 / Time: 0h:14m:39s (0h:5m:26s left)
Optimizing NNI: done in 1.23299 secs using 398.9% CPU
Computing log-likelihood of 98 initial trees ... 9.845 seconds
Current best score: -106570.993

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.29796 secs using 398.9% CPU
Iteration 100 / LogL: -60156.136 / Time: 0h:2m:34s (0h:2m:33s left)
Optimizing NNI: done in 1.4167 secs using 398.9% CPU
Optimizing NNI: done in 1.67701 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.23656 secs using 399.3% CPU
Optimizing NNI: done in 5.6696 secs using 597.9% CPU
Optimizing NNI: done in 1.33491 secs using 398.6% CPU
Optimizing NNI: done in 1.428 secs using 399.1% CPU
Optimizing NNI: done in 1.42413 secs using 398.8% CPU
Optimizing NNI: done in 1.38226 secs using 398.3% CPU
Optimizing NNI: done in 1.21898 secs using 399.2% CPU
Optimizing NNI: done in 6.45202 secs using 597.7% CPU
Optimizing NNI: done in 1.44874 secs using 398.9% CPU
Optimizing NNI: done in 1.29993 secs using 399.2% CPU
Optimizing NNI: done in 1.3324 secs using 399.1% CPU
Iteration 110 / LogL: -60162.103 / Time: 0h:2m:48s (0h:2m:15s left)
Optimizing NNI: done in 1.22946 secs using 398.8% CPU
Optimizing NNI: done in 5.23122 secs using 596.8% CPU
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Optimizing NNI: done in 1.69628 secs using 398.8% CPU
Iteration 120 / LogL: -60237.090 / Time: 0h:3m:1s (0h:1m:58s left)
Optimizing NNI: done in 4.10281 secs using 597.7% CPU
Optimizing NNI: done in 1.52931 secs using 399.3% CPU
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Iteration 130 / LogL: -60155.069 / Time: 0h:3m:15s (0h:1m:42s left)
Optimizing NNI: done in 1.21895 secs using 399.3% CPU
Optimizing NNI: done in 4.67256 secs using 596.8% CPU
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Optimizing NNI: done in 4.70694 secs using 597.3% CPU
Iteration 170 / LogL: -189550.978 / Time: 0h:15m:29s (0h:4m:29s left)
Optimizing NNI: done in 1.39946 secs using 399.2% CPU
Optimizing NNI: done in 1.3145 secs using 399.4% CPU
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Optimizing NNI: done in 1.15361 secs using 398.9% CPU
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Iteration 140 / LogL: -60146.130 / Time: 0h:3m:28s (0h:1m:27s left)
Optimizing NNI: done in 1.38016 secs using 399.3% CPU
Optimizing NNI: done in 4.0625 secs using 597.2% CPU
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Optimizing NNI: done in 1.21454 secs using 399.6% CPU
BETTER TREE FOUND at iteration 1: -106140.387
Optimizing NNI: done in 4.75889 secs using 596.4% CPU
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Optimizing NNI: done in 1.16339 secs using 398.6% CPU
Optimizing NNI: done in 2.2794 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.52584 secs using 399.1% CPU
Optimizing NNI: done in 4.37282 secs using 597.8% CPU
Optimizing NNI: done in 1.20875 secs using 398.9% CPU
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Iteration 150 / LogL: -60158.778 / Time: 0h:3m:41s (0h:1m:11s left)
Optimizing NNI: done in 1.22363 secs using 398.9% CPU
Optimizing NNI: done in 1.26709 secs using 399% CPU
Optimizing NNI: done in 1.15574 secs using 399% CPU
BETTER TREE FOUND at iteration 2: -106087.108
Optimizing NNI: done in 6.11898 secs using 597.5% CPU
Optimizing NNI: done in 1.08904 secs using 399% CPU
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Iteration 160 / LogL: -60198.988 / Time: 0h:3m:54s (0h:0m:55s left)
Optimizing NNI: done in 2.19442 secs using 398.4% CPU
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Optimizing NNI: done in 6.04082 secs using 598% CPU
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Iteration 10 / LogL: -106369.986 / Time: 0h:2m:14s
Optimizing NNI: done in 1.2894 secs using 398.8% CPU
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Iteration 170 / LogL: -60162.986 / Time: 0h:4m:7s (0h:0m:40s left)
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Optimizing NNI: done in 5.87954 secs using 597.8% CPU
Iteration 180 / LogL: -189627.357 / Time: 0h:16m:23s (0h:3m:34s left)
Optimizing NNI: done in 1.34465 secs using 398.3% CPU
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Optimizing NNI: done in 2.03282 secs using 398.7% CPU
Iteration 20 / LogL: -106190.096 / Time: 0h:2m:34s
Finish initializing candidate tree set (20)
Current best tree score: -106087.108 / CPU time: 126.823
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.28255 secs using 399% CPU
Iteration 180 / LogL: -60162.341 / Time: 0h:4m:21s (0h:0m:26s left)
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 1.19851 secs using 398.7% CPU
BETTER TREE FOUND at iteration 21: -106085.180
Optimizing NNI: done in 1.39063 secs using 398.7% CPU
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BETTER TREE FOUND at iteration 23: -106083.617
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Iteration 190 / LogL: -60165.274 / Time: 0h:4m:34s (0h:0m:11s left)
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BETTER TREE FOUND at iteration 195: -60144.191
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Iteration 200 / LogL: -60144.191 / Time: 0h:4m:47s (0h:2m:17s left)
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 4.07285 secs using 598.5% CPU
Optimizing NNI: done in 1.25184 secs using 398.7% CPU
BETTER TREE FOUND at iteration 30: -106073.491
Iteration 30 / LogL: -106073.491 / Time: 0h:3m:5s (0h:10m:39s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 32: -106069.896
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Iteration 210 / LogL: -60154.149 / Time: 0h:5m:0s (0h:2m:2s left)
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Optimizing NNI: done in 4.24871 secs using 596.9% CPU
Optimizing NNI: done in 1.42646 secs using 399.1% CPU
UPDATE BEST LOG-LIKELIHOOD: -60144.191
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 1.48362 secs using 398.9% CPU
BETTER TREE FOUND at iteration 35: -106065.771
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Iteration 190 / LogL: -189627.351 / Time: 0h:17m:15s (0h:2m:38s left)
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UPDATE BEST LOG-LIKELIHOOD: -60144.191
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Iteration 220 / LogL: -60154.440 / Time: 0h:5m:13s (0h:1m:47s left)
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Iteration 40 / LogL: -106098.504 / Time: 0h:3m:32s (0h:8m:37s left)
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Iteration 230 / LogL: -60144.191 / Time: 0h:5m:26s (0h:1m:32s left)
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Optimizing NNI: done in 2.58601 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 7.98599 secs using 597.4% CPU
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Iteration 240 / LogL: -60155.121 / Time: 0h:5m:40s (0h:1m:18s left)
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BETTER TREE FOUND at iteration 48: -106057.292
Optimizing NNI: done in 6.63913 secs using 597.4% CPU
Optimizing NNI: done in 1.58759 secs using 399% CPU
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BETTER TREE FOUND at iteration 50: -106057.284
Iteration 50 / LogL: -106057.284 / Time: 0h:4m:3s (0h:8m:17s left)
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Iteration 250 / LogL: -60146.010 / Time: 0h:5m:53s (0h:1m:3s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 54: -106054.626
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Iteration 260 / LogL: -60156.106 / Time: 0h:6m:6s (0h:0m:49s left)
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Iteration 200 / LogL: -189544.290 / Time: 0h:18m:17s (0h:1m:44s left)
Optimizing NNI: done in 1.31974 secs using 399.1% CPU
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Iteration 60 / LogL: -106288.950 / Time: 0h:4m:31s (0h:7m:11s left)
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Iteration 270 / LogL: -60151.945 / Time: 0h:6m:20s (0h:0m:35s left)
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Iteration 280 / LogL: -60154.685 / Time: 0h:6m:33s (0h:0m:21s left)
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Iteration 70 / LogL: -106058.190 / Time: 0h:4m:53s (0h:5m:57s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.33182 secs using 399.4% CPU
Iteration 290 / LogL: -60149.082 / Time: 0h:6m:46s (0h:0m:7s left)
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Optimizing NNI: done in 1.23317 secs using 397.9% CPU
BETTER TREE FOUND at iteration 72: -106040.947
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Optimizing NNI: done in 1.46121 secs using 398.9% CPU
Optimizing NNI: done in 1.15898 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 296 ITERATIONS / Time: 0h:6m:53s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60144.191
Optimal log-likelihood: -60144.184
Site proportion and rates:  (0.144,0.088) (0.026,0.245) (0.129,0.339) (0.083,0.343) (0.257,0.725) (0.175,1.288) (0.156,2.266) (0.030,4.786)
Parameters optimization took 1 rounds (0.776 sec)
BEST SCORE FOUND : -60144.184
Total tree length: 43.673

Total number of iterations: 296
CPU time used for tree search: 1608.317 sec (0h:26m:48s)
Wall-clock time used for tree search: 406.747 sec (0h:6m:46s)
Total CPU time used: 1639.871 sec (0h:27m:19s)
Total wall-clock time used: 414.626 sec (0h:6m:54s)

===> START BOOTSTRAP REPLICATE NUMBER 43

Creating bootstrap alignment (seed: 67505)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59812.758
Optimizing NNI: done in 2.51603 secs using 398.7% CPU
2. Current log-likelihood: -59137.098
Optimizing NNI: done in 4.78853 secs using 597.4% CPU
3. Current log-likelihood: -59104.025
4. Current log-likelihood: -59096.175
Optimizing NNI: done in 2.03535 secs using 398.4% CPU
5. Current log-likelihood: -59093.775
6. Current log-likelihood: -59092.995
7. Current log-likelihood: -59092.418
Optimizing NNI: done in 2.22542 secs using 398% CPU
Optimizing NNI: done in 3.92756 secs using 597.4% CPU
Iteration 210 / LogL: -189553.896 / Time: 0h:19m:6s (0h:0m:49s left)
8. Current log-likelihood: -59091.951
9. Current log-likelihood: -59091.631
10. Current log-likelihood: -59091.434
Optimizing NNI: done in 2.29375 secs using 397.9% CPU
11. Current log-likelihood: -59091.320
Optimal log-likelihood: -59091.250
Site proportion and rates:  (0.111,0.059) (0.099,0.188) (0.148,0.349) (0.205,0.598) (0.148,0.942) (0.131,1.444) (0.117,2.247) (0.042,4.958)
Parameters optimization took 11 rounds (7.963 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.95092 secs using 398.4% CPU
Calculating distance matrix: done in 1.08742 secs using 399.8% CPU
Computing ML distances took 1.087607 sec (of wall-clock time) 4.347861 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000330925 secs using 414.6% CPU
Constructing RapidNJ tree: done in 0.00471616 secs using 378% CPU
Computing RapidNJ tree took 0.005098 sec (of wall-clock time) 0.020481 sec (of CPU time)
Optimizing NNI: done in 4.51832 secs using 598% CPU
Log-likelihood of RapidNJ tree: -59153.467
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.40683 secs using 398.1% CPU
Iteration 80 / LogL: -106076.714 / Time: 0h:5m:19s (0h:6m:12s left)
Optimizing NNI: done in 2.2613 secs using 398.6% CPU
5.159 second
Optimizing NNI: done in 5.73948 secs using 597.3% CPU
Optimizing NNI: done in 2.08629 secs using 398.5% CPU
Optimizing NNI: done in 2.63339 secs using 398.5% CPU
Computing log-likelihood of 98 initial trees ... 5.085 seconds
Current best score: -59064.047

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.42829 secs using 598% CPU
Optimizing NNI: done in 2.50731 secs using 398.2% CPU
Optimizing NNI: done in 1.37178 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.27804 secs using 398.1% CPU
BETTER TREE FOUND at iteration 1: -58881.375
Optimizing NNI: done in 0.94853 secs using 399% CPU
Optimizing NNI: done in 2.14871 secs using 398.3% CPU
Optimizing NNI: done in 1.73536 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.66959 secs using 597.5% CPU
Optimizing NNI: done in 2.24226 secs using 398.5% CPU
BETTER TREE FOUND at iteration 3: -58874.014
Optimizing NNI: done in 1.7225 secs using 398.6% CPU
Optimizing NNI: done in 2.5899 secs using 398.8% CPU
Optimizing NNI: done in 2.2381 secs using 398.8% CPU
Optimizing NNI: done in 5.94405 secs using 597.9% CPU
Optimizing NNI: done in 2.38163 secs using 397.7% CPU
Optimizing NNI: done in 1.8468 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.4917 secs using 398.9% CPU
Iteration 90 / LogL: -106058.942 / Time: 0h:5m:43s (0h:5m:16s left)
BETTER TREE FOUND at iteration 6: -58857.821
Optimizing NNI: done in 1.63953 secs using 398.6% CPU
Optimizing NNI: done in 3.03097 secs using 398.5% CPU
Optimizing NNI: done in 6.47187 secs using 597.7% CPU
Optimizing NNI: done in 1.66936 secs using 399.2% CPU
Optimizing NNI: done in 1.96971 secs using 397.8% CPU
Optimizing NNI: done in 1.94772 secs using 399% CPU
Optimizing NNI: done in 2.1708 secs using 398.2% CPU
Optimizing NNI: done in 1.69137 secs using 398.7% CPU
Iteration 10 / LogL: -58925.815 / Time: 0h:0m:43s
Optimizing NNI: done in 2.34044 secs using 397.6% CPU
Optimizing NNI: done in 1.571 secs using 399.4% CPU
Optimizing NNI: done in 0.775445 secs using 399.1% CPU
Optimizing NNI: done in 6.62123 secs using 598.1% CPU
Optimizing NNI: done in 2.14309 secs using 398.5% CPU
Optimizing NNI: done in 1.65592 secs using 399.4% CPU
Optimizing NNI: done in 1.89409 secs using 398.9% CPU
Optimizing NNI: done in 2.38901 secs using 398.5% CPU
Optimizing NNI: done in 1.66357 secs using 399.4% CPU
Optimizing NNI: done in 2.48138 secs using 398.3% CPU
Optimizing NNI: done in 1.6858 secs using 398.8% CPU
Optimizing NNI: done in 7.34429 secs using 597.7% CPU
Optimizing NNI: done in 1.50521 secs using 399.2% CPU
Optimizing NNI: done in 2.27048 secs using 398.4% CPU
Optimizing NNI: done in 1.28188 secs using 399.2% CPU
Optimizing NNI: done in 2.29022 secs using 398% CPU
Optimizing NNI: done in 1.43453 secs using 399.4% CPU
Optimizing NNI: done in 1.20905 secs using 399.2% CPU
Iteration 20 / LogL: -58961.114 / Time: 0h:0m:58s
Finish initializing candidate tree set (20)
Current best tree score: -58857.821 / CPU time: 48.422
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.56761 secs using 398.1% CPU
Iteration 100 / LogL: -106070.286 / Time: 0h:6m:7s (0h:4m:27s left)
Optimizing NNI: done in 6.0468 secs using 598.4% CPU
Optimizing NNI: done in 1.51399 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.83471 secs using 398.6% CPU
BETTER TREE FOUND at iteration 21: -58843.526
Optimizing NNI: done in 1.34743 secs using 399% CPU
Optimizing NNI: done in 2.26808 secs using 398.5% CPU
Optimizing NNI: done in 1.79725 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -58837.397
Optimizing NNI: done in 6.45567 secs using 597.7% CPU
Iteration 220 / LogL: -189558.977 / Time: 0h:20m:7s (0h:0m:-6s left)
TREE SEARCH COMPLETED AFTER 220 ITERATIONS / Time: 0h:20m:7s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -189530.030
Optimizing NNI: done in 2.81952 secs using 397.8% CPU
Optimal log-likelihood: -189530.028
Site proportion and rates:  (0.013,0.093) (0.077,0.233) (0.145,0.386) (0.185,0.547) (0.154,0.762) (0.153,1.048) (0.171,1.615) (0.102,2.638)
Parameters optimization took 1 rounds (0.609 sec)
BEST SCORE FOUND : -189530.028
Total tree length: 151.590

Total number of iterations: 220
CPU time used for tree search: 6883.541 sec (1h:54m:43s)
Wall-clock time used for tree search: 1176.661 sec (0h:19m:36s)
Total CPU time used: 7072.375 sec (1h:57m:52s)
Total wall-clock time used: 1208.374 sec (0h:20m:8s)

===> START BOOTSTRAP REPLICATE NUMBER 12

Creating bootstrap alignment (seed: 70475)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.312 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -193783.541
Optimizing NNI: done in 1.29779 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.02111 secs using 398.5% CPU
BETTER TREE FOUND at iteration 24: -58807.051
Optimizing NNI: done in 1.38046 secs using 398.8% CPU
2. Current log-likelihood: -191458.101
Optimizing NNI: done in 2.53598 secs using 398.3% CPU
Optimizing NNI: done in 1.5005 secs using 399.4% CPU
Optimizing NNI: done in 1.29777 secs using 398.9% CPU
Optimizing NNI: done in 2.0686 secs using 398.6% CPU
3. Current log-likelihood: -191396.436
Optimizing NNI: done in 1.62414 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -58799.075
Optimizing NNI: done in 2.78352 secs using 398.5% CPU
4. Current log-likelihood: -191335.770
Optimizing NNI: done in 1.16727 secs using 399.2% CPU
Optimizing NNI: done in 1.59037 secs using 398.9% CPU
Iteration 30 / LogL: -58842.871 / Time: 0h:1m:17s (0h:4m:22s left)
Optimizing NNI: done in 2.53567 secs using 398.5% CPU
5. Current log-likelihood: -191334.157
Optimizing NNI: done in 1.59322 secs using 398.7% CPU
Optimizing NNI: done in 2.20005 secs using 398.2% CPU
Optimizing NNI: done in 1.35267 secs using 398.1% CPU
6. Current log-likelihood: -191333.742
Optimizing NNI: done in 2.08316 secs using 398.1% CPU
Iteration 110 / LogL: -106231.745 / Time: 0h:6m:30s (0h:3m:42s left)
Optimizing NNI: done in 1.90294 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
7. Current log-likelihood: -191333.444
BETTER TREE FOUND at iteration 33: -58794.777
Optimizing NNI: done in 2.69707 secs using 397.9% CPU
Optimizing NNI: done in 1.48673 secs using 399% CPU
8. Current log-likelihood: -191333.257
Optimizing NNI: done in 1.74269 secs using 398.9% CPU
Optimizing NNI: done in 2.35329 secs using 398.5% CPU
9. Current log-likelihood: -191333.142
Optimizing NNI: done in 1.63767 secs using 399.2% CPU
Optimizing NNI: done in 2.20185 secs using 398.5% CPU
Optimizing NNI: done in 1.47718 secs using 399% CPU
Optimal log-likelihood: -191333.074
Site proportion and rates:  (0.011,0.104) (0.062,0.246) (0.089,0.379) (0.154,0.505) (0.231,0.719) (0.242,1.036) (0.119,1.683) (0.091,2.805)
Parameters optimization took 9 rounds (24.383 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.78801 secs using 398.9% CPU
Optimizing NNI: done in 1.29618 secs using 399.4% CPU
Optimizing NNI: done in 1.16261 secs using 398.4% CPU
Optimizing NNI: done in 2.64689 secs using 399% CPU
Optimizing NNI: done in 1.76755 secs using 399.3% CPU
Iteration 40 / LogL: -58805.110 / Time: 0h:1m:34s (0h:3m:46s left)
Optimizing NNI: done in 1.55223 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.35624 secs using 398.2% CPU
BETTER TREE FOUND at iteration 41: -58790.472
Optimizing NNI: done in 2.23496 secs using 398.4% CPU
Optimizing NNI: done in 1.76892 secs using 398.7% CPU
Optimizing NNI: done in 1.27163 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
Calculating distance matrix: done in 10.0028 secs using 599.9% CPU
Computing ML distances took 10.003378 sec (of wall-clock time) 60.005924 sec (of CPU time)
Optimizing NNI: done in 2.16111 secs using 398.3% CPU
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00119281 secs using 425% CPU
Constructing RapidNJ tree: done in 0.0221632 secs using 680.3% CPU
Computing RapidNJ tree took 0.023442 sec (of wall-clock time) 0.157485 sec (of CPU time)
BETTER TREE FOUND at iteration 43: -58789.708
Log-likelihood of RapidNJ tree: -196355.992
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.60269 secs using 398.6% CPU
Optimizing NNI: done in 2.25636 secs using 398.6% CPU
Optimizing NNI: done in 1.92507 secs using 398.6% CPU
Iteration 120 / LogL: -106044.069 / Time: 0h:6m:53s (0h:3m:0s left)
Optimizing NNI: done in 2.18177 secs using 398.9% CPU
Optimizing NNI: done in 2.04666 secs using 398.3% CPU
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Optimizing NNI: done in 1.47946 secs using 399.2% CPU
Iteration 50 / LogL: -58813.002 / Time: 0h:1m:54s (0h:3m:37s left)
Optimizing NNI: done in 1.56821 secs using 398.5% CPU
Optimizing NNI: done in 2.78689 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.09186 secs using 398.5% CPU
BETTER TREE FOUND at iteration 124: -106035.868
Optimizing NNI: done in 1.84896 secs using 398.5% CPU
Optimizing NNI: done in 2.57042 secs using 398.2% CPU
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Optimizing NNI: done in 1.75091 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.10409 secs using 398.6% CPU
BETTER TREE FOUND at iteration 56: -58788.872
Optimizing NNI: done in 1.74059 secs using 399.1% CPU
Optimizing NNI: done in 3.02668 secs using 398.5% CPU
Optimizing NNI: done in 2.17638 secs using 399% CPU
29.359 second
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Optimizing NNI: done in 1.61162 secs using 398% CPU
Optimizing NNI: done in 1.41825 secs using 398.8% CPU
Iteration 60 / LogL: -58792.471 / Time: 0h:2m:14s (0h:3m:38s left)
Optimizing NNI: done in 2.58527 secs using 398.4% CPU
Iteration 130 / LogL: -106065.661 / Time: 0h:7m:23s (0h:5m:22s left)
Optimizing NNI: done in 1.2033 secs using 399.2% CPU
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Optimizing NNI: done in 2.08222 secs using 398.4% CPU
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Optimizing NNI: done in 1.48675 secs using 399.2% CPU
Computing log-likelihood of 98 initial trees ... 16.035 seconds
Current best score: -191333.074

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.46098 secs using 398.6% CPU
Iteration 70 / LogL: -58843.125 / Time: 0h:2m:28s (0h:3m:4s left)
Optimizing NNI: done in 1.95085 secs using 398.4% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.2863 secs using 399.6% CPU
Optimizing NNI: done in 2.30852 secs using 398.3% CPU
Optimizing NNI: done in 1.26083 secs using 398.5% CPU
Optimizing NNI: done in 1.2094 secs using 399.1% CPU
BETTER TREE FOUND at iteration 1: -190831.750
Optimizing NNI: done in 2.36261 secs using 398.5% CPU
Optimizing NNI: done in 1.41387 secs using 398.7% CPU
Optimizing NNI: done in 2.26637 secs using 398.5% CPU
Iteration 140 / LogL: -106044.157 / Time: 0h:7m:45s (0h:4m:41s left)
Optimizing NNI: done in 1.37231 secs using 398.8% CPU
Optimizing NNI: done in 3.73568 secs using 598.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.57185 secs using 399.2% CPU
Optimizing NNI: done in 2.41187 secs using 398.1% CPU
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Optimizing NNI: done in 1.49658 secs using 399.2% CPU
Iteration 80 / LogL: -58819.642 / Time: 0h:2m:42s (0h:2m:35s left)
BETTER TREE FOUND at iteration 2: -190803.997
Optimizing NNI: done in 1.19945 secs using 398.9% CPU
Optimizing NNI: done in 2.41884 secs using 398.2% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.44264 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 84: -58788.596
Optimizing NNI: done in 1.12662 secs using 399.6% CPU
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Optimizing NNI: done in 1.26374 secs using 398.9% CPU
BETTER TREE FOUND at iteration 3: -190788.858
Optimizing NNI: done in 1.34293 secs using 398.8% CPU
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Iteration 90 / LogL: -58790.802 / Time: 0h:2m:56s (0h:3m:6s left)
Optimizing NNI: done in 3.89002 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.29847 secs using 398.7% CPU
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Iteration 150 / LogL: -106092.318 / Time: 0h:8m:8s (0h:4m:2s left)
Optimizing NNI: done in 1.76278 secs using 399% CPU
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BETTER TREE FOUND at iteration 4: -190725.582
Optimizing NNI: done in 1.55358 secs using 398.4% CPU
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Iteration 100 / LogL: -58812.988 / Time: 0h:3m:11s (0h:2m:42s left)
Optimizing NNI: done in 2.57609 secs using 398.5% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 107: -58786.937
Optimizing NNI: done in 3.80889 secs using 596.7% CPU
Optimizing NNI: done in 2.03348 secs using 397.9% CPU
Iteration 160 / LogL: -106062.913 / Time: 0h:8m:30s (0h:3m:25s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.52078 secs using 399% CPU
Iteration 110 / LogL: -58788.653 / Time: 0h:3m:25s (0h:3m:3s left)
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BETTER TREE FOUND at iteration 10: -190721.945
Iteration 10 / LogL: -190721.945 / Time: 0h:2m:22s
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BETTER TREE FOUND at iteration 115: -58786.935
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Iteration 120 / LogL: -58793.677 / Time: 0h:3m:40s (0h:2m:56s left)
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Iteration 170 / LogL: -106199.579 / Time: 0h:8m:53s (0h:2m:50s left)
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Iteration 130 / LogL: -58786.944 / Time: 0h:3m:55s (0h:2m:34s left)
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BETTER TREE FOUND at iteration 132: -58786.935
Optimizing NNI: done in 1.49757 secs using 398.7% CPU
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Iteration 180 / LogL: -106060.225 / Time: 0h:9m:14s (0h:2m:16s left)
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Optimizing NNI: done in 4.10705 secs using 596.7% CPU
Iteration 20 / LogL: -190828.855 / Time: 0h:3m:2s
Finish initializing candidate tree set (20)
Current best tree score: -190721.945 / CPU time: 146.325
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.45976 secs using 399.3% CPU
Iteration 140 / LogL: -58792.369 / Time: 0h:4m:9s (0h:2m:45s left)
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Iteration 150 / LogL: -58798.389 / Time: 0h:4m:24s (0h:2m:25s left)
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Iteration 190 / LogL: -106037.874 / Time: 0h:9m:36s (0h:1m:43s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.51789 secs using 399% CPU
Optimizing NNI: done in 1.34062 secs using 398.8% CPU
BETTER TREE FOUND at iteration 194: -106033.432
Optimizing NNI: done in 1.62418 secs using 398.1% CPU
Iteration 160 / LogL: -58819.385 / Time: 0h:4m:39s (0h:2m:6s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.89962 secs using 398.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 165: -58786.349
Optimizing NNI: done in 2.39021 secs using 398.1% CPU
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Iteration 200 / LogL: -106125.221 / Time: 0h:10m:0s (0h:4m:43s left)
BETTER TREE FOUND at iteration 29: -190713.310
Optimizing NNI: done in 1.53305 secs using 398.8% CPU
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Iteration 170 / LogL: -58790.243 / Time: 0h:4m:55s (0h:2m:46s left)
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Iteration 30 / LogL: -190900.979 / Time: 0h:3m:50s (0h:13m:7s left)
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Iteration 180 / LogL: -58796.783 / Time: 0h:5m:9s (0h:2m:27s left)
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Iteration 210 / LogL: -106042.108 / Time: 0h:10m:22s (0h:4m:10s left)
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Iteration 190 / LogL: -58786.504 / Time: 0h:5m:24s (0h:2m:8s left)
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Iteration 220 / LogL: -106059.073 / Time: 0h:10m:43s (0h:3m:37s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 199: -58785.919
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BETTER TREE FOUND at iteration 39: -190707.787
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 200: -58785.784
Iteration 200 / LogL: -58785.784 / Time: 0h:5m:40s (0h:2m:50s left)
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Iteration 40 / LogL: -190766.976 / Time: 0h:4m:37s (0h:11m:44s left)
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BETTER TREE FOUND at iteration 207: -58785.780
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Iteration 210 / LogL: -58787.948 / Time: 0h:5m:54s (0h:2m:44s left)
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Iteration 230 / LogL: -106063.832 / Time: 0h:11m:7s (0h:3m:6s left)
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Iteration 220 / LogL: -58791.143 / Time: 0h:6m:9s (0h:2m:26s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 46: -190705.639
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Iteration 240 / LogL: -106045.834 / Time: 0h:11m:29s (0h:2m:35s left)
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BETTER TREE FOUND at iteration 47: -190704.436
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Iteration 230 / LogL: -58785.899 / Time: 0h:6m:25s (0h:2m:9s left)
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Optimizing NNI: done in 1.40083 secs using 399% CPU
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BETTER TREE FOUND at iteration 49: -190680.848
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Iteration 240 / LogL: -58785.782 / Time: 0h:6m:39s (0h:1m:52s left)
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Iteration 50 / LogL: -190752.923 / Time: 0h:5m:33s (0h:11m:13s left)
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Iteration 250 / LogL: -106170.405 / Time: 0h:11m:51s (0h:2m:5s left)
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BETTER TREE FOUND at iteration 247: -58785.779
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Iteration 250 / LogL: -58803.699 / Time: 0h:6m:55s (0h:2m:41s left)
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Iteration 260 / LogL: -106053.183 / Time: 0h:12m:13s (0h:1m:36s left)
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Iteration 260 / LogL: -58798.757 / Time: 0h:7m:11s (0h:2m:24s left)
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Iteration 280 / LogL: -106047.697 / Time: 0h:12m:59s (0h:4m:2s left)
BETTER TREE FOUND at iteration 66: -190668.966
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TREE SEARCH COMPLETED AFTER 348 ITERATIONS / Time: 0h:9m:19s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58785.779
Optimal log-likelihood: -58785.771
Site proportion and rates:  (0.102,0.054) (0.096,0.174) (0.160,0.347) (0.156,0.554) (0.189,0.868) (0.140,1.451) (0.114,2.262) (0.043,4.911)
Parameters optimization took 1 rounds (0.419 sec)
BEST SCORE FOUND : -58785.771
Total tree length: 46.291

Total number of iterations: 348
CPU time used for tree search: 2178.219 sec (0h:36m:18s)
Wall-clock time used for tree search: 549.785 sec (0h:9m:9s)
Total CPU time used: 2219.139 sec (0h:36m:59s)
Total wall-clock time used: 560.018 sec (0h:9m:20s)

===> START BOOTSTRAP REPLICATE NUMBER 44

Creating bootstrap alignment (seed: 67506)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.042 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61015.155
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Iteration 320 / LogL: -106068.159 / Time: 0h:14m:28s (0h:2m:7s left)
2. Current log-likelihood: -60448.669
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3. Current log-likelihood: -60443.625
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4. Current log-likelihood: -60439.921
5. Current log-likelihood: -60437.420
6. Current log-likelihood: -60436.182
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7. Current log-likelihood: -60435.676
8. Current log-likelihood: -60435.487
Optimizing NNI: done in 1.95531 secs using 397.9% CPU
Optimal log-likelihood: -60435.386
Site proportion and rates:  (0.117,0.059) (0.120,0.175) (0.076,0.402) (0.063,0.418) (0.222,0.685) (0.161,1.191) (0.169,2.079) (0.072,3.058)
Parameters optimization took 8 rounds (6.784 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.07884 secs using 399.7% CPU
Computing ML distances took 1.079033 sec (of wall-clock time) 4.312412 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000399113 secs using 420.7% CPU
Constructing RapidNJ tree: done in 0.00440598 secs using 342.9% CPU
Computing RapidNJ tree took 0.004863 sec (of wall-clock time) 0.017551 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60435.434
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.04968 secs using 398.2% CPU
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5.010 second
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Computing log-likelihood of 98 initial trees ... 5.236 seconds
Current best score: -60372.272

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 90 / LogL: -190659.245 / Time: 0h:8m:34s (0h:7m:42s left)
BETTER TREE FOUND at iteration 1: -60163.175
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Iteration 330 / LogL: -106179.856 / Time: 0h:14m:50s (0h:1m:40s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -60115.342
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Iteration 10 / LogL: -60150.297 / Time: 0h:0m:37s
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Iteration 20 / LogL: -60138.454 / Time: 0h:0m:49s
Finish initializing candidate tree set (20)
Current best tree score: -60115.342 / CPU time: 41.346
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Iteration 360 / LogL: -106109.147 / Time: 0h:15m:54s (0h:0m:18s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.84316 secs using 398.4% CPU
BETTER TREE FOUND at iteration 50: -60098.515
Iteration 50 / LogL: -60098.515 / Time: 0h:1m:35s (0h:3m:14s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 51: -60098.208
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Optimizing NNI: done in 2.13879 secs using 398.5% CPU
TREE SEARCH COMPLETED AFTER 368 ITERATIONS / Time: 0h:16m:12s

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|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106032.878
Optimizing NNI: done in 3.9216 secs using 597.7% CPU
2. Current log-likelihood: -106032.841
Optimizing NNI: done in 1.74639 secs using 398.6% CPU
3. Current log-likelihood: -106032.794
4. Current log-likelihood: -106032.754
Optimizing NNI: done in 1.37468 secs using 399% CPU
5. Current log-likelihood: -106032.719
Optimizing NNI: done in 1.30454 secs using 398.9% CPU
Optimizing NNI: done in 3.96401 secs using 596.9% CPU
Iteration 110 / LogL: -190752.435 / Time: 0h:10m:2s (0h:8m:11s left)
6. Current log-likelihood: -106032.688
Optimizing NNI: done in 1.11822 secs using 399.3% CPU
Iteration 60 / LogL: -60107.309 / Time: 0h:1m:49s (0h:2m:48s left)
7. Current log-likelihood: -106032.671
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8. Current log-likelihood: -106032.646
9. Current log-likelihood: -106032.633
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10. Current log-likelihood: -106032.620
11. Current log-likelihood: -106032.608
Optimizing NNI: done in 1.09048 secs using 399% CPU
Optimizing NNI: done in 4.09544 secs using 597.6% CPU
12. Current log-likelihood: -106032.597
Optimal log-likelihood: -106032.583
Proportion of invariable sites: 0.026
Site proportion and rates:  (0.082,0.023) (0.065,0.076) (0.080,0.166) (0.096,0.286) (0.108,0.432) (0.101,0.651) (0.162,1.018) (0.211,1.789) (0.070,4.250)
Parameters optimization took 12 rounds (9.940 sec)
BEST SCORE FOUND : -106032.583
Total tree length: 179.914

Total number of iterations: 368
CPU time used for tree search: 3731.028 sec (1h:2m:11s)
Wall-clock time used for tree search: 944.657 sec (0h:15m:44s)
Total CPU time used: 3880.972 sec (1h:4m:40s)
Total wall-clock time used: 982.270 sec (0h:16m:22s)

===> START BOOTSTRAP REPLICATE NUMBER 10

Creating bootstrap alignment (seed: 68192)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.088 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.23197 secs using 399.3% CPU
1. Initial log-likelihood: -110721.822
Optimizing NNI: done in 1.16772 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
2. Current log-likelihood: -108395.035
BETTER TREE FOUND at iteration 65: -60095.401
Optimizing NNI: done in 4.33128 secs using 597.3% CPU
3. Current log-likelihood: -108284.234
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Estimate model parameters (epsilon = 0.100)
4. Current log-likelihood: -108278.491
BETTER TREE FOUND at iteration 66: -60094.718
Optimizing NNI: done in 1.22669 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
5. Current log-likelihood: -108278.216
Optimizing NNI: done in 4.1892 secs using 597.5% CPU
BETTER TREE FOUND at iteration 67: -60091.160
Optimal log-likelihood: -108278.176
Proportion of invariable sites: 0.024
Site proportion and rates:  (0.109,0.042) (0.080,0.128) (0.082,0.218) (0.128,0.356) (0.083,0.534) (0.075,0.804) (0.160,1.182) (0.182,1.798) (0.078,3.854)
Parameters optimization took 5 rounds (8.116 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 70 / LogL: -60106.226 / Time: 0h:2m:6s (0h:2m:57s left)
Calculating distance matrix: done in 4.708 secs using 399.9% CPU
Computing ML distances took 4.708424 sec (of wall-clock time) 18.829492 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000802994 secs using 422.3% CPU
Constructing RapidNJ tree: done in 0.00876498 secs using 361.3% CPU
Computing RapidNJ tree took 0.009626 sec (of wall-clock time) 0.036761 sec (of CPU time)
Optimizing NNI: done in 1.12753 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 71: -60085.579
Log-likelihood of RapidNJ tree: -108504.853
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.4633 secs using 399% CPU
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11.145 second
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Iteration 80 / LogL: -60088.714 / Time: 0h:2m:20s (0h:2m:41s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 85: -60083.034
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Optimizing NNI: done in 1.22577 secs using 399.5% CPU
Computing log-likelihood of 98 initial trees ... 10.000 seconds
Current best score: -108278.176

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 120 / LogL: -190674.274 / Time: 0h:10m:46s (0h:7m:8s left)
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BETTER TREE FOUND at iteration 1: -107765.890
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Iteration 90 / LogL: -60091.900 / Time: 0h:2m:34s (0h:2m:45s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 93: -60081.750
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 98: -60080.665
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Iteration 100 / LogL: -60082.059 / Time: 0h:2m:49s (0h:2m:47s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 101: -60080.562
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Estimate model parameters (epsilon = 0.100)
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Iteration 120 / LogL: -60080.608 / Time: 0h:3m:17s (0h:2m:14s left)
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Iteration 130 / LogL: -190708.407 / Time: 0h:11m:31s (0h:8m:29s left)
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BETTER TREE FOUND at iteration 130: -60080.561
Iteration 130 / LogL: -60080.561 / Time: 0h:3m:31s (0h:2m:44s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 131: -60078.885
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Iteration 140 / LogL: -60136.169 / Time: 0h:3m:46s (0h:2m:28s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 146: -60075.286
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 149: -60074.962
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Iteration 10 / LogL: -107713.835 / Time: 0h:2m:13s
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Iteration 20 / LogL: -107679.498 / Time: 0h:2m:44s
Finish initializing candidate tree set (20)
Current best tree score: -107624.705 / CPU time: 150.638
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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BETTER TREE FOUND at iteration 23: -107602.329
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 192: -60073.155
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 41: -107591.596
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BETTER TREE FOUND at iteration 50: -107575.624
Iteration 50 / LogL: -107575.624 / Time: 0h:4m:17s (0h:8m:44s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 260 / LogL: -60075.660 / Time: 0h:6m:29s (0h:0m:48s left)
BETTER TREE FOUND at iteration 57: -107571.772
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 179: -190639.227
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Iteration 180 / LogL: -190676.169 / Time: 0h:15m:8s (0h:8m:22s left)
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Iteration 280 / LogL: -60082.882 / Time: 0h:6m:56s (0h:0m:17s left)
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Iteration 290 / LogL: -60073.553 / Time: 0h:7m:9s (0h:0m:2s left)
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TREE SEARCH COMPLETED AFTER 293 ITERATIONS / Time: 0h:7m:14s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60073.155
Optimal log-likelihood: -60073.145
Site proportion and rates:  (0.114,0.058) (0.121,0.172) (0.086,0.420) (0.072,0.420) (0.236,0.728) (0.144,1.278) (0.174,2.193) (0.051,3.261)
Parameters optimization took 1 rounds (0.770 sec)
BEST SCORE FOUND : -60073.145
Total tree length: 42.636

Total number of iterations: 293
CPU time used for tree search: 1684.780 sec (0h:28m:4s)
Wall-clock time used for tree search: 426.067 sec (0h:7m:6s)
Total CPU time used: 1720.675 sec (0h:28m:40s)
Total wall-clock time used: 435.043 sec (0h:7m:15s)

===> START BOOTSTRAP REPLICATE NUMBER 45

Creating bootstrap alignment (seed: 67507)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.058 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58099.223
Optimizing NNI: done in 2.64675 secs using 398% CPU
Optimizing NNI: done in 4.29539 secs using 598% CPU
2. Current log-likelihood: -57560.005
3. Current log-likelihood: -57540.024
Optimizing NNI: done in 2.38668 secs using 398.7% CPU
4. Current log-likelihood: -57533.115
5. Current log-likelihood: -57530.301
6. Current log-likelihood: -57528.867
Optimizing NNI: done in 3.73306 secs using 597.8% CPU
Optimizing NNI: done in 2.33412 secs using 398.4% CPU
7. Current log-likelihood: -57528.059
8. Current log-likelihood: -57527.043
9. Current log-likelihood: -57526.526
Optimizing NNI: done in 2.58447 secs using 398.5% CPU
Optimal log-likelihood: -57526.481
Site proportion and rates:  (0.098,0.060) (0.141,0.202) (0.123,0.319) (0.084,0.511) (0.214,0.774) (0.144,1.252) (0.175,2.352) (0.022,5.753)
Parameters optimization took 9 rounds (7.499 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09434 secs using 399.7% CPU
Computing ML distances took 1.094515 sec (of wall-clock time) 4.374522 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000365019 secs using 422.4% CPU
Constructing RapidNJ tree: done in 0.00449586 secs using 346.9% CPU
Computing RapidNJ tree took 0.004925 sec (of wall-clock time) 0.018775 sec (of CPU time)
Optimizing NNI: done in 4.46604 secs using 597.1% CPU
Log-likelihood of RapidNJ tree: -57513.599
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.46638 secs using 398.6% CPU
Iteration 80 / LogL: -107579.401 / Time: 0h:5m:31s (0h:5m:22s left)
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5.144 second
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Computing log-likelihood of 98 initial trees ... 5.196 seconds
Current best score: -57430.308

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 190 / LogL: -190748.367 / Time: 0h:15m:51s (0h:7m:27s left)
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BETTER TREE FOUND at iteration 1: -57216.208
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Iteration 90 / LogL: -107579.907 / Time: 0h:5m:55s (0h:4m:27s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 7: -57206.267
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Iteration 10 / LogL: -57261.732 / Time: 0h:0m:42s
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Iteration 20 / LogL: -57308.623 / Time: 0h:0m:55s
Finish initializing candidate tree set (20)
Current best tree score: -57206.267 / CPU time: 46.558
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 100 / LogL: -107574.115 / Time: 0h:6m:19s (0h:3m:38s left)
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Iteration 200 / LogL: -190655.302 / Time: 0h:16m:32s (0h:6m:33s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 27: -57199.064
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Iteration 30 / LogL: -57202.768 / Time: 0h:1m:11s (0h:3m:58s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -57194.241
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Iteration 40 / LogL: -57211.976 / Time: 0h:1m:27s (0h:3m:39s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 41: -57191.092
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -57185.148
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 43: -57184.582
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BETTER TREE FOUND at iteration 47: -57179.484
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Iteration 210 / LogL: -190652.243 / Time: 0h:17m:15s (0h:5m:41s left)
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Iteration 120 / LogL: -107597.075 / Time: 0h:7m:8s (0h:2m:13s left)
BETTER TREE FOUND at iteration 49: -57177.453
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BETTER TREE FOUND at iteration 124: -107570.962
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BETTER TREE FOUND at iteration 67: -57176.052
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Iteration 70 / LogL: -57178.579 / Time: 0h:2m:19s (0h:3m:15s left)
BETTER TREE FOUND at iteration 217: -190636.514
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BETTER TREE FOUND at iteration 134: -107567.559
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Iteration 220 / LogL: -190686.647 / Time: 0h:18m:2s (0h:7m:59s left)
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Iteration 140 / LogL: -107578.512 / Time: 0h:8m:7s (0h:5m:29s left)
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Iteration 160 / LogL: -107574.162 / Time: 0h:8m:57s (0h:4m:10s left)
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Iteration 130 / LogL: -57177.356 / Time: 0h:3m:47s (0h:1m:5s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 173: -107565.579
BETTER TREE FOUND at iteration 146: -57175.681
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Iteration 150 / LogL: -57176.618 / Time: 0h:4m:16s (0h:2m:44s left)
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Iteration 180 / LogL: -107573.878 / Time: 0h:9m:49s (0h:5m:6s left)
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Iteration 160 / LogL: -57189.399 / Time: 0h:4m:30s (0h:2m:26s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 162: -57175.512
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 164: -57174.977
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BETTER TREE FOUND at iteration 249: -190636.461
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UPDATE BEST LOG-LIKELIHOOD: -57174.976
Iteration 170 / LogL: -57174.976 / Time: 0h:4m:46s (0h:2m:39s left)
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Iteration 190 / LogL: -57176.832 / Time: 0h:5m:14s (0h:2m:2s left)
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TREE SEARCH COMPLETED AFTER 265 ITERATIONS / Time: 0h:7m:9s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57174.976
Optimal log-likelihood: -57174.975
Site proportion and rates:  (0.101,0.063) (0.180,0.220) (0.127,0.402) (0.192,0.696) (0.162,1.027) (0.140,1.899) (0.079,2.809) (0.019,5.956)
Parameters optimization took 1 rounds (0.316 sec)
BEST SCORE FOUND : -57174.975
Total tree length: 42.531

Total number of iterations: 265
CPU time used for tree search: 1661.328 sec (0h:27m:41s)
Wall-clock time used for tree search: 420.265 sec (0h:7m:0s)
Total CPU time used: 1699.033 sec (0h:28m:19s)
Total wall-clock time used: 429.697 sec (0h:7m:9s)

===> START BOOTSTRAP REPLICATE NUMBER 46

Creating bootstrap alignment (seed: 67508)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.052 seconds

NOTE: 64 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59963.536
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2. Current log-likelihood: -59340.824
3. Current log-likelihood: -59314.590
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4. Current log-likelihood: -59312.426
5. Current log-likelihood: -59312.095
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Optimizing NNI: done in 2.20087 secs using 398.1% CPU
6. Current log-likelihood: -59311.989
Optimal log-likelihood: -59311.924
Site proportion and rates:  (0.095,0.072) (0.130,0.183) (0.089,0.386) (0.076,0.507) (0.237,0.742) (0.147,1.230) (0.168,2.005) (0.058,3.527)
Parameters optimization took 6 rounds (6.454 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.06279 secs using 399.9% CPU
Computing ML distances took 1.063015 sec (of wall-clock time) 4.250837 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000444889 secs using 417.4% CPU
Constructing RapidNJ tree: done in 0.0100129 secs using 396.9% CPU
Computing RapidNJ tree took 0.010520 sec (of wall-clock time) 0.041973 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59348.412
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.24709 secs using 398.5% CPU
Iteration 250 / LogL: -107574.271 / Time: 0h:12m:40s (0h:1m:10s left)
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5.060 second
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Computing log-likelihood of 98 initial trees ... 6.926 seconds
Current best score: -59176.663

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -58965.601
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 288: -190626.389
BETTER TREE FOUND at iteration 256: -107565.266
BETTER TREE FOUND at iteration 2: -58944.902
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 270 / LogL: -107597.369 / Time: 0h:13m:36s (0h:4m:20s left)
BETTER TREE FOUND at iteration 6: -58897.398
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Iteration 10 / LogL: -58966.305 / Time: 0h:1m:15s
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Iteration 20 / LogL: -59015.485 / Time: 0h:1m:39s
Finish initializing candidate tree set (20)
Current best tree score: -58897.398 / CPU time: 90.774
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -58872.882
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 40: -58870.132
Iteration 40 / LogL: -58870.132 / Time: 0h:2m:30s (0h:6m:25s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 50: -58869.102
Iteration 50 / LogL: -58869.102 / Time: 0h:2m:52s (0h:5m:51s left)
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BETTER TREE FOUND at iteration 314: -107562.853
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BETTER TREE FOUND at iteration 54: -58868.861
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Iteration 320 / LogL: -107567.907 / Time: 0h:15m:43s (0h:4m:37s left)
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BETTER TREE FOUND at iteration 59: -58867.483
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Iteration 60 / LogL: -58870.691 / Time: 0h:3m:16s (0h:5m:28s left)
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Iteration 330 / LogL: -107564.169 / Time: 0h:16m:8s (0h:4m:7s left)
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Iteration 70 / LogL: -58899.302 / Time: 0h:3m:39s (0h:4m:43s left)
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Iteration 320 / LogL: -190667.240 / Time: 0h:26m:22s (0h:5m:37s left)
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BETTER TREE FOUND at iteration 336: -107560.716
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BETTER TREE FOUND at iteration 79: -58867.261
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BETTER TREE FOUND at iteration 80: -58865.080
Iteration 80 / LogL: -58865.080 / Time: 0h:4m:2s (0h:5m:7s left)
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BETTER TREE FOUND at iteration 89: -58862.621
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Iteration 90 / LogL: -58909.476 / Time: 0h:4m:20s (0h:4m:49s left)
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Iteration 350 / LogL: -107588.890 / Time: 0h:16m:59s (0h:4m:11s left)
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Iteration 100 / LogL: -58873.056 / Time: 0h:4m:35s (0h:4m:7s left)
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Iteration 330 / LogL: -190650.715 / Time: 0h:27m:17s (0h:4m:48s left)
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BETTER TREE FOUND at iteration 103: -58862.348
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Iteration 360 / LogL: -107565.900 / Time: 0h:17m:23s (0h:3m:40s left)
BETTER TREE FOUND at iteration 110: -58861.993
Iteration 110 / LogL: -58861.993 / Time: 0h:4m:53s (0h:4m:28s left)
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BETTER TREE FOUND at iteration 120: -58860.304
Iteration 120 / LogL: -58860.304 / Time: 0h:5m:10s (0h:4m:21s left)
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Iteration 370 / LogL: -107563.612 / Time: 0h:17m:47s (0h:3m:10s left)
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Iteration 340 / LogL: -190682.479 / Time: 0h:28m:0s (0h:3m:57s left)
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Iteration 130 / LogL: -58869.981 / Time: 0h:5m:26s (0h:3m:47s left)
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Iteration 380 / LogL: -107587.000 / Time: 0h:18m:12s (0h:2m:41s left)
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Iteration 150 / LogL: -58860.549 / Time: 0h:5m:59s (0h:2m:48s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 152: -58858.922
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Iteration 350 / LogL: -190714.913 / Time: 0h:28m:43s (0h:3m:7s left)
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Iteration 390 / LogL: -107572.923 / Time: 0h:18m:36s (0h:2m:12s left)
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Iteration 160 / LogL: -58870.498 / Time: 0h:6m:16s (0h:3m:37s left)
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Iteration 400 / LogL: -107618.945 / Time: 0h:19m:2s (0h:1m:43s left)
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Iteration 170 / LogL: -58867.546 / Time: 0h:6m:32s (0h:3m:10s left)
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BETTER TREE FOUND at iteration 171: -58857.941
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Iteration 360 / LogL: -190712.295 / Time: 0h:29m:24s (0h:2m:17s left)
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Iteration 180 / LogL: -58858.162 / Time: 0h:6m:49s (0h:3m:28s left)
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Iteration 410 / LogL: -107589.523 / Time: 0h:19m:27s (0h:1m:14s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 190: -58857.764
Iteration 190 / LogL: -58857.764 / Time: 0h:7m:7s (0h:3m:46s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.21846 secs using 399.5% CPU
BETTER TREE FOUND at iteration 418: -107557.414
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Iteration 200 / LogL: -58858.647 / Time: 0h:7m:23s (0h:3m:20s left)
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Iteration 420 / LogL: -107604.385 / Time: 0h:19m:54s (0h:4m:39s left)
Optimizing NNI: done in 1.53601 secs using 398.7% CPU
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Iteration 370 / LogL: -190683.112 / Time: 0h:30m:6s (0h:1m:28s left)
Optimizing NNI: done in 1.61817 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.61225 secs using 597.1% CPU
Optimizing NNI: done in 1.20205 secs using 395.2% CPU
Iteration 210 / LogL: -58858.598 / Time: 0h:7m:38s (0h:2m:55s left)
BETTER TREE FOUND at iteration 426: -107557.381
Optimizing NNI: done in 1.41168 secs using 399.1% CPU
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Iteration 430 / LogL: -107570.725 / Time: 0h:20m:18s (0h:4m:32s left)
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Iteration 220 / LogL: -58859.050 / Time: 0h:7m:54s (0h:2m:31s left)
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Optimizing NNI: done in 1.5767 secs using 398.8% CPU
BETTER TREE FOUND at iteration 227: -58857.755
Optimizing NNI: done in 1.76812 secs using 399.5% CPU
Optimizing NNI: done in 2.55246 secs using 398% CPU
Optimizing NNI: done in 4.43591 secs using 598.5% CPU
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Iteration 230 / LogL: -58861.931 / Time: 0h:8m:10s (0h:3m:27s left)
Optimizing NNI: done in 1.60641 secs using 398.9% CPU
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Iteration 440 / LogL: -107571.504 / Time: 0h:20m:43s (0h:4m:3s left)
Optimizing NNI: done in 4.42147 secs using 597.8% CPU
Iteration 380 / LogL: -190827.712 / Time: 0h:30m:50s (0h:0m:39s left)
Optimizing NNI: done in 1.7852 secs using 398.8% CPU
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Iteration 240 / LogL: -58913.649 / Time: 0h:8m:26s (0h:3m:4s left)
Optimizing NNI: done in 2.42878 secs using 398.1% CPU
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Iteration 450 / LogL: -107606.169 / Time: 0h:21m:7s (0h:3m:34s left)
Optimizing NNI: done in 1.60306 secs using 399.1% CPU
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Iteration 250 / LogL: -58869.325 / Time: 0h:8m:41s (0h:2m:41s left)
Optimizing NNI: done in 2.59345 secs using 398.3% CPU
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Optimizing NNI: done in 2.01548 secs using 398.2% CPU
Optimizing NNI: done in 4.04854 secs using 597.9% CPU
TREE SEARCH COMPLETED AFTER 389 ITERATIONS / Time: 0h:31m:29s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -190626.389
Optimizing NNI: done in 1.34007 secs using 398.9% CPU
Optimal log-likelihood: -190626.389
Site proportion and rates:  (0.012,0.102) (0.057,0.245) (0.111,0.375) (0.141,0.512) (0.229,0.725) (0.240,1.042) (0.117,1.676) (0.093,2.791)
Parameters optimization took 1 rounds (0.476 sec)
BEST SCORE FOUND : -190626.389
Total tree length: 151.663

Total number of iterations: 389
CPU time used for tree search: 10926.901 sec (3h:2m:6s)
Wall-clock time used for tree search: 1853.349 sec (0h:30m:53s)
Total CPU time used: 11146.357 sec (3h:5m:46s)
Total wall-clock time used: 1890.219 sec (0h:31m:30s)

===> START BOOTSTRAP REPLICATE NUMBER 13

Creating bootstrap alignment (seed: 70476)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.292 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -201772.816
Optimizing NNI: done in 1.8557 secs using 398.9% CPU
Optimizing NNI: done in 2.52379 secs using 398.1% CPU
2. Current log-likelihood: -199159.986
Optimizing NNI: done in 1.42586 secs using 399.1% CPU
Optimizing NNI: done in 1.12437 secs using 399.2% CPU
Optimizing NNI: done in 2.42675 secs using 398.5% CPU
3. Current log-likelihood: -199142.509
Optimizing NNI: done in 1.36235 secs using 399.1% CPU
Iteration 260 / LogL: -58858.006 / Time: 0h:8m:57s (0h:2m:18s left)
Optimizing NNI: done in 1.60806 secs using 398.9% CPU
Optimizing NNI: done in 2.6287 secs using 397.8% CPU
4. Current log-likelihood: -199132.570
Optimizing NNI: done in 1.50872 secs using 399.4% CPU
Optimizing NNI: done in 2.30701 secs using 397.9% CPU
Iteration 460 / LogL: -107562.957 / Time: 0h:21m:32s (0h:3m:5s left)
5. Current log-likelihood: -199121.645
Optimizing NNI: done in 1.7101 secs using 398.9% CPU
6. Current log-likelihood: -199111.769
Optimizing NNI: done in 1.71337 secs using 398.9% CPU
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Optimizing NNI: done in 1.66347 secs using 398.8% CPU
7. Current log-likelihood: -199099.708
Optimizing NNI: done in 2.18825 secs using 398.4% CPU
Optimizing NNI: done in 1.41678 secs using 399.1% CPU
8. Current log-likelihood: -199095.274
Optimizing NNI: done in 1.61279 secs using 398% CPU
Optimizing NNI: done in 2.98052 secs using 398.8% CPU
Optimizing NNI: done in 1.4954 secs using 399.1% CPU
9. Current log-likelihood: -199092.459
Optimizing NNI: done in 1.59344 secs using 399.2% CPU
Optimizing NNI: done in 2.71652 secs using 398.2% CPU
10. Current log-likelihood: -199091.430
Optimizing NNI: done in 1.70103 secs using 398.7% CPU
Iteration 270 / LogL: -58866.095 / Time: 0h:9m:13s (0h:1m:57s left)
11. Current log-likelihood: -199091.321
Optimizing NNI: done in 2.48456 secs using 397.9% CPU
Optimizing NNI: done in 1.48706 secs using 399.5% CPU
Optimal log-likelihood: -199091.301
Site proportion and rates:  (0.012,0.100) (0.018,0.221) (0.157,0.359) (0.265,0.595) (0.252,0.891) (0.119,1.309) (0.127,1.953) (0.050,3.039)
Parameters optimization took 11 rounds (22.833 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.41841 secs using 399.4% CPU
Optimizing NNI: done in 2.10559 secs using 398.5% CPU
Optimizing NNI: done in 1.75803 secs using 399.1% CPU
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Optimizing NNI: done in 1.6368 secs using 399.1% CPU
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Optimizing NNI: done in 3.07864 secs using 398% CPU
Optimizing NNI: done in 1.68023 secs using 399% CPU
Calculating distance matrix: done in 9.5106 secs using 599.9% CPU
Computing ML distances took 9.511190 sec (of wall-clock time) 57.055595 sec (of CPU time)
Optimizing NNI: done in 2.74076 secs using 398.2% CPU
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00133586 secs using 701% CPU
Constructing RapidNJ tree: done in 0.0231409 secs using 691.5% CPU
Computing RapidNJ tree took 0.024558 sec (of wall-clock time) 0.170489 sec (of CPU time)
Optimizing NNI: done in 1.64007 secs using 399.4% CPU
Optimizing NNI: done in 1.60752 secs using 399.2% CPU
Optimizing NNI: done in 2.38776 secs using 397.5% CPU
Iteration 470 / LogL: -107561.945 / Time: 0h:21m:57s (0h:2m:37s left)
Log-likelihood of RapidNJ tree: -203728.185
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.52717 secs using 399.3% CPU
Optimizing NNI: done in 1.58395 secs using 399.3% CPU
Iteration 280 / LogL: -58878.819 / Time: 0h:9m:29s (0h:1m:35s left)
Optimizing NNI: done in 2.76472 secs using 398.4% CPU
Optimizing NNI: done in 1.72787 secs using 399.1% CPU
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Optimizing NNI: done in 1.94936 secs using 397.9% CPU
Iteration 290 / LogL: -58859.086 / Time: 0h:9m:47s (0h:1m:15s left)
Optimizing NNI: done in 2.55943 secs using 398.3% CPU
Optimizing NNI: done in 2.24516 secs using 397.7% CPU
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Optimizing NNI: done in 2.18548 secs using 398.3% CPU
Iteration 480 / LogL: -107585.523 / Time: 0h:22m:24s (0h:2m:9s left)
Optimizing NNI: done in 2.67417 secs using 398.2% CPU
Optimizing NNI: done in 2.71492 secs using 397.9% CPU
Optimizing NNI: done in 2.15478 secs using 398.4% CPU
30.438 second
Optimizing NNI: done in 2.48957 secs using 398.4% CPU
Optimizing NNI: done in 2.09473 secs using 398.8% CPU
Optimizing NNI: done in 1.56439 secs using 399.1% CPU
Optimizing NNI: done in 2.2003 secs using 397.4% CPU
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Optimizing NNI: done in 2.43733 secs using 398.2% CPU
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Optimizing NNI: done in 1.59102 secs using 399% CPU
Optimizing NNI: done in 3.12404 secs using 398.2% CPU
Optimizing NNI: done in 1.55365 secs using 398.9% CPU
Iteration 300 / LogL: -58867.942 / Time: 0h:10m:7s (0h:0m:54s left)
Optimizing NNI: done in 1.5966 secs using 399.1% CPU
Optimizing NNI: done in 2.70637 secs using 398.3% CPU
Optimizing NNI: done in 1.67311 secs using 398.6% CPU
Optimizing NNI: done in 1.41658 secs using 399.1% CPU
Optimizing NNI: done in 2.64659 secs using 397.9% CPU
Optimizing NNI: done in 1.33565 secs using 399.4% CPU
Computing log-likelihood of 98 initial trees ... 16.555 seconds
Current best score: -199091.301

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.09025 secs using 397.9% CPU
Optimizing NNI: done in 1.31469 secs using 398.8% CPU
Optimizing NNI: done in 1.82829 secs using 399.1% CPU
Optimizing NNI: done in 2.4757 secs using 398% CPU
Optimizing NNI: done in 3.46419 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.49056 secs using 398.6% CPU
Optimizing NNI: done in 1.29097 secs using 399.2% CPU
Optimizing NNI: done in 2.38674 secs using 397.5% CPU
Iteration 490 / LogL: -107559.840 / Time: 0h:22m:50s (0h:1m:40s left)
BETTER TREE FOUND at iteration 1: -198417.934
Optimizing NNI: done in 1.72063 secs using 399.3% CPU
Optimizing NNI: done in 2.71476 secs using 397.8% CPU
Optimizing NNI: done in 1.47521 secs using 399.3% CPU
Iteration 310 / LogL: -58880.305 / Time: 0h:10m:22s (0h:0m:34s left)
Optimizing NNI: done in 1.63698 secs using 399% CPU
Optimizing NNI: done in 2.03806 secs using 398% CPU
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Optimizing NNI: done in 1.98133 secs using 398.8% CPU
Optimizing NNI: done in 6.4234 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.36285 secs using 399% CPU
Optimizing NNI: done in 2.35198 secs using 397.7% CPU
Optimizing NNI: done in 1.70485 secs using 399.4% CPU
BETTER TREE FOUND at iteration 2: -198309.662
Optimizing NNI: done in 1.81935 secs using 399.2% CPU
Optimizing NNI: done in 2.89798 secs using 398.5% CPU
Optimizing NNI: done in 1.59213 secs using 398.9% CPU
Optimizing NNI: done in 1.45068 secs using 399% CPU
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Optimizing NNI: done in 2.48276 secs using 397.9% CPU
Optimizing NNI: done in 1.55294 secs using 399.1% CPU
Optimizing NNI: done in 7.04582 secs using 596.3% CPU
Optimizing NNI: done in 1.54081 secs using 398.7% CPU
Iteration 320 / LogL: -58873.929 / Time: 0h:10m:38s (0h:0m:14s left)
Optimizing NNI: done in 2.85017 secs using 397.5% CPU
Optimizing NNI: done in 1.51126 secs using 398.9% CPU
Optimizing NNI: done in 1.54509 secs using 399% CPU
Optimizing NNI: done in 2.61956 secs using 398.2% CPU
Optimizing NNI: done in 1.46226 secs using 399.1% CPU
Optimizing NNI: done in 6.36174 secs using 597.4% CPU
Optimizing NNI: done in 1.5094 secs using 399.1% CPU
Optimizing NNI: done in 2.61121 secs using 398.4% CPU
Iteration 500 / LogL: -107561.355 / Time: 0h:23m:15s (0h:1m:12s left)
Optimizing NNI: done in 1.14041 secs using 399.3% CPU
Optimizing NNI: done in 1.11086 secs using 399.2% CPU
Optimizing NNI: done in 2.67074 secs using 397.6% CPU
Optimizing NNI: done in 1.50159 secs using 399.2% CPU
Optimizing NNI: done in 5.8457 secs using 597.1% CPU
Optimizing NNI: done in 2.04266 secs using 398% CPU
Optimizing NNI: done in 1.56398 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 328 ITERATIONS / Time: 0h:10m:49s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58857.755
2. Current log-likelihood: -58857.743
Optimal log-likelihood: -58857.740
Site proportion and rates:  (0.127,0.083) (0.119,0.203) (0.148,0.445) (0.249,0.714) (0.142,1.219) (0.149,1.929) (0.054,3.034) (0.012,8.028)
Parameters optimization took 2 rounds (0.886 sec)
BEST SCORE FOUND : -58857.740
Total tree length: 44.697

Total number of iterations: 328
CPU time used for tree search: 2541.630 sec (0h:42m:21s)
Wall-clock time used for tree search: 641.224 sec (0h:10m:41s)
Total CPU time used: 2579.197 sec (0h:42m:59s)
Total wall-clock time used: 650.631 sec (0h:10m:50s)

===> START BOOTSTRAP REPLICATE NUMBER 47

Creating bootstrap alignment (seed: 67509)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.058 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61995.221
Optimizing NNI: done in 2.12185 secs using 398.2% CPU
2. Current log-likelihood: -61424.426
3. Current log-likelihood: -61419.750
4. Current log-likelihood: -61402.159
Optimizing NNI: done in 2.40498 secs using 397.8% CPU
5. Current log-likelihood: -61379.753
Optimizing NNI: done in 5.85051 secs using 596.4% CPU
6. Current log-likelihood: -61371.613
7. Current log-likelihood: -61369.830
Optimizing NNI: done in 2.33537 secs using 397.8% CPU
8. Current log-likelihood: -61369.724
Optimal log-likelihood: -61369.681
Site proportion and rates:  (0.120,0.059) (0.068,0.169) (0.112,0.325) (0.061,0.418) (0.208,0.646) (0.190,1.067) (0.209,2.047) (0.031,4.937)
Parameters optimization took 8 rounds (6.782 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10111 secs using 400.1% CPU
Computing ML distances took 1.101294 sec (of wall-clock time) 4.405298 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00037694 secs using 414.7% CPU
Constructing RapidNJ tree: done in 0.00426292 secs using 362.7% CPU
Computing RapidNJ tree took 0.004705 sec (of wall-clock time) 0.017877 sec (of CPU time)
Optimizing NNI: done in 2.54338 secs using 398.4% CPU
Log-likelihood of RapidNJ tree: -61385.575
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.7575 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.42793 secs using 398.2% CPU
Optimizing NNI: done in 2.67814 secs using 398.4% CPU
5.101 second
Optimizing NNI: done in 2.00311 secs using 398.2% CPU
Optimizing NNI: done in 2.25069 secs using 398.2% CPU
Iteration 510 / LogL: -107792.253 / Time: 0h:23m:39s (0h:0m:44s left)
Computing log-likelihood of 98 initial trees ... 5.126 seconds
Current best score: -61240.206

Do NNI search on 20 best initial trees
BETTER TREE FOUND at iteration 7: -198296.073
Optimizing NNI: done in 2.17962 secs using 398.1% CPU
Optimizing NNI: done in 1.27758 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -61018.315
Optimizing NNI: done in 2.48968 secs using 398.2% CPU
Optimizing NNI: done in 1.12748 secs using 399.3% CPU
Optimizing NNI: done in 1.08943 secs using 398.3% CPU
Optimizing NNI: done in 2.39476 secs using 398.4% CPU
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Optimizing NNI: done in 5.63925 secs using 596.4% CPU
Optimizing NNI: done in 1.24404 secs using 398.9% CPU
Optimizing NNI: done in 2.20697 secs using 398.2% CPU
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Optimizing NNI: done in 5.68189 secs using 597.2% CPU
Optimizing NNI: done in 1.10853 secs using 399.1% CPU
Optimizing NNI: done in 2.52752 secs using 397.5% CPU
Optimizing NNI: done in 1.2139 secs using 399.7% CPU
Iteration 10 / LogL: -61100.763 / Time: 0h:0m:32s
Optimizing NNI: done in 1.13419 secs using 398.8% CPU
Optimizing NNI: done in 2.5635 secs using 398.7% CPU
Optimizing NNI: done in 1.19697 secs using 398.7% CPU
Optimizing NNI: done in 1.07943 secs using 399.3% CPU
Optimizing NNI: done in 2.24117 secs using 397.2% CPU
Optimizing NNI: done in 1.08767 secs using 399.3% CPU
Optimizing NNI: done in 6.35135 secs using 597.1% CPU
Iteration 10 / LogL: -198336.167 / Time: 0h:2m:35s
Optimizing NNI: done in 1.28042 secs using 398.7% CPU
Optimizing NNI: done in 2.33571 secs using 398.2% CPU
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Optimizing NNI: done in 1.12333 secs using 398.9% CPU
Optimizing NNI: done in 2.64961 secs using 397.8% CPU
Iteration 520 / LogL: -107557.815 / Time: 0h:24m:3s (0h:0m:16s left)
Optimizing NNI: done in 1.46384 secs using 398.8% CPU
Optimizing NNI: done in 0.991111 secs using 399.3% CPU
Optimizing NNI: done in 6.73977 secs using 597.5% CPU
Optimizing NNI: done in 1.09146 secs using 399.3% CPU
Iteration 20 / LogL: -61109.090 / Time: 0h:0m:44s
Finish initializing candidate tree set (20)
Current best tree score: -61018.315 / CPU time: 35.580
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 2.545 secs using 397.7% CPU
Optimizing NNI: done in 1.27515 secs using 398.3% CPU
Optimizing NNI: done in 2.10166 secs using 397.7% CPU
Optimizing NNI: done in 1.26969 secs using 398.7% CPU
Optimizing NNI: done in 1.41189 secs using 399% CPU
Optimizing NNI: done in 2.85031 secs using 397.7% CPU
Optimizing NNI: done in 5.37976 secs using 596.9% CPU
Optimizing NNI: done in 1.71939 secs using 399% CPU
Optimizing NNI: done in 2.16851 secs using 398% CPU
Optimizing NNI: done in 1.48391 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -61016.773
Optimizing NNI: done in 1.28437 secs using 398.8% CPU
Optimizing NNI: done in 2.46373 secs using 398.2% CPU
Optimizing NNI: done in 1.56395 secs using 399.1% CPU
Optimizing NNI: done in 2.08511 secs using 398.1% CPU
Optimizing NNI: done in 6.92881 secs using 595.7% CPU
Optimizing NNI: done in 1.42527 secs using 399.4% CPU
Optimizing NNI: done in 1.55802 secs using 399.2% CPU
Optimizing NNI: done in 2.62483 secs using 398.1% CPU
TREE SEARCH COMPLETED AFTER 527 ITERATIONS / Time: 0h:24m:20s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -107557.381
Optimizing NNI: done in 1.5524 secs using 399.1% CPU
Iteration 30 / LogL: -61038.971 / Time: 0h:0m:59s (0h:3m:15s left)
2. Current log-likelihood: -107557.369
Optimal log-likelihood: -107557.358
Proportion of invariable sites: 0.022
Site proportion and rates:  (0.064,0.027) (0.099,0.080) (0.102,0.191) (0.134,0.338) (0.089,0.524) (0.098,0.851) (0.181,1.283) (0.141,1.895) (0.070,4.222)
Parameters optimization took 2 rounds (2.435 sec)
BEST SCORE FOUND : -107557.358
Total tree length: 191.166

Total number of iterations: 527
CPU time used for tree search: 5723.653 sec (1h:35m:23s)
Wall-clock time used for tree search: 1445.764 sec (0h:24m:5s)
Total CPU time used: 5790.492 sec (1h:36m:30s)
Total wall-clock time used: 1462.503 sec (0h:24m:22s)

===> START BOOTSTRAP REPLICATE NUMBER 11

Creating bootstrap alignment (seed: 68193)...
Optimizing NNI: done in 1.49198 secs using 399.4% CPU

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.086 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 101 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104067.158
Optimizing NNI: done in 1.41018 secs using 399% CPU
Optimizing NNI: done in 6.53353 secs using 596.3% CPU
2. Current log-likelihood: -102095.882
Optimizing NNI: done in 1.24051 secs using 398.9% CPU
3. Current log-likelihood: -102017.281
Optimizing NNI: done in 1.56773 secs using 398.8% CPU
4. Current log-likelihood: -101991.787
Optimizing NNI: done in 1.23517 secs using 399% CPU
Optimizing NNI: done in 1.14894 secs using 399.3% CPU
5. Current log-likelihood: -101989.174
Optimizing NNI: done in 1.28127 secs using 398.9% CPU
6. Current log-likelihood: -101987.961
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Optimizing NNI: done in 1.49102 secs using 398.9% CPU
7. Current log-likelihood: -101987.261
Optimizing NNI: done in 1.26094 secs using 399.2% CPU
8. Current log-likelihood: -101986.788
Optimizing NNI: done in 1.62781 secs using 398.7% CPU
Iteration 40 / LogL: -61018.342 / Time: 0h:1m:13s (0h:2m:40s left)
9. Current log-likelihood: -101986.473
Optimizing NNI: done in 1.27701 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
10. Current log-likelihood: -101986.329
BETTER TREE FOUND at iteration 41: -61012.880
Optimizing NNI: done in 6.4457 secs using 597% CPU
11. Current log-likelihood: -101986.211
Optimizing NNI: done in 1.09262 secs using 398.9% CPU
Optimal log-likelihood: -101986.074
Proportion of invariable sites: 0.014
Site proportion and rates:  (0.128,0.049) (0.129,0.164) (0.022,0.259) (0.118,0.342) (0.121,0.544) (0.102,0.882) (0.133,1.386) (0.176,2.091) (0.057,3.824)
Parameters optimization took 11 rounds (17.156 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.5503 secs using 399.2% CPU
Optimizing NNI: done in 1.49556 secs using 398.6% CPU
Optimizing NNI: done in 1.39199 secs using 398.9% CPU
Optimizing NNI: done in 6.35789 secs using 597% CPU
Calculating distance matrix: done in 4.67773 secs using 399.8% CPU
Computing ML distances took 4.678123 sec (of wall-clock time) 18.704371 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000806093 secs using 141.4% CPU
Constructing RapidNJ tree: done in 0.00890803 secs using 360.5% CPU
Computing RapidNJ tree took 0.009780 sec (of wall-clock time) 0.034856 sec (of CPU time)
Optimizing NNI: done in 1.32447 secs using 398.5% CPU
Log-likelihood of RapidNJ tree: -102211.421
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.6642 secs using 399.4% CPU
Optimizing NNI: done in 1.50699 secs using 399% CPU
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Optimizing NNI: done in 1.63352 secs using 399.4% CPU
Iteration 50 / LogL: -61016.834 / Time: 0h:1m:29s (0h:2m:45s left)
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Optimizing NNI: done in 1.54082 secs using 399.5% CPU
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10.612 second
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.30582 secs using 399.1% CPU
Optimizing NNI: done in 1.61934 secs using 399% CPU
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Optimizing NNI: done in 1.5661 secs using 399.2% CPU
Computing log-likelihood of 98 initial trees ... 9.501 seconds
Current best score: -101986.074

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.56996 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 60: -61011.828
Iteration 60 / LogL: -61011.828 / Time: 0h:1m:45s (0h:2m:58s left)
Optimizing NNI: done in 1.2685 secs using 399.4% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.60441 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 62: -61011.566
Optimizing NNI: done in 1.52558 secs using 398.6% CPU
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BETTER TREE FOUND at iteration 1: -101412.352
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.60785 secs using 398.1% CPU
Iteration 70 / LogL: -61039.993 / Time: 0h:2m:0s (0h:2m:40s left)
Optimizing NNI: done in 1.43625 secs using 399.4% CPU
Optimizing NNI: done in 1.47734 secs using 398.9% CPU
BETTER TREE FOUND at iteration 2: -101376.173
BETTER TREE FOUND at iteration 19: -198266.663
Optimizing NNI: done in 1.36662 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.70145 secs using 399.4% CPU
Optimizing NNI: done in 1.79388 secs using 398.7% CPU
BETTER TREE FOUND at iteration 4: -101346.218
Optimizing NNI: done in 1.29524 secs using 398.8% CPU
Optimizing NNI: done in 1.96238 secs using 398.6% CPU
Optimizing NNI: done in 8.12302 secs using 596.9% CPU
Iteration 20 / LogL: -198370.585 / Time: 0h:4m:10s
Finish initializing candidate tree set (20)
Current best tree score: -198266.663 / CPU time: 215.260
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.34148 secs using 399.1% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.52932 secs using 399.3% CPU
Iteration 80 / LogL: -61039.696 / Time: 0h:2m:15s (0h:2m:20s left)
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BETTER TREE FOUND at iteration 6: -101324.170
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 85: -61010.212
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -198228.967
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Estimate model parameters (epsilon = 0.100)
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Iteration 90 / LogL: -61021.317 / Time: 0h:2m:30s (0h:2m:40s left)
BETTER TREE FOUND at iteration 8: -101303.675
Optimizing NNI: done in 1.29296 secs using 398.1% CPU
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Iteration 10 / LogL: -101341.101 / Time: 0h:1m:34s
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Iteration 100 / LogL: -61018.927 / Time: 0h:2m:44s (0h:2m:21s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.20439 secs using 398.9% CPU
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BETTER TREE FOUND at iteration 104: -61009.724
Optimizing NNI: done in 1.41315 secs using 399.2% CPU
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Optimizing NNI: done in 1.77232 secs using 398.8% CPU
Iteration 20 / LogL: -101496.515 / Time: 0h:1m:57s
Finish initializing candidate tree set (20)
Current best tree score: -101303.675 / CPU time: 94.013
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.50087 secs using 398.8% CPU
Iteration 110 / LogL: -61135.195 / Time: 0h:2m:59s (0h:2m:34s left)
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Iteration 30 / LogL: -198307.361 / Time: 0h:5m:6s (0h:16m:12s left)
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Iteration 120 / LogL: -61022.683 / Time: 0h:3m:13s (0h:2m:16s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 29: -101296.884
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Iteration 30 / LogL: -101345.560 / Time: 0h:2m:24s (0h:8m:14s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 132: -61008.620
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 134: -61008.412
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BETTER TREE FOUND at iteration 34: -198216.392
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Iteration 140 / LogL: -61009.537 / Time: 0h:3m:42s (0h:2m:30s left)
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Iteration 40 / LogL: -101330.612 / Time: 0h:2m:45s (0h:6m:17s left)
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Iteration 150 / LogL: -61016.768 / Time: 0h:3m:57s (0h:2m:13s left)
Optimizing NNI: done in 4.79706 secs using 596.8% CPU
Optimizing NNI: done in 1.54338 secs using 398.9% CPU
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Optimizing NNI: done in 5.41384 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.0221 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.5002 secs using 398.5% CPU
Optimizing NNI: done in 1.43042 secs using 399.1% CPU
BETTER TREE FOUND at iteration 49: -101289.086
BETTER TREE FOUND at iteration 39: -198210.287
Optimizing NNI: done in 1.43147 secs using 399.4% CPU
Optimizing NNI: done in 1.96227 secs using 398.6% CPU
Iteration 50 / LogL: -101317.990 / Time: 0h:3m:6s (0h:6m:17s left)
Optimizing NNI: done in 1.1265 secs using 398.1% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.47371 secs using 399% CPU
Iteration 160 / LogL: -61012.367 / Time: 0h:4m:11s (0h:1m:56s left)
BETTER TREE FOUND at iteration 51: -101271.110
Optimizing NNI: done in 1.21603 secs using 398.5% CPU
Optimizing NNI: done in 5.40437 secs using 596.8% CPU
Iteration 40 / LogL: -198391.719 / Time: 0h:6m:11s (0h:15m:41s left)
Optimizing NNI: done in 1.31974 secs using 399.6% CPU
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Iteration 170 / LogL: -61012.294 / Time: 0h:4m:25s (0h:1m:40s left)
Optimizing NNI: done in 2.07185 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.67018 secs using 399.4% CPU
Optimizing NNI: done in 1.31521 secs using 399.1% CPU
BETTER TREE FOUND at iteration 43: -198207.465
Optimizing NNI: done in 1.98153 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.19516 secs using 399.2% CPU
Optimizing NNI: done in 1.38434 secs using 399.1% CPU
BETTER TREE FOUND at iteration 60: -101269.607
Iteration 60 / LogL: -101269.607 / Time: 0h:3m:31s (0h:5m:58s left)
Optimizing NNI: done in 1.38744 secs using 399.1% CPU
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Iteration 180 / LogL: -61012.338 / Time: 0h:4m:39s (0h:1m:24s left)
Optimizing NNI: done in 5.65461 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.20529 secs using 399.4% CPU
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BETTER TREE FOUND at iteration 45: -198203.303
Optimizing NNI: done in 1.40575 secs using 399.2% CPU
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BETTER TREE FOUND at iteration 187: -61008.412
Optimizing NNI: done in 1.94208 secs using 399% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.56798 secs using 398.6% CPU
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Iteration 190 / LogL: -61021.112 / Time: 0h:4m:53s (0h:2m:30s left)
BETTER TREE FOUND at iteration 69: -101265.054
Optimizing NNI: done in 1.53607 secs using 399.5% CPU
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Iteration 70 / LogL: -101266.581 / Time: 0h:3m:54s (0h:5m:36s left)
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Iteration 200 / LogL: -61012.135 / Time: 0h:5m:7s (0h:2m:14s left)
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Iteration 50 / LogL: -198246.177 / Time: 0h:7m:11s (0h:13m:56s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.34511 secs using 399.1% CPU
BETTER TREE FOUND at iteration 78: -101264.142
Optimizing NNI: done in 1.2444 secs using 398.9% CPU
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Iteration 80 / LogL: -101307.009 / Time: 0h:4m:17s (0h:5m:19s left)
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Iteration 210 / LogL: -61008.712 / Time: 0h:5m:22s (0h:1m:58s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.72936 secs using 597.1% CPU
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BETTER TREE FOUND at iteration 214: -61007.445
Optimizing NNI: done in 1.35066 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.60205 secs using 398.7% CPU
BETTER TREE FOUND at iteration 88: -101258.895
Optimizing NNI: done in 1.25566 secs using 399.3% CPU
Iteration 220 / LogL: -61025.312 / Time: 0h:5m:38s (0h:2m:25s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.38942 secs using 399.1% CPU
BETTER TREE FOUND at iteration 90: -101253.762
Iteration 90 / LogL: -101253.762 / Time: 0h:4m:43s (0h:5m:18s left)
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Iteration 230 / LogL: -61273.514 / Time: 0h:5m:53s (0h:2m:9s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.0397 secs using 398.7% CPU
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BETTER TREE FOUND at iteration 59: -198200.831
Optimizing NNI: done in 1.38844 secs using 399% CPU
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Iteration 100 / LogL: -101310.399 / Time: 0h:5m:4s (0h:4m:36s left)
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Iteration 240 / LogL: -61009.292 / Time: 0h:6m:8s (0h:1m:53s left)
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Iteration 60 / LogL: -198244.231 / Time: 0h:8m:8s (0h:13m:39s left)
Optimizing NNI: done in 1.45861 secs using 399.1% CPU
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Iteration 250 / LogL: -61036.994 / Time: 0h:6m:22s (0h:1m:38s left)
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Iteration 110 / LogL: -101348.390 / Time: 0h:5m:24s (0h:3m:58s left)
Optimizing NNI: done in 1.54554 secs using 399.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.32772 secs using 398.6% CPU
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BETTER TREE FOUND at iteration 63: -198199.795
Optimizing NNI: done in 1.42158 secs using 398.8% CPU
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Iteration 260 / LogL: -61033.556 / Time: 0h:6m:37s (0h:1m:22s left)
Optimizing NNI: done in 1.29991 secs using 398.9% CPU
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Iteration 120 / LogL: -101259.370 / Time: 0h:5m:44s (0h:3m:22s left)
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Iteration 270 / LogL: -61029.865 / Time: 0h:6m:50s (0h:1m:7s left)
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Iteration 280 / LogL: -61016.375 / Time: 0h:7m:5s (0h:0m:51s left)
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Iteration 130 / LogL: -101254.535 / Time: 0h:6m:4s (0h:2m:49s left)
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Iteration 70 / LogL: -198301.022 / Time: 0h:9m:6s (0h:12m:16s left)
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Iteration 290 / LogL: -61015.049 / Time: 0h:7m:19s (0h:0m:36s left)
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Iteration 140 / LogL: -101262.147 / Time: 0h:6m:24s (0h:2m:18s left)
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Iteration 300 / LogL: -61019.203 / Time: 0h:7m:33s (0h:0m:21s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 148: -101253.442
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Iteration 310 / LogL: -61013.245 / Time: 0h:7m:47s (0h:0m:6s left)
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Iteration 150 / LogL: -101291.259 / Time: 0h:6m:46s (0h:4m:27s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 151: -101250.382
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Optimizing NNI: done in 2.14291 secs using 398.9% CPU
Optimizing NNI: done in 1.31907 secs using 398.6% CPU
TREE SEARCH COMPLETED AFTER 315 ITERATIONS / Time: 0h:7m:54s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -61007.445
Optimal log-likelihood: -61007.441
Site proportion and rates:  (0.118,0.059) (0.068,0.168) (0.116,0.337) (0.052,0.340) (0.226,0.648) (0.182,1.096) (0.207,2.037) (0.030,5.164)
Parameters optimization took 1 rounds (0.354 sec)
BEST SCORE FOUND : -61007.441
Total tree length: 46.504

Total number of iterations: 315
CPU time used for tree search: 1842.530 sec (0h:30m:42s)
Wall-clock time used for tree search: 465.537 sec (0h:7m:45s)
Total CPU time used: 1878.416 sec (0h:31m:18s)
Total wall-clock time used: 474.505 sec (0h:7m:54s)

===> START BOOTSTRAP REPLICATE NUMBER 48

Creating bootstrap alignment (seed: 67510)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.049 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -57233.159
2. Current log-likelihood: -56710.749
3. Current log-likelihood: -56702.882
Optimizing NNI: done in 2.38526 secs using 398.9% CPU
Optimizing NNI: done in 4.94846 secs using 598.2% CPU
4. Current log-likelihood: -56701.619
5. Current log-likelihood: -56700.967
Optimizing NNI: done in 1.72928 secs using 399% CPU
6. Current log-likelihood: -56700.306
7. Current log-likelihood: -56699.298
8. Current log-likelihood: -56697.479
Optimizing NNI: done in 1.92928 secs using 398.8% CPU
9. Current log-likelihood: -56694.082
10. Current log-likelihood: -56690.557
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Iteration 80 / LogL: -198205.226 / Time: 0h:10m:0s (0h:10m:30s left)
Optimizing NNI: done in 2.06462 secs using 398.6% CPU
11. Current log-likelihood: -56689.449
12. Current log-likelihood: -56689.122
13. Current log-likelihood: -56688.877
Optimizing NNI: done in 2.23402 secs using 398.4% CPU
14. Current log-likelihood: -56688.533
15. Current log-likelihood: -56687.937
16. Current log-likelihood: -56686.875
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17. Current log-likelihood: -56685.390
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18. Current log-likelihood: -56684.166
19. Current log-likelihood: -56683.497
Optimizing NNI: done in 2.13194 secs using 399% CPU
20. Current log-likelihood: -56683.163
21. Current log-likelihood: -56682.990
Optimizing NNI: done in 2.05987 secs using 398.9% CPU
Iteration 160 / LogL: -101265.437 / Time: 0h:7m:9s (0h:4m:5s left)
Optimal log-likelihood: -56682.890
Site proportion and rates:  (0.096,0.073) (0.173,0.190) (0.145,0.421) (0.185,0.677) (0.153,1.066) (0.113,1.733) (0.120,2.640) (0.014,6.888)
Parameters optimization took 21 rounds (16.234 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.08593 secs using 399.9% CPU
Computing ML distances took 1.086105 sec (of wall-clock time) 4.342825 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000344992 secs using 401.7% CPU
Constructing RapidNJ tree: done in 0.00423384 secs using 370.9% CPU
Computing RapidNJ tree took 0.004636 sec (of wall-clock time) 0.017609 sec (of CPU time)
Optimizing NNI: done in 1.95152 secs using 398.9% CPU
Log-likelihood of RapidNJ tree: -56777.179
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.50966 secs using 597.5% CPU
Optimizing NNI: done in 1.77923 secs using 399.2% CPU
Optimizing NNI: done in 1.93336 secs using 399.3% CPU
4.919 second
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Optimizing NNI: done in 1.76089 secs using 399.2% CPU
Computing log-likelihood of 98 initial trees ... 5.118 seconds
Current best score: -56649.164

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -56454.627
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -56422.262
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Iteration 170 / LogL: -101255.320 / Time: 0h:7m:28s (0h:3m:35s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 8: -56405.367
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BETTER TREE FOUND at iteration 178: -101249.823
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Iteration 180 / LogL: -101270.319 / Time: 0h:7m:50s (0h:4m:17s left)
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Iteration 20 / LogL: -56486.768 / Time: 0h:0m:58s
Finish initializing candidate tree set (20)
Current best tree score: -56405.367 / CPU time: 40.331
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Iteration 90 / LogL: -198260.286 / Time: 0h:10m:56s (0h:8m:57s left)
BETTER TREE FOUND at iteration 22: -56378.966
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Iteration 190 / LogL: -101246.531 / Time: 0h:8m:13s (0h:4m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 46: -56374.022
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Iteration 110 / LogL: -56385.376 / Time: 0h:3m:7s (0h:1m:27s left)
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Optimizing NNI: done in 2.05719 secs using 398.3% CPU
Optimizing NNI: done in 1.25177 secs using 398.9% CPU
Optimizing NNI: done in 1.50454 secs using 398.6% CPU
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Optimizing NNI: done in 1.86391 secs using 399% CPU
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Optimizing NNI: done in 1.79488 secs using 398.9% CPU
Optimizing NNI: done in 1.1362 secs using 398.9% CPU
Optimizing NNI: done in 1.31343 secs using 398.6% CPU
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Optimizing NNI: done in 5.45473 secs using 598% CPU
Optimizing NNI: done in 1.33 secs using 398.8% CPU
Optimizing NNI: done in 1.38781 secs using 399.4% CPU
Iteration 120 / LogL: -56397.973 / Time: 0h:3m:20s (0h:1m:8s left)
Optimizing NNI: done in 1.8819 secs using 399.1% CPU
Optimizing NNI: done in 1.2749 secs using 398.7% CPU
Optimizing NNI: done in 2.0725 secs using 399% CPU
Iteration 250 / LogL: -101263.600 / Time: 0h:10m:15s (0h:1m:41s left)
Optimizing NNI: done in 1.64417 secs using 399% CPU
Optimizing NNI: done in 5.67965 secs using 597.1% CPU
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Optimizing NNI: done in 1.21401 secs using 399.2% CPU
Optimizing NNI: done in 1.03215 secs using 399.1% CPU
Optimizing NNI: done in 1.95706 secs using 398.9% CPU
Optimizing NNI: done in 1.11489 secs using 398.7% CPU
Optimizing NNI: done in 1.23564 secs using 398.7% CPU
Optimizing NNI: done in 2.25714 secs using 398.4% CPU
Optimizing NNI: done in 1.09636 secs using 399.2% CPU
Optimizing NNI: done in 5.05458 secs using 597.5% CPU
Optimizing NNI: done in 1.24764 secs using 398.5% CPU
Optimizing NNI: done in 1.94839 secs using 398.9% CPU
Optimizing NNI: done in 1.31942 secs using 399% CPU
Optimizing NNI: done in 1.74457 secs using 398.7% CPU
Optimizing NNI: done in 1.10683 secs using 399.2% CPU
Iteration 130 / LogL: -56374.261 / Time: 0h:3m:32s (0h:0m:51s left)
Optimizing NNI: done in 1.22201 secs using 399.3% CPU
Optimizing NNI: done in 1.99723 secs using 398.6% CPU
Optimizing NNI: done in 5.55546 secs using 596.9% CPU
Optimizing NNI: done in 1.44988 secs using 398.9% CPU
Optimizing NNI: done in 1.65425 secs using 398.8% CPU
Optimizing NNI: done in 1.30127 secs using 399.1% CPU
Optimizing NNI: done in 1.71877 secs using 398.9% CPU
Optimizing NNI: done in 1.59465 secs using 398.8% CPU
Optimizing NNI: done in 1.20527 secs using 398.9% CPU
Optimizing NNI: done in 2.33121 secs using 398.7% CPU
Optimizing NNI: done in 1.15475 secs using 398.7% CPU
Optimizing NNI: done in 5.52394 secs using 597.6% CPU
Optimizing NNI: done in 0.968622 secs using 399.1% CPU
Optimizing NNI: done in 2.30972 secs using 398.9% CPU
Iteration 260 / LogL: -101276.557 / Time: 0h:10m:35s (0h:1m:16s left)
Optimizing NNI: done in 1.56479 secs using 399.2% CPU
Optimizing NNI: done in 1.80715 secs using 398.5% CPU
Optimizing NNI: done in 1.5881 secs using 398.8% CPU
Optimizing NNI: done in 1.20923 secs using 398.9% CPU
Iteration 140 / LogL: -56373.608 / Time: 0h:3m:46s (0h:0m:34s left)
Optimizing NNI: done in 5.45495 secs using 597.6% CPU
Iteration 120 / LogL: -198287.722 / Time: 0h:13m:39s (0h:9m:45s left)
Optimizing NNI: done in 2.29876 secs using 399.2% CPU
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Optimizing NNI: done in 1.74936 secs using 398.1% CPU
Optimizing NNI: done in 5.12612 secs using 597.8% CPU
Optimizing NNI: done in 1.53223 secs using 399% CPU
Optimizing NNI: done in 1.83818 secs using 398.8% CPU
Optimizing NNI: done in 1.32281 secs using 399.1% CPU
Optimizing NNI: done in 0.910701 secs using 399% CPU
Optimizing NNI: done in 2.36562 secs using 398.4% CPU
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Optimizing NNI: done in 2.09159 secs using 398.9% CPU
Optimizing NNI: done in 1.16238 secs using 398.8% CPU
Iteration 150 / LogL: -56389.288 / Time: 0h:3m:58s (0h:0m:17s left)
Optimizing NNI: done in 1.72941 secs using 398.8% CPU
Optimizing NNI: done in 1.63186 secs using 399.2% CPU
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Optimizing NNI: done in 1.30452 secs using 398.9% CPU
Optimizing NNI: done in 1.76491 secs using 398.8% CPU
Iteration 270 / LogL: -101247.039 / Time: 0h:10m:55s (0h:0m:51s left)
Optimizing NNI: done in 1.11011 secs using 398.7% CPU
Optimizing NNI: done in 1.73341 secs using 399% CPU
Optimizing NNI: done in 1.20391 secs using 399% CPU
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Optimizing NNI: done in 1.59315 secs using 398.7% CPU
Optimizing NNI: done in 4.54563 secs using 597.1% CPU
Optimizing NNI: done in 1.51776 secs using 399% CPU
Optimizing NNI: done in 2.15088 secs using 398.6% CPU
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Optimizing NNI: done in 1.69594 secs using 398.7% CPU
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Optimizing NNI: done in 1.37432 secs using 399.3% CPU
Optimizing NNI: done in 5.18346 secs using 598% CPU
Optimizing NNI: done in 1.72765 secs using 398.4% CPU
Iteration 160 / LogL: -56392.408 / Time: 0h:4m:13s (0h:0m:1s left)
Optimizing NNI: done in 2.01732 secs using 398.9% CPU
Optimizing NNI: done in 1.4751 secs using 399.2% CPU
Optimizing NNI: done in 1.84482 secs using 399.2% CPU
Optimizing NNI: done in 1.59768 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 162 ITERATIONS / Time: 0h:4m:16s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -56373.199
Optimizing NNI: done in 4.8141 secs using 597.3% CPU
Optimal log-likelihood: -56373.192
Site proportion and rates:  (0.106,0.073) (0.160,0.196) (0.132,0.397) (0.187,0.652) (0.162,1.023) (0.109,1.658) (0.128,2.662) (0.015,6.420)
Parameters optimization took 1 rounds (0.440 sec)
BEST SCORE FOUND : -56373.192
Total tree length: 40.685

Total number of iterations: 162
CPU time used for tree search: 934.455 sec (0h:15m:34s)
Wall-clock time used for tree search: 237.811 sec (0h:3m:57s)
Total CPU time used: 1010.344 sec (0h:16m:50s)
Total wall-clock time used: 256.827 sec (0h:4m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 49

Creating bootstrap alignment (seed: 67511)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 59 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -62749.743
2. Current log-likelihood: -62170.760
Optimizing NNI: done in 2.39995 secs using 398.6% CPU
3. Current log-likelihood: -62146.778
4. Current log-likelihood: -62139.350
Optimizing NNI: done in 1.79674 secs using 399.1% CPU
5. Current log-likelihood: -62138.562
Optimal log-likelihood: -62138.492
Site proportion and rates:  (0.086,0.071) (0.091,0.182) (0.138,0.331) (0.058,0.392) (0.262,0.713) (0.146,1.220) (0.176,2.034) (0.044,4.266)
Parameters optimization took 5 rounds (3.905 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.90616 secs using 398.8% CPU
Iteration 280 / LogL: -101247.271 / Time: 0h:11m:14s (0h:0m:26s left)
Calculating distance matrix: done in 1.09448 secs using 399.8% CPU
Computing ML distances took 1.094654 sec (of wall-clock time) 4.375789 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.0003438 secs using 420% CPU
Constructing RapidNJ tree: done in 0.00427198 secs using 332.4% CPU
Computing RapidNJ tree took 0.004670 sec (of wall-clock time) 0.017818 sec (of CPU time)
Optimizing NNI: done in 5.43878 secs using 596.8% CPU
Log-likelihood of RapidNJ tree: -62098.501
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.90457 secs using 398.8% CPU
Optimizing NNI: done in 2.0933 secs using 398.6% CPU
Optimizing NNI: done in 1.95756 secs using 399.2% CPU
5.206 second
Optimizing NNI: done in 6.63891 secs using 597.2% CPU
Optimizing NNI: done in 1.97594 secs using 399.2% CPU
Optimizing NNI: done in 1.74773 secs using 398.9% CPU
Computing log-likelihood of 98 initial trees ... 4.957 seconds
Current best score: -62076.153

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.0486 secs using 398.5% CPU
Optimizing NNI: done in 5.00192 secs using 597% CPU
Optimizing NNI: done in 1.31695 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.51793 secs using 398.6% CPU
BETTER TREE FOUND at iteration 1: -61855.819
Optimizing NNI: done in 1.1445 secs using 399.1% CPU
Optimizing NNI: done in 1.92919 secs using 399.2% CPU
Optimizing NNI: done in 1.32025 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.21687 secs using 597.5% CPU
Iteration 130 / LogL: -198202.062 / Time: 0h:14m:32s (0h:8m:26s left)
Optimizing NNI: done in 1.89574 secs using 398.8% CPU
BETTER TREE FOUND at iteration 3: -61847.823
Optimizing NNI: done in 1.19637 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.03534 secs using 399% CPU
Iteration 290 / LogL: -101274.713 / Time: 0h:11m:35s (0h:0m:2s left)
BETTER TREE FOUND at iteration 4: -61807.446
Optimizing NNI: done in 1.76095 secs using 399.2% CPU
Optimizing NNI: done in 1.31132 secs using 398.5% CPU
Optimizing NNI: done in 5.33874 secs using 597% CPU
Optimizing NNI: done in 1.37239 secs using 399.1% CPU
Optimizing NNI: done in 2.05096 secs using 398.5% CPU
TREE SEARCH COMPLETED AFTER 292 ITERATIONS / Time: 0h:11m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101245.116
2. Current log-likelihood: -101245.092
Optimizing NNI: done in 1.34466 secs using 399.1% CPU
Optimal log-likelihood: -101245.081
Proportion of invariable sites: 0.013
Site proportion and rates:  (0.122,0.041) (0.106,0.137) (0.070,0.227) (0.104,0.337) (0.121,0.523) (0.098,0.852) (0.134,1.342) (0.176,2.046) (0.055,4.370)
Parameters optimization took 2 rounds (1.249 sec)
BEST SCORE FOUND : -101245.081
Total tree length: 162.328

Total number of iterations: 292
CPU time used for tree search: 2663.844 sec (0h:44m:23s)
Wall-clock time used for tree search: 676.066 sec (0h:11m:16s)
Total CPU time used: 2760.798 sec (0h:46m:0s)
Total wall-clock time used: 700.369 sec (0h:11m:40s)

===> START BOOTSTRAP REPLICATE NUMBER 12

Creating bootstrap alignment (seed: 68194)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.104 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105536.638
Optimizing NNI: done in 1.22866 secs using 398.7% CPU
2. Current log-likelihood: -103576.982
Optimizing NNI: done in 4.72663 secs using 598.2% CPU
Optimizing NNI: done in 1.5453 secs using 398.6% CPU
3. Current log-likelihood: -103508.330
Optimizing NNI: done in 1.23048 secs using 399% CPU
Iteration 10 / LogL: -61836.523 / Time: 0h:0m:33s
Optimizing NNI: done in 1.45903 secs using 398.9% CPU
4. Current log-likelihood: -103488.381
Optimizing NNI: done in 1.37178 secs using 399.2% CPU
5. Current log-likelihood: -103486.327
Optimizing NNI: done in 5.25942 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.33081 secs using 398.6% CPU
6. Current log-likelihood: -103486.188
7. Current log-likelihood: -103486.084
Optimizing NNI: done in 1.38024 secs using 398.6% CPU
BETTER TREE FOUND at iteration 133: -198191.788
Optimal log-likelihood: -103485.941
Proportion of invariable sites: 0.022
Site proportion and rates:  (0.079,0.038) (0.087,0.121) (0.077,0.206) (0.135,0.326) (0.113,0.536) (0.109,0.837) (0.164,1.306) (0.149,1.944) (0.065,4.168)
Parameters optimization took 7 rounds (10.307 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.59782 secs using 398.2% CPU
Optimizing NNI: done in 1.04589 secs using 398.9% CPU
Optimizing NNI: done in 1.2296 secs using 399.2% CPU
Optimizing NNI: done in 1.48634 secs using 398.4% CPU
Calculating distance matrix: done in 4.68121 secs using 400% CPU
Computing ML distances took 4.681607 sec (of wall-clock time) 18.723389 sec (of CPU time)
Optimizing NNI: done in 5.15382 secs using 596.7% CPU
Setting up auxiliary I and S matrices: done in 0.000807047 secs using 324.4% CPU
Constructing RapidNJ tree: done in 0.00891209 secs using 450.1% CPU
Computing RapidNJ tree took 0.009780 sec (of wall-clock time) 0.044482 sec (of CPU time)
Optimizing NNI: done in 1.32458 secs using 399.5% CPU
Log-likelihood of RapidNJ tree: -103862.259
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.47084 secs using 398.7% CPU
Iteration 20 / LogL: -61826.989 / Time: 0h:0m:47s
Finish initializing candidate tree set (20)
Current best tree score: -61807.446 / CPU time: 42.008
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.57729 secs using 398.8% CPU
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Optimizing NNI: done in 1.23568 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
10.561 second
BETTER TREE FOUND at iteration 26: -61797.057
Optimizing NNI: done in 8.09435 secs using 597.6% CPU
Optimizing NNI: done in 1.62442 secs using 398.7% CPU
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Optimizing NNI: done in 1.48848 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.65025 secs using 597.2% CPU
Computing log-likelihood of 98 initial trees ... 9.656 seconds
Current best score: -103485.941

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.78066 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.38452 secs using 597.2% CPU
BETTER TREE FOUND at iteration 1: -102918.655
BETTER TREE FOUND at iteration 30: -61791.675
Iteration 30 / LogL: -61791.675 / Time: 0h:1m:13s (0h:4m:14s left)
Optimizing NNI: done in 2.4326 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.2951 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.89562 secs using 398.7% CPU
BETTER TREE FOUND at iteration 2: -102833.167
Optimizing NNI: done in 1.49579 secs using 398.5% CPU
BETTER TREE FOUND at iteration 139: -198190.325
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -61791.043
Optimizing NNI: done in 5.01704 secs using 597.7% CPU
Iteration 140 / LogL: -198258.367 / Time: 0h:15m:33s (0h:11m:4s left)
Optimizing NNI: done in 2.6502 secs using 399.3% CPU
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Optimizing NNI: done in 1.26404 secs using 399.7% CPU
Iteration 40 / LogL: -61807.641 / Time: 0h:1m:29s (0h:3m:39s left)
Optimizing NNI: done in 2.15478 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.94228 secs using 398% CPU
BETTER TREE FOUND at iteration 41: -61778.706
Optimizing NNI: done in 4.77478 secs using 596% CPU
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Iteration 10 / LogL: -102895.803 / Time: 0h:1m:4s
Optimizing NNI: done in 1.59817 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.58163 secs using 398.7% CPU
BETTER TREE FOUND at iteration 46: -61776.753
Optimizing NNI: done in 1.26817 secs using 398.7% CPU
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Optimizing NNI: done in 1.60121 secs using 399.2% CPU
Optimizing NNI: done in 1.46621 secs using 398.3% CPU
Iteration 50 / LogL: -61803.104 / Time: 0h:1m:46s (0h:3m:28s left)
Optimizing NNI: done in 2.47018 secs using 399% CPU
Optimizing NNI: done in 1.36182 secs using 398.7% CPU
Optimizing NNI: done in 5.41229 secs using 597.2% CPU
Optimizing NNI: done in 2.36549 secs using 398.8% CPU
Optimizing NNI: done in 1.79636 secs using 399% CPU
Optimizing NNI: done in 1.72204 secs using 398.7% CPU
Optimizing NNI: done in 2.66463 secs using 398.7% CPU
Optimizing NNI: done in 1.25902 secs using 398.7% CPU
Optimizing NNI: done in 1.71064 secs using 398.8% CPU
Optimizing NNI: done in 5.10237 secs using 597.5% CPU
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Optimizing NNI: done in 1.34651 secs using 399.1% CPU
Optimizing NNI: done in 2.45911 secs using 398.4% CPU
Iteration 20 / LogL: -102956.196 / Time: 0h:1m:27s
Finish initializing candidate tree set (20)
Current best tree score: -102833.167 / CPU time: 71.119
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.5413 secs using 399.3% CPU
Optimizing NNI: done in 2.22202 secs using 398.7% CPU
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Optimizing NNI: done in 5.41194 secs using 597.2% CPU
Optimizing NNI: done in 1.41223 secs using 398.7% CPU
Iteration 60 / LogL: -61790.082 / Time: 0h:2m:1s (0h:2m:56s left)
Optimizing NNI: done in 1.95219 secs using 398.6% CPU
Optimizing NNI: done in 1.29963 secs using 399% CPU
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Optimizing NNI: done in 2.06328 secs using 398.9% CPU
Optimizing NNI: done in 1.49583 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -61771.736
Optimizing NNI: done in 4.65945 secs using 597.6% CPU
Optimizing NNI: done in 2.45098 secs using 398.5% CPU
Optimizing NNI: done in 1.28385 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 66: -61770.599
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Estimate model parameters (epsilon = 0.100)
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TREE SEARCH COMPLETED AFTER 197 ITERATIONS / Time: 0h:5m:26s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -61764.783
Optimizing NNI: done in 2.05708 secs using 399.2% CPU
2. Current log-likelihood: -61764.746
3. Current log-likelihood: -61764.720
Optimizing NNI: done in 1.72033 secs using 399.1% CPU
4. Current log-likelihood: -61764.701
5. Current log-likelihood: -61764.687
6. Current log-likelihood: -61764.675
Optimal log-likelihood: -61764.669
Site proportion and rates:  (0.087,0.074) (0.119,0.197) (0.171,0.371) (0.225,0.681) (0.115,0.989) (0.130,1.553) (0.121,2.347) (0.032,4.742)
Parameters optimization took 6 rounds (3.769 sec)
BEST SCORE FOUND : -61764.669
Total tree length: 46.617

Total number of iterations: 197
CPU time used for tree search: 1264.698 sec (0h:21m:4s)
Wall-clock time used for tree search: 320.865 sec (0h:5m:20s)
Total CPU time used: 1302.325 sec (0h:21m:42s)
Total wall-clock time used: 330.269 sec (0h:5m:30s)

===> START BOOTSTRAP REPLICATE NUMBER 50

Creating bootstrap alignment (seed: 67512)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58541.713
Optimizing NNI: done in 4.68821 secs using 597.3% CPU
Optimizing NNI: done in 2.2236 secs using 398.5% CPU
2. Current log-likelihood: -57927.251
3. Current log-likelihood: -57904.556
4. Current log-likelihood: -57892.253
Optimizing NNI: done in 2.19847 secs using 398.9% CPU
5. Current log-likelihood: -57875.539
6. Current log-likelihood: -57873.739
Optimizing NNI: done in 2.02738 secs using 398.6% CPU
Optimal log-likelihood: -57873.615
Site proportion and rates:  (0.114,0.061) (0.138,0.170) (0.086,0.373) (0.088,0.377) (0.203,0.697) (0.158,1.180) (0.178,2.147) (0.036,5.448)
Parameters optimization took 6 rounds (4.861 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.59333 secs using 597.8% CPU
Calculating distance matrix: done in 1.1126 secs using 400% CPU
Computing ML distances took 1.112775 sec (of wall-clock time) 4.450359 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000369787 secs using 427.3% CPU
Constructing RapidNJ tree: done in 0.00434279 secs using 365.6% CPU
Computing RapidNJ tree took 0.004768 sec (of wall-clock time) 0.018153 sec (of CPU time)
Log-likelihood of RapidNJ tree: -58014.399
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.98484 secs using 398.8% CPU
Iteration 110 / LogL: -102825.917 / Time: 0h:5m:6s (0h:4m:1s left)
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5.057 second
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Iteration 190 / LogL: -198202.442 / Time: 0h:19m:52s (0h:5m:8s left)
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Optimizing NNI: done in 2.06898 secs using 398.3% CPU
Computing log-likelihood of 98 initial trees ... 5.108 seconds
Current best score: -57847.258

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 115: -102802.239
BETTER TREE FOUND at iteration 1: -57521.583
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BETTER TREE FOUND at iteration 3: -57494.832
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Iteration 120 / LogL: -103146.473 / Time: 0h:5m:29s (0h:4m:23s left)
BETTER TREE FOUND at iteration 9: -57482.053
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Iteration 10 / LogL: -57558.572 / Time: 0h:0m:31s
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BETTER TREE FOUND at iteration 124: -102798.229
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BETTER TREE FOUND at iteration 195: -198185.282
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Iteration 20 / LogL: -57581.087 / Time: 0h:0m:43s
Finish initializing candidate tree set (20)
Current best tree score: -57482.053 / CPU time: 37.139
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 23: -57469.216
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Iteration 130 / LogL: -102817.352 / Time: 0h:5m:51s (0h:4m:15s left)
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BETTER TREE FOUND at iteration 25: -57464.867
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Iteration 30 / LogL: -57483.245 / Time: 0h:0m:58s (0h:3m:11s left)
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BETTER TREE FOUND at iteration 33: -57459.930
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Iteration 200 / LogL: -198242.937 / Time: 0h:20m:47s (0h:9m:55s left)
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Iteration 50 / LogL: -57467.734 / Time: 0h:1m:25s (0h:2m:25s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 55: -57450.185
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Iteration 150 / LogL: -102831.869 / Time: 0h:6m:33s (0h:3m:15s left)
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Iteration 60 / LogL: -57486.119 / Time: 0h:1m:40s (0h:2m:41s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 62: -57448.424
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BETTER TREE FOUND at iteration 156: -102794.797
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BETTER TREE FOUND at iteration 67: -57448.416
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Estimate model parameters (epsilon = 0.100)
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Iteration 70 / LogL: -57458.435 / Time: 0h:1m:53s (0h:2m:39s left)
BETTER TREE FOUND at iteration 158: -102790.128
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Iteration 160 / LogL: -102902.255 / Time: 0h:6m:58s (0h:4m:17s left)
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Iteration 210 / LogL: -198248.346 / Time: 0h:21m:39s (0h:8m:48s left)
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Iteration 80 / LogL: -57450.169 / Time: 0h:2m:7s (0h:2m:19s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 83: -57447.933
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Iteration 170 / LogL: -102801.737 / Time: 0h:7m:19s (0h:3m:48s left)
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Iteration 90 / LogL: -57448.448 / Time: 0h:2m:20s (0h:2m:27s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 95: -57446.145
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BETTER TREE FOUND at iteration 97: -57446.142
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UPDATE BEST LOG-LIKELIHOOD: -57446.141
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Iteration 100 / LogL: -57462.999 / Time: 0h:2m:34s (0h:2m:31s left)
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Iteration 180 / LogL: -102800.720 / Time: 0h:7m:40s (0h:3m:20s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 110 / LogL: -57475.306 / Time: 0h:2m:47s (0h:2m:13s left)
BETTER TREE FOUND at iteration 219: -198182.833
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Iteration 220 / LogL: -198193.670 / Time: 0h:22m:34s (0h:10m:12s left)
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Iteration 120 / LogL: -57447.908 / Time: 0h:3m:1s (0h:1m:57s left)
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Iteration 130 / LogL: -57456.178 / Time: 0h:3m:13s (0h:1m:40s left)
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BETTER TREE FOUND at iteration 131: -57444.747
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BETTER TREE FOUND at iteration 133: -57444.743
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BETTER TREE FOUND at iteration 200: -102788.355
Iteration 200 / LogL: -102788.355 / Time: 0h:8m:25s (0h:4m:13s left)
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Iteration 140 / LogL: -57460.397 / Time: 0h:3m:27s (0h:2m:18s left)
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Iteration 150 / LogL: -57444.747 / Time: 0h:3m:39s (0h:2m:2s left)
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Iteration 230 / LogL: -198265.345 / Time: 0h:23m:26s (0h:9m:6s left)
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Iteration 230 / LogL: -57449.119 / Time: 0h:5m:23s (0h:0m:4s left)
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TREE SEARCH COMPLETED AFTER 234 ITERATIONS / Time: 0h:5m:29s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57444.743
2. Current log-likelihood: -57444.726
3. Current log-likelihood: -57444.714
4. Current log-likelihood: -57444.701
5. Current log-likelihood: -57444.689
Optimizing NNI: done in 2.26971 secs using 399.1% CPU
Iteration 260 / LogL: -102813.459 / Time: 0h:10m:30s (0h:1m:37s left)
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Iteration 250 / LogL: -198220.569 / Time: 0h:25m:11s (0h:6m:58s left)
6. Current log-likelihood: -57444.676
7. Current log-likelihood: -57444.664
8. Current log-likelihood: -57444.652
9. Current log-likelihood: -57444.640
10. Current log-likelihood: -57444.628
Optimizing NNI: done in 2.18193 secs using 398.4% CPU
11. Current log-likelihood: -57444.617
12. Current log-likelihood: -57444.606
13. Current log-likelihood: -57444.595
14. Current log-likelihood: -57444.584
Optimal log-likelihood: -57444.569
Site proportion and rates:  (0.102,0.059) (0.153,0.161) (0.083,0.374) (0.085,0.374) (0.199,0.696) (0.171,1.206) (0.168,2.178) (0.039,5.057)
Parameters optimization took 14 rounds (6.021 sec)
BEST SCORE FOUND : -57444.569
Total tree length: 45.027

Total number of iterations: 234
CPU time used for tree search: 1272.716 sec (0h:21m:12s)
Wall-clock time used for tree search: 322.707 sec (0h:5m:22s)
Total CPU time used: 1322.132 sec (0h:22m:2s)
Total wall-clock time used: 335.078 sec (0h:5m:35s)

===> START BOOTSTRAP REPLICATE NUMBER 51

Creating bootstrap alignment (seed: 67513)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.056 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -56405.571
Optimizing NNI: done in 2.2502 secs using 398.4% CPU
Optimizing NNI: done in 4.76062 secs using 597% CPU
2. Current log-likelihood: -55818.115
3. Current log-likelihood: -55803.769
Optimizing NNI: done in 2.14548 secs using 398.2% CPU
4. Current log-likelihood: -55795.915
5. Current log-likelihood: -55784.233
6. Current log-likelihood: -55779.490
Optimizing NNI: done in 2.07404 secs using 398.8% CPU
7. Current log-likelihood: -55778.799
Optimizing NNI: done in 5.05909 secs using 597% CPU
Optimal log-likelihood: -55778.696
Site proportion and rates:  (0.121,0.059) (0.135,0.190) (0.116,0.394) (0.097,0.429) (0.243,0.809) (0.149,1.555) (0.099,2.490) (0.039,5.301)
Parameters optimization took 7 rounds (5.965 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.10461 secs using 399.9% CPU
Computing ML distances took 1.104803 sec (of wall-clock time) 4.417445 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000374079 secs using 306.4% CPU
Constructing RapidNJ tree: done in 0.00430417 secs using 335.6% CPU
Computing RapidNJ tree took 0.004729 sec (of wall-clock time) 0.016983 sec (of CPU time)
Log-likelihood of RapidNJ tree: -55918.817
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.91644 secs using 399.2% CPU
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4.979 second
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Iteration 270 / LogL: -102788.936 / Time: 0h:10m:52s (0h:1m:12s left)
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Computing log-likelihood of 98 initial trees ... 5.305 seconds
Current best score: -55711.487

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -55513.556
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Iteration 260 / LogL: -198281.641 / Time: 0h:26m:3s (0h:5m:56s left)
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Iteration 20 / LogL: -55563.064 / Time: 0h:0m:52s
Finish initializing candidate tree set (20)
Current best tree score: -55513.556 / CPU time: 44.963
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -55497.732
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Optimizing NNI: done in 5.39729 secs using 598% CPU
Optimizing NNI: done in 1.75412 secs using 399.3% CPU
BETTER TREE FOUND at iteration 316: -102783.154
Optimizing NNI: done in 1.64134 secs using 399% CPU
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Iteration 50 / LogL: -55502.399 / Time: 0h:1m:58s (0h:3m:49s left)
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Iteration 320 / LogL: -102795.643 / Time: 0h:12m:39s (0h:3m:48s left)
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Iteration 60 / LogL: -55481.506 / Time: 0h:2m:14s (0h:3m:13s left)
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Iteration 330 / LogL: -102815.044 / Time: 0h:12m:59s (0h:3m:23s left)
Optimizing NNI: done in 4.89264 secs using 598.1% CPU
Optimizing NNI: done in 1.33018 secs using 399.1% CPU
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Optimizing NNI: done in 2.28012 secs using 398.5% CPU
BETTER TREE FOUND at iteration 67: -55468.508
Optimizing NNI: done in 1.52731 secs using 399.1% CPU
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BETTER TREE FOUND at iteration 70: -55462.690
Iteration 70 / LogL: -55462.690 / Time: 0h:2m:32s (0h:3m:40s left)
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Iteration 280 / LogL: -198277.144 / Time: 0h:27m:51s (0h:8m:34s left)
Optimizing NNI: done in 1.57913 secs using 399.4% CPU
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BETTER TREE FOUND at iteration 76: -55461.594
Optimizing NNI: done in 2.27539 secs using 398.7% CPU
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Iteration 340 / LogL: -102784.176 / Time: 0h:13m:20s (0h:2m:59s left)
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Iteration 80 / LogL: -55462.309 / Time: 0h:2m:48s (0h:3m:24s left)
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Iteration 90 / LogL: -55472.790 / Time: 0h:3m:3s (0h:2m:57s left)
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Iteration 350 / LogL: -102787.077 / Time: 0h:13m:42s (0h:2m:35s left)
Optimizing NNI: done in 1.22904 secs using 398.6% CPU
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Iteration 100 / LogL: -55524.797 / Time: 0h:3m:18s (0h:2m:32s left)
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BETTER TREE FOUND at iteration 101: -55461.585
Optimizing NNI: done in 1.88469 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.4125 secs using 597.3% CPU
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BETTER TREE FOUND at iteration 357: -102782.598
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Iteration 290 / LogL: -198354.346 / Time: 0h:28m:42s (0h:7m:32s left)
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BETTER TREE FOUND at iteration 106: -55461.584
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Iteration 360 / LogL: -102788.731 / Time: 0h:14m:5s (0h:3m:48s left)
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Iteration 110 / LogL: -55652.438 / Time: 0h:3m:34s (0h:3m:8s left)
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BETTER TREE FOUND at iteration 114: -55461.584
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Iteration 120 / LogL: -55464.639 / Time: 0h:3m:49s (0h:3m:1s left)
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Iteration 370 / LogL: -102797.514 / Time: 0h:14m:25s (0h:3m:24s left)
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Iteration 130 / LogL: -55487.371 / Time: 0h:4m:5s (0h:2m:39s left)
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Iteration 380 / LogL: -102791.846 / Time: 0h:14m:47s (0h:3m:0s left)
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Iteration 300 / LogL: -198216.825 / Time: 0h:29m:32s (0h:6m:31s left)
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Iteration 140 / LogL: -55479.149 / Time: 0h:4m:21s (0h:2m:18s left)
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Iteration 390 / LogL: -102784.256 / Time: 0h:15m:7s (0h:2m:36s left)
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Iteration 150 / LogL: -55471.339 / Time: 0h:4m:36s (0h:1m:58s left)
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Iteration 160 / LogL: -55492.980 / Time: 0h:4m:51s (0h:1m:38s left)
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Iteration 400 / LogL: -102821.810 / Time: 0h:15m:28s (0h:2m:12s left)
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Iteration 170 / LogL: -55492.926 / Time: 0h:5m:6s (0h:1m:19s left)
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Iteration 310 / LogL: -198198.503 / Time: 0h:30m:23s (0h:5m:30s left)
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Iteration 410 / LogL: -102826.836 / Time: 0h:15m:48s (0h:1m:49s left)
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Iteration 180 / LogL: -55480.260 / Time: 0h:5m:21s (0h:1m:0s left)
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Iteration 420 / LogL: -102814.604 / Time: 0h:16m:10s (0h:1m:25s left)
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Optimizing NNI: done in 2.07619 secs using 398.5% CPU
Optimizing NNI: done in 1.70298 secs using 399% CPU
Iteration 200 / LogL: -55472.662 / Time: 0h:5m:51s (0h:0m:24s left)
Optimizing NNI: done in 2.22352 secs using 398.6% CPU
Optimizing NNI: done in 1.51458 secs using 398.7% CPU
Optimizing NNI: done in 2.03106 secs using 398.9% CPU
Optimizing NNI: done in 5.56542 secs using 596.5% CPU
Optimizing NNI: done in 1.66972 secs using 398.9% CPU
Optimizing NNI: done in 1.51813 secs using 398.3% CPU
Optimizing NNI: done in 2.21773 secs using 398.6% CPU
Iteration 430 / LogL: -102791.251 / Time: 0h:16m:31s (0h:1m:2s left)
Optimizing NNI: done in 1.48245 secs using 399.2% CPU
Optimizing NNI: done in 1.93837 secs using 398.8% CPU
Optimizing NNI: done in 1.53807 secs using 398.7% CPU
Optimizing NNI: done in 5.08022 secs using 597.6% CPU
Iteration 320 / LogL: -198218.214 / Time: 0h:31m:15s (0h:4m:30s left)
Optimizing NNI: done in 1.34774 secs using 399.2% CPU
Optimizing NNI: done in 2.4135 secs using 398.8% CPU
Optimizing NNI: done in 1.65145 secs using 399.4% CPU
Optimizing NNI: done in 2.16455 secs using 398.3% CPU
Optimizing NNI: done in 1.7935 secs using 398.2% CPU
Optimizing NNI: done in 5.22152 secs using 598% CPU
Optimizing NNI: done in 1.77676 secs using 398.7% CPU
Optimizing NNI: done in 1.66768 secs using 398.9% CPU
Optimizing NNI: done in 2.39791 secs using 398.7% CPU
Optimizing NNI: done in 2.05626 secs using 398.7% CPU
Iteration 210 / LogL: -55476.840 / Time: 0h:6m:8s (0h:0m:7s left)
Optimizing NNI: done in 2.05235 secs using 399% CPU
Optimizing NNI: done in 1.90308 secs using 399.3% CPU
Optimizing NNI: done in 5.33994 secs using 597.3% CPU
Optimizing NNI: done in 2.06092 secs using 398.7% CPU
Optimizing NNI: done in 1.80506 secs using 398.9% CPU
Optimizing NNI: done in 1.53661 secs using 399.2% CPU
Optimizing NNI: done in 2.18569 secs using 398.5% CPU
Optimizing NNI: done in 1.4475 secs using 399.2% CPU
Optimizing NNI: done in 1.9442 secs using 398.6% CPU
Optimizing NNI: done in 5.49481 secs using 597.9% CPU
Optimizing NNI: done in 1.56959 secs using 398.5% CPU
TREE SEARCH COMPLETED AFTER 215 ITERATIONS / Time: 0h:6m:16s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -55461.584
2. Current log-likelihood: -55461.552
3. Current log-likelihood: -55461.533
Optimizing NNI: done in 2.29188 secs using 398.4% CPU
Iteration 440 / LogL: -102806.553 / Time: 0h:16m:53s (0h:0m:39s left)
4. Current log-likelihood: -55461.502
5. Current log-likelihood: -55461.486
6. Current log-likelihood: -55461.467
Optimizing NNI: done in 2.29474 secs using 398.8% CPU
Optimizing NNI: done in 5.02544 secs using 597.2% CPU
7. Current log-likelihood: -55461.452
8. Current log-likelihood: -55461.437
9. Current log-likelihood: -55461.423
10. Current log-likelihood: -55461.408
Optimizing NNI: done in 2.11496 secs using 398.7% CPU
11. Current log-likelihood: -55461.394
12. Current log-likelihood: -55461.380
13. Current log-likelihood: -55461.366
Optimizing NNI: done in 2.06281 secs using 398.7% CPU
14. Current log-likelihood: -55461.352
15. Current log-likelihood: -55461.340
16. Current log-likelihood: -55461.329
Optimizing NNI: done in 4.55548 secs using 597.2% CPU
17. Current log-likelihood: -55461.318
18. Current log-likelihood: -55461.305
Optimizing NNI: done in 2.35978 secs using 398.6% CPU
19. Current log-likelihood: -55461.294
20. Current log-likelihood: -55461.284
21. Current log-likelihood: -55461.273
22. Current log-likelihood: -55461.262
Optimizing NNI: done in 2.00789 secs using 398.7% CPU
23. Current log-likelihood: -55461.249
24. Current log-likelihood: -55461.239
25. Current log-likelihood: -55461.228
Optimizing NNI: done in 4.46646 secs using 597.8% CPU
Optimal log-likelihood: -55461.213
Site proportion and rates:  (0.104,0.053) (0.142,0.171) (0.194,0.382) (0.184,0.709) (0.121,0.994) (0.113,1.634) (0.102,2.466) (0.040,5.267)
Parameters optimization took 25 rounds (14.021 sec)
BEST SCORE FOUND : -55461.213
Total tree length: 44.095

Total number of iterations: 215
CPU time used for tree search: 1456.075 sec (0h:24m:16s)
Wall-clock time used for tree search: 368.554 sec (0h:6m:8s)
Total CPU time used: 1543.305 sec (0h:25m:43s)
Total wall-clock time used: 390.417 sec (0h:6m:30s)

===> START BOOTSTRAP REPLICATE NUMBER 52

Creating bootstrap alignment (seed: 67514)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61497.821
Optimizing NNI: done in 2.15569 secs using 399% CPU
2. Current log-likelihood: -60906.175
3. Current log-likelihood: -60897.799
4. Current log-likelihood: -60892.333
Optimizing NNI: done in 2.16757 secs using 399.3% CPU
5. Current log-likelihood: -60874.708
6. Current log-likelihood: -60872.048
Optimizing NNI: done in 4.84796 secs using 597.3% CPU
7. Current log-likelihood: -60869.944
Optimizing NNI: done in 2.0446 secs using 398.8% CPU
8. Current log-likelihood: -60867.623
9. Current log-likelihood: -60865.973
Optimizing NNI: done in 2.1441 secs using 398.5% CPU
10. Current log-likelihood: -60865.192
11. Current log-likelihood: -60864.923
Optimal log-likelihood: -60864.830
Site proportion and rates:  (0.105,0.059) (0.076,0.189) (0.200,0.362) (0.147,0.571) (0.190,0.919) (0.176,1.645) (0.082,2.512) (0.023,6.722)
Parameters optimization took 11 rounds (8.536 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.34099 secs using 398.9% CPU
Iteration 450 / LogL: -102788.576 / Time: 0h:17m:15s (0h:0m:16s left)
Calculating distance matrix: done in 1.10351 secs using 399.9% CPU
Computing ML distances took 1.103690 sec (of wall-clock time) 4.413284 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00036788 secs using 414.5% CPU
Constructing RapidNJ tree: done in 0.00441909 secs using 395% CPU
Computing RapidNJ tree took 0.004842 sec (of wall-clock time) 0.019421 sec (of CPU time)
Optimizing NNI: done in 5.42695 secs using 597.5% CPU
Log-likelihood of RapidNJ tree: -60882.422
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.91635 secs using 399.2% CPU
Optimizing NNI: done in 1.8607 secs using 398.7% CPU
Optimizing NNI: done in 1.62977 secs using 398.8% CPU
Optimizing NNI: done in 5.08807 secs using 597.4% CPU
5.322 second
Optimizing NNI: done in 2.14771 secs using 398.9% CPU
Optimizing NNI: done in 1.97263 secs using 398.5% CPU
Optimizing NNI: done in 4.91246 secs using 597.7% CPU
Iteration 330 / LogL: -198196.062 / Time: 0h:32m:5s (0h:3m:30s left)
Computing log-likelihood of 98 initial trees ... 5.209 seconds
Current best score: -60709.486

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.02413 secs using 398.6% CPU
Optimizing NNI: done in 1.65184 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.68858 secs using 398.6% CPU
Optimizing NNI: done in 2.09779 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 458 ITERATIONS / Time: 0h:17m:30s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102782.598
Optimizing NNI: done in 5.40344 secs using 597.7% CPU
2. Current log-likelihood: -102782.588
3. Current log-likelihood: -102782.577
4. Current log-likelihood: -102782.567
5. Current log-likelihood: -102782.556
Optimal log-likelihood: -102782.542
Proportion of invariable sites: 0.022
Site proportion and rates:  (0.082,0.035) (0.075,0.113) (0.082,0.189) (0.136,0.316) (0.112,0.518) (0.115,0.827) (0.158,1.289) (0.156,1.944) (0.062,4.318)
Parameters optimization took 5 rounds (3.060 sec)
BEST SCORE FOUND : -102782.542
Total tree length: 164.791

Total number of iterations: 458
CPU time used for tree search: 4093.024 sec (1h:8m:13s)
Wall-clock time used for tree search: 1034.504 sec (0h:17m:14s)
Total CPU time used: 4170.051 sec (1h:9m:30s)
Total wall-clock time used: 1053.798 sec (0h:17m:33s)

===> START BOOTSTRAP REPLICATE NUMBER 13

Creating bootstrap alignment (seed: 68195)...

BETTER TREE FOUND at iteration 1: -60537.001
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.088 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 101 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105152.668
Optimizing NNI: done in 1.34256 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
2. Current log-likelihood: -102967.777
Optimizing NNI: done in 4.72539 secs using 597.5% CPU
BETTER TREE FOUND at iteration 2: -60502.081
3. Current log-likelihood: -102913.442
Optimizing NNI: done in 1.33062 secs using 399.3% CPU
4. Current log-likelihood: -102913.341
Optimizing NNI: done in 1.63875 secs using 399.4% CPU
Optimal log-likelihood: -102913.326
Proportion of invariable sites: 0.043
Site proportion and rates:  (0.094,0.039) (0.101,0.124) (0.057,0.213) (0.118,0.320) (0.092,0.493) (0.089,0.716) (0.143,1.067) (0.186,1.894) (0.076,4.230)
Parameters optimization took 4 rounds (6.141 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.56321 secs using 398.4% CPU
Optimizing NNI: done in 5.18946 secs using 597.4% CPU
Optimizing NNI: done in 1.19287 secs using 398.5% CPU
Optimizing NNI: done in 1.48307 secs using 398.9% CPU
Calculating distance matrix: done in 4.71903 secs using 399.9% CPU
Computing ML distances took 4.719424 sec (of wall-clock time) 18.872418 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000802994 secs using 421.4% CPU
Constructing RapidNJ tree: done in 0.00874615 secs using 347.7% CPU
Computing RapidNJ tree took 0.009613 sec (of wall-clock time) 0.035634 sec (of CPU time)
Optimizing NNI: done in 1.5782 secs using 398.7% CPU
Log-likelihood of RapidNJ tree: -103339.727
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.80482 secs using 598.1% CPU
Optimizing NNI: done in 1.34677 secs using 398.9% CPU
Optimizing NNI: done in 1.5743 secs using 398.7% CPU
Iteration 10 / LogL: -60543.978 / Time: 0h:0m:42s
Optimizing NNI: done in 1.1313 secs using 399% CPU
Optimizing NNI: done in 1.50247 secs using 398.8% CPU
Optimizing NNI: done in 5.38666 secs using 597.5% CPU
Optimizing NNI: done in 1.57681 secs using 398.6% CPU
Optimizing NNI: done in 0.956208 secs using 398.1% CPU
Optimizing NNI: done in 1.43293 secs using 398.9% CPU
Optimizing NNI: done in 1.30039 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
10.486 second
Optimizing NNI: done in 4.92538 secs using 597.4% CPU
BETTER TREE FOUND at iteration 16: -60491.026
Optimizing NNI: done in 1.46129 secs using 399% CPU
Optimizing NNI: done in 1.77154 secs using 399% CPU
Optimizing NNI: done in 4.71234 secs using 597% CPU
Optimizing NNI: done in 1.31952 secs using 399.1% CPU
Optimizing NNI: done in 1.66728 secs using 399% CPU
Iteration 20 / LogL: -60597.621 / Time: 0h:0m:58s
Finish initializing candidate tree set (20)
Current best tree score: -60491.026 / CPU time: 48.002
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.28851 secs using 398.7% CPU
Computing log-likelihood of 98 initial trees ... 9.836 seconds
Current best score: -102913.326

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.84333 secs using 597.5% CPU
Optimizing NNI: done in 1.58997 secs using 398.8% CPU
Optimizing NNI: done in 1.87949 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.24155 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -60484.764
Optimizing NNI: done in 1.46711 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.35926 secs using 597.6% CPU
BETTER TREE FOUND at iteration 24: -60475.078
Optimizing NNI: done in 1.2039 secs using 398.8% CPU
Optimizing NNI: done in 1.40809 secs using 398.8% CPU
Optimizing NNI: done in 1.06337 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.01551 secs using 597% CPU
Iteration 340 / LogL: -198201.810 / Time: 0h:32m:56s (0h:2m:31s left)
BETTER TREE FOUND at iteration 27: -60473.605
Optimizing NNI: done in 1.42634 secs using 398.7% CPU
Optimizing NNI: done in 1.10478 secs using 398.5% CPU
Optimizing NNI: done in 1.23325 secs using 399.1% CPU
Iteration 30 / LogL: -60475.394 / Time: 0h:1m:15s (0h:4m:13s left)
Optimizing NNI: done in 5.10193 secs using 597.6% CPU
Optimizing NNI: done in 1.28031 secs using 399.1% CPU
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Optimizing NNI: done in 1.16027 secs using 398.7% CPU
BETTER TREE FOUND at iteration 1: -102302.208
Optimizing NNI: done in 1.11887 secs using 398.9% CPU
Optimizing NNI: done in 1.04699 secs using 398.6% CPU
Optimizing NNI: done in 2.47914 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.18771 secs using 398.4% CPU
Optimizing NNI: done in 5.62325 secs using 596.7% CPU
Optimizing NNI: done in 1.70834 secs using 398.7% CPU
Iteration 40 / LogL: -60497.610 / Time: 0h:1m:28s (0h:3m:16s left)
BETTER TREE FOUND at iteration 2: -102265.372
Optimizing NNI: done in 1.08115 secs using 399% CPU
Optimizing NNI: done in 1.20145 secs using 398.6% CPU
Optimizing NNI: done in 1.98266 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.24784 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 43: -60472.924
Optimizing NNI: done in 5.36435 secs using 597.9% CPU
Optimizing NNI: done in 1.47354 secs using 398.9% CPU
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BETTER TREE FOUND at iteration 3: -102238.094
Optimizing NNI: done in 1.43663 secs using 398.8% CPU
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Optimizing NNI: done in 1.74676 secs using 399% CPU
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Iteration 50 / LogL: -60474.232 / Time: 0h:1m:42s (0h:3m:15s left)
Optimizing NNI: done in 1.54286 secs using 399.3% CPU
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Optimizing NNI: done in 1.31898 secs using 399.1% CPU
Optimizing NNI: done in 2.0598 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.45464 secs using 399.1% CPU
Optimizing NNI: done in 1.51886 secs using 398.9% CPU
Optimizing NNI: done in 4.73324 secs using 597.3% CPU
Optimizing NNI: done in 1.18945 secs using 399.5% CPU
Optimizing NNI: done in 1.46573 secs using 399.1% CPU
Optimizing NNI: done in 1.18759 secs using 398% CPU
Iteration 60 / LogL: -60476.384 / Time: 0h:1m:56s (0h:2m:44s left)
Optimizing NNI: done in 1.463 secs using 399.2% CPU
Optimizing NNI: done in 5.38424 secs using 597.7% CPU
Optimizing NNI: done in 1.3023 secs using 399% CPU
BETTER TREE FOUND at iteration 9: -102219.925
Optimizing NNI: done in 1.25392 secs using 399.2% CPU
Optimizing NNI: done in 1.28815 secs using 399.1% CPU
Optimizing NNI: done in 2.729 secs using 398.6% CPU
Iteration 10 / LogL: -102300.046 / Time: 0h:1m:34s
Optimizing NNI: done in 1.56278 secs using 399% CPU
Optimizing NNI: done in 5.58787 secs using 596.4% CPU
Iteration 350 / LogL: -198230.923 / Time: 0h:33m:50s (0h:1m:33s left)
Optimizing NNI: done in 1.17974 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.89085 secs using 398.5% CPU
BETTER TREE FOUND at iteration 66: -60471.359
Optimizing NNI: done in 1.54052 secs using 398.9% CPU
Optimizing NNI: done in 2.92045 secs using 398.6% CPU
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Iteration 70 / LogL: -60472.973 / Time: 0h:2m:11s (0h:3m:3s left)
Optimizing NNI: done in 1.812 secs using 398.4% CPU
Optimizing NNI: done in 1.71656 secs using 398.6% CPU
Optimizing NNI: done in 4.77918 secs using 597.1% CPU
Optimizing NNI: done in 2.4202 secs using 398.1% CPU
Optimizing NNI: done in 1.25578 secs using 398.6% CPU
Optimizing NNI: done in 1.48105 secs using 399.1% CPU
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Optimizing NNI: done in 1.14765 secs using 399.1% CPU
Optimizing NNI: done in 4.99559 secs using 596.9% CPU
Optimizing NNI: done in 1.43683 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.02781 secs using 398.9% CPU
BETTER TREE FOUND at iteration 75: -60470.763
Optimizing NNI: done in 1.74102 secs using 398.7% CPU
Optimizing NNI: done in 2.94039 secs using 398.6% CPU
Optimizing NNI: done in 1.27881 secs using 399% CPU
Optimizing NNI: done in 5.30331 secs using 598.1% CPU
Optimizing NNI: done in 1.22819 secs using 399.5% CPU
Optimizing NNI: done in 2.45998 secs using 398.7% CPU
Optimizing NNI: done in 1.08405 secs using 398.6% CPU
Optimizing NNI: done in 1.12874 secs using 399% CPU
Iteration 80 / LogL: -60473.309 / Time: 0h:2m:26s (0h:2m:56s left)
Optimizing NNI: done in 2.52607 secs using 398.6% CPU
Iteration 20 / LogL: -102221.108 / Time: 0h:1m:59s
Finish initializing candidate tree set (20)
Current best tree score: -102219.925 / CPU time: 107.122
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.7519 secs using 398.9% CPU
Optimizing NNI: done in 4.70695 secs using 596.9% CPU
Optimizing NNI: done in 1.85513 secs using 398.6% CPU
Optimizing NNI: done in 1.3188 secs using 398.8% CPU
Optimizing NNI: done in 1.79172 secs using 398.4% CPU
Optimizing NNI: done in 2.69785 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.3969 secs using 398.6% CPU
BETTER TREE FOUND at iteration 22: -102182.982
Optimizing NNI: done in 4.90937 secs using 597.3% CPU
Optimizing NNI: done in 1.3904 secs using 399.3% CPU
Optimizing NNI: done in 1.96971 secs using 398.9% CPU
Optimizing NNI: done in 1.46661 secs using 399% CPU
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Optimizing NNI: done in 2.45298 secs using 399% CPU
Optimizing NNI: done in 4.8469 secs using 597.6% CPU
Optimizing NNI: done in 1.68824 secs using 399% CPU
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Optimizing NNI: done in 1.33158 secs using 398.6% CPU
Iteration 90 / LogL: -60478.265 / Time: 0h:2m:41s (0h:2m:34s left)
Optimizing NNI: done in 2.09442 secs using 399.1% CPU
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Optimizing NNI: done in 4.76829 secs using 597.3% CPU
Optimizing NNI: done in 1.98702 secs using 398.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.82793 secs using 399.3% CPU
BETTER TREE FOUND at iteration 92: -60469.934
Optimizing NNI: done in 1.51588 secs using 398.8% CPU
Optimizing NNI: done in 1.85782 secs using 399% CPU
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Iteration 30 / LogL: -102200.083 / Time: 0h:2m:22s (0h:7m:31s left)
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Iteration 360 / LogL: -198249.028 / Time: 0h:34m:40s (0h:0m:34s left)
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Iteration 100 / LogL: -60471.480 / Time: 0h:2m:57s (0h:2m:44s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 35: -102170.009
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Iteration 110 / LogL: -60475.099 / Time: 0h:3m:10s (0h:2m:23s left)
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Iteration 40 / LogL: -102247.491 / Time: 0h:2m:48s (0h:6m:49s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 42: -102162.921
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 119: -60469.203
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BETTER TREE FOUND at iteration 127: -60467.449
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Iteration 50 / LogL: -102195.900 / Time: 0h:3m:12s (0h:6m:1s left)
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TREE SEARCH COMPLETED AFTER 367 ITERATIONS / Time: 0h:35m:37s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -198180.807
Optimizing NNI: done in 2.119 secs using 398.6% CPU
Optimizing NNI: done in 1.54046 secs using 398.8% CPU
Optimal log-likelihood: -198180.804
Site proportion and rates:  (0.019,0.120) (0.145,0.335) (0.176,0.531) (0.221,0.721) (0.185,1.017) (0.111,1.477) (0.109,2.132) (0.035,3.261)
Parameters optimization took 1 rounds (1.139 sec)
BEST SCORE FOUND : -198180.804
Total tree length: 153.766

Total number of iterations: 367
CPU time used for tree search: 12401.715 sec (3h:26m:41s)
Wall-clock time used for tree search: 2101.987 sec (0h:35m:1s)
Total CPU time used: 12618.746 sec (3h:30m:18s)
Total wall-clock time used: 2138.409 sec (0h:35m:38s)

===> START BOOTSTRAP REPLICATE NUMBER 14

Creating bootstrap alignment (seed: 70477)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.256 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -195819.617
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Iteration 140 / LogL: -60488.847 / Time: 0h:3m:53s (0h:2m:26s left)
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2. Current log-likelihood: -192964.334
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3. Current log-likelihood: -192943.281
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4. Current log-likelihood: -192941.989
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Iteration 60 / LogL: -102255.141 / Time: 0h:3m:34s (0h:4m:57s left)
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5. Current log-likelihood: -192941.195
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Iteration 150 / LogL: -60483.372 / Time: 0h:4m:7s (0h:2m:7s left)
6. Current log-likelihood: -192940.799
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7. Current log-likelihood: -192940.586
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Optimizing NNI: done in 1.17021 secs using 398.6% CPU
Optimal log-likelihood: -192940.470
Site proportion and rates:  (0.011,0.097) (0.036,0.223) (0.113,0.345) (0.215,0.508) (0.139,0.716) (0.218,0.987) (0.158,1.522) (0.110,2.614)
Parameters optimization took 7 rounds (19.727 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 65: -102162.227
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Iteration 160 / LogL: -60471.065 / Time: 0h:4m:21s (0h:1m:50s left)
Calculating distance matrix: done in 9.53701 secs using 599.9% CPU
Computing ML distances took 9.537636 sec (of wall-clock time) 57.212712 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00168991 secs using 419.7% CPU
Constructing RapidNJ tree: done in 0.0338941 secs using 634.6% CPU
Computing RapidNJ tree took 0.035665 sec (of wall-clock time) 0.222808 sec (of CPU time)
Optimizing NNI: done in 2.05367 secs using 398.6% CPU
Optimizing NNI: done in 1.69528 secs using 398.9% CPU
Log-likelihood of RapidNJ tree: -196773.053
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.16759 secs using 398.3% CPU
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Iteration 70 / LogL: -102168.310 / Time: 0h:3m:58s (0h:5m:27s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 167: -60467.393
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 76: -102157.700
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Iteration 80 / LogL: -102175.145 / Time: 0h:4m:22s (0h:5m:18s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 177: -60464.474
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30.068 second
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 178: -60461.112
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 180: -60460.129
Iteration 180 / LogL: -60460.129 / Time: 0h:5m:0s (0h:2m:47s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 186: -60459.812
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Iteration 90 / LogL: -102165.849 / Time: 0h:4m:44s (0h:4m:34s left)
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Computing log-likelihood of 98 initial trees ... 21.271 seconds
Current best score: -192940.470

Do NNI search on 20 best initial trees
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Iteration 190 / LogL: -60496.343 / Time: 0h:5m:15s (0h:2m:40s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 201: -60459.561
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -192411.479 / Time: 0h:3m:5s
Finish initializing candidate tree set (20)
Current best tree score: -192288.242 / CPU time: 153.374
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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TREE SEARCH COMPLETED AFTER 177 ITERATIONS / Time: 0h:7m:58s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102157.700
Optimizing NNI: done in 1.40641 secs using 398.5% CPU
Iteration 320 / LogL: -60474.996 / Time: 0h:8m:27s (0h:2m:5s left)
Optimal log-likelihood: -102157.689
Proportion of invariable sites: 0.042
Site proportion and rates:  (0.087,0.034) (0.098,0.102) (0.064,0.191) (0.117,0.300) (0.117,0.496) (0.077,0.734) (0.133,1.057) (0.187,1.837) (0.076,4.445)
Parameters optimization took 1 rounds (1.223 sec)
BEST SCORE FOUND : -102157.689
Total tree length: 170.495

Total number of iterations: 177
CPU time used for tree search: 1828.477 sec (0h:30m:28s)
Wall-clock time used for tree search: 466.482 sec (0h:7m:46s)
Total CPU time used: 1881.087 sec (0h:31m:21s)
Total wall-clock time used: 479.644 sec (0h:7m:59s)

===> START BOOTSTRAP REPLICATE NUMBER 14

Creating bootstrap alignment (seed: 68196)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.089 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -101796.953
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BETTER TREE FOUND at iteration 37: -192222.797
2. Current log-likelihood: -99844.394
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3. Current log-likelihood: -99770.644
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5. Current log-likelihood: -99765.354
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Iteration 330 / LogL: -60459.036 / Time: 0h:8m:42s (0h:1m:49s left)
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13. Current log-likelihood: -99750.524
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 333: -60457.015
14. Current log-likelihood: -99750.420
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15. Current log-likelihood: -99750.298
Optimal log-likelihood: -99750.208
Proportion of invariable sites: 0.030
Site proportion and rates:  (0.109,0.038) (0.069,0.124) (0.120,0.221) (0.132,0.368) (0.136,0.633) (0.094,0.932) (0.115,1.445) (0.124,2.161) (0.070,4.375)
Parameters optimization took 15 rounds (22.915 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Estimate model parameters (epsilon = 0.100)
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Computing ML distances took 4.715070 sec (of wall-clock time) 18.855165 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000721931 secs using 386.5% CPU
Constructing RapidNJ tree: done in 0.00871301 secs using 364.8% CPU
Computing RapidNJ tree took 0.009495 sec (of wall-clock time) 0.037066 sec (of CPU time)
Optimizing NNI: done in 1.20705 secs using 399.5% CPU
Log-likelihood of RapidNJ tree: -100043.716
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.61616 secs using 399.2% CPU
Iteration 340 / LogL: -60460.601 / Time: 0h:8m:57s (0h:2m:27s left)
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10.431 second
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Computing log-likelihood of 98 initial trees ... 10.071 seconds
Current best score: -99750.208

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 390 / LogL: -60540.137 / Time: 0h:10m:12s (0h:1m:7s left)
Optimizing NNI: done in 2.58581 secs using 398.5% CPU
Optimizing NNI: done in 1.38126 secs using 399.2% CPU
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Optimizing NNI: done in 5.28431 secs using 596.9% CPU
Iteration 60 / LogL: -192915.531 / Time: 0h:6m:27s (0h:10m:10s left)
Optimizing NNI: done in 2.81067 secs using 398.5% CPU
Optimizing NNI: done in 1.2202 secs using 398.8% CPU
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Optimizing NNI: done in 1.42578 secs using 398.6% CPU
Optimizing NNI: done in 3.16408 secs using 398.8% CPU
Iteration 20 / LogL: -99340.745 / Time: 0h:1m:56s
Finish initializing candidate tree set (20)
Current best tree score: -99291.327 / CPU time: 87.553
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 4.19911 secs using 598.2% CPU
Optimizing NNI: done in 1.31803 secs using 398.9% CPU
Optimizing NNI: done in 2.16428 secs using 398.8% CPU
Optimizing NNI: done in 1.29177 secs using 399.1% CPU
Iteration 400 / LogL: -60458.864 / Time: 0h:10m:26s (0h:0m:51s left)
Optimizing NNI: done in 1.46721 secs using 398.6% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.49127 secs using 399.3% CPU
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Optimizing NNI: done in 1.95436 secs using 398.5% CPU
BETTER TREE FOUND at iteration 63: -192179.544
Optimizing NNI: done in 1.5205 secs using 399.1% CPU
Optimizing NNI: done in 2.31544 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.48581 secs using 399% CPU
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Optimizing NNI: done in 4.12731 secs using 597.5% CPU
Optimizing NNI: done in 1.56571 secs using 398.8% CPU
BETTER TREE FOUND at iteration 409: -60457.011
Optimizing NNI: done in 1.46644 secs using 399.1% CPU
Iteration 410 / LogL: -60461.116 / Time: 0h:10m:42s (0h:2m:35s left)
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Optimizing NNI: done in 4.57199 secs using 597.9% CPU
Optimizing NNI: done in 1.67553 secs using 399.4% CPU
BETTER TREE FOUND at iteration 26: -99286.787
Optimizing NNI: done in 1.46038 secs using 398.8% CPU
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Optimizing NNI: done in 1.33437 secs using 399.5% CPU
Iteration 420 / LogL: -60461.047 / Time: 0h:10m:56s (0h:2m:19s left)
Optimizing NNI: done in 4.0067 secs using 598.1% CPU
Optimizing NNI: done in 1.21958 secs using 398.7% CPU
Optimizing NNI: done in 1.56892 secs using 398.8% CPU
BETTER TREE FOUND at iteration 30: -99284.636
Iteration 30 / LogL: -99284.636 / Time: 0h:2m:32s (0h:8m:45s left)
Optimizing NNI: done in 1.68124 secs using 399.1% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.24532 secs using 399.5% CPU
Optimizing NNI: done in 4.1656 secs using 597.6% CPU
Iteration 70 / LogL: -192203.312 / Time: 0h:7m:12s (0h:9m:43s left)
BETTER TREE FOUND at iteration 32: -99274.053
Optimizing NNI: done in 1.43857 secs using 398.8% CPU
Optimizing NNI: done in 1.24607 secs using 399% CPU
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Iteration 430 / LogL: -60498.277 / Time: 0h:11m:11s (0h:2m:3s left)
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Iteration 40 / LogL: -99274.388 / Time: 0h:2m:56s (0h:6m:56s left)
Optimizing NNI: done in 1.48933 secs using 398.8% CPU
Iteration 440 / LogL: -60457.385 / Time: 0h:11m:24s (0h:1m:47s left)
Optimizing NNI: done in 1.71662 secs using 398.9% CPU
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Optimizing NNI: done in 1.54194 secs using 398.5% CPU
BETTER TREE FOUND at iteration 447: -60457.011
Optimizing NNI: done in 4.28605 secs using 597.9% CPU
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Optimizing NNI: done in 1.44295 secs using 399.1% CPU
Iteration 450 / LogL: -60509.224 / Time: 0h:11m:39s (0h:2m:31s left)
Optimizing NNI: done in 1.95101 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.48974 secs using 597.7% CPU
Optimizing NNI: done in 1.51358 secs using 399% CPU
BETTER TREE FOUND at iteration 454: -60457.010
BETTER TREE FOUND at iteration 50: -99272.842
Iteration 50 / LogL: -99272.842 / Time: 0h:3m:18s (0h:6m:45s left)
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Iteration 80 / LogL: -192206.592 / Time: 0h:7m:56s (0h:8m:20s left)
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Iteration 460 / LogL: -60460.878 / Time: 0h:11m:54s (0h:2m:26s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 58: -99267.702
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Iteration 470 / LogL: -60468.231 / Time: 0h:12m:7s (0h:2m:10s left)
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Iteration 60 / LogL: -99286.600 / Time: 0h:3m:42s (0h:6m:10s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 63: -99266.304
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Iteration 480 / LogL: -60462.265 / Time: 0h:12m:22s (0h:1m:54s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 65: -99262.141
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Iteration 90 / LogL: -192256.345 / Time: 0h:8m:38s (0h:7m:5s left)
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Iteration 490 / LogL: -60459.573 / Time: 0h:12m:36s (0h:1m:38s left)
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Iteration 70 / LogL: -99302.472 / Time: 0h:4m:10s (0h:5m:44s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 500 / LogL: -60458.530 / Time: 0h:12m:50s (0h:1m:23s left)
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BETTER TREE FOUND at iteration 76: -99258.490
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Iteration 80 / LogL: -99293.367 / Time: 0h:4m:33s (0h:5m:32s left)
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Iteration 510 / LogL: -60466.360 / Time: 0h:13m:4s (0h:1m:7s left)
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Iteration 100 / LogL: -192319.582 / Time: 0h:9m:21s (0h:5m:57s left)
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Iteration 520 / LogL: -60468.182 / Time: 0h:13m:19s (0h:0m:52s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 88: -99256.501
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 90: -99253.179
Iteration 90 / LogL: -99253.179 / Time: 0h:5m:2s (0h:5m:39s left)
Optimizing NNI: done in 1.32661 secs using 398.6% CPU
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Iteration 530 / LogL: -60459.040 / Time: 0h:13m:35s (0h:0m:36s left)
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Iteration 540 / LogL: -60458.266 / Time: 0h:13m:50s (0h:0m:21s left)
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Iteration 100 / LogL: -99272.224 / Time: 0h:5m:26s (0h:4m:56s left)
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Iteration 110 / LogL: -192253.981 / Time: 0h:10m:4s (0h:4m:54s left)
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Iteration 550 / LogL: -60457.255 / Time: 0h:14m:4s (0h:0m:6s left)
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Optimizing NNI: done in 1.29948 secs using 399.6% CPU
TREE SEARCH COMPLETED AFTER 555 ITERATIONS / Time: 0h:14m:10s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60457.010
Optimal log-likelihood: -60457.002
Site proportion and rates:  (0.101,0.056) (0.092,0.193) (0.202,0.366) (0.170,0.628) (0.195,1.025) (0.160,1.843) (0.055,2.690) (0.024,6.281)
Parameters optimization took 1 rounds (0.366 sec)
BEST SCORE FOUND : -60457.002
Total tree length: 46.008

Total number of iterations: 555
CPU time used for tree search: 3337.368 sec (0h:55m:37s)
Wall-clock time used for tree search: 840.554 sec (0h:14m:0s)
Total CPU time used: 3380.197 sec (0h:56m:20s)
Total wall-clock time used: 851.269 sec (0h:14m:11s)

===> START BOOTSTRAP REPLICATE NUMBER 53

Creating bootstrap alignment (seed: 67515)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59549.504
Optimizing NNI: done in 2.37828 secs using 398.8% CPU
2. Current log-likelihood: -58984.014
3. Current log-likelihood: -58940.682
4. Current log-likelihood: -58930.143
Optimizing NNI: done in 2.44602 secs using 398.7% CPU
5. Current log-likelihood: -58926.492
Optimizing NNI: done in 4.33872 secs using 597.8% CPU
6. Current log-likelihood: -58925.710
Optimizing NNI: done in 1.94395 secs using 398.4% CPU
Iteration 110 / LogL: -99676.568 / Time: 0h:5m:48s (0h:4m:15s left)
7. Current log-likelihood: -58925.453
8. Current log-likelihood: -58925.338
Optimal log-likelihood: -58925.282
Site proportion and rates:  (0.121,0.071) (0.092,0.185) (0.146,0.368) (0.176,0.557) (0.191,0.841) (0.092,1.424) (0.137,2.197) (0.046,5.061)
Parameters optimization took 8 rounds (6.061 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.93349 secs using 398.8% CPU
Calculating distance matrix: done in 1.11452 secs using 400% CPU
Computing ML distances took 1.114703 sec (of wall-clock time) 4.458151 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000406981 secs using 423.1% CPU
Constructing RapidNJ tree: done in 0.00444412 secs using 360.7% CPU
Computing RapidNJ tree took 0.004918 sec (of wall-clock time) 0.018757 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59256.158
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.01365 secs using 597.5% CPU
Optimizing NNI: done in 2.30107 secs using 398.3% CPU
Optimizing NNI: done in 2.59376 secs using 398.3% CPU
5.121 second
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Optimizing NNI: done in 4.07534 secs using 597.4% CPU
Computing log-likelihood of 98 initial trees ... 5.116 seconds
Current best score: -58925.282

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -58812.335
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 117: -99252.780
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Estimate model parameters (epsilon = 0.100)
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Iteration 120 / LogL: -192260.703 / Time: 0h:10m:48s (0h:3m:54s left)
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Iteration 120 / LogL: -99268.096 / Time: 0h:6m:14s (0h:5m:5s left)
BETTER TREE FOUND at iteration 4: -58758.136
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 5: -58749.313
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 13: -58746.691
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Iteration 130 / LogL: -99260.012 / Time: 0h:6m:35s (0h:4m:26s left)
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Iteration 20 / LogL: -58768.378 / Time: 0h:0m:58s
Finish initializing candidate tree set (20)
Current best tree score: -58746.691 / CPU time: 50.337
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 25: -58735.033
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 137: -99252.542
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 141: -192178.919
BETTER TREE FOUND at iteration 62: -58734.893
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 152: -192172.602
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Iteration 120 / LogL: -58824.362 / Time: 0h:3m:25s (0h:1m:15s left)
Optimizing NNI: done in 2.06156 secs using 398.6% CPU
Optimizing NNI: done in 4.7008 secs using 597.6% CPU
Iteration 160 / LogL: -192236.972 / Time: 0h:13m:44s (0h:7m:56s left)
Optimizing NNI: done in 1.38382 secs using 399.3% CPU
Optimizing NNI: done in 2.25996 secs using 398.3% CPU
Optimizing NNI: done in 1.49572 secs using 399.4% CPU
Optimizing NNI: done in 1.41469 secs using 399.1% CPU
Optimizing NNI: done in 3.80953 secs using 597.9% CPU
Optimizing NNI: done in 2.39878 secs using 398.5% CPU
Iteration 200 / LogL: -99260.129 / Time: 0h:9m:13s (0h:2m:7s left)
Optimizing NNI: done in 1.21515 secs using 399.3% CPU
Optimizing NNI: done in 1.16749 secs using 398.8% CPU
Optimizing NNI: done in 2.33299 secs using 398.6% CPU
Optimizing NNI: done in 1.342 secs using 398.7% CPU
Optimizing NNI: done in 4.53518 secs using 597.6% CPU
Optimizing NNI: done in 1.35337 secs using 398.6% CPU
Optimizing NNI: done in 2.35115 secs using 398.4% CPU
Optimizing NNI: done in 1.82612 secs using 398.5% CPU
Optimizing NNI: done in 2.26274 secs using 398.5% CPU
Optimizing NNI: done in 1.39064 secs using 398.7% CPU
Optimizing NNI: done in 4.0181 secs using 597% CPU
Optimizing NNI: done in 2.2658 secs using 398.6% CPU
Optimizing NNI: done in 1.46927 secs using 399.2% CPU
Iteration 130 / LogL: -58752.291 / Time: 0h:3m:39s (0h:0m:57s left)
Optimizing NNI: done in 1.28308 secs using 398.8% CPU
Optimizing NNI: done in 2.26092 secs using 399% CPU
Optimizing NNI: done in 1.06614 secs using 398.8% CPU
Optimizing NNI: done in 3.68635 secs using 598.2% CPU
Optimizing NNI: done in 1.41106 secs using 399.2% CPU
Optimizing NNI: done in 2.13848 secs using 399.1% CPU
Optimizing NNI: done in 1.54883 secs using 399% CPU
Optimizing NNI: done in 2.14849 secs using 398.8% CPU
Optimizing NNI: done in 1.34788 secs using 398.9% CPU
Optimizing NNI: done in 4.46417 secs using 597.6% CPU
Optimizing NNI: done in 1.39847 secs using 399.5% CPU
Optimizing NNI: done in 2.18018 secs using 398.3% CPU
Optimizing NNI: done in 1.27064 secs using 398.9% CPU
Optimizing NNI: done in 1.25035 secs using 399.4% CPU
Optimizing NNI: done in 2.08912 secs using 398.5% CPU
Optimizing NNI: done in 4.11611 secs using 596.8% CPU
Optimizing NNI: done in 1.50656 secs using 399.4% CPU
Optimizing NNI: done in 2.15815 secs using 399.1% CPU
Iteration 210 / LogL: -99260.412 / Time: 0h:9m:35s (0h:1m:39s left)
Optimizing NNI: done in 1.41026 secs using 398.7% CPU
Iteration 140 / LogL: -58735.792 / Time: 0h:3m:52s (0h:0m:40s left)
Optimizing NNI: done in 1.81279 secs using 398.8% CPU
Optimizing NNI: done in 1.29801 secs using 398.9% CPU
Optimizing NNI: done in 4.14596 secs using 598% CPU
Optimizing NNI: done in 1.33605 secs using 398.7% CPU
Optimizing NNI: done in 2.16732 secs using 398.6% CPU
Optimizing NNI: done in 1.40654 secs using 398.7% CPU
Optimizing NNI: done in 1.35168 secs using 398.9% CPU
Optimizing NNI: done in 2.07716 secs using 398.6% CPU
Optimizing NNI: done in 3.97698 secs using 597.8% CPU
Optimizing NNI: done in 1.55893 secs using 399.1% CPU
Optimizing NNI: done in 2.45425 secs using 399.1% CPU
Optimizing NNI: done in 1.60295 secs using 398.9% CPU
Optimizing NNI: done in 1.52736 secs using 399.2% CPU
Optimizing NNI: done in 2.44095 secs using 398.5% CPU
Optimizing NNI: done in 4.30667 secs using 597.3% CPU
Optimizing NNI: done in 1.55492 secs using 399.2% CPU
Optimizing NNI: done in 2.01932 secs using 398.7% CPU
Optimizing NNI: done in 1.39329 secs using 399% CPU
Optimizing NNI: done in 3.87558 secs using 597.6% CPU
Iteration 170 / LogL: -192308.038 / Time: 0h:14m:25s (0h:7m:0s left)
Optimizing NNI: done in 1.73013 secs using 398.9% CPU
Iteration 150 / LogL: -58742.257 / Time: 0h:4m:7s (0h:0m:23s left)
Optimizing NNI: done in 3.46654 secs using 398.3% CPU
Optimizing NNI: done in 1.45371 secs using 399.2% CPU
Optimizing NNI: done in 1.52093 secs using 398.8% CPU
Optimizing NNI: done in 2.24251 secs using 398.5% CPU
Optimizing NNI: done in 3.89903 secs using 597.5% CPU
Optimizing NNI: done in 1.42698 secs using 399.3% CPU
Optimizing NNI: done in 1.90166 secs using 398% CPU
Optimizing NNI: done in 1.46709 secs using 398.7% CPU
Optimizing NNI: done in 1.34032 secs using 399.6% CPU
Optimizing NNI: done in 4.05453 secs using 597.8% CPU
Optimizing NNI: done in 2.48591 secs using 399% CPU
Iteration 220 / LogL: -99382.699 / Time: 0h:9m:58s (0h:1m:11s left)
Optimizing NNI: done in 1.42901 secs using 399.1% CPU
Optimizing NNI: done in 1.41573 secs using 399.2% CPU
Optimizing NNI: done in 2.51633 secs using 398.2% CPU
Optimizing NNI: done in 1.67127 secs using 398.5% CPU
Optimizing NNI: done in 4.659 secs using 598.5% CPU
Optimizing NNI: done in 2.57495 secs using 399.1% CPU
Optimizing NNI: done in 1.45443 secs using 399.2% CPU
Optimizing NNI: done in 1.47257 secs using 399.6% CPU
Iteration 160 / LogL: -58755.275 / Time: 0h:4m:22s (0h:0m:6s left)
Optimizing NNI: done in 2.75908 secs using 398.9% CPU
Optimizing NNI: done in 1.41083 secs using 399% CPU
Optimizing NNI: done in 3.79852 secs using 598.1% CPU
Optimizing NNI: done in 1.62565 secs using 398.7% CPU
Optimizing NNI: done in 2.10889 secs using 398.8% CPU
Optimizing NNI: done in 1.40488 secs using 399% CPU
Optimizing NNI: done in 3.84366 secs using 597.7% CPU
Optimizing NNI: done in 2.48108 secs using 398.3% CPU
Optimizing NNI: done in 1.44338 secs using 398.8% CPU
Optimizing NNI: done in 1.47375 secs using 398.5% CPU
TREE SEARCH COMPLETED AFTER 165 ITERATIONS / Time: 0h:4m:29s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58734.888
Optimizing NNI: done in 2.24073 secs using 398.7% CPU
Optimal log-likelihood: -58734.878
Site proportion and rates:  (0.109,0.070) (0.113,0.182) (0.200,0.405) (0.158,0.653) (0.136,0.872) (0.090,1.341) (0.144,2.148) (0.051,4.716)
Parameters optimization took 1 rounds (0.565 sec)
BEST SCORE FOUND : -58734.878
Total tree length: 46.045

Total number of iterations: 165
CPU time used for tree search: 1031.044 sec (0h:17m:11s)
Wall-clock time used for tree search: 262.161 sec (0h:4m:22s)
Total CPU time used: 1064.320 sec (0h:17m:44s)
Total wall-clock time used: 270.477 sec (0h:4m:30s)

===> START BOOTSTRAP REPLICATE NUMBER 54

Creating bootstrap alignment (seed: 67516)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.051 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60870.219
Optimizing NNI: done in 3.32223 secs using 596.9% CPU
2. Current log-likelihood: -60247.495
3. Current log-likelihood: -60234.208
Optimizing NNI: done in 2.17695 secs using 398.7% CPU
4. Current log-likelihood: -60225.672
5. Current log-likelihood: -60216.528
Optimizing NNI: done in 1.90978 secs using 398.7% CPU
6. Current log-likelihood: -60215.568
Optimal log-likelihood: -60215.535
Site proportion and rates:  (0.110,0.062) (0.108,0.192) (0.132,0.361) (0.105,0.497) (0.187,0.798) (0.189,1.348) (0.132,2.280) (0.037,4.526)
Parameters optimization took 6 rounds (5.013 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.95111 secs using 597.4% CPU
Optimizing NNI: done in 2.04521 secs using 398.5% CPU
Calculating distance matrix: done in 1.08991 secs using 399.9% CPU
Computing ML distances took 1.090085 sec (of wall-clock time) 4.358690 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000400066 secs using 418.9% CPU
Constructing RapidNJ tree: done in 0.00430918 secs using 462% CPU
Computing RapidNJ tree took 0.004762 sec (of wall-clock time) 0.022638 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60277.080
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.18652 secs using 399.3% CPU
Iteration 230 / LogL: -99289.760 / Time: 0h:10m:22s (0h:0m:43s left)
Optimizing NNI: done in 1.94731 secs using 398.9% CPU
Optimizing NNI: done in 4.61085 secs using 597.6% CPU
5.149 second
Optimizing NNI: done in 2.17786 secs using 398.9% CPU
Optimizing NNI: done in 2.22768 secs using 398.5% CPU
Optimizing NNI: done in 5.1798 secs using 597.7% CPU
Optimizing NNI: done in 2.39084 secs using 398.5% CPU
Computing log-likelihood of 98 initial trees ... 6.166 seconds
Current best score: -60098.240

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.22973 secs using 398.3% CPU
Optimizing NNI: done in 1.50336 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.86219 secs using 596.5% CPU
Iteration 180 / LogL: -192190.553 / Time: 0h:15m:9s (0h:6m:5s left)
BETTER TREE FOUND at iteration 1: -59914.236
Optimizing NNI: done in 2.06282 secs using 399% CPU
Optimizing NNI: done in 1.59647 secs using 398.8% CPU
Optimizing NNI: done in 2.29483 secs using 398.6% CPU
Optimizing NNI: done in 1.57939 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.96104 secs using 597.2% CPU
Optimizing NNI: done in 2.47359 secs using 398.6% CPU
Optimizing NNI: done in 4.05174 secs using 598.2% CPU
Optimizing NNI: done in 2.36466 secs using 398.6% CPU
BETTER TREE FOUND at iteration 3: -59899.486
Optimizing NNI: done in 1.61763 secs using 399.3% CPU
Optimizing NNI: done in 2.54589 secs using 398.8% CPU
Iteration 240 / LogL: -99255.869 / Time: 0h:10m:45s (0h:0m:16s left)
Optimizing NNI: done in 1.64445 secs using 399.3% CPU
Optimizing NNI: done in 4.17423 secs using 597.6% CPU
Optimizing NNI: done in 2.50078 secs using 398.6% CPU
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Optimizing NNI: done in 1.70628 secs using 397.4% CPU
Optimizing NNI: done in 2.28605 secs using 398.6% CPU
Optimizing NNI: done in 4.11609 secs using 597.7% CPU
Optimizing NNI: done in 1.9675 secs using 399% CPU
Optimizing NNI: done in 2.31391 secs using 398.4% CPU
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Optimizing NNI: done in 2.31058 secs using 398.8% CPU
Optimizing NNI: done in 1.49656 secs using 399.3% CPU
Iteration 10 / LogL: -59905.456 / Time: 0h:0m:40s
Optimizing NNI: done in 5.0901 secs using 596.8% CPU
Optimizing NNI: done in 1.6775 secs using 398.7% CPU
Optimizing NNI: done in 2.08929 secs using 398.9% CPU
Optimizing NNI: done in 1.10717 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.12021 secs using 398.9% CPU
BETTER TREE FOUND at iteration 12: -59891.013
Optimizing NNI: done in 3.84589 secs using 597.6% CPU
Optimizing NNI: done in 1.65298 secs using 399.2% CPU
Optimizing NNI: done in 2.25294 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 247 ITERATIONS / Time: 0h:11m:1s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -99252.071
Optimal log-likelihood: -99252.062
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.109,0.032) (0.066,0.118) (0.127,0.214) (0.127,0.359) (0.127,0.595) (0.109,0.915) (0.122,1.426) (0.120,2.207) (0.065,4.664)
Parameters optimization took 1 rounds (0.780 sec)
BEST SCORE FOUND : -99252.062
Total tree length: 155.494

Total number of iterations: 247
CPU time used for tree search: 2489.404 sec (0h:41m:29s)
Wall-clock time used for tree search: 632.382 sec (0h:10m:32s)
Total CPU time used: 2607.756 sec (0h:43m:27s)
Total wall-clock time used: 662.065 sec (0h:11m:2s)

===> START BOOTSTRAP REPLICATE NUMBER 15

Creating bootstrap alignment (seed: 68197)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.075 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -103755.313
Optimizing NNI: done in 1.36521 secs using 399% CPU
Optimizing NNI: done in 1.76028 secs using 398.8% CPU
Optimizing NNI: done in 4.00347 secs using 597.4% CPU
2. Current log-likelihood: -101907.617
Optimizing NNI: done in 1.50589 secs using 398.4% CPU
3. Current log-likelihood: -101803.948
Optimizing NNI: done in 1.5849 secs using 398.8% CPU
4. Current log-likelihood: -101797.195
Optimizing NNI: done in 3.82302 secs using 597.2% CPU
Optimizing NNI: done in 1.60756 secs using 399% CPU
Optimal log-likelihood: -101797.080
Proportion of invariable sites: 0.031
Site proportion and rates:  (0.097,0.046) (0.067,0.122) (0.088,0.220) (0.100,0.344) (0.063,0.444) (0.156,0.708) (0.138,1.177) (0.205,1.915) (0.055,4.378)
Parameters optimization took 4 rounds (6.596 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.49821 secs using 398.7% CPU
Optimizing NNI: done in 1.64524 secs using 398.8% CPU
Iteration 20 / LogL: -59943.787 / Time: 0h:0m:57s
Finish initializing candidate tree set (20)
Current best tree score: -59891.013 / CPU time: 51.282
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.2513 secs using 597.4% CPU
Calculating distance matrix: done in 4.64501 secs using 399.9% CPU
Computing ML distances took 4.645268 sec (of wall-clock time) 18.577077 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000700951 secs using 95.3% CPU
Constructing RapidNJ tree: done in 0.00853491 secs using 393.3% CPU
Computing RapidNJ tree took 0.009299 sec (of wall-clock time) 0.034743 sec (of CPU time)
Optimizing NNI: done in 1.60212 secs using 399.3% CPU
Log-likelihood of RapidNJ tree: -102078.890
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.57069 secs using 398.6% CPU
Optimizing NNI: done in 1.45284 secs using 398.9% CPU
Optimizing NNI: done in 4.8446 secs using 597.2% CPU
Iteration 190 / LogL: -192208.923 / Time: 0h:15m:52s (0h:5m:12s left)
Optimizing NNI: done in 1.35061 secs using 398.5% CPU
Optimizing NNI: done in 1.40089 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -59883.860
Optimizing NNI: done in 1.60707 secs using 398.6% CPU
Optimizing NNI: done in 5.47202 secs using 597.8% CPU
Optimizing NNI: done in 1.48248 secs using 398.8% CPU
10.347 second
Optimizing NNI: done in 1.57748 secs using 399.2% CPU
Optimizing NNI: done in 1.71564 secs using 398.2% CPU
Optimizing NNI: done in 4.78002 secs using 597.7% CPU
Optimizing NNI: done in 1.54472 secs using 398.5% CPU
Iteration 30 / LogL: -59893.114 / Time: 0h:1m:14s (0h:4m:5s left)
Optimizing NNI: done in 1.47027 secs using 399% CPU
Optimizing NNI: done in 4.09955 secs using 597.8% CPU
Optimizing NNI: done in 1.66552 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -59883.261
Computing log-likelihood of 98 initial trees ... 9.888 seconds
Current best score: -101797.080

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.76463 secs using 399.4% CPU
Optimizing NNI: done in 4.07167 secs using 598.1% CPU
Optimizing NNI: done in 1.38917 secs using 399% CPU
Optimizing NNI: done in 2.23709 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.44917 secs using 399.1% CPU
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Optimizing NNI: done in 4.10144 secs using 598% CPU
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Optimizing NNI: done in 4.47234 secs using 597.3% CPU
Optimizing NNI: done in 1.44609 secs using 398.9% CPU
Iteration 40 / LogL: -59897.802 / Time: 0h:1m:31s (0h:3m:36s left)
Optimizing NNI: done in 1.24046 secs using 399.3% CPU
Optimizing NNI: done in 4.24881 secs using 597.9% CPU
Optimizing NNI: done in 1.81373 secs using 399.1% CPU
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Optimizing NNI: done in 1.26765 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 47: -59882.267
Optimizing NNI: done in 3.95422 secs using 598.2% CPU
Optimizing NNI: done in 1.59662 secs using 398.6% CPU
Optimizing NNI: done in 1.4432 secs using 398.9% CPU
Optimizing NNI: done in 1.48498 secs using 399.1% CPU
Iteration 50 / LogL: -59892.793 / Time: 0h:1m:47s (0h:3m:33s left)
Optimizing NNI: done in 3.84771 secs using 598.1% CPU
Iteration 200 / LogL: -192237.809 / Time: 0h:16m:37s (0h:4m:20s left)
BETTER TREE FOUND at iteration 1: -101237.660
Optimizing NNI: done in 1.48546 secs using 399.3% CPU
Optimizing NNI: done in 1.63154 secs using 397.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.42423 secs using 398.9% CPU
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Optimizing NNI: done in 1.42785 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -101180.401
BETTER TREE FOUND at iteration 56: -59879.830
Optimizing NNI: done in 1.88909 secs using 398% CPU
Optimizing NNI: done in 1.47697 secs using 398.9% CPU
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Optimizing NNI: done in 1.47066 secs using 399% CPU
Iteration 60 / LogL: -59882.835 / Time: 0h:2m:3s (0h:3m:21s left)
Optimizing NNI: done in 4.29657 secs using 597.3% CPU
Optimizing NNI: done in 2.47107 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.88577 secs using 399.3% CPU
Optimizing NNI: done in 1.95801 secs using 399.1% CPU
BETTER TREE FOUND at iteration 7: -101177.658
Optimizing NNI: done in 1.47691 secs using 399.3% CPU
Optimizing NNI: done in 4.55678 secs using 597.7% CPU
Optimizing NNI: done in 1.55081 secs using 398.9% CPU
Optimizing NNI: done in 2.56672 secs using 398.2% CPU
Optimizing NNI: done in 1.51979 secs using 398.6% CPU
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Optimizing NNI: done in 1.9446 secs using 399% CPU
Optimizing NNI: done in 4.10881 secs using 597.8% CPU
Optimizing NNI: done in 2.43668 secs using 399% CPU
Iteration 10 / LogL: -101249.790 / Time: 0h:1m:27s
Optimizing NNI: done in 1.91633 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.50139 secs using 399.1% CPU
BETTER TREE FOUND at iteration 67: -59874.874
Optimizing NNI: done in 4.3517 secs using 598.2% CPU
Optimizing NNI: done in 2.07514 secs using 398.6% CPU
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Optimizing NNI: done in 1.36791 secs using 398.9% CPU
Iteration 70 / LogL: -59877.943 / Time: 0h:2m:22s (0h:3m:20s left)
Optimizing NNI: done in 4.24882 secs using 597.3% CPU
Optimizing NNI: done in 1.54032 secs using 399% CPU
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Iteration 210 / LogL: -192266.209 / Time: 0h:17m:20s (0h:3m:29s left)
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Iteration 80 / LogL: -59877.561 / Time: 0h:2m:37s (0h:2m:53s left)
Optimizing NNI: done in 2.55867 secs using 397.4% CPU
Iteration 20 / LogL: -101195.925 / Time: 0h:1m:50s
Finish initializing candidate tree set (20)
Current best tree score: -101177.658 / CPU time: 97.678
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.54497 secs using 399% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.14095 secs using 398.4% CPU
BETTER TREE FOUND at iteration 87: -59869.376
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Iteration 90 / LogL: -59878.838 / Time: 0h:2m:54s (0h:3m:10s left)
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Iteration 30 / LogL: -101201.607 / Time: 0h:2m:13s (0h:5m:54s left)
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Iteration 100 / LogL: -59875.573 / Time: 0h:3m:10s (0h:2m:47s left)
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Iteration 220 / LogL: -192235.909 / Time: 0h:18m:3s (0h:2m:38s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 221: -192170.589
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BETTER TREE FOUND at iteration 38: -101175.589
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Iteration 110 / LogL: -59873.045 / Time: 0h:3m:25s (0h:2m:24s left)
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BETTER TREE FOUND at iteration 39: -101172.105
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Iteration 40 / LogL: -101181.949 / Time: 0h:2m:40s (0h:6m:48s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 114: -59864.676
Optimizing NNI: done in 2.25588 secs using 398.5% CPU
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Iteration 120 / LogL: -59887.039 / Time: 0h:3m:41s (0h:2m:54s left)
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Iteration 50 / LogL: -101266.987 / Time: 0h:3m:2s (0h:5m:32s left)
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Iteration 130 / LogL: -59867.736 / Time: 0h:3m:57s (0h:2m:34s left)
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Iteration 230 / LogL: -192199.821 / Time: 0h:18m:49s (0h:7m:28s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 133: -59863.015
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BETTER TREE FOUND at iteration 55: -101169.769
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 231: -192164.398
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Iteration 140 / LogL: -59863.650 / Time: 0h:4m:13s (0h:2m:49s left)
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Iteration 60 / LogL: -101173.530 / Time: 0h:3m:26s (0h:5m:32s left)
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Iteration 150 / LogL: -59868.570 / Time: 0h:4m:28s (0h:2m:29s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 237: -192150.288
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Iteration 70 / LogL: -101169.829 / Time: 0h:3m:49s (0h:4m:42s left)
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Iteration 160 / LogL: -59867.997 / Time: 0h:4m:43s (0h:2m:9s left)
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Iteration 240 / LogL: -192218.795 / Time: 0h:19m:36s (0h:7m:57s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 164: -59862.756
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Iteration 80 / LogL: -101179.570 / Time: 0h:4m:11s (0h:3m:58s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 180 / LogL: -59866.005 / Time: 0h:5m:15s (0h:2m:27s left)
BETTER TREE FOUND at iteration 87: -101166.094
Optimizing NNI: done in 1.45319 secs using 398.5% CPU
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Iteration 90 / LogL: -101211.751 / Time: 0h:4m:34s (0h:4m:58s left)
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Iteration 250 / LogL: -192337.608 / Time: 0h:20m:19s (0h:7m:5s left)
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Iteration 190 / LogL: -59862.761 / Time: 0h:5m:30s (0h:2m:9s left)
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Iteration 100 / LogL: -101178.040 / Time: 0h:4m:55s (0h:4m:19s left)
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Iteration 210 / LogL: -59871.377 / Time: 0h:5m:59s (0h:1m:32s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 110 / LogL: -101209.479 / Time: 0h:5m:15s (0h:3m:43s left)
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BETTER TREE FOUND at iteration 212: -59861.795
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Estimate model parameters (epsilon = 0.100)
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Iteration 260 / LogL: -192168.323 / Time: 0h:21m:1s (0h:6m:14s left)
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BETTER TREE FOUND at iteration 113: -101163.964
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Iteration 220 / LogL: -59879.677 / Time: 0h:6m:16s (0h:2m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 237: -59861.345
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 288: -192144.406
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Iteration 330 / LogL: -59865.221 / Time: 0h:9m:4s (0h:0m:11s left)
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Iteration 300 / LogL: -192162.950 / Time: 0h:23m:58s (0h:7m:3s left)
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Optimizing NNI: done in 1.64949 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 338 ITERATIONS / Time: 0h:9m:15s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59861.345
Optimal log-likelihood: -59861.342
Site proportion and rates:  (0.109,0.062) (0.103,0.189) (0.153,0.351) (0.149,0.579) (0.169,0.915) (0.168,1.483) (0.110,2.327) (0.039,4.497)
Parameters optimization took 1 rounds (0.462 sec)
BEST SCORE FOUND : -59861.342
Total tree length: 44.371

Total number of iterations: 338
CPU time used for tree search: 2176.164 sec (0h:36m:16s)
Wall-clock time used for tree search: 549.266 sec (0h:9m:9s)
Total CPU time used: 2204.813 sec (0h:36m:44s)
Total wall-clock time used: 556.421 sec (0h:9m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 55

Creating bootstrap alignment (seed: 67517)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60594.611
Optimizing NNI: done in 2.23199 secs using 398.9% CPU
2. Current log-likelihood: -60000.323
Optimizing NNI: done in 4.71268 secs using 597.2% CPU
3. Current log-likelihood: -59993.214
4. Current log-likelihood: -59992.414
Optimizing NNI: done in 1.9995 secs using 398.8% CPU
Iteration 200 / LogL: -101173.809 / Time: 0h:8m:31s (0h:0m:33s left)
5. Current log-likelihood: -59991.808
6. Current log-likelihood: -59989.760
7. Current log-likelihood: -59974.688
Optimizing NNI: done in 1.87516 secs using 398.9% CPU
8. Current log-likelihood: -59972.421
Optimizing NNI: done in 4.46757 secs using 597.4% CPU
9. Current log-likelihood: -59972.040
10. Current log-likelihood: -59971.543
Optimizing NNI: done in 2.42638 secs using 398.1% CPU
11. Current log-likelihood: -59970.529
12. Current log-likelihood: -59968.509
13. Current log-likelihood: -59966.291
Optimizing NNI: done in 2.2383 secs using 398.2% CPU
14. Current log-likelihood: -59965.343
Optimizing NNI: done in 4.19945 secs using 597.9% CPU
15. Current log-likelihood: -59965.071
Optimal log-likelihood: -59964.989
Site proportion and rates:  (0.088,0.062) (0.150,0.186) (0.125,0.388) (0.229,0.629) (0.137,0.990) (0.107,1.602) (0.134,2.347) (0.030,5.118)
Parameters optimization took 15 rounds (11.025 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.04369 secs using 398.9% CPU
Calculating distance matrix: done in 1.0903 secs using 399.8% CPU
Computing ML distances took 1.090467 sec (of wall-clock time) 4.360039 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000351191 secs using 412.6% CPU
Constructing RapidNJ tree: done in 0.00429797 secs using 346.7% CPU
Computing RapidNJ tree took 0.004703 sec (of wall-clock time) 0.018869 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59979.964
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.2505 secs using 399% CPU
Optimizing NNI: done in 4.3796 secs using 597.8% CPU
Optimizing NNI: done in 1.9762 secs using 398.5% CPU
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5.137 second
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Optimizing NNI: done in 6.67589 secs using 597.7% CPU
Optimizing NNI: done in 2.11428 secs using 398.6% CPU
Computing log-likelihood of 98 initial trees ... 5.117 seconds
Current best score: -59915.895

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.96397 secs using 398.6% CPU
Iteration 210 / LogL: -101172.495 / Time: 0h:8m:52s (0h:0m:7s left)
Optimizing NNI: done in 1.56749 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.03937 secs using 398.9% CPU
Optimizing NNI: done in 5.08149 secs using 597.8% CPU
BETTER TREE FOUND at iteration 1: -59690.150
Optimizing NNI: done in 2.16396 secs using 398.1% CPU
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Optimizing NNI: done in 1.94038 secs using 398.1% CPU
TREE SEARCH COMPLETED AFTER 214 ITERATIONS / Time: 0h:9m:1s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101163.964
2. Current log-likelihood: -101163.954
Optimal log-likelihood: -101163.945
Proportion of invariable sites: 0.031
Site proportion and rates:  (0.092,0.041) (0.069,0.108) (0.089,0.213) (0.116,0.344) (0.064,0.478) (0.145,0.708) (0.152,1.202) (0.189,1.941) (0.055,4.525)
Parameters optimization took 2 rounds (1.508 sec)
BEST SCORE FOUND : -101163.945
Total tree length: 161.862

Total number of iterations: 214
CPU time used for tree search: 2075.678 sec (0h:34m:35s)
Wall-clock time used for tree search: 528.715 sec (0h:8m:48s)
Total CPU time used: 2131.304 sec (0h:35m:31s)
Total wall-clock time used: 542.631 sec (0h:9m:2s)

===> START BOOTSTRAP REPLICATE NUMBER 16

Creating bootstrap alignment (seed: 68198)...

Optimizing NNI: done in 1.72988 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.114 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -110308.980
Optimizing NNI: done in 4.30789 secs using 597% CPU
BETTER TREE FOUND at iteration 5: -59666.021
2. Current log-likelihood: -108282.244
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3. Current log-likelihood: -108226.303
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Optimizing NNI: done in 4.651 secs using 596.3% CPU
Iteration 310 / LogL: -192153.189 / Time: 0h:24m:45s (0h:6m:14s left)
4. Current log-likelihood: -108223.691
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5. Current log-likelihood: -108222.616
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Iteration 10 / LogL: -59725.113 / Time: 0h:0m:42s
Optimizing NNI: done in 0.925595 secs using 398.4% CPU
6. Current log-likelihood: -108221.779
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7. Current log-likelihood: -108221.186
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8. Current log-likelihood: -108220.733
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9. Current log-likelihood: -108220.372
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10. Current log-likelihood: -108220.140
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11. Current log-likelihood: -108219.977
Optimizing NNI: done in 1.07074 secs using 398.9% CPU
Optimizing NNI: done in 4.3907 secs using 597.4% CPU
Optimal log-likelihood: -108219.829
Proportion of invariable sites: 0.036
Site proportion and rates:  (0.058,0.036) (0.111,0.113) (0.036,0.192) (0.115,0.308) (0.085,0.458) (0.149,0.677) (0.156,1.066) (0.181,1.840) (0.073,4.155)
Parameters optimization took 11 rounds (19.380 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Optimizing NNI: done in 1.30077 secs using 398.5% CPU
Iteration 20 / LogL: -59791.660 / Time: 0h:0m:55s
Finish initializing candidate tree set (20)
Current best tree score: -59666.021 / CPU time: 42.087
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.58485 secs using 399% CPU
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Calculating distance matrix: done in 4.72693 secs using 399.9% CPU
Computing ML distances took 4.727297 sec (of wall-clock time) 18.905850 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00074482 secs using 282.4% CPU
Constructing RapidNJ tree: done in 0.00885296 secs using 394.7% CPU
Computing RapidNJ tree took 0.009666 sec (of wall-clock time) 0.037530 sec (of CPU time)
Optimizing NNI: done in 1.39609 secs using 399.2% CPU
Log-likelihood of RapidNJ tree: -108661.591
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.49608 secs using 398.6% CPU
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10.778 second
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Iteration 30 / LogL: -59696.810 / Time: 0h:1m:10s (0h:3m:2s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 34: -59662.123
Optimizing NNI: done in 1.49513 secs using 399.3% CPU
Computing log-likelihood of 98 initial trees ... 10.308 seconds
Current best score: -108219.829

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 45: -59658.430
BETTER TREE FOUND at iteration 1: -107789.450
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Iteration 60 / LogL: -59664.381 / Time: 0h:2m:0s (0h:3m:1s left)
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Iteration 10 / LogL: -107962.867 / Time: 0h:1m:33s
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -107776.139 / Time: 0h:1m:59s
Finish initializing candidate tree set (20)
Current best tree score: -107717.682 / CPU time: 94.004
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -59654.556
Iteration 130 / LogL: -59654.556 / Time: 0h:3m:46s (0h:2m:13s left)
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BETTER TREE FOUND at iteration 57: -107666.396
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Iteration 360 / LogL: -192227.755 / Time: 0h:28m:30s (0h:5m:52s left)
Optimizing NNI: done in 2.65341 secs using 398.9% CPU
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Iteration 160 / LogL: -59668.427 / Time: 0h:4m:31s (0h:1m:18s left)
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Optimizing NNI: done in 2.07719 secs using 398% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 162: -59652.935
Optimizing NNI: done in 2.27144 secs using 398.9% CPU
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Iteration 70 / LogL: -107671.681 / Time: 0h:4m:3s (0h:5m:6s left)
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Iteration 170 / LogL: -59699.995 / Time: 0h:4m:47s (0h:2m:36s left)
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Iteration 80 / LogL: -107745.013 / Time: 0h:4m:23s (0h:4m:17s left)
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Iteration 180 / LogL: -59667.555 / Time: 0h:5m:1s (0h:2m:18s left)
Optimizing NNI: done in 2.1487 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.31864 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -59652.933
Optimizing NNI: done in 4.46355 secs using 597.2% CPU
BETTER TREE FOUND at iteration 82: -107665.610
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Iteration 370 / LogL: -192196.669 / Time: 0h:29m:13s (0h:5m:4s left)
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Iteration 190 / LogL: -59691.765 / Time: 0h:5m:16s (0h:2m:0s left)
Optimizing NNI: done in 1.79522 secs using 399.1% CPU
Optimizing NNI: done in 1.7308 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 191: -59652.792
Optimizing NNI: done in 2.12441 secs using 397.9% CPU
Iteration 90 / LogL: -107731.496 / Time: 0h:4m:45s (0h:4m:55s left)
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Iteration 200 / LogL: -59687.063 / Time: 0h:5m:32s (0h:2m:31s left)
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Iteration 100 / LogL: -107673.457 / Time: 0h:5m:6s (0h:4m:13s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 210: -59652.714
Iteration 210 / LogL: -59652.714 / Time: 0h:5m:48s (0h:2m:46s left)
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Iteration 380 / LogL: -192191.024 / Time: 0h:29m:54s (0h:4m:15s left)
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Iteration 110 / LogL: -107703.759 / Time: 0h:5m:28s (0h:3m:36s left)
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Iteration 220 / LogL: -59659.516 / Time: 0h:6m:3s (0h:2m:29s left)
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Iteration 230 / LogL: -59663.022 / Time: 0h:6m:18s (0h:2m:12s left)
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Iteration 120 / LogL: -107849.089 / Time: 0h:5m:49s (0h:3m:2s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.20212 secs using 398.7% CPU
BETTER TREE FOUND at iteration 236: -59652.667
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Iteration 390 / LogL: -192184.442 / Time: 0h:30m:36s (0h:3m:27s left)
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BETTER TREE FOUND at iteration 239: -59652.663
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Iteration 240 / LogL: -59657.453 / Time: 0h:6m:34s (0h:2m:43s left)
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Iteration 130 / LogL: -107693.460 / Time: 0h:6m:10s (0h:2m:29s left)
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Iteration 250 / LogL: -59654.441 / Time: 0h:6m:49s (0h:2m:26s left)
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Iteration 260 / LogL: -59659.188 / Time: 0h:7m:5s (0h:2m:9s left)
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Iteration 140 / LogL: -107893.869 / Time: 0h:6m:32s (0h:1m:58s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.00906 secs using 398.7% CPU
BETTER TREE FOUND at iteration 262: -59642.527
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Iteration 400 / LogL: -192199.142 / Time: 0h:31m:18s (0h:2m:40s left)
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Iteration 270 / LogL: -59654.336 / Time: 0h:7m:23s (0h:2m:31s left)
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Iteration 150 / LogL: -107751.306 / Time: 0h:6m:53s (0h:1m:28s left)
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Iteration 280 / LogL: -59657.239 / Time: 0h:7m:38s (0h:2m:14s left)
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Iteration 160 / LogL: -107687.319 / Time: 0h:7m:15s (0h:1m:0s left)
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Iteration 290 / LogL: -59705.392 / Time: 0h:7m:53s (0h:1m:58s left)
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Iteration 410 / LogL: -192173.975 / Time: 0h:32m:2s (0h:1m:52s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 293: -59641.187
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Iteration 300 / LogL: -59641.194 / Time: 0h:8m:11s (0h:2m:32s left)
Optimizing NNI: done in 2.00871 secs using 399% CPU
Iteration 170 / LogL: -107696.359 / Time: 0h:7m:36s (0h:0m:32s left)
Optimizing NNI: done in 1.60731 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.99559 secs using 399.1% CPU
BETTER TREE FOUND at iteration 301: -59640.794
Optimizing NNI: done in 1.76144 secs using 399.1% CPU
Optimizing NNI: done in 4.89074 secs using 597.6% CPU
Optimizing NNI: done in 2.27985 secs using 398.7% CPU
Optimizing NNI: done in 1.42006 secs using 398.8% CPU
Optimizing NNI: done in 1.75299 secs using 399.2% CPU
Optimizing NNI: done in 1.44189 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.21421 secs using 398.8% CPU
Optimizing NNI: done in 3.98561 secs using 598.2% CPU
BETTER TREE FOUND at iteration 304: -59639.400
Optimizing NNI: done in 1.16665 secs using 399.8% CPU
Optimizing NNI: done in 2.02589 secs using 399% CPU
Optimizing NNI: done in 1.62594 secs using 398.7% CPU
Optimizing NNI: done in 2.2777 secs using 398.5% CPU
Optimizing NNI: done in 4.42768 secs using 597.7% CPU
Optimizing NNI: done in 1.67656 secs using 398.7% CPU
Optimizing NNI: done in 1.48449 secs using 398.9% CPU
Optimizing NNI: done in 2.0833 secs using 398.9% CPU
Optimizing NNI: done in 1.50334 secs using 399.3% CPU
Optimizing NNI: done in 2.11512 secs using 398.7% CPU
Optimizing NNI: done in 4.31469 secs using 597.1% CPU
Optimizing NNI: done in 1.74051 secs using 399% CPU
Iteration 310 / LogL: -59645.545 / Time: 0h:8m:28s (0h:2m:34s left)
Optimizing NNI: done in 1.79224 secs using 398.6% CPU
Optimizing NNI: done in 1.50802 secs using 399.4% CPU
Optimizing NNI: done in 1.89141 secs using 398.9% CPU
Optimizing NNI: done in 3.94225 secs using 596.5% CPU
Optimizing NNI: done in 2.64226 secs using 399% CPU
Iteration 180 / LogL: -107749.403 / Time: 0h:7m:58s (0h:0m:5s left)
Optimizing NNI: done in 1.24213 secs using 399.1% CPU
Optimizing NNI: done in 2.17146 secs using 398.9% CPU
Optimizing NNI: done in 1.74221 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.2891 secs using 597.5% CPU
Optimizing NNI: done in 1.99946 secs using 398.6% CPU
BETTER TREE FOUND at iteration 314: -59638.279
Optimizing NNI: done in 1.51968 secs using 398.9% CPU
Optimizing NNI: done in 2.3314 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 183 ITERATIONS / Time: 0h:8m:4s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -107665.610
Optimizing NNI: done in 1.48851 secs using 399% CPU
Optimal log-likelihood: -107665.603
Proportion of invariable sites: 0.036
Site proportion and rates:  (0.054,0.031) (0.103,0.098) (0.050,0.176) (0.109,0.302) (0.087,0.437) (0.149,0.677) (0.166,1.068) (0.175,1.853) (0.071,4.287)
Parameters optimization took 1 rounds (0.924 sec)
BEST SCORE FOUND : -107665.603
Total tree length: 172.367

Total number of iterations: 183
CPU time used for tree search: 1800.128 sec (0h:30m:0s)
Wall-clock time used for tree search: 459.587 sec (0h:7m:39s)
Total CPU time used: 1904.789 sec (0h:31m:44s)
Total wall-clock time used: 485.825 sec (0h:8m:5s)

===> START BOOTSTRAP REPLICATE NUMBER 17

Creating bootstrap alignment (seed: 68199)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.126 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -103985.806
Optimizing NNI: done in 4.20574 secs using 597.7% CPU
Iteration 420 / LogL: -192175.498 / Time: 0h:32m:46s (0h:1m:5s left)
Optimizing NNI: done in 1.32536 secs using 398.8% CPU
2. Current log-likelihood: -102054.627
Optimizing NNI: done in 1.53342 secs using 398.8% CPU
3. Current log-likelihood: -101906.001
Optimizing NNI: done in 1.4092 secs using 399.4% CPU
Optimizing NNI: done in 4.61203 secs using 597.7% CPU
4. Current log-likelihood: -101900.387
Optimizing NNI: done in 1.53184 secs using 399.1% CPU
Iteration 320 / LogL: -59697.136 / Time: 0h:8m:45s (0h:2m:34s left)
5. Current log-likelihood: -101900.224
Optimizing NNI: done in 1.8274 secs using 398.3% CPU
Optimal log-likelihood: -101900.200
Proportion of invariable sites: 0.030
Site proportion and rates:  (0.124,0.042) (0.088,0.129) (0.065,0.220) (0.067,0.310) (0.126,0.460) (0.121,0.718) (0.115,1.149) (0.196,1.887) (0.067,4.460)
Parameters optimization took 5 rounds (7.588 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.56461 secs using 398.9% CPU
Optimizing NNI: done in 4.31522 secs using 597.7% CPU
Optimizing NNI: done in 1.25713 secs using 398.3% CPU
Optimizing NNI: done in 1.53816 secs using 399% CPU
Calculating distance matrix: done in 4.7469 secs using 399.9% CPU
Computing ML distances took 4.747252 sec (of wall-clock time) 18.985503 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000736952 secs using 405.9% CPU
Constructing RapidNJ tree: done in 0.00894809 secs using 352.3% CPU
Computing RapidNJ tree took 0.009759 sec (of wall-clock time) 0.037268 sec (of CPU time)
Optimizing NNI: done in 1.35854 secs using 399.1% CPU
Log-likelihood of RapidNJ tree: -102298.072
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.13892 secs using 597.5% CPU
Optimizing NNI: done in 1.39076 secs using 398.2% CPU
Optimizing NNI: done in 1.48545 secs using 398.8% CPU
Optimizing NNI: done in 1.73252 secs using 398.6% CPU
Optimizing NNI: done in 4.20224 secs using 597% CPU
Optimizing NNI: done in 1.44489 secs using 399.1% CPU
Optimizing NNI: done in 1.94622 secs using 398.8% CPU
Iteration 330 / LogL: -59645.618 / Time: 0h:9m:1s (0h:2m:18s left)
Optimizing NNI: done in 4.0996 secs using 598.2% CPU
Optimizing NNI: done in 1.40844 secs using 398.8% CPU
Optimizing NNI: done in 1.3323 secs using 399.2% CPU
10.661 second
Optimizing NNI: done in 1.631 secs using 398.4% CPU
Optimizing NNI: done in 4.26509 secs using 597.4% CPU
Optimizing NNI: done in 1.59491 secs using 399.2% CPU
Optimizing NNI: done in 1.64145 secs using 398.9% CPU
Optimizing NNI: done in 1.47891 secs using 398.9% CPU
Optimizing NNI: done in 4.44789 secs using 597.2% CPU
Optimizing NNI: done in 1.56379 secs using 398.8% CPU
Optimizing NNI: done in 1.72332 secs using 399% CPU
Computing log-likelihood of 98 initial trees ... 10.016 seconds
Current best score: -101900.200

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.41653 secs using 398.9% CPU
Optimizing NNI: done in 3.95344 secs using 596.1% CPU
Optimizing NNI: done in 1.46641 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.78788 secs using 398.7% CPU
Iteration 340 / LogL: -59646.351 / Time: 0h:9m:17s (0h:2m:1s left)
Optimizing NNI: done in 1.67234 secs using 399.1% CPU
Optimizing NNI: done in 4.35794 secs using 596.7% CPU
Optimizing NNI: done in 1.43432 secs using 399% CPU
Optimizing NNI: done in 1.80208 secs using 399.2% CPU
Optimizing NNI: done in 3.73772 secs using 598.5% CPU
Iteration 430 / LogL: -192160.907 / Time: 0h:33m:29s (0h:0m:18s left)
Optimizing NNI: done in 1.71436 secs using 398.9% CPU
Optimizing NNI: done in 2.02445 secs using 399% CPU
Optimizing NNI: done in 1.50272 secs using 398.6% CPU
Optimizing NNI: done in 3.96957 secs using 597.3% CPU
Optimizing NNI: done in 1.29582 secs using 399.4% CPU
Optimizing NNI: done in 1.68085 secs using 398.7% CPU
Optimizing NNI: done in 1.53645 secs using 398.5% CPU
Optimizing NNI: done in 4.31666 secs using 597.6% CPU
Optimizing NNI: done in 1.31127 secs using 398.8% CPU
Iteration 350 / LogL: -59639.552 / Time: 0h:9m:33s (0h:1m:45s left)
Optimizing NNI: done in 1.62194 secs using 398.5% CPU
Optimizing NNI: done in 4.20458 secs using 596.1% CPU
Optimizing NNI: done in 1.72098 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 352: -59637.562
Optimizing NNI: done in 1.93387 secs using 398.7% CPU
Optimizing NNI: done in 4.24296 secs using 598% CPU
Optimizing NNI: done in 1.39227 secs using 398.9% CPU
Optimizing NNI: done in 1.42126 secs using 399.4% CPU
Optimizing NNI: done in 1.36299 secs using 399% CPU
Optimizing NNI: done in 1.50125 secs using 399.2% CPU
Optimizing NNI: done in 4.43062 secs using 598.1% CPU
TREE SEARCH COMPLETED AFTER 435 ITERATIONS / Time: 0h:33m:50s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192139.055
Optimal log-likelihood: -192139.050
Site proportion and rates:  (0.012,0.103) (0.044,0.233) (0.129,0.361) (0.193,0.520) (0.125,0.701) (0.225,0.972) (0.161,1.512) (0.111,2.625)
Parameters optimization took 1 rounds (0.710 sec)
BEST SCORE FOUND : -192139.050
Total tree length: 152.336

Total number of iterations: 435
CPU time used for tree search: 11792.776 sec (3h:16m:32s)
Wall-clock time used for tree search: 1998.996 sec (0h:33m:18s)
Total CPU time used: 11985.714 sec (3h:19m:45s)
Total wall-clock time used: 2031.389 sec (0h:33m:51s)

===> START BOOTSTRAP REPLICATE NUMBER 15

Creating bootstrap alignment (seed: 70478)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.285 seconds

NOTE: 242 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -200918.186
Optimizing NNI: done in 1.6842 secs using 398.5% CPU
Optimizing NNI: done in 1.47689 secs using 398.4% CPU
2. Current log-likelihood: -198317.436
Optimizing NNI: done in 1.64486 secs using 398.9% CPU
Iteration 360 / LogL: -59667.752 / Time: 0h:9m:49s (0h:2m:31s left)
BETTER TREE FOUND at iteration 1: -101496.364
Optimizing NNI: done in 1.47034 secs using 399.2% CPU
3. Current log-likelihood: -198291.861
Optimizing NNI: done in 2.06838 secs using 398.2% CPU
Optimizing NNI: done in 1.71816 secs using 399.2% CPU
4. Current log-likelihood: -198290.000
Optimizing NNI: done in 1.54855 secs using 398.9% CPU
Optimizing NNI: done in 2.13353 secs using 397.9% CPU
5. Current log-likelihood: -198288.444
Optimizing NNI: done in 1.6845 secs using 399% CPU
Optimizing NNI: done in 1.6577 secs using 398.9% CPU
Optimizing NNI: done in 1.45269 secs using 398.7% CPU
Optimizing NNI: done in 1.61486 secs using 399.3% CPU
6. Current log-likelihood: -198286.840
Optimizing NNI: done in 1.38558 secs using 398.4% CPU
Optimizing NNI: done in 1.62668 secs using 398.5% CPU
7. Current log-likelihood: -198285.480
Optimizing NNI: done in 1.78133 secs using 398.8% CPU
Optimizing NNI: done in 2.7266 secs using 398.5% CPU
8. Current log-likelihood: -198284.742
Optimizing NNI: done in 1.59097 secs using 399.2% CPU
Optimizing NNI: done in 1.85052 secs using 398.3% CPU
Optimizing NNI: done in 1.93816 secs using 399% CPU
9. Current log-likelihood: -198284.418
Optimizing NNI: done in 1.2068 secs using 398.9% CPU
Iteration 370 / LogL: -59668.204 / Time: 0h:10m:5s (0h:2m:14s left)
Optimizing NNI: done in 2.32822 secs using 398.9% CPU
10. Current log-likelihood: -198284.297
Optimizing NNI: done in 1.51573 secs using 398.6% CPU
Optimizing NNI: done in 1.73268 secs using 398.9% CPU
Iteration 10 / LogL: -101716.935 / Time: 0h:1m:28s
Optimizing NNI: done in 1.56961 secs using 399.1% CPU
Optimal log-likelihood: -198284.256
Site proportion and rates:  (0.021,0.103) (0.052,0.251) (0.122,0.395) (0.181,0.542) (0.175,0.745) (0.191,1.001) (0.154,1.591) (0.105,2.603)
Parameters optimization took 10 rounds (23.020 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.03218 secs using 398.4% CPU
Optimizing NNI: done in 1.40718 secs using 399.1% CPU
Optimizing NNI: done in 1.72057 secs using 399.1% CPU
Optimizing NNI: done in 1.76908 secs using 399% CPU
Optimizing NNI: done in 1.6137 secs using 398.9% CPU
Optimizing NNI: done in 2.97718 secs using 398.1% CPU
Optimizing NNI: done in 1.63227 secs using 398.7% CPU
Optimizing NNI: done in 1.56553 secs using 398.2% CPU
Optimizing NNI: done in 1.72088 secs using 399% CPU
Optimizing NNI: done in 1.41575 secs using 399% CPU
Calculating distance matrix: done in 9.97511 secs using 599.9% CPU
Computing ML distances took 9.975686 sec (of wall-clock time) 59.841954 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00148606 secs using 411.6% CPU
Constructing RapidNJ tree: done in 0.0227211 secs using 664.5% CPU
Computing RapidNJ tree took 0.024284 sec (of wall-clock time) 0.157745 sec (of CPU time)
Optimizing NNI: done in 2.7621 secs using 398.7% CPU
Optimizing NNI: done in 1.53095 secs using 398.9% CPU
Optimizing NNI: done in 1.59917 secs using 399% CPU
Optimizing NNI: done in 1.68858 secs using 399.3% CPU
Iteration 380 / LogL: -59637.856 / Time: 0h:10m:21s (0h:1m:58s left)
Optimizing NNI: done in 2.0072 secs using 398.8% CPU
Optimizing NNI: done in 1.58754 secs using 399.2% CPU
Log-likelihood of RapidNJ tree: -203491.746
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.54217 secs using 399% CPU
Optimizing NNI: done in 2.76501 secs using 398.4% CPU
Optimizing NNI: done in 1.7624 secs using 399% CPU
Optimizing NNI: done in 2.27165 secs using 398.6% CPU
Optimizing NNI: done in 1.57481 secs using 399.1% CPU
Optimizing NNI: done in 1.42541 secs using 398.3% CPU
Optimizing NNI: done in 2.95155 secs using 398.3% CPU
Iteration 20 / LogL: -101541.941 / Time: 0h:1m:50s
Finish initializing candidate tree set (20)
Current best tree score: -101496.364 / CPU time: 97.213
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.31095 secs using 398.9% CPU
Optimizing NNI: done in 1.24189 secs using 399.2% CPU
Optimizing NNI: done in 1.33473 secs using 399.4% CPU
Optimizing NNI: done in 2.89142 secs using 398.2% CPU
Optimizing NNI: done in 1.57142 secs using 398.4% CPU
Optimizing NNI: done in 2.72366 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.53671 secs using 398.4% CPU
Iteration 390 / LogL: -59639.785 / Time: 0h:10m:36s (0h:1m:41s left)
Optimizing NNI: done in 1.81476 secs using 398.9% CPU
Optimizing NNI: done in 1.65648 secs using 399.2% CPU
Optimizing NNI: done in 1.49486 secs using 399.2% CPU
BETTER TREE FOUND at iteration 22: -101482.964
Optimizing NNI: done in 1.71426 secs using 399.1% CPU
Optimizing NNI: done in 1.60965 secs using 399% CPU
Optimizing NNI: done in 2.95393 secs using 398.6% CPU
Optimizing NNI: done in 1.5531 secs using 399.2% CPU
Optimizing NNI: done in 1.64202 secs using 399.3% CPU
Optimizing NNI: done in 3.00226 secs using 398.5% CPU
Optimizing NNI: done in 1.79642 secs using 399.1% CPU
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Optimizing NNI: done in 1.7773 secs using 398.9% CPU
Optimizing NNI: done in 1.33236 secs using 398.9% CPU
Iteration 400 / LogL: -59664.901 / Time: 0h:10m:53s (0h:1m:25s left)
29.632 second
Optimizing NNI: done in 1.73372 secs using 398.4% CPU
Optimizing NNI: done in 3.22575 secs using 398.5% CPU
Optimizing NNI: done in 1.27319 secs using 398.9% CPU
Optimizing NNI: done in 1.86219 secs using 399% CPU
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Optimizing NNI: done in 1.65714 secs using 399.3% CPU
Optimizing NNI: done in 1.98375 secs using 398.9% CPU
Iteration 30 / LogL: -101512.908 / Time: 0h:2m:23s (0h:7m:33s left)
Optimizing NNI: done in 1.67793 secs using 398.8% CPU
Optimizing NNI: done in 1.83468 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.56389 secs using 398.7% CPU
Optimizing NNI: done in 2.01056 secs using 398.8% CPU
BETTER TREE FOUND at iteration 31: -101474.588
Optimizing NNI: done in 2.01839 secs using 398.9% CPU
Iteration 410 / LogL: -59642.511 / Time: 0h:11m:10s (0h:1m:8s left)
Computing log-likelihood of 98 initial trees ... 16.773 seconds
Current best score: -198284.256

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.17117 secs using 398.6% CPU
Optimizing NNI: done in 1.37532 secs using 399.3% CPU
Optimizing NNI: done in 2.0058 secs using 398.3% CPU
Optimizing NNI: done in 1.6893 secs using 399.3% CPU
Optimizing NNI: done in 2.96874 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.81561 secs using 399.1% CPU
Optimizing NNI: done in 2.53282 secs using 398.3% CPU
Optimizing NNI: done in 1.33166 secs using 398.6% CPU
BETTER TREE FOUND at iteration 1: -197540.843
Optimizing NNI: done in 2.30101 secs using 398.3% CPU
Optimizing NNI: done in 1.86103 secs using 398.5% CPU
Optimizing NNI: done in 1.52598 secs using 397.7% CPU
Optimizing NNI: done in 1.97242 secs using 398.7% CPU
Optimizing NNI: done in 4.47066 secs using 596.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.93927 secs using 399% CPU
Optimizing NNI: done in 2.16024 secs using 398.1% CPU
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Optimizing NNI: done in 2.7071 secs using 398.6% CPU
Optimizing NNI: done in 1.94446 secs using 398.6% CPU
BETTER TREE FOUND at iteration 2: -197470.484
Optimizing NNI: done in 1.66766 secs using 399.1% CPU
Iteration 420 / LogL: -59647.925 / Time: 0h:11m:27s (0h:0m:52s left)
Optimizing NNI: done in 2.54101 secs using 398.7% CPU
Optimizing NNI: done in 1.28827 secs using 399.4% CPU
Optimizing NNI: done in 1.31359 secs using 399.2% CPU
Optimizing NNI: done in 2.03922 secs using 398.3% CPU
Iteration 40 / LogL: -101869.585 / Time: 0h:2m:49s (0h:6m:36s left)
Optimizing NNI: done in 4.73211 secs using 596.9% CPU
Optimizing NNI: done in 1.23323 secs using 399.5% CPU
Optimizing NNI: done in 2.39282 secs using 398.3% CPU
Optimizing NNI: done in 1.69405 secs using 398.7% CPU
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Optimizing NNI: done in 2.3482 secs using 399% CPU
Optimizing NNI: done in 4.26613 secs using 597% CPU
Optimizing NNI: done in 1.40363 secs using 399.1% CPU
Optimizing NNI: done in 1.57906 secs using 399.1% CPU
Optimizing NNI: done in 2.64529 secs using 398.2% CPU
Optimizing NNI: done in 1.44308 secs using 398.9% CPU
Optimizing NNI: done in 4.14623 secs using 597.1% CPU
Optimizing NNI: done in 2.29994 secs using 398.4% CPU
Optimizing NNI: done in 1.76437 secs using 399.1% CPU
Optimizing NNI: done in 1.94619 secs using 398.5% CPU
Optimizing NNI: done in 1.75881 secs using 398.9% CPU
Iteration 430 / LogL: -59650.484 / Time: 0h:11m:42s (0h:0m:36s left)
Optimizing NNI: done in 1.40772 secs using 398.8% CPU
Optimizing NNI: done in 4.38261 secs using 596.8% CPU
Optimizing NNI: done in 2.52846 secs using 398.5% CPU
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Optimizing NNI: done in 2.04716 secs using 398.6% CPU
Optimizing NNI: done in 1.78533 secs using 399.1% CPU
Optimizing NNI: done in 4.30724 secs using 598.1% CPU
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Optimizing NNI: done in 1.6051 secs using 399.2% CPU
Optimizing NNI: done in 1.34237 secs using 398.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -59637.561
Optimizing NNI: done in 4.15479 secs using 597.4% CPU
Optimizing NNI: done in 2.44478 secs using 398.9% CPU
Iteration 50 / LogL: -101491.326 / Time: 0h:3m:12s (0h:5m:18s left)
Optimizing NNI: done in 1.6152 secs using 399% CPU
Optimizing NNI: done in 1.43877 secs using 399.4% CPU
Optimizing NNI: done in 2.67456 secs using 398.3% CPU
Optimizing NNI: done in 3.88935 secs using 597.9% CPU
Optimizing NNI: done in 1.63173 secs using 399% CPU
Optimizing NNI: done in 2.2836 secs using 398.1% CPU
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Iteration 440 / LogL: -59670.444 / Time: 0h:11m:58s (0h:0m:19s left)
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Iteration 10 / LogL: -197525.240 / Time: 0h:2m:15s
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Iteration 450 / LogL: -59644.170 / Time: 0h:12m:12s (0h:0m:3s left)
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Iteration 60 / LogL: -101508.425 / Time: 0h:3m:34s (0h:4m:18s left)
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Optimizing NNI: done in 1.55442 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 453 ITERATIONS / Time: 0h:12m:17s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59637.561
Optimal log-likelihood: -59637.556
Site proportion and rates:  (0.089,0.060) (0.139,0.176) (0.142,0.381) (0.242,0.650) (0.141,1.071) (0.119,1.780) (0.103,2.524) (0.025,5.390)
Parameters optimization took 1 rounds (0.338 sec)
BEST SCORE FOUND : -59637.556
Total tree length: 44.852

Total number of iterations: 453
CPU time used for tree search: 2873.546 sec (0h:47m:53s)
Wall-clock time used for tree search: 724.130 sec (0h:12m:4s)
Total CPU time used: 2929.081 sec (0h:48m:49s)
Total wall-clock time used: 738.045 sec (0h:12m:18s)

===> START BOOTSTRAP REPLICATE NUMBER 56

Creating bootstrap alignment (seed: 67518)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60447.573
Optimizing NNI: done in 1.8452 secs using 398.4% CPU
2. Current log-likelihood: -59826.925
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3. Current log-likelihood: -59823.082
4. Current log-likelihood: -59822.892
5. Current log-likelihood: -59822.758
Optimizing NNI: done in 2.51636 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
6. Current log-likelihood: -59822.639
7. Current log-likelihood: -59822.505
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8. Current log-likelihood: -59822.307
BETTER TREE FOUND at iteration 63: -101473.230
9. Current log-likelihood: -59821.964
10. Current log-likelihood: -59821.265
11. Current log-likelihood: -59819.660
Optimizing NNI: done in 2.3434 secs using 398.5% CPU
12. Current log-likelihood: -59815.326
13. Current log-likelihood: -59805.103
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Optimizing NNI: done in 2.05355 secs using 398.9% CPU
14. Current log-likelihood: -59773.677
15. Current log-likelihood: -59771.858
Optimal log-likelihood: -59771.799
Site proportion and rates:  (0.102,0.059) (0.107,0.171) (0.093,0.393) (0.110,0.394) (0.248,0.748) (0.172,1.274) (0.140,2.282) (0.028,6.104)
Parameters optimization took 15 rounds (11.167 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.10363 secs using 399.9% CPU
Computing ML distances took 1.103806 sec (of wall-clock time) 4.413690 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000390053 secs using 373.5% CPU
Constructing RapidNJ tree: done in 0.00433993 secs using 241.1% CPU
Computing RapidNJ tree took 0.004785 sec (of wall-clock time) 0.013230 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59534.350
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.82659 secs using 398.5% CPU
Optimizing NNI: done in 4.45503 secs using 597.1% CPU
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5.206 second
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Iteration 70 / LogL: -101475.185 / Time: 0h:3m:58s (0h:5m:20s left)
Optimizing NNI: done in 6.59066 secs using 597.2% CPU
Optimizing NNI: done in 2.49903 secs using 398% CPU
Computing log-likelihood of 98 initial trees ... 5.346 seconds
Current best score: -59477.146

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -59242.278
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -197564.238 / Time: 0h:3m:1s
Finish initializing candidate tree set (20)
Current best tree score: -197470.484 / CPU time: 142.414
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
BETTER TREE FOUND at iteration 73: -101463.256
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 5: -59233.541
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Iteration 10 / LogL: -59279.891 / Time: 0h:0m:38s
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Iteration 80 / LogL: -101509.275 / Time: 0h:4m:22s (0h:5m:8s left)
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Iteration 20 / LogL: -59278.409 / Time: 0h:0m:50s
Finish initializing candidate tree set (20)
Current best tree score: -59233.541 / CPU time: 37.783
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Iteration 90 / LogL: -101474.835 / Time: 0h:4m:44s (0h:4m:25s left)
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Iteration 50 / LogL: -59211.688 / Time: 0h:1m:41s (0h:3m:26s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 60 / LogL: -59207.485 / Time: 0h:1m:57s (0h:3m:19s left)
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UPDATE BEST LOG-LIKELIHOOD: -59202.726
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Iteration 110 / LogL: -59220.617 / Time: 0h:3m:16s (0h:2m:6s left)
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Iteration 150 / LogL: -101469.764 / Time: 0h:6m:59s (0h:1m:4s left)
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Iteration 120 / LogL: -59208.032 / Time: 0h:3m:31s (0h:1m:46s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 158: -101462.133
Optimizing NNI: done in 4.63691 secs using 597.7% CPU
Iteration 60 / LogL: -197470.965 / Time: 0h:6m:14s (0h:8m:40s left)
BETTER TREE FOUND at iteration 127: -59201.301
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Iteration 160 / LogL: -101509.794 / Time: 0h:7m:23s (0h:4m:33s left)
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Iteration 130 / LogL: -59210.697 / Time: 0h:3m:47s (0h:2m:50s left)
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BETTER TREE FOUND at iteration 137: -59200.242
Optimizing NNI: done in 1.92892 secs using 398.7% CPU
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BETTER TREE FOUND at iteration 139: -59199.489
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Iteration 140 / LogL: -59206.096 / Time: 0h:4m:3s (0h:2m:53s left)
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Iteration 170 / LogL: -101483.675 / Time: 0h:7m:46s (0h:4m:2s left)
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BETTER TREE FOUND at iteration 66: -197442.579
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Iteration 150 / LogL: -59201.594 / Time: 0h:4m:18s (0h:2m:34s left)
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BETTER TREE FOUND at iteration 153: -59199.344
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BETTER TREE FOUND at iteration 154: -59198.866
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Iteration 180 / LogL: -101468.116 / Time: 0h:8m:8s (0h:3m:32s left)
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BETTER TREE FOUND at iteration 158: -59198.862
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Iteration 70 / LogL: -197459.134 / Time: 0h:7m:5s (0h:9m:51s left)
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Iteration 160 / LogL: -59204.408 / Time: 0h:4m:34s (0h:2m:49s left)
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Iteration 170 / LogL: -59218.503 / Time: 0h:4m:49s (0h:2m:30s left)
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Iteration 190 / LogL: -101516.546 / Time: 0h:8m:29s (0h:3m:3s left)
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Iteration 180 / LogL: -59215.893 / Time: 0h:5m:4s (0h:2m:12s left)
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Iteration 200 / LogL: -101475.648 / Time: 0h:8m:52s (0h:2m:35s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 189: -59198.567
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Iteration 190 / LogL: -59227.745 / Time: 0h:5m:20s (0h:2m:47s left)
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Iteration 80 / LogL: -197451.889 / Time: 0h:7m:56s (0h:8m:37s left)
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Iteration 200 / LogL: -59210.541 / Time: 0h:5m:34s (0h:2m:29s left)
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Iteration 210 / LogL: -101476.028 / Time: 0h:9m:13s (0h:2m:7s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 213: -101460.459
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Iteration 210 / LogL: -59200.185 / Time: 0h:5m:49s (0h:2m:12s left)
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Optimizing NNI: done in 1.29599 secs using 398.9% CPU
BETTER TREE FOUND at iteration 214: -59198.564
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Iteration 220 / LogL: -101485.941 / Time: 0h:9m:36s (0h:4m:4s left)
BETTER TREE FOUND at iteration 86: -197440.977
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Iteration 220 / LogL: -59210.007 / Time: 0h:6m:4s (0h:2m:36s left)
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BETTER TREE FOUND at iteration 221: -59198.563
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Iteration 230 / LogL: -59211.580 / Time: 0h:6m:18s (0h:2m:30s left)
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Iteration 90 / LogL: -197441.854 / Time: 0h:8m:51s (0h:9m:32s left)
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Iteration 230 / LogL: -101471.512 / Time: 0h:9m:58s (0h:3m:36s left)
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BETTER TREE FOUND at iteration 234: -59198.563
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Iteration 240 / LogL: -59200.084 / Time: 0h:6m:32s (0h:2m:34s left)
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Iteration 240 / LogL: -101487.803 / Time: 0h:10m:20s (0h:3m:9s left)
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Iteration 250 / LogL: -59213.772 / Time: 0h:6m:47s (0h:2m:17s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 270 / LogL: -59204.341 / Time: 0h:7m:16s (0h:1m:43s left)
BETTER TREE FOUND at iteration 98: -197433.899
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 318: -59197.310
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TREE SEARCH COMPLETED AFTER 314 ITERATIONS / Time: 0h:13m:4s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101460.459
Optimal log-likelihood: -101460.454
Proportion of invariable sites: 0.030
Site proportion and rates:  (0.107,0.033) (0.094,0.097) (0.077,0.202) (0.065,0.292) (0.126,0.427) (0.107,0.663) (0.118,1.025) (0.210,1.777) (0.067,4.971)
Parameters optimization took 1 rounds (0.651 sec)
BEST SCORE FOUND : -101460.454
Total tree length: 174.151

Total number of iterations: 314
CPU time used for tree search: 3039.496 sec (0h:50m:39s)
Wall-clock time used for tree search: 770.972 sec (0h:12m:50s)
Total CPU time used: 3096.618 sec (0h:51m:36s)
Total wall-clock time used: 785.269 sec (0h:13m:5s)

===> START BOOTSTRAP REPLICATE NUMBER 18

Creating bootstrap alignment (seed: 68200)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -109650.511
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2. Current log-likelihood: -107641.884
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Iteration 360 / LogL: -59205.445 / Time: 0h:9m:30s (0h:1m:32s left)
3. Current log-likelihood: -107530.372
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4. Current log-likelihood: -107523.886
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5. Current log-likelihood: -107522.475
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6. Current log-likelihood: -107521.616
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7. Current log-likelihood: -107520.917
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8. Current log-likelihood: -107520.419
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9. Current log-likelihood: -107519.930
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10. Current log-likelihood: -107519.773
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Iteration 370 / LogL: -59199.679 / Time: 0h:9m:45s (0h:1m:16s left)
11. Current log-likelihood: -107519.595
12. Current log-likelihood: -107519.380
Optimizing NNI: done in 1.34569 secs using 398.8% CPU
Optimizing NNI: done in 1.38288 secs using 398.9% CPU
BETTER TREE FOUND at iteration 372: -59197.305
Optimal log-likelihood: -107519.243
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.081,0.039) (0.089,0.122) (0.084,0.208) (0.092,0.326) (0.088,0.509) (0.114,0.733) (0.176,1.188) (0.175,1.910) (0.068,3.927)
Parameters optimization took 12 rounds (20.879 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 4.66185 secs using 399.6% CPU
Computing ML distances took 4.662094 sec (of wall-clock time) 18.628346 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000714064 secs using 395.8% CPU
Constructing RapidNJ tree: done in 0.00830603 secs using 505.7% CPU
Computing RapidNJ tree took 0.009089 sec (of wall-clock time) 0.045401 sec (of CPU time)
Log-likelihood of RapidNJ tree: -107856.357
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.68259 secs using 398.9% CPU
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Iteration 380 / LogL: -59207.147 / Time: 0h:9m:59s (0h:2m:25s left)
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11.289 second
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Iteration 130 / LogL: -197676.118 / Time: 0h:12m:44s (0h:6m:42s left)
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Iteration 390 / LogL: -59414.842 / Time: 0h:10m:14s (0h:2m:9s left)
Computing log-likelihood of 98 initial trees ... 10.090 seconds
Current best score: -107519.243

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 400 / LogL: -59200.926 / Time: 0h:10m:29s (0h:1m:53s left)
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Iteration 410 / LogL: -59221.538 / Time: 0h:10m:44s (0h:1m:37s left)
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BETTER TREE FOUND at iteration 1: -107088.830
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -106977.974
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Iteration 420 / LogL: -59197.305 / Time: 0h:10m:59s (0h:1m:21s left)
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Iteration 140 / LogL: -197484.059 / Time: 0h:13m:40s (0h:5m:42s left)
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Iteration 10 / LogL: -107040.147 / Time: 0h:1m:45s
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Iteration 430 / LogL: -59248.877 / Time: 0h:11m:13s (0h:1m:5s left)
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Iteration 440 / LogL: -59201.460 / Time: 0h:11m:28s (0h:0m:50s left)
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Iteration 20 / LogL: -107134.876 / Time: 0h:2m:6s
Finish initializing candidate tree set (20)
Current best tree score: -106977.974 / CPU time: 99.898
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.55023 secs using 398.8% CPU
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Iteration 450 / LogL: -59214.240 / Time: 0h:11m:42s (0h:0m:34s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 26: -106969.135
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Optimizing NNI: done in 1.69139 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.59352 secs using 398.7% CPU
BETTER TREE FOUND at iteration 27: -106968.007
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Iteration 460 / LogL: -59200.790 / Time: 0h:11m:57s (0h:0m:18s left)
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Iteration 30 / LogL: -106978.905 / Time: 0h:2m:30s (0h:8m:24s left)
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Iteration 150 / LogL: -197478.932 / Time: 0h:14m:31s (0h:4m:40s left)
Optimizing NNI: done in 1.45119 secs using 399.4% CPU
Optimizing NNI: done in 1.98723 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 1.37299 secs using 398.9% CPU
BETTER TREE FOUND at iteration 31: -106965.938
Optimizing NNI: done in 4.96844 secs using 596.2% CPU
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Optimizing NNI: done in 1.85642 secs using 398.4% CPU
Optimizing NNI: done in 1.70445 secs using 399.6% CPU
Iteration 470 / LogL: -59217.510 / Time: 0h:12m:12s (0h:0m:3s left)
Optimizing NNI: done in 1.70827 secs using 398% CPU
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Optimizing NNI: done in 1.43804 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 473 ITERATIONS / Time: 0h:12m:16s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59197.305
Optimizing NNI: done in 1.82959 secs using 398.9% CPU
2. Current log-likelihood: -59197.284
3. Current log-likelihood: -59197.271
4. Current log-likelihood: -59197.257
Optimizing NNI: done in 3.72439 secs using 597.7% CPU
5. Current log-likelihood: -59197.242
6. Current log-likelihood: -59197.227
Optimizing NNI: done in 2.03052 secs using 398.6% CPU
7. Current log-likelihood: -59197.212
8. Current log-likelihood: -59197.198
9. Current log-likelihood: -59197.183
Optimizing NNI: done in 2.14635 secs using 398.1% CPU
Iteration 40 / LogL: -107049.021 / Time: 0h:2m:53s (0h:6m:45s left)
10. Current log-likelihood: -59197.165
11. Current log-likelihood: -59197.144
12. Current log-likelihood: -59197.111
Optimizing NNI: done in 4.62183 secs using 597.6% CPU
Optimizing NNI: done in 1.87451 secs using 398.8% CPU
13. Current log-likelihood: -59197.071
14. Current log-likelihood: -59197.020
Optimizing NNI: done in 1.95386 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
15. Current log-likelihood: -59196.966
16. Current log-likelihood: -59196.918
BETTER TREE FOUND at iteration 42: -106960.948
17. Current log-likelihood: -59196.877
18. Current log-likelihood: -59196.844
Optimizing NNI: done in 4.77071 secs using 597.3% CPU
19. Current log-likelihood: -59196.813
Optimizing NNI: done in 2.00418 secs using 399% CPU
20. Current log-likelihood: -59196.783
21. Current log-likelihood: -59196.752
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22. Current log-likelihood: -59196.722
23. Current log-likelihood: -59196.689
Optimizing NNI: done in 4.48843 secs using 597.6% CPU
Optimizing NNI: done in 1.87187 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
24. Current log-likelihood: -59196.658
25. Current log-likelihood: -59196.623
26. Current log-likelihood: -59196.589
27. Current log-likelihood: -59196.551
BETTER TREE FOUND at iteration 45: -106960.094
28. Current log-likelihood: -59196.515
29. Current log-likelihood: -59196.476
Optimizing NNI: done in 4.47775 secs using 597.2% CPU
Optimizing NNI: done in 1.79096 secs using 398.6% CPU
30. Current log-likelihood: -59196.440
31. Current log-likelihood: -59196.403
32. Current log-likelihood: -59196.366
Optimizing NNI: done in 1.99348 secs using 399.4% CPU
33. Current log-likelihood: -59196.332
34. Current log-likelihood: -59196.301
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Optimizing NNI: done in 4.51343 secs using 597.6% CPU
35. Current log-likelihood: -59196.271
36. Current log-likelihood: -59196.245
Optimizing NNI: done in 1.73636 secs using 398.8% CPU
37. Current log-likelihood: -59196.221
38. Current log-likelihood: -59196.199
39. Current log-likelihood: -59196.179
Optimizing NNI: done in 2.12695 secs using 399.1% CPU
Iteration 50 / LogL: -106979.603 / Time: 0h:3m:17s (0h:6m:23s left)
40. Current log-likelihood: -59196.163
41. Current log-likelihood: -59196.146
42. Current log-likelihood: -59196.133
Optimizing NNI: done in 5.42146 secs using 596.9% CPU
Iteration 160 / LogL: -197521.843 / Time: 0h:15m:19s (0h:3m:39s left)
Optimizing NNI: done in 2.01785 secs using 398.9% CPU
43. Current log-likelihood: -59196.119
44. Current log-likelihood: -59196.106
45. Current log-likelihood: -59196.094
Optimizing NNI: done in 1.78238 secs using 398.4% CPU
46. Current log-likelihood: -59196.082
47. Current log-likelihood: -59196.071
48. Current log-likelihood: -59196.059
49. Current log-likelihood: -59196.048
Optimizing NNI: done in 1.8767 secs using 399% CPU
50. Current log-likelihood: -59196.035
51. Current log-likelihood: -59196.024
52. Current log-likelihood: -59196.013
Optimizing NNI: done in 5.57903 secs using 597.6% CPU
Optimizing NNI: done in 1.98834 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
53. Current log-likelihood: -59196.001
54. Current log-likelihood: -59195.990
55. Current log-likelihood: -59195.979
56. Current log-likelihood: -59195.969
57. Current log-likelihood: -59195.959
Optimal log-likelihood: -59195.944
Site proportion and rates:  (0.088,0.055) (0.109,0.151) (0.199,0.378) (0.078,0.544) (0.218,0.825) (0.156,1.388) (0.124,2.371) (0.028,6.165)
Parameters optimization took 57 rounds (39.031 sec)
BEST SCORE FOUND : -59195.944
Total tree length: 45.764

Total number of iterations: 473
CPU time used for tree search: 2872.107 sec (0h:47m:52s)
Wall-clock time used for tree search: 723.665 sec (0h:12m:3s)
Total CPU time used: 3077.918 sec (0h:51m:17s)
Total wall-clock time used: 775.319 sec (0h:12m:55s)

===> START BOOTSTRAP REPLICATE NUMBER 57

Creating bootstrap alignment (seed: 67519)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.041 seconds

NOTE: 64 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61687.685
BETTER TREE FOUND at iteration 54: -106950.374
2. Current log-likelihood: -61135.408
3. Current log-likelihood: -61132.404
Optimizing NNI: done in 5.21715 secs using 597.7% CPU
Optimizing NNI: done in 2.06484 secs using 398.8% CPU
Optimal log-likelihood: -61132.295
Site proportion and rates:  (0.107,0.056) (0.107,0.177) (0.096,0.408) (0.130,0.452) (0.102,0.774) (0.194,1.000) (0.117,1.706) (0.146,2.762)
Parameters optimization took 3 rounds (2.707 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.07627 secs using 399.9% CPU
Computing ML distances took 1.076445 sec (of wall-clock time) 4.304143 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000355959 secs using 402.3% CPU
Constructing RapidNJ tree: done in 0.00433493 secs using 367.4% CPU
Computing RapidNJ tree took 0.004754 sec (of wall-clock time) 0.018070 sec (of CPU time)
Log-likelihood of RapidNJ tree: -61310.031
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.20019 secs using 398.6% CPU
Optimizing NNI: done in 1.92896 secs using 398.8% CPU
Optimizing NNI: done in 4.90326 secs using 597.7% CPU
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5.097 second
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Optimizing NNI: done in 5.1956 secs using 598% CPU
Optimizing NNI: done in 1.888 secs using 398.6% CPU
Iteration 60 / LogL: -106984.794 / Time: 0h:3m:41s (0h:5m:52s left)
Computing log-likelihood of 98 initial trees ... 5.245 seconds
Current best score: -61112.700

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.31594 secs using 398.3% CPU
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -60984.829
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 62: -106949.732
BETTER TREE FOUND at iteration 165: -197433.475
BETTER TREE FOUND at iteration 2: -60897.037
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Iteration 10 / LogL: -60935.700 / Time: 0h:0m:30s
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Iteration 70 / LogL: -106954.564 / Time: 0h:4m:5s (0h:5m:26s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 18: -60888.769
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Iteration 170 / LogL: -197916.546 / Time: 0h:16m:12s (0h:9m:6s left)
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Iteration 20 / LogL: -60982.444 / Time: 0h:0m:47s
Finish initializing candidate tree set (20)
Current best tree score: -60888.769 / CPU time: 43.396
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -60877.567
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Estimate model parameters (epsilon = 0.100)
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Iteration 80 / LogL: -106984.036 / Time: 0h:4m:25s (0h:4m:35s left)
BETTER TREE FOUND at iteration 24: -60868.305
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 83: -106941.902
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 30: -60864.115
Iteration 30 / LogL: -60864.115 / Time: 0h:1m:13s (0h:4m:11s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 90 / LogL: -106944.289 / Time: 0h:4m:51s (0h:5m:4s left)
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BETTER TREE FOUND at iteration 35: -60854.866
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Iteration 40 / LogL: -60865.548 / Time: 0h:1m:31s (0h:3m:43s left)
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Iteration 180 / LogL: -197452.729 / Time: 0h:17m:1s (0h:8m:4s left)
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TREE SEARCH COMPLETED AFTER 184 ITERATIONS / Time: 0h:7m:59s

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|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106941.902
Optimizing NNI: done in 1.68426 secs using 399.3% CPU
Optimal log-likelihood: -106941.896
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.077,0.030) (0.074,0.100) (0.101,0.192) (0.087,0.308) (0.098,0.488) (0.118,0.733) (0.177,1.194) (0.168,1.910) (0.067,4.141)
Parameters optimization took 1 rounds (0.793 sec)
BEST SCORE FOUND : -106941.896
Total tree length: 168.957

Total number of iterations: 184
CPU time used for tree search: 1770.180 sec (0h:29m:30s)
Wall-clock time used for tree search: 452.589 sec (0h:7m:32s)
Total CPU time used: 1880.317 sec (0h:31m:20s)
Total wall-clock time used: 480.209 sec (0h:8m:0s)

===> START BOOTSTRAP REPLICATE NUMBER 19

Creating bootstrap alignment (seed: 68201)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.114 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106775.731
Optimizing NNI: done in 1.61401 secs using 398.7% CPU
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2. Current log-likelihood: -104515.890
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3. Current log-likelihood: -104430.942
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4. Current log-likelihood: -104416.678
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5. Current log-likelihood: -104414.982
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6. Current log-likelihood: -104414.740
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Iteration 220 / LogL: -197477.251 / Time: 0h:20m:9s (0h:4m:8s left)
Optimal log-likelihood: -104414.645
Proportion of invariable sites: 0.020
Site proportion and rates:  (0.140,0.045) (0.077,0.128) (0.052,0.221) (0.081,0.318) (0.119,0.500) (0.124,0.771) (0.181,1.298) (0.126,1.844) (0.082,3.983)
Parameters optimization took 6 rounds (9.640 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 160 / LogL: -60834.915 / Time: 0h:4m:44s (0h:0m:33s left)
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Calculating distance matrix: done in 4.77401 secs using 399.9% CPU
Computing ML distances took 4.774253 sec (of wall-clock time) 19.090768 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000701904 secs using 406.8% CPU
Constructing RapidNJ tree: done in 0.008564 secs using 346.1% CPU
Computing RapidNJ tree took 0.009335 sec (of wall-clock time) 0.032556 sec (of CPU time)
Optimizing NNI: done in 1.43039 secs using 399.4% CPU
Log-likelihood of RapidNJ tree: -104467.637
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.52689 secs using 399.1% CPU
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10.497 second
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Iteration 170 / LogL: -60855.161 / Time: 0h:5m:0s (0h:0m:16s left)
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Optimizing NNI: done in 4.46915 secs using 597.4% CPU
Computing log-likelihood of 98 initial trees ... 9.919 seconds
Current best score: -104414.645

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -103887.199
Optimizing NNI: done in 1.68174 secs using 399.2% CPU
Iteration 180 / LogL: -60854.043 / Time: 0h:5m:16s (0h:0m:-2s left)
TREE SEARCH COMPLETED AFTER 180 ITERATIONS / Time: 0h:5m:16s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60821.958
Optimizing NNI: done in 4.1149 secs using 597.7% CPU
2. Current log-likelihood: -60821.924
Optimizing NNI: done in 1.5916 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
3. Current log-likelihood: -60821.892
4. Current log-likelihood: -60821.850
5. Current log-likelihood: -60821.795
6. Current log-likelihood: -60821.713
7. Current log-likelihood: -60821.572
Optimizing NNI: done in 4.75615 secs using 597% CPU
8. Current log-likelihood: -60821.281
9. Current log-likelihood: -60820.354
10. Current log-likelihood: -60816.994
11. Current log-likelihood: -60810.339
12. Current log-likelihood: -60806.266
Optimizing NNI: done in 4.62625 secs using 597.2% CPU
Iteration 230 / LogL: -197475.904 / Time: 0h:20m:54s (0h:3m:11s left)
13. Current log-likelihood: -60806.007
14. Current log-likelihood: -60805.947
15. Current log-likelihood: -60805.909
16. Current log-likelihood: -60805.880
17. Current log-likelihood: -60805.856
18. Current log-likelihood: -60805.831
Optimizing NNI: done in 4.52056 secs using 597.5% CPU
19. Current log-likelihood: -60805.807
20. Current log-likelihood: -60805.784
21. Current log-likelihood: -60805.759
22. Current log-likelihood: -60805.732
23. Current log-likelihood: -60805.704
24. Current log-likelihood: -60805.674
Optimizing NNI: done in 4.81007 secs using 596.3% CPU
25. Current log-likelihood: -60805.643
26. Current log-likelihood: -60805.611
27. Current log-likelihood: -60805.578
28. Current log-likelihood: -60805.543
29. Current log-likelihood: -60805.507
Optimizing NNI: done in 4.50263 secs using 597.2% CPU
30. Current log-likelihood: -60805.469
31. Current log-likelihood: -60805.431
BETTER TREE FOUND at iteration 2: -103724.338
32. Current log-likelihood: -60805.389
33. Current log-likelihood: -60805.348
34. Current log-likelihood: -60805.306
Optimizing NNI: done in 2.27204 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.93699 secs using 597.4% CPU
35. Current log-likelihood: -60805.267
36. Current log-likelihood: -60805.227
37. Current log-likelihood: -60805.193
38. Current log-likelihood: -60805.160
BETTER TREE FOUND at iteration 3: -103675.214
39. Current log-likelihood: -60805.130
40. Current log-likelihood: -60805.106
Optimizing NNI: done in 4.57122 secs using 597.1% CPU
41. Current log-likelihood: -60805.083
42. Current log-likelihood: -60805.063
Optimizing NNI: done in 2.65032 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
43. Current log-likelihood: -60805.046
44. Current log-likelihood: -60805.031
45. Current log-likelihood: -60805.018
Optimizing NNI: done in 3.98175 secs using 596.4% CPU
Optimal log-likelihood: -60805.006
Site proportion and rates:  (0.113,0.055) (0.113,0.183) (0.199,0.423) (0.084,0.666) (0.226,0.945) (0.107,1.584) (0.136,2.503) (0.021,5.177)
Parameters optimization took 45 rounds (36.977 sec)
BEST SCORE FOUND : -60805.006
Total tree length: 44.039

Total number of iterations: 180
CPU time used for tree search: 1231.026 sec (0h:20m:31s)
Wall-clock time used for tree search: 312.280 sec (0h:5m:12s)
Total CPU time used: 1395.327 sec (0h:23m:15s)
Total wall-clock time used: 353.508 sec (0h:5m:53s)

===> START BOOTSTRAP REPLICATE NUMBER 58

Creating bootstrap alignment (seed: 67520)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.049 seconds

NOTE: 64 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58977.720
2. Current log-likelihood: -58448.294
3. Current log-likelihood: -58430.542
BETTER TREE FOUND at iteration 4: -103669.641
4. Current log-likelihood: -58425.396
5. Current log-likelihood: -58424.779
Optimizing NNI: done in 1.88156 secs using 398.2% CPU
6. Current log-likelihood: -58424.597
Optimal log-likelihood: -58424.486
Site proportion and rates:  (0.110,0.060) (0.103,0.180) (0.092,0.392) (0.101,0.459) (0.220,0.740) (0.158,1.196) (0.156,2.145) (0.060,3.412)
Parameters optimization took 6 rounds (4.659 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 5.27077 secs using 597.6% CPU
Calculating distance matrix: done in 1.06653 secs using 399.9% CPU
Computing ML distances took 1.066720 sec (of wall-clock time) 4.266116 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000351191 secs using 392.9% CPU
Constructing RapidNJ tree: done in 0.00438499 secs using 384.2% CPU
Computing RapidNJ tree took 0.004802 sec (of wall-clock time) 0.019290 sec (of CPU time)
Optimizing NNI: done in 1.99554 secs using 398.6% CPU
Log-likelihood of RapidNJ tree: -58198.037
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.46172 secs using 398.3% CPU
Optimizing NNI: done in 5.30687 secs using 597.2% CPU
Optimizing NNI: done in 2.3661 secs using 398.5% CPU
5.103 second
Optimizing NNI: done in 2.0807 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -103654.769
Computing log-likelihood of 98 initial trees ... 5.289 seconds
Current best score: -58086.361

Do NNI search on 20 best initial trees
Optimizing NNI: done in 7.0429 secs using 597.7% CPU
Optimizing NNI: done in 2.0673 secs using 399.1% CPU
Iteration 10 / LogL: -103704.036 / Time: 0h:1m:39s
Optimizing NNI: done in 1.91217 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.97844 secs using 399.2% CPU
Optimizing NNI: done in 5.0161 secs using 597.5% CPU
Iteration 240 / LogL: -197436.106 / Time: 0h:21m:43s (0h:2m:16s left)
Optimizing NNI: done in 2.64375 secs using 398.6% CPU
BETTER TREE FOUND at iteration 1: -57842.604
Optimizing NNI: done in 1.26323 secs using 398.8% CPU
Optimizing NNI: done in 2.32392 secs using 398.7% CPU
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Optimizing NNI: done in 1.25374 secs using 399.1% CPU
Iteration 10 / LogL: -57942.348 / Time: 0h:0m:35s
Optimizing NNI: done in 2.15928 secs using 398.8% CPU
Optimizing NNI: done in 1.29293 secs using 399.4% CPU
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Optimizing NNI: done in 2.5762 secs using 398.9% CPU
Iteration 20 / LogL: -103715.564 / Time: 0h:2m:2s
Finish initializing candidate tree set (20)
Current best tree score: -103654.769 / CPU time: 106.291
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.48622 secs using 399.2% CPU
Optimizing NNI: done in 2.18933 secs using 399.1% CPU
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Optimizing NNI: done in 1.43095 secs using 398.3% CPU
Iteration 20 / LogL: -57927.004 / Time: 0h:0m:49s
Finish initializing candidate tree set (20)
Current best tree score: -57842.604 / CPU time: 42.417
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.58536 secs using 398.8% CPU
Optimizing NNI: done in 1.4503 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.15599 secs using 598% CPU
Optimizing NNI: done in 2.97501 secs using 398% CPU
BETTER TREE FOUND at iteration 21: -57815.805
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.27684 secs using 398.6% CPU
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BETTER TREE FOUND at iteration 26: -103651.666
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.18768 secs using 597.1% CPU
BETTER TREE FOUND at iteration 28: -103651.342
Optimizing NNI: done in 2.86245 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.50206 secs using 597.8% CPU
BETTER TREE FOUND at iteration 29: -103643.288
BETTER TREE FOUND at iteration 25: -57803.401
Optimizing NNI: done in 1.42608 secs using 398.8% CPU
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Iteration 30 / LogL: -103649.757 / Time: 0h:2m:33s (0h:8m:42s left)
Optimizing NNI: done in 1.16112 secs using 399% CPU
Optimizing NNI: done in 4.80665 secs using 597% CPU
Iteration 250 / LogL: -197488.043 / Time: 0h:22m:34s (0h:1m:21s left)
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Iteration 30 / LogL: -57815.938 / Time: 0h:1m:16s (0h:4m:9s left)
Optimizing NNI: done in 2.49397 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.30418 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -57803.195
BETTER TREE FOUND at iteration 35: -103636.767
Optimizing NNI: done in 1.72778 secs using 399% CPU
Optimizing NNI: done in 4.39427 secs using 596.7% CPU
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Iteration 40 / LogL: -57804.418 / Time: 0h:1m:31s (0h:3m:45s left)
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Iteration 40 / LogL: -103648.543 / Time: 0h:2m:59s (0h:7m:15s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.39615 secs using 398.3% CPU
BETTER TREE FOUND at iteration 47: -57798.391
Optimizing NNI: done in 1.66323 secs using 399% CPU
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Iteration 50 / LogL: -57803.711 / Time: 0h:1m:47s (0h:3m:32s left)
Optimizing NNI: done in 2.48332 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -103636.429
Optimizing NNI: done in 1.60105 secs using 399.3% CPU
Optimizing NNI: done in 4.45008 secs using 598% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.35878 secs using 399% CPU
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BETTER TREE FOUND at iteration 46: -103631.970
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Iteration 260 / LogL: -197467.829 / Time: 0h:23m:21s (0h:0m:27s left)
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Iteration 60 / LogL: -57814.747 / Time: 0h:2m:2s (0h:3m:0s left)
Optimizing NNI: done in 1.51539 secs using 399.2% CPU
Optimizing NNI: done in 2.36072 secs using 398.2% CPU
Iteration 50 / LogL: -103647.065 / Time: 0h:3m:25s (0h:6m:42s left)
Optimizing NNI: done in 1.29338 secs using 399.2% CPU
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Optimizing NNI: done in 2.15805 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.2763 secs using 399% CPU
Iteration 70 / LogL: -57808.391 / Time: 0h:2m:16s (0h:2m:32s left)
Optimizing NNI: done in 1.40091 secs using 399.1% CPU
BETTER TREE FOUND at iteration 55: -103621.883
Optimizing NNI: done in 1.33969 secs using 399.4% CPU
Optimizing NNI: done in 4.88647 secs using 597.3% CPU
Optimizing NNI: done in 1.22115 secs using 398.6% CPU
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Optimizing NNI: done in 1.32386 secs using 399% CPU
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Optimizing NNI: done in 1.4687 secs using 399% CPU
Optimizing NNI: done in 5.05348 secs using 596.8% CPU
Optimizing NNI: done in 1.63647 secs using 399.1% CPU
Optimizing NNI: done in 3.07277 secs using 398.4% CPU
Optimizing NNI: done in 1.35778 secs using 398.6% CPU
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Optimizing NNI: done in 2.66452 secs using 398.5% CPU
Optimizing NNI: done in 1.23944 secs using 399.4% CPU
Iteration 80 / LogL: -57823.076 / Time: 0h:2m:30s (0h:2m:7s left)
Optimizing NNI: done in 5.40357 secs using 597.4% CPU
TREE SEARCH COMPLETED AFTER 266 ITERATIONS / Time: 0h:23m:52s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -197433.475
Optimizing NNI: done in 2.31238 secs using 398.7% CPU
Iteration 60 / LogL: -103634.579 / Time: 0h:3m:53s (0h:6m:15s left)
Optimizing NNI: done in 1.48854 secs using 398.8% CPU
Optimal log-likelihood: -197433.464
Site proportion and rates:  (0.021,0.103) (0.051,0.257) (0.107,0.375) (0.198,0.538) (0.182,0.751) (0.182,1.011) (0.152,1.590) (0.106,2.597)
Parameters optimization took 1 rounds (1.302 sec)
BEST SCORE FOUND : -197433.464
Total tree length: 152.343

Total number of iterations: 266
CPU time used for tree search: 8173.646 sec (2h:16m:13s)
Wall-clock time used for tree search: 1393.086 sec (0h:23m:13s)
Total CPU time used: 8414.237 sec (2h:20m:14s)
Total wall-clock time used: 1433.458 sec (0h:23m:53s)

===> START BOOTSTRAP REPLICATE NUMBER 16

Creating bootstrap alignment (seed: 70479)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.256 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196053.127
Optimizing NNI: done in 1.38224 secs using 399.5% CPU
Optimizing NNI: done in 2.36982 secs using 398.5% CPU
2. Current log-likelihood: -193422.625
Optimizing NNI: done in 1.53892 secs using 399.5% CPU
Optimizing NNI: done in 1.19968 secs using 399.1% CPU
Optimizing NNI: done in 2.39844 secs using 398.4% CPU
3. Current log-likelihood: -193376.622
Optimizing NNI: done in 1.63858 secs using 398.9% CPU
Optimizing NNI: done in 1.19727 secs using 399.2% CPU
Optimizing NNI: done in 2.46535 secs using 398.9% CPU
4. Current log-likelihood: -193368.793
Optimizing NNI: done in 1.74613 secs using 399.1% CPU
Optimizing NNI: done in 2.08269 secs using 398.6% CPU
5. Current log-likelihood: -193363.584
Optimizing NNI: done in 1.51592 secs using 399.3% CPU
Optimizing NNI: done in 1.22973 secs using 398.9% CPU
Optimizing NNI: done in 2.41116 secs using 398.9% CPU
6. Current log-likelihood: -193359.458
Optimizing NNI: done in 1.46172 secs using 399.5% CPU
Iteration 90 / LogL: -57811.989 / Time: 0h:2m:45s (0h:1m:45s left)
7. Current log-likelihood: -193358.182
Optimizing NNI: done in 2.54386 secs using 398.7% CPU
Optimizing NNI: done in 1.51932 secs using 398.5% CPU
8. Current log-likelihood: -193357.887
Optimizing NNI: done in 1.57388 secs using 398.8% CPU
Optimizing NNI: done in 2.59364 secs using 398.6% CPU
Optimizing NNI: done in 1.46914 secs using 399.3% CPU
Optimal log-likelihood: -193357.785
Site proportion and rates:  (0.003,0.108) (0.056,0.242) (0.118,0.353) (0.205,0.544) (0.176,0.752) (0.184,1.020) (0.121,1.562) (0.137,2.368)
Parameters optimization took 8 rounds (17.293 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.47821 secs using 399.2% CPU
Optimizing NNI: done in 2.20828 secs using 399% CPU
Optimizing NNI: done in 1.60305 secs using 398.9% CPU
Optimizing NNI: done in 1.14577 secs using 398.6% CPU
Optimizing NNI: done in 3.05065 secs using 398.4% CPU
Optimizing NNI: done in 1.68731 secs using 399% CPU
Optimizing NNI: done in 2.509 secs using 398.8% CPU
Iteration 70 / LogL: -103657.342 / Time: 0h:4m:18s (0h:5m:17s left)
Optimizing NNI: done in 1.20673 secs using 399.1% CPU
Optimizing NNI: done in 1.66608 secs using 399.1% CPU
Optimizing NNI: done in 2.0943 secs using 397.7% CPU
Optimizing NNI: done in 1.31578 secs using 399.2% CPU
Iteration 100 / LogL: -57827.656 / Time: 0h:3m:0s (0h:1m:25s left)
Calculating distance matrix: done in 10.1204 secs using 599.8% CPU
Computing ML distances took 10.120971 sec (of wall-clock time) 60.709861 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00134802 secs using 675.8% CPU
Constructing RapidNJ tree: done in 0.0229349 secs using 675.9% CPU
Computing RapidNJ tree took 0.024362 sec (of wall-clock time) 0.165061 sec (of CPU time)
Optimizing NNI: done in 1.13047 secs using 398.8% CPU
Optimizing NNI: done in 2.71737 secs using 398% CPU
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Optimizing NNI: done in 2.43693 secs using 398.5% CPU
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Optimizing NNI: done in 2.30472 secs using 398.4% CPU
Optimizing NNI: done in 1.45869 secs using 399.3% CPU
Log-likelihood of RapidNJ tree: -198150.620
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.36373 secs using 398.6% CPU
Optimizing NNI: done in 1.66797 secs using 398.8% CPU
Optimizing NNI: done in 1.49578 secs using 399% CPU
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Optimizing NNI: done in 1.24626 secs using 399.2% CPU
Optimizing NNI: done in 1.08057 secs using 399.4% CPU
Iteration 110 / LogL: -57804.374 / Time: 0h:3m:14s (0h:1m:5s left)
Optimizing NNI: done in 1.45203 secs using 399% CPU
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Optimizing NNI: done in 2.80834 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 80: -103620.277
Iteration 80 / LogL: -103620.277 / Time: 0h:4m:43s (0h:5m:58s left)
Optimizing NNI: done in 1.75637 secs using 398.8% CPU
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Iteration 120 / LogL: -57800.340 / Time: 0h:3m:29s (0h:0m:47s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 84: -103617.942
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30.758 second
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Iteration 130 / LogL: -57810.728 / Time: 0h:3m:43s (0h:0m:29s left)
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Iteration 90 / LogL: -103778.775 / Time: 0h:5m:8s (0h:5m:25s left)
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Optimizing NNI: done in 2.47972 secs using 398.7% CPU
Computing log-likelihood of 98 initial trees ... 16.482 seconds
Current best score: -193357.785

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.49557 secs using 399.5% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.7245 secs using 399.3% CPU
Iteration 140 / LogL: -57800.312 / Time: 0h:3m:58s (0h:0m:11s left)
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BETTER TREE FOUND at iteration 1: -192882.347
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 1.34732 secs using 399.6% CPU
TREE SEARCH COMPLETED AFTER 148 ITERATIONS / Time: 0h:4m:9s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57798.391
2. Current log-likelihood: -57798.347
3. Current log-likelihood: -57798.316
Optimizing NNI: done in 2.28252 secs using 398.4% CPU
Iteration 100 / LogL: -103674.932 / Time: 0h:5m:32s (0h:4m:42s left)
4. Current log-likelihood: -57798.295
5. Current log-likelihood: -57798.280
BETTER TREE FOUND at iteration 2: -192881.621
Optimal log-likelihood: -57798.272
Site proportion and rates:  (0.136,0.073) (0.065,0.184) (0.159,0.360) (0.273,0.685) (0.116,1.097) (0.100,1.652) (0.130,2.485) (0.021,5.600)
Parameters optimization took 5 rounds (3.455 sec)
BEST SCORE FOUND : -57798.272
Total tree length: 41.858

Total number of iterations: 148
CPU time used for tree search: 954.728 sec (0h:15m:54s)
Wall-clock time used for tree search: 243.002 sec (0h:4m:3s)
Total CPU time used: 995.240 sec (0h:16m:35s)
Total wall-clock time used: 253.134 sec (0h:4m:13s)

===> START BOOTSTRAP REPLICATE NUMBER 59

Creating bootstrap alignment (seed: 67521)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60652.671
Optimizing NNI: done in 2.58655 secs using 398.2% CPU
2. Current log-likelihood: -60009.802
3. Current log-likelihood: -60004.701
4. Current log-likelihood: -60000.480
Optimizing NNI: done in 1.93574 secs using 398.2% CPU
5. Current log-likelihood: -59990.162
Optimizing NNI: done in 4.55374 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
6. Current log-likelihood: -59968.470
Optimizing NNI: done in 1.74612 secs using 398.5% CPU
7. Current log-likelihood: -59964.281
8. Current log-likelihood: -59964.135
Optimal log-likelihood: -59964.132
Site proportion and rates:  (0.095,0.063) (0.088,0.179) (0.107,0.357) (0.080,0.360) (0.239,0.697) (0.176,1.138) (0.192,2.166) (0.023,5.555)
Parameters optimization took 8 rounds (5.931 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.08645 secs using 398% CPU
Calculating distance matrix: done in 1.08302 secs using 400% CPU
Computing ML distances took 1.083198 sec (of wall-clock time) 4.332125 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000408173 secs using 421.9% CPU
Constructing RapidNJ tree: done in 0.00437999 secs using 394.2% CPU
Computing RapidNJ tree took 0.004856 sec (of wall-clock time) 0.019506 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59785.127
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.16869 secs using 399% CPU
Optimizing NNI: done in 1.97208 secs using 398.8% CPU
4.878 second
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Computing log-likelihood of 98 initial trees ... 5.247 seconds
Current best score: -59701.836

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 110 / LogL: -103623.259 / Time: 0h:5m:53s (0h:4m:0s left)
BETTER TREE FOUND at iteration 1: -59481.892
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BETTER TREE FOUND at iteration 3: -59477.960
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Estimate model parameters (epsilon = 0.100)
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Iteration 120 / LogL: -103665.905 / Time: 0h:6m:15s (0h:3m:22s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 10: -59415.810
Iteration 10 / LogL: -59415.810 / Time: 0h:0m:45s
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Iteration 20 / LogL: -59493.078 / Time: 0h:0m:58s
Finish initializing candidate tree set (20)
Current best tree score: -59415.810 / CPU time: 50.894
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 130 / LogL: -103671.257 / Time: 0h:6m:38s (0h:2m:46s left)
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Iteration 30 / LogL: -59438.061 / Time: 0h:1m:14s (0h:4m:5s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 50: -59397.164
Iteration 50 / LogL: -59397.164 / Time: 0h:1m:47s (0h:3m:39s left)
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Iteration 20 / LogL: -192792.305 / Time: 0h:3m:58s
Finish initializing candidate tree set (20)
Current best tree score: -192720.176 / CPU time: 203.690
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 82: -59394.428
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Iteration 210 / LogL: -59423.828 / Time: 0h:5m:36s (0h:0m:-2s left)
TREE SEARCH COMPLETED AFTER 210 ITERATIONS / Time: 0h:5m:36s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59394.389
Optimal log-likelihood: -59394.386
Site proportion and rates:  (0.101,0.067) (0.116,0.208) (0.103,0.390) (0.075,0.411) (0.246,0.734) (0.152,1.219) (0.183,2.199) (0.024,5.409)
Parameters optimization took 1 rounds (0.411 sec)
BEST SCORE FOUND : -59394.386
Total tree length: 43.871

Total number of iterations: 210
CPU time used for tree search: 1297.376 sec (0h:21m:37s)
Wall-clock time used for tree search: 328.710 sec (0h:5m:28s)
Total CPU time used: 1330.183 sec (0h:22m:10s)
Total wall-clock time used: 336.907 sec (0h:5m:36s)

===> START BOOTSTRAP REPLICATE NUMBER 60

Creating bootstrap alignment (seed: 67522)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.041 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61073.131
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2. Current log-likelihood: -60480.705
3. Current log-likelihood: -60454.603
4. Current log-likelihood: -60447.846
Optimizing NNI: done in 2.09432 secs using 397.8% CPU
5. Current log-likelihood: -60442.997
6. Current log-likelihood: -60442.482
Optimizing NNI: done in 4.42383 secs using 598.2% CPU
Optimal log-likelihood: -60442.425
Site proportion and rates:  (0.106,0.061) (0.134,0.190) (0.066,0.425) (0.165,0.476) (0.199,0.801) (0.128,1.305) (0.170,2.169) (0.031,5.267)
Parameters optimization took 6 rounds (4.820 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.10268 secs using 400% CPU
Computing ML distances took 1.102857 sec (of wall-clock time) 4.411043 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000397921 secs using 174.2% CPU
Constructing RapidNJ tree: done in 0.00436187 secs using 222.2% CPU
Computing RapidNJ tree took 0.004824 sec (of wall-clock time) 0.012378 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60365.044
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.17398 secs using 397.7% CPU
Iteration 250 / LogL: -103624.380 / Time: 0h:11m:18s (0h:2m:29s left)
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5.187 second
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Computing log-likelihood of 98 initial trees ... 5.233 seconds
Current best score: -60254.315

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 10 / LogL: -60069.235 / Time: 0h:0m:34s
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Iteration 70 / LogL: -192674.243 / Time: 0h:8m:0s (0h:8m:14s left)
Optimizing NNI: done in 1.22986 secs using 398.6% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.48624 secs using 398.7% CPU
BETTER TREE FOUND at iteration 266: -103614.030
Optimizing NNI: done in 1.4212 secs using 399.4% CPU
Iteration 20 / LogL: -60042.262 / Time: 0h:0m:47s
Finish initializing candidate tree set (20)
Current best tree score: -60015.268 / CPU time: 41.328
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.62364 secs using 399% CPU
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BETTER TREE FOUND at iteration 25: -60007.695
Optimizing NNI: done in 2.2389 secs using 397.9% CPU
Iteration 270 / LogL: -103642.666 / Time: 0h:12m:7s (0h:4m:19s left)
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BETTER TREE FOUND at iteration 26: -60004.630
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Iteration 30 / LogL: -60021.790 / Time: 0h:1m:4s (0h:3m:34s left)
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BETTER TREE FOUND at iteration 33: -60000.504
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Iteration 280 / LogL: -103641.596 / Time: 0h:12m:30s (0h:3m:51s left)
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Iteration 40 / LogL: -60014.618 / Time: 0h:1m:19s (0h:3m:10s left)
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Iteration 80 / LogL: -192754.905 / Time: 0h:8m:46s (0h:6m:46s left)
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Iteration 50 / LogL: -60011.702 / Time: 0h:1m:34s (0h:2m:40s left)
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Iteration 290 / LogL: -103628.144 / Time: 0h:12m:52s (0h:3m:23s left)
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Iteration 60 / LogL: -60011.816 / Time: 0h:1m:47s (0h:2m:13s left)
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BETTER TREE FOUND at iteration 67: -59999.770
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Iteration 70 / LogL: -60002.257 / Time: 0h:2m:3s (0h:2m:53s left)
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BETTER TREE FOUND at iteration 71: -59999.198
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Iteration 300 / LogL: -103633.386 / Time: 0h:13m:17s (0h:2m:55s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 72: -59998.732
Optimizing NNI: done in 2.39448 secs using 397.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 73: -59997.317
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Iteration 90 / LogL: -192816.340 / Time: 0h:9m:32s (0h:5m:28s left)
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Iteration 80 / LogL: -59998.963 / Time: 0h:2m:18s (0h:2m:43s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 83: -59996.048
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Iteration 310 / LogL: -103636.628 / Time: 0h:13m:40s (0h:2m:28s left)
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Iteration 90 / LogL: -59997.334 / Time: 0h:2m:33s (0h:2m:40s left)
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Iteration 100 / LogL: -60004.876 / Time: 0h:2m:46s (0h:2m:19s left)
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Iteration 320 / LogL: -103619.809 / Time: 0h:14m:3s (0h:2m:1s left)
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Iteration 110 / LogL: -60003.538 / Time: 0h:2m:59s (0h:2m:0s left)
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Iteration 100 / LogL: -192677.981 / Time: 0h:10m:18s (0h:4m:15s left)
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Iteration 120 / LogL: -60007.614 / Time: 0h:3m:13s (0h:1m:42s left)
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Iteration 330 / LogL: -103635.679 / Time: 0h:14m:25s (0h:1m:34s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.4372 secs using 399% CPU
BETTER TREE FOUND at iteration 331: -103613.497
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Iteration 130 / LogL: -60011.560 / Time: 0h:3m:27s (0h:1m:25s left)
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Iteration 340 / LogL: -103691.298 / Time: 0h:14m:50s (0h:3m:59s left)
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Iteration 110 / LogL: -192692.543 / Time: 0h:11m:4s (0h:3m:8s left)
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Iteration 150 / LogL: -60013.007 / Time: 0h:3m:53s (0h:0m:51s left)
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Iteration 350 / LogL: -103624.298 / Time: 0h:15m:12s (0h:3m:31s left)
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Iteration 160 / LogL: -60008.407 / Time: 0h:4m:7s (0h:0m:35s left)
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UPDATE BEST LOG-LIKELIHOOD: -59995.358
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UPDATE BEST LOG-LIKELIHOOD: -59995.095
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TREE SEARCH COMPLETED AFTER 432 ITERATIONS / Time: 0h:18m:18s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -103613.497
Optimal log-likelihood: -103613.497
Proportion of invariable sites: 0.019
Site proportion and rates:  (0.121,0.034) (0.085,0.095) (0.062,0.187) (0.081,0.307) (0.093,0.452) (0.126,0.671) (0.166,1.126) (0.166,1.696) (0.082,4.362)
Parameters optimization took 1 rounds (0.487 sec)
BEST SCORE FOUND : -103613.497
Total tree length: 177.772

Total number of iterations: 432
CPU time used for tree search: 4281.248 sec (1h:11m:21s)
Wall-clock time used for tree search: 1082.607 sec (0h:18m:2s)
Total CPU time used: 4346.203 sec (1h:12m:26s)
Total wall-clock time used: 1098.867 sec (0h:18m:18s)

===> START BOOTSTRAP REPLICATE NUMBER 20

Creating bootstrap alignment (seed: 68202)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.104 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 110 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -111129.730
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Iteration 290 / LogL: -59995.762 / Time: 0h:7m:9s (0h:1m:41s left)
2. Current log-likelihood: -109095.865
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3. Current log-likelihood: -109024.285
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4. Current log-likelihood: -109022.442
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10. Current log-likelihood: -109020.888
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Iteration 300 / LogL: -60000.840 / Time: 0h:7m:23s (0h:1m:26s left)
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11. Current log-likelihood: -109019.297
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13. Current log-likelihood: -109007.796
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14. Current log-likelihood: -109006.760
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15. Current log-likelihood: -109006.613
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16. Current log-likelihood: -109006.511
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Optimizing NNI: done in 4.20349 secs using 598.2% CPU
Optimal log-likelihood: -109006.389
Proportion of invariable sites: 0.031
Site proportion and rates:  (0.085,0.037) (0.065,0.116) (0.118,0.217) (0.128,0.384) (0.118,0.609) (0.100,0.890) (0.142,1.285) (0.150,1.826) (0.064,4.633)
Parameters optimization took 16 rounds (26.657 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 310 / LogL: -60040.511 / Time: 0h:7m:37s (0h:1m:11s left)
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Calculating distance matrix: done in 4.66353 secs using 399.9% CPU
Computing ML distances took 4.663772 sec (of wall-clock time) 18.650669 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000741005 secs using 413.8% CPU
Constructing RapidNJ tree: done in 0.00872111 secs using 353.1% CPU
Computing RapidNJ tree took 0.009528 sec (of wall-clock time) 0.036309 sec (of CPU time)
Optimizing NNI: done in 1.38719 secs using 398.8% CPU
Log-likelihood of RapidNJ tree: -109128.024
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.45461 secs using 399% CPU
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Iteration 320 / LogL: -60000.529 / Time: 0h:7m:50s (0h:0m:56s left)
10.792 second
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Iteration 160 / LogL: -192663.219 / Time: 0h:15m:9s (0h:5m:31s left)
Optimizing NNI: done in 1.40855 secs using 399.3% CPU
UPDATE BEST LOG-LIKELIHOOD: -59995.094
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 161: -192645.668
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Computing log-likelihood of 98 initial trees ... 10.658 seconds
Current best score: -109006.389

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 330 / LogL: -59999.447 / Time: 0h:8m:4s (0h:0m:41s left)
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BETTER TREE FOUND at iteration 8: -108468.859
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Iteration 170 / LogL: -192724.955 / Time: 0h:15m:59s (0h:8m:36s left)
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TREE SEARCH COMPLETED AFTER 359 ITERATIONS / Time: 0h:8m:46s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59995.094
Optimizing NNI: done in 2.23549 secs using 398.3% CPU
Iteration 10 / LogL: -108493.668 / Time: 0h:1m:39s
Optimal log-likelihood: -59995.089
Site proportion and rates:  (0.103,0.060) (0.139,0.189) (0.062,0.449) (0.158,0.450) (0.213,0.785) (0.123,1.323) (0.170,2.183) (0.032,5.162)
Parameters optimization took 1 rounds (0.364 sec)
BEST SCORE FOUND : -59995.089
Total tree length: 45.946

Total number of iterations: 359
CPU time used for tree search: 2060.740 sec (0h:34m:20s)
Wall-clock time used for tree search: 520.210 sec (0h:8m:40s)
Total CPU time used: 2087.621 sec (0h:34m:47s)
Total wall-clock time used: 526.924 sec (0h:8m:46s)

===> START BOOTSTRAP REPLICATE NUMBER 61

Creating bootstrap alignment (seed: 67523)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 64 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60652.824
Optimizing NNI: done in 4.82455 secs using 597.6% CPU
2. Current log-likelihood: -60045.454
3. Current log-likelihood: -60036.182
Optimizing NNI: done in 2.31129 secs using 398.7% CPU
4. Current log-likelihood: -60016.416
5. Current log-likelihood: -59991.396
6. Current log-likelihood: -59989.540
Optimizing NNI: done in 2.46638 secs using 398.8% CPU
Optimizing NNI: done in 4.52944 secs using 597.5% CPU
Optimal log-likelihood: -59989.498
Site proportion and rates:  (0.142,0.082) (0.074,0.168) (0.104,0.332) (0.096,0.436) (0.134,0.626) (0.213,1.003) (0.199,2.064) (0.037,5.153)
Parameters optimization took 6 rounds (5.008 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.12328 secs using 399.9% CPU
Computing ML distances took 1.123473 sec (of wall-clock time) 4.492250 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000354052 secs using 405.3% CPU
Constructing RapidNJ tree: done in 0.00443196 secs using 363.8% CPU
Computing RapidNJ tree took 0.004846 sec (of wall-clock time) 0.019384 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60098.774
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.73463 secs using 398.9% CPU
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Optimizing NNI: done in 5.68075 secs using 597.6% CPU
5.023 second
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.74452 secs using 595.8% CPU
Computing log-likelihood of 98 initial trees ... 5.272 seconds
Current best score: -59989.498

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 15: -108464.142
BETTER TREE FOUND at iteration 1: -59814.020
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 4: -59746.745
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Iteration 20 / LogL: -108547.942 / Time: 0h:2m:9s
Finish initializing candidate tree set (20)
Current best tree score: -108464.142 / CPU time: 97.206
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 180 / LogL: -192756.211 / Time: 0h:16m:49s (0h:7m:36s left)
BETTER TREE FOUND at iteration 18: -59740.784
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Iteration 20 / LogL: -59787.106 / Time: 0h:0m:47s
Finish initializing candidate tree set (20)
Current best tree score: -59740.784 / CPU time: 40.865
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 40 / LogL: -59763.744 / Time: 0h:1m:15s (0h:2m:31s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 79: -59734.341
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Iteration 70 / LogL: -108442.021 / Time: 0h:4m:23s (0h:5m:43s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 106: -59730.612
Optimizing NNI: done in 2.20435 secs using 398.3% CPU
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Iteration 110 / LogL: -59731.631 / Time: 0h:2m:56s (0h:2m:35s left)
Optimizing NNI: done in 2.40768 secs using 398.2% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.31056 secs using 399.1% CPU
Optimizing NNI: done in 1.40729 secs using 398.9% CPU
BETTER TREE FOUND at iteration 76: -108419.891
Optimizing NNI: done in 1.27877 secs using 399.1% CPU
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Iteration 210 / LogL: -192689.513 / Time: 0h:19m:11s (0h:4m:40s left)
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Iteration 120 / LogL: -59730.660 / Time: 0h:3m:9s (0h:2m:17s left)
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Iteration 80 / LogL: -108424.540 / Time: 0h:4m:50s (0h:5m:52s left)
Optimizing NNI: done in 4.48733 secs using 597.9% CPU
Optimizing NNI: done in 1.34124 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 121: -59729.924
Optimizing NNI: done in 1.327 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 126: -59729.884
Optimizing NNI: done in 4.58603 secs using 597.8% CPU
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Iteration 130 / LogL: -59733.116 / Time: 0h:3m:25s (0h:2m:32s left)
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Iteration 90 / LogL: -108442.968 / Time: 0h:5m:13s (0h:5m:3s left)
Optimizing NNI: done in 4.70474 secs using 597.3% CPU
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Iteration 140 / LogL: -59814.678 / Time: 0h:3m:39s (0h:2m:15s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.57491 secs using 399.4% CPU
Iteration 150 / LogL: -59731.031 / Time: 0h:3m:52s (0h:1m:58s left)
BETTER TREE FOUND at iteration 97: -108411.619
Optimizing NNI: done in 5.19734 secs using 597.1% CPU
Iteration 220 / LogL: -192912.806 / Time: 0h:19m:58s (0h:3m:44s left)
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Iteration 100 / LogL: -108431.722 / Time: 0h:5m:40s (0h:5m:33s left)
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Iteration 160 / LogL: -59752.752 / Time: 0h:4m:7s (0h:1m:42s left)
Optimizing NNI: done in 4.26664 secs using 598% CPU
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Iteration 170 / LogL: -59731.451 / Time: 0h:4m:21s (0h:1m:26s left)
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Iteration 110 / LogL: -108490.179 / Time: 0h:6m:3s (0h:4m:50s left)
Optimizing NNI: done in 1.47167 secs using 399% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.49165 secs using 399% CPU
BETTER TREE FOUND at iteration 112: -108411.000
Optimizing NNI: done in 4.45215 secs using 597% CPU
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Iteration 180 / LogL: -59730.664 / Time: 0h:4m:35s (0h:1m:10s left)
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Iteration 230 / LogL: -192703.455 / Time: 0h:20m:44s (0h:2m:48s left)
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Iteration 120 / LogL: -108450.095 / Time: 0h:6m:27s (0h:4m:59s left)
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Optimizing NNI: done in 1.31446 secs using 399.5% CPU
Iteration 190 / LogL: -59740.321 / Time: 0h:4m:49s (0h:0m:55s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 196: -59729.847
Optimizing NNI: done in 2.34248 secs using 398.6% CPU
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Iteration 200 / LogL: -59729.886 / Time: 0h:5m:4s (0h:2m:26s left)
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Iteration 130 / LogL: -108441.468 / Time: 0h:6m:50s (0h:4m:20s left)
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Iteration 210 / LogL: -59731.924 / Time: 0h:5m:18s (0h:2m:10s left)
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BETTER TREE FOUND at iteration 138: -108410.996
Optimizing NNI: done in 1.39065 secs using 399% CPU
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Iteration 240 / LogL: -192699.224 / Time: 0h:21m:34s (0h:1m:53s left)
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Iteration 220 / LogL: -59751.327 / Time: 0h:5m:32s (0h:1m:55s left)
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Iteration 140 / LogL: -108412.543 / Time: 0h:7m:11s (0h:5m:4s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.27207 secs using 398.8% CPU
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BETTER TREE FOUND at iteration 241: -192642.471
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Iteration 230 / LogL: -59738.315 / Time: 0h:5m:45s (0h:1m:39s left)
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Iteration 150 / LogL: -108414.155 / Time: 0h:7m:33s (0h:4m:27s left)
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Iteration 240 / LogL: -59745.096 / Time: 0h:5m:58s (0h:1m:24s left)
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BETTER TREE FOUND at iteration 242: -59729.839
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 247: -192641.851
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Iteration 250 / LogL: -59740.598 / Time: 0h:6m:12s (0h:2m:17s left)
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Iteration 160 / LogL: -108411.127 / Time: 0h:7m:56s (0h:3m:53s left)
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Iteration 250 / LogL: -192648.933 / Time: 0h:22m:30s (0h:8m:45s left)
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Iteration 260 / LogL: -59729.932 / Time: 0h:6m:26s (0h:2m:2s left)
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Iteration 170 / LogL: -108422.611 / Time: 0h:8m:18s (0h:3m:20s left)
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Iteration 270 / LogL: -59743.125 / Time: 0h:6m:40s (0h:1m:47s left)
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Iteration 280 / LogL: -59734.102 / Time: 0h:6m:54s (0h:1m:32s left)
Optimizing NNI: done in 1.50004 secs using 399% CPU
Optimizing NNI: done in 2.33646 secs using 398.6% CPU
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Iteration 180 / LogL: -108414.285 / Time: 0h:8m:40s (0h:2m:48s left)
Optimizing NNI: done in 1.72714 secs using 399.1% CPU
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Optimizing NNI: done in 2.17319 secs using 398.8% CPU
Optimizing NNI: done in 1.31578 secs using 399.3% CPU
Iteration 290 / LogL: -59753.304 / Time: 0h:7m:8s (0h:1m:17s left)
Optimizing NNI: done in 4.84371 secs using 597.2% CPU
Optimizing NNI: done in 2.18588 secs using 398.8% CPU
Optimizing NNI: done in 1.36732 secs using 399% CPU
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Iteration 260 / LogL: -192648.367 / Time: 0h:23m:17s (0h:7m:49s left)
Optimizing NNI: done in 2.06158 secs using 398.7% CPU
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Optimizing NNI: done in 2.26984 secs using 398.7% CPU
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Iteration 300 / LogL: -59742.762 / Time: 0h:7m:21s (0h:1m:2s left)
Optimizing NNI: done in 4.94156 secs using 597.4% CPU
Optimizing NNI: done in 1.18794 secs using 399.4% CPU
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Iteration 190 / LogL: -108426.527 / Time: 0h:9m:2s (0h:2m:17s left)
Optimizing NNI: done in 1.43716 secs using 398.5% CPU
Optimizing NNI: done in 2.53748 secs using 398.7% CPU
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Optimizing NNI: done in 1.13346 secs using 399% CPU
Optimizing NNI: done in 2.4915 secs using 398.5% CPU
Optimizing NNI: done in 1.2622 secs using 399.1% CPU
Optimizing NNI: done in 4.51616 secs using 597.5% CPU
Optimizing NNI: done in 1.17463 secs using 399.2% CPU
Optimizing NNI: done in 2.22758 secs using 398.4% CPU
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Optimizing NNI: done in 2.10511 secs using 398.5% CPU
Optimizing NNI: done in 1.17691 secs using 399.2% CPU
Iteration 310 / LogL: -59741.547 / Time: 0h:7m:35s (0h:0m:47s left)
Optimizing NNI: done in 1.37187 secs using 398.7% CPU
Optimizing NNI: done in 4.63722 secs using 596.7% CPU
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Optimizing NNI: done in 1.32874 secs using 399.5% CPU
Optimizing NNI: done in 2.4111 secs using 398.9% CPU
Optimizing NNI: done in 1.69235 secs using 399% CPU
Optimizing NNI: done in 1.32585 secs using 398.7% CPU
Optimizing NNI: done in 1.89446 secs using 398.9% CPU
Optimizing NNI: done in 4.61958 secs using 596.9% CPU
Optimizing NNI: done in 1.43653 secs using 398.9% CPU
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Optimizing NNI: done in 1.49951 secs using 399% CPU
Optimizing NNI: done in 1.20028 secs using 399% CPU
Optimizing NNI: done in 2.22451 secs using 398.7% CPU
Iteration 200 / LogL: -108479.183 / Time: 0h:9m:24s (0h:1m:47s left)
Optimizing NNI: done in 4.86641 secs using 597.7% CPU
Optimizing NNI: done in 1.15306 secs using 398.9% CPU
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Iteration 320 / LogL: -59883.043 / Time: 0h:7m:49s (0h:0m:32s left)
Optimizing NNI: done in 2.09833 secs using 398.6% CPU
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Optimizing NNI: done in 4.34922 secs using 597.6% CPU
Optimizing NNI: done in 1.43814 secs using 399% CPU
Optimizing NNI: done in 1.98194 secs using 398.6% CPU
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Optimizing NNI: done in 2.25036 secs using 398.9% CPU
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Optimizing NNI: done in 1.212 secs using 398.9% CPU
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Optimizing NNI: done in 4.3742 secs using 597.7% CPU
Iteration 270 / LogL: -192653.226 / Time: 0h:24m:4s (0h:6m:53s left)
Optimizing NNI: done in 2.22869 secs using 398.3% CPU
Optimizing NNI: done in 1.37796 secs using 399.1% CPU
Optimizing NNI: done in 1.38125 secs using 398.9% CPU
Iteration 330 / LogL: -59764.614 / Time: 0h:8m:2s (0h:0m:17s left)
Optimizing NNI: done in 2.10487 secs using 398.5% CPU
Optimizing NNI: done in 1.41656 secs using 399.2% CPU
Optimizing NNI: done in 4.33169 secs using 597% CPU
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Optimizing NNI: done in 1.46025 secs using 399.4% CPU
Optimizing NNI: done in 1.87219 secs using 399.1% CPU
Iteration 210 / LogL: -108416.425 / Time: 0h:9m:46s (0h:1m:18s left)
Optimizing NNI: done in 1.55101 secs using 399% CPU
Optimizing NNI: done in 4.34939 secs using 597.8% CPU
Optimizing NNI: done in 2.4179 secs using 398.8% CPU
Optimizing NNI: done in 1.30984 secs using 399.1% CPU
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Optimizing NNI: done in 2.21001 secs using 398.8% CPU
Optimizing NNI: done in 1.41946 secs using 399.1% CPU
Optimizing NNI: done in 4.58684 secs using 597.5% CPU
Optimizing NNI: done in 2.10253 secs using 398.5% CPU
Optimizing NNI: done in 1.54262 secs using 399.5% CPU
Optimizing NNI: done in 1.28613 secs using 398.8% CPU
Optimizing NNI: done in 2.01158 secs using 398.7% CPU
Optimizing NNI: done in 1.23734 secs using 399.4% CPU
Iteration 340 / LogL: -59737.166 / Time: 0h:8m:16s (0h:0m:2s left)
Optimizing NNI: done in 4.08617 secs using 597.8% CPU
Optimizing NNI: done in 1.36919 secs using 399.2% CPU
Optimizing NNI: done in 2.79768 secs using 398.6% CPU
Optimizing NNI: done in 1.22349 secs using 399.2% CPU
Optimizing NNI: done in 1.41451 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 343 ITERATIONS / Time: 0h:8m:20s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59729.839
Optimizing NNI: done in 2.00585 secs using 398.5% CPU
Optimal log-likelihood: -59729.829
Site proportion and rates:  (0.156,0.083) (0.083,0.204) (0.094,0.379) (0.089,0.413) (0.154,0.657) (0.194,1.050) (0.193,2.091) (0.037,5.166)
Parameters optimization took 1 rounds (0.702 sec)
BEST SCORE FOUND : -59729.829
Total tree length: 48.500

Total number of iterations: 343
CPU time used for tree search: 1957.689 sec (0h:32m:37s)
Wall-clock time used for tree search: 494.248 sec (0h:8m:14s)
Total CPU time used: 1986.629 sec (0h:33m:6s)
Total wall-clock time used: 501.474 sec (0h:8m:21s)

===> START BOOTSTRAP REPLICATE NUMBER 62

Creating bootstrap alignment (seed: 67524)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.042 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -57481.171
2. Current log-likelihood: -56946.309
Optimizing NNI: done in 4.98599 secs using 597.2% CPU
Optimizing NNI: done in 1.93327 secs using 398.5% CPU
3. Current log-likelihood: -56942.396
4. Current log-likelihood: -56940.528
Optimizing NNI: done in 2.04119 secs using 398.7% CPU
5. Current log-likelihood: -56935.497
6. Current log-likelihood: -56913.849
Optimizing NNI: done in 1.97208 secs using 398.5% CPU
7. Current log-likelihood: -56896.409
Optimizing NNI: done in 4.54682 secs using 597.1% CPU
8. Current log-likelihood: -56894.243
9. Current log-likelihood: -56893.951
Optimizing NNI: done in 2.23403 secs using 399.2% CPU
Iteration 220 / LogL: -108487.742 / Time: 0h:10m:8s (0h:0m:50s left)
Optimal log-likelihood: -56893.914
Site proportion and rates:  (0.113,0.063) (0.159,0.206) (0.037,0.416) (0.154,0.438) (0.189,0.722) (0.147,1.280) (0.180,2.300) (0.020,6.864)
Parameters optimization took 9 rounds (7.958 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09923 secs using 399.9% CPU
Computing ML distances took 1.099409 sec (of wall-clock time) 4.396077 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000365019 secs using 190.7% CPU
Constructing RapidNJ tree: done in 0.00439286 secs using 329.4% CPU
Computing RapidNJ tree took 0.004818 sec (of wall-clock time) 0.016351 sec (of CPU time)
Log-likelihood of RapidNJ tree: -56930.203
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.16185 secs using 398.3% CPU
Optimizing NNI: done in 4.74122 secs using 597.8% CPU
Optimizing NNI: done in 2.33426 secs using 398.6% CPU
5.097 second
Optimizing NNI: done in 2.37164 secs using 398.4% CPU
Optimizing NNI: done in 2.40629 secs using 398.8% CPU
Optimizing NNI: done in 6.74977 secs using 597.9% CPU
Optimizing NNI: done in 2.28537 secs using 399% CPU
Computing log-likelihood of 98 initial trees ... 5.284 seconds
Current best score: -56893.914

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.24645 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.37735 secs using 398.6% CPU
Optimizing NNI: done in 5.28455 secs using 597.7% CPU
BETTER TREE FOUND at iteration 1: -56717.917
Optimizing NNI: done in 0.811874 secs using 399.7% CPU
Optimizing NNI: done in 2.31279 secs using 399.1% CPU
Optimizing NNI: done in 1.33234 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -56710.054
Optimizing NNI: done in 2.22882 secs using 399% CPU
Optimizing NNI: done in 4.27208 secs using 597.2% CPU
Iteration 280 / LogL: -192661.417 / Time: 0h:24m:52s (0h:5m:58s left)
Optimizing NNI: done in 1.12562 secs using 398.6% CPU
Optimizing NNI: done in 1.29624 secs using 399.2% CPU
Optimizing NNI: done in 2.30967 secs using 399.1% CPU
Optimizing NNI: done in 1.25554 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.41993 secs using 398.3% CPU
Iteration 230 / LogL: -108421.193 / Time: 0h:10m:32s (0h:0m:22s left)
BETTER TREE FOUND at iteration 6: -56699.114
Optimizing NNI: done in 4.64473 secs using 597% CPU
Optimizing NNI: done in 1.21234 secs using 398.3% CPU
Optimizing NNI: done in 2.09744 secs using 399% CPU
Optimizing NNI: done in 1.12115 secs using 398.8% CPU
Optimizing NNI: done in 1.37638 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.37551 secs using 398.6% CPU
Optimizing NNI: done in 4.62372 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -56691.746
Optimizing NNI: done in 1.52066 secs using 399.1% CPU
Iteration 10 / LogL: -56709.854 / Time: 0h:0m:37s
Optimizing NNI: done in 2.12016 secs using 398% CPU
Optimizing NNI: done in 1.15926 secs using 399% CPU
BETTER TREE FOUND at iteration 282: -192641.157
Optimizing NNI: done in 1.1121 secs using 399.2% CPU
Optimizing NNI: done in 2.51176 secs using 398.4% CPU
Optimizing NNI: done in 1.29704 secs using 399% CPU
Optimizing NNI: done in 2.38307 secs using 398.7% CPU
Optimizing NNI: done in 1.56734 secs using 399% CPU
Optimizing NNI: done in 1.21 secs using 399.3% CPU
Optimizing NNI: done in 4.71583 secs using 596.7% CPU
Optimizing NNI: done in 2.09164 secs using 399% CPU
Optimizing NNI: done in 1.33653 secs using 398.8% CPU
Optimizing NNI: done in 1.35222 secs using 399.1% CPU
Optimizing NNI: done in 2.30876 secs using 398.5% CPU
Optimizing NNI: done in 1.34363 secs using 398.6% CPU
Optimizing NNI: done in 1.95188 secs using 398.9% CPU
Optimizing NNI: done in 4.95168 secs using 596.9% CPU
Optimizing NNI: done in 1.27811 secs using 398.7% CPU
Optimizing NNI: done in 1.20493 secs using 399.2% CPU
Iteration 20 / LogL: -56769.749 / Time: 0h:0m:50s
Finish initializing candidate tree set (20)
Current best tree score: -56691.746 / CPU time: 41.368
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.50779 secs using 398.6% CPU
TREE SEARCH COMPLETED AFTER 239 ITERATIONS / Time: 0h:10m:52s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -108410.996
Optimizing NNI: done in 1.49668 secs using 399.5% CPU
2. Current log-likelihood: -108410.931
Optimizing NNI: done in 1.29105 secs using 398.4% CPU
Optimal log-likelihood: -108410.920
Proportion of invariable sites: 0.030
Site proportion and rates:  (0.085,0.033) (0.062,0.107) (0.124,0.211) (0.121,0.375) (0.121,0.591) (0.107,0.903) (0.129,1.294) (0.157,1.809) (0.064,4.716)
Parameters optimization took 2 rounds (2.100 sec)
BEST SCORE FOUND : -108410.920
Total tree length: 174.975

Total number of iterations: 239
CPU time used for tree search: 2439.896 sec (0h:40m:39s)
Wall-clock time used for tree search: 620.138 sec (0h:10m:20s)
Total CPU time used: 2577.771 sec (0h:42m:57s)
Total wall-clock time used: 654.711 sec (0h:10m:54s)

===> START BOOTSTRAP REPLICATE NUMBER 21

Creating bootstrap alignment (seed: 68203)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105823.723
Optimizing NNI: done in 4.88618 secs using 597.1% CPU
Optimizing NNI: done in 1.37907 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
2. Current log-likelihood: -103765.077
BETTER TREE FOUND at iteration 23: -56683.417
3. Current log-likelihood: -103687.065
Optimizing NNI: done in 1.41355 secs using 399.3% CPU
4. Current log-likelihood: -103685.536
Optimizing NNI: done in 4.7018 secs using 597.2% CPU
Optimizing NNI: done in 1.64107 secs using 398.6% CPU
Optimal log-likelihood: -103685.421
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.094,0.040) (0.081,0.126) (0.090,0.223) (0.089,0.333) (0.111,0.433) (0.117,0.710) (0.106,1.174) (0.199,1.872) (0.080,3.844)
Parameters optimization took 4 rounds (6.603 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.22304 secs using 399.3% CPU
Optimizing NNI: done in 1.43886 secs using 399.2% CPU
Optimizing NNI: done in 1.40544 secs using 399.7% CPU
Optimizing NNI: done in 4.79678 secs using 596.8% CPU
Optimizing NNI: done in 1.31781 secs using 398.9% CPU
Calculating distance matrix: done in 4.72565 secs using 399.9% CPU
Computing ML distances took 4.725904 sec (of wall-clock time) 18.900445 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000720024 secs using 403.3% CPU
Constructing RapidNJ tree: done in 0.00860095 secs using 344.6% CPU
Computing RapidNJ tree took 0.009381 sec (of wall-clock time) 0.034598 sec (of CPU time)
Log-likelihood of RapidNJ tree: -103925.588
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.39481 secs using 398.9% CPU
Iteration 30 / LogL: -56692.120 / Time: 0h:1m:6s (0h:3m:32s left)
Optimizing NNI: done in 1.37028 secs using 398.6% CPU
Optimizing NNI: done in 4.83913 secs using 597.2% CPU
Optimizing NNI: done in 1.48931 secs using 399.1% CPU
Optimizing NNI: done in 1.43458 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -56683.330
Optimizing NNI: done in 1.33869 secs using 398.4% CPU
Optimizing NNI: done in 1.48171 secs using 399.1% CPU
Optimizing NNI: done in 6.3911 secs using 597.1% CPU
Optimizing NNI: done in 1.26814 secs using 399.4% CPU
Optimizing NNI: done in 1.35856 secs using 398.6% CPU
10.536 second
Optimizing NNI: done in 1.70102 secs using 399.1% CPU
Optimizing NNI: done in 1.42249 secs using 399.2% CPU
Optimizing NNI: done in 5.70065 secs using 597.3% CPU
Iteration 290 / LogL: -192689.501 / Time: 0h:25m:47s (0h:8m:12s left)
Optimizing NNI: done in 1.39139 secs using 399.4% CPU
Iteration 40 / LogL: -56685.612 / Time: 0h:1m:21s (0h:3m:13s left)
Optimizing NNI: done in 1.60994 secs using 399% CPU
Optimizing NNI: done in 1.46145 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -56676.627
Optimizing NNI: done in 4.46933 secs using 597.3% CPU
Optimizing NNI: done in 1.3807 secs using 398.9% CPU
Computing log-likelihood of 98 initial trees ... 9.778 seconds
Current best score: -103685.421

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.3747 secs using 399.1% CPU
Optimizing NNI: done in 1.89536 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
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Iteration 50 / LogL: -56684.177 / Time: 0h:1m:36s (0h:3m:1s left)
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Iteration 60 / LogL: -56679.956 / Time: 0h:1m:50s (0h:2m:33s left)
Optimizing NNI: done in 1.34623 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 61: -56667.152
BETTER TREE FOUND at iteration 1: -103127.217
Optimizing NNI: done in 1.559 secs using 398.9% CPU
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BETTER TREE FOUND at iteration 63: -56666.696
Optimizing NNI: done in 1.56581 secs using 399% CPU
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Iteration 70 / LogL: -56684.611 / Time: 0h:2m:5s (0h:2m:49s left)
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Iteration 300 / LogL: -192699.313 / Time: 0h:26m:33s (0h:7m:16s left)
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BETTER TREE FOUND at iteration 2: -102993.337
Optimizing NNI: done in 1.50358 secs using 398.5% CPU
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Iteration 80 / LogL: -56685.996 / Time: 0h:2m:19s (0h:2m:26s left)
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BETTER TREE FOUND at iteration 3: -102991.604
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Iteration 90 / LogL: -56675.044 / Time: 0h:2m:33s (0h:2m:5s left)
BETTER TREE FOUND at iteration 4: -102913.336
Optimizing NNI: done in 1.47303 secs using 398.8% CPU
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Iteration 10 / LogL: -102956.330 / Time: 0h:1m:52s
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Iteration 100 / LogL: -56681.192 / Time: 0h:2m:46s (0h:1m:46s left)
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Iteration 310 / LogL: -192663.513 / Time: 0h:27m:20s (0h:6m:22s left)
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BETTER TREE FOUND at iteration 108: -56666.696
Optimizing NNI: done in 1.89852 secs using 398.5% CPU
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Iteration 110 / LogL: -56677.412 / Time: 0h:3m:0s (0h:2m:41s left)
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Iteration 20 / LogL: -103040.307 / Time: 0h:2m:16s
Finish initializing candidate tree set (20)
Current best tree score: -102913.336 / CPU time: 124.206
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.17768 secs using 398.6% CPU
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Iteration 120 / LogL: -56666.700 / Time: 0h:3m:13s (0h:2m:23s left)
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Iteration 130 / LogL: -56687.268 / Time: 0h:3m:27s (0h:2m:5s left)
Optimizing NNI: done in 2.07257 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 29: -102907.526
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Iteration 30 / LogL: -103027.132 / Time: 0h:2m:39s (0h:9m:3s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 33: -102900.463
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Iteration 140 / LogL: -56676.219 / Time: 0h:3m:42s (0h:1m:48s left)
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Iteration 320 / LogL: -192675.228 / Time: 0h:28m:8s (0h:5m:28s left)
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Iteration 40 / LogL: -102902.347 / Time: 0h:3m:0s (0h:7m:10s left)
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Iteration 150 / LogL: -56681.324 / Time: 0h:3m:55s (0h:1m:31s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 323: -192637.900
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BETTER TREE FOUND at iteration 42: -102896.632
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Iteration 160 / LogL: -56685.858 / Time: 0h:4m:9s (0h:1m:15s left)
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Iteration 50 / LogL: -102900.717 / Time: 0h:3m:22s (0h:6m:19s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.51671 secs using 398.9% CPU
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Iteration 170 / LogL: -56670.797 / Time: 0h:4m:23s (0h:0m:59s left)
BETTER TREE FOUND at iteration 53: -102889.128
Optimizing NNI: done in 1.4145 secs using 399.1% CPU
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Iteration 330 / LogL: -192688.909 / Time: 0h:28m:57s (0h:8m:11s left)
Optimizing NNI: done in 1.2692 secs using 398.6% CPU
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Iteration 180 / LogL: -56683.062 / Time: 0h:4m:36s (0h:0m:43s left)
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Iteration 60 / LogL: -103002.133 / Time: 0h:3m:43s (0h:5m:51s left)
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Optimizing NNI: done in 1.33411 secs using 399.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -56666.695
Optimizing NNI: done in 2.0071 secs using 398.5% CPU
Optimizing NNI: done in 4.95457 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.33868 secs using 398.4% CPU
BETTER TREE FOUND at iteration 333: -192636.251
Optimizing NNI: done in 1.7735 secs using 398.9% CPU
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Iteration 190 / LogL: -56666.696 / Time: 0h:4m:50s (0h:0m:27s left)
Optimizing NNI: done in 4.61064 secs using 596.8% CPU
Optimizing NNI: done in 1.88576 secs using 398.5% CPU
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Iteration 70 / LogL: -102899.401 / Time: 0h:4m:2s (0h:4m:51s left)
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Iteration 200 / LogL: -56678.229 / Time: 0h:5m:5s (0h:0m:12s left)
Optimizing NNI: done in 1.19618 secs using 399.1% CPU
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Iteration 80 / LogL: -102901.590 / Time: 0h:4m:21s (0h:4m:1s left)
Optimizing NNI: done in 1.50452 secs using 399.3% CPU
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Optimizing NNI: done in 1.9153 secs using 398.9% CPU
Optimizing NNI: done in 1.65286 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 209 ITERATIONS / Time: 0h:5m:18s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -56666.695
Optimizing NNI: done in 4.66293 secs using 598% CPU
Iteration 340 / LogL: -192686.908 / Time: 0h:29m:44s (0h:8m:9s left)
Optimal log-likelihood: -56666.689
Site proportion and rates:  (0.109,0.063) (0.151,0.201) (0.161,0.422) (0.039,0.422) (0.188,0.714) (0.151,1.282) (0.181,2.286) (0.020,6.723)
Parameters optimization took 1 rounds (0.335 sec)
BEST SCORE FOUND : -56666.689
Total tree length: 42.075

Total number of iterations: 209
CPU time used for tree search: 1217.844 sec (0h:20m:17s)
Wall-clock time used for tree search: 308.948 sec (0h:5m:8s)
Total CPU time used: 1256.973 sec (0h:20m:56s)
Total wall-clock time used: 318.733 sec (0h:5m:18s)

===> START BOOTSTRAP REPLICATE NUMBER 63

Creating bootstrap alignment (seed: 67525)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.036 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59292.453
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2. Current log-likelihood: -58763.882
3. Current log-likelihood: -58757.593
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4. Current log-likelihood: -58745.005
5. Current log-likelihood: -58698.365
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6. Current log-likelihood: -58695.366
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Optimal log-likelihood: -58695.309
Site proportion and rates:  (0.100,0.062) (0.115,0.169) (0.137,0.330) (0.078,0.481) (0.165,0.647) (0.184,1.108) (0.180,2.061) (0.041,5.087)
Parameters optimization took 6 rounds (4.804 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.0993 secs using 400% CPU
Computing ML distances took 1.099480 sec (of wall-clock time) 4.397209 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000406027 secs using 420.4% CPU
Constructing RapidNJ tree: done in 0.00434685 secs using 326.9% CPU
Computing RapidNJ tree took 0.004808 sec (of wall-clock time) 0.018313 sec (of CPU time)
Log-likelihood of RapidNJ tree: -58714.242
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.88168 secs using 398.5% CPU
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5.136 second
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Iteration 90 / LogL: -102910.024 / Time: 0h:4m:39s (0h:3m:18s left)
Computing log-likelihood of 98 initial trees ... 5.258 seconds
Current best score: -58695.309

Do NNI search on 20 best initial trees
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Iteration 20 / LogL: -58471.337 / Time: 0h:0m:45s
Finish initializing candidate tree set (20)
Current best tree score: -58376.513 / CPU time: 39.657
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 187: -102883.371
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TREE SEARCH COMPLETED AFTER 177 ITERATIONS / Time: 0h:4m:27s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58356.674
Optimal log-likelihood: -58356.663
Site proportion and rates:  (0.100,0.062) (0.116,0.165) (0.037,0.351) (0.142,0.351) (0.202,0.629) (0.182,1.107) (0.180,2.072) (0.042,5.058)
Parameters optimization took 1 rounds (0.452 sec)
BEST SCORE FOUND : -58356.663
Total tree length: 46.579

Total number of iterations: 177
CPU time used for tree search: 1026.673 sec (0h:17m:6s)
Wall-clock time used for tree search: 261.024 sec (0h:4m:21s)
Total CPU time used: 1053.838 sec (0h:17m:33s)
Total wall-clock time used: 267.799 sec (0h:4m:27s)

===> START BOOTSTRAP REPLICATE NUMBER 64

Creating bootstrap alignment (seed: 67526)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.056 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61054.391
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2. Current log-likelihood: -60467.690
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3. Current log-likelihood: -60463.799
4. Current log-likelihood: -60463.586
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5. Current log-likelihood: -60463.083
6. Current log-likelihood: -60455.887
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Iteration 220 / LogL: -102898.628 / Time: 0h:8m:57s (0h:2m:44s left)
7. Current log-likelihood: -60402.085
8. Current log-likelihood: -60398.873
Optimizing NNI: done in 1.82857 secs using 398.2% CPU
Optimal log-likelihood: -60398.798
Site proportion and rates:  (0.148,0.081) (0.036,0.179) (0.155,0.333) (0.120,0.514) (0.190,0.732) (0.141,1.227) (0.166,2.084) (0.044,4.780)
Parameters optimization took 8 rounds (7.123 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10463 secs using 399.9% CPU
Computing ML distances took 1.104809 sec (of wall-clock time) 4.417526 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000394106 secs using 424.3% CPU
Constructing RapidNJ tree: done in 0.00433993 secs using 369.5% CPU
Computing RapidNJ tree took 0.004793 sec (of wall-clock time) 0.018251 sec (of CPU time)
Optimizing NNI: done in 1.6907 secs using 399.3% CPU
Log-likelihood of RapidNJ tree: -60496.235
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.51976 secs using 597.3% CPU
Iteration 400 / LogL: -192767.295 / Time: 0h:34m:21s (0h:2m:50s left)
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5.217 second
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Computing log-likelihood of 98 initial trees ... 5.237 seconds
Current best score: -60398.798

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -60211.668
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Iteration 230 / LogL: -102997.828 / Time: 0h:9m:15s (0h:2m:18s left)
BETTER TREE FOUND at iteration 2: -60199.178
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -60195.372 / Time: 0h:0m:49s
Finish initializing candidate tree set (20)
Current best tree score: -60175.862 / CPU time: 40.288
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 70 / LogL: -60143.625 / Time: 0h:2m:7s (0h:2m:49s left)
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Optimizing NNI: done in 1.45057 secs using 399.2% CPU
Optimizing NNI: done in 4.63764 secs using 597.3% CPU
Optimizing NNI: done in 1.31574 secs using 399% CPU
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Optimizing NNI: done in 1.35504 secs using 399.5% CPU
Optimizing NNI: done in 1.68457 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 288 ITERATIONS / Time: 0h:11m:4s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102883.371
Optimal log-likelihood: -102883.357
Proportion of invariable sites: 0.032
Site proportion and rates:  (0.076,0.030) (0.089,0.093) (0.093,0.201) (0.103,0.311) (0.115,0.447) (0.107,0.701) (0.107,1.134) (0.199,1.823) (0.079,4.160)
Parameters optimization took 1 rounds (0.600 sec)
BEST SCORE FOUND : -102883.357
Total tree length: 173.516

Total number of iterations: 288
CPU time used for tree search: 2569.243 sec (0h:42m:49s)
Wall-clock time used for tree search: 652.213 sec (0h:10m:52s)
Total CPU time used: 2621.591 sec (0h:43m:41s)
Total wall-clock time used: 665.313 sec (0h:11m:5s)

===> START BOOTSTRAP REPLICATE NUMBER 22

Creating bootstrap alignment (seed: 68204)...

Optimizing NNI: done in 1.12605 secs using 398.9% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105431.416
Optimizing NNI: done in 4.67944 secs using 597.9% CPU
Optimizing NNI: done in 1.38148 secs using 399.3% CPU
2. Current log-likelihood: -103618.276
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3. Current log-likelihood: -103484.651
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4. Current log-likelihood: -103478.203
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5. Current log-likelihood: -103477.526
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6. Current log-likelihood: -103476.959
Optimizing NNI: done in 1.64423 secs using 398.8% CPU
Iteration 80 / LogL: -60142.347 / Time: 0h:2m:21s (0h:2m:27s left)
7. Current log-likelihood: -103476.448
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8. Current log-likelihood: -103475.993
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9. Current log-likelihood: -103475.580
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10. Current log-likelihood: -103475.215
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11. Current log-likelihood: -103474.884
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12. Current log-likelihood: -103474.586
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Iteration 430 / LogL: -192657.292 / Time: 0h:36m:44s (0h:7m:27s left)
Optimizing NNI: done in 1.21446 secs using 399.2% CPU
13. Current log-likelihood: -103474.316
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Optimizing NNI: done in 1.22548 secs using 398.7% CPU
Iteration 90 / LogL: -60176.459 / Time: 0h:2m:35s (0h:2m:5s left)
14. Current log-likelihood: -103474.067
Optimizing NNI: done in 3.77202 secs using 597.1% CPU
Optimizing NNI: done in 1.49932 secs using 398.6% CPU
15. Current log-likelihood: -103473.921
Optimizing NNI: done in 1.11657 secs using 399.6% CPU
Optimizing NNI: done in 1.28801 secs using 399.4% CPU
16. Current log-likelihood: -103473.783
Optimizing NNI: done in 1.38082 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.63837 secs using 596.5% CPU
17. Current log-likelihood: -103473.655
BETTER TREE FOUND at iteration 94: -60135.855
18. Current log-likelihood: -103473.535
Optimizing NNI: done in 1.20853 secs using 399.2% CPU
19. Current log-likelihood: -103473.423
Optimizing NNI: done in 1.36339 secs using 398.7% CPU
20. Current log-likelihood: -103473.317
Optimizing NNI: done in 4.47796 secs using 597.6% CPU
Optimizing NNI: done in 1.32841 secs using 399.3% CPU
Optimal log-likelihood: -103473.160
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.092,0.039) (0.096,0.116) (0.092,0.225) (0.080,0.313) (0.115,0.487) (0.129,0.751) (0.127,1.236) (0.175,1.944) (0.065,4.485)
Parameters optimization took 20 rounds (33.877 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.65564 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 98: -60134.168
Optimizing NNI: done in 4.83206 secs using 596.9% CPU
Optimizing NNI: done in 1.19855 secs using 399.4% CPU
Calculating distance matrix: done in 4.66215 secs using 399.9% CPU
Computing ML distances took 4.662399 sec (of wall-clock time) 18.646339 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000748158 secs using 50.66% CPU
Constructing RapidNJ tree: done in 0.00869584 secs using 378.4% CPU
Computing RapidNJ tree took 0.009524 sec (of wall-clock time) 0.034557 sec (of CPU time)
Optimizing NNI: done in 1.29964 secs using 399.1% CPU
Iteration 100 / LogL: -60139.981 / Time: 0h:2m:51s (0h:2m:49s left)
Log-likelihood of RapidNJ tree: -103751.371
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.32109 secs using 399.2% CPU
Optimizing NNI: done in 4.21935 secs using 597.5% CPU
Optimizing NNI: done in 1.67941 secs using 399.2% CPU
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Optimizing NNI: done in 1.28273 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 106: -60133.014
Optimizing NNI: done in 1.41921 secs using 398.9% CPU
10.760 second
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Optimizing NNI: done in 1.26215 secs using 399.6% CPU
Optimizing NNI: done in 1.38096 secs using 399.5% CPU
Iteration 110 / LogL: -60138.817 / Time: 0h:3m:7s (0h:2m:44s left)
Optimizing NNI: done in 1.44466 secs using 399% CPU
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Optimizing NNI: done in 1.21638 secs using 399.4% CPU
Optimizing NNI: done in 1.3481 secs using 399.3% CPU
Computing log-likelihood of 98 initial trees ... 10.293 seconds
Current best score: -103473.160

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.98774 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 116: -60132.242
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Optimizing NNI: done in 4.51337 secs using 596.8% CPU
Iteration 440 / LogL: -192639.412 / Time: 0h:37m:31s (0h:6m:34s left)
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Optimizing NNI: done in 1.42482 secs using 399.1% CPU
Iteration 120 / LogL: -60139.709 / Time: 0h:3m:21s (0h:2m:42s left)
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BETTER TREE FOUND at iteration 1: -102986.933
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 5: -102936.408
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Iteration 130 / LogL: -60153.845 / Time: 0h:3m:35s (0h:2m:23s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 133: -60129.879
BETTER TREE FOUND at iteration 6: -102884.084
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Iteration 10 / LogL: -102926.006 / Time: 0h:1m:34s
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Iteration 140 / LogL: -60164.416 / Time: 0h:3m:49s (0h:2m:33s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 15: -102874.255
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Iteration 150 / LogL: -60130.111 / Time: 0h:4m:2s (0h:2m:14s left)
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Iteration 450 / LogL: -192808.505 / Time: 0h:38m:17s (0h:5m:42s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 18: -102869.248
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Iteration 20 / LogL: -102925.967 / Time: 0h:2m:0s
Finish initializing candidate tree set (20)
Current best tree score: -102869.248 / CPU time: 80.960
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 160 / LogL: -60159.006 / Time: 0h:4m:15s (0h:1m:57s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -102867.257
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Iteration 170 / LogL: -60143.924 / Time: 0h:4m:29s (0h:1m:40s left)
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Iteration 30 / LogL: -102876.322 / Time: 0h:2m:24s (0h:7m:37s left)
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Iteration 460 / LogL: -193093.064 / Time: 0h:39m:3s (0h:4m:50s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 40: -102865.179
Iteration 40 / LogL: -102865.179 / Time: 0h:2m:47s (0h:7m:8s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 43: -102863.011
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Iteration 50 / LogL: -102871.018 / Time: 0h:3m:10s (0h:6m:1s left)
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Iteration 220 / LogL: -60130.652 / Time: 0h:5m:35s (0h:0m:19s left)
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 1.61203 secs using 398.4% CPU
BETTER TREE FOUND at iteration 470: -192631.142
Iteration 470 / LogL: -192631.142 / Time: 0h:39m:52s (0h:8m:30s left)
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Iteration 60 / LogL: -102919.761 / Time: 0h:3m:30s (0h:4m:56s left)
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Iteration 230 / LogL: -60136.445 / Time: 0h:5m:48s (0h:0m:4s left)
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TREE SEARCH COMPLETED AFTER 234 ITERATIONS / Time: 0h:5m:53s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60129.879
Optimizing NNI: done in 4.2437 secs using 597.2% CPU
Optimal log-likelihood: -60129.875
Site proportion and rates:  (0.148,0.081) (0.040,0.180) (0.164,0.340) (0.077,0.505) (0.205,0.700) (0.160,1.201) (0.163,2.109) (0.044,4.743)
Parameters optimization took 1 rounds (0.842 sec)
BEST SCORE FOUND : -60129.875
Total tree length: 47.108

Total number of iterations: 234
CPU time used for tree search: 1361.239 sec (0h:22m:41s)
Wall-clock time used for tree search: 344.927 sec (0h:5m:44s)
Total CPU time used: 1399.533 sec (0h:23m:19s)
Total wall-clock time used: 354.517 sec (0h:5m:54s)

===> START BOOTSTRAP REPLICATE NUMBER 65

Creating bootstrap alignment (seed: 67527)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.064 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60000.693
2. Current log-likelihood: -59439.853
Optimizing NNI: done in 2.0808 secs using 398.3% CPU
3. Current log-likelihood: -59401.254
4. Current log-likelihood: -59385.225
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5. Current log-likelihood: -59382.077
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6. Current log-likelihood: -59381.950
Optimizing NNI: done in 1.95091 secs using 398% CPU
Optimal log-likelihood: -59381.912
Site proportion and rates:  (0.091,0.062) (0.135,0.169) (0.098,0.336) (0.086,0.400) (0.207,0.691) (0.127,1.110) (0.223,1.990) (0.034,5.192)
Parameters optimization took 6 rounds (5.141 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09737 secs using 399.8% CPU
Computing ML distances took 1.097553 sec (of wall-clock time) 4.387444 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000371218 secs using 227.4% CPU
Constructing RapidNJ tree: done in 0.00440598 secs using 286.6% CPU
Computing RapidNJ tree took 0.004833 sec (of wall-clock time) 0.015423 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59421.284
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.00338 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 69: -102861.138
5.147 second
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Iteration 70 / LogL: -102867.420 / Time: 0h:3m:54s (0h:5m:35s left)
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Optimizing NNI: done in 2.33984 secs using 398.6% CPU
Computing log-likelihood of 98 initial trees ... 5.102 seconds
Current best score: -59268.516

Do NNI search on 20 best initial trees
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BETTER TREE FOUND at iteration 1: -59052.619
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -59039.407
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Iteration 480 / LogL: -192695.251 / Time: 0h:40m:38s (0h:7m:38s left)
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Iteration 10 / LogL: -59088.141 / Time: 0h:0m:33s
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Iteration 80 / LogL: -102888.826 / Time: 0h:4m:15s (0h:4m:48s left)
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Iteration 20 / LogL: -59109.413 / Time: 0h:0m:44s
Finish initializing candidate tree set (20)
Current best tree score: -59039.407 / CPU time: 37.906
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -59038.833
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Estimate model parameters (epsilon = 0.100)
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Iteration 90 / LogL: -102871.997 / Time: 0h:4m:37s (0h:4m:6s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 46: -59011.483
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BETTER TREE FOUND at iteration 49: -59010.169
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Estimate model parameters (epsilon = 0.100)
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Iteration 60 / LogL: -59026.223 / Time: 0h:1m:44s (0h:2m:37s left)
BETTER TREE FOUND at iteration 110: -102856.198
Iteration 110 / LogL: -102856.198 / Time: 0h:5m:26s (0h:4m:59s left)
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BETTER TREE FOUND at iteration 147: -102855.622
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 126: -59007.795
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UPDATE BEST LOG-LIKELIHOOD: -59007.794
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Iteration 200 / LogL: -59009.140 / Time: 0h:4m:53s (0h:0m:38s left)
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BETTER TREE FOUND at iteration 200: -102853.826
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TREE SEARCH COMPLETED AFTER 227 ITERATIONS / Time: 0h:5m:29s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59007.794
Optimal log-likelihood: -59007.786
Site proportion and rates:  (0.096,0.064) (0.126,0.168) (0.100,0.356) (0.088,0.356) (0.202,0.702) (0.122,1.045) (0.233,1.961) (0.035,5.234)
Parameters optimization took 1 rounds (0.441 sec)
BEST SCORE FOUND : -59007.786
Total tree length: 45.270

Total number of iterations: 227
CPU time used for tree search: 1272.600 sec (0h:21m:12s)
Wall-clock time used for tree search: 322.705 sec (0h:5m:22s)
Total CPU time used: 1301.105 sec (0h:21m:41s)
Total wall-clock time used: 329.824 sec (0h:5m:29s)

===> START BOOTSTRAP REPLICATE NUMBER 66

Creating bootstrap alignment (seed: 67528)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59545.267
Optimizing NNI: done in 4.13482 secs using 597.3% CPU
2. Current log-likelihood: -59038.968
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3. Current log-likelihood: -59008.600
4. Current log-likelihood: -58992.630
5. Current log-likelihood: -58989.693
Optimizing NNI: done in 2.16948 secs using 398.2% CPU
6. Current log-likelihood: -58989.518
Optimal log-likelihood: -58989.486
Site proportion and rates:  (0.117,0.064) (0.122,0.184) (0.074,0.391) (0.085,0.401) (0.240,0.704) (0.155,1.226) (0.180,2.187) (0.027,5.795)
Parameters optimization took 6 rounds (4.678 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.0811 secs using 399.9% CPU
Computing ML distances took 1.081272 sec (of wall-clock time) 4.324214 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000394106 secs using 390.8% CPU
Constructing RapidNJ tree: done in 0.00433207 secs using 327.2% CPU
Computing RapidNJ tree took 0.004781 sec (of wall-clock time) 0.017886 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59076.116
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.85072 secs using 398.7% CPU
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Iteration 220 / LogL: -103059.630 / Time: 0h:9m:22s (0h:3m:25s left)
4.949 second
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Computing log-likelihood of 98 initial trees ... 5.090 seconds
Current best score: -58944.504

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 550 / LogL: -192646.050 / Time: 0h:46m:1s (0h:1m:40s left)
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Iteration 10 / LogL: -58757.104 / Time: 0h:0m:30s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 12: -58645.519
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -58685.448 / Time: 0h:0m:43s
Finish initializing candidate tree set (20)
Current best tree score: -58645.519 / CPU time: 37.775
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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BETTER TREE FOUND at iteration 236: -102853.015
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -58634.679
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Iteration 240 / LogL: -102854.618 / Time: 0h:10m:5s (0h:4m:3s left)
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Iteration 30 / LogL: -58660.315 / Time: 0h:0m:59s (0h:3m:9s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.03303 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -58629.668
BETTER TREE FOUND at iteration 245: -102852.523
Optimizing NNI: done in 1.36789 secs using 399% CPU
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Optimizing NNI: done in 4.65366 secs using 597.8% CPU
Iteration 560 / LogL: -192644.321 / Time: 0h:46m:49s (0h:0m:50s left)
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Iteration 40 / LogL: -58670.271 / Time: 0h:1m:14s (0h:2m:56s left)
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Iteration 250 / LogL: -102873.472 / Time: 0h:10m:26s (0h:3m:59s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.9475 secs using 398.6% CPU
BETTER TREE FOUND at iteration 43: -58624.778
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Iteration 50 / LogL: -58697.226 / Time: 0h:1m:29s (0h:2m:50s left)
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Iteration 260 / LogL: -102853.981 / Time: 0h:10m:47s (0h:3m:32s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 58: -58620.931
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Iteration 60 / LogL: -58625.808 / Time: 0h:1m:45s (0h:2m:55s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 66: -58618.566
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Iteration 270 / LogL: -102870.293 / Time: 0h:11m:8s (0h:3m:6s left)
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Iteration 70 / LogL: -58624.788 / Time: 0h:1m:59s (0h:2m:46s left)
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Iteration 570 / LogL: -192640.381 / Time: 0h:47m:37s (0h:0m:0s left)
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Optimizing NNI: done in 4.37744 secs using 597.7% CPU
TREE SEARCH COMPLETED AFTER 571 ITERATIONS / Time: 0h:47m:41s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192631.142
Optimizing NNI: done in 2.04487 secs using 398.9% CPU
Optimizing NNI: done in 1.29409 secs using 398.7% CPU
Optimal log-likelihood: -192631.139
Site proportion and rates:  (0.048,0.220) (0.138,0.357) (0.217,0.552) (0.177,0.770) (0.164,1.035) (0.100,1.506) (0.127,2.137) (0.029,3.168)
Parameters optimization took 1 rounds (1.253 sec)
BEST SCORE FOUND : -192631.139
Total tree length: 153.593

Total number of iterations: 571
CPU time used for tree search: 16726.851 sec (4h:38m:46s)
Wall-clock time used for tree search: 2826.215 sec (0h:47m:6s)
Total CPU time used: 16944.932 sec (4h:42m:24s)
Total wall-clock time used: 2862.772 sec (0h:47m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 17

Creating bootstrap alignment (seed: 70480)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.346 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199493.165
Optimizing NNI: done in 1.31285 secs using 399.2% CPU
Optimizing NNI: done in 1.90626 secs using 399.1% CPU
Optimizing NNI: done in 1.39486 secs using 399% CPU
2. Current log-likelihood: -196778.129
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3. Current log-likelihood: -196751.091
Optimizing NNI: done in 1.24228 secs using 398.4% CPU
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4. Current log-likelihood: -196749.608
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Iteration 80 / LogL: -58658.514 / Time: 0h:2m:13s (0h:2m:25s left)
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5. Current log-likelihood: -196749.039
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Optimizing NNI: done in 2.23535 secs using 398.5% CPU
Iteration 280 / LogL: -102873.810 / Time: 0h:11m:29s (0h:2m:40s left)
6. Current log-likelihood: -196748.601
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7. Current log-likelihood: -196748.214
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Optimizing NNI: done in 1.90001 secs using 399.3% CPU
8. Current log-likelihood: -196747.844
Optimizing NNI: done in 1.63376 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 86: -58617.643
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9. Current log-likelihood: -196747.474
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10. Current log-likelihood: -196747.110
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11. Current log-likelihood: -196746.774
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Iteration 90 / LogL: -58630.144 / Time: 0h:2m:28s (0h:2m:39s left)
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12. Current log-likelihood: -196746.485
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13. Current log-likelihood: -196746.266
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14. Current log-likelihood: -196746.119
Optimizing NNI: done in 1.23595 secs using 399.2% CPU
Optimizing NNI: done in 1.9302 secs using 398.8% CPU
Optimizing NNI: done in 1.30486 secs using 398.5% CPU
15. Current log-likelihood: -196746.011
Optimizing NNI: done in 2.09107 secs using 399.1% CPU
Optimizing NNI: done in 1.37968 secs using 398.6% CPU
Optimal log-likelihood: -196745.936
Site proportion and rates:  (0.014,0.100) (0.035,0.191) (0.105,0.332) (0.213,0.540) (0.117,0.714) (0.213,0.968) (0.186,1.480) (0.117,2.366)
Parameters optimization took 15 rounds (32.364 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.34055 secs using 399.5% CPU
Optimizing NNI: done in 2.19592 secs using 398.4% CPU
Iteration 290 / LogL: -102866.218 / Time: 0h:11m:51s (0h:2m:15s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 100: -58615.655
Iteration 100 / LogL: -58615.655 / Time: 0h:2m:42s (0h:2m:43s left)
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Calculating distance matrix: done in 9.66327 secs using 599.8% CPU
Computing ML distances took 9.663912 sec (of wall-clock time) 57.965221 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.001297 secs using 520.3% CPU
Constructing RapidNJ tree: done in 0.0226281 secs using 661% CPU
Computing RapidNJ tree took 0.023997 sec (of wall-clock time) 0.157817 sec (of CPU time)
Optimizing NNI: done in 1.33923 secs using 399.4% CPU
Optimizing NNI: done in 2.02781 secs using 398.6% CPU
Log-likelihood of RapidNJ tree: -200743.928
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.37217 secs using 399.2% CPU
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Iteration 110 / LogL: -58616.304 / Time: 0h:2m:55s (0h:2m:24s left)
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Iteration 300 / LogL: -102855.064 / Time: 0h:12m:15s (0h:1m:50s left)
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Iteration 120 / LogL: -58617.499 / Time: 0h:3m:9s (0h:2m:7s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.92938 secs using 398.5% CPU
BETTER TREE FOUND at iteration 123: -58615.255
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30.846 second
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 129: -58615.154
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Iteration 130 / LogL: -58617.044 / Time: 0h:3m:23s (0h:2m:36s left)
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Iteration 310 / LogL: -102868.512 / Time: 0h:12m:41s (0h:1m:26s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 136: -58614.321
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 137: -58613.434
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Optimizing NNI: done in 1.15911 secs using 399% CPU
Computing log-likelihood of 98 initial trees ... 16.425 seconds
Current best score: -196745.936

Do NNI search on 20 best initial trees
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Iteration 140 / LogL: -58618.340 / Time: 0h:3m:38s (0h:2m:32s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -196238.329
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Iteration 320 / LogL: -102916.759 / Time: 0h:13m:1s (0h:1m:1s left)
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Iteration 150 / LogL: -58614.498 / Time: 0h:3m:52s (0h:2m:15s left)
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Iteration 160 / LogL: -58629.789 / Time: 0h:4m:6s (0h:1m:59s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 330 / LogL: -102853.182 / Time: 0h:13m:22s (0h:0m:36s left)
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BETTER TREE FOUND at iteration 6: -196224.960
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 167: -58605.885
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Iteration 170 / LogL: -58614.572 / Time: 0h:4m:20s (0h:2m:29s left)
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Optimizing NNI: done in 1.54368 secs using 399.3% CPU
Optimizing NNI: done in 4.03922 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.23049 secs using 399.2% CPU
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Optimizing NNI: done in 1.32474 secs using 399.2% CPU
Optimizing NNI: done in 1.80851 secs using 398.8% CPU
Iteration 340 / LogL: -102869.389 / Time: 0h:13m:42s (0h:0m:12s left)
Optimizing NNI: done in 1.31941 secs using 399.1% CPU
BETTER TREE FOUND at iteration 9: -196190.188
Optimizing NNI: done in 1.44004 secs using 398.9% CPU
Optimizing NNI: done in 1.96196 secs using 398.3% CPU
Optimizing NNI: done in 1.27089 secs using 398.6% CPU
Iteration 180 / LogL: -58621.344 / Time: 0h:4m:34s (0h:2m:13s left)
Optimizing NNI: done in 2.16085 secs using 398.8% CPU
Optimizing NNI: done in 1.49812 secs using 399.3% CPU
Optimizing NNI: done in 3.97198 secs using 597.6% CPU
Iteration 10 / LogL: -196340.996 / Time: 0h:2m:30s
Optimizing NNI: done in 1.23965 secs using 399.9% CPU
Optimizing NNI: done in 2.0629 secs using 398.1% CPU
Optimizing NNI: done in 1.29008 secs using 398.9% CPU
Optimizing NNI: done in 1.69826 secs using 398.7% CPU
Optimizing NNI: done in 1.30268 secs using 399.3% CPU
Optimizing NNI: done in 3.33006 secs using 597.4% CPU
Optimizing NNI: done in 1.92671 secs using 399% CPU
Optimizing NNI: done in 1.55232 secs using 399.3% CPU
Optimizing NNI: done in 1.5002 secs using 399.5% CPU
Optimizing NNI: done in 2.12991 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 346 ITERATIONS / Time: 0h:13m:54s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102852.523
Optimal log-likelihood: -102852.520
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.092,0.037) (0.089,0.107) (0.096,0.207) (0.088,0.313) (0.129,0.507) (0.118,0.781) (0.125,1.263) (0.169,1.965) (0.064,4.525)
Parameters optimization took 1 rounds (0.630 sec)
BEST SCORE FOUND : -102852.520
Total tree length: 160.675

Total number of iterations: 346
CPU time used for tree search: 3137.588 sec (0h:52m:17s)
Wall-clock time used for tree search: 795.182 sec (0h:13m:15s)
Total CPU time used: 3298.774 sec (0h:54m:58s)
Total wall-clock time used: 835.640 sec (0h:13m:55s)

===> START BOOTSTRAP REPLICATE NUMBER 23

Creating bootstrap alignment (seed: 68205)...

Optimizing NNI: done in 1.26388 secs using 398.8% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.128 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -100150.253
Optimizing NNI: done in 4.32176 secs using 596.7% CPU
Optimizing NNI: done in 1.36657 secs using 399.2% CPU
2. Current log-likelihood: -98332.942
Optimizing NNI: done in 1.33253 secs using 399.2% CPU
3. Current log-likelihood: -98245.628
Optimizing NNI: done in 1.5452 secs using 399.3% CPU
Iteration 190 / LogL: -58632.486 / Time: 0h:4m:48s (0h:1m:57s left)
Optimizing NNI: done in 4.01827 secs using 597.5% CPU
Optimizing NNI: done in 1.24997 secs using 398.5% CPU
4. Current log-likelihood: -98199.895
Optimizing NNI: done in 1.6269 secs using 398.8% CPU
5. Current log-likelihood: -98197.081
Optimizing NNI: done in 1.24762 secs using 399.2% CPU
Optimizing NNI: done in 4.2141 secs using 596.2% CPU
6. Current log-likelihood: -98196.749
Optimizing NNI: done in 1.1621 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 194: -58605.327
7. Current log-likelihood: -98196.553
Optimizing NNI: done in 1.41509 secs using 399% CPU
8. Current log-likelihood: -98196.401
Optimizing NNI: done in 4.19038 secs using 596.8% CPU
Optimizing NNI: done in 1.26584 secs using 398.8% CPU
9. Current log-likelihood: -98196.275
Optimizing NNI: done in 1.35271 secs using 399.4% CPU
Optimal log-likelihood: -98196.138
Proportion of invariable sites: 0.042
Site proportion and rates:  (0.120,0.041) (0.087,0.128) (0.065,0.217) (0.122,0.363) (0.111,0.568) (0.128,0.847) (0.163,1.394) (0.110,2.286) (0.051,5.350)
Parameters optimization took 9 rounds (15.007 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.35946 secs using 398.6% CPU
Optimizing NNI: done in 3.68232 secs using 597.3% CPU
Optimizing NNI: done in 1.21963 secs using 398.5% CPU
Optimizing NNI: done in 1.44006 secs using 399.8% CPU
Iteration 200 / LogL: -58607.383 / Time: 0h:5m:2s (0h:2m:22s left)
Optimizing NNI: done in 1.15644 secs using 398.8% CPU
Calculating distance matrix: done in 4.70025 secs using 399.9% CPU
Computing ML distances took 4.700492 sec (of wall-clock time) 18.798941 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000693083 secs using 255.8% CPU
Constructing RapidNJ tree: done in 0.00864196 secs using 361.7% CPU
Computing RapidNJ tree took 0.009391 sec (of wall-clock time) 0.036211 sec (of CPU time)
Optimizing NNI: done in 4.10894 secs using 596.4% CPU
Optimizing NNI: done in 1.50212 secs using 398.8% CPU
Log-likelihood of RapidNJ tree: -98495.649
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.38064 secs using 399.1% CPU
Optimizing NNI: done in 1.43652 secs using 398.9% CPU
Optimizing NNI: done in 3.96495 secs using 597% CPU
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Optimizing NNI: done in 4.1799 secs using 596.8% CPU
Optimizing NNI: done in 1.47177 secs using 398.9% CPU
Optimizing NNI: done in 1.26363 secs using 399.2% CPU
10.432 second
Optimizing NNI: done in 1.51716 secs using 399.3% CPU
Iteration 210 / LogL: -58616.914 / Time: 0h:5m:16s (0h:2m:7s left)
Optimizing NNI: done in 4.04061 secs using 597.5% CPU
Iteration 20 / LogL: -196295.048 / Time: 0h:3m:11s
Finish initializing candidate tree set (20)
Current best tree score: -196190.188 / CPU time: 147.037
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.35988 secs using 399% CPU
Optimizing NNI: done in 1.18574 secs using 398.2% CPU
Optimizing NNI: done in 1.22452 secs using 398.6% CPU
Optimizing NNI: done in 3.9468 secs using 597.4% CPU
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Optimizing NNI: done in 1.19424 secs using 398.7% CPU
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Optimizing NNI: done in 1.21618 secs using 399% CPU
Optimizing NNI: done in 4.73107 secs using 597% CPU
Computing log-likelihood of 98 initial trees ... 10.204 seconds
Current best score: -98196.138

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.36434 secs using 399.1% CPU
Optimizing NNI: done in 1.37652 secs using 399% CPU
Optimizing NNI: done in 2.13824 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.38636 secs using 399.4% CPU
Iteration 220 / LogL: -58613.413 / Time: 0h:5m:29s (0h:1m:51s left)
Optimizing NNI: done in 4.0789 secs using 597.3% CPU
Optimizing NNI: done in 1.16723 secs using 398.7% CPU
Optimizing NNI: done in 1.28816 secs using 399% CPU
Optimizing NNI: done in 1.52049 secs using 399.1% CPU
Optimizing NNI: done in 4.29266 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.21045 secs using 398.7% CPU
Optimizing NNI: done in 1.37243 secs using 399.2% CPU
Optimizing NNI: done in 1.09812 secs using 399.2% CPU
Optimizing NNI: done in 1.36454 secs using 399.2% CPU
BETTER TREE FOUND at iteration 24: -196180.786
Optimizing NNI: done in 1.42196 secs using 399.3% CPU
Optimizing NNI: done in 1.41108 secs using 398.8% CPU
Optimizing NNI: done in 1.28704 secs using 399.3% CPU
Iteration 230 / LogL: -58628.855 / Time: 0h:5m:42s (0h:1m:35s left)
Optimizing NNI: done in 4.40977 secs using 597.7% CPU
Optimizing NNI: done in 1.09875 secs using 399.2% CPU
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Optimizing NNI: done in 1.20934 secs using 399.4% CPU
BETTER TREE FOUND at iteration 1: -97724.853
Optimizing NNI: done in 1.185 secs using 399% CPU
Optimizing NNI: done in 1.80742 secs using 398.5% CPU
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Optimizing NNI: done in 4.39027 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.46483 secs using 398.8% CPU
Optimizing NNI: done in 1.84346 secs using 398.7% CPU
Optimizing NNI: done in 1.35293 secs using 398.9% CPU
BETTER TREE FOUND at iteration 27: -196153.576
Optimizing NNI: done in 1.92145 secs using 398.7% CPU
Optimizing NNI: done in 1.15365 secs using 399% CPU
Iteration 240 / LogL: -58607.288 / Time: 0h:5m:55s (0h:1m:20s left)
Optimizing NNI: done in 1.80425 secs using 398.8% CPU
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Optimizing NNI: done in 1.16307 secs using 399.2% CPU
Optimizing NNI: done in 4.30894 secs using 598% CPU
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Optimizing NNI: done in 1.14645 secs using 399.8% CPU
Optimizing NNI: done in 1.35344 secs using 399% CPU
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Optimizing NNI: done in 1.57151 secs using 399% CPU
Optimizing NNI: done in 1.36464 secs using 398.4% CPU
Optimizing NNI: done in 2.83686 secs using 398% CPU
Iteration 10 / LogL: -97725.966 / Time: 0h:1m:24s
Optimizing NNI: done in 4.49922 secs using 597.9% CPU
Iteration 30 / LogL: -196306.101 / Time: 0h:4m:2s (0h:13m:29s left)
Optimizing NNI: done in 1.43756 secs using 399% CPU
Iteration 250 / LogL: -58632.576 / Time: 0h:6m:9s (0h:1m:5s left)
Optimizing NNI: done in 1.94524 secs using 398.3% CPU
Optimizing NNI: done in 1.40546 secs using 399.1% CPU
Optimizing NNI: done in 1.13774 secs using 398.6% CPU
Optimizing NNI: done in 2.33388 secs using 397.9% CPU
Optimizing NNI: done in 4.44189 secs using 597.5% CPU
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Optimizing NNI: done in 1.62155 secs using 398% CPU
Optimizing NNI: done in 4.21048 secs using 598% CPU
Optimizing NNI: done in 1.16237 secs using 399.4% CPU
Optimizing NNI: done in 1.34401 secs using 398.6% CPU
Optimizing NNI: done in 3.04768 secs using 398.9% CPU
Optimizing NNI: done in 1.2693 secs using 399.8% CPU
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Optimizing NNI: done in 2.06737 secs using 398.1% CPU
Optimizing NNI: done in 4.31162 secs using 597.8% CPU
Optimizing NNI: done in 1.3119 secs using 399.2% CPU
Iteration 260 / LogL: -58618.374 / Time: 0h:6m:22s (0h:0m:50s left)
Optimizing NNI: done in 1.18646 secs using 399.2% CPU
Optimizing NNI: done in 2.3966 secs using 398.5% CPU
Optimizing NNI: done in 1.39983 secs using 399.4% CPU
Optimizing NNI: done in 2.12322 secs using 398.5% CPU
Optimizing NNI: done in 4.31496 secs using 597.6% CPU
Optimizing NNI: done in 1.36608 secs using 399% CPU
Optimizing NNI: done in 2.01576 secs using 397.8% CPU
Optimizing NNI: done in 1.49809 secs using 398.4% CPU
Optimizing NNI: done in 1.5685 secs using 399.4% CPU
Optimizing NNI: done in 1.86004 secs using 398.2% CPU
Iteration 20 / LogL: -97806.231 / Time: 0h:1m:45s
Finish initializing candidate tree set (20)
Current best tree score: -97724.853 / CPU time: 84.303
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.27967 secs using 597.2% CPU
Optimizing NNI: done in 1.23968 secs using 399% CPU
Optimizing NNI: done in 2.21552 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.25531 secs using 398.8% CPU
Optimizing NNI: done in 1.15657 secs using 398.9% CPU
Optimizing NNI: done in 1.46279 secs using 398.9% CPU
Optimizing NNI: done in 4.60809 secs using 596.9% CPU
Optimizing NNI: done in 1.34681 secs using 399.2% CPU
Iteration 270 / LogL: -58607.252 / Time: 0h:6m:36s (0h:0m:35s left)
Optimizing NNI: done in 1.34286 secs using 399.4% CPU
BETTER TREE FOUND at iteration 21: -97723.650
Optimizing NNI: done in 3.95595 secs using 597.2% CPU
Optimizing NNI: done in 1.74815 secs using 399.2% CPU
Optimizing NNI: done in 1.80839 secs using 398.6% CPU
Optimizing NNI: done in 1.48841 secs using 399.2% CPU
Optimizing NNI: done in 2.07931 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.24512 secs using 398.9% CPU
Optimizing NNI: done in 3.76297 secs using 597.5% CPU
Optimizing NNI: done in 1.2094 secs using 398.7% CPU
BETTER TREE FOUND at iteration 23: -97702.697
Optimizing NNI: done in 1.35059 secs using 399.3% CPU
Optimizing NNI: done in 1.44589 secs using 398.4% CPU
Optimizing NNI: done in 2.27736 secs using 398.4% CPU
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Iteration 280 / LogL: -58606.264 / Time: 0h:6m:50s (0h:0m:20s left)
Optimizing NNI: done in 2.50438 secs using 398.5% CPU
Optimizing NNI: done in 1.21411 secs using 398.8% CPU
Optimizing NNI: done in 4.22401 secs using 597.7% CPU
Iteration 40 / LogL: -196195.380 / Time: 0h:4m:45s (0h:10m:36s left)
Optimizing NNI: done in 1.33753 secs using 399% CPU
Optimizing NNI: done in 1.99427 secs using 398.3% CPU
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Optimizing NNI: done in 1.9361 secs using 398.5% CPU
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Optimizing NNI: done in 2.03316 secs using 398.5% CPU
Iteration 30 / LogL: -97707.119 / Time: 0h:2m:15s (0h:7m:14s left)
Optimizing NNI: done in 4.42079 secs using 597.4% CPU
Optimizing NNI: done in 1.30644 secs using 398.9% CPU
Optimizing NNI: done in 2.00036 secs using 398.5% CPU
Optimizing NNI: done in 1.32182 secs using 399% CPU
Optimizing NNI: done in 1.36009 secs using 399.6% CPU
Iteration 290 / LogL: -58609.702 / Time: 0h:7m:3s (0h:0m:5s left)
Optimizing NNI: done in 2.1951 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.34918 secs using 399.5% CPU
Optimizing NNI: done in 4.68258 secs using 597% CPU
Optimizing NNI: done in 1.22435 secs using 399.4% CPU
BETTER TREE FOUND at iteration 32: -97695.465
Optimizing NNI: done in 1.43765 secs using 398.9% CPU
Optimizing NNI: done in 2.3687 secs using 397.9% CPU
Optimizing NNI: done in 1.38234 secs using 398.7% CPU
Optimizing NNI: done in 4.61084 secs using 597.4% CPU
Optimizing NNI: done in 1.185 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 295 ITERATIONS / Time: 0h:7m:10s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58605.327
Optimizing NNI: done in 1.68352 secs using 398.9% CPU
Optimal log-likelihood: -58605.318
Site proportion and rates:  (0.122,0.065) (0.105,0.177) (0.091,0.373) (0.081,0.373) (0.236,0.702) (0.169,1.226) (0.167,2.248) (0.028,5.786)
Parameters optimization took 1 rounds (0.436 sec)
BEST SCORE FOUND : -58605.318
Total tree length: 44.609

Total number of iterations: 295
CPU time used for tree search: 1677.102 sec (0h:27m:57s)
Wall-clock time used for tree search: 423.934 sec (0h:7m:3s)
Total CPU time used: 1703.465 sec (0h:28m:23s)
Total wall-clock time used: 430.517 sec (0h:7m:10s)

===> START BOOTSTRAP REPLICATE NUMBER 67

Creating bootstrap alignment (seed: 67529)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.049 seconds

NOTE: 59 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58280.835
2. Current log-likelihood: -57764.923
Optimizing NNI: done in 1.68158 secs using 398.7% CPU
3. Current log-likelihood: -57762.073
4. Current log-likelihood: -57761.912
5. Current log-likelihood: -57759.457
Optimizing NNI: done in 1.84188 secs using 398.4% CPU
Optimal log-likelihood: -57759.408
Site proportion and rates:  (0.076,0.068) (0.171,0.183) (0.072,0.417) (0.125,0.468) (0.118,0.750) (0.158,0.985) (0.113,1.486) (0.166,2.780)
Parameters optimization took 5 rounds (3.649 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.68727 secs using 597.9% CPU
Calculating distance matrix: done in 1.05814 secs using 399.8% CPU
Computing ML distances took 1.058308 sec (of wall-clock time) 4.230485 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000349998 secs using 119.7% CPU
Constructing RapidNJ tree: done in 0.00436401 secs using 329.5% CPU
Computing RapidNJ tree took 0.004769 sec (of wall-clock time) 0.017140 sec (of CPU time)
Log-likelihood of RapidNJ tree: -57784.122
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.10421 secs using 398% CPU
Optimizing NNI: done in 2.15525 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.47115 secs using 597.6% CPU
5.227 second
BETTER TREE FOUND at iteration 38: -97686.499
Computing log-likelihood of 98 initial trees ... 4.914 seconds
Current best score: -57688.791

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.99456 secs using 398.1% CPU
Optimizing NNI: done in 6.38809 secs using 597.2% CPU
Optimizing NNI: done in 1.01274 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.07212 secs using 398.7% CPU
Iteration 40 / LogL: -97711.416 / Time: 0h:2m:44s (0h:6m:51s left)
Optimizing NNI: done in 1.96596 secs using 398.3% CPU
Optimizing NNI: done in 4.63859 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -57500.746
Optimizing NNI: done in 2.44859 secs using 398.1% CPU
Optimizing NNI: done in 0.945447 secs using 399.3% CPU
Optimizing NNI: done in 0.852812 secs using 398.9% CPU
Optimizing NNI: done in 1.88604 secs using 398.4% CPU
Optimizing NNI: done in 0.92565 secs using 398.7% CPU
BETTER TREE FOUND at iteration 48: -196140.527
Optimizing NNI: done in 1.00596 secs using 399.6% CPU
Optimizing NNI: done in 2.185 secs using 398.6% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.79205 secs using 398.9% CPU
BETTER TREE FOUND at iteration 7: -57482.385
Optimizing NNI: done in 4.44313 secs using 596.9% CPU
Optimizing NNI: done in 0.940892 secs using 399.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.92742 secs using 398.1% CPU
BETTER TREE FOUND at iteration 9: -57472.297
Optimizing NNI: done in 1.008 secs using 398.8% CPU
Iteration 10 / LogL: -57567.742 / Time: 0h:0m:33s
Optimizing NNI: done in 1.84597 secs using 399% CPU
Optimizing NNI: done in 4.55154 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
Iteration 50 / LogL: -196166.714 / Time: 0h:5m:38s (0h:11m:15s left)
Optimizing NNI: done in 1.05479 secs using 398.7% CPU
Optimizing NNI: done in 0.969208 secs using 398.7% CPU
BETTER TREE FOUND at iteration 48: -97684.670
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Iteration 50 / LogL: -97693.163 / Time: 0h:3m:6s (0h:6m:13s left)
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Optimizing NNI: done in 0.89422 secs using 399.3% CPU
Iteration 20 / LogL: -57580.092 / Time: 0h:0m:43s
Finish initializing candidate tree set (20)
Current best tree score: -57472.297 / CPU time: 37.910
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.37183 secs using 399.5% CPU
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BETTER TREE FOUND at iteration 25: -57470.941
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BETTER TREE FOUND at iteration 27: -57466.235
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.23264 secs using 597.9% CPU
BETTER TREE FOUND at iteration 28: -57464.900
BETTER TREE FOUND at iteration 57: -97680.392
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Iteration 30 / LogL: -57486.861 / Time: 0h:0m:59s (0h:3m:22s left)
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BETTER TREE FOUND at iteration 56: -196123.939
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Iteration 60 / LogL: -97684.929 / Time: 0h:3m:30s (0h:5m:45s left)
BETTER TREE FOUND at iteration 33: -57454.781
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Iteration 40 / LogL: -57462.804 / Time: 0h:1m:14s (0h:2m:56s left)
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BETTER TREE FOUND at iteration 42: -57449.458
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BETTER TREE FOUND at iteration 43: -57440.137
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Iteration 60 / LogL: -196152.387 / Time: 0h:6m:25s (0h:10m:27s left)
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BETTER TREE FOUND at iteration 45: -57436.919
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Iteration 70 / LogL: -97692.309 / Time: 0h:3m:51s (0h:4m:51s left)
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BETTER TREE FOUND at iteration 46: -57435.300
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BETTER TREE FOUND at iteration 47: -57434.391
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BETTER TREE FOUND at iteration 62: -196120.938
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Iteration 50 / LogL: -57449.100 / Time: 0h:1m:32s (0h:3m:2s left)
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Optimizing NNI: done in 4.58525 secs using 597.5% CPU
BETTER TREE FOUND at iteration 56: -57433.456
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.36444 secs using 398.6% CPU
BETTER TREE FOUND at iteration 57: -57429.619
Optimizing NNI: done in 4.01773 secs using 596.1% CPU
Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 65: -196110.851
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Iteration 80 / LogL: -97737.747 / Time: 0h:4m:12s (0h:4m:5s left)
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Iteration 60 / LogL: -57443.195 / Time: 0h:1m:47s (0h:2m:56s left)
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BETTER TREE FOUND at iteration 66: -196110.138
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Iteration 70 / LogL: -57448.614 / Time: 0h:2m:0s (0h:2m:31s left)
Optimizing NNI: done in 4.46389 secs using 597.1% CPU
Optimizing NNI: done in 1.16256 secs using 398.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -57429.619
Optimizing NNI: done in 2.14075 secs using 398.6% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 72: -57429.354
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Iteration 90 / LogL: -97685.559 / Time: 0h:4m:33s (0h:3m:25s left)
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Iteration 70 / LogL: -196179.322 / Time: 0h:7m:13s (0h:10m:3s left)
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Iteration 80 / LogL: -57430.498 / Time: 0h:2m:13s (0h:2m:35s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 82: -57424.731
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 86: -57419.176
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Iteration 90 / LogL: -57438.428 / Time: 0h:2m:27s (0h:2m:38s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 100: -97678.681
Iteration 100 / LogL: -97678.681 / Time: 0h:4m:56s (0h:4m:59s left)
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UPDATE BEST LOG-LIKELIHOOD: -57419.176
Optimizing NNI: done in 4.92338 secs using 595.9% CPU
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Iteration 100 / LogL: -57423.143 / Time: 0h:2m:39s (0h:2m:18s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 105: -57418.614
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Iteration 110 / LogL: -97708.533 / Time: 0h:5m:17s (0h:4m:21s left)
Optimizing NNI: done in 1.28403 secs using 399% CPU
Optimizing NNI: done in 1.24632 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -57418.612
Iteration 110 / LogL: -57418.612 / Time: 0h:2m:52s (0h:2m:30s left)
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Iteration 80 / LogL: -196138.422 / Time: 0h:7m:59s (0h:8m:41s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.40111 secs using 399.1% CPU
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BETTER TREE FOUND at iteration 81: -196102.797
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Iteration 120 / LogL: -57421.638 / Time: 0h:3m:5s (0h:2m:12s left)
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Iteration 120 / LogL: -97715.898 / Time: 0h:5m:38s (0h:3m:47s left)
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Iteration 130 / LogL: -57435.404 / Time: 0h:3m:18s (0h:1m:55s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.14757 secs using 398.9% CPU
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Iteration 140 / LogL: -57427.456 / Time: 0h:3m:31s (0h:1m:38s left)
BETTER TREE FOUND at iteration 87: -196100.098
Optimizing NNI: done in 1.43413 secs using 399% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.45581 secs using 399.3% CPU
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BETTER TREE FOUND at iteration 130: -97676.575
Iteration 130 / LogL: -97676.575 / Time: 0h:6m:2s (0h:4m:40s left)
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Iteration 150 / LogL: -57424.972 / Time: 0h:3m:44s (0h:1m:22s left)
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Iteration 90 / LogL: -196136.848 / Time: 0h:8m:50s (0h:9m:37s left)
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Iteration 160 / LogL: -57438.387 / Time: 0h:3m:56s (0h:1m:6s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 140: -97675.940
Iteration 140 / LogL: -97675.940 / Time: 0h:6m:32s (0h:4m:42s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 146: -97674.868
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Iteration 100 / LogL: -196166.074 / Time: 0h:9m:33s (0h:8m:23s left)
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TREE SEARCH COMPLETED AFTER 206 ITERATIONS / Time: 0h:4m:55s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57418.612
Optimal log-likelihood: -57418.612
Site proportion and rates:  (0.078,0.067) (0.184,0.195) (0.057,0.490) (0.171,0.496) (0.160,0.923) (0.069,0.923) (0.115,1.495) (0.165,2.801)
Parameters optimization took 1 rounds (0.257 sec)
BEST SCORE FOUND : -57418.612
Total tree length: 40.013

Total number of iterations: 206
CPU time used for tree search: 1144.532 sec (0h:19m:4s)
Wall-clock time used for tree search: 290.653 sec (0h:4m:50s)
Total CPU time used: 1166.096 sec (0h:19m:26s)
Total wall-clock time used: 296.029 sec (0h:4m:56s)

===> START BOOTSTRAP REPLICATE NUMBER 68

Creating bootstrap alignment (seed: 67530)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.044 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58729.647
2. Current log-likelihood: -58177.710
3. Current log-likelihood: -58169.368
Optimizing NNI: done in 2.38667 secs using 398.5% CPU
4. Current log-likelihood: -58164.998
5. Current log-likelihood: -58160.490
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6. Current log-likelihood: -58149.932
7. Current log-likelihood: -58147.289
Optimizing NNI: done in 1.65689 secs using 397.8% CPU
8. Current log-likelihood: -58145.342
9. Current log-likelihood: -58143.796
10. Current log-likelihood: -58143.255
Optimizing NNI: done in 2.04206 secs using 397.8% CPU
Iteration 160 / LogL: -97686.387 / Time: 0h:7m:29s (0h:4m:3s left)
11. Current log-likelihood: -58143.130
Optimizing NNI: done in 4.28324 secs using 597.9% CPU
Optimal log-likelihood: -58143.083
Site proportion and rates:  (0.095,0.071) (0.139,0.197) (0.120,0.371) (0.215,0.612) (0.179,1.004) (0.110,1.653) (0.117,2.485) (0.025,5.472)
Parameters optimization took 11 rounds (8.171 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09206 secs using 400% CPU
Computing ML distances took 1.092243 sec (of wall-clock time) 4.368618 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000346899 secs using 400.7% CPU
Constructing RapidNJ tree: done in 0.00438881 secs using 306.2% CPU
Computing RapidNJ tree took 0.004792 sec (of wall-clock time) 0.016270 sec (of CPU time)
Optimizing NNI: done in 2.16131 secs using 397.9% CPU
Log-likelihood of RapidNJ tree: -58139.927
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.81199 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 162: -97674.438
5.213 second
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Iteration 110 / LogL: -196382.546 / Time: 0h:10m:19s (0h:7m:17s left)
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Computing log-likelihood of 98 initial trees ... 5.052 seconds
Current best score: -57993.147

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 10 / LogL: -57801.500 / Time: 0h:0m:40s
BETTER TREE FOUND at iteration 173: -97672.692
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Iteration 20 / LogL: -57798.617 / Time: 0h:0m:56s
Finish initializing candidate tree set (20)
Current best tree score: -57745.173 / CPU time: 46.514
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 30 / LogL: -57743.828 / Time: 0h:1m:12s (0h:4m:10s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 121: -57699.296
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BETTER TREE FOUND at iteration 178: -57699.288
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 188: -57699.201
Optimizing NNI: done in 4.31561 secs using 597.3% CPU
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TREE SEARCH COMPLETED AFTER 312 ITERATIONS / Time: 0h:12m:56s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -97669.707
2. Current log-likelihood: -97669.689
Optimizing NNI: done in 1.37096 secs using 398.7% CPU
Iteration 200 / LogL: -57704.101 / Time: 0h:5m:34s (0h:2m:28s left)
3. Current log-likelihood: -97669.673
4. Current log-likelihood: -97669.658
Optimizing NNI: done in 1.5106 secs using 398.9% CPU
5. Current log-likelihood: -97669.643
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6. Current log-likelihood: -97669.628
Optimizing NNI: done in 5.11009 secs using 597% CPU
Iteration 180 / LogL: -196154.355 / Time: 0h:15m:39s (0h:4m:16s left)
7. Current log-likelihood: -97669.613
Optimizing NNI: done in 1.27537 secs using 399% CPU
8. Current log-likelihood: -97669.599
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9. Current log-likelihood: -97669.585
10. Current log-likelihood: -97669.573
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11. Current log-likelihood: -97669.560
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12. Current log-likelihood: -97669.548
13. Current log-likelihood: -97669.536
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14. Current log-likelihood: -97669.525
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15. Current log-likelihood: -97669.513
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16. Current log-likelihood: -97669.502
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17. Current log-likelihood: -97669.491
Optimizing NNI: done in 1.25292 secs using 398.7% CPU
Iteration 210 / LogL: -57711.660 / Time: 0h:5m:48s (0h:2m:10s left)
Optimal log-likelihood: -97669.478
Proportion of invariable sites: 0.041
Site proportion and rates:  (0.109,0.035) (0.084,0.102) (0.079,0.202) (0.134,0.360) (0.132,0.598) (0.117,0.932) (0.148,1.418) (0.105,2.267) (0.050,5.684)
Parameters optimization took 17 rounds (15.965 sec)
BEST SCORE FOUND : -97669.478
Total tree length: 155.787

Total number of iterations: 312
CPU time used for tree search: 2975.308 sec (0h:49m:35s)
Wall-clock time used for tree search: 754.710 sec (0h:12m:34s)
Total CPU time used: 3124.474 sec (0h:52m:4s)
Total wall-clock time used: 792.155 sec (0h:13m:12s)

===> START BOOTSTRAP REPLICATE NUMBER 24

Creating bootstrap alignment (seed: 68206)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.131 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -113330.347
Optimizing NNI: done in 1.34808 secs using 398.6% CPU
Optimizing NNI: done in 4.30437 secs using 597.9% CPU
2. Current log-likelihood: -111113.991
Optimizing NNI: done in 1.45674 secs using 398.8% CPU
Optimizing NNI: done in 1.44011 secs using 399.1% CPU
3. Current log-likelihood: -111065.392
Optimizing NNI: done in 1.40742 secs using 399.1% CPU
4. Current log-likelihood: -111064.860
Optimizing NNI: done in 4.16031 secs using 597.8% CPU
Optimal log-likelihood: -111064.828
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.087,0.050) (0.023,0.113) (0.086,0.192) (0.114,0.300) (0.082,0.409) (0.153,0.645) (0.113,1.023) (0.221,1.688) (0.087,3.713)
Parameters optimization took 4 rounds (6.042 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.30613 secs using 398.9% CPU
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Optimizing NNI: done in 4.373 secs using 598.3% CPU
Calculating distance matrix: done in 4.60765 secs using 399.9% CPU
Computing ML distances took 4.607895 sec (of wall-clock time) 18.427119 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000689983 secs using 380.9% CPU
Constructing RapidNJ tree: done in 0.00851989 secs using 427.3% CPU
Computing RapidNJ tree took 0.009282 sec (of wall-clock time) 0.041020 sec (of CPU time)
Optimizing NNI: done in 1.5581 secs using 399% CPU
Log-likelihood of RapidNJ tree: -111365.976
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.35434 secs using 399% CPU
Optimizing NNI: done in 1.49546 secs using 398.7% CPU
Iteration 220 / LogL: -57844.600 / Time: 0h:6m:3s (0h:1m:52s left)
Optimizing NNI: done in 1.29304 secs using 399.5% CPU
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11.480 second
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Optimizing NNI: done in 1.19337 secs using 399.1% CPU
Iteration 230 / LogL: -57717.005 / Time: 0h:6m:16s (0h:1m:35s left)
Optimizing NNI: done in 1.2225 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 6.2544 secs using 597.7% CPU
BETTER TREE FOUND at iteration 231: -57699.132
Optimizing NNI: done in 1.39394 secs using 399.1% CPU
Optimizing NNI: done in 1.58449 secs using 398.2% CPU
Computing log-likelihood of 98 initial trees ... 9.639 seconds
Current best score: -111064.828

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.19309 secs using 399.1% CPU
Optimizing NNI: done in 1.38166 secs using 398.9% CPU
BETTER TREE FOUND at iteration 1: -110587.170
Optimizing NNI: done in 4.85037 secs using 597.3% CPU
Iteration 190 / LogL: -196153.805 / Time: 0h:16m:27s (0h:3m:23s left)
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Optimizing NNI: done in 1.94606 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 1.56517 secs using 399% CPU
Iteration 240 / LogL: -57701.795 / Time: 0h:6m:31s (0h:2m:28s left)
BETTER TREE FOUND at iteration 2: -110571.240
Optimizing NNI: done in 4.55339 secs using 597.1% CPU
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 4: -110544.179
Optimizing NNI: done in 1.39529 secs using 398.7% CPU
Iteration 250 / LogL: -57699.904 / Time: 0h:6m:45s (0h:2m:11s left)
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Iteration 10 / LogL: -110608.453 / Time: 0h:1m:8s
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Iteration 260 / LogL: -57722.126 / Time: 0h:6m:58s (0h:1m:54s left)
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Iteration 270 / LogL: -57703.575 / Time: 0h:7m:12s (0h:1m:38s left)
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Iteration 200 / LogL: -196173.613 / Time: 0h:17m:13s (0h:2m:30s left)
Optimizing NNI: done in 1.44329 secs using 398.9% CPU
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Iteration 20 / LogL: -110575.728 / Time: 0h:1m:29s
Finish initializing candidate tree set (20)
Current best tree score: -110544.179 / CPU time: 78.080
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.41672 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 278: -57699.130
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BETTER TREE FOUND at iteration 22: -110527.080
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Iteration 280 / LogL: -57770.435 / Time: 0h:7m:26s (0h:2m:36s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 25: -110524.408
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Iteration 290 / LogL: -57707.534 / Time: 0h:7m:40s (0h:2m:20s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 28: -110516.651
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Iteration 30 / LogL: -110517.851 / Time: 0h:1m:59s (0h:6m:42s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 210 / LogL: -196301.275 / Time: 0h:17m:57s (0h:1m:37s left)
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BETTER TREE FOUND at iteration 304: -57699.125
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 35: -110481.927
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Iteration 310 / LogL: -57724.477 / Time: 0h:8m:8s (0h:2m:28s left)
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Iteration 40 / LogL: -110504.544 / Time: 0h:2m:24s (0h:5m:52s left)
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Iteration 320 / LogL: -57707.391 / Time: 0h:8m:22s (0h:2m:12s left)
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Iteration 50 / LogL: -110484.796 / Time: 0h:2m:43s (0h:4m:43s left)
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Iteration 330 / LogL: -57704.317 / Time: 0h:8m:36s (0h:1m:56s left)
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Iteration 220 / LogL: -196120.015 / Time: 0h:18m:42s (0h:0m:46s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 56: -110480.567
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Estimate model parameters (epsilon = 0.100)
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Iteration 340 / LogL: -57737.125 / Time: 0h:8m:50s (0h:1m:40s left)
BETTER TREE FOUND at iteration 57: -110477.091
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 224: -196096.170
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Iteration 350 / LogL: -57706.876 / Time: 0h:9m:4s (0h:1m:24s left)
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Iteration 70 / LogL: -110509.136 / Time: 0h:3m:25s (0h:4m:18s left)
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Iteration 360 / LogL: -57722.975 / Time: 0h:9m:18s (0h:1m:8s left)
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Iteration 230 / LogL: -196104.876 / Time: 0h:19m:32s (0h:8m:1s left)
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Iteration 370 / LogL: -57699.135 / Time: 0h:9m:32s (0h:0m:52s left)
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Iteration 380 / LogL: -57706.333 / Time: 0h:9m:47s (0h:0m:37s left)
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Iteration 90 / LogL: -110500.642 / Time: 0h:4m:3s (0h:3m:2s left)
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Iteration 390 / LogL: -57699.720 / Time: 0h:10m:0s (0h:0m:21s left)
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Iteration 100 / LogL: -110489.070 / Time: 0h:4m:22s (0h:2m:31s left)
Optimizing NNI: done in 4.0922 secs using 597.7% CPU
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Iteration 400 / LogL: -57707.569 / Time: 0h:10m:15s (0h:0m:6s left)
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Optimizing NNI: done in 4.10606 secs using 597.2% CPU
Iteration 240 / LogL: -196171.651 / Time: 0h:20m:17s (0h:7m:7s left)
Optimizing NNI: done in 1.22439 secs using 399.4% CPU
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Optimizing NNI: done in 1.50035 secs using 398.3% CPU
TREE SEARCH COMPLETED AFTER 405 ITERATIONS / Time: 0h:10m:22s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57699.125
2. Current log-likelihood: -57699.096
3. Current log-likelihood: -57699.062
Optimizing NNI: done in 2.02317 secs using 399.1% CPU
4. Current log-likelihood: -57699.030
5. Current log-likelihood: -57698.998
Optimizing NNI: done in 4.54126 secs using 597.5% CPU
6. Current log-likelihood: -57698.969
7. Current log-likelihood: -57698.954
Optimizing NNI: done in 1.91693 secs using 398.6% CPU
8. Current log-likelihood: -57698.936
9. Current log-likelihood: -57698.920
10. Current log-likelihood: -57698.906
Optimizing NNI: done in 1.62173 secs using 398.6% CPU
11. Current log-likelihood: -57698.891
12. Current log-likelihood: -57698.876
13. Current log-likelihood: -57698.863
14. Current log-likelihood: -57698.849
Optimizing NNI: done in 1.80812 secs using 398.5% CPU
Optimizing NNI: done in 4.58052 secs using 596.6% CPU
15. Current log-likelihood: -57698.837
16. Current log-likelihood: -57698.823
17. Current log-likelihood: -57698.811
Optimizing NNI: done in 1.72528 secs using 398.6% CPU
Iteration 110 / LogL: -110677.134 / Time: 0h:4m:41s (0h:2m:1s left)
18. Current log-likelihood: -57698.801
19. Current log-likelihood: -57698.790
Optimal log-likelihood: -57698.776
Site proportion and rates:  (0.064,0.058) (0.152,0.162) (0.208,0.391) (0.164,0.692) (0.171,1.018) (0.124,1.748) (0.093,2.601) (0.026,5.691)
Parameters optimization took 19 rounds (9.699 sec)
BEST SCORE FOUND : -57698.776
Total tree length: 42.216

Total number of iterations: 405
CPU time used for tree search: 2427.971 sec (0h:40m:27s)
Wall-clock time used for tree search: 612.427 sec (0h:10m:12s)
Total CPU time used: 2506.261 sec (0h:41m:46s)
Total wall-clock time used: 632.040 sec (0h:10m:32s)

===> START BOOTSTRAP REPLICATE NUMBER 69

Creating bootstrap alignment (seed: 67531)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -56579.540
2. Current log-likelihood: -56016.632
Optimizing NNI: done in 1.95105 secs using 398.7% CPU
3. Current log-likelihood: -55988.713
Optimizing NNI: done in 4.6043 secs using 597.5% CPU
4. Current log-likelihood: -55982.686
Optimizing NNI: done in 1.97613 secs using 398.9% CPU
5. Current log-likelihood: -55981.921
6. Current log-likelihood: -55981.665
7. Current log-likelihood: -55981.487
Optimizing NNI: done in 1.97952 secs using 398.9% CPU
8. Current log-likelihood: -55981.367
Optimal log-likelihood: -55981.263
Site proportion and rates:  (0.130,0.058) (0.140,0.212) (0.074,0.421) (0.069,0.443) (0.249,0.739) (0.146,1.257) (0.147,2.301) (0.045,4.307)
Parameters optimization took 8 rounds (6.310 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.21738 secs using 597.2% CPU
Calculating distance matrix: done in 1.07736 secs using 399.8% CPU
Computing ML distances took 1.077535 sec (of wall-clock time) 4.307538 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000367165 secs using 423.2% CPU
Constructing RapidNJ tree: done in 0.0044229 secs using 388.3% CPU
Computing RapidNJ tree took 0.004848 sec (of wall-clock time) 0.019469 sec (of CPU time)
Optimizing NNI: done in 2.164 secs using 398.7% CPU
Log-likelihood of RapidNJ tree: -56037.995
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.82912 secs using 398.8% CPU
Optimizing NNI: done in 1.99391 secs using 398.9% CPU
4.952 second
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Optimizing NNI: done in 1.82131 secs using 398.3% CPU
Computing log-likelihood of 98 initial trees ... 5.004 seconds
Current best score: -55903.199

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.40089 secs using 597.6% CPU
Optimizing NNI: done in 1.90131 secs using 398.4% CPU
Iteration 120 / LogL: -110532.668 / Time: 0h:5m:1s (0h:1m:33s left)
Optimizing NNI: done in 1.58369 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.88755 secs using 398.6% CPU
BETTER TREE FOUND at iteration 1: -55690.863
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Iteration 250 / LogL: -196157.439 / Time: 0h:21m:3s (0h:6m:15s left)
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Iteration 10 / LogL: -55774.608 / Time: 0h:0m:33s
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Iteration 130 / LogL: -110492.523 / Time: 0h:5m:20s (0h:1m:7s left)
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Iteration 20 / LogL: -55785.351 / Time: 0h:0m:47s
Finish initializing candidate tree set (20)
Current best tree score: -55690.863 / CPU time: 39.536
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 140 / LogL: -110540.995 / Time: 0h:5m:39s (0h:0m:41s left)
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Iteration 30 / LogL: -55699.506 / Time: 0h:1m:1s (0h:2m:30s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 144: -110476.365
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 34: -55681.784
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 263: -196090.435
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Iteration 50 / LogL: -55677.809 / Time: 0h:1m:35s (0h:2m:49s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 84: -55674.758
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 89: -55674.273
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BETTER TREE FOUND at iteration 285: -196087.697
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BETTER TREE FOUND at iteration 120: -55665.527
Iteration 120 / LogL: -55665.527 / Time: 0h:3m:22s (0h:2m:50s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 132: -55663.610
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Iteration 300 / LogL: -196129.661 / Time: 0h:24m:50s (0h:7m:3s left)
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TREE SEARCH COMPLETED AFTER 245 ITERATIONS / Time: 0h:9m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -110476.365
2. Current log-likelihood: -110476.331
Optimizing NNI: done in 4.92771 secs using 597.6% CPU
Optimizing NNI: done in 1.78297 secs using 399.4% CPU
Iteration 160 / LogL: -55666.662 / Time: 0h:4m:23s (0h:1m:59s left)
3. Current log-likelihood: -110476.281
4. Current log-likelihood: -110476.236
Optimizing NNI: done in 1.62816 secs using 398.7% CPU
5. Current log-likelihood: -110476.193
6. Current log-likelihood: -110476.154
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7. Current log-likelihood: -110476.116
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8. Current log-likelihood: -110476.078
Optimizing NNI: done in 1.57025 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
9. Current log-likelihood: -110476.042
BETTER TREE FOUND at iteration 164: -55663.385
10. Current log-likelihood: -110476.007
Optimizing NNI: done in 1.43442 secs using 399.2% CPU
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11. Current log-likelihood: -110475.974
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12. Current log-likelihood: -110475.942
13. Current log-likelihood: -110475.914
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14. Current log-likelihood: -110475.896
15. Current log-likelihood: -110475.867
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16. Current log-likelihood: -110475.842
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17. Current log-likelihood: -110475.825
18. Current log-likelihood: -110475.800
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Iteration 170 / LogL: -55671.582 / Time: 0h:4m:38s (0h:2m:34s left)
19. Current log-likelihood: -110475.784
20. Current log-likelihood: -110475.767
Optimizing NNI: done in 1.45768 secs using 399% CPU
21. Current log-likelihood: -110475.751
22. Current log-likelihood: -110475.736
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23. Current log-likelihood: -110475.722
24. Current log-likelihood: -110475.705
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25. Current log-likelihood: -110475.692
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26. Current log-likelihood: -110475.678
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27. Current log-likelihood: -110475.664
28. Current log-likelihood: -110475.651
29. Current log-likelihood: -110475.638
Optimizing NNI: done in 1.39283 secs using 398.9% CPU
30. Current log-likelihood: -110475.626
31. Current log-likelihood: -110475.614
Optimizing NNI: done in 1.4037 secs using 398.9% CPU
Optimal log-likelihood: -110475.602
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.071,0.043) (0.038,0.097) (0.087,0.187) (0.105,0.290) (0.090,0.397) (0.136,0.619) (0.122,0.959) (0.231,1.661) (0.087,3.728)
Parameters optimization took 31 rounds (26.343 sec)
BEST SCORE FOUND : -110475.602
Total tree length: 178.669

Total number of iterations: 245
CPU time used for tree search: 2087.775 sec (0h:34m:47s)
Wall-clock time used for tree search: 532.354 sec (0h:8m:52s)
Total CPU time used: 2239.014 sec (0h:37m:19s)
Total wall-clock time used: 570.317 sec (0h:9m:30s)

===> START BOOTSTRAP REPLICATE NUMBER 25

Creating bootstrap alignment (seed: 68207)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.127 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 101 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104264.061
Optimizing NNI: done in 1.47505 secs using 399.4% CPU
2. Current log-likelihood: -102360.757
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3. Current log-likelihood: -102314.433
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4. Current log-likelihood: -102282.863
Optimizing NNI: done in 1.31832 secs using 399.3% CPU
Iteration 180 / LogL: -55691.896 / Time: 0h:4m:53s (0h:2m:17s left)
5. Current log-likelihood: -102279.229
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6. Current log-likelihood: -102271.189
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7. Current log-likelihood: -102266.081
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8. Current log-likelihood: -102264.816
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9. Current log-likelihood: -102262.138
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10. Current log-likelihood: -102258.666
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Optimizing NNI: done in 6.16865 secs using 596.3% CPU
Optimizing NNI: done in 1.36347 secs using 399.2% CPU
11. Current log-likelihood: -102258.049
Optimal log-likelihood: -102258.008
Proportion of invariable sites: 0.028
Site proportion and rates:  (0.108,0.044) (0.115,0.137) (0.131,0.263) (0.098,0.463) (0.134,0.676) (0.079,0.979) (0.127,1.594) (0.130,2.354) (0.050,4.495)
Parameters optimization took 11 rounds (17.426 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 190 / LogL: -55682.460 / Time: 0h:5m:8s (0h:2m:0s left)
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Calculating distance matrix: done in 4.65778 secs using 399.6% CPU
Computing ML distances took 4.658035 sec (of wall-clock time) 18.612211 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000683069 secs using 403.2% CPU
Constructing RapidNJ tree: done in 0.00873017 secs using 380.3% CPU
Computing RapidNJ tree took 0.009466 sec (of wall-clock time) 0.037946 sec (of CPU time)
Optimizing NNI: done in 1.44344 secs using 398.7% CPU
Log-likelihood of RapidNJ tree: -102352.823
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.49948 secs using 399% CPU
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Iteration 310 / LogL: -196692.830 / Time: 0h:25m:48s (0h:6m:15s left)
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Iteration 200 / LogL: -55681.299 / Time: 0h:5m:22s (0h:1m:43s left)
10.749 second
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BETTER TREE FOUND at iteration 205: -55663.380
Optimizing NNI: done in 1.49974 secs using 398.8% CPU
Computing log-likelihood of 98 initial trees ... 9.422 seconds
Current best score: -102258.008

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 210 / LogL: -55665.668 / Time: 0h:5m:36s (0h:2m:33s left)
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BETTER TREE FOUND at iteration 1: -101644.105
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Iteration 220 / LogL: -55663.591 / Time: 0h:5m:51s (0h:2m:16s left)
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Iteration 10 / LogL: -101901.868 / Time: 0h:1m:10s
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BETTER TREE FOUND at iteration 225: -55663.378
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Iteration 230 / LogL: -55685.657 / Time: 0h:6m:5s (0h:2m:31s left)
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Iteration 320 / LogL: -196107.066 / Time: 0h:26m:42s (0h:5m:26s left)
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Iteration 20 / LogL: -101840.894 / Time: 0h:1m:30s
Finish initializing candidate tree set (20)
Current best tree score: -101644.105 / CPU time: 66.300
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 72: -101605.509
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Iteration 330 / LogL: -55713.163 / Time: 0h:8m:30s (0h:0m:7s left)
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TREE SEARCH COMPLETED AFTER 336 ITERATIONS / Time: 0h:8m:39s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -55663.378
2. Current log-likelihood: -55663.356
Optimizing NNI: done in 4.48023 secs using 597.2% CPU
3. Current log-likelihood: -55663.345
4. Current log-likelihood: -55663.334
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5. Current log-likelihood: -55663.321
6. Current log-likelihood: -55663.310
7. Current log-likelihood: -55663.296
8. Current log-likelihood: -55663.285
Optimizing NNI: done in 1.83517 secs using 398.6% CPU
9. Current log-likelihood: -55663.273
10. Current log-likelihood: -55663.262
11. Current log-likelihood: -55663.252
12. Current log-likelihood: -55663.241
Optimal log-likelihood: -55663.226
Site proportion and rates:  (0.125,0.055) (0.145,0.209) (0.071,0.432) (0.065,0.433) (0.245,0.721) (0.160,1.231) (0.141,2.306) (0.048,4.281)
Parameters optimization took 12 rounds (4.604 sec)
BEST SCORE FOUND : -55663.226
Total tree length: 39.884

Total number of iterations: 336
CPU time used for tree search: 2025.811 sec (0h:33m:45s)
Wall-clock time used for tree search: 511.291 sec (0h:8m:31s)
Total CPU time used: 2075.419 sec (0h:34m:35s)
Total wall-clock time used: 523.703 sec (0h:8m:43s)

===> START BOOTSTRAP REPLICATE NUMBER 70

Creating bootstrap alignment (seed: 67532)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.049 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59675.621
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Iteration 80 / LogL: -101615.028 / Time: 0h:3m:56s (0h:4m:35s left)
2. Current log-likelihood: -59079.058
3. Current log-likelihood: -59069.903
4. Current log-likelihood: -59065.789
Optimizing NNI: done in 1.95738 secs using 398.7% CPU
5. Current log-likelihood: -59049.075
6. Current log-likelihood: -59041.168
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Optimizing NNI: done in 2.44059 secs using 398.1% CPU
7. Current log-likelihood: -59039.730
8. Current log-likelihood: -59039.372
9. Current log-likelihood: -59039.209
Optimizing NNI: done in 1.97853 secs using 399.1% CPU
Optimal log-likelihood: -59039.114
Site proportion and rates:  (0.118,0.076) (0.110,0.200) (0.155,0.364) (0.187,0.549) (0.144,0.936) (0.132,1.552) (0.125,2.429) (0.029,5.663)
Parameters optimization took 9 rounds (7.862 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09377 secs using 399.8% CPU
Computing ML distances took 1.093941 sec (of wall-clock time) 4.373256 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000346184 secs using 420.6% CPU
Constructing RapidNJ tree: done in 0.00439787 secs using 329.8% CPU
Computing RapidNJ tree took 0.004796 sec (of wall-clock time) 0.016234 sec (of CPU time)
Optimizing NNI: done in 4.11309 secs using 597% CPU
Log-likelihood of RapidNJ tree: -59033.613
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.47141 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 85: -101602.689
5.085 second
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Computing log-likelihood of 98 initial trees ... 5.109 seconds
Current best score: -58849.721

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -58679.503
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Iteration 90 / LogL: -101610.100 / Time: 0h:4m:21s (0h:4m:38s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 6: -58671.587
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Iteration 10 / LogL: -58715.363 / Time: 0h:0m:37s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 13: -58646.065
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Iteration 100 / LogL: -101607.465 / Time: 0h:4m:43s (0h:4m:3s left)
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Iteration 20 / LogL: -58769.692 / Time: 0h:0m:51s
Finish initializing candidate tree set (20)
Current best tree score: -58646.065 / CPU time: 42.184
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 106: -101595.679
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 39: -58640.213
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 59: -58635.106
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BETTER TREE FOUND at iteration 73: -58633.290
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Iteration 140 / LogL: -101661.464 / Time: 0h:6m:11s (0h:2m:56s left)
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Optimizing NNI: done in 4.16752 secs using 597.5% CPU
TREE SEARCH COMPLETED AFTER 386 ITERATIONS / Time: 0h:31m:32s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -196087.697
Optimizing NNI: done in 1.16488 secs using 398.7% CPU
Optimal log-likelihood: -196087.686
Site proportion and rates:  (0.018,0.109) (0.045,0.220) (0.105,0.356) (0.238,0.569) (0.124,0.791) (0.173,1.009) (0.179,1.479) (0.118,2.356)
Parameters optimization took 1 rounds (1.597 sec)
BEST SCORE FOUND : -196087.686
Total tree length: 156.745

Total number of iterations: 386
CPU time used for tree search: 10888.814 sec (3h:1m:28s)
Wall-clock time used for tree search: 1848.600 sec (0h:30m:48s)
Total CPU time used: 11161.732 sec (3h:6m:1s)
Total wall-clock time used: 1894.443 sec (0h:31m:34s)

===> START BOOTSTRAP REPLICATE NUMBER 18

Creating bootstrap alignment (seed: 70481)...

Optimizing NNI: done in 2.07711 secs using 399.1% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.289 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199419.965
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 78: -58633.199
2. Current log-likelihood: -196648.411
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3. Current log-likelihood: -196623.853
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Iteration 80 / LogL: -58634.460 / Time: 0h:2m:23s (0h:2m:58s left)
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4. Current log-likelihood: -196623.121
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5. Current log-likelihood: -196622.841
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6. Current log-likelihood: -196622.700
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Optimizing NNI: done in 2.51106 secs using 398.6% CPU
Optimal log-likelihood: -196622.631
Site proportion and rates:  (0.009,0.092) (0.053,0.216) (0.083,0.335) (0.148,0.455) (0.215,0.639) (0.209,0.953) (0.172,1.564) (0.111,2.582)
Parameters optimization took 6 rounds (13.873 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 150 / LogL: -101612.733 / Time: 0h:6m:34s (0h:2m:28s left)
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Calculating distance matrix: done in 10.3612 secs using 599.9% CPU
Computing ML distances took 10.361759 sec (of wall-clock time) 62.157926 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00127792 secs using 430.9% CPU
Constructing RapidNJ tree: done in 0.022573 secs using 675% CPU
Computing RapidNJ tree took 0.023923 sec (of wall-clock time) 0.159205 sec (of CPU time)
Optimizing NNI: done in 2.14688 secs using 398.6% CPU
Optimizing NNI: done in 1.66355 secs using 398.8% CPU
Log-likelihood of RapidNJ tree: -200811.417
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.32014 secs using 399.6% CPU
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 96: -58632.658
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 105: -58627.745
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30.613 second
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Computing log-likelihood of 98 initial trees ... 16.707 seconds
Current best score: -196622.631

Do NNI search on 20 best initial trees
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Iteration 120 / LogL: -58648.665 / Time: 0h:3m:33s (0h:2m:32s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -196015.547
BETTER TREE FOUND at iteration 129: -58626.873
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Optimizing NNI: done in 1.61635 secs using 399.3% CPU
Optimizing NNI: done in 2.00886 secs using 398.5% CPU
Optimizing NNI: done in 1.50713 secs using 398.6% CPU
Optimizing NNI: done in 1.28399 secs using 399.1% CPU
Optimizing NNI: done in 1.68386 secs using 398.2% CPU
Optimizing NNI: done in 4.01403 secs using 597.7% CPU
Optimizing NNI: done in 1.26689 secs using 399.3% CPU
Optimizing NNI: done in 2.0008 secs using 398.5% CPU
TREE SEARCH COMPLETED AFTER 207 ITERATIONS / Time: 0h:8m:38s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101595.679
2. Current log-likelihood: -101595.667
Optimizing NNI: done in 1.5518 secs using 398.8% CPU
Optimal log-likelihood: -101595.654
Proportion of invariable sites: 0.028
Site proportion and rates:  (0.108,0.040) (0.103,0.124) (0.142,0.248) (0.094,0.454) (0.134,0.657) (0.080,0.951) (0.134,1.585) (0.132,2.343) (0.045,4.915)
Parameters optimization took 2 rounds (1.194 sec)
BEST SCORE FOUND : -101595.654
Total tree length: 160.854

Total number of iterations: 207
CPU time used for tree search: 1941.163 sec (0h:32m:21s)
Wall-clock time used for tree search: 494.941 sec (0h:8m:14s)
Total CPU time used: 2040.610 sec (0h:34m:0s)
Total wall-clock time used: 519.908 sec (0h:8m:39s)

===> START BOOTSTRAP REPLICATE NUMBER 26

Creating bootstrap alignment (seed: 68208)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.087 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -107239.462
Optimizing NNI: done in 3.69462 secs using 597.2% CPU
Optimizing NNI: done in 1.36063 secs using 398.8% CPU
2. Current log-likelihood: -105371.470
Optimizing NNI: done in 1.62799 secs using 398.7% CPU
3. Current log-likelihood: -105274.720
Optimizing NNI: done in 1.39654 secs using 399.2% CPU
Optimizing NNI: done in 4.01954 secs using 597.2% CPU
Optimizing NNI: done in 1.20805 secs using 398.4% CPU
Iteration 170 / LogL: -58629.158 / Time: 0h:4m:49s (0h:1m:40s left)
4. Current log-likelihood: -105267.627
Optimizing NNI: done in 1.48437 secs using 399.3% CPU
5. Current log-likelihood: -105267.397
Optimizing NNI: done in 1.52058 secs using 398.6% CPU
Optimal log-likelihood: -105267.378
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.098,0.040) (0.059,0.126) (0.105,0.225) (0.097,0.331) (0.131,0.500) (0.101,0.766) (0.134,1.241) (0.187,1.961) (0.053,4.811)
Parameters optimization took 5 rounds (8.325 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.28979 secs using 597.3% CPU
Optimizing NNI: done in 1.40132 secs using 398.9% CPU
Optimizing NNI: done in 1.53821 secs using 398.9% CPU
Optimizing NNI: done in 1.50965 secs using 398.3% CPU
Optimizing NNI: done in 4.07007 secs using 598% CPU
Calculating distance matrix: done in 4.58909 secs using 399.9% CPU
Computing ML distances took 4.589333 sec (of wall-clock time) 18.351885 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000695944 secs using 251.7% CPU
Constructing RapidNJ tree: done in 0.0086751 secs using 418.3% CPU
Computing RapidNJ tree took 0.009437 sec (of wall-clock time) 0.038326 sec (of CPU time)
Optimizing NNI: done in 1.17419 secs using 398.5% CPU
Log-likelihood of RapidNJ tree: -105301.366
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.42426 secs using 398.5% CPU
Optimizing NNI: done in 1.65065 secs using 399.4% CPU
Optimizing NNI: done in 4.70264 secs using 597.1% CPU
Optimizing NNI: done in 1.27242 secs using 399.1% CPU
Optimizing NNI: done in 1.20516 secs using 398.6% CPU
Iteration 180 / LogL: -58666.065 / Time: 0h:5m:3s (0h:1m:23s left)
Optimizing NNI: done in 1.43895 secs using 398.6% CPU
Optimizing NNI: done in 1.51415 secs using 398.4% CPU
Optimizing NNI: done in 5.11537 secs using 597.2% CPU
Optimizing NNI: done in 1.42546 secs using 399% CPU
Optimizing NNI: done in 1.24578 secs using 398.7% CPU
10.697 second
Optimizing NNI: done in 1.43851 secs using 398.9% CPU
Optimizing NNI: done in 4.92782 secs using 597% CPU
Iteration 20 / LogL: -196126.948 / Time: 0h:2m:53s
Finish initializing candidate tree set (20)
Current best tree score: -195948.397 / CPU time: 147.469
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.45905 secs using 399.7% CPU
Optimizing NNI: done in 1.67524 secs using 398.9% CPU
Optimizing NNI: done in 1.3804 secs using 399.1% CPU
Optimizing NNI: done in 4.35325 secs using 598.1% CPU
Optimizing NNI: done in 1.44881 secs using 399% CPU
Optimizing NNI: done in 1.22577 secs using 397.7% CPU
Iteration 190 / LogL: -58636.276 / Time: 0h:5m:17s (0h:1m:5s left)
Computing log-likelihood of 98 initial trees ... 9.933 seconds
Current best score: -105267.378

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.69987 secs using 399.2% CPU
Optimizing NNI: done in 4.1115 secs using 598% CPU
Optimizing NNI: done in 1.44507 secs using 399.4% CPU
Optimizing NNI: done in 2.29118 secs using 397.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.26182 secs using 399.2% CPU
Optimizing NNI: done in 1.27451 secs using 399.4% CPU
Optimizing NNI: done in 4.10775 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.26379 secs using 398.5% CPU
Optimizing NNI: done in 1.3925 secs using 399.3% CPU
Optimizing NNI: done in 1.79847 secs using 398.9% CPU
BETTER TREE FOUND at iteration 23: -195947.505
Optimizing NNI: done in 1.484 secs using 398.9% CPU
Optimizing NNI: done in 1.42208 secs using 399.5% CPU
Optimizing NNI: done in 3.67926 secs using 597.7% CPU
Optimizing NNI: done in 1.47697 secs using 399.3% CPU
Iteration 200 / LogL: -58628.462 / Time: 0h:5m:32s (0h:0m:48s left)
Optimizing NNI: done in 1.25128 secs using 398.8% CPU
BETTER TREE FOUND at iteration 1: -104754.293
Optimizing NNI: done in 1.79492 secs using 398.3% CPU
Optimizing NNI: done in 1.75092 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.32674 secs using 597.9% CPU
Optimizing NNI: done in 1.40741 secs using 398.1% CPU
Optimizing NNI: done in 1.34182 secs using 398.9% CPU
Optimizing NNI: done in 1.57589 secs using 398.5% CPU
BETTER TREE FOUND at iteration 2: -104752.698
Optimizing NNI: done in 4.33582 secs using 596.8% CPU
Optimizing NNI: done in 1.59158 secs using 398.7% CPU
Optimizing NNI: done in 2.06399 secs using 398.7% CPU
Optimizing NNI: done in 1.44823 secs using 399.3% CPU
Optimizing NNI: done in 1.53134 secs using 398.3% CPU
Optimizing NNI: done in 1.43605 secs using 399.2% CPU
Optimizing NNI: done in 4.45312 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.51721 secs using 398.9% CPU
Optimizing NNI: done in 1.48545 secs using 399% CPU
Optimizing NNI: done in 1.63318 secs using 399.2% CPU
Iteration 210 / LogL: -58640.569 / Time: 0h:5m:47s (0h:0m:31s left)
Optimizing NNI: done in 2.30238 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.60555 secs using 399.1% CPU
BETTER TREE FOUND at iteration 27: -195915.514
Optimizing NNI: done in 1.57996 secs using 399.2% CPU
Optimizing NNI: done in 1.42925 secs using 398.9% CPU
BETTER TREE FOUND at iteration 6: -104679.739
Optimizing NNI: done in 1.25664 secs using 399% CPU
Optimizing NNI: done in 4.1706 secs using 597% CPU
Optimizing NNI: done in 2.0883 secs using 398.2% CPU
Optimizing NNI: done in 1.40576 secs using 399.1% CPU
Optimizing NNI: done in 1.34841 secs using 399% CPU
Optimizing NNI: done in 2.92479 secs using 398.9% CPU
Optimizing NNI: done in 1.79455 secs using 399% CPU
Optimizing NNI: done in 4.57382 secs using 597.5% CPU
Optimizing NNI: done in 1.88628 secs using 398.9% CPU
Optimizing NNI: done in 1.53252 secs using 399.1% CPU
Optimizing NNI: done in 1.46115 secs using 398.6% CPU
Optimizing NNI: done in 2.20291 secs using 398.7% CPU
Iteration 10 / LogL: -104735.605 / Time: 0h:1m:17s
Optimizing NNI: done in 1.37227 secs using 399% CPU
Iteration 220 / LogL: -58631.958 / Time: 0h:6m:2s (0h:0m:14s left)
Optimizing NNI: done in 4.47494 secs using 596.8% CPU
Iteration 30 / LogL: -195944.138 / Time: 0h:3m:44s (0h:12m:30s left)
Optimizing NNI: done in 1.43683 secs using 399.1% CPU
Optimizing NNI: done in 2.25658 secs using 398.5% CPU
Optimizing NNI: done in 1.67022 secs using 399% CPU
Optimizing NNI: done in 2.72417 secs using 398% CPU
Optimizing NNI: done in 1.23131 secs using 398.9% CPU
Optimizing NNI: done in 4.72528 secs using 597.5% CPU
Optimizing NNI: done in 1.46678 secs using 399% CPU
Optimizing NNI: done in 1.90871 secs using 398.7% CPU
Optimizing NNI: done in 1.39923 secs using 398.6% CPU
Optimizing NNI: done in 1.49552 secs using 399.1% CPU
Optimizing NNI: done in 2.83 secs using 398.8% CPU
Optimizing NNI: done in 4.67302 secs using 597.4% CPU
Optimizing NNI: done in 1.38334 secs using 399.3% CPU
Optimizing NNI: done in 1.85272 secs using 397.9% CPU
Optimizing NNI: done in 1.28747 secs using 398.6% CPU
Optimizing NNI: done in 1.38777 secs using 399.1% CPU
Optimizing NNI: done in 1.99559 secs using 398.9% CPU
Optimizing NNI: done in 4.39717 secs using 597.7% CPU
Optimizing NNI: done in 1.47455 secs using 399.1% CPU
Iteration 230 / LogL: -58628.563 / Time: 0h:6m:16s (0h:0m:-2s left)
TREE SEARCH COMPLETED AFTER 230 ITERATIONS / Time: 0h:6m:16s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58626.873
Optimal log-likelihood: -58626.868
Site proportion and rates:  (0.133,0.081) (0.089,0.198) (0.189,0.370) (0.186,0.604) (0.122,0.963) (0.119,1.540) (0.134,2.390) (0.028,6.045)
Parameters optimization took 1 rounds (0.646 sec)
BEST SCORE FOUND : -58626.868
Total tree length: 44.747

Total number of iterations: 230
CPU time used for tree search: 1449.486 sec (0h:24m:9s)
Wall-clock time used for tree search: 367.078 sec (0h:6m:7s)
Total CPU time used: 1490.858 sec (0h:24m:50s)
Total wall-clock time used: 377.430 sec (0h:6m:17s)

===> START BOOTSTRAP REPLICATE NUMBER 71

Creating bootstrap alignment (seed: 67533)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 60 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60251.228
Optimizing NNI: done in 2.53434 secs using 398.8% CPU
2. Current log-likelihood: -59701.682
3. Current log-likelihood: -59692.365
Optimizing NNI: done in 1.83325 secs using 399% CPU
4. Current log-likelihood: -59689.286
Optimizing NNI: done in 3.72462 secs using 597.8% CPU
5. Current log-likelihood: -59672.224
Optimizing NNI: done in 1.66607 secs using 398.7% CPU
6. Current log-likelihood: -59664.490
7. Current log-likelihood: -59660.802
8. Current log-likelihood: -59659.464
Optimizing NNI: done in 2.50063 secs using 398.3% CPU
Iteration 20 / LogL: -104714.756 / Time: 0h:1m:39s
Finish initializing candidate tree set (20)
Current best tree score: -104679.739 / CPU time: 85.664
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
9. Current log-likelihood: -59658.959
Optimizing NNI: done in 4.11704 secs using 597.6% CPU
10. Current log-likelihood: -59658.705
11. Current log-likelihood: -59658.518
Optimizing NNI: done in 2.19438 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
12. Current log-likelihood: -59658.356
13. Current log-likelihood: -59658.204
14. Current log-likelihood: -59658.062
15. Current log-likelihood: -59657.931
Optimizing NNI: done in 4.08779 secs using 598.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -104660.582
16. Current log-likelihood: -59657.809
17. Current log-likelihood: -59657.696
BETTER TREE FOUND at iteration 36: -195907.669
18. Current log-likelihood: -59657.588
Optimizing NNI: done in 2.03367 secs using 398.6% CPU
19. Current log-likelihood: -59657.486
Optimal log-likelihood: -59657.329
Site proportion and rates:  (0.096,0.056) (0.114,0.193) (0.154,0.405) (0.198,0.592) (0.169,0.900) (0.149,1.630) (0.100,2.527) (0.021,6.941)
Parameters optimization took 19 rounds (14.788 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.29984 secs using 398.2% CPU
Calculating distance matrix: done in 1.08806 secs using 399.8% CPU
Computing ML distances took 1.088242 sec (of wall-clock time) 4.350196 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000403166 secs using 425.9% CPU
Constructing RapidNJ tree: done in 0.00469685 secs using 348% CPU
Computing RapidNJ tree took 0.005151 sec (of wall-clock time) 0.019688 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59703.853
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.91714 secs using 597.2% CPU
Optimizing NNI: done in 2.12834 secs using 398.5% CPU
Optimizing NNI: done in 2.78014 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
5.211 second
BETTER TREE FOUND at iteration 25: -104653.736
Optimizing NNI: done in 6.03492 secs using 597% CPU
Optimizing NNI: done in 2.26187 secs using 398.7% CPU
Computing log-likelihood of 98 initial trees ... 4.968 seconds
Current best score: -59657.329

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.994819 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.56426 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.60871 secs using 597% CPU
BETTER TREE FOUND at iteration 1: -59524.158
BETTER TREE FOUND at iteration 27: -104651.894
Optimizing NNI: done in 1.04921 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -59507.745
Optimizing NNI: done in 2.30312 secs using 398.1% CPU
Optimizing NNI: done in 0.691737 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.87259 secs using 596.4% CPU
Iteration 40 / LogL: -195949.055 / Time: 0h:4m:33s (0h:11m:11s left)
BETTER TREE FOUND at iteration 3: -59466.433
Optimizing NNI: done in 2.51792 secs using 398.7% CPU
Optimizing NNI: done in 1.29658 secs using 398.9% CPU
Optimizing NNI: done in 1.29224 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.60995 secs using 398.5% CPU
Iteration 30 / LogL: -104749.253 / Time: 0h:2m:10s (0h:7m:16s left)
Optimizing NNI: done in 4.84166 secs using 597.2% CPU
Optimizing NNI: done in 2.01343 secs using 398.3% CPU
BETTER TREE FOUND at iteration 5: -59451.083
Optimizing NNI: done in 1.2169 secs using 399.2% CPU
Optimizing NNI: done in 2.37795 secs using 398.3% CPU
Optimizing NNI: done in 1.3192 secs using 399% CPU
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Optimizing NNI: done in 1.30374 secs using 399.3% CPU
Optimizing NNI: done in 1.25367 secs using 398.7% CPU
Iteration 10 / LogL: -59553.526 / Time: 0h:0m:45s
Optimizing NNI: done in 2.02405 secs using 398.7% CPU
Optimizing NNI: done in 0.998985 secs using 399.3% CPU
Optimizing NNI: done in 5.13942 secs using 596.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.46788 secs using 398.9% CPU
Optimizing NNI: done in 2.40033 secs using 398.3% CPU
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Optimizing NNI: done in 2.07204 secs using 399% CPU
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Optimizing NNI: done in 2.68815 secs using 398.6% CPU
Optimizing NNI: done in 1.15409 secs using 399.3% CPU
BETTER TREE FOUND at iteration 43: -195886.105
Optimizing NNI: done in 1.13767 secs using 398.9% CPU
Optimizing NNI: done in 2.54653 secs using 398.5% CPU
Optimizing NNI: done in 1.37061 secs using 398.4% CPU
Optimizing NNI: done in 2.00983 secs using 398.5% CPU
Optimizing NNI: done in 1.34002 secs using 399% CPU
Iteration 20 / LogL: -59461.020 / Time: 0h:0m:58s
Finish initializing candidate tree set (20)
Current best tree score: -59451.083 / CPU time: 41.788
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 3.64245 secs using 597.8% CPU
Optimizing NNI: done in 1.48856 secs using 399.3% CPU
Optimizing NNI: done in 2.25245 secs using 398.3% CPU
Iteration 40 / LogL: -104672.295 / Time: 0h:2m:33s (0h:5m:42s left)
Optimizing NNI: done in 1.27757 secs using 398.7% CPU
Optimizing NNI: done in 1.52377 secs using 399.5% CPU
Optimizing NNI: done in 2.62897 secs using 398.6% CPU
Optimizing NNI: done in 1.3391 secs using 398.7% CPU
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Optimizing NNI: done in 2.28094 secs using 398.5% CPU
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Optimizing NNI: done in 1.30399 secs using 399.4% CPU
Optimizing NNI: done in 0.992101 secs using 398.5% CPU
Optimizing NNI: done in 2.52966 secs using 398.3% CPU
Optimizing NNI: done in 4.73765 secs using 596.9% CPU
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Optimizing NNI: done in 2.62552 secs using 398.5% CPU
Optimizing NNI: done in 1.41198 secs using 399.5% CPU
Optimizing NNI: done in 1.45271 secs using 399.1% CPU
Iteration 30 / LogL: -59478.952 / Time: 0h:1m:11s (0h:3m:5s left)
Optimizing NNI: done in 2.16058 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.32507 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.93143 secs using 596.6% CPU
BETTER TREE FOUND at iteration 31: -59444.162
BETTER TREE FOUND at iteration 45: -104649.310
Optimizing NNI: done in 1.24447 secs using 399.2% CPU
Optimizing NNI: done in 1.31121 secs using 399.3% CPU
Optimizing NNI: done in 2.15006 secs using 398.7% CPU
Optimizing NNI: done in 4.4393 secs using 597.4% CPU
Optimizing NNI: done in 1.23031 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.44943 secs using 398.1% CPU
BETTER TREE FOUND at iteration 34: -59441.281
Optimizing NNI: done in 1.19622 secs using 399.1% CPU
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Optimizing NNI: done in 4.55383 secs using 597.5% CPU
Optimizing NNI: done in 1.3656 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -59424.086
Optimizing NNI: done in 2.24553 secs using 398.2% CPU
Optimizing NNI: done in 1.2744 secs using 398.5% CPU
Optimizing NNI: done in 1.1914 secs using 399.5% CPU
Optimizing NNI: done in 2.61527 secs using 398.7% CPU
Iteration 50 / LogL: -104705.650 / Time: 0h:3m:0s (0h:5m:49s left)
Optimizing NNI: done in 4.79629 secs using 597.9% CPU
Iteration 50 / LogL: -195912.886 / Time: 0h:5m:27s (0h:10m:20s left)
Optimizing NNI: done in 1.1751 secs using 399.6% CPU
Optimizing NNI: done in 1.16016 secs using 398.9% CPU
Iteration 40 / LogL: -59432.633 / Time: 0h:1m:28s (0h:3m:38s left)
Optimizing NNI: done in 2.20992 secs using 398.8% CPU
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Optimizing NNI: done in 2.21604 secs using 398.7% CPU
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Optimizing NNI: done in 2.17628 secs using 398.7% CPU
Optimizing NNI: done in 1.34573 secs using 399% CPU
Optimizing NNI: done in 0.987753 secs using 399.3% CPU
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Optimizing NNI: done in 1.02815 secs using 399.5% CPU
Optimizing NNI: done in 4.14357 secs using 597.7% CPU
Optimizing NNI: done in 1.19805 secs using 398.9% CPU
Optimizing NNI: done in 2.01288 secs using 398.7% CPU
Optimizing NNI: done in 1.25469 secs using 398.9% CPU
Optimizing NNI: done in 1.15557 secs using 399.5% CPU
Optimizing NNI: done in 2.26982 secs using 398.2% CPU
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Iteration 50 / LogL: -59431.104 / Time: 0h:1m:41s (0h:2m:57s left)
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BETTER TREE FOUND at iteration 51: -59423.606
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BETTER TREE FOUND at iteration 58: -104648.661
Optimizing NNI: done in 5.10641 secs using 597% CPU
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BETTER TREE FOUND at iteration 56: -59422.838
Optimizing NNI: done in 2.1865 secs using 398.5% CPU
Iteration 60 / LogL: -104668.183 / Time: 0h:3m:24s (0h:5m:39s left)
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Iteration 60 / LogL: -59426.028 / Time: 0h:1m:55s (0h:3m:7s left)
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BETTER TREE FOUND at iteration 63: -59422.831
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Iteration 70 / LogL: -59424.120 / Time: 0h:2m:8s (0h:2m:53s left)
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Iteration 70 / LogL: -104752.148 / Time: 0h:3m:47s (0h:4m:50s left)
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Iteration 80 / LogL: -59430.999 / Time: 0h:2m:21s (0h:2m:28s left)
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Iteration 90 / LogL: -59429.075 / Time: 0h:2m:34s (0h:2m:6s left)
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Iteration 80 / LogL: -104694.217 / Time: 0h:4m:11s (0h:4m:7s left)
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Iteration 100 / LogL: -59458.998 / Time: 0h:2m:46s (0h:1m:45s left)
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Iteration 110 / LogL: -59423.485 / Time: 0h:2m:59s (0h:1m:27s left)
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Iteration 70 / LogL: -195900.129 / Time: 0h:6m:59s (0h:7m:23s left)
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Iteration 90 / LogL: -104661.882 / Time: 0h:4m:35s (0h:3m:30s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.29652 secs using 399.3% CPU
BETTER TREE FOUND at iteration 92: -104645.550
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Iteration 120 / LogL: -59423.572 / Time: 0h:3m:12s (0h:1m:9s left)
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Iteration 130 / LogL: -59464.604 / Time: 0h:3m:24s (0h:0m:52s left)
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Iteration 100 / LogL: -104651.136 / Time: 0h:4m:59s (0h:4m:38s left)
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BETTER TREE FOUND at iteration 140: -59422.830
Iteration 140 / LogL: -59422.830 / Time: 0h:3m:36s (0h:2m:35s left)
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Iteration 80 / LogL: -195961.392 / Time: 0h:7m:45s (0h:6m:10s left)
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Iteration 110 / LogL: -104699.720 / Time: 0h:5m:22s (0h:4m:2s left)
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Iteration 160 / LogL: -59423.995 / Time: 0h:4m:1s (0h:2m:1s left)
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Iteration 120 / LogL: -104653.363 / Time: 0h:5m:44s (0h:3m:28s left)
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Iteration 170 / LogL: -59496.869 / Time: 0h:4m:14s (0h:1m:45s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 126: -104645.230
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Iteration 180 / LogL: -59440.626 / Time: 0h:4m:26s (0h:1m:29s left)
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Iteration 90 / LogL: -195915.129 / Time: 0h:8m:31s (0h:5m:4s left)
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Iteration 200 / LogL: -59448.414 / Time: 0h:4m:52s (0h:0m:58s left)
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Iteration 210 / LogL: -59429.074 / Time: 0h:5m:5s (0h:0m:43s left)
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Iteration 220 / LogL: -59425.011 / Time: 0h:5m:18s (0h:0m:29s left)
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Iteration 240 / LogL: -59483.957 / Time: 0h:5m:43s (0h:0m:0s left)
Optimizing NNI: done in 1.21249 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 241 ITERATIONS / Time: 0h:5m:44s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59422.830
Optimizing NNI: done in 2.39833 secs using 398.8% CPU
Iteration 160 / LogL: -104675.524 / Time: 0h:7m:18s (0h:3m:1s left)
2. Current log-likelihood: -59422.801
3. Current log-likelihood: -59422.785
4. Current log-likelihood: -59422.759
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5. Current log-likelihood: -59422.744
6. Current log-likelihood: -59422.729
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7. Current log-likelihood: -59422.715
8. Current log-likelihood: -59422.702
9. Current log-likelihood: -59422.688
10. Current log-likelihood: -59422.676
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11. Current log-likelihood: -59422.661
12. Current log-likelihood: -59422.648
13. Current log-likelihood: -59422.635
14. Current log-likelihood: -59422.623
15. Current log-likelihood: -59422.609
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16. Current log-likelihood: -59422.597
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17. Current log-likelihood: -59422.585
18. Current log-likelihood: -59422.572
19. Current log-likelihood: -59422.560
20. Current log-likelihood: -59422.549
21. Current log-likelihood: -59422.538
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22. Current log-likelihood: -59422.527
23. Current log-likelihood: -59422.516
24. Current log-likelihood: -59422.505
25. Current log-likelihood: -59422.494
26. Current log-likelihood: -59422.482
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27. Current log-likelihood: -59422.471
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28. Current log-likelihood: -59422.461
29. Current log-likelihood: -59422.451
30. Current log-likelihood: -59422.438
31. Current log-likelihood: -59422.428
32. Current log-likelihood: -59422.418
Optimizing NNI: done in 2.30362 secs using 398.4% CPU
Optimal log-likelihood: -59422.403
Site proportion and rates:  (0.093,0.050) (0.117,0.188) (0.138,0.400) (0.200,0.569) (0.176,0.885) (0.124,1.525) (0.130,2.419) (0.021,6.892)
Parameters optimization took 32 rounds (14.541 sec)
BEST SCORE FOUND : -59422.403
Total tree length: 45.299

Total number of iterations: 241
CPU time used for tree search: 1294.213 sec (0h:21m:34s)
Wall-clock time used for tree search: 328.181 sec (0h:5m:28s)
Total CPU time used: 1417.781 sec (0h:23m:37s)
Total wall-clock time used: 359.166 sec (0h:5m:59s)

===> START BOOTSTRAP REPLICATE NUMBER 72

Creating bootstrap alignment (seed: 67534)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.058 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -56962.224
2. Current log-likelihood: -56433.514
3. Current log-likelihood: -56425.091
Optimizing NNI: done in 2.15882 secs using 398.3% CPU
Optimizing NNI: done in 4.53815 secs using 597.9% CPU
4. Current log-likelihood: -56413.628
5. Current log-likelihood: -56386.836
Optimizing NNI: done in 2.36473 secs using 398.3% CPU
6. Current log-likelihood: -56385.157
Optimal log-likelihood: -56385.103
Site proportion and rates:  (0.106,0.061) (0.140,0.185) (0.115,0.371) (0.106,0.498) (0.177,0.779) (0.171,1.251) (0.150,2.258) (0.035,5.163)
Parameters optimization took 6 rounds (5.182 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.08453 secs using 399.7% CPU
Computing ML distances took 1.084718 sec (of wall-clock time) 4.335184 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000368118 secs using 421.9% CPU
Constructing RapidNJ tree: done in 0.00441408 secs using 343.9% CPU
Computing RapidNJ tree took 0.004850 sec (of wall-clock time) 0.017457 sec (of CPU time)
Optimizing NNI: done in 2.2495 secs using 398.4% CPU
Optimizing NNI: done in 4.71973 secs using 597.4% CPU
Iteration 110 / LogL: -195937.657 / Time: 0h:10m:5s (0h:3m:3s left)
Log-likelihood of RapidNJ tree: -56440.535
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.08826 secs using 398.3% CPU
Iteration 170 / LogL: -104655.824 / Time: 0h:7m:41s (0h:2m:32s left)
Optimizing NNI: done in 2.52992 secs using 398.4% CPU
5.044 second
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Computing log-likelihood of 98 initial trees ... 5.104 seconds
Current best score: -56385.103

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -56254.312
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -56245.278 / Time: 0h:1m:9s
Finish initializing candidate tree set (20)
Current best tree score: -56190.961 / CPU time: 62.133
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 50 / LogL: -56182.677 / Time: 0h:2m:3s (0h:4m:12s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 110: -56178.088
Iteration 110 / LogL: -56178.088 / Time: 0h:3m:35s (0h:3m:17s left)
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UPDATE BEST LOG-LIKELIHOOD: -56178.079
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 177: -56177.739
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TREE SEARCH COMPLETED AFTER 300 ITERATIONS / Time: 0h:12m:53s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -104644.563
Optimal log-likelihood: -104644.552
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.099,0.039) (0.061,0.123) (0.131,0.228) (0.147,0.401) (0.118,0.636) (0.091,0.994) (0.160,1.504) (0.108,2.177) (0.052,4.986)
Parameters optimization took 1 rounds (0.806 sec)
BEST SCORE FOUND : -104644.552
Total tree length: 158.116

Total number of iterations: 300
CPU time used for tree search: 2992.107 sec (0h:49m:52s)
Wall-clock time used for tree search: 758.919 sec (0h:12m:38s)
Total CPU time used: 3052.677 sec (0h:50m:52s)
Total wall-clock time used: 774.079 sec (0h:12m:54s)

===> START BOOTSTRAP REPLICATE NUMBER 27

Creating bootstrap alignment (seed: 68209)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.103 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 109 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -108879.526
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2. Current log-likelihood: -106823.201
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4. Current log-likelihood: -106731.150
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5. Current log-likelihood: -106730.392
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6. Current log-likelihood: -106729.831
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7. Current log-likelihood: -106729.387
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Iteration 190 / LogL: -56183.010 / Time: 0h:5m:32s (0h:2m:33s left)
8. Current log-likelihood: -106729.027
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9. Current log-likelihood: -106728.732
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10. Current log-likelihood: -106728.487
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Estimate model parameters (epsilon = 0.100)
11. Current log-likelihood: -106728.351
BETTER TREE FOUND at iteration 193: -56177.476
12. Current log-likelihood: -106728.220
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13. Current log-likelihood: -106728.106
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14. Current log-likelihood: -106728.006
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Optimal log-likelihood: -106727.867
Proportion of invariable sites: 0.020
Site proportion and rates:  (0.112,0.034) (0.098,0.111) (0.074,0.216) (0.054,0.281) (0.072,0.377) (0.111,0.604) (0.144,0.996) (0.241,1.765) (0.075,3.886)
Parameters optimization took 14 rounds (20.375 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 4.89747 secs using 399.9% CPU
Computing ML distances took 4.897748 sec (of wall-clock time) 19.585496 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000756979 secs using 404.5% CPU
Constructing RapidNJ tree: done in 0.00875497 secs using 367.5% CPU
Computing RapidNJ tree took 0.009579 sec (of wall-clock time) 0.037474 sec (of CPU time)
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Iteration 200 / LogL: -56189.383 / Time: 0h:5m:47s (0h:2m:42s left)
Log-likelihood of RapidNJ tree: -106807.067
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.4752 secs using 398.6% CPU
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10.880 second
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Iteration 210 / LogL: -56194.697 / Time: 0h:6m:2s (0h:2m:23s left)
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Computing log-likelihood of 98 initial trees ... 10.124 seconds
Current best score: -106727.867

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -106069.623
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 221: -56177.466
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BETTER TREE FOUND at iteration 2: -106065.147
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Iteration 230 / LogL: -56197.335 / Time: 0h:6m:31s (0h:2m:35s left)
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UPDATE BEST LOG-LIKELIHOOD: -56177.462
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Iteration 240 / LogL: -56178.009 / Time: 0h:6m:46s (0h:2m:17s left)
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Iteration 10 / LogL: -106111.938 / Time: 0h:1m:27s
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Iteration 250 / LogL: -56185.136 / Time: 0h:7m:1s (0h:2m:0s left)
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UPDATE BEST LOG-LIKELIHOOD: -56177.462
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Iteration 20 / LogL: -106369.591 / Time: 0h:1m:58s
Finish initializing candidate tree set (20)
Current best tree score: -106054.443 / CPU time: 92.007
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 300 / LogL: -56179.207 / Time: 0h:8m:15s (0h:0m:34s left)
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BETTER TREE FOUND at iteration 40: -106019.447
Iteration 40 / LogL: -106019.447 / Time: 0h:2m:55s (0h:7m:29s left)
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Iteration 310 / LogL: -56184.636 / Time: 0h:8m:30s (0h:0m:18s left)
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Iteration 50 / LogL: -106039.367 / Time: 0h:3m:20s (0h:6m:31s left)
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Iteration 320 / LogL: -56183.292 / Time: 0h:8m:44s (0h:0m:1s left)
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TREE SEARCH COMPLETED AFTER 322 ITERATIONS / Time: 0h:8m:46s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -56177.462
Optimizing NNI: done in 2.19856 secs using 398.1% CPU
2. Current log-likelihood: -56177.431
3. Current log-likelihood: -56177.416
4. Current log-likelihood: -56177.384
Optimizing NNI: done in 4.48192 secs using 597.7% CPU
Optimizing NNI: done in 1.66357 secs using 398.9% CPU
5. Current log-likelihood: -56177.352
6. Current log-likelihood: -56177.323
7. Current log-likelihood: -56177.305
Optimizing NNI: done in 1.98986 secs using 398.6% CPU
8. Current log-likelihood: -56177.273
9. Current log-likelihood: -56177.244
10. Current log-likelihood: -56177.227
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Iteration 220 / LogL: -195902.167 / Time: 0h:18m:51s (0h:2m:29s left)
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11. Current log-likelihood: -56177.198
12. Current log-likelihood: -56177.183
13. Current log-likelihood: -56177.164
14. Current log-likelihood: -56177.146
Optimizing NNI: done in 2.13789 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
15. Current log-likelihood: -56177.115
16. Current log-likelihood: -56177.100
17. Current log-likelihood: -56177.084
BETTER TREE FOUND at iteration 57: -106007.601
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18. Current log-likelihood: -56177.067
19. Current log-likelihood: -56177.051
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23. Current log-likelihood: -56176.974
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25. Current log-likelihood: -56176.928
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26. Current log-likelihood: -56176.916
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28. Current log-likelihood: -56176.887
Optimizing NNI: done in 1.98874 secs using 398.7% CPU
Iteration 60 / LogL: -106175.515 / Time: 0h:3m:42s (0h:6m:5s left)
29. Current log-likelihood: -56176.871
30. Current log-likelihood: -56176.857
31. Current log-likelihood: -56176.842
32. Current log-likelihood: -56176.828
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34. Current log-likelihood: -56176.798
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36. Current log-likelihood: -56176.770
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39. Current log-likelihood: -56176.731
40. Current log-likelihood: -56176.716
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Optimizing NNI: done in 4.49568 secs using 598.1% CPU
44. Current log-likelihood: -56176.671
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45. Current log-likelihood: -56176.660
46. Current log-likelihood: -56176.646
47. Current log-likelihood: -56176.635
Optimizing NNI: done in 1.64346 secs using 398.9% CPU
48. Current log-likelihood: -56176.625
49. Current log-likelihood: -56176.611
50. Current log-likelihood: -56176.600
Optimizing NNI: done in 1.66356 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
51. Current log-likelihood: -56176.590
Optimizing NNI: done in 4.35276 secs using 597.4% CPU
52. Current log-likelihood: -56176.577
Optimal log-likelihood: -56176.561
Site proportion and rates:  (0.086,0.052) (0.148,0.155) (0.189,0.375) (0.202,0.708) (0.173,1.158) (0.132,2.010) (0.043,2.878) (0.027,6.311)
Parameters optimization took 52 rounds (29.756 sec)
BEST SCORE FOUND : -56176.561
Total tree length: 43.324

Total number of iterations: 322
CPU time used for tree search: 2059.910 sec (0h:34m:19s)
Wall-clock time used for tree search: 520.061 sec (0h:8m:40s)
Total CPU time used: 2206.151 sec (0h:36m:46s)
Total wall-clock time used: 556.731 sec (0h:9m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 73

Creating bootstrap alignment (seed: 67535)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61271.020
2. Current log-likelihood: -60668.005
BETTER TREE FOUND at iteration 66: -106006.578
3. Current log-likelihood: -60659.679
4. Current log-likelihood: -60643.238
Optimizing NNI: done in 1.99517 secs using 398.7% CPU
5. Current log-likelihood: -60620.523
Optimizing NNI: done in 4.60329 secs using 597.6% CPU
6. Current log-likelihood: -60619.058
Optimal log-likelihood: -60618.985
Site proportion and rates:  (0.104,0.058) (0.114,0.182) (0.117,0.354) (0.107,0.570) (0.183,0.744) (0.183,1.197) (0.158,2.208) (0.034,4.950)
Parameters optimization took 6 rounds (4.982 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.13965 secs using 398.7% CPU
Calculating distance matrix: done in 1.10413 secs using 399.9% CPU
Computing ML distances took 1.104306 sec (of wall-clock time) 4.415433 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000329971 secs using 388.2% CPU
Constructing RapidNJ tree: done in 0.00442791 secs using 259.7% CPU
Computing RapidNJ tree took 0.004817 sec (of wall-clock time) 0.014328 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60544.607
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.94319 secs using 398.5% CPU
Optimizing NNI: done in 4.98743 secs using 596.8% CPU
Optimizing NNI: done in 1.9282 secs using 399.2% CPU
Iteration 70 / LogL: -106283.426 / Time: 0h:4m:4s (0h:5m:40s left)
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4.905 second
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Optimizing NNI: done in 1.81826 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Computing log-likelihood of 98 initial trees ... 5.117 seconds
Current best score: -60376.706

Do NNI search on 20 best initial trees
BETTER TREE FOUND at iteration 73: -106004.083
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -60170.925
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Iteration 230 / LogL: -195883.246 / Time: 0h:19m:38s (0h:1m:37s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 5: -60149.737
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Iteration 80 / LogL: -106009.617 / Time: 0h:4m:28s (0h:5m:15s left)
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Iteration 10 / LogL: -60211.013 / Time: 0h:0m:35s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 83: -106003.154
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Iteration 20 / LogL: -60266.054 / Time: 0h:0m:48s
Finish initializing candidate tree set (20)
Current best tree score: -60149.737 / CPU time: 41.733
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Iteration 90 / LogL: -106096.990 / Time: 0h:4m:51s (0h:5m:4s left)
BETTER TREE FOUND at iteration 25: -60148.601
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 26: -60141.064
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 27: -60139.796
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Iteration 30 / LogL: -60139.994 / Time: 0h:1m:7s (0h:3m:45s left)
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Iteration 240 / LogL: -195893.674 / Time: 0h:20m:26s (0h:0m:46s left)
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Iteration 100 / LogL: -106045.310 / Time: 0h:5m:12s (0h:4m:21s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 40: -60137.410
Iteration 40 / LogL: -60137.410 / Time: 0h:1m:22s (0h:3m:32s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 110 / LogL: -106027.484 / Time: 0h:5m:31s (0h:3m:42s left)
BETTER TREE FOUND at iteration 49: -60133.589
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Iteration 50 / LogL: -60140.586 / Time: 0h:1m:39s (0h:3m:19s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 57: -60130.468
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Iteration 60 / LogL: -60138.656 / Time: 0h:1m:54s (0h:3m:8s left)
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Iteration 120 / LogL: -106014.920 / Time: 0h:5m:51s (0h:3m:6s left)
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Iteration 250 / LogL: -195923.849 / Time: 0h:21m:12s (0h:0m:-6s left)
TREE SEARCH COMPLETED AFTER 250 ITERATIONS / Time: 0h:21m:12s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -195874.539
Optimizing NNI: done in 1.61016 secs using 399.2% CPU
Optimal log-likelihood: -195874.539
Site proportion and rates:  (0.010,0.093) (0.071,0.235) (0.115,0.373) (0.141,0.511) (0.179,0.653) (0.210,0.971) (0.165,1.598) (0.109,2.591)
Parameters optimization took 1 rounds (0.490 sec)
BEST SCORE FOUND : -195874.539
Total tree length: 159.149

Total number of iterations: 250
CPU time used for tree search: 7292.788 sec (2h:1m:32s)
Wall-clock time used for tree search: 1246.419 sec (0h:20m:46s)
Total CPU time used: 7453.255 sec (2h:4m:13s)
Total wall-clock time used: 1273.344 sec (0h:21m:13s)

===> START BOOTSTRAP REPLICATE NUMBER 19

Creating bootstrap alignment (seed: 70482)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.317 seconds

NOTE: 230 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.07688 secs using 398.8% CPU
1. Initial log-likelihood: -199290.906
Optimizing NNI: done in 1.45646 secs using 398.7% CPU
Optimizing NNI: done in 2.0963 secs using 398.9% CPU
Optimizing NNI: done in 1.36032 secs using 399.3% CPU
2. Current log-likelihood: -196794.766
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3. Current log-likelihood: -196776.760
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4. Current log-likelihood: -196775.971
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5. Current log-likelihood: -196774.997
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6. Current log-likelihood: -196773.177
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Iteration 70 / LogL: -60138.001 / Time: 0h:2m:9s (0h:2m:43s left)
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7. Current log-likelihood: -196769.894
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8. Current log-likelihood: -196766.345
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9. Current log-likelihood: -196764.703
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Iteration 130 / LogL: -106017.306 / Time: 0h:6m:11s (0h:2m:32s left)
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10. Current log-likelihood: -196764.232
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11. Current log-likelihood: -196764.114
Optimizing NNI: done in 1.3006 secs using 399.1% CPU
Optimizing NNI: done in 2.34513 secs using 399% CPU
Optimal log-likelihood: -196764.093
Site proportion and rates:  (0.012,0.098) (0.066,0.266) (0.133,0.382) (0.178,0.558) (0.166,0.766) (0.168,1.001) (0.145,1.520) (0.132,2.393)
Parameters optimization took 11 rounds (22.956 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 80 / LogL: -60149.679 / Time: 0h:2m:22s (0h:2m:18s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 81: -60128.909
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BETTER TREE FOUND at iteration 134: -106001.460
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Calculating distance matrix: done in 10.303 secs using 599.9% CPU
Computing ML distances took 10.303589 sec (of wall-clock time) 61.809113 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00134301 secs using 687.3% CPU
Constructing RapidNJ tree: done in 0.0217791 secs using 671.7% CPU
Computing RapidNJ tree took 0.023212 sec (of wall-clock time) 0.157301 sec (of CPU time)
Optimizing NNI: done in 1.31789 secs using 398.8% CPU
Optimizing NNI: done in 1.85959 secs using 398.6% CPU
Optimizing NNI: done in 1.29015 secs using 398.9% CPU
Log-likelihood of RapidNJ tree: -200650.563
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.87297 secs using 398.8% CPU
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Iteration 90 / LogL: -60137.930 / Time: 0h:2m:38s (0h:2m:42s left)
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Iteration 140 / LogL: -106042.733 / Time: 0h:6m:35s (0h:4m:27s left)
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Iteration 100 / LogL: -60133.938 / Time: 0h:2m:51s (0h:2m:20s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 102: -60126.662
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30.073 second
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Iteration 150 / LogL: -106015.812 / Time: 0h:7m:0s (0h:3m:56s left)
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Computing log-likelihood of 98 initial trees ... 15.981 seconds
Current best score: -196764.093

Do NNI search on 20 best initial trees
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Iteration 120 / LogL: -60126.996 / Time: 0h:3m:20s (0h:2m:18s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -196013.205
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Iteration 130 / LogL: -60127.238 / Time: 0h:3m:34s (0h:1m:59s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 166: -106000.979
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Estimate model parameters (epsilon = 0.100)
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Iteration 10 / LogL: -196127.838 / Time: 0h:2m:9s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 160: -60117.303
Iteration 160 / LogL: -60117.303 / Time: 0h:4m:17s (0h:2m:41s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 190 / LogL: -106010.719 / Time: 0h:8m:24s (0h:3m:22s left)
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Iteration 170 / LogL: -60120.084 / Time: 0h:4m:35s (0h:2m:34s left)
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Iteration 200 / LogL: -106023.200 / Time: 0h:8m:44s (0h:2m:53s left)
Optimizing NNI: done in 4.09903 secs using 595.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.31597 secs using 398.6% CPU
Iteration 180 / LogL: -60116.792 / Time: 0h:4m:50s (0h:2m:17s left)
Optimizing NNI: done in 1.57025 secs using 398.7% CPU
Optimizing NNI: done in 2.2216 secs using 398.8% CPU
BETTER TREE FOUND at iteration 20: -196009.744
Iteration 20 / LogL: -196009.744 / Time: 0h:2m:54s
Finish initializing candidate tree set (20)
Current best tree score: -196009.744 / CPU time: 137.812
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 21: -196005.877
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BETTER TREE FOUND at iteration 189: -60112.218
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Iteration 190 / LogL: -60114.961 / Time: 0h:5m:5s (0h:2m:40s left)
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BETTER TREE FOUND at iteration 191: -60111.811
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Iteration 210 / LogL: -106009.423 / Time: 0h:9m:4s (0h:2m:25s left)
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BETTER TREE FOUND at iteration 23: -195982.516
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Iteration 200 / LogL: -60113.852 / Time: 0h:5m:21s (0h:2m:26s left)
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Iteration 220 / LogL: -106021.365 / Time: 0h:9m:25s (0h:1m:58s left)
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Iteration 210 / LogL: -60129.815 / Time: 0h:5m:36s (0h:2m:10s left)
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BETTER TREE FOUND at iteration 28: -195978.580
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BETTER TREE FOUND at iteration 225: -105999.570
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Iteration 30 / LogL: -195992.115 / Time: 0h:3m:50s (0h:12m:59s left)
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Iteration 230 / LogL: -60120.509 / Time: 0h:6m:7s (0h:1m:37s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 34: -195946.262
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Iteration 240 / LogL: -106046.316 / Time: 0h:10m:8s (0h:3m:36s left)
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Iteration 240 / LogL: -60112.584 / Time: 0h:6m:22s (0h:1m:21s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 249: -105998.739
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Iteration 250 / LogL: -106010.326 / Time: 0h:10m:31s (0h:4m:11s left)
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Iteration 250 / LogL: -60134.458 / Time: 0h:6m:38s (0h:1m:5s left)
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Iteration 40 / LogL: -196025.718 / Time: 0h:4m:43s (0h:11m:21s left)
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Iteration 260 / LogL: -60124.050 / Time: 0h:6m:53s (0h:0m:49s left)
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Iteration 260 / LogL: -106021.922 / Time: 0h:10m:52s (0h:3m:44s left)
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BETTER TREE FOUND at iteration 264: -60111.806
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Iteration 270 / LogL: -60123.897 / Time: 0h:7m:8s (0h:2m:29s left)
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BETTER TREE FOUND at iteration 274: -60111.805
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Iteration 270 / LogL: -106000.469 / Time: 0h:11m:11s (0h:3m:17s left)
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Iteration 280 / LogL: -60117.470 / Time: 0h:7m:23s (0h:2m:29s left)
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Iteration 50 / LogL: -196142.493 / Time: 0h:5m:34s (0h:9m:32s left)
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Iteration 280 / LogL: -106023.617 / Time: 0h:11m:31s (0h:2m:50s left)
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Iteration 290 / LogL: -60136.859 / Time: 0h:7m:38s (0h:2m:13s left)
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Iteration 300 / LogL: -60124.170 / Time: 0h:7m:54s (0h:1m:57s left)
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Iteration 290 / LogL: -106010.785 / Time: 0h:11m:50s (0h:2m:25s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 291: -105997.738
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Iteration 310 / LogL: -60116.133 / Time: 0h:8m:9s (0h:1m:41s left)
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Iteration 320 / LogL: -60131.511 / Time: 0h:8m:24s (0h:1m:25s left)
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Iteration 70 / LogL: -195971.026 / Time: 0h:7m:10s (0h:6m:38s left)
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Iteration 350 / LogL: -60156.405 / Time: 0h:9m:9s (0h:0m:37s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 327: -105997.414
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Iteration 370 / LogL: -60117.902 / Time: 0h:9m:40s (0h:0m:6s left)
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Iteration 340 / LogL: -106008.330 / Time: 0h:13m:36s (0h:3m:29s left)
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TREE SEARCH COMPLETED AFTER 375 ITERATIONS / Time: 0h:9m:48s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60111.805
Optimizing NNI: done in 1.94611 secs using 398.8% CPU
2. Current log-likelihood: -60111.789
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3. Current log-likelihood: -60111.777
4. Current log-likelihood: -60111.764
5. Current log-likelihood: -60111.753
6. Current log-likelihood: -60111.741
Optimizing NNI: done in 1.91883 secs using 398.6% CPU
7. Current log-likelihood: -60111.730
8. Current log-likelihood: -60111.719
9. Current log-likelihood: -60111.708
10. Current log-likelihood: -60111.698
11. Current log-likelihood: -60111.687
Optimizing NNI: done in 1.86839 secs using 398.6% CPU
12. Current log-likelihood: -60111.677
13. Current log-likelihood: -60111.667
Optimizing NNI: done in 4.19781 secs using 597.6% CPU
Optimal log-likelihood: -60111.652
Site proportion and rates:  (0.091,0.053) (0.125,0.169) (0.125,0.352) (0.135,0.568) (0.209,0.834) (0.133,1.346) (0.147,2.251) (0.033,5.018)
Parameters optimization took 13 rounds (5.052 sec)
BEST SCORE FOUND : -60111.652
Total tree length: 46.329

Total number of iterations: 375
CPU time used for tree search: 2306.737 sec (0h:38m:26s)
Wall-clock time used for tree search: 581.817 sec (0h:9m:41s)
Total CPU time used: 2353.263 sec (0h:39m:13s)
Total wall-clock time used: 593.461 sec (0h:9m:53s)

===> START BOOTSTRAP REPLICATE NUMBER 74

Creating bootstrap alignment (seed: 67536)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.059 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58759.091
Optimizing NNI: done in 1.73612 secs using 399.2% CPU
2. Current log-likelihood: -58194.155
3. Current log-likelihood: -58181.370
4. Current log-likelihood: -58173.561
Optimizing NNI: done in 1.96831 secs using 398.9% CPU
5. Current log-likelihood: -58167.555
6. Current log-likelihood: -58162.070
Optimizing NNI: done in 4.35545 secs using 597.6% CPU
Iteration 80 / LogL: -195979.950 / Time: 0h:7m:59s (0h:5m:27s left)
Optimizing NNI: done in 2.00066 secs using 398.6% CPU
7. Current log-likelihood: -58161.628
Optimal log-likelihood: -58161.573
Site proportion and rates:  (0.107,0.064) (0.086,0.194) (0.162,0.367) (0.056,0.487) (0.273,0.787) (0.141,1.366) (0.149,2.379) (0.026,4.875)
Parameters optimization took 7 rounds (5.421 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.06388 secs using 399.9% CPU
Computing ML distances took 1.064059 sec (of wall-clock time) 4.254493 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000368118 secs using 420.8% CPU
Constructing RapidNJ tree: done in 0.00439692 secs using 347.3% CPU
Computing RapidNJ tree took 0.004820 sec (of wall-clock time) 0.017375 sec (of CPU time)
Optimizing NNI: done in 2.05079 secs using 398.7% CPU
Iteration 350 / LogL: -106000.304 / Time: 0h:13m:55s (0h:3m:4s left)
Log-likelihood of RapidNJ tree: -58099.284
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.05264 secs using 399% CPU
Optimizing NNI: done in 4.63157 secs using 597.4% CPU
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5.132 second
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Computing log-likelihood of 98 initial trees ... 5.160 seconds
Current best score: -58073.991

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -57799.979
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Iteration 360 / LogL: -106045.112 / Time: 0h:14m:15s (0h:2m:39s left)
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Iteration 10 / LogL: -57818.251 / Time: 0h:0m:34s
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Iteration 370 / LogL: -106015.689 / Time: 0h:14m:35s (0h:2m:15s left)
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Iteration 20 / LogL: -57921.031 / Time: 0h:0m:48s
Finish initializing candidate tree set (20)
Current best tree score: -57799.979 / CPU time: 41.083
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 90 / LogL: -195959.489 / Time: 0h:8m:50s (0h:4m:22s left)
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Iteration 30 / LogL: -57814.330 / Time: 0h:1m:3s (0h:2m:35s left)
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Iteration 380 / LogL: -106001.489 / Time: 0h:14m:56s (0h:1m:51s left)
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Iteration 40 / LogL: -57825.598 / Time: 0h:1m:17s (0h:2m:1s left)
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Iteration 390 / LogL: -105999.999 / Time: 0h:15m:17s (0h:1m:27s left)
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Iteration 50 / LogL: -57824.331 / Time: 0h:1m:31s (0h:1m:35s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 55: -57792.844
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Iteration 100 / LogL: -195977.850 / Time: 0h:9m:39s (0h:3m:18s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 58: -57788.425
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -57788.357
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 127: -195942.573
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Iteration 160 / LogL: -57827.002 / Time: 0h:4m:2s (0h:0m:7s left)
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TREE SEARCH COMPLETED AFTER 166 ITERATIONS / Time: 0h:4m:10s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57788.357
Optimizing NNI: done in 1.99706 secs using 398.7% CPU
2. Current log-likelihood: -57788.339
3. Current log-likelihood: -57788.326
4. Current log-likelihood: -57788.314
Optimizing NNI: done in 2.07474 secs using 399% CPU
Iteration 470 / LogL: -106002.781 / Time: 0h:18m:1s (0h:2m:6s left)
5. Current log-likelihood: -57788.301
6. Current log-likelihood: -57788.289
Optimizing NNI: done in 4.9592 secs using 596.9% CPU
Iteration 130 / LogL: -195944.954 / Time: 0h:12m:9s (0h:9m:8s left)
7. Current log-likelihood: -57788.278
Optimizing NNI: done in 1.9755 secs using 399.2% CPU
Optimal log-likelihood: -57788.265
Site proportion and rates:  (0.107,0.065) (0.094,0.196) (0.186,0.367) (0.149,0.666) (0.176,0.902) (0.121,1.425) (0.142,2.452) (0.025,5.053)
Parameters optimization took 7 rounds (5.009 sec)
BEST SCORE FOUND : -57788.265
Total tree length: 41.345

Total number of iterations: 166
CPU time used for tree search: 954.747 sec (0h:15m:54s)
Wall-clock time used for tree search: 243.026 sec (0h:4m:3s)
Total CPU time used: 1003.321 sec (0h:16m:43s)
Total wall-clock time used: 255.182 sec (0h:4m:15s)

===> START BOOTSTRAP REPLICATE NUMBER 75

Creating bootstrap alignment (seed: 67537)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.058 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61559.935
2. Current log-likelihood: -61030.257
Optimizing NNI: done in 1.85761 secs using 399% CPU
3. Current log-likelihood: -61021.049
4. Current log-likelihood: -61018.727
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5. Current log-likelihood: -61017.872
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6. Current log-likelihood: -61017.423
7. Current log-likelihood: -61017.137
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8. Current log-likelihood: -61016.858
9. Current log-likelihood: -61016.377
10. Current log-likelihood: -61014.305
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11. Current log-likelihood: -61005.922
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12. Current log-likelihood: -61005.058
13. Current log-likelihood: -61004.836
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14. Current log-likelihood: -61004.652
15. Current log-likelihood: -61004.498
16. Current log-likelihood: -61004.350
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17. Current log-likelihood: -61004.204
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18. Current log-likelihood: -61004.039
19. Current log-likelihood: -61003.834
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20. Current log-likelihood: -61003.556
21. Current log-likelihood: -61003.191
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22. Current log-likelihood: -61002.717
23. Current log-likelihood: -61002.107
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24. Current log-likelihood: -61001.351
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Iteration 480 / LogL: -106000.099 / Time: 0h:18m:21s (0h:1m:43s left)
25. Current log-likelihood: -61000.502
26. Current log-likelihood: -60999.724
27. Current log-likelihood: -60999.192
Optimizing NNI: done in 2.1823 secs using 398.5% CPU
28. Current log-likelihood: -60998.920
29. Current log-likelihood: -60998.791
Optimal log-likelihood: -60998.739
Site proportion and rates:  (0.089,0.057) (0.126,0.194) (0.180,0.388) (0.216,0.718) (0.146,1.103) (0.133,1.781) (0.094,2.581) (0.016,6.725)
Parameters optimization took 29 rounds (21.525 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.79876 secs using 398.9% CPU
Optimizing NNI: done in 5.38988 secs using 597.4% CPU
Calculating distance matrix: done in 1.09284 secs using 399.9% CPU
Computing ML distances took 1.093022 sec (of wall-clock time) 4.370511 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000400066 secs using 395.2% CPU
Constructing RapidNJ tree: done in 0.00453496 secs using 385.3% CPU
Computing RapidNJ tree took 0.004992 sec (of wall-clock time) 0.020560 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60989.138
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.78418 secs using 398.5% CPU
Optimizing NNI: done in 1.71732 secs using 398.7% CPU
Optimizing NNI: done in 1.8476 secs using 398.4% CPU
5.178 second
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Optimizing NNI: done in 2.00686 secs using 398.9% CPU
Computing log-likelihood of 98 initial trees ... 5.135 seconds
Current best score: -60940.984

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 490 / LogL: -106002.741 / Time: 0h:18m:40s (0h:1m:20s left)
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BETTER TREE FOUND at iteration 1: -60747.302
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -60713.081
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Iteration 10 / LogL: -60767.068 / Time: 0h:0m:52s
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Iteration 500 / LogL: -106017.179 / Time: 0h:19m:0s (0h:0m:57s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 13: -60701.673
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Iteration 140 / LogL: -195986.219 / Time: 0h:13m:12s (0h:8m:15s left)
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Iteration 20 / LogL: -60767.927 / Time: 0h:1m:9s
Finish initializing candidate tree set (20)
Current best tree score: -60701.673 / CPU time: 46.073
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.05241 secs using 398.8% CPU
Optimizing NNI: done in 8.06212 secs using 597.5% CPU
Optimizing NNI: done in 1.68977 secs using 399% CPU
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Iteration 510 / LogL: -106180.936 / Time: 0h:19m:21s (0h:0m:34s left)
Optimizing NNI: done in 8.28351 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.48637 secs using 398.7% CPU
Optimizing NNI: done in 1.84707 secs using 398.5% CPU
BETTER TREE FOUND at iteration 142: -195938.170
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 29: -60698.568
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Iteration 30 / LogL: -60711.112 / Time: 0h:1m:26s (0h:4m:55s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 7.85699 secs using 597.5% CPU
BETTER TREE FOUND at iteration 31: -60698.102
Optimizing NNI: done in 2.23503 secs using 398.6% CPU
Optimizing NNI: done in 1.46493 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -60693.278
Optimizing NNI: done in 2.14984 secs using 398.4% CPU
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Iteration 520 / LogL: -106016.697 / Time: 0h:19m:41s (0h:0m:11s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 37: -60690.839
Optimizing NNI: done in 1.76305 secs using 399.2% CPU
Optimizing NNI: done in 2.18216 secs using 398.8% CPU
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Iteration 40 / LogL: -60750.878 / Time: 0h:1m:46s (0h:4m:23s left)
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Optimizing NNI: done in 2.09159 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 526 ITERATIONS / Time: 0h:19m:54s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -105996.974
Optimizing NNI: done in 8.30357 secs using 597.4% CPU
2. Current log-likelihood: -105996.956
Optimizing NNI: done in 1.53855 secs using 399.1% CPU
3. Current log-likelihood: -105996.933
4. Current log-likelihood: -105996.920
5. Current log-likelihood: -105996.907
Optimizing NNI: done in 1.38032 secs using 398.4% CPU
6. Current log-likelihood: -105996.894
7. Current log-likelihood: -105996.883
Optimizing NNI: done in 1.58439 secs using 398.9% CPU
8. Current log-likelihood: -105996.871
9. Current log-likelihood: -105996.858
10. Current log-likelihood: -105996.847
Optimizing NNI: done in 1.5747 secs using 399.4% CPU
11. Current log-likelihood: -105996.836
12. Current log-likelihood: -105996.825
Optimizing NNI: done in 6.75861 secs using 598% CPU
Optimizing NNI: done in 1.36855 secs using 398.9% CPU
13. Current log-likelihood: -105996.815
14. Current log-likelihood: -105996.805
Optimizing NNI: done in 1.46393 secs using 398.8% CPU
Optimal log-likelihood: -105996.793
Proportion of invariable sites: 0.019
Site proportion and rates:  (0.104,0.029) (0.101,0.099) (0.099,0.211) (0.059,0.327) (0.050,0.391) (0.099,0.595) (0.141,0.962) (0.248,1.711) (0.079,3.883)
Parameters optimization took 14 rounds (9.231 sec)
BEST SCORE FOUND : -105996.793
Total tree length: 179.937

Total number of iterations: 526
CPU time used for tree search: 4625.112 sec (1h:17m:5s)
Wall-clock time used for tree search: 1168.107 sec (0h:19m:28s)
Total CPU time used: 4767.933 sec (1h:19m:27s)
Total wall-clock time used: 1203.910 sec (0h:20m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 28

Creating bootstrap alignment (seed: 68210)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.131 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104859.446
Optimizing NNI: done in 1.41152 secs using 398.9% CPU
Iteration 50 / LogL: -60720.056 / Time: 0h:2m:1s (0h:3m:34s left)
2. Current log-likelihood: -103001.242
Optimizing NNI: done in 1.40027 secs using 398.7% CPU
3. Current log-likelihood: -102894.620
Optimizing NNI: done in 1.43112 secs using 398.6% CPU
Optimizing NNI: done in 1.41895 secs using 398.6% CPU
4. Current log-likelihood: -102871.941
Optimizing NNI: done in 8.17935 secs using 597.3% CPU
5. Current log-likelihood: -102871.014
Optimizing NNI: done in 1.35101 secs using 399.1% CPU
6. Current log-likelihood: -102870.723
Optimizing NNI: done in 1.85182 secs using 398.9% CPU
7. Current log-likelihood: -102870.598
8. Current log-likelihood: -102870.487
Optimizing NNI: done in 1.36425 secs using 398.8% CPU
Optimal log-likelihood: -102870.344
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.110,0.044) (0.075,0.126) (0.115,0.213) (0.096,0.356) (0.077,0.515) (0.110,0.749) (0.162,1.283) (0.158,2.025) (0.068,4.057)
Parameters optimization took 8 rounds (10.990 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.37641 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 57: -60689.871
Optimizing NNI: done in 8.12558 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.39281 secs using 398.9% CPU
Calculating distance matrix: done in 4.75005 secs using 399.9% CPU
Computing ML distances took 4.750304 sec (of wall-clock time) 18.996263 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000739098 secs using 189.6% CPU
Constructing RapidNJ tree: done in 0.00883412 secs using 474.4% CPU
Computing RapidNJ tree took 0.009643 sec (of wall-clock time) 0.044969 sec (of CPU time)
Optimizing NNI: done in 1.73516 secs using 398.7% CPU
BETTER TREE FOUND at iteration 149: -195936.947
Log-likelihood of RapidNJ tree: -103020.127
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.4748 secs using 399.2% CPU
Iteration 60 / LogL: -60692.701 / Time: 0h:2m:18s (0h:3m:46s left)
Optimizing NNI: done in 1.57134 secs using 399.1% CPU
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Optimizing NNI: done in 7.59135 secs using 597.8% CPU
Iteration 150 / LogL: -195959.271 / Time: 0h:14m:35s (0h:9m:41s left)
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Optimizing NNI: done in 1.29969 secs using 399.2% CPU
10.878 second
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Optimizing NNI: done in 1.56759 secs using 399.1% CPU
Iteration 70 / LogL: -60690.761 / Time: 0h:2m:32s (0h:3m:12s left)
Optimizing NNI: done in 1.55051 secs using 399% CPU
Optimizing NNI: done in 1.36978 secs using 398.4% CPU
Optimizing NNI: done in 1.48418 secs using 398.4% CPU
Computing log-likelihood of 98 initial trees ... 9.982 seconds
Current best score: -102870.344

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.4049 secs using 399.3% CPU
Optimizing NNI: done in 1.77051 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
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Iteration 80 / LogL: -60757.674 / Time: 0h:2m:47s (0h:2m:42s left)
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BETTER TREE FOUND at iteration 1: -102418.127
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BETTER TREE FOUND at iteration 87: -60689.869
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Iteration 90 / LogL: -60694.825 / Time: 0h:3m:2s (0h:3m:18s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 99: -60689.480
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Iteration 100 / LogL: -60690.980 / Time: 0h:3m:18s (0h:3m:17s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 101: -60688.123
BETTER TREE FOUND at iteration 9: -102398.157
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Iteration 10 / LogL: -102457.477 / Time: 0h:1m:24s
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BETTER TREE FOUND at iteration 108: -60688.116
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Iteration 110 / LogL: -60704.124 / Time: 0h:3m:33s (0h:3m:12s left)
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Iteration 160 / LogL: -195950.446 / Time: 0h:15m:52s (0h:8m:53s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 120 / LogL: -60857.027 / Time: 0h:3m:48s (0h:2m:48s left)
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BETTER TREE FOUND at iteration 17: -102379.417
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Iteration 130 / LogL: -60691.091 / Time: 0h:4m:3s (0h:2m:27s left)
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Iteration 20 / LogL: -102461.316 / Time: 0h:2m:3s
Finish initializing candidate tree set (20)
Current best tree score: -102379.417 / CPU time: 106.975
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 150: -60688.006
Iteration 150 / LogL: -60688.006 / Time: 0h:4m:32s (0h:3m:3s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 170: -60686.718
Iteration 170 / LogL: -60686.718 / Time: 0h:5m:3s (0h:2m:59s left)
BETTER TREE FOUND at iteration 41: -102371.849
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Iteration 180 / LogL: -60742.503 / Time: 0h:5m:18s (0h:2m:40s left)
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Iteration 180 / LogL: -195946.324 / Time: 0h:17m:32s (0h:6m:45s left)
Optimizing NNI: done in 1.26068 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.97132 secs using 399% CPU
Iteration 50 / LogL: -102397.355 / Time: 0h:3m:23s (0h:6m:18s left)
BETTER TREE FOUND at iteration 183: -60686.469
Optimizing NNI: done in 1.21873 secs using 399% CPU
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Iteration 190 / LogL: -60709.447 / Time: 0h:5m:34s (0h:2m:44s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.4709 secs using 398.8% CPU
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Iteration 200 / LogL: -60690.300 / Time: 0h:5m:48s (0h:2m:25s left)
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BETTER TREE FOUND at iteration 60: -102369.947
Iteration 60 / LogL: -102369.947 / Time: 0h:3m:51s (0h:6m:32s left)
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Iteration 210 / LogL: -60690.699 / Time: 0h:6m:3s (0h:2m:7s left)
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Iteration 190 / LogL: -195997.479 / Time: 0h:18m:21s (0h:5m:43s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 70: -102369.178
Iteration 70 / LogL: -102369.178 / Time: 0h:4m:17s (0h:6m:12s left)
Optimizing NNI: done in 1.55636 secs using 398.9% CPU
Iteration 220 / LogL: -60707.966 / Time: 0h:6m:18s (0h:1m:48s left)
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BETTER TREE FOUND at iteration 223: -60685.932
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Iteration 230 / LogL: -60688.321 / Time: 0h:6m:34s (0h:2m:40s left)
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Iteration 80 / LogL: -102379.232 / Time: 0h:4m:38s (0h:5m:17s left)
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BETTER TREE FOUND at iteration 239: -60685.730
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Iteration 240 / LogL: -60692.502 / Time: 0h:6m:50s (0h:2m:49s left)
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Iteration 200 / LogL: -196034.619 / Time: 0h:19m:9s (0h:4m:43s left)
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Iteration 90 / LogL: -102385.615 / Time: 0h:5m:1s (0h:4m:30s left)
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Iteration 250 / LogL: -60700.028 / Time: 0h:7m:4s (0h:2m:31s left)
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Iteration 260 / LogL: -60687.430 / Time: 0h:7m:19s (0h:2m:14s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 261: -60685.699
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Iteration 100 / LogL: -102391.652 / Time: 0h:5m:22s (0h:3m:47s left)
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Iteration 270 / LogL: -60783.090 / Time: 0h:7m:34s (0h:2m:33s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 109: -102368.275
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Iteration 110 / LogL: -102392.492 / Time: 0h:5m:45s (0h:5m:14s left)
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Iteration 210 / LogL: -195985.738 / Time: 0h:19m:57s (0h:3m:43s left)
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Iteration 280 / LogL: -60685.942 / Time: 0h:7m:49s (0h:2m:16s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 115: -102363.966
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Iteration 290 / LogL: -60696.368 / Time: 0h:8m:4s (0h:1m:59s left)
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Iteration 120 / LogL: -102399.633 / Time: 0h:6m:7s (0h:4m:53s left)
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Iteration 300 / LogL: -60708.237 / Time: 0h:8m:19s (0h:1m:41s left)
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Iteration 130 / LogL: -102378.130 / Time: 0h:6m:29s (0h:4m:16s left)
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Iteration 310 / LogL: -60687.640 / Time: 0h:8m:34s (0h:1m:24s left)
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Iteration 220 / LogL: -196085.044 / Time: 0h:20m:45s (0h:2m:44s left)
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BETTER TREE FOUND at iteration 315: -60685.693
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 222: -195935.045
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Iteration 320 / LogL: -60692.982 / Time: 0h:8m:48s (0h:2m:37s left)
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Iteration 140 / LogL: -102368.119 / Time: 0h:6m:50s (0h:3m:41s left)
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UPDATE BEST LOG-LIKELIHOOD: -60685.693
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BETTER TREE FOUND at iteration 234: -195933.346
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TREE SEARCH COMPLETED AFTER 416 ITERATIONS / Time: 0h:11m:11s

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|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60685.693
Optimizing NNI: done in 2.08045 secs using 398.8% CPU
2. Current log-likelihood: -60685.682
Optimal log-likelihood: -60685.674
Site proportion and rates:  (0.089,0.056) (0.136,0.197) (0.181,0.395) (0.226,0.738) (0.152,1.170) (0.121,1.974) (0.079,2.640) (0.015,6.989)
Parameters optimization took 2 rounds (0.772 sec)
BEST SCORE FOUND : -60685.674
Total tree length: 46.303

Total number of iterations: 416
CPU time used for tree search: 2569.077 sec (0h:42m:49s)
Wall-clock time used for tree search: 647.787 sec (0h:10m:47s)
Total CPU time used: 2664.884 sec (0h:44m:24s)
Total wall-clock time used: 671.810 sec (0h:11m:11s)

===> START BOOTSTRAP REPLICATE NUMBER 76

Creating bootstrap alignment (seed: 67538)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.042 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58958.482
2. Current log-likelihood: -58429.585
Optimizing NNI: done in 2.09805 secs using 398.5% CPU
3. Current log-likelihood: -58423.571
4. Current log-likelihood: -58416.423
Optimizing NNI: done in 1.90792 secs using 398.9% CPU
Optimizing NNI: done in 4.34474 secs using 598.2% CPU
5. Current log-likelihood: -58402.332
6. Current log-likelihood: -58393.177
7. Current log-likelihood: -58392.268
Optimizing NNI: done in 2.03426 secs using 398.6% CPU
Optimal log-likelihood: -58392.228
Site proportion and rates:  (0.136,0.080) (0.030,0.184) (0.149,0.357) (0.070,0.372) (0.250,0.679) (0.187,1.228) (0.148,2.334) (0.030,5.328)
Parameters optimization took 7 rounds (5.916 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.08621 secs using 399.9% CPU
Computing ML distances took 1.086389 sec (of wall-clock time) 4.343984 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000355959 secs using 300.9% CPU
Constructing RapidNJ tree: done in 0.00439215 secs using 285.2% CPU
Computing RapidNJ tree took 0.004802 sec (of wall-clock time) 0.015267 sec (of CPU time)
Optimizing NNI: done in 2.05457 secs using 398.8% CPU
Log-likelihood of RapidNJ tree: -58529.682
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.59566 secs using 597.6% CPU
Optimizing NNI: done in 2.038 secs using 398.9% CPU
Optimizing NNI: done in 2.02609 secs using 398.3% CPU
4.940 second
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Iteration 210 / LogL: -102366.467 / Time: 0h:9m:25s (0h:0m:13s left)
Optimizing NNI: done in 2.15939 secs using 398.4% CPU
Computing log-likelihood of 98 initial trees ... 5.063 seconds
Current best score: -58391.122

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -58194.183
Optimizing NNI: done in 2.01997 secs using 398.3% CPU
Optimizing NNI: done in 0.988811 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -58183.070
Optimizing NNI: done in 2.42274 secs using 398.4% CPU
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TREE SEARCH COMPLETED AFTER 216 ITERATIONS / Time: 0h:9m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102363.966
Optimizing NNI: done in 1.14881 secs using 398.7% CPU
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2. Current log-likelihood: -102363.902
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4. Current log-likelihood: -102363.763
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Iteration 10 / LogL: -58230.082 / Time: 0h:0m:32s
5. Current log-likelihood: -102363.711
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6. Current log-likelihood: -102363.661
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10. Current log-likelihood: -102363.467
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11. Current log-likelihood: -102363.422
12. Current log-likelihood: -102363.377
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14. Current log-likelihood: -102363.291
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Iteration 20 / LogL: -58207.387 / Time: 0h:0m:43s
Finish initializing candidate tree set (20)
Current best tree score: -58183.070 / CPU time: 35.462
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
15. Current log-likelihood: -102363.249
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Iteration 260 / LogL: -195961.279 / Time: 0h:24m:6s (0h:6m:53s left)
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Estimate model parameters (epsilon = 0.100)
16. Current log-likelihood: -102363.208
BETTER TREE FOUND at iteration 21: -58181.700
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Estimate model parameters (epsilon = 0.100)
17. Current log-likelihood: -102363.165
BETTER TREE FOUND at iteration 22: -58173.104
18. Current log-likelihood: -102363.123
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19. Current log-likelihood: -102363.084
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20. Current log-likelihood: -102363.043
21. Current log-likelihood: -102363.008
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -58172.444
22. Current log-likelihood: -102362.975
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23. Current log-likelihood: -102362.938
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24. Current log-likelihood: -102362.905
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26. Current log-likelihood: -102362.865
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Estimate model parameters (epsilon = 0.100)
27. Current log-likelihood: -102362.834
BETTER TREE FOUND at iteration 29: -58169.591
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28. Current log-likelihood: -102362.803
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Iteration 30 / LogL: -58183.195 / Time: 0h:0m:59s (0h:3m:23s left)
29. Current log-likelihood: -102362.785
30. Current log-likelihood: -102362.767
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31. Current log-likelihood: -102362.748
32. Current log-likelihood: -102362.730
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -58168.523
33. Current log-likelihood: -102362.710
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34. Current log-likelihood: -102362.691
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36. Current log-likelihood: -102362.655
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Estimate model parameters (epsilon = 0.100)
38. Current log-likelihood: -102362.620
BETTER TREE FOUND at iteration 35: -58167.045
39. Current log-likelihood: -102362.603
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40. Current log-likelihood: -102362.585
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42. Current log-likelihood: -102362.551
43. Current log-likelihood: -102362.535
Optimizing NNI: done in 1.19204 secs using 398.3% CPU
44. Current log-likelihood: -102362.519
Optimizing NNI: done in 1.19153 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
45. Current log-likelihood: -102362.503
Optimizing NNI: done in 4.24211 secs using 598% CPU
BETTER TREE FOUND at iteration 39: -58166.439
46. Current log-likelihood: -102362.487
47. Current log-likelihood: -102362.471
Optimizing NNI: done in 0.919806 secs using 398.7% CPU
Iteration 40 / LogL: -58167.458 / Time: 0h:1m:12s (0h:3m:4s left)
48. Current log-likelihood: -102362.455
Optimizing NNI: done in 1.18253 secs using 398.1% CPU
49. Current log-likelihood: -102362.437
Optimizing NNI: done in 1.35327 secs using 398.7% CPU
50. Current log-likelihood: -102362.418
Optimizing NNI: done in 1.13446 secs using 398.4% CPU
51. Current log-likelihood: -102362.402
Optimizing NNI: done in 5.01909 secs using 597.6% CPU
52. Current log-likelihood: -102362.387
Optimizing NNI: done in 1.06657 secs using 399.2% CPU
53. Current log-likelihood: -102362.371
54. Current log-likelihood: -102362.355
Optimizing NNI: done in 1.34484 secs using 398.8% CPU
55. Current log-likelihood: -102362.340
56. Current log-likelihood: -102362.325
Optimizing NNI: done in 1.30519 secs using 398.8% CPU
57. Current log-likelihood: -102362.310
58. Current log-likelihood: -102362.295
Optimizing NNI: done in 4.60548 secs using 597.6% CPU
Optimizing NNI: done in 1.2425 secs using 399.3% CPU
59. Current log-likelihood: -102362.280
60. Current log-likelihood: -102362.265
Optimizing NNI: done in 1.15004 secs using 399.4% CPU
61. Current log-likelihood: -102362.250
Optimizing NNI: done in 1.22595 secs using 398.9% CPU
62. Current log-likelihood: -102362.235
63. Current log-likelihood: -102362.220
Optimizing NNI: done in 1.11778 secs using 397.6% CPU
Iteration 50 / LogL: -58181.674 / Time: 0h:1m:25s (0h:2m:34s left)
64. Current log-likelihood: -102362.206
65. Current log-likelihood: -102362.192
Optimizing NNI: done in 1.38398 secs using 399.2% CPU
66. Current log-likelihood: -102362.177
Optimizing NNI: done in 5.43041 secs using 597.4% CPU
67. Current log-likelihood: -102362.163
Optimizing NNI: done in 1.24678 secs using 399.3% CPU
68. Current log-likelihood: -102362.149
69. Current log-likelihood: -102362.136
Optimizing NNI: done in 1.25917 secs using 399.6% CPU
70. Current log-likelihood: -102362.121
71. Current log-likelihood: -102362.108
Optimizing NNI: done in 1.3951 secs using 399% CPU
72. Current log-likelihood: -102362.094
73. Current log-likelihood: -102362.080
Optimizing NNI: done in 1.2315 secs using 399.3% CPU
Optimizing NNI: done in 5.12596 secs using 597.4% CPU
Iteration 270 / LogL: -196022.977 / Time: 0h:24m:54s (0h:5m:55s left)
74. Current log-likelihood: -102362.067
75. Current log-likelihood: -102362.053
Optimizing NNI: done in 1.36946 secs using 398.8% CPU
76. Current log-likelihood: -102362.040
77. Current log-likelihood: -102362.026
Optimizing NNI: done in 1.17399 secs using 398.5% CPU
78. Current log-likelihood: -102362.013
Optimizing NNI: done in 1.10998 secs using 399.5% CPU
79. Current log-likelihood: -102361.999
80. Current log-likelihood: -102361.986
Optimizing NNI: done in 1.30449 secs using 398.8% CPU
Optimizing NNI: done in 4.54093 secs using 598% CPU
81. Current log-likelihood: -102361.973
82. Current log-likelihood: -102361.960
Optimizing NNI: done in 1.22947 secs using 399% CPU
Iteration 60 / LogL: -58174.745 / Time: 0h:1m:37s (0h:2m:10s left)
83. Current log-likelihood: -102361.947
84. Current log-likelihood: -102361.934
Optimizing NNI: done in 1.16327 secs using 399.1% CPU
85. Current log-likelihood: -102361.921
Optimizing NNI: done in 1.20213 secs using 399.6% CPU
86. Current log-likelihood: -102361.908
Optimizing NNI: done in 4.58154 secs using 597.1% CPU
87. Current log-likelihood: -102361.896
Optimizing NNI: done in 1.17068 secs using 399% CPU
88. Current log-likelihood: -102361.883
Optimizing NNI: done in 1.08923 secs using 398.8% CPU
89. Current log-likelihood: -102361.870
90. Current log-likelihood: -102361.858
Optimizing NNI: done in 1.0961 secs using 399.4% CPU
91. Current log-likelihood: -102361.846
92. Current log-likelihood: -102361.833
Optimizing NNI: done in 1.24426 secs using 398.9% CPU
93. Current log-likelihood: -102361.821
Optimizing NNI: done in 1.43024 secs using 399.3% CPU
94. Current log-likelihood: -102361.809
Optimizing NNI: done in 5.1931 secs using 597.2% CPU
95. Current log-likelihood: -102361.798
Optimizing NNI: done in 1.28632 secs using 399.1% CPU
96. Current log-likelihood: -102361.786
97. Current log-likelihood: -102361.775
98. Current log-likelihood: -102361.762
Optimizing NNI: done in 1.5858 secs using 399.1% CPU
99. Current log-likelihood: -102361.750
Optimal log-likelihood: -102361.750
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.086,0.033) (0.076,0.094) (0.147,0.193) (0.119,0.378) (0.091,0.584) (0.083,0.844) (0.156,1.302) (0.149,2.040) (0.065,4.405)
Parameters optimization took 99 rounds (82.249 sec)
BEST SCORE FOUND : -102361.750
Total tree length: 162.227

Total number of iterations: 216
CPU time used for tree search: 2209.052 sec (0h:36m:49s)
Wall-clock time used for tree search: 562.316 sec (0h:9m:22s)
Total CPU time used: 2604.526 sec (0h:43m:24s)
Total wall-clock time used: 661.586 sec (0h:11m:1s)

===> START BOOTSTRAP REPLICATE NUMBER 29

Creating bootstrap alignment (seed: 68211)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.101 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -107753.968
Optimizing NNI: done in 1.26167 secs using 399.3% CPU
Iteration 70 / LogL: -58169.644 / Time: 0h:1m:50s (0h:1m:50s left)
Optimizing NNI: done in 3.96607 secs using 597.8% CPU
2. Current log-likelihood: -105980.354
Optimizing NNI: done in 1.22518 secs using 399% CPU
Optimizing NNI: done in 1.23106 secs using 399.1% CPU
3. Current log-likelihood: -105865.554
Optimizing NNI: done in 1.15107 secs using 398.8% CPU
4. Current log-likelihood: -105847.655
Optimizing NNI: done in 1.24594 secs using 399% CPU
Optimizing NNI: done in 5.85655 secs using 597% CPU
Optimizing NNI: done in 1.11419 secs using 399% CPU
5. Current log-likelihood: -105846.831
Optimizing NNI: done in 1.40803 secs using 399% CPU
6. Current log-likelihood: -105846.355
Optimizing NNI: done in 1.20382 secs using 399.3% CPU
7. Current log-likelihood: -105845.899
Optimizing NNI: done in 1.13845 secs using 399.3% CPU
Optimizing NNI: done in 1.05292 secs using 398.8% CPU
Optimizing NNI: done in 5.32737 secs using 597.3% CPU
8. Current log-likelihood: -105845.444
Optimizing NNI: done in 1.23398 secs using 398.7% CPU
Iteration 80 / LogL: -58170.695 / Time: 0h:2m:2s (0h:1m:31s left)
9. Current log-likelihood: -105844.987
Optimizing NNI: done in 1.09297 secs using 398.3% CPU
Optimizing NNI: done in 1.00279 secs using 399.2% CPU
10. Current log-likelihood: -105844.531
Optimizing NNI: done in 1.06062 secs using 398.8% CPU
11. Current log-likelihood: -105844.084
Optimizing NNI: done in 5.09313 secs using 597.2% CPU
Optimizing NNI: done in 1.1667 secs using 398.7% CPU
12. Current log-likelihood: -105843.648
Optimizing NNI: done in 1.12119 secs using 399.6% CPU
Optimizing NNI: done in 1.32201 secs using 399% CPU
13. Current log-likelihood: -105843.220
Optimizing NNI: done in 1.24554 secs using 399.1% CPU
14. Current log-likelihood: -105842.807
Optimizing NNI: done in 4.70524 secs using 598% CPU
Optimizing NNI: done in 1.21352 secs using 399% CPU
15. Current log-likelihood: -105842.405
Optimizing NNI: done in 1.16437 secs using 399.6% CPU
16. Current log-likelihood: -105842.041
Optimizing NNI: done in 1.32382 secs using 399.3% CPU
Iteration 90 / LogL: -58246.458 / Time: 0h:2m:14s (0h:1m:14s left)
17. Current log-likelihood: -105841.694
Optimizing NNI: done in 1.62592 secs using 398.9% CPU
Optimizing NNI: done in 4.54043 secs using 597.2% CPU
Optimizing NNI: done in 1.25557 secs using 399.4% CPU
18. Current log-likelihood: -105841.364
Optimizing NNI: done in 1.13491 secs using 398.8% CPU
19. Current log-likelihood: -105841.049
Optimizing NNI: done in 1.36249 secs using 398.6% CPU
20. Current log-likelihood: -105840.751
Optimizing NNI: done in 4.73402 secs using 597.6% CPU
Iteration 280 / LogL: -195968.577 / Time: 0h:25m:43s (0h:4m:58s left)
Optimizing NNI: done in 1.22072 secs using 398.7% CPU
21. Current log-likelihood: -105840.472
Optimizing NNI: done in 1.24332 secs using 398.9% CPU
Optimizing NNI: done in 1.19259 secs using 399.7% CPU
22. Current log-likelihood: -105840.205
Optimizing NNI: done in 1.14363 secs using 398.9% CPU
23. Current log-likelihood: -105839.954
Optimizing NNI: done in 4.4956 secs using 596.7% CPU
Optimizing NNI: done in 1.23662 secs using 399.3% CPU
24. Current log-likelihood: -105839.796
Optimizing NNI: done in 1.38313 secs using 399.5% CPU
Iteration 100 / LogL: -58190.216 / Time: 0h:2m:27s (0h:0m:58s left)
25. Current log-likelihood: -105839.559
Optimizing NNI: done in 1.36911 secs using 399.4% CPU
26. Current log-likelihood: -105839.421
Optimizing NNI: done in 1.18027 secs using 398.5% CPU
Optimizing NNI: done in 4.39516 secs using 597.3% CPU
27. Current log-likelihood: -105839.281
Optimizing NNI: done in 1.1765 secs using 399.1% CPU
28. Current log-likelihood: -105839.146
Optimizing NNI: done in 1.28186 secs using 399.2% CPU
29. Current log-likelihood: -105839.017
Optimizing NNI: done in 1.48418 secs using 399% CPU
30. Current log-likelihood: -105838.898
Optimizing NNI: done in 5.01937 secs using 597.2% CPU
Optimizing NNI: done in 1.51603 secs using 399.1% CPU
31. Current log-likelihood: -105838.782
Optimizing NNI: done in 1.25214 secs using 398.6% CPU
32. Current log-likelihood: -105838.672
Optimizing NNI: done in 1.33734 secs using 398.9% CPU
33. Current log-likelihood: -105838.570
Optimizing NNI: done in 1.29986 secs using 398.7% CPU
Optimal log-likelihood: -105838.423
Proportion of invariable sites: 0.034
Site proportion and rates:  (0.071,0.034) (0.101,0.108) (0.086,0.201) (0.093,0.317) (0.092,0.521) (0.154,0.797) (0.107,1.229) (0.200,1.940) (0.062,4.056)
Parameters optimization took 33 rounds (49.950 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.85182 secs using 597.1% CPU
Optimizing NNI: done in 1.19215 secs using 398.9% CPU
Iteration 110 / LogL: -58166.496 / Time: 0h:2m:40s (0h:0m:42s left)
Optimizing NNI: done in 1.22478 secs using 399.5% CPU
Optimizing NNI: done in 1.19889 secs using 398.8% CPU
Optimizing NNI: done in 1.31519 secs using 398.8% CPU
Calculating distance matrix: done in 4.57207 secs using 400% CPU
Computing ML distances took 4.572316 sec (of wall-clock time) 18.286841 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000720978 secs using 414.3% CPU
Constructing RapidNJ tree: done in 0.0084579 secs using 364.7% CPU
Computing RapidNJ tree took 0.009241 sec (of wall-clock time) 0.035124 sec (of CPU time)
Optimizing NNI: done in 4.78371 secs using 598.4% CPU
Log-likelihood of RapidNJ tree: -106106.346
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.34868 secs using 399% CPU
Optimizing NNI: done in 1.08101 secs using 398% CPU
Optimizing NNI: done in 1.19996 secs using 399.3% CPU
Optimizing NNI: done in 1.26918 secs using 398.9% CPU
Optimizing NNI: done in 1.39298 secs using 399.2% CPU
Optimizing NNI: done in 6.45192 secs using 597.7% CPU
Optimizing NNI: done in 1.05519 secs using 398.8% CPU
Optimizing NNI: done in 1.26682 secs using 399.1% CPU
Iteration 120 / LogL: -58199.968 / Time: 0h:2m:53s (0h:0m:27s left)
Optimizing NNI: done in 1.02914 secs using 399.1% CPU
Optimizing NNI: done in 1.26684 secs using 398% CPU
10.475 second
Optimizing NNI: done in 1.28542 secs using 399.2% CPU
Optimizing NNI: done in 5.35031 secs using 597.3% CPU
Optimizing NNI: done in 1.23847 secs using 398.9% CPU
Optimizing NNI: done in 1.13946 secs using 399.2% CPU
Optimizing NNI: done in 1.30063 secs using 399.2% CPU
Optimizing NNI: done in 4.59558 secs using 598.1% CPU
Optimizing NNI: done in 1.3294 secs using 398.9% CPU
Optimizing NNI: done in 1.32798 secs using 398.5% CPU
Optimizing NNI: done in 1.07827 secs using 398.6% CPU
Optimizing NNI: done in 1.30985 secs using 399% CPU
Iteration 130 / LogL: -58200.729 / Time: 0h:3m:5s (0h:0m:12s left)
Optimizing NNI: done in 4.31353 secs using 597.5% CPU
Computing log-likelihood of 98 initial trees ... 10.105 seconds
Current best score: -105838.423

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.13038 secs using 399.2% CPU
Optimizing NNI: done in 1.46556 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.1532 secs using 399.6% CPU
Optimizing NNI: done in 1.19945 secs using 399.2% CPU
Optimizing NNI: done in 1.25481 secs using 398.8% CPU
Optimizing NNI: done in 5.04736 secs using 597.3% CPU
Iteration 290 / LogL: -196066.497 / Time: 0h:26m:33s (0h:4m:2s left)
Optimizing NNI: done in 1.24594 secs using 398.7% CPU
Optimizing NNI: done in 1.13072 secs using 399.2% CPU
Optimizing NNI: done in 1.18287 secs using 398.7% CPU
Optimizing NNI: done in 1.34236 secs using 399.1% CPU
Optimizing NNI: done in 4.35954 secs using 597.8% CPU
BETTER TREE FOUND at iteration 1: -105489.141
Optimizing NNI: done in 1.17101 secs using 399.1% CPU
Optimizing NNI: done in 1.27254 secs using 399.4% CPU
Iteration 140 / LogL: -58201.762 / Time: 0h:3m:17s (0h:0m:-2s left)
TREE SEARCH COMPLETED AFTER 140 ITERATIONS / Time: 0h:3m:17s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58166.439
Optimal log-likelihood: -58166.438
Site proportion and rates:  (0.140,0.081) (0.019,0.189) (0.154,0.350) (0.072,0.351) (0.262,0.691) (0.175,1.223) (0.148,2.344) (0.031,5.299)
Parameters optimization took 1 rounds (0.262 sec)
BEST SCORE FOUND : -58166.438
Total tree length: 42.579

Total number of iterations: 140
CPU time used for tree search: 742.831 sec (0h:12m:22s)
Wall-clock time used for tree search: 189.785 sec (0h:3m:9s)
Total CPU time used: 775.774 sec (0h:12m:55s)
Total wall-clock time used: 198.014 sec (0h:3m:18s)

===> START BOOTSTRAP REPLICATE NUMBER 77

Creating bootstrap alignment (seed: 67539)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.041 seconds

NOTE: 59 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -57719.526
2. Current log-likelihood: -57165.723
Optimizing NNI: done in 2.87429 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
3. Current log-likelihood: -57155.348
4. Current log-likelihood: -57139.889
Optimizing NNI: done in 5.24465 secs using 597.9% CPU
BETTER TREE FOUND at iteration 2: -105303.765
5. Current log-likelihood: -57114.062
6. Current log-likelihood: -57111.494
7. Current log-likelihood: -57111.215
Optimizing NNI: done in 1.72519 secs using 398.7% CPU
8. Current log-likelihood: -57111.000
9. Current log-likelihood: -57110.786
10. Current log-likelihood: -57110.541
Optimizing NNI: done in 4.56353 secs using 597.7% CPU
11. Current log-likelihood: -57110.240
Optimizing NNI: done in 2.87043 secs using 398.5% CPU
12. Current log-likelihood: -57109.875
13. Current log-likelihood: -57109.490
Optimizing NNI: done in 1.76699 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
14. Current log-likelihood: -57109.144
15. Current log-likelihood: -57108.902
16. Current log-likelihood: -57108.763
Optimal log-likelihood: -57108.695
Site proportion and rates:  (0.129,0.059) (0.105,0.186) (0.126,0.329) (0.225,0.610) (0.162,0.963) (0.070,1.481) (0.157,2.375) (0.026,6.223)
Parameters optimization took 16 rounds (11.469 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
BETTER TREE FOUND at iteration 5: -105297.889
Calculating distance matrix: done in 1.09883 secs using 400% CPU
Computing ML distances took 1.099004 sec (of wall-clock time) 4.395327 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000347137 secs using 401.9% CPU
Constructing RapidNJ tree: done in 0.00445104 secs using 341.2% CPU
Computing RapidNJ tree took 0.004858 sec (of wall-clock time) 0.019432 sec (of CPU time)
Optimizing NNI: done in 5.56581 secs using 598% CPU
Log-likelihood of RapidNJ tree: -56968.057
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.14042 secs using 398.8% CPU
Optimizing NNI: done in 1.95479 secs using 398.2% CPU
Optimizing NNI: done in 1.80792 secs using 398.6% CPU
5.101 second
Optimizing NNI: done in 7.43517 secs using 597.1% CPU
Optimizing NNI: done in 2.53723 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -105285.794
Computing log-likelihood of 98 initial trees ... 4.922 seconds
Current best score: -56968.057

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.866986 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.46551 secs using 597% CPU
Optimizing NNI: done in 2.17481 secs using 398.3% CPU
Iteration 10 / LogL: -105346.527 / Time: 0h:1m:53s
BETTER TREE FOUND at iteration 1: -56709.611
Optimizing NNI: done in 1.14084 secs using 399.6% CPU
Optimizing NNI: done in 1.51437 secs using 398% CPU
Optimizing NNI: done in 1.23465 secs using 399.4% CPU
Optimizing NNI: done in 2.28438 secs using 398.3% CPU
Optimizing NNI: done in 1.07128 secs using 398.9% CPU
Optimizing NNI: done in 4.51465 secs using 597.5% CPU
Optimizing NNI: done in 1.1069 secs using 399.2% CPU
Optimizing NNI: done in 1.15061 secs using 398.4% CPU
Optimizing NNI: done in 2.55076 secs using 398.8% CPU
Optimizing NNI: done in 1.20809 secs using 398.9% CPU
Optimizing NNI: done in 1.79496 secs using 398.8% CPU
Optimizing NNI: done in 1.15853 secs using 399.3% CPU
Optimizing NNI: done in 4.16445 secs using 597.5% CPU
Optimizing NNI: done in 1.22254 secs using 399% CPU
Optimizing NNI: done in 1.2525 secs using 399.4% CPU
Iteration 10 / LogL: -56786.676 / Time: 0h:0m:36s
Optimizing NNI: done in 2.81433 secs using 398.6% CPU
Optimizing NNI: done in 1.20646 secs using 399.2% CPU
Optimizing NNI: done in 2.22749 secs using 398.6% CPU
Optimizing NNI: done in 1.24574 secs using 399.3% CPU
Optimizing NNI: done in 5.57032 secs using 597.5% CPU
Optimizing NNI: done in 1.10817 secs using 399.2% CPU
Optimizing NNI: done in 2.4756 secs using 398.3% CPU
Optimizing NNI: done in 1.37039 secs using 399.3% CPU
Optimizing NNI: done in 1.0808 secs using 398.8% CPU
Optimizing NNI: done in 1.9365 secs using 398.9% CPU
Optimizing NNI: done in 1.21074 secs using 398.2% CPU
Optimizing NNI: done in 1.12333 secs using 398.1% CPU
Optimizing NNI: done in 5.46933 secs using 597.4% CPU
Iteration 300 / LogL: -195971.374 / Time: 0h:27m:25s (0h:3m:7s left)
Optimizing NNI: done in 2.26502 secs using 398.6% CPU
Optimizing NNI: done in 1.26093 secs using 398.8% CPU
Optimizing NNI: done in 1.33354 secs using 398.8% CPU
Optimizing NNI: done in 2.45795 secs using 398.4% CPU
Iteration 20 / LogL: -105340.626 / Time: 0h:2m:15s
Finish initializing candidate tree set (20)
Current best tree score: -105285.794 / CPU time: 79.879
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.33915 secs using 399.1% CPU
Iteration 20 / LogL: -56751.319 / Time: 0h:0m:48s
Finish initializing candidate tree set (20)
Current best tree score: -56709.611 / CPU time: 35.425
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 3.97655 secs using 597.8% CPU
Optimizing NNI: done in 1.99791 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.23293 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -105260.095
Optimizing NNI: done in 2.01284 secs using 398.8% CPU
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TREE SEARCH COMPLETED AFTER 335 ITERATIONS / Time: 0h:30m:11s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -195933.346
Optimal log-likelihood: -195933.343
Site proportion and rates:  (0.012,0.099) (0.072,0.269) (0.136,0.384) (0.175,0.566) (0.184,0.788) (0.145,1.017) (0.151,1.548) (0.124,2.434)
Parameters optimization took 1 rounds (0.687 sec)
BEST SCORE FOUND : -195933.343
Total tree length: 149.606

Total number of iterations: 335
CPU time used for tree search: 10453.718 sec (2h:54m:13s)
Wall-clock time used for tree search: 1775.237 sec (0h:29m:35s)
Total CPU time used: 10674.081 sec (2h:57m:54s)
Total wall-clock time used: 1812.219 sec (0h:30m:12s)

===> START BOOTSTRAP REPLICATE NUMBER 20

Creating bootstrap alignment (seed: 70483)...

Optimizing NNI: done in 2.08418 secs using 398.3% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.290 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199538.068
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2. Current log-likelihood: -196772.880
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3. Current log-likelihood: -196754.212
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4. Current log-likelihood: -196753.906
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5. Current log-likelihood: -196753.799
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Optimal log-likelihood: -196753.750
Site proportion and rates:  (0.003,0.106) (0.057,0.211) (0.058,0.322) (0.102,0.389) (0.241,0.587) (0.267,0.957) (0.141,1.512) (0.131,2.429)
Parameters optimization took 5 rounds (11.382 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 100 / LogL: -105261.763 / Time: 0h:5m:13s (0h:4m:3s left)
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Calculating distance matrix: done in 10.43 secs using 599.9% CPU
Computing ML distances took 10.430561 sec (of wall-clock time) 62.569649 sec (of CPU time)
Optimizing NNI: done in 1.31595 secs using 398.6% CPU
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00132799 secs using 540% CPU
Constructing RapidNJ tree: done in 0.022331 secs using 677.4% CPU
Computing RapidNJ tree took 0.023732 sec (of wall-clock time) 0.160380 sec (of CPU time)
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Log-likelihood of RapidNJ tree: -200912.160
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.26583 secs using 398.1% CPU
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30.484 second
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Optimizing NNI: done in 1.03259 secs using 399% CPU
Optimizing NNI: done in 2.06547 secs using 398.6% CPU
Iteration 120 / LogL: -105254.641 / Time: 0h:6m:5s (0h:2m:54s left)
Optimizing NNI: done in 1.38927 secs using 399.1% CPU
Optimizing NNI: done in 1.18033 secs using 398.6% CPU
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Optimizing NNI: done in 1.58272 secs using 398.7% CPU
Optimizing NNI: done in 2.02771 secs using 398.7% CPU
Optimizing NNI: done in 1.26631 secs using 399% CPU
Iteration 170 / LogL: -56631.692 / Time: 0h:4m:41s (0h:0m:18s left)
Optimizing NNI: done in 1.28075 secs using 398.4% CPU
Optimizing NNI: done in 2.12837 secs using 398.8% CPU
Optimizing NNI: done in 1.13232 secs using 398.7% CPU
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Optimizing NNI: done in 2.123 secs using 398.9% CPU
Optimizing NNI: done in 1.46517 secs using 398.6% CPU
Optimizing NNI: done in 1.77335 secs using 398.5% CPU
Computing log-likelihood of 98 initial trees ... 16.921 seconds
Current best score: -196753.750

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.37733 secs using 398.7% CPU
Optimizing NNI: done in 1.34583 secs using 398.5% CPU
Optimizing NNI: done in 2.00374 secs using 398.4% CPU
Optimizing NNI: done in 2.88423 secs using 596.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.51197 secs using 399% CPU
Optimizing NNI: done in 2.27894 secs using 399% CPU
Optimizing NNI: done in 1.45168 secs using 399.4% CPU
BETTER TREE FOUND at iteration 1: -196264.300
Optimizing NNI: done in 1.82061 secs using 398.9% CPU
Optimizing NNI: done in 1.42239 secs using 398.9% CPU
Optimizing NNI: done in 1.70695 secs using 398.9% CPU
Iteration 180 / LogL: -56622.169 / Time: 0h:4m:55s (0h:0m:1s left)
Optimizing NNI: done in 2.04798 secs using 398.6% CPU
Optimizing NNI: done in 3.69652 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.4913 secs using 399.1% CPU
Optimizing NNI: done in 2.32602 secs using 398.9% CPU
Iteration 130 / LogL: -105255.589 / Time: 0h:6m:26s (0h:2m:20s left)
Optimizing NNI: done in 1.2906 secs using 399.5% CPU
TREE SEARCH COMPLETED AFTER 182 ITERATIONS / Time: 0h:4m:58s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -56622.060
Optimal log-likelihood: -56622.054
Site proportion and rates:  (0.121,0.057) (0.110,0.181) (0.136,0.336) (0.234,0.615) (0.184,1.067) (0.119,1.974) (0.072,2.766) (0.024,6.269)
Parameters optimization took 1 rounds (0.392 sec)
BEST SCORE FOUND : -56622.054
Total tree length: 43.052

Total number of iterations: 182
CPU time used for tree search: 1123.455 sec (0h:18m:43s)
Wall-clock time used for tree search: 285.378 sec (0h:4m:45s)
Total CPU time used: 1176.979 sec (0h:19m:36s)
Total wall-clock time used: 298.782 sec (0h:4m:58s)

===> START BOOTSTRAP REPLICATE NUMBER 78

Creating bootstrap alignment (seed: 67540)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.035 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59705.508
2. Current log-likelihood: -59105.407
Optimizing NNI: done in 2.21622 secs using 398.4% CPU
3. Current log-likelihood: -59095.389
4. Current log-likelihood: -59085.965
BETTER TREE FOUND at iteration 2: -196200.687
5. Current log-likelihood: -59073.389
Optimizing NNI: done in 2.39596 secs using 398.6% CPU
6. Current log-likelihood: -59063.583
7. Current log-likelihood: -59062.375
8. Current log-likelihood: -59062.188
Optimizing NNI: done in 2.05886 secs using 398.5% CPU
Optimizing NNI: done in 3.87059 secs using 597.1% CPU
Optimal log-likelihood: -59062.146
Site proportion and rates:  (0.139,0.076) (0.057,0.197) (0.145,0.328) (0.168,0.574) (0.204,0.898) (0.119,1.453) (0.142,2.350) (0.025,5.700)
Parameters optimization took 8 rounds (6.688 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.08216 secs using 399.9% CPU
Computing ML distances took 1.082346 sec (of wall-clock time) 4.327656 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000345945 secs using 105.5% CPU
Constructing RapidNJ tree: done in 0.00444603 secs using 356.4% CPU
Computing RapidNJ tree took 0.004851 sec (of wall-clock time) 0.018592 sec (of CPU time)
Optimizing NNI: done in 1.84265 secs using 398.8% CPU
Log-likelihood of RapidNJ tree: -59086.878
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.7192 secs using 398.8% CPU
Optimizing NNI: done in 3.69251 secs using 596.4% CPU
Optimizing NNI: done in 1.85883 secs using 398.6% CPU
5.068 second
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Optimizing NNI: done in 3.86012 secs using 596.9% CPU
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Optimizing NNI: done in 2.20752 secs using 398.2% CPU
Optimizing NNI: done in 4.09599 secs using 597% CPU
Computing log-likelihood of 98 initial trees ... 5.306 seconds
Current best score: -58960.744

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.80808 secs using 398.6% CPU
Iteration 140 / LogL: -105304.615 / Time: 0h:6m:46s (0h:1m:48s left)
Optimizing NNI: done in 1.61214 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.23858 secs using 398.1% CPU
BETTER TREE FOUND at iteration 1: -58732.679
Optimizing NNI: done in 3.83681 secs using 597.6% CPU
Optimizing NNI: done in 1.19928 secs using 398.3% CPU
Optimizing NNI: done in 2.2167 secs using 398.5% CPU
Optimizing NNI: done in 1.43711 secs using 399% CPU
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Optimizing NNI: done in 3.81604 secs using 597.8% CPU
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Optimizing NNI: done in 0.989603 secs using 398.9% CPU
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Optimizing NNI: done in 2.06179 secs using 398.9% CPU
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Optimizing NNI: done in 3.7148 secs using 597.1% CPU
Optimizing NNI: done in 1.8254 secs using 398.8% CPU
Optimizing NNI: done in 1.36981 secs using 399.4% CPU
Optimizing NNI: done in 1.17668 secs using 399.2% CPU
Optimizing NNI: done in 2.37648 secs using 398.7% CPU
Optimizing NNI: done in 3.63308 secs using 597.7% CPU
Iteration 10 / LogL: -196264.035 / Time: 0h:2m:0s
Optimizing NNI: done in 1.50626 secs using 399.1% CPU
Iteration 10 / LogL: -58765.873 / Time: 0h:0m:33s
Optimizing NNI: done in 2.35265 secs using 398.5% CPU
Optimizing NNI: done in 1.55572 secs using 399.1% CPU
Optimizing NNI: done in 1.14976 secs using 399.4% CPU
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Optimizing NNI: done in 4.13723 secs using 597.8% CPU
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Optimizing NNI: done in 1.27748 secs using 399.3% CPU
Optimizing NNI: done in 2.18082 secs using 398.4% CPU
Iteration 150 / LogL: -105255.875 / Time: 0h:7m:8s (0h:1m:17s left)
Optimizing NNI: done in 3.92715 secs using 596.7% CPU
Optimizing NNI: done in 1.23727 secs using 398.6% CPU
Optimizing NNI: done in 1.34624 secs using 398.8% CPU
Optimizing NNI: done in 1.94883 secs using 398.9% CPU
Optimizing NNI: done in 1.44879 secs using 399.1% CPU
Optimizing NNI: done in 2.03739 secs using 398.4% CPU
Optimizing NNI: done in 4.1213 secs using 597.4% CPU
Optimizing NNI: done in 1.33648 secs using 399% CPU
Optimizing NNI: done in 1.26862 secs using 399.2% CPU
Iteration 20 / LogL: -58758.576 / Time: 0h:0m:47s
Finish initializing candidate tree set (20)
Current best tree score: -58732.679 / CPU time: 38.491
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.91626 secs using 398.5% CPU
Optimizing NNI: done in 1.58247 secs using 398.9% CPU
Optimizing NNI: done in 3.92811 secs using 596.9% CPU
Optimizing NNI: done in 2.40189 secs using 398.7% CPU
Optimizing NNI: done in 1.66853 secs using 399% CPU
Optimizing NNI: done in 1.70179 secs using 399% CPU
Optimizing NNI: done in 2.68324 secs using 398.4% CPU
Optimizing NNI: done in 3.62377 secs using 597.7% CPU
Optimizing NNI: done in 1.45626 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.92349 secs using 398.6% CPU
BETTER TREE FOUND at iteration 24: -58730.415
Optimizing NNI: done in 1.9038 secs using 399.1% CPU
Optimizing NNI: done in 1.59514 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.34553 secs using 596.7% CPU
BETTER TREE FOUND at iteration 25: -58712.698
Optimizing NNI: done in 2.18527 secs using 398.3% CPU
Optimizing NNI: done in 1.16823 secs using 398.5% CPU
Optimizing NNI: done in 1.96678 secs using 398.8% CPU
Optimizing NNI: done in 1.5646 secs using 399.2% CPU
Optimizing NNI: done in 3.86381 secs using 597.9% CPU
Optimizing NNI: done in 1.69993 secs using 399.5% CPU
Optimizing NNI: done in 2.70357 secs using 397.8% CPU
Iteration 160 / LogL: -105269.830 / Time: 0h:7m:30s (0h:0m:48s left)
Optimizing NNI: done in 1.39526 secs using 398.9% CPU
Optimizing NNI: done in 2.19176 secs using 397.9% CPU
Optimizing NNI: done in 4.05376 secs using 597.2% CPU
Optimizing NNI: done in 1.40422 secs using 398.4% CPU
Iteration 30 / LogL: -58720.272 / Time: 0h:1m:5s (0h:3m:35s left)
Optimizing NNI: done in 1.54095 secs using 399.1% CPU
Optimizing NNI: done in 2.27704 secs using 398.7% CPU
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Optimizing NNI: done in 1.97727 secs using 398.6% CPU
Optimizing NNI: done in 4.4603 secs using 597.7% CPU
Optimizing NNI: done in 1.60487 secs using 398% CPU
Optimizing NNI: done in 2.16205 secs using 399% CPU
Optimizing NNI: done in 2.04407 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.58337 secs using 598.2% CPU
Iteration 20 / LogL: -196269.757 / Time: 0h:2m:40s
Finish initializing candidate tree set (20)
Current best tree score: -196200.687 / CPU time: 132.055
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.9246 secs using 398.8% CPU
BETTER TREE FOUND at iteration 34: -58706.428
Optimizing NNI: done in 1.46958 secs using 399.1% CPU
Optimizing NNI: done in 2.25952 secs using 398.2% CPU
Optimizing NNI: done in 1.6244 secs using 399.5% CPU
Optimizing NNI: done in 1.66442 secs using 398.7% CPU
Optimizing NNI: done in 4.74571 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.66353 secs using 399% CPU
Optimizing NNI: done in 1.96671 secs using 399% CPU
BETTER TREE FOUND at iteration 21: -196196.413
Optimizing NNI: done in 1.78758 secs using 398.9% CPU
Optimizing NNI: done in 1.85996 secs using 398.7% CPU
Optimizing NNI: done in 1.363 secs using 398.8% CPU
Optimizing NNI: done in 1.79756 secs using 398.7% CPU
Iteration 170 / LogL: -105265.635 / Time: 0h:7m:50s (0h:0m:19s left)
Optimizing NNI: done in 1.47573 secs using 398.8% CPU
Iteration 40 / LogL: -58737.708 / Time: 0h:1m:23s (0h:3m:21s left)
Optimizing NNI: done in 1.42928 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.92897 secs using 596.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.08913 secs using 398.6% CPU
BETTER TREE FOUND at iteration 41: -58703.770
Optimizing NNI: done in 1.94912 secs using 398.7% CPU
Optimizing NNI: done in 1.67227 secs using 398.4% CPU
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Optimizing NNI: done in 1.32693 secs using 398.9% CPU
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Optimizing NNI: done in 2.31776 secs using 398.5% CPU
Optimizing NNI: done in 1.58298 secs using 398.8% CPU
Optimizing NNI: done in 2.14527 secs using 399.1% CPU
Optimizing NNI: done in 1.46727 secs using 398.7% CPU
Optimizing NNI: done in 1.31697 secs using 398.9% CPU
Optimizing NNI: done in 2.3677 secs using 398.8% CPU
Optimizing NNI: done in 1.20539 secs using 398.8% CPU
Iteration 50 / LogL: -58727.658 / Time: 0h:1m:39s (0h:3m:3s left)
Optimizing NNI: done in 1.32973 secs using 399% CPU
Optimizing NNI: done in 2.23458 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 178 ITERATIONS / Time: 0h:8m:8s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -105251.923
2. Current log-likelihood: -105251.912
Optimizing NNI: done in 1.62136 secs using 398.9% CPU
3. Current log-likelihood: -105251.900
4. Current log-likelihood: -105251.890
Optimizing NNI: done in 1.47216 secs using 398.7% CPU
5. Current log-likelihood: -105251.880
Optimal log-likelihood: -105251.867
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.069,0.033) (0.106,0.105) (0.117,0.219) (0.105,0.385) (0.091,0.630) (0.123,0.871) (0.100,1.273) (0.195,1.948) (0.061,4.053)
Parameters optimization took 5 rounds (3.408 sec)
BEST SCORE FOUND : -105251.867
Total tree length: 158.818

Total number of iterations: 178
CPU time used for tree search: 1691.593 sec (0h:28m:11s)
Wall-clock time used for tree search: 432.152 sec (0h:7m:12s)
Total CPU time used: 1927.845 sec (0h:32m:7s)
Total wall-clock time used: 491.436 sec (0h:8m:11s)

===> START BOOTSTRAP REPLICATE NUMBER 30

Creating bootstrap alignment (seed: 68212)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.118 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106939.028
Optimizing NNI: done in 1.32834 secs using 399.5% CPU
2. Current log-likelihood: -105064.013
Optimizing NNI: done in 1.66396 secs using 398.1% CPU
Optimizing NNI: done in 1.44819 secs using 399.3% CPU
3. Current log-likelihood: -104936.202
Optimizing NNI: done in 1.3708 secs using 399% CPU
4. Current log-likelihood: -104927.445
Optimizing NNI: done in 1.58849 secs using 398.8% CPU
BETTER TREE FOUND at iteration 22: -196178.241
5. Current log-likelihood: -104927.263
Optimizing NNI: done in 1.75501 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimal log-likelihood: -104927.230
Proportion of invariable sites: 0.030
Site proportion and rates:  (0.098,0.044) (0.061,0.120) (0.079,0.205) (0.124,0.331) (0.078,0.483) (0.149,0.707) (0.142,1.209) (0.184,1.985) (0.055,4.563)
Parameters optimization took 5 rounds (8.187 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
BETTER TREE FOUND at iteration 59: -58702.834
Optimizing NNI: done in 1.55629 secs using 399.2% CPU
Iteration 60 / LogL: -58741.329 / Time: 0h:1m:54s (0h:3m:12s left)
Optimizing NNI: done in 1.57718 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.80865 secs using 596.7% CPU
Calculating distance matrix: done in 4.6254 secs using 399.9% CPU
Computing ML distances took 4.625652 sec (of wall-clock time) 18.496397 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000715971 secs using 438.7% CPU
Constructing RapidNJ tree: done in 0.00873899 secs using 363.4% CPU
Computing RapidNJ tree took 0.009513 sec (of wall-clock time) 0.034922 sec (of CPU time)
BETTER TREE FOUND at iteration 61: -58701.548
Log-likelihood of RapidNJ tree: -104909.026
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.40923 secs using 399.3% CPU
Optimizing NNI: done in 1.7195 secs using 399.2% CPU
Optimizing NNI: done in 4.70185 secs using 597.5% CPU
Optimizing NNI: done in 1.75405 secs using 399% CPU
Optimizing NNI: done in 1.673 secs using 398.9% CPU
Optimizing NNI: done in 4.13342 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.04123 secs using 399% CPU
Optimizing NNI: done in 1.7138 secs using 399.3% CPU
10.513 second
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Optimizing NNI: done in 1.64466 secs using 399% CPU
BETTER TREE FOUND at iteration 25: -196172.386
Optimizing NNI: done in 1.7903 secs using 399.3% CPU
Iteration 70 / LogL: -58704.797 / Time: 0h:2m:13s (0h:2m:56s left)
Optimizing NNI: done in 1.79028 secs using 398.8% CPU
Optimizing NNI: done in 4.27273 secs using 598.1% CPU
Optimizing NNI: done in 1.98032 secs using 398.2% CPU
Computing log-likelihood of 98 initial trees ... 9.632 seconds
Current best score: -104909.026

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.03623 secs using 399.3% CPU
Optimizing NNI: done in 2.07019 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.63398 secs using 597.8% CPU
Optimizing NNI: done in 1.73765 secs using 398.4% CPU
Optimizing NNI: done in 1.53649 secs using 398.5% CPU
Optimizing NNI: done in 1.40417 secs using 398.9% CPU
Optimizing NNI: done in 4.69532 secs using 598% CPU
Optimizing NNI: done in 1.66738 secs using 399.5% CPU
Optimizing NNI: done in 1.56889 secs using 399.1% CPU
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Optimizing NNI: done in 4.29371 secs using 597.5% CPU
Optimizing NNI: done in 1.41122 secs using 398.6% CPU
Iteration 80 / LogL: -58733.765 / Time: 0h:2m:30s (0h:2m:34s left)
BETTER TREE FOUND at iteration 1: -104255.825
Optimizing NNI: done in 1.41081 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 81: -58697.095
Optimizing NNI: done in 1.77717 secs using 398.1% CPU
Optimizing NNI: done in 4.08317 secs using 597.9% CPU
Iteration 30 / LogL: -196174.366 / Time: 0h:4m:1s (0h:13m:9s left)
Optimizing NNI: done in 2.00782 secs using 398.8% CPU
Optimizing NNI: done in 1.42072 secs using 399.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.54416 secs using 399.1% CPU
Optimizing NNI: done in 4.93609 secs using 598% CPU
Optimizing NNI: done in 1.2139 secs using 398.8% CPU
BETTER TREE FOUND at iteration 3: -104235.027
Optimizing NNI: done in 1.63828 secs using 398.8% CPU
Optimizing NNI: done in 1.83132 secs using 399% CPU
Optimizing NNI: done in 4.27045 secs using 597.6% CPU
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Optimizing NNI: done in 4.22311 secs using 597.7% CPU
Optimizing NNI: done in 1.5652 secs using 398.5% CPU
Iteration 90 / LogL: -58707.367 / Time: 0h:2m:48s (0h:2m:52s left)
Optimizing NNI: done in 2.01817 secs using 398.7% CPU
Optimizing NNI: done in 1.44707 secs using 398.8% CPU
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Optimizing NNI: done in 2.18226 secs using 398% CPU
Optimizing NNI: done in 4.06864 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.71604 secs using 399.2% CPU
Optimizing NNI: done in 1.61864 secs using 399.1% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.45396 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 34: -196164.885
BETTER TREE FOUND at iteration 95: -58696.297
Optimizing NNI: done in 1.74031 secs using 399.1% CPU
Optimizing NNI: done in 1.77891 secs using 398.9% CPU
Optimizing NNI: done in 4.61011 secs using 596.5% CPU
Optimizing NNI: done in 1.69569 secs using 399.1% CPU
BETTER TREE FOUND at iteration 9: -104227.655
Optimizing NNI: done in 1.55463 secs using 398.6% CPU
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Iteration 10 / LogL: -104404.893 / Time: 0h:1m:20s
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Iteration 100 / LogL: -58712.997 / Time: 0h:3m:5s (0h:2m:58s left)
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Iteration 110 / LogL: -58719.719 / Time: 0h:3m:20s (0h:2m:36s left)
Optimizing NNI: done in 2.13734 secs using 399.1% CPU
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Optimizing NNI: done in 4.70323 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.54975 secs using 398.8% CPU
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Optimizing NNI: done in 1.53205 secs using 398.7% CPU
Optimizing NNI: done in 1.60818 secs using 398.8% CPU
BETTER TREE FOUND at iteration 40: -196162.510
Iteration 40 / LogL: -196162.510 / Time: 0h:4m:54s (0h:12m:34s left)
Optimizing NNI: done in 3.30607 secs using 398.1% CPU
Iteration 20 / LogL: -104338.899 / Time: 0h:1m:43s
Finish initializing candidate tree set (20)
Current best tree score: -104227.655 / CPU time: 88.925
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.57709 secs using 398.3% CPU
Optimizing NNI: done in 2.23827 secs using 398.8% CPU
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BETTER TREE FOUND at iteration 21: -104210.514
BETTER TREE FOUND at iteration 117: -58695.949
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BETTER TREE FOUND at iteration 118: -58694.518
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Iteration 140 / LogL: -58709.235 / Time: 0h:4m:11s (0h:2m:20s left)
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Iteration 40 / LogL: -104231.256 / Time: 0h:2m:34s (0h:5m:19s left)
Optimizing NNI: done in 1.5358 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 145: -58693.775
Optimizing NNI: done in 2.16787 secs using 398% CPU
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Iteration 50 / LogL: -196158.379 / Time: 0h:5m:49s (0h:10m:48s left)
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BETTER TREE FOUND at iteration 147: -58693.726
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Iteration 150 / LogL: -58704.432 / Time: 0h:4m:29s (0h:2m:55s left)
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BETTER TREE FOUND at iteration 46: -104204.298
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Iteration 160 / LogL: -58699.422 / Time: 0h:4m:45s (0h:2m:36s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 55: -196145.286
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BETTER TREE FOUND at iteration 52: -104203.028
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Iteration 170 / LogL: -58693.728 / Time: 0h:5m:0s (0h:2m:16s left)
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Iteration 60 / LogL: -104230.961 / Time: 0h:3m:25s (0h:5m:20s left)
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Iteration 60 / LogL: -196209.490 / Time: 0h:6m:39s (0h:10m:43s left)
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Iteration 180 / LogL: -58923.849 / Time: 0h:5m:15s (0h:1m:58s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 63: -104199.191
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BETTER TREE FOUND at iteration 63: -196133.863
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Iteration 190 / LogL: -58709.147 / Time: 0h:5m:31s (0h:1m:39s left)
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Iteration 200 / LogL: -58707.864 / Time: 0h:5m:47s (0h:1m:22s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 72: -196124.071
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BETTER TREE FOUND at iteration 222: -58693.256
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Iteration 90 / LogL: -104201.490 / Time: 0h:4m:42s (0h:5m:4s left)
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Iteration 230 / LogL: -58703.981 / Time: 0h:6m:35s (0h:2m:38s left)
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Iteration 240 / LogL: -58740.904 / Time: 0h:6m:50s (0h:2m:20s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 100: -104196.949
Iteration 100 / LogL: -104196.949 / Time: 0h:5m:7s (0h:5m:10s left)
BETTER TREE FOUND at iteration 241: -58693.083
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BETTER TREE FOUND at iteration 242: -58692.515
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BETTER TREE FOUND at iteration 83: -196117.078
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Iteration 250 / LogL: -58721.337 / Time: 0h:7m:8s (0h:2m:38s left)
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Iteration 110 / LogL: -104434.978 / Time: 0h:5m:33s (0h:4m:35s left)
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Iteration 260 / LogL: -58704.235 / Time: 0h:7m:24s (0h:2m:20s left)
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Optimizing NNI: done in 2.21412 secs using 398% CPU
Optimizing NNI: done in 4.30099 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.65875 secs using 398.9% CPU
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BETTER TREE FOUND at iteration 88: -196116.232
Optimizing NNI: done in 1.43315 secs using 398.9% CPU
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Iteration 270 / LogL: -58710.441 / Time: 0h:7m:40s (0h:2m:3s left)
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Iteration 120 / LogL: -104210.902 / Time: 0h:5m:57s (0h:4m:0s left)
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Iteration 90 / LogL: -196151.534 / Time: 0h:9m:9s (0h:10m:4s left)
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Iteration 280 / LogL: -58754.796 / Time: 0h:7m:56s (0h:1m:45s left)
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Iteration 130 / LogL: -104213.720 / Time: 0h:6m:22s (0h:3m:27s left)
Optimizing NNI: done in 1.47864 secs using 399.1% CPU
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Iteration 290 / LogL: -58692.920 / Time: 0h:8m:12s (0h:1m:28s left)
Optimizing NNI: done in 1.78294 secs using 399.4% CPU
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Iteration 100 / LogL: -196130.542 / Time: 0h:9m:52s (0h:8m:46s left)
Optimizing NNI: done in 2.48888 secs using 398.2% CPU
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Iteration 300 / LogL: -58711.256 / Time: 0h:8m:28s (0h:1m:11s left)
Optimizing NNI: done in 2.23171 secs using 398.2% CPU
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Iteration 140 / LogL: -104219.181 / Time: 0h:6m:46s (0h:2m:55s left)
Optimizing NNI: done in 1.32373 secs using 399.4% CPU
Optimizing NNI: done in 1.91066 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.69183 secs using 397.6% CPU
BETTER TREE FOUND at iteration 303: -58692.255
Optimizing NNI: done in 4.40629 secs using 598.2% CPU
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Iteration 310 / LogL: -58717.626 / Time: 0h:8m:45s (0h:2m:38s left)
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Iteration 150 / LogL: -104218.151 / Time: 0h:7m:10s (0h:2m:24s left)
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Iteration 320 / LogL: -58699.483 / Time: 0h:9m:1s (0h:2m:20s left)
Optimizing NNI: done in 2.18674 secs using 398.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.39358 secs using 398.9% CPU
Optimizing NNI: done in 2.70817 secs using 398.6% CPU
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BETTER TREE FOUND at iteration 109: -196109.098
Optimizing NNI: done in 2.30031 secs using 398.3% CPU
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Iteration 110 / LogL: -196333.821 / Time: 0h:10m:37s (0h:9m:38s left)
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Iteration 330 / LogL: -58695.150 / Time: 0h:9m:18s (0h:2m:3s left)
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Iteration 160 / LogL: -104223.480 / Time: 0h:7m:34s (0h:1m:54s left)
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Iteration 340 / LogL: -58699.540 / Time: 0h:9m:34s (0h:1m:46s left)
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Iteration 170 / LogL: -104228.669 / Time: 0h:7m:58s (0h:1m:24s left)
Optimizing NNI: done in 1.80813 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.55721 secs using 398.7% CPU
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BETTER TREE FOUND at iteration 118: -196108.657
Optimizing NNI: done in 1.82359 secs using 399.5% CPU
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Iteration 350 / LogL: -58699.913 / Time: 0h:9m:51s (0h:1m:29s left)
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Iteration 120 / LogL: -196115.715 / Time: 0h:11m:23s (0h:9m:22s left)
Optimizing NNI: done in 2.36323 secs using 398.3% CPU
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Iteration 180 / LogL: -104209.241 / Time: 0h:8m:22s (0h:0m:56s left)
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Iteration 360 / LogL: -58696.771 / Time: 0h:10m:7s (0h:1m:12s left)
Optimizing NNI: done in 1.4711 secs using 398.1% CPU
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Iteration 370 / LogL: -58701.023 / Time: 0h:10m:23s (0h:0m:55s left)
Optimizing NNI: done in 5.22145 secs using 597.7% CPU
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Iteration 190 / LogL: -104198.550 / Time: 0h:8m:47s (0h:0m:27s left)
Optimizing NNI: done in 4.21391 secs using 597.6% CPU
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Iteration 380 / LogL: -58726.063 / Time: 0h:10m:40s (0h:0m:38s left)
Optimizing NNI: done in 4.67682 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.24979 secs using 398% CPU
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Optimizing NNI: done in 1.16546 secs using 399.3% CPU
BETTER TREE FOUND at iteration 130: -196106.780
Iteration 130 / LogL: -196106.780 / Time: 0h:12m:12s (0h:9m:27s left)
Optimizing NNI: done in 2.25838 secs using 398.7% CPU
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Iteration 200 / LogL: -104211.780 / Time: 0h:9m:11s (0h:0m:0s left)
Optimizing NNI: done in 2.0016 secs using 399% CPU
Iteration 390 / LogL: -58692.485 / Time: 0h:10m:56s (0h:0m:21s left)
Optimizing NNI: done in 2.13008 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 201 ITERATIONS / Time: 0h:9m:13s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -104196.949
Optimizing NNI: done in 3.85349 secs using 598.1% CPU
Optimizing NNI: done in 1.15759 secs using 399% CPU
2. Current log-likelihood: -104196.922
Optimizing NNI: done in 1.48348 secs using 398.4% CPU
3. Current log-likelihood: -104196.887
Optimizing NNI: done in 1.74791 secs using 398.9% CPU
4. Current log-likelihood: -104196.866
5. Current log-likelihood: -104196.838
Optimizing NNI: done in 4.37144 secs using 597.6% CPU
6. Current log-likelihood: -104196.822
Optimizing NNI: done in 1.75796 secs using 399% CPU
7. Current log-likelihood: -104196.807
8. Current log-likelihood: -104196.793
9. Current log-likelihood: -104196.778
Optimizing NNI: done in 2.02355 secs using 399% CPU
10. Current log-likelihood: -104196.764
11. Current log-likelihood: -104196.750
Optimizing NNI: done in 4.12012 secs using 598.5% CPU
Optimizing NNI: done in 1.77406 secs using 398.7% CPU
12. Current log-likelihood: -104196.737
13. Current log-likelihood: -104196.725
14. Current log-likelihood: -104196.712
Optimizing NNI: done in 1.68108 secs using 398.7% CPU
15. Current log-likelihood: -104196.700
16. Current log-likelihood: -104196.688
Optimizing NNI: done in 1.71488 secs using 398.9% CPU
17. Current log-likelihood: -104196.677
Optimizing NNI: done in 4.26893 secs using 597.8% CPU
18. Current log-likelihood: -104196.666
Optimizing NNI: done in 1.52773 secs using 399.1% CPU
Optimal log-likelihood: -104196.651
Proportion of invariable sites: 0.030
Site proportion and rates:  (0.097,0.041) (0.061,0.117) (0.094,0.208) (0.150,0.358) (0.161,0.637) (0.094,1.004) (0.152,1.512) (0.116,2.226) (0.046,5.031)
Parameters optimization took 18 rounds (14.477 sec)
BEST SCORE FOUND : -104196.651
Total tree length: 164.778

Total number of iterations: 201
CPU time used for tree search: 2116.646 sec (0h:35m:16s)
Wall-clock time used for tree search: 539.201 sec (0h:8m:59s)
Total CPU time used: 2231.226 sec (0h:37m:11s)
Total wall-clock time used: 567.927 sec (0h:9m:27s)

===> START BOOTSTRAP REPLICATE NUMBER 31

Creating bootstrap alignment (seed: 68213)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.101 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106560.190
Optimizing NNI: done in 1.63323 secs using 399.1% CPU
Iteration 400 / LogL: -58706.992 / Time: 0h:11m:13s (0h:0m:5s left)
2. Current log-likelihood: -104344.614
Optimizing NNI: done in 4.15963 secs using 597.5% CPU
Optimizing NNI: done in 1.8106 secs using 399.6% CPU
3. Current log-likelihood: -104268.275
Optimizing NNI: done in 1.6456 secs using 398.5% CPU
4. Current log-likelihood: -104267.078
Optimizing NNI: done in 1.66063 secs using 399.2% CPU
5. Current log-likelihood: -104266.920
Optimizing NNI: done in 1.63981 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 404 ITERATIONS / Time: 0h:11m:20s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58692.255
Optimizing NNI: done in 5.31915 secs using 597.1% CPU
Optimal log-likelihood: -104266.785
Proportion of invariable sites: 0.019
Site proportion and rates:  (0.102,0.045) (0.066,0.121) (0.097,0.200) (0.113,0.334) (0.081,0.500) (0.133,0.714) (0.145,1.151) (0.176,1.765) (0.068,4.690)
Parameters optimization took 5 rounds (8.041 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
2. Current log-likelihood: -58692.232
3. Current log-likelihood: -58692.216
4. Current log-likelihood: -58692.202
5. Current log-likelihood: -58692.190
6. Current log-likelihood: -58692.179
Optimal log-likelihood: -58692.172
Site proportion and rates:  (0.133,0.075) (0.067,0.194) (0.161,0.344) (0.190,0.644) (0.179,0.952) (0.121,1.489) (0.125,2.430) (0.024,5.924)
Parameters optimization took 6 rounds (4.431 sec)
BEST SCORE FOUND : -58692.172
Total tree length: 43.290

Total number of iterations: 404
CPU time used for tree search: 2664.511 sec (0h:44m:24s)
Wall-clock time used for tree search: 671.639 sec (0h:11m:11s)
Total CPU time used: 2716.879 sec (0h:45m:16s)
Total wall-clock time used: 684.752 sec (0h:11m:24s)

===> START BOOTSTRAP REPLICATE NUMBER 79

Creating bootstrap alignment (seed: 67541)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.041 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -62490.653
Optimizing NNI: done in 4.55691 secs using 597% CPU
Calculating distance matrix: done in 4.68544 secs using 399.9% CPU
Computing ML distances took 4.685685 sec (of wall-clock time) 18.738561 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000710964 secs using 44.59% CPU
Constructing RapidNJ tree: done in 0.00865197 secs using 364.7% CPU
Computing RapidNJ tree took 0.009417 sec (of wall-clock time) 0.033005 sec (of CPU time)
2. Current log-likelihood: -61817.959
Log-likelihood of RapidNJ tree: -104455.243
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 3. Current log-likelihood: -61799.307
4. Current log-likelihood: -61790.296
5. Current log-likelihood: -61788.026
6. Current log-likelihood: -61787.754
Optimizing NNI: done in 4.45925 secs using 597.7% CPU
Iteration 140 / LogL: -196290.557 / Time: 0h:12m:56s (0h:8m:22s left)
Optimal log-likelihood: -61787.697
Site proportion and rates:  (0.098,0.075) (0.078,0.181) (0.174,0.349) (0.050,0.583) (0.202,0.701) (0.187,1.101) (0.175,2.136) (0.035,4.757)
Parameters optimization took 6 rounds (5.008 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.0942 secs using 399.8% CPU
Computing ML distances took 1.094379 sec (of wall-clock time) 4.374978 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000404835 secs using 201.1% CPU
Constructing RapidNJ tree: done in 0.00438118 secs using 311.6% CPU
Computing RapidNJ tree took 0.004837 sec (of wall-clock time) 0.016443 sec (of CPU time)
Log-likelihood of RapidNJ tree: -61766.951
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.97196 secs using 597.7% CPU
4.909 second
10.634 second
Optimizing NNI: done in 5.32027 secs using 597.1% CPU
Computing log-likelihood of 98 initial trees ... 5.310 seconds
Current best score: -61730.260

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.51301 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.64124 secs using 597.6% CPU
Computing log-likelihood of 98 initial trees ... 9.667 seconds
Current best score: -104266.785

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.94931 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.98609 secs using 597.9% CPU
Optimizing NNI: done in 3.90217 secs using 597.7% CPU
BETTER TREE FOUND at iteration 1: -61515.050
Optimizing NNI: done in 1.61456 secs using 398.9% CPU
Optimizing NNI: done in 1.76984 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -103668.242
Optimizing NNI: done in 5.13239 secs using 597.4% CPU
BETTER TREE FOUND at iteration 3: -61508.084
Optimizing NNI: done in 2.03174 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.74564 secs using 399.1% CPU
Optimizing NNI: done in 1.67307 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.24671 secs using 596.8% CPU
BETTER TREE FOUND at iteration 5: -61489.267
BETTER TREE FOUND at iteration 2: -103640.395
Optimizing NNI: done in 1.84698 secs using 399.3% CPU
Optimizing NNI: done in 4.26884 secs using 598.6% CPU
Optimizing NNI: done in 2.32918 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.55119 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -61486.173
Optimizing NNI: done in 1.76264 secs using 398.1% CPU
BETTER TREE FOUND at iteration 3: -103584.352
Optimizing NNI: done in 5.14185 secs using 597.6% CPU
Optimizing NNI: done in 1.08365 secs using 398.8% CPU
Optimizing NNI: done in 0.931423 secs using 399.2% CPU
Iteration 10 / LogL: -61506.184 / Time: 0h:0m:49s
Optimizing NNI: done in 1.85789 secs using 398.6% CPU
Optimizing NNI: done in 1.69956 secs using 398.8% CPU
Optimizing NNI: done in 4.25981 secs using 598% CPU
Iteration 150 / LogL: -196116.626 / Time: 0h:13m:44s (0h:7m:22s left)
Optimizing NNI: done in 1.47805 secs using 398.7% CPU
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Optimizing NNI: done in 2.79131 secs using 397.9% CPU
Optimizing NNI: done in 4.86838 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.67092 secs using 398.4% CPU
Optimizing NNI: done in 2.78118 secs using 399.2% CPU
Optimizing NNI: done in 2.10351 secs using 399% CPU
BETTER TREE FOUND at iteration 151: -196106.019
Optimizing NNI: done in 1.73728 secs using 399% CPU
Optimizing NNI: done in 2.86501 secs using 398.6% CPU
Optimizing NNI: done in 1.53579 secs using 399.3% CPU
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Optimizing NNI: done in 1.74477 secs using 398.7% CPU
Optimizing NNI: done in 1.6975 secs using 398.9% CPU
Iteration 20 / LogL: -61586.075 / Time: 0h:1m:6s
Finish initializing candidate tree set (20)
Current best tree score: -61486.173 / CPU time: 59.482
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.43093 secs using 398.4% CPU
Iteration 10 / LogL: -103591.281 / Time: 0h:1m:18s
Optimizing NNI: done in 1.7582 secs using 398.4% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.10156 secs using 398.9% CPU
BETTER TREE FOUND at iteration 23: -61477.552
Optimizing NNI: done in 4.48468 secs using 597.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.29257 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -61469.697
BETTER TREE FOUND at iteration 15: -103574.134
Optimizing NNI: done in 2.06704 secs using 398.8% CPU
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Iteration 30 / LogL: -61475.432 / Time: 0h:1m:26s (0h:4m:47s left)
Optimizing NNI: done in 2.87975 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.4594 secs using 399.1% CPU
Optimizing NNI: done in 1.52453 secs using 398.9% CPU
Optimizing NNI: done in 4.22973 secs using 598% CPU
BETTER TREE FOUND at iteration 17: -103569.528
Optimizing NNI: done in 1.88266 secs using 398.8% CPU
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Optimizing NNI: done in 1.3803 secs using 399.3% CPU
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Optimizing NNI: done in 1.99885 secs using 398.3% CPU
Iteration 20 / LogL: -103622.552 / Time: 0h:1m:50s
Finish initializing candidate tree set (20)
Current best tree score: -103569.528 / CPU time: 96.304
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.3931 secs using 399% CPU
Optimizing NNI: done in 4.3636 secs using 597.5% CPU
Iteration 160 / LogL: -196279.386 / Time: 0h:14m:30s (0h:8m:18s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 21: -103568.668
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.22099 secs using 398.9% CPU
BETTER TREE FOUND at iteration 40: -61466.391
Iteration 40 / LogL: -61466.391 / Time: 0h:1m:45s (0h:4m:30s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -103567.907
BETTER TREE FOUND at iteration 43: -61456.386
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Iteration 50 / LogL: -61471.899 / Time: 0h:2m:3s (0h:3m:53s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.70688 secs using 399.1% CPU
BETTER TREE FOUND at iteration 30: -103558.658
Iteration 30 / LogL: -103558.658 / Time: 0h:2m:17s (0h:7m:55s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 52: -61454.949
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -103554.269
BETTER TREE FOUND at iteration 55: -61448.633
Optimizing NNI: done in 4.47905 secs using 597.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.02407 secs using 399.1% CPU
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Iteration 170 / LogL: -196113.286 / Time: 0h:15m:15s (0h:7m:18s left)
BETTER TREE FOUND at iteration 60: -61439.373
Iteration 60 / LogL: -61439.373 / Time: 0h:2m:24s (0h:4m:4s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -103543.706
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Iteration 40 / LogL: -103551.985 / Time: 0h:2m:43s (0h:6m:51s left)
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Iteration 70 / LogL: -61470.641 / Time: 0h:2m:40s (0h:3m:28s left)
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Iteration 50 / LogL: -103555.852 / Time: 0h:3m:5s (0h:5m:33s left)
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Iteration 80 / LogL: -61461.341 / Time: 0h:2m:56s (0h:2m:59s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 54: -103542.730
BETTER TREE FOUND at iteration 84: -61436.862
Optimizing NNI: done in 2.48597 secs using 398.2% CPU
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Iteration 180 / LogL: -196166.774 / Time: 0h:15m:58s (0h:6m:20s left)
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Iteration 90 / LogL: -61473.386 / Time: 0h:3m:16s (0h:3m:27s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 61: -103540.497
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Iteration 100 / LogL: -61441.226 / Time: 0h:3m:32s (0h:2m:59s left)
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Iteration 70 / LogL: -103559.346 / Time: 0h:3m:53s (0h:5m:8s left)
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Iteration 110 / LogL: -61450.986 / Time: 0h:3m:49s (0h:2m:35s left)
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Iteration 190 / LogL: -196128.678 / Time: 0h:16m:40s (0h:5m:22s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 111: -61427.102
Optimizing NNI: done in 5.29401 secs using 597.4% CPU
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Iteration 80 / LogL: -103568.631 / Time: 0h:4m:16s (0h:4m:22s left)
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BETTER TREE FOUND at iteration 81: -103537.929
Optimizing NNI: done in 1.78672 secs using 398.9% CPU
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Iteration 120 / LogL: -61442.431 / Time: 0h:4m:9s (0h:3m:10s left)
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BETTER TREE FOUND at iteration 195: -196102.185
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Iteration 90 / LogL: -103551.930 / Time: 0h:4m:38s (0h:4m:44s left)
BETTER TREE FOUND at iteration 130: -61426.453
Iteration 130 / LogL: -61426.453 / Time: 0h:4m:27s (0h:3m:27s left)
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BETTER TREE FOUND at iteration 131: -61426.146
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Iteration 200 / LogL: -196124.134 / Time: 0h:17m:29s (0h:8m:20s left)
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Iteration 140 / LogL: -61451.917 / Time: 0h:4m:44s (0h:3m:6s left)
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Iteration 100 / LogL: -103583.151 / Time: 0h:4m:58s (0h:4m:3s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 147: -61425.783
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Iteration 150 / LogL: -61426.190 / Time: 0h:5m:2s (0h:3m:16s left)
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BETTER TREE FOUND at iteration 110: -103535.126
Iteration 110 / LogL: -103535.126 / Time: 0h:5m:20s (0h:4m:53s left)
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BETTER TREE FOUND at iteration 154: -61422.258
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Iteration 160 / LogL: -61458.744 / Time: 0h:5m:20s (0h:3m:9s left)
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Iteration 210 / LogL: -196138.242 / Time: 0h:18m:13s (0h:7m:24s left)
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Iteration 120 / LogL: -103539.869 / Time: 0h:5m:40s (0h:4m:17s left)
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Iteration 170 / LogL: -61456.565 / Time: 0h:5m:35s (0h:2m:46s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 174: -61421.945
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Iteration 180 / LogL: -61423.674 / Time: 0h:5m:50s (0h:3m:3s left)
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Iteration 130 / LogL: -103543.940 / Time: 0h:6m:2s (0h:3m:44s left)
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Iteration 220 / LogL: -196124.636 / Time: 0h:18m:55s (0h:6m:28s left)
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Iteration 190 / LogL: -61423.467 / Time: 0h:6m:5s (0h:2m:42s left)
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Iteration 140 / LogL: -103562.452 / Time: 0h:6m:26s (0h:3m:14s left)
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Iteration 200 / LogL: -61432.806 / Time: 0h:6m:25s (0h:2m:23s left)
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Iteration 150 / LogL: -103542.442 / Time: 0h:6m:58s (0h:2m:48s left)
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Iteration 230 / LogL: -196112.106 / Time: 0h:19m:40s (0h:5m:34s left)
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Iteration 220 / LogL: -61442.569 / Time: 0h:7m:12s (0h:1m:46s left)
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Iteration 160 / LogL: -103548.904 / Time: 0h:7m:30s (0h:2m:21s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.4684 secs using 398.2% CPU
BETTER TREE FOUND at iteration 163: -103534.281
Optimizing NNI: done in 4.26165 secs using 597.9% CPU
Iteration 240 / LogL: -196181.398 / Time: 0h:20m:22s (0h:4m:41s left)
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UPDATE BEST LOG-LIKELIHOOD: -61421.942
Optimizing NNI: done in 3.03069 secs using 398.6% CPU
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Iteration 230 / LogL: -61425.396 / Time: 0h:7m:34s (0h:1m:27s left)
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Iteration 170 / LogL: -103540.541 / Time: 0h:7m:58s (0h:4m:23s left)
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Iteration 240 / LogL: -61457.124 / Time: 0h:7m:51s (0h:1m:7s left)
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Iteration 250 / LogL: -61434.074 / Time: 0h:8m:7s (0h:0m:46s left)
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Iteration 260 / LogL: -61439.695 / Time: 0h:8m:22s (0h:0m:27s left)
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Iteration 190 / LogL: -103567.511 / Time: 0h:8m:42s (0h:3m:21s left)
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Iteration 270 / LogL: -61422.573 / Time: 0h:8m:38s (0h:0m:7s left)
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TREE SEARCH COMPLETED AFTER 275 ITERATIONS / Time: 0h:8m:46s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -61421.942
Optimal log-likelihood: -61421.936
Site proportion and rates:  (0.091,0.076) (0.092,0.173) (0.166,0.356) (0.158,0.607) (0.226,0.896) (0.127,1.580) (0.108,2.387) (0.032,4.999)
Parameters optimization took 1 rounds (0.336 sec)
BEST SCORE FOUND : -61421.936
Total tree length: 46.496

Total number of iterations: 275
CPU time used for tree search: 2060.222 sec (0h:34m:20s)
Wall-clock time used for tree search: 520.170 sec (0h:8m:40s)
Total CPU time used: 2088.401 sec (0h:34m:48s)
Total wall-clock time used: 527.207 sec (0h:8m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 80

Creating bootstrap alignment (seed: 67542)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 66 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60754.423
2. Current log-likelihood: -60132.792
Optimizing NNI: done in 4.32813 secs using 598.2% CPU
Optimizing NNI: done in 2.52224 secs using 398.7% CPU
3. Current log-likelihood: -60116.614
4. Current log-likelihood: -60096.093
5. Current log-likelihood: -60084.770
Optimizing NNI: done in 2.11765 secs using 398.9% CPU
6. Current log-likelihood: -60084.082
Optimal log-likelihood: -60084.039
Site proportion and rates:  (0.104,0.057) (0.100,0.183) (0.080,0.409) (0.141,0.475) (0.240,0.758) (0.145,1.303) (0.163,2.197) (0.026,5.613)
Parameters optimization took 6 rounds (4.977 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.79167 secs using 398.4% CPU
Iteration 200 / LogL: -103545.513 / Time: 0h:9m:5s (0h:2m:52s left)
Calculating distance matrix: done in 1.09343 secs using 400% CPU
Computing ML distances took 1.093593 sec (of wall-clock time) 4.373712 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000396967 secs using 421.4% CPU
Constructing RapidNJ tree: done in 0.00439692 secs using 310.2% CPU
Computing RapidNJ tree took 0.004857 sec (of wall-clock time) 0.018511 sec (of CPU time)
Optimizing NNI: done in 4.5029 secs using 597.4% CPU
Log-likelihood of RapidNJ tree: -59931.944
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.45939 secs using 398.9% CPU
Optimizing NNI: done in 1.88393 secs using 398.4% CPU
Optimizing NNI: done in 4.48363 secs using 597.7% CPU
Iteration 260 / LogL: -196167.807 / Time: 0h:21m:49s (0h:2m:56s left)
5.151 second
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Computing log-likelihood of 98 initial trees ... 5.542 seconds
Current best score: -59826.696

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -59624.716
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Iteration 210 / LogL: -103543.361 / Time: 0h:9m:27s (0h:2m:23s left)
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Iteration 10 / LogL: -59705.517 / Time: 0h:0m:31s
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Iteration 20 / LogL: -59666.030 / Time: 0h:0m:45s
Finish initializing candidate tree set (20)
Current best tree score: -59624.716 / CPU time: 38.900
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -59623.170
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Estimate model parameters (epsilon = 0.100)
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Iteration 270 / LogL: -196121.351 / Time: 0h:22m:34s (0h:2m:5s left)
BETTER TREE FOUND at iteration 26: -59615.084
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Iteration 230 / LogL: -103546.630 / Time: 0h:10m:11s (0h:1m:28s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 37: -59607.327
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 53: -59593.512
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Iteration 280 / LogL: -196130.602 / Time: 0h:23m:20s (0h:1m:15s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 55: -59593.189
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Iteration 60 / LogL: -59597.635 / Time: 0h:1m:51s (0h:2m:59s left)
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Iteration 250 / LogL: -103542.578 / Time: 0h:10m:55s (0h:0m:34s left)
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Iteration 70 / LogL: -59619.390 / Time: 0h:2m:5s (0h:2m:45s left)
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Iteration 260 / LogL: -103596.189 / Time: 0h:11m:18s (0h:0m:7s left)
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Iteration 80 / LogL: -59604.329 / Time: 0h:2m:19s (0h:2m:22s left)
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Iteration 290 / LogL: -196147.324 / Time: 0h:24m:5s (0h:0m:24s left)
Optimizing NNI: done in 1.20606 secs using 398.8% CPU
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Optimizing NNI: done in 2.63875 secs using 398.4% CPU
TREE SEARCH COMPLETED AFTER 264 ITERATIONS / Time: 0h:11m:27s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -103534.281
Optimal log-likelihood: -103534.274
Proportion of invariable sites: 0.019
Site proportion and rates:  (0.103,0.039) (0.061,0.113) (0.103,0.189) (0.124,0.335) (0.106,0.534) (0.107,0.775) (0.135,1.163) (0.176,1.775) (0.067,4.753)
Parameters optimization took 1 rounds (0.613 sec)
BEST SCORE FOUND : -103534.274
Total tree length: 173.398

Total number of iterations: 264
CPU time used for tree search: 2653.122 sec (0h:44m:13s)
Wall-clock time used for tree search: 673.502 sec (0h:11m:13s)
Total CPU time used: 2711.740 sec (0h:45m:11s)
Total wall-clock time used: 688.170 sec (0h:11m:28s)

===> START BOOTSTRAP REPLICATE NUMBER 32

Creating bootstrap alignment (seed: 68214)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.114 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -111026.655
Optimizing NNI: done in 1.31991 secs using 399% CPU
Optimizing NNI: done in 1.44892 secs using 398.7% CPU
2. Current log-likelihood: -109099.042
Optimizing NNI: done in 4.7272 secs using 597.4% CPU
Optimizing NNI: done in 1.1806 secs using 399.3% CPU
3. Current log-likelihood: -108993.708
Optimizing NNI: done in 1.35116 secs using 398.7% CPU
Iteration 90 / LogL: -59593.235 / Time: 0h:2m:32s (0h:2m:1s left)
4. Current log-likelihood: -108987.514
Optimizing NNI: done in 1.46239 secs using 399% CPU
Optimizing NNI: done in 4.05509 secs using 597.8% CPU
5. Current log-likelihood: -108986.297
Optimizing NNI: done in 1.72344 secs using 399.5% CPU
6. Current log-likelihood: -108985.381
Optimizing NNI: done in 1.37965 secs using 399.2% CPU
Optimizing NNI: done in 3.69679 secs using 597.7% CPU
Optimizing NNI: done in 1.36644 secs using 398.8% CPU
7. Current log-likelihood: -108984.645
Optimizing NNI: done in 1.24349 secs using 399.5% CPU
8. Current log-likelihood: -108984.221
Optimizing NNI: done in 1.39251 secs using 398.5% CPU
9. Current log-likelihood: -108983.865
Optimizing NNI: done in 4.08556 secs using 597.6% CPU
Optimizing NNI: done in 1.36276 secs using 399.3% CPU
10. Current log-likelihood: -108983.610
Optimizing NNI: done in 0.983321 secs using 399.5% CPU
Optimizing NNI: done in 1.24393 secs using 398.6% CPU
11. Current log-likelihood: -108983.484
12. Current log-likelihood: -108983.360
Optimizing NNI: done in 1.3859 secs using 399% CPU
Iteration 100 / LogL: -59606.103 / Time: 0h:2m:46s (0h:1m:42s left)
Optimizing NNI: done in 4.22513 secs using 597% CPU
Optimal log-likelihood: -108983.234
Proportion of invariable sites: 0.023
Site proportion and rates:  (0.053,0.036) (0.094,0.115) (0.069,0.204) (0.107,0.314) (0.093,0.442) (0.113,0.640) (0.188,1.094) (0.193,1.840) (0.067,3.996)
Parameters optimization took 12 rounds (19.320 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.5709 secs using 399% CPU
Optimizing NNI: done in 1.26589 secs using 399% CPU
Optimizing NNI: done in 1.22052 secs using 398.8% CPU
Optimizing NNI: done in 4.07023 secs using 597.5% CPU
TREE SEARCH COMPLETED AFTER 296 ITERATIONS / Time: 0h:24m:30s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -196102.185
Optimizing NNI: done in 1.49132 secs using 399.2% CPU
Optimal log-likelihood: -196102.176
Site proportion and rates:  (0.005,0.124) (0.063,0.219) (0.135,0.359) (0.191,0.547) (0.103,0.707) (0.234,0.982) (0.146,1.549) (0.123,2.471)
Parameters optimization took 1 rounds (1.363 sec)
BEST SCORE FOUND : -196102.176
Calculating distance matrix: done in 4.57405 secs using 399.9% CPU
Computing ML distances took 4.574306 sec (of wall-clock time) 18.292953 sec (of CPU time)
Total tree length: 158.033

Total number of iterations: 296
CPU time used for tree search: 8460.798 sec (2h:21m:0s)
Wall-clock time used for tree search: 1441.490 sec (0h:24m:1s)
Total CPU time used: 8640.580 sec (2h:24m:0s)
Total wall-clock time used: 1471.646 sec (0h:24m:31s)
Setting up auxiliary I and S matrices: done in 0.000740051 secs using 269.2% CPU
Constructing RapidNJ tree: done in 0.00884199 secs using 427.8% CPU
Computing RapidNJ tree took 0.009643 sec (of wall-clock time) 0.040514 sec (of CPU time)

===> START BOOTSTRAP REPLICATE NUMBER 21

Creating bootstrap alignment (seed: 70484)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.289 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -198664.185
Optimizing NNI: done in 1.33874 secs using 398.9% CPU
Log-likelihood of RapidNJ tree: -109092.872
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.45477 secs using 398.6% CPU
2. Current log-likelihood: -196000.359
Optimizing NNI: done in 1.38705 secs using 399% CPU
Optimizing NNI: done in 1.36445 secs using 399.6% CPU
3. Current log-likelihood: -195955.830
Optimizing NNI: done in 1.19431 secs using 399.1% CPU
Optimizing NNI: done in 0.988835 secs using 399% CPU
Iteration 110 / LogL: -59593.720 / Time: 0h:3m:0s (0h:1m:24s left)
4. Current log-likelihood: -195947.523
Optimizing NNI: done in 1.37683 secs using 399% CPU
Optimizing NNI: done in 1.57641 secs using 399.1% CPU
5. Current log-likelihood: -195944.109
Optimizing NNI: done in 0.976481 secs using 399.3% CPU
10.707 second
Optimizing NNI: done in 1.30628 secs using 398.9% CPU
6. Current log-likelihood: -195942.704
Optimizing NNI: done in 1.43087 secs using 398.9% CPU
7. Current log-likelihood: -195941.834
Optimizing NNI: done in 1.44062 secs using 398.9% CPU
Optimizing NNI: done in 1.16234 secs using 398.6% CPU
8. Current log-likelihood: -195941.386
Optimizing NNI: done in 1.57705 secs using 398.9% CPU
9. Current log-likelihood: -195941.211
Optimizing NNI: done in 1.53969 secs using 398.6% CPU
Optimal log-likelihood: -195941.130
Site proportion and rates:  (0.023,0.125) (0.042,0.242) (0.104,0.348) (0.220,0.535) (0.207,0.786) (0.174,1.046) (0.131,1.649) (0.099,2.739)
Parameters optimization took 9 rounds (20.961 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.59947 secs using 398.6% CPU
Iteration 120 / LogL: -59593.593 / Time: 0h:3m:14s (0h:1m:6s left)
Computing log-likelihood of 98 initial trees ... 10.002 seconds
Current best score: -108983.234

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.33746 secs using 398.9% CPU
Optimizing NNI: done in 2.26262 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.35629 secs using 399.1% CPU
Optimizing NNI: done in 1.08768 secs using 399.1% CPU
Optimizing NNI: done in 1.40767 secs using 398.9% CPU
Optimizing NNI: done in 1.41909 secs using 398.9% CPU
Optimizing NNI: done in 1.40478 secs using 398.9% CPU
Optimizing NNI: done in 1.41244 secs using 398.9% CPU
Calculating distance matrix: done in 10.2776 secs using 599.9% CPU
Computing ML distances took 10.278150 sec (of wall-clock time) 61.658287 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00133395 secs using 535.4% CPU
Constructing RapidNJ tree: done in 0.023658 secs using 676.8% CPU
Computing RapidNJ tree took 0.025068 sec (of wall-clock time) 0.168403 sec (of CPU time)
Optimizing NNI: done in 1.47069 secs using 398.9% CPU
Log-likelihood of RapidNJ tree: -199953.455
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.28813 secs using 398.3% CPU
Optimizing NNI: done in 1.23992 secs using 399% CPU
Iteration 130 / LogL: -59606.700 / Time: 0h:3m:27s (0h:0m:49s left)
Optimizing NNI: done in 1.55667 secs using 398.6% CPU
Optimizing NNI: done in 1.44082 secs using 399.1% CPU
Optimizing NNI: done in 1.37325 secs using 398.3% CPU
Optimizing NNI: done in 1.40054 secs using 398.9% CPU
Optimizing NNI: done in 1.30259 secs using 399% CPU
BETTER TREE FOUND at iteration 1: -108440.312
Optimizing NNI: done in 1.47959 secs using 399.1% CPU
Optimizing NNI: done in 1.55761 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.65724 secs using 399% CPU
Optimizing NNI: done in 1.47056 secs using 398.9% CPU
Optimizing NNI: done in 1.43198 secs using 398.8% CPU
BETTER TREE FOUND at iteration 2: -108370.469
Optimizing NNI: done in 1.28084 secs using 399% CPU
Iteration 140 / LogL: -59605.365 / Time: 0h:3m:42s (0h:0m:33s left)
Optimizing NNI: done in 1.53183 secs using 399.3% CPU
Optimizing NNI: done in 2.4798 secs using 398.3% CPU
Optimizing NNI: done in 1.35454 secs using 398.8% CPU
Optimizing NNI: done in 1.19898 secs using 398.5% CPU
Optimizing NNI: done in 3.23724 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.66639 secs using 399% CPU
Optimizing NNI: done in 1.30004 secs using 399.4% CPU
Optimizing NNI: done in 1.45515 secs using 399.2% CPU
Optimizing NNI: done in 1.43583 secs using 399.3% CPU
Optimizing NNI: done in 1.35322 secs using 399.3% CPU
BETTER TREE FOUND at iteration 4: -108366.078
Optimizing NNI: done in 1.45946 secs using 399.6% CPU
Optimizing NNI: done in 1.35727 secs using 399.2% CPU
Iteration 150 / LogL: -59625.339 / Time: 0h:3m:56s (0h:0m:17s left)
Optimizing NNI: done in 1.49861 secs using 399% CPU
30.652 second
Optimizing NNI: done in 1.59514 secs using 398.7% CPU
Optimizing NNI: done in 2.28408 secs using 398.1% CPU
Optimizing NNI: done in 1.18144 secs using 399.3% CPU
Optimizing NNI: done in 1.30187 secs using 398.9% CPU
Optimizing NNI: done in 1.91866 secs using 398.8% CPU
Optimizing NNI: done in 1.32807 secs using 399.1% CPU
Optimizing NNI: done in 2.07033 secs using 398.3% CPU
Optimizing NNI: done in 1.42105 secs using 399.1% CPU
Optimizing NNI: done in 1.18955 secs using 399.4% CPU
Optimizing NNI: done in 2.1496 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.35616 secs using 399.1% CPU
Optimizing NNI: done in 1.30894 secs using 398.3% CPU
Optimizing NNI: done in 1.18137 secs using 399% CPU
BETTER TREE FOUND at iteration 9: -108356.967
Optimizing NNI: done in 1.31044 secs using 398.5% CPU
Iteration 160 / LogL: -59600.777 / Time: 0h:4m:9s (0h:0m:1s left)
Optimizing NNI: done in 1.24034 secs using 398.9% CPU
Optimizing NNI: done in 2.29002 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.34648 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 162 ITERATIONS / Time: 0h:4m:12s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59593.184
Computing log-likelihood of 98 initial trees ... 16.144 seconds
Current best score: -195941.130

Do NNI search on 20 best initial trees
2. Current log-likelihood: -59593.143
3. Current log-likelihood: -59593.105
4. Current log-likelihood: -59593.085
5. Current log-likelihood: -59593.070
6. Current log-likelihood: -59593.060
BETTER TREE FOUND at iteration 10: -108349.281
Iteration 10 / LogL: -108349.281 / Time: 0h:1m:47s
Optimal log-likelihood: -59593.046
Site proportion and rates:  (0.100,0.056) (0.099,0.183) (0.083,0.409) (0.098,0.421) (0.295,0.726) (0.145,1.351) (0.155,2.261) (0.026,5.558)
Parameters optimization took 6 rounds (4.377 sec)
BEST SCORE FOUND : -59593.046
Total tree length: 45.402

Total number of iterations: 162
CPU time used for tree search: 965.789 sec (0h:16m:5s)
Wall-clock time used for tree search: 245.836 sec (0h:4m:5s)
Total CPU time used: 1009.697 sec (0h:16m:49s)
Total wall-clock time used: 256.825 sec (0h:4m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 81

Creating bootstrap alignment (seed: 67543)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.071 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60498.313
Optimizing NNI: done in 3.88794 secs using 596.9% CPU
Estimate model parameters (epsilon = 0.100)
2. Current log-likelihood: -59925.632
3. Current log-likelihood: -59905.707
Optimizing NNI: done in 2.87392 secs using 397.9% CPU
4. Current log-likelihood: -59881.065
5. Current log-likelihood: -59876.207
6. Current log-likelihood: -59875.861
BETTER TREE FOUND at iteration 1: -195375.398
Optimizing NNI: done in 2.14076 secs using 398.6% CPU
Optimal log-likelihood: -59875.804
Site proportion and rates:  (0.112,0.066) (0.071,0.179) (0.146,0.336) (0.061,0.387) (0.245,0.708) (0.154,1.183) (0.176,2.138) (0.036,4.923)
Parameters optimization took 6 rounds (4.999 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09468 secs using 399.9% CPU
Computing ML distances took 1.094876 sec (of wall-clock time) 4.377870 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000336885 secs using 395.1% CPU
Constructing RapidNJ tree: done in 0.00450897 secs using 396.3% CPU
Computing RapidNJ tree took 0.004914 sec (of wall-clock time) 0.019682 sec (of CPU time)
Optimizing NNI: done in 1.8143 secs using 398.6% CPU
Log-likelihood of RapidNJ tree: -60145.658
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.51605 secs using 398.3% CPU
Optimizing NNI: done in 4.73935 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.73296 secs using 399.2% CPU
4.993 second
Optimizing NNI: done in 1.78761 secs using 398.7% CPU
Optimizing NNI: done in 2.50161 secs using 398.2% CPU
BETTER TREE FOUND at iteration 2: -195350.953
Computing log-likelihood of 98 initial trees ... 5.389 seconds
Current best score: -59875.804

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.02457 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.98598 secs using 398.1% CPU
Optimizing NNI: done in 1.29133 secs using 399.2% CPU
BETTER TREE FOUND at iteration 1: -59791.698
Optimizing NNI: done in 4.6303 secs using 597.6% CPU
Optimizing NNI: done in 1.22888 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.52148 secs using 398.8% CPU
Iteration 20 / LogL: -108594.229 / Time: 0h:2m:9s
Finish initializing candidate tree set (20)
Current best tree score: -108349.281 / CPU time: 104.023
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
BETTER TREE FOUND at iteration 2: -59755.582
Optimizing NNI: done in 2.1622 secs using 398.5% CPU
Optimizing NNI: done in 1.33554 secs using 399.3% CPU
Optimizing NNI: done in 4.59096 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.41717 secs using 399.2% CPU
Optimizing NNI: done in 2.08978 secs using 398.6% CPU
Optimizing NNI: done in 1.53726 secs using 398.3% CPU
Optimizing NNI: done in 1.83239 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -195336.616
Optimizing NNI: done in 1.25084 secs using 399.2% CPU
Optimizing NNI: done in 1.30195 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -59745.264
BETTER TREE FOUND at iteration 23: -108340.939
Optimizing NNI: done in 1.271 secs using 399.3% CPU
Optimizing NNI: done in 4.41861 secs using 597.1% CPU
Optimizing NNI: done in 1.311 secs using 398.9% CPU
Optimizing NNI: done in 2.09942 secs using 398.6% CPU
Optimizing NNI: done in 1.3469 secs using 399.5% CPU
Iteration 10 / LogL: -59810.819 / Time: 0h:0m:34s
Optimizing NNI: done in 1.85934 secs using 398.2% CPU
Optimizing NNI: done in 1.20476 secs using 398.9% CPU
Optimizing NNI: done in 1.32507 secs using 398.8% CPU
Optimizing NNI: done in 4.90794 secs using 596.8% CPU
Optimizing NNI: done in 1.88905 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.29367 secs using 399.1% CPU
Optimizing NNI: done in 1.33382 secs using 399% CPU
BETTER TREE FOUND at iteration 26: -108339.425
Optimizing NNI: done in 1.49964 secs using 399% CPU
Optimizing NNI: done in 4.24904 secs using 597.9% CPU
Optimizing NNI: done in 1.21418 secs using 398.8% CPU
Optimizing NNI: done in 2.89721 secs using 397.9% CPU
Optimizing NNI: done in 1.29131 secs using 398.7% CPU
Optimizing NNI: done in 1.37596 secs using 399.1% CPU
Optimizing NNI: done in 1.90957 secs using 399% CPU
Optimizing NNI: done in 4.51972 secs using 596.7% CPU
Optimizing NNI: done in 1.44839 secs using 398.2% CPU
Optimizing NNI: done in 1.88925 secs using 398.9% CPU
Optimizing NNI: done in 1.46473 secs using 399% CPU
Iteration 20 / LogL: -59825.761 / Time: 0h:0m:48s
Finish initializing candidate tree set (20)
Current best tree score: -59745.264 / CPU time: 41.647
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.86076 secs using 398.8% CPU
Iteration 30 / LogL: -108353.983 / Time: 0h:2m:37s (0h:8m:41s left)
Optimizing NNI: done in 1.35788 secs using 399.3% CPU
Optimizing NNI: done in 4.35201 secs using 597.7% CPU
Optimizing NNI: done in 1.43629 secs using 398.9% CPU
Optimizing NNI: done in 2.13771 secs using 398.5% CPU
Optimizing NNI: done in 1.52026 secs using 399.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.9561 secs using 398.6% CPU
BETTER TREE FOUND at iteration 23: -59742.458
Optimizing NNI: done in 4.12193 secs using 596.6% CPU
Iteration 10 / LogL: -195369.200 / Time: 0h:2m:18s
Optimizing NNI: done in 1.54273 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.01514 secs using 398.5% CPU
BETTER TREE FOUND at iteration 24: -59741.764
Optimizing NNI: done in 2.33732 secs using 398.6% CPU
Optimizing NNI: done in 1.33855 secs using 399.4% CPU
Optimizing NNI: done in 4.3928 secs using 598.1% CPU
Optimizing NNI: done in 1.36797 secs using 399% CPU
Optimizing NNI: done in 2.01796 secs using 398.5% CPU
Optimizing NNI: done in 1.40766 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -59738.472
Optimizing NNI: done in 2.18152 secs using 399% CPU
Optimizing NNI: done in 4.10534 secs using 597.5% CPU
Optimizing NNI: done in 1.64279 secs using 398.9% CPU
Optimizing NNI: done in 1.98872 secs using 398.2% CPU
Optimizing NNI: done in 1.60465 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -59737.006
Optimizing NNI: done in 1.99986 secs using 398.3% CPU
Optimizing NNI: done in 3.49614 secs using 597.9% CPU
Optimizing NNI: done in 1.33981 secs using 399.5% CPU
Iteration 30 / LogL: -59754.767 / Time: 0h:1m:7s (0h:3m:49s left)
Optimizing NNI: done in 1.79587 secs using 398.8% CPU
Optimizing NNI: done in 1.41578 secs using 399.2% CPU
Optimizing NNI: done in 1.3509 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.95257 secs using 398.8% CPU
Iteration 40 / LogL: -108356.723 / Time: 0h:2m:58s (0h:6m:33s left)
Optimizing NNI: done in 4.26624 secs using 597.7% CPU
BETTER TREE FOUND at iteration 32: -59734.640
Optimizing NNI: done in 1.93224 secs using 399.2% CPU
Optimizing NNI: done in 1.57085 secs using 399% CPU
Optimizing NNI: done in 1.71869 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.36562 secs using 398.7% CPU
Optimizing NNI: done in 4.32354 secs using 597.2% CPU
Optimizing NNI: done in 1.75153 secs using 399.1% CPU
BETTER TREE FOUND at iteration 42: -108325.417
Optimizing NNI: done in 1.5366 secs using 399% CPU
Optimizing NNI: done in 1.87808 secs using 398.6% CPU
Optimizing NNI: done in 1.30254 secs using 399.3% CPU
Optimizing NNI: done in 4.47171 secs using 597.3% CPU
Optimizing NNI: done in 1.58286 secs using 399% CPU
Optimizing NNI: done in 1.32617 secs using 398.8% CPU
Optimizing NNI: done in 1.80276 secs using 398.7% CPU
Optimizing NNI: done in 1.32608 secs using 399.3% CPU
Optimizing NNI: done in 1.46196 secs using 398.8% CPU
Iteration 40 / LogL: -59738.504 / Time: 0h:1m:23s (0h:3m:16s left)
Optimizing NNI: done in 1.82266 secs using 398.4% CPU
Optimizing NNI: done in 4.78652 secs using 597.2% CPU
Optimizing NNI: done in 1.34058 secs using 399% CPU
Optimizing NNI: done in 1.9364 secs using 398.6% CPU
Optimizing NNI: done in 1.31351 secs using 399.5% CPU
Optimizing NNI: done in 1.34842 secs using 398.9% CPU
Optimizing NNI: done in 1.96872 secs using 399.1% CPU
Optimizing NNI: done in 1.42171 secs using 398.9% CPU
Optimizing NNI: done in 4.48109 secs using 597.8% CPU
Optimizing NNI: done in 1.83683 secs using 397.6% CPU
Optimizing NNI: done in 1.34206 secs using 399.6% CPU
Optimizing NNI: done in 2.05016 secs using 398.5% CPU
Iteration 50 / LogL: -108352.173 / Time: 0h:3m:19s (0h:6m:14s left)
Optimizing NNI: done in 1.65242 secs using 399% CPU
Optimizing NNI: done in 1.23866 secs using 398% CPU
Optimizing NNI: done in 1.85055 secs using 399.1% CPU
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Optimizing NNI: done in 1.48607 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.01846 secs using 597% CPU
Iteration 20 / LogL: -195404.103 / Time: 0h:3m:2s
Finish initializing candidate tree set (20)
Current best tree score: -195336.616 / CPU time: 149.230
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 50: -59727.251
Iteration 50 / LogL: -59727.251 / Time: 0h:1m:39s (0h:3m:22s left)
Optimizing NNI: done in 2.02374 secs using 399.2% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.0757 secs using 398.5% CPU
Optimizing NNI: done in 1.60921 secs using 398.9% CPU
BETTER TREE FOUND at iteration 22: -195318.965
Optimizing NNI: done in 1.78651 secs using 398.8% CPU
Iteration 60 / LogL: -108329.165 / Time: 0h:3m:38s (0h:5m:4s left)
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Optimizing NNI: done in 1.2884 secs using 398.9% CPU
Iteration 60 / LogL: -59730.977 / Time: 0h:1m:53s (0h:2m:52s left)
Optimizing NNI: done in 1.5241 secs using 399.3% CPU
Optimizing NNI: done in 4.6558 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 61: -108323.033
Optimizing NNI: done in 1.69594 secs using 398.8% CPU
Optimizing NNI: done in 1.62023 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -195281.021
Optimizing NNI: done in 1.64893 secs using 398.9% CPU
BETTER TREE FOUND at iteration 63: -59725.514
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Iteration 70 / LogL: -59789.012 / Time: 0h:2m:8s (0h:2m:53s left)
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Iteration 70 / LogL: -108336.379 / Time: 0h:4m:1s (0h:5m:17s left)
Optimizing NNI: done in 1.583 secs using 399% CPU
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Optimizing NNI: done in 1.43967 secs using 398.8% CPU
Iteration 80 / LogL: -59733.439 / Time: 0h:2m:23s (0h:2m:30s left)
Optimizing NNI: done in 1.9507 secs using 398.7% CPU
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Optimizing NNI: done in 4.04463 secs using 597.9% CPU
Iteration 30 / LogL: -195309.942 / Time: 0h:3m:53s (0h:12m:28s left)
Optimizing NNI: done in 1.28447 secs using 399% CPU
Optimizing NNI: done in 1.97498 secs using 398.4% CPU
Optimizing NNI: done in 1.42917 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 86: -59721.779
Optimizing NNI: done in 1.8442 secs using 398.6% CPU
Iteration 80 / LogL: -108370.734 / Time: 0h:4m:21s (0h:4m:27s left)
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Iteration 90 / LogL: -59924.963 / Time: 0h:2m:38s (0h:2m:50s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.32805 secs using 398.7% CPU
Optimizing NNI: done in 1.38355 secs using 399% CPU
BETTER TREE FOUND at iteration 86: -108321.798
Optimizing NNI: done in 4.23802 secs using 597.3% CPU
Optimizing NNI: done in 1.40941 secs using 399% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.53182 secs using 398.9% CPU
Iteration 100 / LogL: -59740.312 / Time: 0h:2m:52s (0h:2m:30s left)
Optimizing NNI: done in 1.61501 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.60225 secs using 399.2% CPU
BETTER TREE FOUND at iteration 35: -195261.099
Optimizing NNI: done in 1.26598 secs using 398.7% CPU
BETTER TREE FOUND at iteration 89: -108318.967
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.31628 secs using 398.9% CPU
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BETTER TREE FOUND at iteration 90: -108312.282
Iteration 90 / LogL: -108312.282 / Time: 0h:4m:48s (0h:5m:24s left)
Optimizing NNI: done in 1.36519 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.59013 secs using 597.4% CPU
Optimizing NNI: done in 2.03075 secs using 398.8% CPU
BETTER TREE FOUND at iteration 108: -59718.517
Optimizing NNI: done in 2.1087 secs using 398.2% CPU
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Iteration 110 / LogL: -59724.355 / Time: 0h:3m:8s (0h:2m:48s left)
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Optimizing NNI: done in 4.10668 secs using 597.5% CPU
Iteration 40 / LogL: -195295.699 / Time: 0h:4m:41s (0h:11m:24s left)
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Iteration 100 / LogL: -108376.067 / Time: 0h:5m:8s (0h:4m:39s left)
Optimizing NNI: done in 1.33118 secs using 398.4% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.41024 secs using 399.4% CPU
Iteration 120 / LogL: -59728.930 / Time: 0h:3m:21s (0h:2m:28s left)
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BETTER TREE FOUND at iteration 41: -195250.174
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 106: -108308.234
Optimizing NNI: done in 1.20083 secs using 399.1% CPU
Iteration 130 / LogL: -59734.029 / Time: 0h:3m:34s (0h:2m:9s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.77641 secs using 398.7% CPU
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BETTER TREE FOUND at iteration 43: -195216.928
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Iteration 110 / LogL: -108326.915 / Time: 0h:5m:30s (0h:4m:51s left)
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Iteration 140 / LogL: -59720.009 / Time: 0h:3m:48s (0h:1m:51s left)
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Iteration 120 / LogL: -108352.491 / Time: 0h:5m:50s (0h:4m:13s left)
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Iteration 150 / LogL: -59719.929 / Time: 0h:4m:3s (0h:1m:34s left)
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Iteration 50 / LogL: -195272.983 / Time: 0h:5m:36s (0h:10m:38s left)
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Iteration 160 / LogL: -59719.126 / Time: 0h:4m:17s (0h:1m:17s left)
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Iteration 130 / LogL: -108320.158 / Time: 0h:6m:10s (0h:3m:38s left)
Optimizing NNI: done in 1.49346 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 167: -59717.632
Optimizing NNI: done in 1.96979 secs using 398.3% CPU
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Iteration 170 / LogL: -59718.958 / Time: 0h:4m:32s (0h:2m:36s left)
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Iteration 140 / LogL: -108322.670 / Time: 0h:6m:31s (0h:3m:5s left)
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Iteration 180 / LogL: -59726.956 / Time: 0h:4m:46s (0h:2m:18s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.86253 secs using 398.6% CPU
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BETTER TREE FOUND at iteration 59: -195209.676
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Iteration 190 / LogL: -59777.905 / Time: 0h:5m:0s (0h:2m:2s left)
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Iteration 60 / LogL: -195221.969 / Time: 0h:6m:25s (0h:10m:45s left)
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Iteration 150 / LogL: -108355.204 / Time: 0h:6m:50s (0h:2m:34s left)
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Iteration 160 / LogL: -108406.225 / Time: 0h:7m:9s (0h:2m:4s left)
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Iteration 210 / LogL: -59781.618 / Time: 0h:5m:27s (0h:1m:29s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 168: -108307.580
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 73: -195205.785
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 200: -108307.174
Iteration 200 / LogL: -108307.174 / Time: 0h:8m:33s (0h:4m:17s left)
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TREE SEARCH COMPLETED AFTER 268 ITERATIONS / Time: 0h:6m:49s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59717.632
Optimal log-likelihood: -59717.628
Site proportion and rates:  (0.110,0.065) (0.076,0.176) (0.141,0.344) (0.055,0.353) (0.256,0.695) (0.159,1.189) (0.167,2.193) (0.035,5.057)
Parameters optimization took 1 rounds (0.379 sec)
BEST SCORE FOUND : -59717.628
Total tree length: 46.020

Total number of iterations: 268
CPU time used for tree search: 1594.893 sec (0h:26m:34s)
Wall-clock time used for tree search: 403.396 sec (0h:6m:43s)
Total CPU time used: 1622.803 sec (0h:27m:2s)
Total wall-clock time used: 410.366 sec (0h:6m:50s)

===> START BOOTSTRAP REPLICATE NUMBER 82

Creating bootstrap alignment (seed: 67544)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.065 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -56747.334
2. Current log-likelihood: -56185.472
Optimizing NNI: done in 4.10565 secs using 597.7% CPU
Optimizing NNI: done in 2.32376 secs using 398.8% CPU
3. Current log-likelihood: -56168.847
4. Current log-likelihood: -56152.824
5. Current log-likelihood: -56140.134
Optimizing NNI: done in 2.21536 secs using 398.6% CPU
6. Current log-likelihood: -56139.134
Optimal log-likelihood: -56139.050
Site proportion and rates:  (0.108,0.059) (0.134,0.207) (0.089,0.413) (0.152,0.551) (0.184,0.766) (0.171,1.254) (0.131,2.366) (0.030,5.917)
Parameters optimization took 6 rounds (4.841 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.70629 secs using 398.8% CPU
Optimizing NNI: done in 4.18639 secs using 598.2% CPU
Calculating distance matrix: done in 1.08202 secs using 400% CPU
Computing ML distances took 1.082198 sec (of wall-clock time) 4.328294 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000408173 secs using 422.1% CPU
Constructing RapidNJ tree: done in 0.00445604 secs using 393.4% CPU
Computing RapidNJ tree took 0.004917 sec (of wall-clock time) 0.019744 sec (of CPU time)
Log-likelihood of RapidNJ tree: -56177.180
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.76413 secs using 398.8% CPU
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5.065 second
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Iteration 210 / LogL: -108346.758 / Time: 0h:8m:53s (0h:3m:49s left)
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Computing log-likelihood of 98 initial trees ... 5.064 seconds
Current best score: -56015.494

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -55804.111
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Iteration 90 / LogL: -195617.828 / Time: 0h:8m:42s (0h:8m:7s left)
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Iteration 10 / LogL: -55830.113 / Time: 0h:0m:30s
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Iteration 220 / LogL: -108322.215 / Time: 0h:9m:12s (0h:3m:21s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -55842.680 / Time: 0h:0m:43s
Finish initializing candidate tree set (20)
Current best tree score: -55804.111 / CPU time: 36.870
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
BETTER TREE FOUND at iteration 93: -195185.268
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -55786.243
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Iteration 230 / LogL: -108317.524 / Time: 0h:9m:31s (0h:2m:54s left)
BETTER TREE FOUND at iteration 25: -55782.482
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -55781.279
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 101: -195182.512
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 102: -195180.433
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TREE SEARCH COMPLETED AFTER 129 ITERATIONS / Time: 0h:3m:10s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -55781.279
Optimal log-likelihood: -55781.272
Site proportion and rates:  (0.104,0.058) (0.132,0.204) (0.099,0.402) (0.128,0.546) (0.193,0.743) (0.177,1.219) (0.134,2.358) (0.032,5.667)
Parameters optimization took 1 rounds (0.822 sec)
BEST SCORE FOUND : -55781.272
Total tree length: 42.343

Total number of iterations: 129
CPU time used for tree search: 718.804 sec (0h:11m:58s)
Wall-clock time used for tree search: 183.849 sec (0h:3m:3s)
Total CPU time used: 747.750 sec (0h:12m:27s)
Total wall-clock time used: 191.078 sec (0h:3m:11s)

===> START BOOTSTRAP REPLICATE NUMBER 83

Creating bootstrap alignment (seed: 67545)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.050 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59462.537
Optimizing NNI: done in 1.70925 secs using 399% CPU
2. Current log-likelihood: -58911.390
3. Current log-likelihood: -58904.187
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Iteration 300 / LogL: -108290.821 / Time: 0h:11m:51s (0h:2m:34s left)
4. Current log-likelihood: -58903.797
5. Current log-likelihood: -58903.688
Optimal log-likelihood: -58903.586
Site proportion and rates:  (0.095,0.062) (0.099,0.183) (0.095,0.356) (0.168,0.505) (0.119,0.798) (0.179,1.068) (0.183,1.972) (0.063,3.360)
Parameters optimization took 5 rounds (3.772 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.05451 secs using 399.6% CPU
Computing ML distances took 1.054695 sec (of wall-clock time) 4.214151 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000355005 secs using 297.5% CPU
Constructing RapidNJ tree: done in 0.004421 secs using 354.9% CPU
Computing RapidNJ tree took 0.004832 sec (of wall-clock time) 0.018498 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59025.816
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.98835 secs using 398.7% CPU
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5.084 second
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Computing log-likelihood of 98 initial trees ... 5.200 seconds
Current best score: -58849.770

Do NNI search on 20 best initial trees
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Iteration 20 / LogL: -58713.098 / Time: 0h:0m:44s
Finish initializing candidate tree set (20)
Current best tree score: -58681.926 / CPU time: 39.659
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 60 / LogL: -58869.515 / Time: 0h:1m:54s (0h:2m:50s left)
Optimizing NNI: done in 1.84557 secs using 399.1% CPU
Optimizing NNI: done in 4.30318 secs using 597.8% CPU
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Optimizing NNI: done in 1.53526 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 66: -58638.637
Optimizing NNI: done in 5.25671 secs using 597.3% CPU
Optimizing NNI: done in 2.06885 secs using 398.5% CPU
Iteration 360 / LogL: -108434.061 / Time: 0h:13m:54s (0h:2m:58s left)
Optimizing NNI: done in 1.55192 secs using 399% CPU
Optimizing NNI: done in 1.96378 secs using 399.1% CPU
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Iteration 70 / LogL: -58638.639 / Time: 0h:2m:10s (0h:3m:1s left)
Optimizing NNI: done in 2.03976 secs using 398.3% CPU
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Optimizing NNI: done in 4.61024 secs using 597.1% CPU
Iteration 150 / LogL: -195181.020 / Time: 0h:13m:39s (0h:7m:58s left)
Optimizing NNI: done in 1.77853 secs using 398.9% CPU
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Optimizing NNI: done in 1.59115 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.07212 secs using 399% CPU
BETTER TREE FOUND at iteration 76: -58634.839
Optimizing NNI: done in 1.38497 secs using 399% CPU
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Optimizing NNI: done in 4.13735 secs using 596.8% CPU
Optimizing NNI: done in 1.30406 secs using 399.1% CPU
Optimizing NNI: done in 1.88327 secs using 399% CPU
Iteration 370 / LogL: -108306.493 / Time: 0h:14m:14s (0h:2m:35s left)
Optimizing NNI: done in 1.30925 secs using 399.1% CPU
Optimizing NNI: done in 1.50354 secs using 399.4% CPU
BETTER TREE FOUND at iteration 80: -58634.838
Iteration 80 / LogL: -58634.838 / Time: 0h:2m:26s (0h:3m:5s left)
Optimizing NNI: done in 2.32405 secs using 399.2% CPU
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Optimizing NNI: done in 1.61105 secs using 399% CPU
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Optimizing NNI: done in 1.60569 secs using 399.1% CPU
Iteration 90 / LogL: -58638.508 / Time: 0h:2m:42s (0h:2m:43s left)
Optimizing NNI: done in 2.01924 secs using 398.8% CPU
Optimizing NNI: done in 1.63908 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 91: -58631.960
Optimizing NNI: done in 4.10516 secs using 597.5% CPU
Optimizing NNI: done in 1.95592 secs using 398.6% CPU
Iteration 380 / LogL: -108288.840 / Time: 0h:14m:34s (0h:2m:11s left)
Optimizing NNI: done in 1.49056 secs using 398.8% CPU
Optimizing NNI: done in 1.85245 secs using 398.4% CPU
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Optimizing NNI: done in 4.16115 secs using 597.5% CPU
Iteration 160 / LogL: -195191.354 / Time: 0h:14m:23s (0h:6m:58s left)
Optimizing NNI: done in 1.30421 secs using 399% CPU
Iteration 100 / LogL: -58722.048 / Time: 0h:2m:58s (0h:2m:43s left)
Optimizing NNI: done in 2.08662 secs using 398.8% CPU
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Optimizing NNI: done in 1.90629 secs using 398.8% CPU
Iteration 390 / LogL: -108288.072 / Time: 0h:14m:55s (0h:1m:48s left)
Optimizing NNI: done in 1.43304 secs using 398.9% CPU
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Iteration 110 / LogL: -58648.222 / Time: 0h:3m:13s (0h:2m:23s left)
Optimizing NNI: done in 1.57259 secs using 399% CPU
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Optimizing NNI: done in 1.68154 secs using 398.7% CPU
Optimizing NNI: done in 2.18804 secs using 398.3% CPU
Iteration 400 / LogL: -108293.305 / Time: 0h:15m:15s (0h:1m:24s left)
Optimizing NNI: done in 1.70578 secs using 399.2% CPU
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Optimizing NNI: done in 1.66628 secs using 398.5% CPU
Optimizing NNI: done in 1.53482 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 120: -58628.373
Iteration 120 / LogL: -58628.373 / Time: 0h:3m:30s (0h:2m:56s left)
Optimizing NNI: done in 1.7768 secs using 398.8% CPU
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Optimizing NNI: done in 3.89685 secs using 596.9% CPU
Iteration 170 / LogL: -195181.665 / Time: 0h:15m:6s (0h:5m:59s left)
Optimizing NNI: done in 1.82942 secs using 398.7% CPU
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Iteration 410 / LogL: -108308.565 / Time: 0h:15m:34s (0h:1m:1s left)
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Iteration 130 / LogL: -58680.242 / Time: 0h:3m:45s (0h:2m:37s left)
Optimizing NNI: done in 1.28625 secs using 398.5% CPU
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Optimizing NNI: done in 1.98823 secs using 399% CPU
Optimizing NNI: done in 4.25369 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.4079 secs using 399.3% CPU
Optimizing NNI: done in 1.89675 secs using 398.7% CPU
BETTER TREE FOUND at iteration 173: -195170.599
Optimizing NNI: done in 1.6631 secs using 398.7% CPU
Optimizing NNI: done in 2.22081 secs using 399% CPU
Optimizing NNI: done in 1.45098 secs using 398.7% CPU
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Iteration 140 / LogL: -58668.025 / Time: 0h:4m:0s (0h:2m:18s left)
Optimizing NNI: done in 2.12675 secs using 398.4% CPU
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Iteration 420 / LogL: -108332.007 / Time: 0h:15m:55s (0h:0m:38s left)
Optimizing NNI: done in 1.30476 secs using 398.8% CPU
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Iteration 150 / LogL: -58636.893 / Time: 0h:4m:15s (0h:2m:0s left)
Optimizing NNI: done in 1.76955 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.78464 secs using 398.5% CPU
Iteration 430 / LogL: -108287.296 / Time: 0h:16m:15s (0h:0m:15s left)
BETTER TREE FOUND at iteration 156: -58625.901
Optimizing NNI: done in 4.50251 secs using 597.5% CPU
Iteration 180 / LogL: -195212.420 / Time: 0h:15m:53s (0h:8m:15s left)
Optimizing NNI: done in 1.93297 secs using 398.8% CPU
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Iteration 160 / LogL: -58644.763 / Time: 0h:4m:32s (0h:2m:44s left)
Optimizing NNI: done in 1.57068 secs using 399.3% CPU
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Optimizing NNI: done in 4.66822 secs using 597% CPU
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Optimizing NNI: done in 1.52414 secs using 399.2% CPU
Optimizing NNI: done in 1.94066 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 438 ITERATIONS / Time: 0h:16m:32s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -108285.707
Optimizing NNI: done in 1.58003 secs using 398.7% CPU
Optimal log-likelihood: -108285.693
Proportion of invariable sites: 0.022
Site proportion and rates:  (0.053,0.028) (0.102,0.111) (0.087,0.219) (0.071,0.325) (0.110,0.429) (0.108,0.645) (0.201,1.107) (0.184,1.891) (0.061,4.233)
Parameters optimization took 1 rounds (0.777 sec)
BEST SCORE FOUND : -108285.693
Total tree length: 174.497

Total number of iterations: 438
CPU time used for tree search: 3824.109 sec (1h:3m:44s)
Wall-clock time used for tree search: 967.277 sec (0h:16m:7s)
Total CPU time used: 3927.728 sec (1h:5m:27s)
Total wall-clock time used: 993.256 sec (0h:16m:33s)

===> START BOOTSTRAP REPLICATE NUMBER 33

Creating bootstrap alignment (seed: 68215)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -100483.981
Optimizing NNI: done in 1.46712 secs using 398.8% CPU
Optimizing NNI: done in 4.73966 secs using 597.3% CPU
2. Current log-likelihood: -98755.421
Optimizing NNI: done in 1.40549 secs using 398.7% CPU
3. Current log-likelihood: -98723.259
Optimizing NNI: done in 1.59372 secs using 399% CPU
Iteration 170 / LogL: -58641.564 / Time: 0h:4m:48s (0h:2m:26s left)
4. Current log-likelihood: -98716.908
Optimizing NNI: done in 3.82251 secs using 596.4% CPU
Optimizing NNI: done in 1.51897 secs using 399.1% CPU
5. Current log-likelihood: -98714.832
Optimizing NNI: done in 1.41513 secs using 399.5% CPU
6. Current log-likelihood: -98714.114
Optimizing NNI: done in 1.6566 secs using 399.1% CPU
7. Current log-likelihood: -98713.554
Optimizing NNI: done in 1.52732 secs using 398.7% CPU
Optimizing NNI: done in 4.85961 secs using 598% CPU
8. Current log-likelihood: -98713.023
Optimizing NNI: done in 1.3884 secs using 398.9% CPU
9. Current log-likelihood: -98712.518
Optimizing NNI: done in 1.42104 secs using 399.2% CPU
10. Current log-likelihood: -98712.046
Optimizing NNI: done in 1.21679 secs using 399.4% CPU
Optimizing NNI: done in 4.376 secs using 597.1% CPU
Optimizing NNI: done in 1.28339 secs using 399.4% CPU
11. Current log-likelihood: -98711.612
Optimizing NNI: done in 1.17925 secs using 399.1% CPU
12. Current log-likelihood: -98711.204
Optimizing NNI: done in 1.80982 secs using 398.9% CPU
Iteration 180 / LogL: -58630.330 / Time: 0h:5m:2s (0h:2m:8s left)
13. Current log-likelihood: -98710.824
Optimizing NNI: done in 4.21644 secs using 597.7% CPU
Optimizing NNI: done in 1.28644 secs using 398.7% CPU
14. Current log-likelihood: -98710.464
Optimizing NNI: done in 1.59416 secs using 399.5% CPU
15. Current log-likelihood: -98710.130
Optimizing NNI: done in 1.63458 secs using 398.6% CPU
16. Current log-likelihood: -98709.825
Optimizing NNI: done in 4.47498 secs using 598.2% CPU
Optimizing NNI: done in 1.45204 secs using 399.1% CPU
17. Current log-likelihood: -98709.536
18. Current log-likelihood: -98709.362
Optimizing NNI: done in 1.58361 secs using 399% CPU
Optimizing NNI: done in 1.24984 secs using 399.2% CPU
19. Current log-likelihood: -98709.190
Optimizing NNI: done in 4.6308 secs using 597.9% CPU
Iteration 190 / LogL: -195238.165 / Time: 0h:16m:37s (0h:7m:18s left)
Optimizing NNI: done in 1.33222 secs using 399.1% CPU
20. Current log-likelihood: -98709.012
Optimizing NNI: done in 1.47684 secs using 399.4% CPU
21. Current log-likelihood: -98708.840
22. Current log-likelihood: -98708.641
Optimizing NNI: done in 1.6509 secs using 398.9% CPU
Optimizing NNI: done in 4.68766 secs using 597.8% CPU
23. Current log-likelihood: -98708.363
Optimizing NNI: done in 1.91849 secs using 399% CPU
Iteration 190 / LogL: -58723.709 / Time: 0h:5m:17s (0h:1m:50s left)
24. Current log-likelihood: -98707.652
Optimizing NNI: done in 1.61354 secs using 399.1% CPU
25. Current log-likelihood: -98684.993
Optimizing NNI: done in 1.2916 secs using 398.6% CPU
Optimizing NNI: done in 4.1538 secs using 596.9% CPU
26. Current log-likelihood: -98668.725
Optimizing NNI: done in 1.41374 secs using 399.3% CPU
Optimizing NNI: done in 1.33684 secs using 398.5% CPU
27. Current log-likelihood: -98667.630
Optimizing NNI: done in 1.38467 secs using 398.7% CPU
Optimal log-likelihood: -98667.561
Proportion of invariable sites: 0.036
Site proportion and rates:  (0.086,0.037) (0.104,0.116) (0.086,0.228) (0.135,0.375) (0.114,0.589) (0.119,1.009) (0.125,1.642) (0.171,2.408) (0.023,4.760)
Parameters optimization took 27 rounds (41.311 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.21731 secs using 597.4% CPU
Optimizing NNI: done in 1.55271 secs using 399% CPU
Optimizing NNI: done in 1.63865 secs using 399.3% CPU
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Calculating distance matrix: done in 4.61203 secs using 399.9% CPU
Computing ML distances took 4.612426 sec (of wall-clock time) 18.444709 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000710011 secs using 463% CPU
Constructing RapidNJ tree: done in 0.00893188 secs using 363.2% CPU
Computing RapidNJ tree took 0.009703 sec (of wall-clock time) 0.035783 sec (of CPU time)
Log-likelihood of RapidNJ tree: -99003.578
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.48482 secs using 399.1% CPU
Optimizing NNI: done in 1.49801 secs using 398.8% CPU
Iteration 200 / LogL: -58628.089 / Time: 0h:5m:32s (0h:1m:33s left)
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10.643 second
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Computing log-likelihood of 98 initial trees ... 10.050 seconds
Current best score: -98667.561

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 215: -58625.901
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Iteration 200 / LogL: -195173.407 / Time: 0h:17m:21s (0h:6m:21s left)
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Iteration 230 / LogL: -58639.503 / Time: 0h:6m:16s (0h:2m:19s left)
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Iteration 210 / LogL: -195215.026 / Time: 0h:18m:6s (0h:5m:27s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 250 / LogL: -58651.890 / Time: 0h:6m:46s (0h:1m:46s left)
BETTER TREE FOUND at iteration 211: -195165.016
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 14: -98188.616
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Iteration 260 / LogL: -58644.113 / Time: 0h:7m:2s (0h:1m:29s left)
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Iteration 20 / LogL: -98240.053 / Time: 0h:2m:26s
Finish initializing candidate tree set (20)
Current best tree score: -98188.616 / CPU time: 99.141
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Iteration 220 / LogL: -195215.510 / Time: 0h:18m:51s (0h:7m:50s left)
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BETTER TREE FOUND at iteration 27: -98186.458
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 30: -98177.388
Iteration 30 / LogL: -98177.388 / Time: 0h:3m:0s (0h:10m:20s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 300 / LogL: -58687.513 / Time: 0h:8m:3s (0h:0m:24s left)
BETTER TREE FOUND at iteration 38: -98174.772
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 39: -98166.332
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Iteration 40 / LogL: -98174.734 / Time: 0h:3m:27s (0h:8m:45s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 310 / LogL: -58628.723 / Time: 0h:8m:17s (0h:0m:8s left)
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BETTER TREE FOUND at iteration 43: -98160.724
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TREE SEARCH COMPLETED AFTER 316 ITERATIONS / Time: 0h:8m:26s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58625.901
Optimizing NNI: done in 1.76705 secs using 397.7% CPU
2. Current log-likelihood: -58625.850
3. Current log-likelihood: -58625.813
4. Current log-likelihood: -58625.780
Optimizing NNI: done in 2.00819 secs using 398% CPU
Optimizing NNI: done in 4.65768 secs using 597.8% CPU
5. Current log-likelihood: -58625.752
6. Current log-likelihood: -58625.731
Optimizing NNI: done in 1.93448 secs using 398.5% CPU
7. Current log-likelihood: -58625.710
8. Current log-likelihood: -58625.693
9. Current log-likelihood: -58625.678
Optimizing NNI: done in 2.04161 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
10. Current log-likelihood: -58625.664
11. Current log-likelihood: -58625.653
Optimizing NNI: done in 4.49034 secs using 597.4% CPU
BETTER TREE FOUND at iteration 49: -98160.199
Optimal log-likelihood: -58625.643
Site proportion and rates:  (0.099,0.064) (0.093,0.181) (0.090,0.364) (0.095,0.423) (0.150,0.645) (0.222,1.017) (0.178,1.921) (0.074,3.263)
Parameters optimization took 11 rounds (8.124 sec)
BEST SCORE FOUND : -58625.643
Total tree length: 40.590

Total number of iterations: 316
CPU time used for tree search: 1985.596 sec (0h:33m:5s)
Wall-clock time used for tree search: 501.365 sec (0h:8m:21s)
Total CPU time used: 2038.862 sec (0h:33m:58s)
Total wall-clock time used: 514.703 sec (0h:8m:34s)

===> START BOOTSTRAP REPLICATE NUMBER 84

Creating bootstrap alignment (seed: 67546)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.064 seconds

NOTE: 64 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59702.087
2. Current log-likelihood: -59125.926
3. Current log-likelihood: -59103.489
Optimizing NNI: done in 2.33376 secs using 398.4% CPU
Iteration 50 / LogL: -98176.532 / Time: 0h:3m:53s (0h:7m:51s left)
4. Current log-likelihood: -59094.441
Optimizing NNI: done in 3.36276 secs using 597.8% CPU
5. Current log-likelihood: -59093.283
6. Current log-likelihood: -59093.161
Optimizing NNI: done in 2.14874 secs using 398.2% CPU
Optimal log-likelihood: -59093.100
Site proportion and rates:  (0.090,0.067) (0.111,0.178) (0.102,0.367) (0.091,0.423) (0.249,0.710) (0.131,1.198) (0.187,2.119) (0.040,4.286)
Parameters optimization took 6 rounds (4.767 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.08673 secs using 400% CPU
Computing ML distances took 1.086905 sec (of wall-clock time) 4.347100 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000365973 secs using 424.3% CPU
Constructing RapidNJ tree: done in 0.00433707 secs using 355.5% CPU
Computing RapidNJ tree took 0.004767 sec (of wall-clock time) 0.018150 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59121.450
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.9056 secs using 398.3% CPU
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4.979 second
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Optimizing NNI: done in 4.41236 secs using 598.2% CPU
Estimate model parameters (epsilon = 0.100)
Computing log-likelihood of 98 initial trees ... 5.223 seconds
Current best score: -58955.491

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.34244 secs using 398.3% CPU
Optimizing NNI: done in 1.32023 secs using 399.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 239: -195160.805
Optimizing NNI: done in 2.11821 secs using 398.6% CPU
BETTER TREE FOUND at iteration 1: -58791.538
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Iteration 240 / LogL: -195194.394 / Time: 0h:20m:22s (0h:8m:26s left)
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Iteration 60 / LogL: -98176.675 / Time: 0h:4m:14s (0h:6m:23s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.3611 secs using 398.5% CPU
Iteration 10 / LogL: -58807.351 / Time: 0h:0m:32s
Optimizing NNI: done in 0.95144 secs using 399% CPU
BETTER TREE FOUND at iteration 64: -98150.784
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 15: -58786.674
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Optimizing NNI: done in 1.30729 secs using 399% CPU
Iteration 20 / LogL: -58834.082 / Time: 0h:0m:45s
Finish initializing candidate tree set (20)
Current best tree score: -58786.674 / CPU time: 39.399
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.86622 secs using 398.7% CPU
Iteration 70 / LogL: -98157.357 / Time: 0h:4m:38s (0h:6m:18s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -58780.381
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BETTER TREE FOUND at iteration 23: -58774.799
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BETTER TREE FOUND at iteration 27: -58773.975
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BETTER TREE FOUND at iteration 28: -58766.973
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Iteration 30 / LogL: -58767.921 / Time: 0h:1m:6s (0h:3m:44s left)
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Iteration 80 / LogL: -98212.710 / Time: 0h:4m:57s (0h:5m:16s left)
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Iteration 250 / LogL: -195201.785 / Time: 0h:21m:7s (0h:7m:32s left)
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BETTER TREE FOUND at iteration 33: -58766.548
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BETTER TREE FOUND at iteration 34: -58763.638
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BETTER TREE FOUND at iteration 84: -98149.323
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Iteration 40 / LogL: -58775.692 / Time: 0h:1m:24s (0h:3m:22s left)
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 1.19625 secs using 399.2% CPU
BETTER TREE FOUND at iteration 87: -98145.059
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BETTER TREE FOUND at iteration 254: -195157.688
BETTER TREE FOUND at iteration 42: -58760.904
Optimizing NNI: done in 2.38215 secs using 398.3% CPU
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Iteration 90 / LogL: -98156.529 / Time: 0h:5m:24s (0h:5m:53s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.07279 secs using 596.7% CPU
BETTER TREE FOUND at iteration 47: -58760.634
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Iteration 50 / LogL: -58984.755 / Time: 0h:1m:41s (0h:3m:20s left)
Optimizing NNI: done in 2.30576 secs using 396.8% CPU
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BETTER TREE FOUND at iteration 53: -58760.574
Optimizing NNI: done in 1.94584 secs using 398% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.32479 secs using 399.3% CPU
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BETTER TREE FOUND at iteration 259: -195157.237
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Iteration 100 / LogL: -98155.022 / Time: 0h:5m:46s (0h:5m:4s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 59: -58757.948
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Iteration 260 / LogL: -195200.778 / Time: 0h:21m:58s (0h:8m:23s left)
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Iteration 70 / LogL: -58761.148 / Time: 0h:2m:13s (0h:2m:51s left)
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Iteration 110 / LogL: -98247.096 / Time: 0h:6m:7s (0h:4m:19s left)
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BETTER TREE FOUND at iteration 74: -58756.938
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BETTER TREE FOUND at iteration 75: -58752.596
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Iteration 80 / LogL: -58755.678 / Time: 0h:2m:30s (0h:3m:1s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 82: -58747.507
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Iteration 120 / LogL: -98152.108 / Time: 0h:6m:28s (0h:3m:38s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 270 / LogL: -195177.933 / Time: 0h:22m:46s (0h:8m:17s left)
BETTER TREE FOUND at iteration 89: -58747.164
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Iteration 90 / LogL: -58769.333 / Time: 0h:2m:48s (0h:3m:7s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 128: -98142.576
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Iteration 130 / LogL: -98155.629 / Time: 0h:6m:52s (0h:5m:12s left)
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Iteration 110 / LogL: -58753.447 / Time: 0h:3m:18s (0h:2m:23s left)
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Iteration 140 / LogL: -98156.881 / Time: 0h:7m:13s (0h:4m:34s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 115: -58747.018
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Iteration 280 / LogL: -195170.641 / Time: 0h:23m:33s (0h:7m:25s left)
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Iteration 120 / LogL: -58758.056 / Time: 0h:3m:32s (0h:2m:49s left)
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BETTER TREE FOUND at iteration 146: -98140.223
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BETTER TREE FOUND at iteration 124: -58747.010
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Iteration 150 / LogL: -98141.513 / Time: 0h:7m:36s (0h:4m:54s left)
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Iteration 130 / LogL: -58764.020 / Time: 0h:3m:48s (0h:2m:46s left)
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Iteration 140 / LogL: -58758.507 / Time: 0h:4m:3s (0h:2m:27s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.53588 secs using 399.5% CPU
BETTER TREE FOUND at iteration 159: -98138.964
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Iteration 160 / LogL: -98304.881 / Time: 0h:7m:58s (0h:4m:58s left)
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Iteration 290 / LogL: -195164.725 / Time: 0h:24m:16s (0h:6m:33s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.03144 secs using 398% CPU
BETTER TREE FOUND at iteration 150: -58746.340
Iteration 150 / LogL: -58746.340 / Time: 0h:4m:19s (0h:2m:53s left)
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BETTER TREE FOUND at iteration 173: -98138.415
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BETTER TREE FOUND at iteration 167: -58746.122
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TREE SEARCH COMPLETED AFTER 268 ITERATIONS / Time: 0h:7m:18s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58746.122
Optimal log-likelihood: -58746.116
Site proportion and rates:  (0.103,0.070) (0.102,0.190) (0.113,0.398) (0.100,0.398) (0.264,0.770) (0.117,1.385) (0.162,2.202) (0.037,4.421)
Parameters optimization took 1 rounds (0.719 sec)
BEST SCORE FOUND : -58746.116
Total tree length: 43.798

Total number of iterations: 268
CPU time used for tree search: 1711.632 sec (0h:28m:31s)
Wall-clock time used for tree search: 432.618 sec (0h:7m:12s)
Total CPU time used: 1740.096 sec (0h:29m:0s)
Total wall-clock time used: 439.725 sec (0h:7m:19s)

===> START BOOTSTRAP REPLICATE NUMBER 85

Creating bootstrap alignment (seed: 67547)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.036 seconds

NOTE: 61 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61819.184
Optimizing NNI: done in 1.96356 secs using 398.4% CPU
2. Current log-likelihood: -61243.901
3. Current log-likelihood: -61229.738
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4. Current log-likelihood: -61216.122
5. Current log-likelihood: -61213.149
6. Current log-likelihood: -61212.966
Optimizing NNI: done in 1.97762 secs using 398.1% CPU
Optimal log-likelihood: -61212.892
Site proportion and rates:  (0.078,0.059) (0.150,0.172) (0.078,0.364) (0.092,0.429) (0.189,0.684) (0.185,1.109) (0.192,1.992) (0.036,5.111)
Parameters optimization took 6 rounds (5.214 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10554 secs using 400% CPU
Computing ML distances took 1.105725 sec (of wall-clock time) 4.422155 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000372887 secs using 105.1% CPU
Constructing RapidNJ tree: done in 0.00430489 secs using 293.9% CPU
Computing RapidNJ tree took 0.004737 sec (of wall-clock time) 0.015008 sec (of CPU time)
Optimizing NNI: done in 1.9656 secs using 398.3% CPU
Log-likelihood of RapidNJ tree: -61410.593
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.76798 secs using 596.9% CPU
Optimizing NNI: done in 2.22811 secs using 398.3% CPU
Iteration 250 / LogL: -98145.842 / Time: 0h:11m:19s (0h:2m:41s left)
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5.241 second
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Computing log-likelihood of 98 initial trees ... 4.987 seconds
Current best score: -61212.892

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -61027.339
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -61022.087
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Estimate model parameters (epsilon = 0.100)
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Iteration 340 / LogL: -195224.371 / Time: 0h:28m:0s (0h:2m:18s left)
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BETTER TREE FOUND at iteration 10: -61009.602
Iteration 10 / LogL: -61009.602 / Time: 0h:0m:46s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 268: -98137.766
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Iteration 270 / LogL: -98153.667 / Time: 0h:12m:5s (0h:4m:24s left)
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Iteration 20 / LogL: -61022.476 / Time: 0h:1m:2s
Finish initializing candidate tree set (20)
Current best tree score: -61009.602 / CPU time: 55.536
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 21: -61006.951
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BETTER TREE FOUND at iteration 346: -195154.989
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BETTER TREE FOUND at iteration 26: -60999.427
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Iteration 280 / LogL: -98142.641 / Time: 0h:12m:27s (0h:3m:55s left)
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Iteration 30 / LogL: -61007.588 / Time: 0h:1m:22s (0h:4m:33s left)
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Iteration 350 / LogL: -195192.402 / Time: 0h:28m:50s (0h:7m:56s left)
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BETTER TREE FOUND at iteration 39: -60999.205
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Iteration 290 / LogL: -98147.256 / Time: 0h:12m:49s (0h:3m:27s left)
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Iteration 40 / LogL: -61014.796 / Time: 0h:1m:40s (0h:4m:14s left)
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BETTER TREE FOUND at iteration 45: -60997.999
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Iteration 50 / LogL: -60998.847 / Time: 0h:1m:57s (0h:3m:46s left)
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Iteration 300 / LogL: -98174.159 / Time: 0h:13m:10s (0h:2m:59s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 55: -60997.327
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Iteration 60 / LogL: -61020.495 / Time: 0h:2m:13s (0h:3m:34s left)
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Optimizing NNI: done in 3.82567 secs using 597.3% CPU
Iteration 360 / LogL: -195208.932 / Time: 0h:29m:35s (0h:7m:5s left)
BETTER TREE FOUND at iteration 61: -60995.533
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BETTER TREE FOUND at iteration 62: -60994.268
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 361: -195154.313
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Iteration 310 / LogL: -98146.177 / Time: 0h:13m:33s (0h:2m:32s left)
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Iteration 70 / LogL: -61002.834 / Time: 0h:2m:30s (0h:3m:21s left)
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Iteration 320 / LogL: -98250.006 / Time: 0h:13m:55s (0h:2m:5s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 87: -60991.829
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Iteration 370 / LogL: -195162.658 / Time: 0h:30m:21s (0h:7m:29s left)
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Iteration 90 / LogL: -61006.084 / Time: 0h:3m:3s (0h:3m:20s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 330 / LogL: -98173.257 / Time: 0h:14m:19s (0h:1m:39s left)
BETTER TREE FOUND at iteration 93: -60989.225
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Iteration 100 / LogL: -61035.314 / Time: 0h:3m:20s (0h:3m:8s left)
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BETTER TREE FOUND at iteration 102: -60988.654
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BETTER TREE FOUND at iteration 338: -98136.149
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Iteration 340 / LogL: -98185.173 / Time: 0h:14m:42s (0h:4m:14s left)
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Iteration 110 / LogL: -60992.050 / Time: 0h:3m:37s (0h:3m:3s left)
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BETTER TREE FOUND at iteration 112: -60988.372
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BETTER TREE FOUND at iteration 113: -60988.012
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Iteration 380 / LogL: -195206.285 / Time: 0h:31m:6s (0h:6m:38s left)
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Iteration 350 / LogL: -98164.620 / Time: 0h:15m:4s (0h:3m:48s left)
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BETTER TREE FOUND at iteration 127: -60987.795
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Iteration 130 / LogL: -60998.514 / Time: 0h:4m:13s (0h:3m:10s left)
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Iteration 360 / LogL: -98146.919 / Time: 0h:15m:26s (0h:3m:21s left)
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Iteration 140 / LogL: -60991.128 / Time: 0h:4m:29s (0h:2m:48s left)
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Iteration 390 / LogL: -195190.229 / Time: 0h:31m:50s (0h:5m:48s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 370 / LogL: -98152.825 / Time: 0h:15m:48s (0h:2m:54s left)
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BETTER TREE FOUND at iteration 391: -195150.223
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TREE SEARCH COMPLETED AFTER 439 ITERATIONS / Time: 0h:18m:22s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -98136.149
Optimal log-likelihood: -98136.136
Proportion of invariable sites: 0.035
Site proportion and rates:  (0.077,0.029) (0.101,0.095) (0.098,0.211) (0.131,0.359) (0.120,0.564) (0.117,0.994) (0.138,1.632) (0.164,2.428) (0.019,5.834)
Parameters optimization took 1 rounds (0.780 sec)
BEST SCORE FOUND : -98136.136
Total tree length: 144.582

Total number of iterations: 439
CPU time used for tree search: 4170.079 sec (1h:9m:30s)
Wall-clock time used for tree search: 1054.920 sec (0h:17m:34s)
Total CPU time used: 4361.837 sec (1h:12m:41s)
Total wall-clock time used: 1103.040 sec (0h:18m:23s)

===> START BOOTSTRAP REPLICATE NUMBER 34

Creating bootstrap alignment (seed: 68216)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.116 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -109862.084
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2. Current log-likelihood: -107686.916
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3. Current log-likelihood: -107574.361
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5. Current log-likelihood: -107569.876
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6. Current log-likelihood: -107569.688
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7. Current log-likelihood: -107569.519
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Iteration 250 / LogL: -60987.759 / Time: 0h:7m:23s (0h:2m:29s left)
8. Current log-likelihood: -107569.415
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9. Current log-likelihood: -107569.288
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Optimal log-likelihood: -107569.181
Proportion of invariable sites: 0.030
Site proportion and rates:  (0.112,0.045) (0.088,0.127) (0.065,0.217) (0.095,0.313) (0.074,0.405) (0.127,0.703) (0.143,1.179) (0.193,1.892) (0.072,3.967)
Parameters optimization took 9 rounds (12.679 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Computing ML distances took 4.667186 sec (of wall-clock time) 18.664654 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000681877 secs using 398.8% CPU
Constructing RapidNJ tree: done in 0.00879288 secs using 366.4% CPU
Computing RapidNJ tree took 0.009544 sec (of wall-clock time) 0.037284 sec (of CPU time)
Optimizing NNI: done in 1.48699 secs using 399.1% CPU
Log-likelihood of RapidNJ tree: -107678.472
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.34995 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 262: -60984.802
11.172 second
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Computing log-likelihood of 98 initial trees ... 9.871 seconds
Current best score: -107569.181

Do NNI search on 20 best initial trees
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BETTER TREE FOUND at iteration 2: -106991.224
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Iteration 10 / LogL: -107036.163 / Time: 0h:1m:24s
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BETTER TREE FOUND at iteration 297: -60984.166
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Iteration 300 / LogL: -60986.927 / Time: 0h:8m:41s (0h:2m:49s left)
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BETTER TREE FOUND at iteration 444: -195146.202
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Iteration 310 / LogL: -60992.863 / Time: 0h:8m:57s (0h:2m:31s left)
Optimizing NNI: done in 2.90425 secs using 398.4% CPU
BETTER TREE FOUND at iteration 447: -195134.828
Optimizing NNI: done in 1.34156 secs using 398.6% CPU
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BETTER TREE FOUND at iteration 311: -60984.058
Optimizing NNI: done in 2.7017 secs using 398.3% CPU
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Optimizing NNI: done in 2.77928 secs using 398.4% CPU
Iteration 20 / LogL: -107088.470 / Time: 0h:1m:50s
Finish initializing candidate tree set (20)
Current best tree score: -106931.952 / CPU time: 92.063
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.51534 secs using 398.5% CPU
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Iteration 450 / LogL: -195168.972 / Time: 0h:36m:31s (0h:7m:53s left)
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BETTER TREE FOUND at iteration 21: -106924.813
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Iteration 320 / LogL: -60986.934 / Time: 0h:9m:13s (0h:2m:37s left)
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BETTER TREE FOUND at iteration 26: -106918.943
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Iteration 330 / LogL: -61001.535 / Time: 0h:9m:29s (0h:2m:20s left)
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Optimizing NNI: done in 4.50896 secs using 598% CPU
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BETTER TREE FOUND at iteration 30: -106911.559
Iteration 30 / LogL: -106911.559 / Time: 0h:2m:27s (0h:8m:27s left)
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Iteration 340 / LogL: -60985.318 / Time: 0h:9m:45s (0h:2m:2s left)
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Iteration 460 / LogL: -195162.133 / Time: 0h:37m:14s (0h:7m:3s left)
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Iteration 350 / LogL: -60986.357 / Time: 0h:10m:0s (0h:1m:44s left)
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Iteration 40 / LogL: -106966.566 / Time: 0h:2m:49s (0h:6m:31s left)
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Iteration 360 / LogL: -61010.675 / Time: 0h:10m:15s (0h:1m:27s left)
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Iteration 50 / LogL: -107000.139 / Time: 0h:3m:12s (0h:5m:14s left)
Optimizing NNI: done in 4.1568 secs using 597.6% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.13928 secs using 596.9% CPU
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Iteration 370 / LogL: -60984.930 / Time: 0h:10m:30s (0h:1m:10s left)
BETTER TREE FOUND at iteration 52: -106910.730
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 371: -60983.502
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Iteration 470 / LogL: -195202.175 / Time: 0h:37m:59s (0h:6m:14s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 379: -60983.002
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Iteration 380 / LogL: -60991.461 / Time: 0h:10m:47s (0h:2m:49s left)
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Iteration 60 / LogL: -106924.651 / Time: 0h:3m:37s (0h:5m:39s left)
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Iteration 390 / LogL: -60990.608 / Time: 0h:11m:2s (0h:2m:31s left)
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Iteration 70 / LogL: -106921.261 / Time: 0h:4m:1s (0h:4m:46s left)
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Iteration 400 / LogL: -60990.398 / Time: 0h:11m:17s (0h:2m:14s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 402: -60981.857
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Iteration 480 / LogL: -195206.108 / Time: 0h:38m:44s (0h:5m:25s left)
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Iteration 410 / LogL: -60996.226 / Time: 0h:11m:34s (0h:2m:36s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 420 / LogL: -60982.987 / Time: 0h:11m:50s (0h:2m:19s left)
BETTER TREE FOUND at iteration 87: -106909.690
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Iteration 90 / LogL: -106914.516 / Time: 0h:4m:45s (0h:5m:11s left)
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Iteration 430 / LogL: -61007.309 / Time: 0h:12m:6s (0h:2m:1s left)
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Iteration 490 / LogL: -195146.111 / Time: 0h:39m:28s (0h:4m:36s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 433: -60981.662
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Estimate model parameters (epsilon = 0.100)
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Iteration 440 / LogL: -60988.784 / Time: 0h:12m:21s (0h:2m:37s left)
BETTER TREE FOUND at iteration 100: -106906.440
Iteration 100 / LogL: -106906.440 / Time: 0h:5m:10s (0h:5m:13s left)
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Iteration 450 / LogL: -60993.244 / Time: 0h:12m:37s (0h:2m:20s left)
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Iteration 110 / LogL: -107121.711 / Time: 0h:5m:34s (0h:4m:35s left)
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BETTER TREE FOUND at iteration 457: -60981.660
Optimizing NNI: done in 2.09151 secs using 398.6% CPU
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Iteration 500 / LogL: -195138.320 / Time: 0h:40m:11s (0h:3m:47s left)
Optimizing NNI: done in 1.56438 secs using 398.6% CPU
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Iteration 460 / LogL: -60990.174 / Time: 0h:12m:53s (0h:2m:43s left)
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Iteration 470 / LogL: -60983.032 / Time: 0h:13m:8s (0h:2m:26s left)
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Iteration 480 / LogL: -60991.472 / Time: 0h:13m:24s (0h:2m:9s left)
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Iteration 130 / LogL: -106948.821 / Time: 0h:6m:18s (0h:3m:25s left)
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Iteration 510 / LogL: -195151.247 / Time: 0h:40m:55s (0h:2m:58s left)
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Iteration 490 / LogL: -60983.552 / Time: 0h:13m:39s (0h:1m:52s left)
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Iteration 140 / LogL: -106928.242 / Time: 0h:6m:41s (0h:2m:53s left)
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Iteration 500 / LogL: -60991.079 / Time: 0h:13m:55s (0h:1m:35s left)
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Iteration 510 / LogL: -60985.137 / Time: 0h:14m:12s (0h:1m:18s left)
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Iteration 150 / LogL: -106931.049 / Time: 0h:7m:2s (0h:2m:21s left)
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Iteration 520 / LogL: -195161.116 / Time: 0h:41m:39s (0h:2m:10s left)
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Iteration 520 / LogL: -61024.698 / Time: 0h:14m:27s (0h:1m:1s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 157: -106905.761
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BETTER TREE FOUND at iteration 159: -106905.166
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Iteration 160 / LogL: -106919.857 / Time: 0h:7m:28s (0h:4m:38s left)
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Iteration 530 / LogL: -60994.828 / Time: 0h:14m:42s (0h:0m:45s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 540: -60981.572
Iteration 540 / LogL: -60981.572 / Time: 0h:14m:58s (0h:2m:46s left)
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Iteration 530 / LogL: -195174.834 / Time: 0h:42m:24s (0h:1m:21s left)
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Iteration 550 / LogL: -60982.988 / Time: 0h:15m:14s (0h:2m:29s left)
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Iteration 180 / LogL: -106929.007 / Time: 0h:8m:12s (0h:3m:37s left)
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BETTER TREE FOUND at iteration 557: -60981.572
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Iteration 560 / LogL: -60981.649 / Time: 0h:15m:29s (0h:2m:41s left)
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Iteration 570 / LogL: -60989.031 / Time: 0h:15m:44s (0h:2m:24s left)
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Iteration 190 / LogL: -106923.121 / Time: 0h:8m:34s (0h:3m:7s left)
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Iteration 540 / LogL: -195144.166 / Time: 0h:43m:7s (0h:0m:33s left)
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Iteration 580 / LogL: -60986.492 / Time: 0h:15m:59s (0h:2m:7s left)
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Iteration 200 / LogL: -106988.591 / Time: 0h:8m:55s (0h:2m:38s left)
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Iteration 590 / LogL: -61002.051 / Time: 0h:16m:15s (0h:1m:50s left)
Optimizing NNI: done in 1.82154 secs using 398.9% CPU
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Optimizing NNI: done in 4.39806 secs using 596.9% CPU
TREE SEARCH COMPLETED AFTER 548 ITERATIONS / Time: 0h:43m:43s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
Optimizing NNI: done in 1.57846 secs using 398.8% CPU
1. Initial log-likelihood: -195134.828
Optimizing NNI: done in 2.16588 secs using 398.8% CPU
Optimizing NNI: done in 1.65307 secs using 398.9% CPU
2. Current log-likelihood: -195134.812
Optimal log-likelihood: -195134.803
Site proportion and rates:  (0.026,0.130) (0.069,0.280) (0.071,0.354) (0.219,0.530) (0.199,0.772) (0.178,1.022) (0.139,1.632) (0.100,2.743)
Parameters optimization took 2 rounds (2.763 sec)
BEST SCORE FOUND : -195134.803
Total tree length: 159.464

Total number of iterations: 548
CPU time used for tree search: 15316.936 sec (4h:15m:16s)
Wall-clock time used for tree search: 2589.692 sec (0h:43m:9s)
Total CPU time used: 15533.851 sec (4h:18m:53s)
Total wall-clock time used: 2626.090 sec (0h:43m:46s)

===> START BOOTSTRAP REPLICATE NUMBER 22

Creating bootstrap alignment (seed: 70485)...

Optimizing NNI: done in 1.70097 secs using 398.5% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.312 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -195826.173
Optimizing NNI: done in 1.63798 secs using 398.5% CPU
Optimizing NNI: done in 1.63008 secs using 399% CPU
Optimizing NNI: done in 2.2858 secs using 398.8% CPU
Iteration 210 / LogL: -106964.341 / Time: 0h:9m:16s (0h:2m:10s left)
2. Current log-likelihood: -193423.177
Optimizing NNI: done in 1.51815 secs using 398.7% CPU
Optimizing NNI: done in 2.538 secs using 398.6% CPU
Optimizing NNI: done in 1.49163 secs using 399.2% CPU
Iteration 600 / LogL: -60984.810 / Time: 0h:16m:31s (0h:1m:34s left)
3. Current log-likelihood: -193333.622
Optimizing NNI: done in 1.05561 secs using 399.2% CPU
Optimizing NNI: done in 2.08344 secs using 398.6% CPU
4. Current log-likelihood: -193310.479
Optimizing NNI: done in 1.69362 secs using 399.2% CPU
Optimizing NNI: done in 1.24532 secs using 399.2% CPU
Optimizing NNI: done in 2.2263 secs using 399% CPU
5. Current log-likelihood: -193301.816
Optimizing NNI: done in 1.92372 secs using 399.1% CPU
Optimizing NNI: done in 2.31456 secs using 398.4% CPU
6. Current log-likelihood: -193300.858
Optimizing NNI: done in 1.40211 secs using 398.8% CPU
Optimizing NNI: done in 1.92213 secs using 398.4% CPU
Optimizing NNI: done in 1.33397 secs using 398.9% CPU
Optimal log-likelihood: -193300.773
Site proportion and rates:  (0.011,0.082) (0.040,0.210) (0.094,0.346) (0.240,0.521) (0.154,0.744) (0.212,1.035) (0.176,1.694) (0.073,2.755)
Parameters optimization took 6 rounds (14.116 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.41004 secs using 399.1% CPU
Optimizing NNI: done in 2.35896 secs using 399.1% CPU
Optimizing NNI: done in 1.33115 secs using 399.5% CPU
Optimizing NNI: done in 1.49584 secs using 398.8% CPU
Optimizing NNI: done in 2.23781 secs using 399% CPU
Optimizing NNI: done in 1.42416 secs using 398.7% CPU
Iteration 610 / LogL: -60981.572 / Time: 0h:16m:45s (0h:1m:17s left)
Optimizing NNI: done in 2.20875 secs using 398.6% CPU
Optimizing NNI: done in 1.6216 secs using 399.2% CPU
Optimizing NNI: done in 1.67923 secs using 399.6% CPU
Optimizing NNI: done in 2.70121 secs using 398.7% CPU
Calculating distance matrix: done in 9.95232 secs using 599.9% CPU
Computing ML distances took 9.952852 sec (of wall-clock time) 59.702549 sec (of CPU time)
Optimizing NNI: done in 1.46304 secs using 399.4% CPU
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00129294 secs using 672.8% CPU
Constructing RapidNJ tree: done in 0.0224669 secs using 685.4% CPU
Computing RapidNJ tree took 0.023837 sec (of wall-clock time) 0.163829 sec (of CPU time)
Optimizing NNI: done in 2.08764 secs using 399.1% CPU
Iteration 220 / LogL: -106918.261 / Time: 0h:9m:39s (0h:1m:43s left)
Optimizing NNI: done in 1.7813 secs using 399.2% CPU
Log-likelihood of RapidNJ tree: -196638.421
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.13348 secs using 398.5% CPU
Optimizing NNI: done in 1.49735 secs using 399.2% CPU
Optimizing NNI: done in 1.79284 secs using 398.6% CPU
Optimizing NNI: done in 2.34565 secs using 398.6% CPU
Optimizing NNI: done in 1.28366 secs using 399.5% CPU
Optimizing NNI: done in 1.98658 secs using 398.9% CPU
Optimizing NNI: done in 1.49039 secs using 399.2% CPU
Optimizing NNI: done in 1.94771 secs using 398.7% CPU
Optimizing NNI: done in 2.46104 secs using 398.6% CPU
Optimizing NNI: done in 1.71637 secs using 398.6% CPU
Optimizing NNI: done in 2.08775 secs using 399% CPU
Iteration 620 / LogL: -60986.864 / Time: 0h:17m:2s (0h:1m:1s left)
Optimizing NNI: done in 1.53263 secs using 398.8% CPU
Optimizing NNI: done in 1.97557 secs using 398.6% CPU
Optimizing NNI: done in 1.81281 secs using 398.8% CPU
Optimizing NNI: done in 2.29091 secs using 398.9% CPU
Optimizing NNI: done in 1.96196 secs using 398.8% CPU
Optimizing NNI: done in 2.42781 secs using 398.5% CPU
Optimizing NNI: done in 2.1916 secs using 398.5% CPU
Optimizing NNI: done in 2.47039 secs using 398.2% CPU
Optimizing NNI: done in 2.2289 secs using 398.9% CPU
Optimizing NNI: done in 1.92951 secs using 399% CPU
Iteration 230 / LogL: -106907.250 / Time: 0h:10m:1s (0h:1m:16s left)
Optimizing NNI: done in 2.27388 secs using 398.7% CPU
Optimizing NNI: done in 2.04215 secs using 398.6% CPU
Optimizing NNI: done in 1.93957 secs using 398.1% CPU
Optimizing NNI: done in 1.79463 secs using 399.2% CPU
Optimizing NNI: done in 1.96243 secs using 398.8% CPU
Optimizing NNI: done in 2.22607 secs using 398.8% CPU
Optimizing NNI: done in 2.34686 secs using 398.6% CPU
Optimizing NNI: done in 2.12641 secs using 398.9% CPU
Optimizing NNI: done in 2.02916 secs using 399% CPU
Iteration 630 / LogL: -60984.748 / Time: 0h:17m:22s (0h:0m:44s left)
29.715 second
Optimizing NNI: done in 2.35935 secs using 396.1% CPU
Optimizing NNI: done in 1.93782 secs using 398.6% CPU
Optimizing NNI: done in 2.0438 secs using 398.9% CPU
Optimizing NNI: done in 1.86958 secs using 398.7% CPU
Optimizing NNI: done in 1.60115 secs using 398.8% CPU
Optimizing NNI: done in 2.52499 secs using 398.2% CPU
Optimizing NNI: done in 1.58437 secs using 398.7% CPU
Optimizing NNI: done in 2.47693 secs using 398.7% CPU
Optimizing NNI: done in 2.01179 secs using 399.3% CPU
Optimizing NNI: done in 2.55099 secs using 399.3% CPU
Optimizing NNI: done in 2.22067 secs using 398.6% CPU
Optimizing NNI: done in 1.69506 secs using 398.4% CPU
Optimizing NNI: done in 2.16056 secs using 398.8% CPU
Iteration 240 / LogL: -106971.083 / Time: 0h:10m:23s (0h:0m:49s left)
Optimizing NNI: done in 2.17178 secs using 398.7% CPU
Optimizing NNI: done in 2.15182 secs using 398.4% CPU
Computing log-likelihood of 98 initial trees ... 16.459 seconds
Current best score: -193268.414

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.06313 secs using 398.6% CPU
Optimizing NNI: done in 1.92514 secs using 398.4% CPU
Optimizing NNI: done in 2.01926 secs using 399.1% CPU
Optimizing NNI: done in 2.46712 secs using 398.9% CPU
Iteration 640 / LogL: -60992.293 / Time: 0h:17m:42s (0h:0m:28s left)
Optimizing NNI: done in 4.49079 secs using 596.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.90861 secs using 398.4% CPU
Optimizing NNI: done in 1.80244 secs using 398.4% CPU
Optimizing NNI: done in 1.55728 secs using 398.2% CPU
Optimizing NNI: done in 2.33868 secs using 398.9% CPU
Optimizing NNI: done in 1.42783 secs using 398.9% CPU
Optimizing NNI: done in 1.79796 secs using 398.3% CPU
Optimizing NNI: done in 1.69987 secs using 398.8% CPU
Optimizing NNI: done in 1.66241 secs using 398.9% CPU
Optimizing NNI: done in 2.68971 secs using 398.8% CPU
Optimizing NNI: done in 1.21546 secs using 398.7% CPU
BETTER TREE FOUND at iteration 1: -192493.353
Optimizing NNI: done in 2.34165 secs using 398.2% CPU
Optimizing NNI: done in 1.51636 secs using 398.9% CPU
Optimizing NNI: done in 1.58903 secs using 398.8% CPU
Optimizing NNI: done in 1.88349 secs using 399% CPU
Optimizing NNI: done in 1.43742 secs using 399.1% CPU
Optimizing NNI: done in 4.18943 secs using 597.3% CPU
Optimizing NNI: done in 2.29561 secs using 398.9% CPU
Iteration 250 / LogL: -106911.552 / Time: 0h:10m:45s (0h:0m:23s left)
Optimizing NNI: done in 1.74146 secs using 398.9% CPU
Iteration 650 / LogL: -60992.178 / Time: 0h:17m:58s (0h:0m:11s left)
Optimizing NNI: done in 2.02163 secs using 398.8% CPU
Optimizing NNI: done in 2.99976 secs using 596.6% CPU
Optimizing NNI: done in 1.49007 secs using 399.4% CPU
Optimizing NNI: done in 1.84664 secs using 399.2% CPU
Optimizing NNI: done in 2.11364 secs using 399.2% CPU
Optimizing NNI: done in 1.54487 secs using 399% CPU
Optimizing NNI: done in 1.96554 secs using 398.7% CPU
Optimizing NNI: done in 4.29745 secs using 596.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.51158 secs using 399.2% CPU
BETTER TREE FOUND at iteration 654: -60981.571
Optimizing NNI: done in 1.86482 secs using 398.2% CPU
Optimizing NNI: done in 1.09175 secs using 398.6% CPU
Optimizing NNI: done in 1.37209 secs using 399% CPU
Optimizing NNI: done in 2.10468 secs using 398.7% CPU
BETTER TREE FOUND at iteration 4: -192488.554
Optimizing NNI: done in 1.54777 secs using 398.8% CPU
Optimizing NNI: done in 2.0195 secs using 398.7% CPU
Optimizing NNI: done in 1.53135 secs using 398.4% CPU
Optimizing NNI: done in 1.58269 secs using 398.6% CPU
Optimizing NNI: done in 2.4534 secs using 398.7% CPU
Optimizing NNI: done in 4.46367 secs using 596.5% CPU
Optimizing NNI: done in 1.2726 secs using 399% CPU
Iteration 660 / LogL: -61005.342 / Time: 0h:18m:13s (0h:2m:35s left)
Optimizing NNI: done in 2.16496 secs using 398.6% CPU
Optimizing NNI: done in 1.53005 secs using 399.4% CPU
Optimizing NNI: done in 3.56159 secs using 597.8% CPU
Optimizing NNI: done in 1.49001 secs using 398.9% CPU
Optimizing NNI: done in 2.00988 secs using 398.3% CPU
Optimizing NNI: done in 1.2985 secs using 398.6% CPU
Optimizing NNI: done in 2.49018 secs using 398.6% CPU
Iteration 260 / LogL: -106908.364 / Time: 0h:11m:6s (0h:0m:-3s left)
TREE SEARCH COMPLETED AFTER 260 ITERATIONS / Time: 0h:11m:6s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106905.166
Optimizing NNI: done in 1.62627 secs using 399.1% CPU
2. Current log-likelihood: -106905.133
Optimizing NNI: done in 1.29168 secs using 399.3% CPU
3. Current log-likelihood: -106905.077
Optimizing NNI: done in 5.06372 secs using 596.7% CPU
4. Current log-likelihood: -106905.034
Optimizing NNI: done in 1.50034 secs using 398.8% CPU
5. Current log-likelihood: -106904.995
Optimizing NNI: done in 1.57221 secs using 399.1% CPU
6. Current log-likelihood: -106904.957
7. Current log-likelihood: -106904.919
Optimizing NNI: done in 1.58934 secs using 399% CPU
Optimizing NNI: done in 4.15117 secs using 597.6% CPU
8. Current log-likelihood: -106904.886
Optimizing NNI: done in 1.21151 secs using 399.3% CPU
9. Current log-likelihood: -106904.854
10. Current log-likelihood: -106904.826
Optimizing NNI: done in 1.36154 secs using 399.3% CPU
Iteration 670 / LogL: -60987.379 / Time: 0h:18m:27s (0h:2m:19s left)
11. Current log-likelihood: -106904.806
12. Current log-likelihood: -106904.778
Optimizing NNI: done in 1.53066 secs using 399.1% CPU
13. Current log-likelihood: -106904.758
Optimizing NNI: done in 4.50319 secs using 596.5% CPU
14. Current log-likelihood: -106904.732
Optimizing NNI: done in 1.62315 secs using 398.7% CPU
15. Current log-likelihood: -106904.713
16. Current log-likelihood: -106904.688
17. Current log-likelihood: -106904.671
Optimizing NNI: done in 1.50796 secs using 399.2% CPU
18. Current log-likelihood: -106904.653
19. Current log-likelihood: -106904.634
20. Current log-likelihood: -106904.615
Optimizing NNI: done in 4.1136 secs using 596.1% CPU
Iteration 10 / LogL: -192621.701 / Time: 0h:2m:7s
Optimizing NNI: done in 1.52365 secs using 399.2% CPU
21. Current log-likelihood: -106904.597
22. Current log-likelihood: -106904.578
Optimizing NNI: done in 1.587 secs using 398.9% CPU
23. Current log-likelihood: -106904.560
24. Current log-likelihood: -106904.543
Optimizing NNI: done in 1.41861 secs using 398.6% CPU
25. Current log-likelihood: -106904.526
Optimizing NNI: done in 3.40726 secs using 596.8% CPU
26. Current log-likelihood: -106904.509
27. Current log-likelihood: -106904.493
28. Current log-likelihood: -106904.478
Optimizing NNI: done in 1.75349 secs using 398.8% CPU
29. Current log-likelihood: -106904.462
30. Current log-likelihood: -106904.447
31. Current log-likelihood: -106904.432
Optimizing NNI: done in 1.49709 secs using 399% CPU
32. Current log-likelihood: -106904.418
33. Current log-likelihood: -106904.404
Optimizing NNI: done in 1.49485 secs using 398.3% CPU
Optimizing NNI: done in 4.49247 secs using 596.8% CPU
34. Current log-likelihood: -106904.390
35. Current log-likelihood: -106904.375
Optimizing NNI: done in 1.40982 secs using 398.8% CPU
Iteration 680 / LogL: -61006.621 / Time: 0h:18m:43s (0h:2m:2s left)
36. Current log-likelihood: -106904.361
37. Current log-likelihood: -106904.348
Optimizing NNI: done in 1.30862 secs using 399.1% CPU
38. Current log-likelihood: -106904.334
39. Current log-likelihood: -106904.321
Optimizing NNI: done in 4.20365 secs using 597.7% CPU
Optimizing NNI: done in 1.51379 secs using 399.4% CPU
40. Current log-likelihood: -106904.309
41. Current log-likelihood: -106904.297
42. Current log-likelihood: -106904.284
Optimizing NNI: done in 1.50931 secs using 398.8% CPU
43. Current log-likelihood: -106904.272
44. Current log-likelihood: -106904.261
Optimizing NNI: done in 1.5579 secs using 398.9% CPU
45. Current log-likelihood: -106904.249
46. Current log-likelihood: -106904.239
Optimizing NNI: done in 4.33105 secs using 597.2% CPU
Optimal log-likelihood: -106904.227
Proportion of invariable sites: 0.030
Site proportion and rates:  (0.104,0.039) (0.071,0.105) (0.074,0.186) (0.125,0.304) (0.063,0.412) (0.122,0.695) (0.155,1.163) (0.190,1.925) (0.068,4.124)
Parameters optimization took 46 rounds (31.645 sec)
BEST SCORE FOUND : -106904.227
Total tree length: 170.607

Total number of iterations: 260
CPU time used for tree search: 2551.545 sec (0h:42m:31s)
Wall-clock time used for tree search: 648.420 sec (0h:10m:48s)
Total CPU time used: 2751.583 sec (0h:45m:51s)
Total wall-clock time used: 698.615 sec (0h:11m:38s)

===> START BOOTSTRAP REPLICATE NUMBER 35

Creating bootstrap alignment (seed: 68217)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.115 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104639.791
Optimizing NNI: done in 1.77795 secs using 398.8% CPU
Optimizing NNI: done in 1.64613 secs using 399% CPU
2. Current log-likelihood: -102352.423
Optimizing NNI: done in 1.42924 secs using 399% CPU
3. Current log-likelihood: -102276.934
Optimizing NNI: done in 1.43519 secs using 399.1% CPU
Optimizing NNI: done in 5.26339 secs using 596.8% CPU
4. Current log-likelihood: -102275.260
Optimizing NNI: done in 1.28046 secs using 398.8% CPU
Optimal log-likelihood: -102275.147
Proportion of invariable sites: 0.030
Site proportion and rates:  (0.113,0.037) (0.100,0.119) (0.042,0.202) (0.119,0.298) (0.095,0.471) (0.115,0.724) (0.120,1.164) (0.174,1.807) (0.093,3.864)
Parameters optimization took 4 rounds (6.843 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.60556 secs using 398.9% CPU
Iteration 690 / LogL: -60993.442 / Time: 0h:18m:58s (0h:1m:45s left)
Optimizing NNI: done in 3.75336 secs using 597.2% CPU
Optimizing NNI: done in 1.62969 secs using 399.6% CPU
Optimizing NNI: done in 1.46438 secs using 398.5% CPU
Calculating distance matrix: done in 4.74406 secs using 400% CPU
Computing ML distances took 4.744506 sec (of wall-clock time) 18.975911 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000702858 secs using 275.3% CPU
Constructing RapidNJ tree: done in 0.00851917 secs using 366.3% CPU
Computing RapidNJ tree took 0.009285 sec (of wall-clock time) 0.035995 sec (of CPU time)
Optimizing NNI: done in 1.34662 secs using 399.2% CPU
Log-likelihood of RapidNJ tree: -102542.257
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.32628 secs using 597.5% CPU
Optimizing NNI: done in 1.17033 secs using 399% CPU
Optimizing NNI: done in 1.41342 secs using 399% CPU
UPDATE BEST LOG-LIKELIHOOD: -60981.570
Optimizing NNI: done in 1.65977 secs using 399.4% CPU
Optimizing NNI: done in 1.69676 secs using 398.8% CPU
Optimizing NNI: done in 5.28114 secs using 597.5% CPU
Optimizing NNI: done in 1.34601 secs using 398.9% CPU
Optimizing NNI: done in 1.21067 secs using 399.5% CPU
Optimizing NNI: done in 1.4099 secs using 399% CPU
Iteration 700 / LogL: -61005.172 / Time: 0h:19m:13s (0h:1m:29s left)
10.701 second
Optimizing NNI: done in 1.48423 secs using 399.3% CPU
Optimizing NNI: done in 1.53209 secs using 399.4% CPU
Optimizing NNI: done in 7.16189 secs using 596.8% CPU
Optimizing NNI: done in 1.55755 secs using 398.9% CPU
Optimizing NNI: done in 1.6591 secs using 399.4% CPU
Optimizing NNI: done in 3.35331 secs using 597.9% CPU
Iteration 20 / LogL: -192645.841 / Time: 0h:2m:53s
Finish initializing candidate tree set (20)
Current best tree score: -192488.554 / CPU time: 146.521
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.45126 secs using 399% CPU
Optimizing NNI: done in 1.339 secs using 398.7% CPU
Optimizing NNI: done in 1.628 secs using 399.5% CPU
Optimizing NNI: done in 4.89487 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.2101 secs using 398.9% CPU
Computing log-likelihood of 98 initial trees ... 10.929 seconds
Current best score: -102275.147

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.80488 secs using 399.2% CPU
Optimizing NNI: done in 1.93615 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -192452.716
Optimizing NNI: done in 1.3402 secs using 398.7% CPU
Iteration 710 / LogL: -60983.635 / Time: 0h:19m:28s (0h:1m:12s left)
Optimizing NNI: done in 1.71321 secs using 398.4% CPU
Optimizing NNI: done in 1.369 secs using 399.5% CPU
Optimizing NNI: done in 4.69593 secs using 598.2% CPU
Optimizing NNI: done in 1.78889 secs using 399.2% CPU
Optimizing NNI: done in 1.48331 secs using 398.8% CPU
Optimizing NNI: done in 2.00724 secs using 399% CPU
Optimizing NNI: done in 5.15849 secs using 597.1% CPU
Optimizing NNI: done in 1.62145 secs using 399.5% CPU
Optimizing NNI: done in 1.54781 secs using 398.9% CPU
Optimizing NNI: done in 1.72776 secs using 399.2% CPU
Optimizing NNI: done in 4.77793 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.73655 secs using 399.3% CPU
Optimizing NNI: done in 1.75031 secs using 398.8% CPU
Iteration 720 / LogL: -61010.425 / Time: 0h:19m:45s (0h:0m:56s left)
BETTER TREE FOUND at iteration 24: -192413.533
Optimizing NNI: done in 1.29392 secs using 399% CPU
Optimizing NNI: done in 1.5703 secs using 399.1% CPU
Optimizing NNI: done in 1.70435 secs using 399% CPU
Optimizing NNI: done in 4.60547 secs using 597.3% CPU
Optimizing NNI: done in 1.63861 secs using 398.7% CPU
BETTER TREE FOUND at iteration 1: -101799.537
Optimizing NNI: done in 1.32964 secs using 399.1% CPU
Optimizing NNI: done in 1.23753 secs using 399.4% CPU
Optimizing NNI: done in 1.9624 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.92606 secs using 597% CPU
Optimizing NNI: done in 1.5345 secs using 398.8% CPU
Optimizing NNI: done in 1.55769 secs using 398.8% CPU
Optimizing NNI: done in 1.74075 secs using 399.2% CPU
Optimizing NNI: done in 4.45732 secs using 597.8% CPU
BETTER TREE FOUND at iteration 2: -101774.285
Optimizing NNI: done in 1.79031 secs using 398.8% CPU
Iteration 730 / LogL: -60990.174 / Time: 0h:20m:0s (0h:0m:39s left)
Optimizing NNI: done in 1.38875 secs using 399.3% CPU
Optimizing NNI: done in 1.32312 secs using 399.1% CPU
Optimizing NNI: done in 3.04999 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.80493 secs using 596.6% CPU
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Iteration 30 / LogL: -192444.024 / Time: 0h:3m:47s (0h:12m:16s left)
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BETTER TREE FOUND at iteration 3: -101731.837
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Estimate model parameters (epsilon = 0.100)
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Iteration 750 / LogL: -60996.947 / Time: 0h:20m:31s (0h:0m:6s left)
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BETTER TREE FOUND at iteration 10: -101686.224
Iteration 10 / LogL: -101686.224 / Time: 0h:1m:46s
Optimizing NNI: done in 1.66933 secs using 398.6% CPU
TREE SEARCH COMPLETED AFTER 755 ITERATIONS / Time: 0h:20m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60981.570
Optimal log-likelihood: -60981.563
Site proportion and rates:  (0.077,0.062) (0.138,0.159) (0.159,0.366) (0.211,0.658) (0.151,1.047) (0.144,1.657) (0.087,2.370) (0.033,5.290)
Parameters optimization took 1 rounds (0.397 sec)
BEST SCORE FOUND : -60981.563
Total tree length: 48.475

Total number of iterations: 755
CPU time used for tree search: 4899.121 sec (1h:21m:39s)
Wall-clock time used for tree search: 1231.813 sec (0h:20m:31s)
Total CPU time used: 4930.090 sec (1h:22m:10s)
Total wall-clock time used: 1239.549 sec (0h:20m:39s)

===> START BOOTSTRAP REPLICATE NUMBER 86

Creating bootstrap alignment (seed: 67548)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.035 seconds

NOTE: 65 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59647.418
2. Current log-likelihood: -59105.569
Optimizing NNI: done in 3.3217 secs using 398.3% CPU
3. Current log-likelihood: -59102.033
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4. Current log-likelihood: -59098.879
5. Current log-likelihood: -59083.972
Optimizing NNI: done in 2.62824 secs using 398.4% CPU
6. Current log-likelihood: -59073.117
7. Current log-likelihood: -59067.266
8. Current log-likelihood: -59066.642
Optimizing NNI: done in 3.02917 secs using 398.4% CPU
Optimal log-likelihood: -59066.600
Site proportion and rates:  (0.125,0.063) (0.111,0.187) (0.083,0.418) (0.113,0.429) (0.239,0.795) (0.161,1.384) (0.142,2.293) (0.026,5.693)
Parameters optimization took 8 rounds (7.002 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.10148 secs using 400.1% CPU
Computing ML distances took 1.101670 sec (of wall-clock time) 4.407152 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00041604 secs using 185.8% CPU
Constructing RapidNJ tree: done in 0.00434613 secs using 346.8% CPU
Computing RapidNJ tree took 0.004817 sec (of wall-clock time) 0.018361 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59107.203
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.61152 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 14: -101666.680
Optimizing NNI: done in 5.48978 secs using 597% CPU
5.225 second
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Computing log-likelihood of 98 initial trees ... 5.298 seconds
Current best score: -59056.221

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 40: -192390.561
Iteration 40 / LogL: -192390.561 / Time: 0h:4m:38s (0h:11m:52s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -101777.427 / Time: 0h:2m:18s
Finish initializing candidate tree set (20)
Current best tree score: -101666.680 / CPU time: 125.227
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 42: -192387.300
BETTER TREE FOUND at iteration 9: -58830.536
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Iteration 10 / LogL: -58884.532 / Time: 0h:0m:37s
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Iteration 20 / LogL: -58862.046 / Time: 0h:0m:50s
Finish initializing candidate tree set (20)
Current best tree score: -58830.536 / CPU time: 42.230
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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UPDATE BEST LOG-LIKELIHOOD: -58802.666
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Iteration 140 / LogL: -58802.801 / Time: 0h:3m:58s (0h:2m:30s left)
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UPDATE BEST LOG-LIKELIHOOD: -58799.921
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 129: -101638.660
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 102: -192363.561
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 155: -101637.936
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Iteration 160 / LogL: -101728.357 / Time: 0h:7m:49s (0h:4m:40s left)
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TREE SEARCH COMPLETED AFTER 229 ITERATIONS / Time: 0h:6m:8s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58799.921
Optimizing NNI: done in 4.39522 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.1136 secs using 398.8% CPU
2. Current log-likelihood: -58799.895
3. Current log-likelihood: -58799.875
4. Current log-likelihood: -58799.852
5. Current log-likelihood: -58799.828
Optimizing NNI: done in 2.21156 secs using 398.8% CPU
6. Current log-likelihood: -58799.802
BETTER TREE FOUND at iteration 113: -192362.843
7. Current log-likelihood: -58799.774
Optimizing NNI: done in 1.79088 secs using 398.4% CPU
8. Current log-likelihood: -58799.743
9. Current log-likelihood: -58799.708
10. Current log-likelihood: -58799.666
Optimizing NNI: done in 1.9194 secs using 398.7% CPU
11. Current log-likelihood: -58799.614
12. Current log-likelihood: -58799.552
13. Current log-likelihood: -58799.477
Optimizing NNI: done in 2.20371 secs using 398.3% CPU
Optimizing NNI: done in 4.76237 secs using 597.5% CPU
14. Current log-likelihood: -58799.385
15. Current log-likelihood: -58799.275
16. Current log-likelihood: -58799.154
Optimizing NNI: done in 2.28494 secs using 398.7% CPU
17. Current log-likelihood: -58799.032
18. Current log-likelihood: -58798.919
19. Current log-likelihood: -58798.820
Optimizing NNI: done in 1.89515 secs using 398.9% CPU
Iteration 170 / LogL: -101639.065 / Time: 0h:8m:10s (0h:4m:6s left)
Optimizing NNI: done in 4.20063 secs using 597.8% CPU
20. Current log-likelihood: -58798.734
21. Current log-likelihood: -58798.658
Optimizing NNI: done in 1.67595 secs using 398.5% CPU
22. Current log-likelihood: -58798.591
23. Current log-likelihood: -58798.531
24. Current log-likelihood: -58798.476
Optimizing NNI: done in 2.13824 secs using 398.5% CPU
25. Current log-likelihood: -58798.426
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26. Current log-likelihood: -58798.380
27. Current log-likelihood: -58798.340
Optimizing NNI: done in 2.04304 secs using 398.7% CPU
28. Current log-likelihood: -58798.307
29. Current log-likelihood: -58798.278
30. Current log-likelihood: -58798.251
Optimizing NNI: done in 2.42858 secs using 398.4% CPU
31. Current log-likelihood: -58798.229
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32. Current log-likelihood: -58798.207
33. Current log-likelihood: -58798.190
Optimizing NNI: done in 2.083 secs using 398.9% CPU
34. Current log-likelihood: -58798.174
35. Current log-likelihood: -58798.159
36. Current log-likelihood: -58798.147
37. Current log-likelihood: -58798.135
Optimizing NNI: done in 2.44602 secs using 398.8% CPU
Optimizing NNI: done in 4.46778 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
38. Current log-likelihood: -58798.124
39. Current log-likelihood: -58798.113
40. Current log-likelihood: -58798.102
Optimizing NNI: done in 1.98476 secs using 398.7% CPU
Optimal log-likelihood: -58798.091
Site proportion and rates:  (0.108,0.056) (0.120,0.167) (0.183,0.402) (0.156,0.690) (0.134,0.971) (0.143,1.488) (0.130,2.297) (0.026,5.799)
Parameters optimization took 40 rounds (28.595 sec)
BEST SCORE FOUND : -58798.091
Total tree length: 44.020

Total number of iterations: 229
CPU time used for tree search: 1420.591 sec (0h:23m:40s)
Wall-clock time used for tree search: 359.908 sec (0h:5m:59s)
Total CPU time used: 1569.163 sec (0h:26m:9s)
Total wall-clock time used: 397.164 sec (0h:6m:37s)

===> START BOOTSTRAP REPLICATE NUMBER 87

Creating bootstrap alignment (seed: 67549)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.058 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -57698.715
2. Current log-likelihood: -57211.134
BETTER TREE FOUND at iteration 118: -192360.926
Optimizing NNI: done in 2.07159 secs using 398.8% CPU
3. Current log-likelihood: -57204.781
4. Current log-likelihood: -57199.912
5. Current log-likelihood: -57181.053
Optimizing NNI: done in 2.54357 secs using 398.5% CPU
6. Current log-likelihood: -57174.763
7. Current log-likelihood: -57173.760
8. Current log-likelihood: -57173.253
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Iteration 180 / LogL: -101643.527 / Time: 0h:8m:32s (0h:3m:34s left)
9. Current log-likelihood: -57172.707
10. Current log-likelihood: -57172.140
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11. Current log-likelihood: -57171.633
12. Current log-likelihood: -57171.245
13. Current log-likelihood: -57170.971
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Optimizing NNI: done in 2.2006 secs using 398.3% CPU
14. Current log-likelihood: -57170.785
15. Current log-likelihood: -57170.658
Optimal log-likelihood: -57170.556
Site proportion and rates:  (0.092,0.058) (0.156,0.191) (0.172,0.386) (0.148,0.616) (0.173,0.978) (0.089,1.509) (0.137,2.369) (0.033,5.462)
Parameters optimization took 15 rounds (12.296 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 1.09718 secs using 400% CPU
Computing ML distances took 1.097362 sec (of wall-clock time) 4.388851 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000394106 secs using 425.5% CPU
Constructing RapidNJ tree: done in 0.00431013 secs using 384.9% CPU
Computing RapidNJ tree took 0.004768 sec (of wall-clock time) 0.019169 sec (of CPU time)
Log-likelihood of RapidNJ tree: -57027.723
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.11322 secs using 398.9% CPU
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4.903 second
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Computing log-likelihood of 98 initial trees ... 5.080 seconds
Current best score: -56966.121

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Iteration 20 / LogL: -56822.009 / Time: 0h:0m:54s
Finish initializing candidate tree set (20)
Current best tree score: -56755.367 / CPU time: 40.662
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 129: -56684.954
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 213: -56684.866
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TREE SEARCH COMPLETED AFTER 335 ITERATIONS / Time: 0h:14m:24s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101637.817
Optimal log-likelihood: -101637.812
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.104,0.030) (0.093,0.092) (0.050,0.169) (0.130,0.281) (0.110,0.479) (0.109,0.744) (0.108,1.163) (0.177,1.798) (0.090,4.056)
Parameters optimization took 1 rounds (0.779 sec)
BEST SCORE FOUND : -101637.812
Total tree length: 181.658

Total number of iterations: 335
CPU time used for tree search: 3363.409 sec (0h:56m:3s)
Wall-clock time used for tree search: 851.759 sec (0h:14m:11s)
Total CPU time used: 3417.667 sec (0h:56m:57s)
Total wall-clock time used: 865.347 sec (0h:14m:25s)

===> START BOOTSTRAP REPLICATE NUMBER 36

Creating bootstrap alignment (seed: 68218)...

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Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.115 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 100 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104383.946
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Iteration 220 / LogL: -56701.612 / Time: 0h:6m:0s (0h:2m:33s left)
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2. Current log-likelihood: -102288.369
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3. Current log-likelihood: -102223.994
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4. Current log-likelihood: -102222.727
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5. Current log-likelihood: -102221.911
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6. Current log-likelihood: -102221.235
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7. Current log-likelihood: -102220.773
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8. Current log-likelihood: -102220.404
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9. Current log-likelihood: -102220.109
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10. Current log-likelihood: -102219.986
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Iteration 230 / LogL: -56694.497 / Time: 0h:6m:14s (0h:2m:15s left)
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Iteration 200 / LogL: -192364.952 / Time: 0h:17m:5s (0h:1m:58s left)
11. Current log-likelihood: -102219.867
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12. Current log-likelihood: -102219.745
Optimizing NNI: done in 1.34125 secs using 399.3% CPU
Optimal log-likelihood: -102219.631
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.104,0.036) (0.080,0.114) (0.061,0.196) (0.094,0.295) (0.099,0.442) (0.134,0.674) (0.150,1.091) (0.162,1.784) (0.083,4.371)
Parameters optimization took 12 rounds (17.699 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 4.68656 secs using 399.9% CPU
Computing ML distances took 4.686831 sec (of wall-clock time) 18.742169 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000686884 secs using 417% CPU
Constructing RapidNJ tree: done in 0.008811 secs using 362.4% CPU
Computing RapidNJ tree took 0.009557 sec (of wall-clock time) 0.037309 sec (of CPU time)
Optimizing NNI: done in 1.10291 secs using 398.6% CPU
Log-likelihood of RapidNJ tree: -102756.037
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.25099 secs using 596.8% CPU
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Iteration 240 / LogL: -56685.487 / Time: 0h:6m:27s (0h:1m:58s left)
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10.601 second
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Iteration 250 / LogL: -56701.438 / Time: 0h:6m:41s (0h:1m:41s left)
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Computing log-likelihood of 98 initial trees ... 9.524 seconds
Current best score: -102219.631

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 258: -56684.517
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Iteration 260 / LogL: -56691.590 / Time: 0h:6m:56s (0h:2m:37s left)
BETTER TREE FOUND at iteration 1: -101844.397
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BETTER TREE FOUND at iteration 2: -101796.735
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 8: -101796.096
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Iteration 10 / LogL: -101880.160 / Time: 0h:1m:21s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 280: -56684.447
Iteration 280 / LogL: -56684.447 / Time: 0h:7m:24s (0h:2m:39s left)
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Iteration 290 / LogL: -56687.976 / Time: 0h:7m:38s (0h:2m:22s left)
Optimizing NNI: done in 1.34695 secs using 399.2% CPU
Optimizing NNI: done in 2.29114 secs using 398% CPU
Iteration 20 / LogL: -101897.295 / Time: 0h:1m:40s
Finish initializing candidate tree set (20)
Current best tree score: -101796.096 / CPU time: 77.490
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.48555 secs using 398.4% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.52836 secs using 398.5% CPU
Optimizing NNI: done in 1.28162 secs using 398.6% CPU
BETTER TREE FOUND at iteration 220: -192351.701
Iteration 220 / LogL: -192351.701 / Time: 0h:18m:39s (0h:8m:31s left)
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Iteration 300 / LogL: -56686.291 / Time: 0h:7m:51s (0h:2m:6s left)
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BETTER TREE FOUND at iteration 27: -101784.531
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BETTER TREE FOUND at iteration 28: -101780.120
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Iteration 30 / LogL: -101793.164 / Time: 0h:2m:2s (0h:6m:55s left)
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Iteration 310 / LogL: -56689.110 / Time: 0h:8m:5s (0h:1m:49s left)
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Iteration 320 / LogL: -56685.826 / Time: 0h:8m:19s (0h:1m:33s left)
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Iteration 40 / LogL: -101787.150 / Time: 0h:2m:25s (0h:5m:27s left)
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Iteration 330 / LogL: -56684.449 / Time: 0h:8m:32s (0h:1m:17s left)
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Iteration 230 / LogL: -192353.806 / Time: 0h:19m:26s (0h:7m:38s left)
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BETTER TREE FOUND at iteration 335: -56684.446
Optimizing NNI: done in 1.57835 secs using 398.5% CPU
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Optimizing NNI: done in 1.84331 secs using 398.6% CPU
Iteration 50 / LogL: -101788.812 / Time: 0h:2m:42s (0h:4m:19s left)
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Iteration 340 / LogL: -56685.330 / Time: 0h:8m:46s (0h:2m:27s left)
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 1.36734 secs using 399% CPU
BETTER TREE FOUND at iteration 58: -101779.739
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Optimizing NNI: done in 1.33444 secs using 398.7% CPU
Iteration 350 / LogL: -56685.899 / Time: 0h:9m:0s (0h:2m:11s left)
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Iteration 60 / LogL: -101809.578 / Time: 0h:3m:3s (0h:5m:4s left)
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UPDATE BEST LOG-LIKELIHOOD: -56684.446
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Iteration 240 / LogL: -192396.182 / Time: 0h:20m:7s (0h:6m:44s left)
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Iteration 360 / LogL: -56690.448 / Time: 0h:9m:19s (0h:1m:56s left)
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Iteration 70 / LogL: -101785.822 / Time: 0h:3m:28s (0h:4m:25s left)
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Iteration 370 / LogL: -56689.646 / Time: 0h:9m:40s (0h:1m:42s left)
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Iteration 80 / LogL: -101786.158 / Time: 0h:3m:52s (0h:3m:49s left)
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Iteration 380 / LogL: -56729.709 / Time: 0h:10m:1s (0h:1m:27s left)
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Iteration 250 / LogL: -192356.406 / Time: 0h:20m:51s (0h:5m:51s left)
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 1.70316 secs using 398.7% CPU
BETTER TREE FOUND at iteration 89: -101776.008
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Iteration 90 / LogL: -101781.736 / Time: 0h:4m:21s (0h:4m:50s left)
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Iteration 390 / LogL: -56688.315 / Time: 0h:10m:21s (0h:1m:11s left)
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Iteration 400 / LogL: -56699.035 / Time: 0h:10m:34s (0h:0m:55s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 258: -192351.500
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Iteration 100 / LogL: -101783.029 / Time: 0h:4m:44s (0h:4m:16s left)
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Iteration 260 / LogL: -192385.236 / Time: 0h:21m:38s (0h:8m:11s left)
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Iteration 410 / LogL: -56714.472 / Time: 0h:10m:48s (0h:0m:39s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 107: -101775.069
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Iteration 420 / LogL: -56752.860 / Time: 0h:11m:2s (0h:0m:23s left)
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Iteration 110 / LogL: -101775.383 / Time: 0h:5m:10s (0h:4m:35s left)
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Iteration 430 / LogL: -56687.972 / Time: 0h:11m:15s (0h:0m:7s left)
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Optimizing NNI: done in 1.48393 secs using 399.3% CPU
TREE SEARCH COMPLETED AFTER 436 ITERATIONS / Time: 0h:11m:24s

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|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -56684.446
Optimal log-likelihood: -56684.445
Site proportion and rates:  (0.138,0.072) (0.117,0.224) (0.167,0.375) (0.158,0.651) (0.163,1.012) (0.072,1.452) (0.150,2.279) (0.034,5.513)
Parameters optimization took 1 rounds (0.178 sec)
BEST SCORE FOUND : -56684.445
Total tree length: 42.771

Total number of iterations: 436
CPU time used for tree search: 2660.817 sec (0h:44m:20s)
Wall-clock time used for tree search: 670.760 sec (0h:11m:10s)
Total CPU time used: 2717.202 sec (0h:45m:17s)
Total wall-clock time used: 684.889 sec (0h:11m:24s)

===> START BOOTSTRAP REPLICATE NUMBER 88

Creating bootstrap alignment (seed: 67550)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.052 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -57927.520
2. Current log-likelihood: -57403.856
Optimizing NNI: done in 2.48498 secs using 398.7% CPU
3. Current log-likelihood: -57398.082
Optimizing NNI: done in 4.03252 secs using 597.2% CPU
4. Current log-likelihood: -57397.436
5. Current log-likelihood: -57397.158
Optimizing NNI: done in 2.62467 secs using 398.6% CPU
6. Current log-likelihood: -57397.040
Optimal log-likelihood: -57396.984
Site proportion and rates:  (0.106,0.058) (0.102,0.185) (0.099,0.413) (0.094,0.433) (0.222,0.777) (0.144,1.158) (0.139,1.889) (0.093,3.114)
Parameters optimization took 6 rounds (5.067 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.25901 secs using 398.6% CPU
Calculating distance matrix: done in 1.04912 secs using 400% CPU
Computing ML distances took 1.049309 sec (of wall-clock time) 4.196398 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00039196 secs using 163.5% CPU
Constructing RapidNJ tree: done in 0.00434899 secs using 313.7% CPU
Computing RapidNJ tree took 0.004812 sec (of wall-clock time) 0.016333 sec (of CPU time)
Log-likelihood of RapidNJ tree: -57525.235
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 4.62329 secs using 596.8% CPU
Iteration 270 / LogL: -192381.973 / Time: 0h:22m:22s (0h:7m:19s left)
Optimizing NNI: done in 2.05836 secs using 399.1% CPU
Iteration 120 / LogL: -101777.154 / Time: 0h:5m:33s (0h:4m:3s left)
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5.336 second
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Optimizing NNI: done in 2.07923 secs using 395.7% CPU
Computing log-likelihood of 98 initial trees ... 5.191 seconds
Current best score: -57268.944

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -57111.578
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Iteration 130 / LogL: -101792.997 / Time: 0h:5m:54s (0h:3m:31s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 10 / LogL: -57107.766 / Time: 0h:0m:38s
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Estimate model parameters (epsilon = 0.100)
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Iteration 140 / LogL: -101785.626 / Time: 0h:6m:13s (0h:2m:59s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 17: -57070.146
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Iteration 280 / LogL: -192418.443 / Time: 0h:23m:9s (0h:6m:28s left)
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Iteration 20 / LogL: -57116.361 / Time: 0h:0m:57s
Finish initializing candidate tree set (20)
Current best tree score: -57070.146 / CPU time: 50.529
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -57020.869
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Iteration 160 / LogL: -101778.050 / Time: 0h:6m:51s (0h:2m:1s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 170 / LogL: -101783.521 / Time: 0h:7m:10s (0h:1m:34s left)
BETTER TREE FOUND at iteration 45: -57011.813
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 50: -57010.822
Iteration 50 / LogL: -57010.822 / Time: 0h:1m:56s (0h:3m:56s left)
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Iteration 60 / LogL: -57027.434 / Time: 0h:2m:12s (0h:3m:22s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 62: -57008.696
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TREE SEARCH COMPLETED AFTER 208 ITERATIONS / Time: 0h:8m:23s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101775.069
2. Current log-likelihood: -101775.043
Optimizing NNI: done in 1.75669 secs using 398.5% CPU
Optimizing NNI: done in 4.24327 secs using 596.8% CPU
3. Current log-likelihood: -101775.001
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5. Current log-likelihood: -101774.917
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7. Current log-likelihood: -101774.837
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Iteration 90 / LogL: -57010.820 / Time: 0h:3m:4s (0h:2m:29s left)
8. Current log-likelihood: -101774.794
9. Current log-likelihood: -101774.756
Optimizing NNI: done in 1.50543 secs using 399.6% CPU
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Iteration 310 / LogL: -192385.748 / Time: 0h:25m:24s (0h:3m:56s left)
12. Current log-likelihood: -101774.634
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14. Current log-likelihood: -101774.551
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18. Current log-likelihood: -101774.392
19. Current log-likelihood: -101774.351
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Optimizing NNI: done in 1.95275 secs using 398.7% CPU
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24. Current log-likelihood: -101774.155
25. Current log-likelihood: -101774.115
Optimizing NNI: done in 1.60995 secs using 398.8% CPU
Iteration 100 / LogL: -57079.391 / Time: 0h:3m:21s (0h:2m:5s left)
26. Current log-likelihood: -101774.078
Optimizing NNI: done in 4.11327 secs using 597.7% CPU
27. Current log-likelihood: -101774.040
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31. Current log-likelihood: -101773.890
32. Current log-likelihood: -101773.851
Optimizing NNI: done in 1.80238 secs using 399.1% CPU
33. Current log-likelihood: -101773.814
Optimizing NNI: done in 1.6103 secs using 398.9% CPU
Optimizing NNI: done in 3.47905 secs using 597.4% CPU
34. Current log-likelihood: -101773.777
35. Current log-likelihood: -101773.739
Optimizing NNI: done in 1.54907 secs using 398.6% CPU
36. Current log-likelihood: -101773.706
Optimizing NNI: done in 1.73995 secs using 398.8% CPU
37. Current log-likelihood: -101773.669
Optimizing NNI: done in 4.76534 secs using 597.4% CPU
Optimizing NNI: done in 1.62669 secs using 399.2% CPU
38. Current log-likelihood: -101773.635
39. Current log-likelihood: -101773.600
Optimizing NNI: done in 1.94351 secs using 399.5% CPU
40. Current log-likelihood: -101773.567
Optimizing NNI: done in 1.34039 secs using 398.8% CPU
Iteration 110 / LogL: -57008.981 / Time: 0h:3m:37s (0h:1m:43s left)
41. Current log-likelihood: -101773.532
Optimizing NNI: done in 4.18263 secs using 597.3% CPU
42. Current log-likelihood: -101773.503
Optimizing NNI: done in 1.4393 secs using 399.1% CPU
43. Current log-likelihood: -101773.485
44. Current log-likelihood: -101773.467
45. Current log-likelihood: -101773.449
Optimizing NNI: done in 1.70635 secs using 399.3% CPU
46. Current log-likelihood: -101773.431
47. Current log-likelihood: -101773.413
Optimizing NNI: done in 1.66734 secs using 398.8% CPU
48. Current log-likelihood: -101773.395
Optimizing NNI: done in 4.55866 secs using 597.1% CPU
49. Current log-likelihood: -101773.378
50. Current log-likelihood: -101773.361
Optimizing NNI: done in 1.62812 secs using 399.2% CPU
51. Current log-likelihood: -101773.343
52. Current log-likelihood: -101773.327
53. Current log-likelihood: -101773.310
Optimizing NNI: done in 1.61876 secs using 398.8% CPU
54. Current log-likelihood: -101773.290
Optimizing NNI: done in 1.19934 secs using 398.7% CPU
55. Current log-likelihood: -101773.264
Optimizing NNI: done in 4.55078 secs using 597% CPU
56. Current log-likelihood: -101773.249
57. Current log-likelihood: -101773.233
58. Current log-likelihood: -101773.218
Optimizing NNI: done in 1.92228 secs using 399.2% CPU
59. Current log-likelihood: -101773.202
60. Current log-likelihood: -101773.187
61. Current log-likelihood: -101773.171
Optimizing NNI: done in 1.69888 secs using 398.3% CPU
62. Current log-likelihood: -101773.156
63. Current log-likelihood: -101773.141
Optimizing NNI: done in 4.10467 secs using 598.1% CPU
Iteration 320 / LogL: -192555.514 / Time: 0h:26m:7s (0h:3m:6s left)
64. Current log-likelihood: -101773.126
Optimizing NNI: done in 1.72818 secs using 398.7% CPU
65. Current log-likelihood: -101773.110
66. Current log-likelihood: -101773.095
67. Current log-likelihood: -101773.081
Optimizing NNI: done in 1.33317 secs using 399% CPU
Iteration 120 / LogL: -57023.691 / Time: 0h:3m:53s (0h:1m:22s left)
68. Current log-likelihood: -101773.065
Optimizing NNI: done in 1.47757 secs using 399.4% CPU
69. Current log-likelihood: -101773.051
70. Current log-likelihood: -101773.036
Optimizing NNI: done in 4.46441 secs using 598.2% CPU
71. Current log-likelihood: -101773.021
Optimizing NNI: done in 1.77715 secs using 398.5% CPU
72. Current log-likelihood: -101773.007
Optimizing NNI: done in 1.34305 secs using 398.9% CPU
73. Current log-likelihood: -101772.992
74. Current log-likelihood: -101772.978
Optimizing NNI: done in 1.69053 secs using 398.4% CPU
75. Current log-likelihood: -101772.964
Optimizing NNI: done in 3.87598 secs using 597.5% CPU
76. Current log-likelihood: -101772.951
77. Current log-likelihood: -101772.938
Optimizing NNI: done in 1.70064 secs using 398.9% CPU
78. Current log-likelihood: -101772.924
79. Current log-likelihood: -101772.911
Optimizing NNI: done in 1.75841 secs using 399% CPU
80. Current log-likelihood: -101772.897
81. Current log-likelihood: -101772.884
Optimizing NNI: done in 4.60387 secs using 597.1% CPU
Optimizing NNI: done in 1.66621 secs using 399.1% CPU
82. Current log-likelihood: -101772.871
83. Current log-likelihood: -101772.858
84. Current log-likelihood: -101772.845
Optimizing NNI: done in 1.97003 secs using 399.1% CPU
85. Current log-likelihood: -101772.832
86. Current log-likelihood: -101772.819
Optimizing NNI: done in 1.63634 secs using 398.9% CPU
87. Current log-likelihood: -101772.807
Optimizing NNI: done in 4.35443 secs using 597.7% CPU
88. Current log-likelihood: -101772.796
89. Current log-likelihood: -101772.783
Optimizing NNI: done in 1.56385 secs using 398.8% CPU
Iteration 130 / LogL: -57009.725 / Time: 0h:4m:10s (0h:1m:2s left)
90. Current log-likelihood: -101772.771
91. Current log-likelihood: -101772.759
Optimizing NNI: done in 1.55101 secs using 399.2% CPU
92. Current log-likelihood: -101772.747
93. Current log-likelihood: -101772.736
Optimizing NNI: done in 1.61209 secs using 398.9% CPU
Optimizing NNI: done in 4.18912 secs using 597.5% CPU
94. Current log-likelihood: -101772.725
95. Current log-likelihood: -101772.714
96. Current log-likelihood: -101772.703
Optimizing NNI: done in 1.81628 secs using 399.3% CPU
Optimal log-likelihood: -101772.689
Proportion of invariable sites: 0.032
Site proportion and rates:  (0.084,0.028) (0.082,0.088) (0.069,0.175) (0.084,0.268) (0.109,0.407) (0.135,0.647) (0.157,1.054) (0.166,1.784) (0.082,4.429)
Parameters optimization took 96 rounds (77.450 sec)
BEST SCORE FOUND : -101772.689
Total tree length: 165.871

Total number of iterations: 208
CPU time used for tree search: 1883.030 sec (0h:31m:23s)
Wall-clock time used for tree search: 480.366 sec (0h:8m:0s)
Total CPU time used: 2284.919 sec (0h:38m:4s)
Total wall-clock time used: 581.281 sec (0h:9m:41s)

===> START BOOTSTRAP REPLICATE NUMBER 37

Creating bootstrap alignment (seed: 68219)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.090 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -115788.957
Optimizing NNI: done in 1.53082 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 134: -57008.317
2. Current log-likelihood: -113594.372
Optimizing NNI: done in 4.77733 secs using 597.2% CPU
Optimizing NNI: done in 1.5245 secs using 398.9% CPU
3. Current log-likelihood: -113498.653
Optimizing NNI: done in 1.61613 secs using 399.4% CPU
4. Current log-likelihood: -113491.905
Optimizing NNI: done in 1.40861 secs using 398.6% CPU
5. Current log-likelihood: -113489.672
Optimizing NNI: done in 4.58457 secs using 597.5% CPU
Optimizing NNI: done in 1.9387 secs using 399% CPU
6. Current log-likelihood: -113488.053
Optimizing NNI: done in 1.80712 secs using 399.1% CPU
7. Current log-likelihood: -113486.601
Optimizing NNI: done in 1.71049 secs using 399% CPU
Iteration 140 / LogL: -57022.876 / Time: 0h:4m:27s (0h:3m:1s left)
Optimizing NNI: done in 4.83606 secs using 597.8% CPU
8. Current log-likelihood: -113485.517
Optimizing NNI: done in 1.81191 secs using 399% CPU
9. Current log-likelihood: -113484.481
Optimizing NNI: done in 1.52542 secs using 399.1% CPU
10. Current log-likelihood: -113483.748
Optimizing NNI: done in 4.1458 secs using 596.9% CPU
Estimate model parameters (epsilon = 0.100)
11. Current log-likelihood: -113482.866
Optimizing NNI: done in 1.86121 secs using 399.5% CPU
Optimizing NNI: done in 1.20882 secs using 399% CPU
BETTER TREE FOUND at iteration 329: -192350.078
12. Current log-likelihood: -113482.330
Optimizing NNI: done in 1.90494 secs using 399.3% CPU
13. Current log-likelihood: -113481.659
14. Current log-likelihood: -113481.224
Optimizing NNI: done in 1.77553 secs using 399.1% CPU
Optimizing NNI: done in 4.41045 secs using 597.7% CPU
Iteration 330 / LogL: -192566.854 / Time: 0h:26m:54s (0h:8m:5s left)
15. Current log-likelihood: -113480.704
Optimizing NNI: done in 1.54201 secs using 399.1% CPU
16. Current log-likelihood: -113480.445
Optimizing NNI: done in 1.61766 secs using 398.4% CPU
17. Current log-likelihood: -113480.165
Optimizing NNI: done in 1.67522 secs using 398.4% CPU
18. Current log-likelihood: -113479.974
Optimizing NNI: done in 4.73884 secs using 597.3% CPU
19. Current log-likelihood: -113479.733
Optimizing NNI: done in 1.86894 secs using 399.1% CPU
Iteration 150 / LogL: -57089.255 / Time: 0h:4m:44s (0h:2m:40s left)
20. Current log-likelihood: -113479.620
Optimizing NNI: done in 1.68924 secs using 398.5% CPU
21. Current log-likelihood: -113479.377
Optimal log-likelihood: -113479.249
Proportion of invariable sites: 0.020
Site proportion and rates:  (0.071,0.032) (0.076,0.100) (0.081,0.199) (0.058,0.251) (0.115,0.363) (0.132,0.612) (0.132,1.001) (0.236,1.681) (0.080,3.859)
Parameters optimization took 21 rounds (32.201 sec)
Optimizing NNI: done in 4.09782 secs using 598% CPU
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.63685 secs using 398.8% CPU
Optimizing NNI: done in 1.81166 secs using 398.8% CPU
Optimizing NNI: done in 1.65772 secs using 398.3% CPU
Optimizing NNI: done in 4.20442 secs using 597.4% CPU
Calculating distance matrix: done in 4.76777 secs using 399.9% CPU
Computing ML distances took 4.768149 sec (of wall-clock time) 19.066467 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000728846 secs using 254% CPU
Constructing RapidNJ tree: done in 0.00843906 secs using 349.5% CPU
Computing RapidNJ tree took 0.009229 sec (of wall-clock time) 0.033734 sec (of CPU time)
Optimizing NNI: done in 1.699 secs using 399.2% CPU
Log-likelihood of RapidNJ tree: -113792.835
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.68249 secs using 399.6% CPU
Optimizing NNI: done in 1.63431 secs using 399.1% CPU
Optimizing NNI: done in 1.50029 secs using 399% CPU
Optimizing NNI: done in 5.87523 secs using 597.6% CPU
Optimizing NNI: done in 1.5737 secs using 398.9% CPU
Optimizing NNI: done in 1.70793 secs using 398.5% CPU
Iteration 160 / LogL: -57047.546 / Time: 0h:5m:1s (0h:2m:20s left)
Optimizing NNI: done in 1.55341 secs using 399% CPU
10.780 second
Optimizing NNI: done in 1.68911 secs using 398.2% CPU
Optimizing NNI: done in 6.50853 secs using 597.4% CPU
Optimizing NNI: done in 1.72831 secs using 399.1% CPU
Optimizing NNI: done in 2.06263 secs using 398.6% CPU
Optimizing NNI: done in 3.95661 secs using 597.9% CPU
Optimizing NNI: done in 1.62332 secs using 399% CPU
Optimizing NNI: done in 1.76352 secs using 399.1% CPU
Optimizing NNI: done in 1.47689 secs using 399% CPU
Optimizing NNI: done in 4.84091 secs using 596.5% CPU
Computing log-likelihood of 98 initial trees ... 10.343 seconds
Current best score: -113479.249

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.46285 secs using 398.8% CPU
UPDATE BEST LOG-LIKELIHOOD: -57008.315
Optimizing NNI: done in 1.36086 secs using 399.4% CPU
Optimizing NNI: done in 2.04031 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.99979 secs using 597.1% CPU
Optimizing NNI: done in 1.48572 secs using 398.9% CPU
Iteration 170 / LogL: -57009.817 / Time: 0h:5m:17s (0h:2m:0s left)
Optimizing NNI: done in 1.74039 secs using 398.9% CPU
Optimizing NNI: done in 1.81931 secs using 399.1% CPU
Optimizing NNI: done in 4.64568 secs using 597.5% CPU
Optimizing NNI: done in 1.29571 secs using 398.7% CPU
Optimizing NNI: done in 1.98759 secs using 398.9% CPU
Optimizing NNI: done in 1.98945 secs using 398.2% CPU
Optimizing NNI: done in 4.60174 secs using 596.4% CPU
Iteration 340 / LogL: -192385.518 / Time: 0h:27m:42s (0h:7m:16s left)
Optimizing NNI: done in 1.51426 secs using 399.3% CPU
Optimizing NNI: done in 1.58966 secs using 398.7% CPU
Optimizing NNI: done in 1.67624 secs using 399% CPU
Optimizing NNI: done in 4.88559 secs using 597.9% CPU
Optimizing NNI: done in 2.01558 secs using 398.2% CPU
Optimizing NNI: done in 2.20669 secs using 398.8% CPU
Iteration 180 / LogL: -57022.609 / Time: 0h:5m:35s (0h:1m:41s left)
Optimizing NNI: done in 4.57399 secs using 596.6% CPU
Optimizing NNI: done in 1.70866 secs using 399% CPU
Optimizing NNI: done in 1.84723 secs using 398.7% CPU
Optimizing NNI: done in 1.84609 secs using 398.7% CPU
Optimizing NNI: done in 4.61567 secs using 597.3% CPU
Optimizing NNI: done in 1.94599 secs using 398.8% CPU
Optimizing NNI: done in 1.93855 secs using 398.6% CPU
Optimizing NNI: done in 4.26401 secs using 596% CPU
BETTER TREE FOUND at iteration 1: -112966.881
Optimizing NNI: done in 1.5693 secs using 398.7% CPU
Optimizing NNI: done in 1.49679 secs using 399.1% CPU
Optimizing NNI: done in 2.30454 secs using 398.3% CPU
Optimizing NNI: done in 1.7113 secs using 398.9% CPU
Optimizing NNI: done in 4.54515 secs using 597.5% CPU
Optimizing NNI: done in 3.13028 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.07904 secs using 398.9% CPU
Optimizing NNI: done in 1.47036 secs using 398.8% CPU
Iteration 190 / LogL: -57027.570 / Time: 0h:5m:53s (0h:1m:22s left)
Optimizing NNI: done in 1.79699 secs using 399% CPU
Optimizing NNI: done in 5.0536 secs using 597.5% CPU
BETTER TREE FOUND at iteration 3: -112865.194
Optimizing NNI: done in 1.46815 secs using 399.4% CPU
Optimizing NNI: done in 1.92472 secs using 398.8% CPU
Optimizing NNI: done in 2.82631 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.49731 secs using 597.1% CPU
Optimizing NNI: done in 1.68807 secs using 398.7% CPU
Optimizing NNI: done in 1.46237 secs using 398.7% CPU
BETTER TREE FOUND at iteration 4: -112832.113
Optimizing NNI: done in 1.84051 secs using 398.4% CPU
Optimizing NNI: done in 4.74385 secs using 596.6% CPU
Optimizing NNI: done in 2.84028 secs using 398.6% CPU
Optimizing NNI: done in 1.82191 secs using 399.1% CPU
Optimizing NNI: done in 2.33722 secs using 398.5% CPU
Optimizing NNI: done in 1.65289 secs using 398.9% CPU
Optimizing NNI: done in 3.95084 secs using 597.3% CPU
Optimizing NNI: done in 1.60398 secs using 399% CPU
Optimizing NNI: done in 2.90986 secs using 397.9% CPU
Optimizing NNI: done in 1.57931 secs using 398.8% CPU
UPDATE BEST LOG-LIKELIHOOD: -57008.315
Iteration 200 / LogL: -57008.315 / Time: 0h:6m:10s (0h:1m:3s left)
Optimizing NNI: done in 1.63202 secs using 399.2% CPU
Optimizing NNI: done in 2.37562 secs using 398.3% CPU
Optimizing NNI: done in 4.9086 secs using 597.2% CPU
Iteration 350 / LogL: -192694.409 / Time: 0h:28m:29s (0h:6m:26s left)
Optimizing NNI: done in 1.75401 secs using 398.9% CPU
Optimizing NNI: done in 2.23217 secs using 398.5% CPU
Optimizing NNI: done in 1.81059 secs using 399% CPU
Optimizing NNI: done in 1.65621 secs using 399.1% CPU
Optimizing NNI: done in 2.61896 secs using 398.7% CPU
Iteration 10 / LogL: -112840.833 / Time: 0h:2m:1s
Optimizing NNI: done in 4.71617 secs using 596.9% CPU
Optimizing NNI: done in 1.58231 secs using 399.1% CPU
Optimizing NNI: done in 2.43354 secs using 398.4% CPU
Optimizing NNI: done in 1.51084 secs using 398.9% CPU
Optimizing NNI: done in 1.91589 secs using 399.2% CPU
Optimizing NNI: done in 2.89472 secs using 398% CPU
Optimizing NNI: done in 4.62157 secs using 597.7% CPU
Optimizing NNI: done in 1.5845 secs using 399% CPU
Optimizing NNI: done in 2.65479 secs using 398.7% CPU
Optimizing NNI: done in 1.46354 secs using 398.9% CPU
Optimizing NNI: done in 1.66886 secs using 398.9% CPU
Iteration 210 / LogL: -57009.332 / Time: 0h:6m:27s (0h:0m:44s left)
Optimizing NNI: done in 4.328 secs using 597.6% CPU
Optimizing NNI: done in 2.59003 secs using 398.2% CPU
Optimizing NNI: done in 1.52569 secs using 399.1% CPU
Optimizing NNI: done in 1.75046 secs using 398.5% CPU
Optimizing NNI: done in 2.45767 secs using 399% CPU
Optimizing NNI: done in 3.99385 secs using 596.3% CPU
Optimizing NNI: done in 1.59939 secs using 399.4% CPU
Optimizing NNI: done in 2.20825 secs using 398.1% CPU
Optimizing NNI: done in 1.87154 secs using 398.8% CPU
Optimizing NNI: done in 2.56316 secs using 398.1% CPU
Optimizing NNI: done in 4.05009 secs using 597.4% CPU
Optimizing NNI: done in 1.728 secs using 398.9% CPU
Optimizing NNI: done in 1.61492 secs using 399% CPU
Optimizing NNI: done in 2.58341 secs using 398.6% CPU
Optimizing NNI: done in 1.86244 secs using 398.9% CPU
Optimizing NNI: done in 4.80034 secs using 597.1% CPU
Optimizing NNI: done in 1.94858 secs using 399.4% CPU
Optimizing NNI: done in 3.24126 secs using 398.1% CPU
Optimizing NNI: done in 1.90608 secs using 398.9% CPU
Optimizing NNI: done in 2.98605 secs using 398.5% CPU
Iteration 20 / LogL: -112871.174 / Time: 0h:2m:28s
Finish initializing candidate tree set (20)
Current best tree score: -112832.113 / CPU time: 110.450
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.56066 secs using 398.2% CPU
Iteration 220 / LogL: -57009.020 / Time: 0h:6m:44s (0h:0m:25s left)
Optimizing NNI: done in 4.1725 secs using 597.6% CPU
Optimizing NNI: done in 1.72668 secs using 398.1% CPU
Optimizing NNI: done in 2.8669 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.85104 secs using 398.8% CPU
Optimizing NNI: done in 4.3933 secs using 597.7% CPU
Optimizing NNI: done in 1.72048 secs using 398.6% CPU
Optimizing NNI: done in 1.62567 secs using 398.4% CPU
BETTER TREE FOUND at iteration 21: -112821.061
Optimizing NNI: done in 3.91929 secs using 597.6% CPU
Optimizing NNI: done in 1.55824 secs using 398.7% CPU
Optimizing NNI: done in 2.4163 secs using 398.3% CPU
Optimizing NNI: done in 1.84387 secs using 399.3% CPU
Optimizing NNI: done in 1.10921 secs using 398.5% CPU
Optimizing NNI: done in 2.35406 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.34125 secs using 399.3% CPU
Optimizing NNI: done in 4.37505 secs using 598.2% CPU
Iteration 360 / LogL: -192431.862 / Time: 0h:29m:13s (0h:5m:36s left)
Optimizing NNI: done in 1.68419 secs using 398.6% CPU
BETTER TREE FOUND at iteration 23: -112805.471
Optimizing NNI: done in 1.5716 secs using 398.8% CPU
Iteration 230 / LogL: -57012.504 / Time: 0h:7m:0s (0h:0m:7s left)
Optimizing NNI: done in 4.60464 secs using 597.6% CPU
Optimizing NNI: done in 1.51488 secs using 398.5% CPU
Optimizing NNI: done in 3.01558 secs using 397.6% CPU
Optimizing NNI: done in 1.67152 secs using 398.9% CPU
Optimizing NNI: done in 2.41774 secs using 398.3% CPU
Optimizing NNI: done in 1.65864 secs using 398.4% CPU
Optimizing NNI: done in 3.97065 secs using 597.4% CPU
Optimizing NNI: done in 1.63558 secs using 398.7% CPU
Optimizing NNI: done in 2.51259 secs using 397.9% CPU
Optimizing NNI: done in 1.58359 secs using 399.2% CPU
TREE SEARCH COMPLETED AFTER 235 ITERATIONS / Time: 0h:7m:9s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57008.315
Optimal log-likelihood: -57008.307
Site proportion and rates:  (0.107,0.059) (0.090,0.177) (0.100,0.406) (0.106,0.406) (0.251,0.799) (0.119,1.220) (0.143,1.947) (0.083,3.249)
Parameters optimization took 1 rounds (0.533 sec)
BEST SCORE FOUND : -57008.307
Total tree length: 39.680

Total number of iterations: 235
CPU time used for tree search: 1669.245 sec (0h:27m:49s)
Wall-clock time used for tree search: 422.433 sec (0h:7m:2s)
Total CPU time used: 1697.752 sec (0h:28m:17s)
Total wall-clock time used: 429.552 sec (0h:7m:9s)

===> START BOOTSTRAP REPLICATE NUMBER 89

Creating bootstrap alignment (seed: 67551)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.049 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60718.831
Optimizing NNI: done in 2.44217 secs using 397.7% CPU
2. Current log-likelihood: -60163.792
Optimizing NNI: done in 4.64652 secs using 597.8% CPU
3. Current log-likelihood: -60149.631
4. Current log-likelihood: -60139.734
Optimizing NNI: done in 1.8685 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
5. Current log-likelihood: -60118.956
6. Current log-likelihood: -60117.244
7. Current log-likelihood: -60117.103
BETTER TREE FOUND at iteration 28: -112803.797
Optimizing NNI: done in 4.48468 secs using 597.3% CPU
Optimal log-likelihood: -60117.017
Site proportion and rates:  (0.139,0.065) (0.026,0.185) (0.170,0.316) (0.032,0.385) (0.236,0.643) (0.170,1.119) (0.199,2.156) (0.028,5.342)
Parameters optimization took 7 rounds (5.966 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Computing ML distances took 1.106262 sec (of wall-clock time) 4.423310 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000403166 secs using 346.8% CPU
Constructing RapidNJ tree: done in 0.00426292 secs using 291.1% CPU
Computing RapidNJ tree took 0.004719 sec (of wall-clock time) 0.014969 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60181.743
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.54094 secs using 397.8% CPU
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5.247 second
BETTER TREE FOUND at iteration 30: -112797.099
Iteration 30 / LogL: -112797.099 / Time: 0h:3m:7s (0h:10m:45s left)
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Computing log-likelihood of 98 initial trees ... 6.273 seconds
Current best score: -60083.196

Do NNI search on 20 best initial trees
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Iteration 20 / LogL: -59895.784 / Time: 0h:1m:1s
Finish initializing candidate tree set (20)
Current best tree score: -59821.786 / CPU time: 53.943
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 140 / LogL: -59800.198 / Time: 0h:4m:11s (0h:1m:59s left)
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Iteration 130 / LogL: -112817.221 / Time: 0h:7m:8s (0h:2m:52s left)
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Optimizing NNI: done in 2.50255 secs using 397.6% CPU
Optimizing NNI: done in 1.432 secs using 398.8% CPU
BETTER TREE FOUND at iteration 146: -59795.760
Optimizing NNI: done in 1.29839 secs using 399.1% CPU
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Iteration 150 / LogL: -59797.150 / Time: 0h:4m:25s (0h:2m:51s left)
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Iteration 420 / LogL: -192371.901 / Time: 0h:33m:57s (0h:0m:43s left)
Optimizing NNI: done in 1.3979 secs using 399% CPU
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Iteration 140 / LogL: -112803.080 / Time: 0h:7m:32s (0h:2m:16s left)
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Iteration 160 / LogL: -59798.096 / Time: 0h:4m:39s (0h:2m:30s left)
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Iteration 170 / LogL: -59839.462 / Time: 0h:4m:52s (0h:2m:11s left)
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Iteration 150 / LogL: -112826.431 / Time: 0h:7m:55s (0h:1m:42s left)
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Iteration 180 / LogL: -59795.763 / Time: 0h:5m:7s (0h:1m:53s left)
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Optimizing NNI: done in 4.52551 secs using 597.4% CPU
Iteration 430 / LogL: -192357.087 / Time: 0h:34m:40s (0h:0m:-5s left)
TREE SEARCH COMPLETED AFTER 430 ITERATIONS / Time: 0h:34m:40s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192350.078
Optimizing NNI: done in 1.21026 secs using 399.5% CPU
2. Current log-likelihood: -192350.066
Optimizing NNI: done in 2.46701 secs using 398.3% CPU
Optimizing NNI: done in 1.13078 secs using 399.3% CPU
Optimal log-likelihood: -192350.058
Site proportion and rates:  (0.012,0.082) (0.045,0.219) (0.113,0.365) (0.239,0.543) (0.182,0.801) (0.172,1.090) (0.165,1.726) (0.072,2.774)
Parameters optimization took 2 rounds (1.729 sec)
BEST SCORE FOUND : -192350.058
Total tree length: 151.261

Total number of iterations: 430
CPU time used for tree search: 12116.429 sec (3h:21m:56s)
Wall-clock time used for tree search: 2053.290 sec (0h:34m:13s)
Total CPU time used: 12289.542 sec (3h:24m:49s)
Total wall-clock time used: 2082.354 sec (0h:34m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 23

Creating bootstrap alignment (seed: 70486)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.313 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -195327.738
Optimizing NNI: done in 1.44712 secs using 398.9% CPU
Optimizing NNI: done in 2.34199 secs using 398.7% CPU
Optimizing NNI: done in 1.51356 secs using 398.7% CPU
2. Current log-likelihood: -192692.889
Optimizing NNI: done in 1.25405 secs using 398.8% CPU
Iteration 190 / LogL: -59798.007 / Time: 0h:5m:20s (0h:1m:35s left)
Optimizing NNI: done in 2.03657 secs using 398.2% CPU
Optimizing NNI: done in 1.48436 secs using 399.6% CPU
3. Current log-likelihood: -192669.166
Optimizing NNI: done in 2.46185 secs using 398.1% CPU
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4. Current log-likelihood: -192667.896
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Optimizing NNI: done in 2.58723 secs using 398% CPU
Iteration 160 / LogL: -112816.203 / Time: 0h:8m:19s (0h:1m:9s left)
Optimizing NNI: done in 1.45161 secs using 398.9% CPU
5. Current log-likelihood: -192665.812
Optimizing NNI: done in 2.16222 secs using 398.4% CPU
Optimizing NNI: done in 1.56826 secs using 399.2% CPU
6. Current log-likelihood: -192658.758
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7. Current log-likelihood: -192645.984
Optimizing NNI: done in 1.42332 secs using 398.5% CPU
Optimizing NNI: done in 2.87732 secs using 397.6% CPU
8. Current log-likelihood: -192641.992
Optimizing NNI: done in 1.38703 secs using 399.3% CPU
Optimizing NNI: done in 1.32275 secs using 399.2% CPU
Iteration 200 / LogL: -59795.959 / Time: 0h:5m:35s (0h:1m:17s left)
Optimizing NNI: done in 2.29563 secs using 398.4% CPU
9. Current log-likelihood: -192641.564
Optimizing NNI: done in 1.85743 secs using 398.8% CPU
Optimal log-likelihood: -192641.539
Site proportion and rates:  (0.012,0.105) (0.053,0.230) (0.105,0.367) (0.227,0.538) (0.197,0.780) (0.144,1.049) (0.144,1.527) (0.117,2.564)
Parameters optimization took 9 rounds (19.995 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.75735 secs using 398% CPU
Optimizing NNI: done in 1.22083 secs using 398.8% CPU
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Optimizing NNI: done in 2.53773 secs using 398.1% CPU
Optimizing NNI: done in 1.51259 secs using 398.8% CPU
Calculating distance matrix: done in 9.65288 secs using 599.6% CPU
Computing ML distances took 9.653428 sec (of wall-clock time) 57.883530 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00127602 secs using 218.3% CPU
Optimizing NNI: done in 1.44436 secs using 398.9% CPU
Constructing RapidNJ tree: done in 0.022603 secs using 664.9% CPU
Computing RapidNJ tree took 0.023956 sec (of wall-clock time) 0.154277 sec (of CPU time)
Optimizing NNI: done in 2.40008 secs using 398.3% CPU
Optimizing NNI: done in 1.41471 secs using 398.8% CPU
Log-likelihood of RapidNJ tree: -196277.854
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.26483 secs using 399.1% CPU
Iteration 210 / LogL: -59795.773 / Time: 0h:5m:50s (0h:1m:0s left)
Optimizing NNI: done in 2.323 secs using 397.9% CPU
Iteration 170 / LogL: -112797.762 / Time: 0h:8m:43s (0h:0m:37s left)
Optimizing NNI: done in 2.04871 secs using 398.1% CPU
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Optimizing NNI: done in 1.85177 secs using 399% CPU
Iteration 220 / LogL: -59825.608 / Time: 0h:6m:10s (0h:0m:43s left)
Optimizing NNI: done in 2.2687 secs using 398.2% CPU
Optimizing NNI: done in 2.05248 secs using 398.5% CPU
Optimizing NNI: done in 2.04508 secs using 398.3% CPU
Iteration 180 / LogL: -112815.020 / Time: 0h:9m:7s (0h:0m:6s left)
Optimizing NNI: done in 2.20597 secs using 398.6% CPU
Optimizing NNI: done in 1.34256 secs using 398.7% CPU
Optimizing NNI: done in 2.52886 secs using 397.9% CPU
Optimizing NNI: done in 1.71157 secs using 398.7% CPU
Optimizing NNI: done in 2.34644 secs using 398.3% CPU
30.268 second
Optimizing NNI: done in 1.8264 secs using 398.7% CPU
Optimizing NNI: done in 2.24996 secs using 397.8% CPU
TREE SEARCH COMPLETED AFTER 183 ITERATIONS / Time: 0h:9m:14s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -112787.949
Optimizing NNI: done in 1.63244 secs using 399.1% CPU
2. Current log-likelihood: -112787.887
Optimizing NNI: done in 1.91732 secs using 398.7% CPU
3. Current log-likelihood: -112787.805
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4. Current log-likelihood: -112787.722
Optimizing NNI: done in 1.38876 secs using 399.1% CPU
5. Current log-likelihood: -112787.618
Optimizing NNI: done in 1.5484 secs using 399% CPU
Iteration 230 / LogL: -59795.767 / Time: 0h:6m:27s (0h:0m:27s left)
6. Current log-likelihood: -112787.473
Optimizing NNI: done in 1.79112 secs using 398.5% CPU
7. Current log-likelihood: -112787.240
Optimizing NNI: done in 1.66441 secs using 398.8% CPU
8. Current log-likelihood: -112786.776
9. Current log-likelihood: -112785.483
Optimizing NNI: done in 1.94999 secs using 398.7% CPU
10. Current log-likelihood: -112782.060
Optimizing NNI: done in 1.46978 secs using 399.1% CPU
Computing log-likelihood of 98 initial trees ... 16.419 seconds
Current best score: -192641.539

Do NNI search on 20 best initial trees
11. Current log-likelihood: -112779.086
Optimizing NNI: done in 1.78825 secs using 399.1% CPU
12. Current log-likelihood: -112777.766
Optimizing NNI: done in 1.59355 secs using 399.2% CPU
Optimizing NNI: done in 3.30286 secs using 596.7% CPU
Estimate model parameters (epsilon = 0.100)
13. Current log-likelihood: -112777.358
Optimizing NNI: done in 1.45796 secs using 398.8% CPU
Optimizing NNI: done in 1.14788 secs using 398.9% CPU
14. Current log-likelihood: -112777.181
Optimizing NNI: done in 1.23388 secs using 399.5% CPU
BETTER TREE FOUND at iteration 1: -192156.000
15. Current log-likelihood: -112777.094
Optimizing NNI: done in 1.24939 secs using 399.5% CPU
Iteration 240 / LogL: -59880.116 / Time: 0h:6m:43s (0h:0m:10s left)
16. Current log-likelihood: -112777.033
Optimizing NNI: done in 1.54898 secs using 399.2% CPU
17. Current log-likelihood: -112776.982
Optimizing NNI: done in 1.57647 secs using 399.1% CPU
Optimizing NNI: done in 4.16456 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
18. Current log-likelihood: -112776.943
Optimizing NNI: done in 1.02357 secs using 399.2% CPU
19. Current log-likelihood: -112776.901
Optimizing NNI: done in 1.64942 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
20. Current log-likelihood: -112776.861
21. Current log-likelihood: -112776.828
BETTER TREE FOUND at iteration 244: -59789.713
BETTER TREE FOUND at iteration 2: -192062.733
22. Current log-likelihood: -112776.808
Optimizing NNI: done in 1.36021 secs using 398.7% CPU
23. Current log-likelihood: -112776.783
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24. Current log-likelihood: -112776.746
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25. Current log-likelihood: -112776.709
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27. Current log-likelihood: -112776.639
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Iteration 250 / LogL: -59808.972 / Time: 0h:6m:58s (0h:2m:37s left)
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28. Current log-likelihood: -112776.610
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29. Current log-likelihood: -112776.590
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32. Current log-likelihood: -112776.508
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34. Current log-likelihood: -112776.469
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36. Current log-likelihood: -112776.420
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Estimate model parameters (epsilon = 0.100)
37. Current log-likelihood: -112776.402
Optimizing NNI: done in 1.40081 secs using 399% CPU
38. Current log-likelihood: -112776.382
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39. Current log-likelihood: -112776.364
40. Current log-likelihood: -112776.346
Optimizing NNI: done in 1.53361 secs using 399.1% CPU
41. Current log-likelihood: -112776.329
BETTER TREE FOUND at iteration 6: -192045.740
42. Current log-likelihood: -112776.312
Optimizing NNI: done in 1.27225 secs using 398.8% CPU
Iteration 260 / LogL: -59796.508 / Time: 0h:7m:12s (0h:2m:20s left)
43. Current log-likelihood: -112776.295
44. Current log-likelihood: -112776.279
Optimizing NNI: done in 1.53314 secs using 398.7% CPU
45. Current log-likelihood: -112776.262
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47. Current log-likelihood: -112776.231
48. Current log-likelihood: -112776.215
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49. Current log-likelihood: -112776.200
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53. Current log-likelihood: -112776.141
Optimizing NNI: done in 1.30788 secs using 399.3% CPU
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54. Current log-likelihood: -112776.127
55. Current log-likelihood: -112776.116
Optimizing NNI: done in 1.37735 secs using 399.3% CPU
56. Current log-likelihood: -112776.101
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57. Current log-likelihood: -112776.087
58. Current log-likelihood: -112776.073
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59. Current log-likelihood: -112776.059
60. Current log-likelihood: -112776.045
Optimizing NNI: done in 1.34883 secs using 399% CPU
Iteration 270 / LogL: -59794.084 / Time: 0h:7m:25s (0h:2m:2s left)
61. Current log-likelihood: -112776.031
62. Current log-likelihood: -112776.018
Optimizing NNI: done in 1.38171 secs using 399% CPU
63. Current log-likelihood: -112776.007
64. Current log-likelihood: -112775.994
Optimizing NNI: done in 1.41481 secs using 399% CPU
Optimizing NNI: done in 4.08388 secs using 597.5% CPU
Iteration 10 / LogL: -192069.966 / Time: 0h:2m:10s
65. Current log-likelihood: -112775.979
Optimizing NNI: done in 1.25315 secs using 399.2% CPU
66. Current log-likelihood: -112775.966
67. Current log-likelihood: -112775.953
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68. Current log-likelihood: -112775.940
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Optimizing NNI: done in 1.39942 secs using 399.3% CPU
69. Current log-likelihood: -112775.926
Optimizing NNI: done in 1.07968 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
70. Current log-likelihood: -112775.913
BETTER TREE FOUND at iteration 276: -59789.599
71. Current log-likelihood: -112775.900
Optimizing NNI: done in 1.4302 secs using 398.7% CPU
72. Current log-likelihood: -112775.887
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Optimizing NNI: done in 1.2302 secs using 399.2% CPU
73. Current log-likelihood: -112775.875
74. Current log-likelihood: -112775.862
Optimizing NNI: done in 1.25257 secs using 398.3% CPU
75. Current log-likelihood: -112775.850
Optimizing NNI: done in 3.21057 secs using 597% CPU
Optimizing NNI: done in 1.30138 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimal log-likelihood: -112775.837
Proportion of invariable sites: 0.018
Site proportion and rates:  (0.066,0.024) (0.081,0.086) (0.123,0.201) (0.129,0.343) (0.108,0.562) (0.087,0.834) (0.110,1.179) (0.204,1.734) (0.073,4.186)
Parameters optimization took 75 rounds (78.850 sec)
BEST SCORE FOUND : -112775.837
Total tree length: 195.142

Total number of iterations: 183
CPU time used for tree search: 2024.458 sec (0h:33m:44s)
Wall-clock time used for tree search: 516.553 sec (0h:8m:36s)
Total CPU time used: 2489.977 sec (0h:41m:29s)
Total wall-clock time used: 633.437 sec (0h:10m:33s)

===> START BOOTSTRAP REPLICATE NUMBER 38

Creating bootstrap alignment (seed: 68220)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.114 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 109 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104334.078
BETTER TREE FOUND at iteration 280: -59789.537
Iteration 280 / LogL: -59789.537 / Time: 0h:7m:40s (0h:2m:44s left)
Optimizing NNI: done in 1.30086 secs using 399.3% CPU
2. Current log-likelihood: -102347.083
Optimizing NNI: done in 1.17881 secs using 399.3% CPU
3. Current log-likelihood: -102277.978
Optimizing NNI: done in 4.20315 secs using 597.2% CPU
Optimizing NNI: done in 1.35121 secs using 399.2% CPU
4. Current log-likelihood: -102274.259
Optimizing NNI: done in 1.28106 secs using 399.1% CPU
Optimizing NNI: done in 1.29146 secs using 399.5% CPU
5. Current log-likelihood: -102273.171
Optimizing NNI: done in 4.2234 secs using 597.7% CPU
Optimizing NNI: done in 1.40753 secs using 398.9% CPU
6. Current log-likelihood: -102271.787
Optimizing NNI: done in 1.18788 secs using 398.7% CPU
7. Current log-likelihood: -102269.350
Optimizing NNI: done in 1.27731 secs using 399% CPU
8. Current log-likelihood: -102268.011
Optimizing NNI: done in 1.29284 secs using 399.6% CPU
Optimizing NNI: done in 5.11301 secs using 597.1% CPU
9. Current log-likelihood: -102267.297
Optimizing NNI: done in 1.71289 secs using 399% CPU
Iteration 290 / LogL: -59834.994 / Time: 0h:7m:53s (0h:2m:27s left)
Optimizing NNI: done in 1.12059 secs using 398.9% CPU
10. Current log-likelihood: -102266.721
Optimizing NNI: done in 1.26874 secs using 399.1% CPU
11. Current log-likelihood: -102266.228
Optimizing NNI: done in 1.3895 secs using 398.9% CPU
Optimizing NNI: done in 4.65071 secs using 597.2% CPU
12. Current log-likelihood: -102265.777
Optimizing NNI: done in 1.38181 secs using 399.1% CPU
13. Current log-likelihood: -102265.378
Optimizing NNI: done in 1.51636 secs using 399.1% CPU
14. Current log-likelihood: -102265.048
Optimizing NNI: done in 1.29636 secs using 399.3% CPU
Optimizing NNI: done in 4.31525 secs using 596.6% CPU
15. Current log-likelihood: -102264.766
Optimizing NNI: done in 1.33231 secs using 398.9% CPU
Optimizing NNI: done in 1.36832 secs using 399.2% CPU
16. Current log-likelihood: -102264.629
Optimizing NNI: done in 1.35993 secs using 398.9% CPU
17. Current log-likelihood: -102264.512
Optimizing NNI: done in 4.24248 secs using 597.2% CPU
Optimizing NNI: done in 1.32647 secs using 398.9% CPU
Iteration 300 / LogL: -59790.336 / Time: 0h:8m:6s (0h:2m:10s left)
18. Current log-likelihood: -102264.405
Optimizing NNI: done in 1.39259 secs using 399.2% CPU
19. Current log-likelihood: -102264.304
Optimizing NNI: done in 1.16456 secs using 399.4% CPU
Optimal log-likelihood: -102264.193
Proportion of invariable sites: 0.046
Site proportion and rates:  (0.101,0.035) (0.069,0.110) (0.099,0.206) (0.118,0.333) (0.096,0.559) (0.107,0.837) (0.104,1.241) (0.191,1.879) (0.069,4.348)
Parameters optimization took 19 rounds (30.258 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.19047 secs using 597.8% CPU
Iteration 20 / LogL: -192102.539 / Time: 0h:2m:53s
Finish initializing candidate tree set (20)
Current best tree score: -192045.740 / CPU time: 141.756
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.11215 secs using 398.9% CPU
Optimizing NNI: done in 1.22994 secs using 399.5% CPU
Optimizing NNI: done in 1.38945 secs using 398.8% CPU
Optimizing NNI: done in 1.08804 secs using 399.6% CPU
Calculating distance matrix: done in 4.72445 secs using 399.9% CPU
Computing ML distances took 4.724739 sec (of wall-clock time) 18.894551 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000739098 secs using 390.1% CPU
Constructing RapidNJ tree: done in 0.00894594 secs using 380.5% CPU
Computing RapidNJ tree took 0.009756 sec (of wall-clock time) 0.037095 sec (of CPU time)
Optimizing NNI: done in 4.84014 secs using 597.4% CPU
Optimizing NNI: done in 1.37999 secs using 398.8% CPU
Log-likelihood of RapidNJ tree: -102586.687
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.37307 secs using 398.8% CPU
Optimizing NNI: done in 1.2531 secs using 399.5% CPU
Optimizing NNI: done in 1.25782 secs using 399% CPU
Iteration 310 / LogL: -59819.205 / Time: 0h:8m:19s (0h:1m:53s left)
Optimizing NNI: done in 1.10699 secs using 399.7% CPU
Optimizing NNI: done in 6.88963 secs using 597.3% CPU
Optimizing NNI: done in 1.56499 secs using 399% CPU
Optimizing NNI: done in 1.2844 secs using 398.2% CPU
Optimizing NNI: done in 1.27357 secs using 399.7% CPU
Optimizing NNI: done in 1.09664 secs using 399.6% CPU
10.561 second
Optimizing NNI: done in 1.27725 secs using 399% CPU
Optimizing NNI: done in 6.43918 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.52789 secs using 398.8% CPU
Optimizing NNI: done in 1.39013 secs using 399.3% CPU
BETTER TREE FOUND at iteration 23: -192018.812
Optimizing NNI: done in 1.43668 secs using 399.5% CPU
Optimizing NNI: done in 1.53384 secs using 398.7% CPU
Iteration 320 / LogL: -59794.864 / Time: 0h:8m:33s (0h:1m:36s left)
Optimizing NNI: done in 1.30519 secs using 398.8% CPU
Optimizing NNI: done in 1.39597 secs using 398.8% CPU
Optimizing NNI: done in 4.45699 secs using 597.1% CPU
Computing log-likelihood of 98 initial trees ... 10.422 seconds
Current best score: -102264.193

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.35891 secs using 398.4% CPU
Optimizing NNI: done in 1.6566 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.36354 secs using 398.8% CPU
Optimizing NNI: done in 1.51717 secs using 399% CPU
Optimizing NNI: done in 5.03777 secs using 596.5% CPU
BETTER TREE FOUND at iteration 1: -101830.225
Optimizing NNI: done in 1.29033 secs using 398.7% CPU
Optimizing NNI: done in 1.85435 secs using 398.7% CPU
Optimizing NNI: done in 2.7872 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.29853 secs using 399.3% CPU
Optimizing NNI: done in 1.43539 secs using 399.4% CPU
Optimizing NNI: done in 4.98851 secs using 597% CPU
Optimizing NNI: done in 1.39404 secs using 398.7% CPU
Iteration 330 / LogL: -59804.341 / Time: 0h:8m:47s (0h:1m:20s left)
Optimizing NNI: done in 1.35087 secs using 399.3% CPU
Optimizing NNI: done in 1.30323 secs using 399.1% CPU
Optimizing NNI: done in 4.89585 secs using 597.1% CPU
Optimizing NNI: done in 1.40373 secs using 399.3% CPU
Optimizing NNI: done in 1.45088 secs using 398.7% CPU
Optimizing NNI: done in 1.45439 secs using 399.4% CPU
Optimizing NNI: done in 4.48588 secs using 598.2% CPU
Optimizing NNI: done in 1.60417 secs using 399.1% CPU
Optimizing NNI: done in 1.12091 secs using 399% CPU
Optimizing NNI: done in 1.50392 secs using 398.7% CPU
Optimizing NNI: done in 1.33945 secs using 399.1% CPU
Optimizing NNI: done in 5.27416 secs using 597.7% CPU
Optimizing NNI: done in 1.22285 secs using 398.1% CPU
Iteration 340 / LogL: -59818.686 / Time: 0h:9m:1s (0h:1m:3s left)
Optimizing NNI: done in 1.38704 secs using 399.3% CPU
BETTER TREE FOUND at iteration 2: -101780.203
Optimizing NNI: done in 1.52555 secs using 399.4% CPU
Optimizing NNI: done in 1.26505 secs using 399.1% CPU
Optimizing NNI: done in 4.88289 secs using 597.4% CPU
Iteration 30 / LogL: -192314.814 / Time: 0h:3m:48s (0h:12m:12s left)
Optimizing NNI: done in 2.69248 secs using 398.8% CPU
Optimizing NNI: done in 1.36726 secs using 398.7% CPU
Optimizing NNI: done in 1.39954 secs using 398.4% CPU
Optimizing NNI: done in 1.32365 secs using 398.9% CPU
Optimizing NNI: done in 1.50151 secs using 399% CPU
Optimizing NNI: done in 2.49176 secs using 398.9% CPU
Optimizing NNI: done in 5.32407 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.57588 secs using 398.8% CPU
Optimizing NNI: done in 1.65271 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.37726 secs using 398.9% CPU
Optimizing NNI: done in 1.43178 secs using 398.7% CPU
BETTER TREE FOUND at iteration 6: -101759.072
BETTER TREE FOUND at iteration 31: -192005.550
Optimizing NNI: done in 1.52456 secs using 398.9% CPU
Iteration 350 / LogL: -59796.961 / Time: 0h:9m:16s (0h:0m:47s left)
Optimizing NNI: done in 1.22211 secs using 398.4% CPU
Optimizing NNI: done in 3.03267 secs using 398.4% CPU
Optimizing NNI: done in 1.48791 secs using 397.8% CPU
Optimizing NNI: done in 1.27959 secs using 398% CPU
Optimizing NNI: done in 1.77015 secs using 398.8% CPU
Optimizing NNI: done in 5.2277 secs using 597.2% CPU
Optimizing NNI: done in 1.32882 secs using 398.4% CPU
Optimizing NNI: done in 1.66963 secs using 399.1% CPU
Optimizing NNI: done in 1.15695 secs using 399.3% CPU
Optimizing NNI: done in 1.30925 secs using 399.2% CPU
Optimizing NNI: done in 2.70932 secs using 398.3% CPU
Iteration 10 / LogL: -101851.016 / Time: 0h:1m:44s
Optimizing NNI: done in 1.31179 secs using 398.9% CPU
Optimizing NNI: done in 4.92623 secs using 597.4% CPU
Optimizing NNI: done in 1.46931 secs using 398.7% CPU
Optimizing NNI: done in 1.43885 secs using 399.1% CPU
Optimizing NNI: done in 1.0983 secs using 399.9% CPU
Optimizing NNI: done in 2.18964 secs using 398.3% CPU
Optimizing NNI: done in 1.35202 secs using 399.2% CPU
Iteration 360 / LogL: -59817.994 / Time: 0h:9m:29s (0h:0m:31s left)
Optimizing NNI: done in 1.07906 secs using 398.7% CPU
Optimizing NNI: done in 2.32123 secs using 398.7% CPU
Optimizing NNI: done in 5.53249 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.2622 secs using 398.4% CPU
Optimizing NNI: done in 1.26545 secs using 399.4% CPU
Optimizing NNI: done in 2.89964 secs using 398.4% CPU
Optimizing NNI: done in 1.32041 secs using 399.1% CPU
BETTER TREE FOUND at iteration 34: -191985.402
Optimizing NNI: done in 1.11577 secs using 398.9% CPU
Optimizing NNI: done in 2.79604 secs using 398.2% CPU
Optimizing NNI: done in 1.30877 secs using 399.1% CPU
Optimizing NNI: done in 1.51842 secs using 398.3% CPU
Optimizing NNI: done in 1.54368 secs using 399.1% CPU
Optimizing NNI: done in 1.45348 secs using 399.1% CPU
Optimizing NNI: done in 2.05848 secs using 399.2% CPU
Optimizing NNI: done in 1.09646 secs using 399.7% CPU
Optimizing NNI: done in 6.38597 secs using 596.3% CPU
Optimizing NNI: done in 1.45619 secs using 399.2% CPU
Iteration 370 / LogL: -59795.094 / Time: 0h:9m:42s (0h:0m:15s left)
Optimizing NNI: done in 2.12515 secs using 398.6% CPU
Optimizing NNI: done in 1.26617 secs using 399.1% CPU
Optimizing NNI: done in 1.40468 secs using 399.7% CPU
Optimizing NNI: done in 2.90979 secs using 398.9% CPU
Optimizing NNI: done in 4.35433 secs using 597.7% CPU
Optimizing NNI: done in 1.4402 secs using 398.9% CPU
Optimizing NNI: done in 1.39037 secs using 398.7% CPU
Optimizing NNI: done in 2.8551 secs using 398.4% CPU
Iteration 20 / LogL: -101841.961 / Time: 0h:2m:8s
Finish initializing candidate tree set (20)
Current best tree score: -101759.072 / CPU time: 91.856
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.32291 secs using 399.1% CPU
Optimizing NNI: done in 1.825 secs using 398.5% CPU
Optimizing NNI: done in 4.70612 secs using 596.4% CPU
Optimizing NNI: done in 1.24018 secs using 399.4% CPU
Optimizing NNI: done in 1.2296 secs using 399.1% CPU
Optimizing NNI: done in 2.21655 secs using 398.4% CPU
Optimizing NNI: done in 1.67431 secs using 399.3% CPU
Optimizing NNI: done in 4.13694 secs using 597.6% CPU
Optimizing NNI: done in 1.38293 secs using 399% CPU
Optimizing NNI: done in 2.52952 secs using 398.7% CPU
Optimizing NNI: done in 1.15966 secs using 399.2% CPU
Iteration 380 / LogL: -59790.480 / Time: 0h:9m:55s (0h:0m:0s left)
Optimizing NNI: done in 1.39224 secs using 398.5% CPU
TREE SEARCH COMPLETED AFTER 381 ITERATIONS / Time: 0h:9m:57s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59789.537
Optimizing NNI: done in 2.64601 secs using 398.9% CPU
Optimal log-likelihood: -59789.533
Site proportion and rates:  (0.146,0.068) (0.090,0.274) (0.126,0.342) (0.245,0.633) (0.156,1.091) (0.132,1.889) (0.083,2.581) (0.023,5.923)
Parameters optimization took 1 rounds (0.417 sec)
BEST SCORE FOUND : -59789.533
Total tree length: 46.719

Total number of iterations: 381
CPU time used for tree search: 2337.304 sec (0h:38m:57s)
Wall-clock time used for tree search: 589.738 sec (0h:9m:49s)
Total CPU time used: 2368.833 sec (0h:39m:28s)
Total wall-clock time used: 597.618 sec (0h:9m:57s)

===> START BOOTSTRAP REPLICATE NUMBER 90

Creating bootstrap alignment (seed: 67552)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.049 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60781.566
2. Current log-likelihood: -60157.711
Optimizing NNI: done in 4.75243 secs using 596.6% CPU
3. Current log-likelihood: -60147.393
Optimizing NNI: done in 2.66211 secs using 398.9% CPU
4. Current log-likelihood: -60117.502
5. Current log-likelihood: -60111.069
Optimizing NNI: done in 1.93757 secs using 399% CPU
6. Current log-likelihood: -60110.514
Optimal log-likelihood: -60110.453
Site proportion and rates:  (0.091,0.059) (0.144,0.190) (0.089,0.399) (0.115,0.428) (0.197,0.764) (0.166,1.208) (0.159,2.179) (0.039,4.756)
Parameters optimization took 6 rounds (5.370 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.0255 secs using 398.6% CPU
Optimizing NNI: done in 4.92867 secs using 597.5% CPU
Iteration 40 / LogL: -191997.142 / Time: 0h:4m:46s (0h:11m:30s left)
Calculating distance matrix: done in 1.08846 secs using 400% CPU
Computing ML distances took 1.088649 sec (of wall-clock time) 4.353903 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000409842 secs using 225.9% CPU
Constructing RapidNJ tree: done in 0.00434804 secs using 366.9% CPU
Computing RapidNJ tree took 0.004812 sec (of wall-clock time) 0.018694 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60142.129
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.91431 secs using 398.8% CPU
Optimizing NNI: done in 2.32317 secs using 398.3% CPU
5.243 second
Optimizing NNI: done in 2.27221 secs using 398.8% CPU
Iteration 30 / LogL: -101801.097 / Time: 0h:2m:30s (0h:6m:35s left)
Optimizing NNI: done in 6.54824 secs using 597.5% CPU
Optimizing NNI: done in 2.31143 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Computing log-likelihood of 98 initial trees ... 5.094 seconds
Current best score: -60039.274

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.30337 secs using 597.6% CPU
BETTER TREE FOUND at iteration 31: -101751.577
Optimizing NNI: done in 1.42636 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.09176 secs using 398.7% CPU
BETTER TREE FOUND at iteration 1: -59846.154
Optimizing NNI: done in 1.41123 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.06941 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.70404 secs using 597% CPU
BETTER TREE FOUND at iteration 2: -59816.124
Optimizing NNI: done in 1.30755 secs using 397.1% CPU
Optimizing NNI: done in 1.73984 secs using 398.7% CPU
Optimizing NNI: done in 4.80058 secs using 597.7% CPU
Optimizing NNI: done in 1.51928 secs using 398.7% CPU
BETTER TREE FOUND at iteration 33: -101749.954
Optimizing NNI: done in 1.1196 secs using 398.5% CPU
Optimizing NNI: done in 1.24677 secs using 398.7% CPU
Optimizing NNI: done in 2.05708 secs using 398.9% CPU
Optimizing NNI: done in 1.60249 secs using 399% CPU
Optimizing NNI: done in 4.96117 secs using 597.7% CPU
Optimizing NNI: done in 2.39344 secs using 398.8% CPU
Optimizing NNI: done in 1.69506 secs using 398.8% CPU
Optimizing NNI: done in 1.79677 secs using 399.1% CPU
Optimizing NNI: done in 1.40891 secs using 398.3% CPU
Iteration 10 / LogL: -59849.338 / Time: 0h:0m:35s
Optimizing NNI: done in 1.49508 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.02672 secs using 398.6% CPU
Optimizing NNI: done in 4.82985 secs using 597.3% CPU
BETTER TREE FOUND at iteration 11: -59808.050
Optimizing NNI: done in 2.2957 secs using 399.1% CPU
Optimizing NNI: done in 1.55913 secs using 399.3% CPU
Optimizing NNI: done in 1.50499 secs using 399.3% CPU
Optimizing NNI: done in 2.55446 secs using 398.2% CPU
Optimizing NNI: done in 4.93889 secs using 596.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.50532 secs using 398.8% CPU
Optimizing NNI: done in 1.82413 secs using 399.2% CPU
Iteration 40 / LogL: -101886.518 / Time: 0h:3m:2s (0h:7m:13s left)
Optimizing NNI: done in 1.3433 secs using 399.3% CPU
BETTER TREE FOUND at iteration 47: -191983.586
Optimizing NNI: done in 2.12357 secs using 398.9% CPU
Optimizing NNI: done in 1.76702 secs using 398.9% CPU
Optimizing NNI: done in 1.00663 secs using 398.9% CPU
Optimizing NNI: done in 1.90536 secs using 398.7% CPU
Optimizing NNI: done in 1.4485 secs using 399% CPU
Optimizing NNI: done in 4.54924 secs using 597.7% CPU
Optimizing NNI: done in 2.02614 secs using 399.1% CPU
Optimizing NNI: done in 1.4942 secs using 399.2% CPU
Optimizing NNI: done in 1.54804 secs using 399% CPU
Iteration 20 / LogL: -59860.529 / Time: 0h:0m:52s
Finish initializing candidate tree set (20)
Current best tree score: -59808.050 / CPU time: 45.164
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.22936 secs using 398.8% CPU
Optimizing NNI: done in 1.54374 secs using 399.1% CPU
Optimizing NNI: done in 4.88056 secs using 597.3% CPU
Optimizing NNI: done in 1.4925 secs using 399.2% CPU
Optimizing NNI: done in 2.8188 secs using 398.8% CPU
Optimizing NNI: done in 1.50747 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.02135 secs using 398.6% CPU
BETTER TREE FOUND at iteration 23: -59802.228
Optimizing NNI: done in 1.30681 secs using 398.6% CPU
Optimizing NNI: done in 2.35245 secs using 398.9% CPU
Optimizing NNI: done in 5.34347 secs using 597.6% CPU
Iteration 50 / LogL: -191987.363 / Time: 0h:5m:40s (0h:11m:13s left)
Optimizing NNI: done in 1.42929 secs using 399.1% CPU
Optimizing NNI: done in 2.22741 secs using 398.5% CPU
Optimizing NNI: done in 2.15792 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.06681 secs using 398.7% CPU
Optimizing NNI: done in 4.24045 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -59798.446
Optimizing NNI: done in 1.15437 secs using 397.6% CPU
Optimizing NNI: done in 1.90719 secs using 398.7% CPU
Iteration 50 / LogL: -101751.293 / Time: 0h:3m:23s (0h:5m:45s left)
Optimizing NNI: done in 1.23164 secs using 397.1% CPU
BETTER TREE FOUND at iteration 51: -191975.009
Optimizing NNI: done in 2.1299 secs using 399% CPU
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Iteration 30 / LogL: -59817.223 / Time: 0h:1m:10s (0h:3m:51s left)
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BETTER TREE FOUND at iteration 31: -59775.020
Optimizing NNI: done in 1.77771 secs using 399% CPU
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BETTER TREE FOUND at iteration 37: -59774.223
BETTER TREE FOUND at iteration 58: -101747.302
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Optimizing NNI: done in 1.54546 secs using 397.5% CPU
Iteration 40 / LogL: -59777.275 / Time: 0h:1m:29s (0h:3m:42s left)
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BETTER TREE FOUND at iteration 59: -101741.725
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Iteration 60 / LogL: -101757.732 / Time: 0h:3m:50s (0h:6m:27s left)
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Optimizing NNI: done in 4.93242 secs using 597.9% CPU
BETTER TREE FOUND at iteration 49: -59773.079
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Iteration 50 / LogL: -59780.294 / Time: 0h:1m:44s (0h:3m:31s left)
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BETTER TREE FOUND at iteration 54: -59772.297
Optimizing NNI: done in 4.20629 secs using 597.7% CPU
Iteration 60 / LogL: -191996.958 / Time: 0h:6m:31s (0h:10m:4s left)
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Optimizing NNI: done in 2.07487 secs using 398.9% CPU
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BETTER TREE FOUND at iteration 70: -101740.869
Iteration 70 / LogL: -101740.869 / Time: 0h:4m:14s (0h:6m:8s left)
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Iteration 60 / LogL: -59787.800 / Time: 0h:2m:0s (0h:3m:11s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 66: -59770.714
Optimizing NNI: done in 2.12069 secs using 398.5% CPU
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BETTER TREE FOUND at iteration 77: -101735.980
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Iteration 70 / LogL: -59778.659 / Time: 0h:2m:16s (0h:3m:9s left)
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Iteration 80 / LogL: -101770.740 / Time: 0h:4m:38s (0h:5m:41s left)
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Iteration 80 / LogL: -59781.645 / Time: 0h:2m:30s (0h:2m:43s left)
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Iteration 70 / LogL: -192061.503 / Time: 0h:7m:19s (0h:8m:35s left)
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Iteration 90 / LogL: -101740.162 / Time: 0h:5m:1s (0h:4m:54s left)
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Iteration 90 / LogL: -59781.820 / Time: 0h:2m:44s (0h:2m:20s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.39148 secs using 597.5% CPU
BETTER TREE FOUND at iteration 92: -59770.298
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Iteration 100 / LogL: -59809.762 / Time: 0h:3m:0s (0h:2m:47s left)
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Iteration 100 / LogL: -101762.319 / Time: 0h:5m:23s (0h:4m:11s left)
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Iteration 110 / LogL: -59780.281 / Time: 0h:3m:15s (0h:2m:26s left)
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Iteration 80 / LogL: -191988.803 / Time: 0h:8m:6s (0h:7m:17s left)
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Iteration 110 / LogL: -101738.734 / Time: 0h:5m:46s (0h:3m:32s left)
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Iteration 120 / LogL: -59772.230 / Time: 0h:3m:29s (0h:2m:6s left)
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Iteration 130 / LogL: -59778.913 / Time: 0h:3m:44s (0h:1m:48s left)
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Iteration 120 / LogL: -101812.830 / Time: 0h:6m:7s (0h:2m:56s left)
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Iteration 140 / LogL: -59770.579 / Time: 0h:3m:59s (0h:1m:29s left)
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Iteration 130 / LogL: -101770.139 / Time: 0h:6m:29s (0h:2m:22s left)
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Iteration 150 / LogL: -59798.550 / Time: 0h:4m:14s (0h:1m:11s left)
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Iteration 90 / LogL: -192045.272 / Time: 0h:8m:56s (0h:6m:7s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 136: -101734.723
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Iteration 160 / LogL: -59771.755 / Time: 0h:4m:28s (0h:0m:54s left)
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BETTER TREE FOUND at iteration 163: -59768.634
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Iteration 140 / LogL: -101737.361 / Time: 0h:6m:53s (0h:4m:45s left)
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Iteration 170 / LogL: -59792.998 / Time: 0h:4m:44s (0h:2m:36s left)
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Iteration 150 / LogL: -101745.974 / Time: 0h:7m:14s (0h:4m:10s left)
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Iteration 180 / LogL: -59781.051 / Time: 0h:4m:59s (0h:2m:18s left)
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UPDATE BEST LOG-LIKELIHOOD: -101734.718
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Estimate model parameters (epsilon = 0.100)
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TREE SEARCH COMPLETED AFTER 237 ITERATIONS / Time: 0h:10m:30s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101734.718
Optimizing NNI: done in 1.37278 secs using 398.6% CPU
Optimal log-likelihood: -101734.704
Proportion of invariable sites: 0.046
Site proportion and rates:  (0.097,0.033) (0.072,0.098) (0.128,0.220) (0.103,0.364) (0.094,0.596) (0.100,0.867) (0.098,1.264) (0.190,1.877) (0.071,4.213)
Parameters optimization took 1 rounds (0.945 sec)
BEST SCORE FOUND : -101734.704
Total tree length: 170.622

Total number of iterations: 237
CPU time used for tree search: 2337.598 sec (0h:38m:57s)
Wall-clock time used for tree search: 594.200 sec (0h:9m:54s)
Total CPU time used: 2486.656 sec (0h:41m:26s)
Total wall-clock time used: 631.578 sec (0h:10m:31s)

===> START BOOTSTRAP REPLICATE NUMBER 39

Creating bootstrap alignment (seed: 68221)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.089 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 110 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106269.205
Optimizing NNI: done in 4.55718 secs using 597.7% CPU
Optimizing NNI: done in 1.30311 secs using 399.3% CPU
2. Current log-likelihood: -104145.863
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3. Current log-likelihood: -104081.931
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Iteration 310 / LogL: -59769.083 / Time: 0h:8m:17s (0h:0m:25s left)
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4. Current log-likelihood: -104079.397
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5. Current log-likelihood: -104078.089
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6. Current log-likelihood: -104076.924
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Iteration 140 / LogL: -192030.575 / Time: 0h:13m:4s (0h:8m:5s left)
7. Current log-likelihood: -104076.022
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8. Current log-likelihood: -104075.364
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9. Current log-likelihood: -104074.854
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10. Current log-likelihood: -104074.460
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11. Current log-likelihood: -104074.183
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12. Current log-likelihood: -104074.038
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Iteration 320 / LogL: -59780.042 / Time: 0h:8m:32s (0h:0m:9s left)
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13. Current log-likelihood: -104073.916
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14. Current log-likelihood: -104073.792
Optimizing NNI: done in 1.74504 secs using 399.3% CPU
Optimal log-likelihood: -104073.670
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.104,0.034) (0.063,0.107) (0.074,0.184) (0.099,0.302) (0.117,0.471) (0.140,0.738) (0.151,1.213) (0.148,1.861) (0.077,4.256)
Parameters optimization took 14 rounds (22.558 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.85556 secs using 596.8% CPU
Optimizing NNI: done in 2.08124 secs using 398.4% CPU
Optimizing NNI: done in 2.14211 secs using 398.3% CPU
Calculating distance matrix: done in 4.73267 secs using 399.9% CPU
Computing ML distances took 4.732975 sec (of wall-clock time) 18.928787 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00068903 secs using 268.1% CPU
Constructing RapidNJ tree: done in 0.00842905 secs using 324.1% CPU
Computing RapidNJ tree took 0.009183 sec (of wall-clock time) 0.031451 sec (of CPU time)
Optimizing NNI: done in 1.67719 secs using 399% CPU
Log-likelihood of RapidNJ tree: -104536.701
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 1.29379 secs using 398.8% CPU
Optimizing NNI: done in 5.3088 secs using 597.4% CPU
Optimizing NNI: done in 1.53235 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 327 ITERATIONS / Time: 0h:8m:44s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59761.568
2. Current log-likelihood: -59761.554
Optimal log-likelihood: -59761.546
Site proportion and rates:  (0.091,0.058) (0.138,0.182) (0.094,0.415) (0.120,0.421) (0.232,0.799) (0.137,1.289) (0.151,2.226) (0.038,4.786)
Parameters optimization took 2 rounds (1.354 sec)
BEST SCORE FOUND : -59761.546
Total tree length: 45.601

Total number of iterations: 327
CPU time used for tree search: 2050.299 sec (0h:34m:10s)
Wall-clock time used for tree search: 517.959 sec (0h:8m:37s)
Total CPU time used: 2083.401 sec (0h:34m:43s)
Total wall-clock time used: 526.233 sec (0h:8m:46s)

===> START BOOTSTRAP REPLICATE NUMBER 91

Creating bootstrap alignment (seed: 67553)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.051 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60854.426
2. Current log-likelihood: -60245.040
3. Current log-likelihood: -60238.199
4. Current log-likelihood: -60230.874
5. Current log-likelihood: -60206.176
Optimizing NNI: done in 6.21768 secs using 597.7% CPU
6. Current log-likelihood: -60191.141
7. Current log-likelihood: -60189.984
Optimal log-likelihood: -60189.864
Site proportion and rates:  (0.097,0.054) (0.115,0.198) (0.103,0.355) (0.084,0.396) (0.251,0.694) (0.152,1.228) (0.165,2.180) (0.033,5.478)
Parameters optimization took 7 rounds (5.654 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10665 secs using 399.7% CPU
Computing ML distances took 1.106839 sec (of wall-clock time) 4.423722 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000380039 secs using 364.2% CPU
Constructing RapidNJ tree: done in 0.004251 secs using 291% CPU
Computing RapidNJ tree took 0.004696 sec (of wall-clock time) 0.014861 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60428.351
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... 10.704 second
Optimizing NNI: done in 6.1892 secs using 597.1% CPU
5.049 second
Optimizing NNI: done in 5.8364 secs using 595.9% CPU
Computing log-likelihood of 98 initial trees ... 10.571 seconds
Current best score: -104073.670

Do NNI search on 20 best initial trees
Computing log-likelihood of 98 initial trees ... 5.804 seconds
Current best score: -60189.864

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.34995 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.81833 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -59971.180
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -59960.605
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BETTER TREE FOUND at iteration 149: -191965.483
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Iteration 10 / LogL: -60024.650 / Time: 0h:0m:37s
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BETTER TREE FOUND at iteration 1: -103541.405
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Iteration 150 / LogL: -192074.502 / Time: 0h:14m:8s (0h:9m:23s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 13: -59960.387
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 16: -59947.096
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -59977.313 / Time: 0h:0m:55s
Finish initializing candidate tree set (20)
Current best tree score: -59947.096 / CPU time: 48.548
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 7: -103507.655
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Iteration 10 / LogL: -103635.680 / Time: 0h:1m:40s
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Iteration 30 / LogL: -59955.591 / Time: 0h:1m:9s (0h:3m:25s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -59944.921
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Iteration 40 / LogL: -59963.513 / Time: 0h:1m:24s (0h:3m:21s left)
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Iteration 20 / LogL: -103605.766 / Time: 0h:2m:6s
Finish initializing candidate tree set (20)
Current best tree score: -103507.655 / CPU time: 97.479
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 160 / LogL: -192036.793 / Time: 0h:15m:0s (0h:8m:23s left)
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Iteration 50 / LogL: -59946.085 / Time: 0h:1m:38s (0h:2m:46s left)
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BETTER TREE FOUND at iteration 51: -59944.916
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Iteration 60 / LogL: -59950.858 / Time: 0h:1m:51s (0h:2m:52s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -103496.995
Iteration 30 / LogL: -103496.995 / Time: 0h:2m:31s (0h:8m:41s left)
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BETTER TREE FOUND at iteration 65: -59941.875
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Iteration 80 / LogL: -59944.685 / Time: 0h:2m:19s (0h:2m:29s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 90 / LogL: -59945.027 / Time: 0h:2m:32s (0h:2m:8s left)
BETTER TREE FOUND at iteration 45: -103492.123
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Iteration 100 / LogL: -59945.504 / Time: 0h:2m:45s (0h:1m:48s left)
BETTER TREE FOUND at iteration 49: -103487.028
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BETTER TREE FOUND at iteration 109: -59932.646
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Iteration 60 / LogL: -103540.064 / Time: 0h:3m:42s (0h:5m:36s left)
BETTER TREE FOUND at iteration 117: -59930.572
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BETTER TREE FOUND at iteration 70: -103484.094
Iteration 70 / LogL: -103484.094 / Time: 0h:4m:9s (0h:6m:1s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 138: -59930.488
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 186: -191958.029
Optimizing NNI: done in 2.40185 secs using 398.6% CPU
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Iteration 150 / LogL: -59948.817 / Time: 0h:3m:53s (0h:2m:17s left)
Optimizing NNI: done in 2.16961 secs using 398.5% CPU
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Iteration 80 / LogL: -103495.466 / Time: 0h:4m:30s (0h:5m:8s left)
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Iteration 160 / LogL: -59994.002 / Time: 0h:4m:5s (0h:2m:0s left)
Optimizing NNI: done in 4.82156 secs using 597.9% CPU
Iteration 190 / LogL: -191995.106 / Time: 0h:17m:32s (0h:8m:54s left)
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Iteration 170 / LogL: -59958.987 / Time: 0h:4m:18s (0h:1m:44s left)
Optimizing NNI: done in 1.31994 secs using 397.8% CPU
Optimizing NNI: done in 2.28535 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.25951 secs using 597.6% CPU
Optimizing NNI: done in 1.18454 secs using 399.1% CPU
BETTER TREE FOUND at iteration 90: -103483.850
Iteration 90 / LogL: -103483.850 / Time: 0h:4m:54s (0h:5m:30s left)
Optimizing NNI: done in 1.23126 secs using 397.3% CPU
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Iteration 180 / LogL: -59964.483 / Time: 0h:4m:31s (0h:1m:28s left)
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Iteration 190 / LogL: -59993.867 / Time: 0h:4m:44s (0h:1m:12s left)
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Iteration 100 / LogL: -103496.972 / Time: 0h:5m:17s (0h:4m:48s left)
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Iteration 200 / LogL: -192022.023 / Time: 0h:18m:22s (0h:7m:56s left)
Optimizing NNI: done in 2.41541 secs using 398.5% CPU
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Iteration 200 / LogL: -59931.687 / Time: 0h:4m:57s (0h:0m:56s left)
Optimizing NNI: done in 1.05264 secs using 398.9% CPU
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Iteration 110 / LogL: -103510.956 / Time: 0h:5m:40s (0h:4m:9s left)
Optimizing NNI: done in 1.2218 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 209: -59930.365
Optimizing NNI: done in 1.28748 secs using 399% CPU
Iteration 210 / LogL: -59933.506 / Time: 0h:5m:10s (0h:2m:27s left)
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Iteration 220 / LogL: -59946.071 / Time: 0h:5m:23s (0h:2m:11s left)
Optimizing NNI: done in 2.20539 secs using 398.4% CPU
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Iteration 120 / LogL: -103642.055 / Time: 0h:6m:4s (0h:3m:34s left)
Optimizing NNI: done in 1.2593 secs using 399.1% CPU
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Iteration 230 / LogL: -59930.681 / Time: 0h:5m:36s (0h:1m:56s left)
Optimizing NNI: done in 2.61825 secs using 398.4% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 240: -59930.294
Iteration 240 / LogL: -59930.294 / Time: 0h:5m:50s (0h:2m:26s left)
Optimizing NNI: done in 5.02039 secs using 597.6% CPU
Iteration 210 / LogL: -191989.138 / Time: 0h:19m:16s (0h:7m:0s left)
Optimizing NNI: done in 2.52277 secs using 398.4% CPU
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Iteration 130 / LogL: -103585.904 / Time: 0h:6m:27s (0h:3m:0s left)
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Iteration 250 / LogL: -60014.794 / Time: 0h:6m:2s (0h:2m:11s left)
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Iteration 260 / LogL: -59994.916 / Time: 0h:6m:15s (0h:1m:56s left)
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Iteration 140 / LogL: -103505.205 / Time: 0h:6m:51s (0h:2m:27s left)
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Iteration 270 / LogL: -59952.119 / Time: 0h:6m:28s (0h:1m:41s left)
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Iteration 150 / LogL: -103488.682 / Time: 0h:7m:12s (0h:1m:56s left)
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Iteration 220 / LogL: -191969.380 / Time: 0h:20m:7s (0h:6m:3s left)
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Iteration 280 / LogL: -60182.203 / Time: 0h:6m:42s (0h:1m:26s left)
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Iteration 290 / LogL: -59954.757 / Time: 0h:6m:55s (0h:1m:11s left)
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Iteration 160 / LogL: -103524.514 / Time: 0h:7m:35s (0h:1m:25s left)
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Iteration 300 / LogL: -59941.021 / Time: 0h:7m:8s (0h:0m:57s left)
Optimizing NNI: done in 2.69214 secs using 398.1% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.22373 secs using 399.2% CPU
Optimizing NNI: done in 1.25069 secs using 398.9% CPU
BETTER TREE FOUND at iteration 167: -103483.531
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Iteration 310 / LogL: -59963.812 / Time: 0h:7m:21s (0h:0m:42s left)
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Iteration 170 / LogL: -103485.908 / Time: 0h:7m:59s (0h:4m:35s left)
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Iteration 230 / LogL: -191997.829 / Time: 0h:20m:57s (0h:5m:7s left)
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Iteration 320 / LogL: -59932.628 / Time: 0h:7m:34s (0h:0m:28s left)
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Iteration 330 / LogL: -59975.435 / Time: 0h:7m:48s (0h:0m:14s left)
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Iteration 180 / LogL: -103512.677 / Time: 0h:8m:21s (0h:4m:3s left)
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Iteration 340 / LogL: -59930.342 / Time: 0h:8m:1s (0h:0m:0s left)
Optimizing NNI: done in 5.71502 secs using 597.1% CPU
Optimizing NNI: done in 1.86217 secs using 399.1% CPU
Optimizing NNI: done in 1.05232 secs using 398.6% CPU
TREE SEARCH COMPLETED AFTER 341 ITERATIONS / Time: 0h:8m:2s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59930.294
2. Current log-likelihood: -59930.280
3. Current log-likelihood: -59930.267
Optimizing NNI: done in 1.76748 secs using 398.7% CPU
4. Current log-likelihood: -59930.255
5. Current log-likelihood: -59930.242
6. Current log-likelihood: -59930.229
7. Current log-likelihood: -59930.216
8. Current log-likelihood: -59930.204
9. Current log-likelihood: -59930.191
Optimizing NNI: done in 2.1854 secs using 398.5% CPU
10. Current log-likelihood: -59930.180
11. Current log-likelihood: -59930.167
Optimizing NNI: done in 5.6774 secs using 596.9% CPU
12. Current log-likelihood: -59930.154
13. Current log-likelihood: -59930.143
14. Current log-likelihood: -59930.132
Optimizing NNI: done in 2.09591 secs using 398.9% CPU
15. Current log-likelihood: -59930.121
16. Current log-likelihood: -59930.110
17. Current log-likelihood: -59930.099
18. Current log-likelihood: -59930.088
19. Current log-likelihood: -59930.077
Optimizing NNI: done in 2.15899 secs using 398.9% CPU
Iteration 190 / LogL: -103528.886 / Time: 0h:8m:42s (0h:3m:32s left)
20. Current log-likelihood: -59930.066
21. Current log-likelihood: -59930.056
22. Current log-likelihood: -59930.046
23. Current log-likelihood: -59930.036
Optimal log-likelihood: -59930.021
Site proportion and rates:  (0.093,0.050) (0.120,0.192) (0.094,0.365) (0.084,0.374) (0.250,0.673) (0.156,1.192) (0.170,2.177) (0.033,5.465)
Parameters optimization took 23 rounds (9.745 sec)
BEST SCORE FOUND : -59930.021
Total tree length: 46.620

Total number of iterations: 341
CPU time used for tree search: 1878.854 sec (0h:31m:18s)
Wall-clock time used for tree search: 474.859 sec (0h:7m:54s)
Total CPU time used: 1946.636 sec (0h:32m:26s)
Total wall-clock time used: 491.837 sec (0h:8m:11s)

===> START BOOTSTRAP REPLICATE NUMBER 92

Creating bootstrap alignment (seed: 67554)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.058 seconds

NOTE: 63 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59018.407
Optimizing NNI: done in 1.92598 secs using 399.2% CPU
2. Current log-likelihood: -58474.850
Optimizing NNI: done in 5.84292 secs using 597.5% CPU
3. Current log-likelihood: -58461.822
Optimizing NNI: done in 2.18649 secs using 398.4% CPU
4. Current log-likelihood: -58454.822
5. Current log-likelihood: -58433.390
6. Current log-likelihood: -58431.942
Optimizing NNI: done in 2.25852 secs using 398.8% CPU
Optimal log-likelihood: -58431.829
Site proportion and rates:  (0.101,0.056) (0.134,0.182) (0.076,0.409) (0.117,0.443) (0.204,0.731) (0.165,1.201) (0.177,2.256) (0.025,5.504)
Parameters optimization took 6 rounds (5.256 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.90338 secs using 597.6% CPU
Calculating distance matrix: done in 1.07877 secs using 399.6% CPU
Computing ML distances took 1.078962 sec (of wall-clock time) 4.310821 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000383854 secs using 120.1% CPU
Constructing RapidNJ tree: done in 0.0044241 secs using 319.7% CPU
Computing RapidNJ tree took 0.004857 sec (of wall-clock time) 0.016534 sec (of CPU time)
Log-likelihood of RapidNJ tree: -58332.993
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.08728 secs using 399.1% CPU
Optimizing NNI: done in 1.95476 secs using 398.5% CPU
Optimizing NNI: done in 2.19175 secs using 398.9% CPU
5.143 second
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Optimizing NNI: done in 6.96302 secs using 597.4% CPU
Iteration 240 / LogL: -192072.325 / Time: 0h:21m:51s (0h:4m:12s left)
Optimizing NNI: done in 2.19568 secs using 398.5% CPU
Computing log-likelihood of 98 initial trees ... 5.158 seconds
Current best score: -58200.760

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 200 / LogL: -103504.144 / Time: 0h:9m:4s (0h:3m:3s left)
BETTER TREE FOUND at iteration 1: -58013.688
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -57998.434
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -57985.000
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Iteration 10 / LogL: -58007.495 / Time: 0h:0m:32s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 14: -57973.227
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Iteration 210 / LogL: -103508.853 / Time: 0h:9m:25s (0h:2m:34s left)
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Iteration 20 / LogL: -58002.434 / Time: 0h:0m:45s
Finish initializing candidate tree set (20)
Current best tree score: -57973.227 / CPU time: 38.496
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -57948.362
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Iteration 30 / LogL: -57978.814 / Time: 0h:1m:1s (0h:3m:22s left)
BETTER TREE FOUND at iteration 218: -103482.313
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Iteration 250 / LogL: -192131.500 / Time: 0h:22m:44s (0h:3m:17s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 220 / LogL: -103524.336 / Time: 0h:9m:51s (0h:4m:24s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 40: -57917.722
Iteration 40 / LogL: -57917.722 / Time: 0h:1m:18s (0h:3m:22s left)
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Iteration 50 / LogL: -57929.322 / Time: 0h:1m:32s (0h:2m:49s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 53: -57914.846
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 59: -57914.773
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BETTER TREE FOUND at iteration 60: -57914.772
Iteration 60 / LogL: -57914.772 / Time: 0h:1m:46s (0h:3m:0s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 81: -57913.565
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 90: -57913.523
Iteration 90 / LogL: -57913.523 / Time: 0h:2m:27s (0h:2m:45s left)
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Iteration 260 / LogL: -103563.701 / Time: 0h:11m:17s (0h:2m:31s left)
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Iteration 100 / LogL: -57914.820 / Time: 0h:2m:41s (0h:2m:26s left)
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Iteration 270 / LogL: -191985.194 / Time: 0h:24m:21s (0h:1m:26s left)
Optimizing NNI: done in 1.29497 secs using 398.8% CPU
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Optimizing NNI: done in 1.14176 secs using 398.4% CPU
Iteration 110 / LogL: -57914.776 / Time: 0h:2m:54s (0h:2m:7s left)
Optimizing NNI: done in 2.26518 secs using 398.8% CPU
Iteration 270 / LogL: -103485.925 / Time: 0h:11m:39s (0h:2m:4s left)
Optimizing NNI: done in 1.26415 secs using 398% CPU
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Optimizing NNI: done in 2.18026 secs using 398.7% CPU
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Optimizing NNI: done in 4.55643 secs using 597.2% CPU
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Optimizing NNI: done in 2.32 secs using 398.4% CPU
Optimizing NNI: done in 4.99563 secs using 597.9% CPU
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Optimizing NNI: done in 1.95002 secs using 398.6% CPU
Optimizing NNI: done in 1.19751 secs using 399% CPU
Optimizing NNI: done in 1.20383 secs using 399.7% CPU
Iteration 120 / LogL: -57951.319 / Time: 0h:3m:7s (0h:1m:50s left)
Optimizing NNI: done in 2.17259 secs using 398.6% CPU
Optimizing NNI: done in 1.32462 secs using 398.5% CPU
Optimizing NNI: done in 4.87921 secs using 597.7% CPU
Optimizing NNI: done in 1.99036 secs using 398.8% CPU
Optimizing NNI: done in 1.44662 secs using 399.3% CPU
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Optimizing NNI: done in 5.46685 secs using 596.6% CPU
Optimizing NNI: done in 1.34818 secs using 398.9% CPU
Optimizing NNI: done in 2.02356 secs using 398.5% CPU
Iteration 280 / LogL: -103520.473 / Time: 0h:12m:0s (0h:1m:38s left)
Optimizing NNI: done in 1.2653 secs using 398.8% CPU
Optimizing NNI: done in 1.48798 secs using 399.1% CPU
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Optimizing NNI: done in 2.43099 secs using 398.5% CPU
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Optimizing NNI: done in 1.8051 secs using 398.6% CPU
Optimizing NNI: done in 1.22702 secs using 399.3% CPU
Iteration 130 / LogL: -57923.101 / Time: 0h:3m:20s (0h:1m:33s left)
Optimizing NNI: done in 1.18604 secs using 399.4% CPU
Optimizing NNI: done in 2.07148 secs using 398.6% CPU
Optimizing NNI: done in 1.43744 secs using 398.6% CPU
Optimizing NNI: done in 5.20048 secs using 596.7% CPU
Optimizing NNI: done in 2.01255 secs using 398.4% CPU
Optimizing NNI: done in 1.49571 secs using 399% CPU
Optimizing NNI: done in 1.41579 secs using 399.3% CPU
Optimizing NNI: done in 2.38656 secs using 399% CPU
Optimizing NNI: done in 1.19544 secs using 398.9% CPU
Optimizing NNI: done in 4.87441 secs using 597.4% CPU
Optimizing NNI: done in 1.39862 secs using 398.5% CPU
Optimizing NNI: done in 1.88823 secs using 398.9% CPU
Optimizing NNI: done in 1.32598 secs using 399.2% CPU
Optimizing NNI: done in 2.11876 secs using 398.2% CPU
Optimizing NNI: done in 1.39828 secs using 398.8% CPU
Optimizing NNI: done in 1.27626 secs using 399% CPU
Optimizing NNI: done in 4.3073 secs using 597.4% CPU
Iteration 280 / LogL: -191988.829 / Time: 0h:25m:11s (0h:0m:32s left)
Optimizing NNI: done in 2.35668 secs using 398.7% CPU
Optimizing NNI: done in 1.42174 secs using 399.6% CPU
Iteration 140 / LogL: -57917.524 / Time: 0h:3m:34s (0h:1m:17s left)
Optimizing NNI: done in 1.30782 secs using 399.4% CPU
Optimizing NNI: done in 2.56061 secs using 398.6% CPU
Optimizing NNI: done in 1.29917 secs using 398.9% CPU
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Iteration 290 / LogL: -103574.788 / Time: 0h:12m:22s (0h:1m:11s left)
Optimizing NNI: done in 1.14037 secs using 398.9% CPU
Optimizing NNI: done in 5.07023 secs using 597.3% CPU
Optimizing NNI: done in 1.3387 secs using 399.1% CPU
Optimizing NNI: done in 2.2612 secs using 398.7% CPU
Optimizing NNI: done in 1.17911 secs using 399.1% CPU
Optimizing NNI: done in 1.26309 secs using 398.8% CPU
Optimizing NNI: done in 2.5548 secs using 398.9% CPU
Optimizing NNI: done in 4.66712 secs using 597.3% CPU
Optimizing NNI: done in 1.2424 secs using 399.1% CPU
Optimizing NNI: done in 1.28323 secs using 399% CPU
Optimizing NNI: done in 2.00823 secs using 398.9% CPU
Optimizing NNI: done in 1.27744 secs using 399% CPU
Optimizing NNI: done in 1.33554 secs using 399.1% CPU
Iteration 150 / LogL: -57917.871 / Time: 0h:3m:47s (0h:1m:0s left)
Optimizing NNI: done in 2.23545 secs using 399% CPU
Optimizing NNI: done in 4.89761 secs using 597.2% CPU
Optimizing NNI: done in 1.31871 secs using 399% CPU
Optimizing NNI: done in 1.84448 secs using 398.9% CPU
Optimizing NNI: done in 1.309 secs using 399.2% CPU
Optimizing NNI: done in 1.22433 secs using 398.4% CPU
Optimizing NNI: done in 1.92789 secs using 398.7% CPU
Optimizing NNI: done in 1.2199 secs using 398.6% CPU
Optimizing NNI: done in 4.89977 secs using 597.3% CPU
Optimizing NNI: done in 2.36416 secs using 398.5% CPU
Optimizing NNI: done in 1.34926 secs using 399% CPU
Optimizing NNI: done in 1.19412 secs using 398.2% CPU
Optimizing NNI: done in 2.16231 secs using 398.4% CPU
Optimizing NNI: done in 1.20262 secs using 398.8% CPU
Optimizing NNI: done in 1.46825 secs using 398.2% CPU
Optimizing NNI: done in 4.72735 secs using 598% CPU
Optimizing NNI: done in 2.25932 secs using 398.6% CPU
Optimizing NNI: done in 1.32576 secs using 399.2% CPU
Optimizing NNI: done in 2.1929 secs using 398.8% CPU
Iteration 300 / LogL: -103506.912 / Time: 0h:12m:44s (0h:0m:46s left)
Optimizing NNI: done in 1.29207 secs using 399.1% CPU
Iteration 160 / LogL: -57915.299 / Time: 0h:4m:0s (0h:0m:45s left)
Optimizing NNI: done in 1.20516 secs using 398.7% CPU
Optimizing NNI: done in 4.47701 secs using 597.9% CPU
Optimizing NNI: done in 1.03702 secs using 399.1% CPU
Optimizing NNI: done in 2.34162 secs using 398.5% CPU
Optimizing NNI: done in 1.20721 secs using 398.9% CPU
Optimizing NNI: done in 2.12632 secs using 398.5% CPU
Optimizing NNI: done in 1.30311 secs using 398.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -57913.517
Optimizing NNI: done in 1.20079 secs using 398% CPU
Optimizing NNI: done in 1.92776 secs using 399% CPU
Optimizing NNI: done in 4.97492 secs using 597.2% CPU
TREE SEARCH COMPLETED AFTER 287 ITERATIONS / Time: 0h:25m:45s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -191958.029
Optimizing NNI: done in 1.16091 secs using 398.6% CPU
Optimal log-likelihood: -191958.014
Site proportion and rates:  (0.013,0.107) (0.050,0.231) (0.118,0.367) (0.228,0.551) (0.173,0.781) (0.164,1.051) (0.147,1.570) (0.107,2.617)
Parameters optimization took 1 rounds (1.244 sec)
BEST SCORE FOUND : -191958.014
Total tree length: 152.898

Total number of iterations: 287
CPU time used for tree search: 8893.093 sec (2h:28m:13s)
Wall-clock time used for tree search: 1514.151 sec (0h:25m:14s)
Total CPU time used: 9088.507 sec (2h:31m:28s)
Total wall-clock time used: 1546.991 sec (0h:25m:46s)
Optimizing NNI: done in 1.17409 secs using 398.4% CPU

===> START BOOTSTRAP REPLICATE NUMBER 24

Creating bootstrap alignment (seed: 70487)...

Optimizing NNI: done in 2.09451 secs using 398.9% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.323 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196694.600
Optimizing NNI: done in 1.15386 secs using 398.8% CPU
Optimizing NNI: done in 2.22688 secs using 398.9% CPU
Optimizing NNI: done in 1.41461 secs using 398.2% CPU
2. Current log-likelihood: -194053.159
Optimizing NNI: done in 1.50308 secs using 398.4% CPU
Iteration 170 / LogL: -57915.598 / Time: 0h:4m:12s (0h:0m:29s left)
Optimizing NNI: done in 2.21796 secs using 398.4% CPU
Optimizing NNI: done in 1.36455 secs using 398.8% CPU
3. Current log-likelihood: -193948.602
Optimizing NNI: done in 1.95736 secs using 399.1% CPU
Optimizing NNI: done in 1.36015 secs using 398.6% CPU
Optimizing NNI: done in 1.31706 secs using 398.5% CPU
4. Current log-likelihood: -193946.758
Optimizing NNI: done in 2.08113 secs using 398.3% CPU
Optimizing NNI: done in 1.41817 secs using 398.6% CPU
5. Current log-likelihood: -193946.630
Optimizing NNI: done in 1.20018 secs using 398.7% CPU
Optimizing NNI: done in 2.17094 secs using 399% CPU
Optimizing NNI: done in 1.42616 secs using 398.7% CPU
Optimal log-likelihood: -193946.561
Site proportion and rates:  (0.020,0.096) (0.022,0.198) (0.033,0.255) (0.113,0.376) (0.327,0.595) (0.196,0.936) (0.167,1.526) (0.122,2.542)
Parameters optimization took 5 rounds (12.041 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.08077 secs using 398.7% CPU
Iteration 310 / LogL: -103512.729 / Time: 0h:13m:6s (0h:0m:20s left)
Optimizing NNI: done in 1.17148 secs using 398.1% CPU
Optimizing NNI: done in 1.33104 secs using 398.4% CPU
Optimizing NNI: done in 1.87759 secs using 399.1% CPU
Optimizing NNI: done in 1.35871 secs using 398.4% CPU
Optimizing NNI: done in 1.98171 secs using 398.1% CPU
Optimizing NNI: done in 1.07886 secs using 398.3% CPU
Iteration 180 / LogL: -57930.858 / Time: 0h:4m:25s (0h:0m:14s left)
Optimizing NNI: done in 1.41271 secs using 399.2% CPU
Optimizing NNI: done in 2.26351 secs using 398.5% CPU
Optimizing NNI: done in 1.31547 secs using 398.2% CPU
Optimizing NNI: done in 1.86099 secs using 398.5% CPU
Optimizing NNI: done in 1.45844 secs using 398.8% CPU
Calculating distance matrix: done in 10.2438 secs using 599.8% CPU
Computing ML distances took 10.244320 sec (of wall-clock time) 61.446471 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00128794 secs using 550.3% CPU
Optimizing NNI: done in 1.22214 secs using 398.5% CPU
Constructing RapidNJ tree: done in 0.0228641 secs using 673.3% CPU
Computing RapidNJ tree took 0.024220 sec (of wall-clock time) 0.161096 sec (of CPU time)
Optimizing NNI: done in 1.87572 secs using 398.5% CPU
Optimizing NNI: done in 1.55346 secs using 398.4% CPU
Log-likelihood of RapidNJ tree: -198680.809
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.90514 secs using 398.5% CPU
Optimizing NNI: done in 1.27587 secs using 398.6% CPU
Optimizing NNI: done in 1.16899 secs using 398.1% CPU
Optimizing NNI: done in 2.78704 secs using 398.3% CPU
Optimizing NNI: done in 1.1462 secs using 398.6% CPU
Optimizing NNI: done in 1.69365 secs using 398% CPU
Optimizing NNI: done in 2.88247 secs using 398.9% CPU
Optimizing NNI: done in 1.60466 secs using 397.6% CPU
Iteration 190 / LogL: -57913.552 / Time: 0h:4m:39s (0h:0m:0s left)
Optimizing NNI: done in 1.89474 secs using 397.9% CPU
TREE SEARCH COMPLETED AFTER 191 ITERATIONS / Time: 0h:4m:41s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57913.517
Optimizing NNI: done in 2.8096 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 319 ITERATIONS / Time: 0h:13m:26s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -103482.313
2. Current log-likelihood: -57913.507
Optimal log-likelihood: -57913.491
Site proportion and rates:  (0.098,0.054) (0.158,0.192) (0.109,0.440) (0.067,0.440) (0.192,0.728) (0.170,1.164) (0.183,2.286) (0.023,5.632)
Parameters optimization took 2 rounds (0.954 sec)
BEST SCORE FOUND : -57913.491
Total tree length: 42.368

Total number of iterations: 191
CPU time used for tree search: 1081.168 sec (0h:18m:1s)
Wall-clock time used for tree search: 274.957 sec (0h:4m:34s)
Total CPU time used: 1111.915 sec (0h:18m:31s)
Total wall-clock time used: 282.649 sec (0h:4m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 93

Creating bootstrap alignment (seed: 67555)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.052 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -63724.669
2. Current log-likelihood: -63087.697
2. Current log-likelihood: -103482.258
3. Current log-likelihood: -63077.651
4. Current log-likelihood: -63072.078
3. Current log-likelihood: -103482.196
5. Current log-likelihood: -63068.671
4. Current log-likelihood: -103482.135
6. Current log-likelihood: -63066.087
7. Current log-likelihood: -63065.006
8. Current log-likelihood: -63062.862
5. Current log-likelihood: -103482.075
9. Current log-likelihood: -63058.174
10. Current log-likelihood: -63055.265
6. Current log-likelihood: -103482.017
11. Current log-likelihood: -63054.137
12. Current log-likelihood: -63053.741
7. Current log-likelihood: -103481.963
13. Current log-likelihood: -63053.580
8. Current log-likelihood: -103481.911
Optimal log-likelihood: -63053.507
Site proportion and rates:  (0.110,0.056) (0.111,0.194) (0.135,0.374) (0.198,0.570) (0.157,0.911) (0.138,1.611) (0.120,2.319) (0.032,5.197)
Parameters optimization took 13 rounds (11.898 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.11832 secs using 399.2% CPU
Computing ML distances took 1.118537 sec (of wall-clock time) 4.464646 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000440121 secs using 405.8% CPU
Constructing RapidNJ tree: done in 0.00939703 secs using 418.5% CPU
Computing RapidNJ tree took 0.009905 sec (of wall-clock time) 0.041553 sec (of CPU time)
Log-likelihood of RapidNJ tree: -63032.410
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 9. Current log-likelihood: -103481.861
10. Current log-likelihood: -103481.810
11. Current log-likelihood: -103481.761
12. Current log-likelihood: -103481.712
5.269 second
13. Current log-likelihood: -103481.667
30.470 second
14. Current log-likelihood: -103481.623
15. Current log-likelihood: -103481.582
16. Current log-likelihood: -103481.542
17. Current log-likelihood: -103481.502
18. Current log-likelihood: -103481.465
Computing log-likelihood of 98 initial trees ... 6.440 seconds
Current best score: -62976.837

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.08665 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
19. Current log-likelihood: -103481.426
20. Current log-likelihood: -103481.388
BETTER TREE FOUND at iteration 1: -62717.322
21. Current log-likelihood: -103481.351
Optimizing NNI: done in 1.44068 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
22. Current log-likelihood: -103481.313
BETTER TREE FOUND at iteration 2: -62675.735
23. Current log-likelihood: -103481.278
Optimizing NNI: done in 1.27338 secs using 399.3% CPU
24. Current log-likelihood: -103481.243
25. Current log-likelihood: -103481.213
Optimizing NNI: done in 1.5239 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
26. Current log-likelihood: -103481.195
27. Current log-likelihood: -103481.178
BETTER TREE FOUND at iteration 4: -62673.151
28. Current log-likelihood: -103481.158
Computing log-likelihood of 98 initial trees ... 16.604 seconds
Current best score: -193946.561

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.34884 secs using 399.2% CPU
29. Current log-likelihood: -103481.136
30. Current log-likelihood: -103481.105
Optimizing NNI: done in 1.25531 secs using 399.1% CPU
31. Current log-likelihood: -103481.087
32. Current log-likelihood: -103481.070
Optimizing NNI: done in 1.32927 secs using 398.6% CPU
33. Current log-likelihood: -103481.053
Optimizing NNI: done in 3.08374 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
34. Current log-likelihood: -103481.034
Optimizing NNI: done in 1.33055 secs using 399.2% CPU
35. Current log-likelihood: -103481.016
Optimizing NNI: done in 1.43288 secs using 398.9% CPU
36. Current log-likelihood: -103480.999
37. Current log-likelihood: -103480.982
Optimizing NNI: done in 1.67669 secs using 399.1% CPU
Iteration 10 / LogL: -62708.264 / Time: 0h:0m:44s
BETTER TREE FOUND at iteration 1: -193233.785
38. Current log-likelihood: -103480.964
39. Current log-likelihood: -103480.948
Optimizing NNI: done in 1.27275 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
40. Current log-likelihood: -103480.931
BETTER TREE FOUND at iteration 11: -62669.731
41. Current log-likelihood: -103480.915
42. Current log-likelihood: -103480.899
Optimizing NNI: done in 3.58101 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.19251 secs using 399.2% CPU
43. Current log-likelihood: -103480.883
Optimizing NNI: done in 1.15424 secs using 399% CPU
44. Current log-likelihood: -103480.867
45. Current log-likelihood: -103480.851
Optimizing NNI: done in 1.14304 secs using 398.9% CPU
46. Current log-likelihood: -103480.836
Optimizing NNI: done in 1.3841 secs using 398.4% CPU
47. Current log-likelihood: -103480.820
BETTER TREE FOUND at iteration 2: -193159.575
48. Current log-likelihood: -103480.805
Optimizing NNI: done in 1.26851 secs using 398.8% CPU
49. Current log-likelihood: -103480.790
Optimizing NNI: done in 1.40402 secs using 399.2% CPU
50. Current log-likelihood: -103480.775
51. Current log-likelihood: -103480.761
Optimizing NNI: done in 1.4847 secs using 398.1% CPU
Optimizing NNI: done in 3.87249 secs using 597.2% CPU
52. Current log-likelihood: -103480.746
Optimizing NNI: done in 1.00714 secs using 399.3% CPU
53. Current log-likelihood: -103480.732
Optimizing NNI: done in 1.12282 secs using 399.1% CPU
Iteration 20 / LogL: -62754.898 / Time: 0h:0m:58s
Finish initializing candidate tree set (20)
Current best tree score: -62669.731 / CPU time: 44.977
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
54. Current log-likelihood: -103480.717
55. Current log-likelihood: -103480.703
Optimizing NNI: done in 1.73195 secs using 399% CPU
56. Current log-likelihood: -103480.689
Optimizing NNI: done in 4.0522 secs using 598.2% CPU
57. Current log-likelihood: -103480.675
Optimizing NNI: done in 1.54618 secs using 399.4% CPU
58. Current log-likelihood: -103480.661
59. Current log-likelihood: -103480.647
Optimizing NNI: done in 1.20947 secs using 398.3% CPU
60. Current log-likelihood: -103480.633
Optimizing NNI: done in 3.51847 secs using 597.6% CPU
Optimizing NNI: done in 1.58077 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
61. Current log-likelihood: -103480.620
62. Current log-likelihood: -103480.607
BETTER TREE FOUND at iteration 24: -62664.799
63. Current log-likelihood: -103480.593
64. Current log-likelihood: -103480.581
Optimizing NNI: done in 1.41372 secs using 398.9% CPU
Optimizing NNI: done in 3.91973 secs using 596.4% CPU
65. Current log-likelihood: -103480.568
Optimizing NNI: done in 1.3578 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
66. Current log-likelihood: -103480.554
67. Current log-likelihood: -103480.541
BETTER TREE FOUND at iteration 26: -62660.533
68. Current log-likelihood: -103480.529
Optimizing NNI: done in 1.25249 secs using 399.2% CPU
69. Current log-likelihood: -103480.516
70. Current log-likelihood: -103480.504
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Optimizing NNI: done in 1.4563 secs using 399.1% CPU
71. Current log-likelihood: -103480.492
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72. Current log-likelihood: -103480.479
73. Current log-likelihood: -103480.467
Optimizing NNI: done in 1.46077 secs using 399.2% CPU
Iteration 30 / LogL: -62661.396 / Time: 0h:1m:15s (0h:4m:11s left)
74. Current log-likelihood: -103480.455
Optimizing NNI: done in 3.71954 secs using 597.8% CPU
Optimizing NNI: done in 1.14846 secs using 398.6% CPU
75. Current log-likelihood: -103480.443
76. Current log-likelihood: -103480.432
Optimizing NNI: done in 1.27528 secs using 399.3% CPU
77. Current log-likelihood: -103480.420
Optimizing NNI: done in 1.23241 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
78. Current log-likelihood: -103480.408
Optimal log-likelihood: -103480.394
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.092,0.027) (0.066,0.085) (0.090,0.180) (0.105,0.310) (0.142,0.505) (0.120,0.810) (0.152,1.276) (0.131,1.914) (0.076,4.334)
Parameters optimization took 78 rounds (81.119 sec)
BEST SCORE FOUND : -103480.394
Total tree length: 171.683

Total number of iterations: 319
CPU time used for tree search: 3066.597 sec (0h:51m:6s)
Wall-clock time used for tree search: 777.337 sec (0h:12m:57s)
Total CPU time used: 3505.913 sec (0h:58m:25s)
Total wall-clock time used: 887.628 sec (0h:14m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 40

Creating bootstrap alignment (seed: 68222)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.089 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -111197.430
Optimizing NNI: done in 4.11719 secs using 597% CPU
BETTER TREE FOUND at iteration 33: -62656.846
2. Current log-likelihood: -109284.334
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Optimizing NNI: done in 1.57077 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
3. Current log-likelihood: -109159.396
Optimizing NNI: done in 4.29424 secs using 596.9% CPU
Iteration 10 / LogL: -193233.490 / Time: 0h:1m:59s
BETTER TREE FOUND at iteration 35: -62647.666
4. Current log-likelihood: -109151.249
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5. Current log-likelihood: -109148.765
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7. Current log-likelihood: -109144.936
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Iteration 40 / LogL: -62675.719 / Time: 0h:1m:32s (0h:3m:44s left)
8. Current log-likelihood: -109143.459
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9. Current log-likelihood: -109142.369
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10. Current log-likelihood: -109141.466
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11. Current log-likelihood: -109140.757
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12. Current log-likelihood: -109140.207
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Estimate model parameters (epsilon = 0.100)
13. Current log-likelihood: -109139.802
BETTER TREE FOUND at iteration 46: -62644.973
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14. Current log-likelihood: -109139.423
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15. Current log-likelihood: -109139.241
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16. Current log-likelihood: -109139.085
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BETTER TREE FOUND at iteration 49: -62644.973
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17. Current log-likelihood: -109138.885
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Iteration 50 / LogL: -62659.125 / Time: 0h:1m:47s (0h:3m:36s left)
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18. Current log-likelihood: -109138.762
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19. Current log-likelihood: -109138.588
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20. Current log-likelihood: -109138.465
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21. Current log-likelihood: -109138.275
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22. Current log-likelihood: -109138.139
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23. Current log-likelihood: -109137.941
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24. Current log-likelihood: -109137.826
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25. Current log-likelihood: -109137.685
Optimizing NNI: done in 1.49861 secs using 397.6% CPU
Optimizing NNI: done in 1.17972 secs using 397.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimal log-likelihood: -109137.628
Proportion of invariable sites: 0.008
Site proportion and rates:  (0.090,0.035) (0.114,0.112) (0.101,0.230) (0.126,0.395) (0.111,0.626) (0.090,0.915) (0.113,1.243) (0.180,1.917) (0.068,4.024)
Parameters optimization took 25 rounds (40.153 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
BETTER TREE FOUND at iteration 60: -62643.678
Iteration 60 / LogL: -62643.678 / Time: 0h:2m:1s (0h:3m:25s left)
Optimizing NNI: done in 1.36465 secs using 398.6% CPU
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Optimizing NNI: done in 1.2127 secs using 398.6% CPU
Optimizing NNI: done in 1.22957 secs using 398.5% CPU
Calculating distance matrix: done in 4.85989 secs using 399.9% CPU
Computing ML distances took 4.860166 sec (of wall-clock time) 19.435619 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000725985 secs using 177.7% CPU
Constructing RapidNJ tree: done in 0.00880504 secs using 471.8% CPU
Computing RapidNJ tree took 0.009594 sec (of wall-clock time) 0.043789 sec (of CPU time)
Optimizing NNI: done in 3.6458 secs using 597.6% CPU
Iteration 20 / LogL: -193232.967 / Time: 0h:2m:40s
Finish initializing candidate tree set (20)
Current best tree score: -193159.575 / CPU time: 136.009
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.39324 secs using 398.8% CPU
Log-likelihood of RapidNJ tree: -109763.350
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.14452 secs using 398.5% CPU
Optimizing NNI: done in 1.1879 secs using 398.6% CPU
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 21: -193155.123
Optimizing NNI: done in 1.22088 secs using 398.9% CPU
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Iteration 70 / LogL: -62789.316 / Time: 0h:2m:14s (0h:2m:54s left)
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10.407 second
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Iteration 80 / LogL: -62643.678 / Time: 0h:2m:27s (0h:2m:28s left)
Computing log-likelihood of 98 initial trees ... 10.349 seconds
Current best score: -109137.628

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 90 / LogL: -62721.622 / Time: 0h:2m:39s (0h:2m:5s left)
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BETTER TREE FOUND at iteration 1: -108664.442
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 97: -62641.681
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Iteration 30 / LogL: -193258.511 / Time: 0h:3m:27s (0h:10m:50s left)
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Iteration 100 / LogL: -62645.095 / Time: 0h:2m:54s (0h:2m:50s left)
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Iteration 110 / LogL: -62655.779 / Time: 0h:3m:6s (0h:2m:28s left)
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Iteration 10 / LogL: -108702.368 / Time: 0h:1m:48s
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BETTER TREE FOUND at iteration 116: -62641.672
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 13: -108658.741
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Iteration 120 / LogL: -62662.914 / Time: 0h:3m:19s (0h:2m:40s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 38: -193147.093
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Iteration 130 / LogL: -62671.928 / Time: 0h:3m:32s (0h:2m:21s left)
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Iteration 20 / LogL: -108688.604 / Time: 0h:2m:16s
Finish initializing candidate tree set (20)
Current best tree score: -108658.741 / CPU time: 90.272
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 30: -108638.144
Iteration 30 / LogL: -108638.144 / Time: 0h:2m:42s (0h:9m:20s left)
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Iteration 180 / LogL: -62648.485 / Time: 0h:4m:35s (0h:0m:55s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 47: -108629.143
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Iteration 190 / LogL: -62641.695 / Time: 0h:4m:48s (0h:0m:39s left)
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Iteration 50 / LogL: -108655.398 / Time: 0h:3m:28s (0h:6m:51s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 200 / LogL: -62655.002 / Time: 0h:5m:1s (0h:0m:24s left)
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Iteration 210 / LogL: -62644.229 / Time: 0h:5m:14s (0h:0m:9s left)
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Iteration 60 / LogL: -193341.577 / Time: 0h:5m:52s (0h:9m:38s left)
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Optimizing NNI: done in 1.19847 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 217 ITERATIONS / Time: 0h:5m:23s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -62641.672
2. Current log-likelihood: -62641.655
3. Current log-likelihood: -62641.644
Optimizing NNI: done in 1.77036 secs using 398.3% CPU
4. Current log-likelihood: -62641.633
5. Current log-likelihood: -62641.622
Optimal log-likelihood: -62641.607
Site proportion and rates:  (0.112,0.053) (0.095,0.194) (0.136,0.333) (0.213,0.569) (0.166,0.941) (0.099,1.582) (0.140,2.206) (0.039,4.829)
Parameters optimization took 5 rounds (2.240 sec)
BEST SCORE FOUND : -62641.607
Total tree length: 50.726

Total number of iterations: 217
CPU time used for tree search: 1218.397 sec (0h:20m:18s)
Wall-clock time used for tree search: 309.469 sec (0h:5m:9s)
Total CPU time used: 1282.318 sec (0h:21m:22s)
Total wall-clock time used: 325.508 sec (0h:5m:25s)

===> START BOOTSTRAP REPLICATE NUMBER 94

Creating bootstrap alignment (seed: 67556)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.063 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61953.797
Optimizing NNI: done in 1.95859 secs using 398.1% CPU
2. Current log-likelihood: -61341.316
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3. Current log-likelihood: -61319.189
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4. Current log-likelihood: -61308.421
5. Current log-likelihood: -61304.707
6. Current log-likelihood: -61300.475
Optimizing NNI: done in 2.11912 secs using 398.9% CPU
Iteration 70 / LogL: -108636.645 / Time: 0h:4m:9s (0h:4m:38s left)
7. Current log-likelihood: -61296.961
8. Current log-likelihood: -61294.757
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9. Current log-likelihood: -61294.042
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10. Current log-likelihood: -61293.719
11. Current log-likelihood: -61293.504
12. Current log-likelihood: -61293.322
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13. Current log-likelihood: -61293.145
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14. Current log-likelihood: -61292.971
15. Current log-likelihood: -61292.804
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16. Current log-likelihood: -61292.647
17. Current log-likelihood: -61292.503
18. Current log-likelihood: -61292.372
Optimizing NNI: done in 2.16642 secs using 398.8% CPU
19. Current log-likelihood: -61292.253
20. Current log-likelihood: -61292.146
Optimizing NNI: done in 4.51652 secs using 597.5% CPU
Optimal log-likelihood: -61292.026
Site proportion and rates:  (0.096,0.056) (0.111,0.201) (0.172,0.406) (0.162,0.650) (0.210,0.915) (0.142,1.654) (0.083,2.526) (0.024,6.595)
Parameters optimization took 20 rounds (15.617 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.81878 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 75: -108628.906
Calculating distance matrix: done in 1.08515 secs using 399.4% CPU
Computing ML distances took 1.085344 sec (of wall-clock time) 4.334874 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000389099 secs using 128.2% CPU
Constructing RapidNJ tree: done in 0.00443101 secs using 264.6% CPU
Computing RapidNJ tree took 0.004879 sec (of wall-clock time) 0.014556 sec (of CPU time)
Log-likelihood of RapidNJ tree: -61324.925
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.02848 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 76: -108627.944
Optimizing NNI: done in 5.02935 secs using 597.2% CPU
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5.204 second
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Computing log-likelihood of 98 initial trees ... 5.109 seconds
Current best score: -61217.813

Do NNI search on 20 best initial trees
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Iteration 80 / LogL: -108634.327 / Time: 0h:4m:32s (0h:5m:30s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -60974.696
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 16: -60960.894
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Iteration 20 / LogL: -61028.828 / Time: 0h:1m:3s
Finish initializing candidate tree set (20)
Current best tree score: -60960.894 / CPU time: 46.726
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 69: -60935.222
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Iteration 70 / LogL: -60942.730 / Time: 0h:2m:33s (0h:3m:40s left)
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Iteration 140 / LogL: -108662.745 / Time: 0h:6m:38s (0h:3m:40s left)
BETTER TREE FOUND at iteration 94: -193125.545
Optimizing NNI: done in 1.51649 secs using 399.3% CPU
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BETTER TREE FOUND at iteration 74: -60935.213
Optimizing NNI: done in 2.28732 secs using 398.8% CPU
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Iteration 80 / LogL: -60943.180 / Time: 0h:2m:49s (0h:3m:21s left)
Optimizing NNI: done in 2.193 secs using 398.4% CPU
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Iteration 150 / LogL: -108704.197 / Time: 0h:7m:0s (0h:3m:8s left)
Optimizing NNI: done in 1.41271 secs using 399% CPU
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Iteration 100 / LogL: -193137.140 / Time: 0h:9m:0s (0h:8m:32s left)
Optimizing NNI: done in 1.93798 secs using 398.7% CPU
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Iteration 90 / LogL: -60945.381 / Time: 0h:3m:5s (0h:2m:55s left)
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Iteration 160 / LogL: -108650.335 / Time: 0h:7m:19s (0h:2m:37s left)
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Iteration 100 / LogL: -60937.660 / Time: 0h:3m:22s (0h:2m:31s left)
Optimizing NNI: done in 3.70974 secs using 598% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.40849 secs using 598% CPU
BETTER TREE FOUND at iteration 103: -60931.290
Optimizing NNI: done in 1.98808 secs using 398.6% CPU
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Iteration 170 / LogL: -108628.791 / Time: 0h:7m:39s (0h:2m:7s left)
Optimizing NNI: done in 1.55618 secs using 398.7% CPU
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Iteration 110 / LogL: -61111.121 / Time: 0h:3m:38s (0h:3m:6s left)
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Iteration 110 / LogL: -193173.563 / Time: 0h:9m:44s (0h:7m:29s left)
Optimizing NNI: done in 1.81596 secs using 398.1% CPU
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Iteration 120 / LogL: -60938.102 / Time: 0h:3m:53s (0h:2m:42s left)
Optimizing NNI: done in 5.59587 secs using 597% CPU
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Iteration 180 / LogL: -108626.620 / Time: 0h:7m:59s (0h:1m:39s left)
Optimizing NNI: done in 1.83743 secs using 398.9% CPU
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Iteration 130 / LogL: -60942.006 / Time: 0h:4m:8s (0h:2m:20s left)
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Iteration 190 / LogL: -108632.256 / Time: 0h:8m:19s (0h:1m:11s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.61221 secs using 399% CPU
BETTER TREE FOUND at iteration 192: -108626.233
Optimizing NNI: done in 3.88638 secs using 597.6% CPU
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Iteration 140 / LogL: -61039.110 / Time: 0h:4m:24s (0h:1m:59s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.95046 secs using 597.1% CPU
Iteration 120 / LogL: -193140.980 / Time: 0h:10m:27s (0h:6m:30s left)
BETTER TREE FOUND at iteration 142: -60919.786
Optimizing NNI: done in 2.15133 secs using 399.2% CPU
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Iteration 200 / LogL: -108632.947 / Time: 0h:8m:40s (0h:4m:0s left)
Optimizing NNI: done in 1.82247 secs using 399% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 150: -60917.542
Iteration 150 / LogL: -60917.542 / Time: 0h:4m:41s (0h:3m:8s left)
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Iteration 210 / LogL: -108707.102 / Time: 0h:9m:1s (0h:3m:32s left)
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Iteration 160 / LogL: -60963.884 / Time: 0h:4m:57s (0h:2m:48s left)
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Iteration 130 / LogL: -193142.350 / Time: 0h:11m:10s (0h:5m:32s left)
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Iteration 170 / LogL: -60919.837 / Time: 0h:5m:14s (0h:2m:29s left)
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Iteration 220 / LogL: -108629.591 / Time: 0h:9m:21s (0h:3m:4s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.15874 secs using 399% CPU
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BETTER TREE FOUND at iteration 133: -193124.167
Optimizing NNI: done in 1.95469 secs using 399% CPU
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Iteration 180 / LogL: -60956.853 / Time: 0h:5m:31s (0h:2m:9s left)
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Iteration 230 / LogL: -108643.151 / Time: 0h:9m:41s (0h:2m:37s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.92236 secs using 596.8% CPU
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BETTER TREE FOUND at iteration 185: -60916.761
Optimizing NNI: done in 1.79245 secs using 399.1% CPU
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Iteration 190 / LogL: -60932.242 / Time: 0h:5m:49s (0h:2m:55s left)
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Iteration 240 / LogL: -108631.126 / Time: 0h:10m:1s (0h:2m:10s left)
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Iteration 140 / LogL: -193136.571 / Time: 0h:11m:58s (0h:8m:0s left)
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Iteration 200 / LogL: -60919.672 / Time: 0h:6m:6s (0h:2m:36s left)
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Iteration 250 / LogL: -108636.965 / Time: 0h:10m:20s (0h:1m:44s left)
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Iteration 210 / LogL: -61018.000 / Time: 0h:6m:22s (0h:2m:17s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 146: -193115.823
BETTER TREE FOUND at iteration 213: -60915.993
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 228: -60915.454
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Iteration 160 / LogL: -193146.208 / Time: 0h:13m:28s (0h:7m:17s left)
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BETTER TREE FOUND at iteration 249: -60915.439
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Iteration 250 / LogL: -60915.554 / Time: 0h:7m:32s (0h:2m:59s left)
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Iteration 290 / LogL: -108629.683 / Time: 0h:11m:40s (0h:0m:4s left)
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Optimizing NNI: done in 1.96723 secs using 398.3% CPU
TREE SEARCH COMPLETED AFTER 293 ITERATIONS / Time: 0h:11m:46s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -108626.233
Optimizing NNI: done in 1.64795 secs using 399.3% CPU
Optimal log-likelihood: -108626.230
Proportion of invariable sites: 0.007
Site proportion and rates:  (0.087,0.031) (0.103,0.101) (0.090,0.201) (0.094,0.325) (0.119,0.503) (0.109,0.782) (0.133,1.158) (0.184,1.883) (0.073,3.997)
Parameters optimization took 1 rounds (0.775 sec)
BEST SCORE FOUND : -108626.230
Total tree length: 170.468

Total number of iterations: 293
CPU time used for tree search: 2600.361 sec (0h:43m:20s)
Wall-clock time used for tree search: 660.047 sec (0h:11m:0s)
Total CPU time used: 2787.658 sec (0h:46m:27s)
Total wall-clock time used: 707.033 sec (0h:11m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 41

Creating bootstrap alignment (seed: 68223)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.121 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -107057.642
Optimizing NNI: done in 4.7288 secs using 597.1% CPU
Optimizing NNI: done in 1.75464 secs using 398.8% CPU
2. Current log-likelihood: -104867.385
Optimizing NNI: done in 1.14754 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 257: -60914.984
3. Current log-likelihood: -104797.849
Optimizing NNI: done in 1.48613 secs using 398.8% CPU
Optimizing NNI: done in 4.0851 secs using 597.8% CPU
4. Current log-likelihood: -104795.024
Optimizing NNI: done in 1.59894 secs using 399.1% CPU
5. Current log-likelihood: -104794.882
Optimal log-likelihood: -104794.777
Proportion of invariable sites: 0.034
Site proportion and rates:  (0.095,0.042) (0.052,0.118) (0.080,0.205) (0.089,0.309) (0.081,0.427) (0.153,0.669) (0.142,1.018) (0.207,1.807) (0.068,4.284)
Parameters optimization took 5 rounds (7.844 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.76577 secs using 399.1% CPU
Iteration 260 / LogL: -60935.598 / Time: 0h:7m:50s (0h:2m:56s left)
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Optimizing NNI: done in 1.92003 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 261: -60914.673
Optimizing NNI: done in 1.54947 secs using 399.3% CPU
Calculating distance matrix: done in 4.69474 secs using 399.9% CPU
Computing ML distances took 4.695103 sec (of wall-clock time) 18.773069 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000720024 secs using 377.8% CPU
Constructing RapidNJ tree: done in 0.0089829 secs using 400.7% CPU
Computing RapidNJ tree took 0.009761 sec (of wall-clock time) 0.038741 sec (of CPU time)
Log-likelihood of RapidNJ tree: -105294.020
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.6276 secs using 398.3% CPU
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11.228 second
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Iteration 270 / LogL: -60957.236 / Time: 0h:8m:7s (0h:2m:44s left)
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Computing log-likelihood of 98 initial trees ... 9.876 seconds
Current best score: -104794.777

Do NNI search on 20 best initial trees
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Iteration 170 / LogL: -193150.231 / Time: 0h:14m:16s (0h:6m:25s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -104174.070
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Iteration 280 / LogL: -60916.353 / Time: 0h:8m:24s (0h:2m:26s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 289: -60914.524
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Iteration 290 / LogL: -60948.169 / Time: 0h:8m:43s (0h:2m:59s left)
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BETTER TREE FOUND at iteration 5: -104100.405
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Iteration 20 / LogL: -104190.428 / Time: 0h:1m:44s
Finish initializing candidate tree set (20)
Current best tree score: -104100.405 / CPU time: 90.569
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Iteration 320 / LogL: -60942.585 / Time: 0h:9m:33s (0h:2m:3s left)
BETTER TREE FOUND at iteration 23: -104098.292
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Iteration 190 / LogL: -193187.267 / Time: 0h:15m:45s (0h:4m:39s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 32: -104092.952
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Iteration 40 / LogL: -104111.167 / Time: 0h:2m:35s (0h:6m:14s left)
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Iteration 350 / LogL: -60919.755 / Time: 0h:10m:23s (0h:1m:9s left)
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Iteration 200 / LogL: -193196.876 / Time: 0h:16m:27s (0h:3m:48s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 45: -104062.691
BETTER TREE FOUND at iteration 354: -60914.444
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Iteration 50 / LogL: -104105.474 / Time: 0h:2m:59s (0h:5m:47s left)
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Iteration 360 / LogL: -60914.692 / Time: 0h:10m:41s (0h:2m:47s left)
BETTER TREE FOUND at iteration 203: -193106.258
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Iteration 370 / LogL: -60960.891 / Time: 0h:10m:57s (0h:2m:29s left)
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BETTER TREE FOUND at iteration 63: -104061.358
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Iteration 210 / LogL: -193265.682 / Time: 0h:17m:13s (0h:7m:39s left)
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BETTER TREE FOUND at iteration 380: -60914.439
Iteration 380 / LogL: -60914.439 / Time: 0h:11m:14s (0h:2m:57s left)
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Iteration 390 / LogL: -60986.801 / Time: 0h:11m:29s (0h:2m:39s left)
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UPDATE BEST LOG-LIKELIHOOD: -60914.439
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 80: -104060.627
Iteration 80 / LogL: -104060.627 / Time: 0h:4m:11s (0h:5m:17s left)
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BETTER TREE FOUND at iteration 83: -104058.848
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Iteration 450 / LogL: -60933.368 / Time: 0h:13m:6s (0h:0m:52s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 112: -104050.883
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Iteration 460 / LogL: -60917.990 / Time: 0h:13m:21s (0h:0m:34s left)
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Iteration 240 / LogL: -193125.990 / Time: 0h:19m:23s (0h:5m:6s left)
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Iteration 470 / LogL: -60938.847 / Time: 0h:13m:37s (0h:0m:17s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.69877 secs using 597.5% CPU
BETTER TREE FOUND at iteration 127: -104044.989
Optimizing NNI: done in 1.68019 secs using 398.7% CPU
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Iteration 130 / LogL: -104059.612 / Time: 0h:6m:10s (0h:4m:38s left)
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Iteration 480 / LogL: -60914.693 / Time: 0h:13m:53s (0h:0m:0s left)
Optimizing NNI: done in 4.69226 secs using 597.9% CPU
Optimizing NNI: done in 1.95001 secs using 398.5% CPU
Optimizing NNI: done in 2.0333 secs using 398.3% CPU
TREE SEARCH COMPLETED AFTER 481 ITERATIONS / Time: 0h:13m:55s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60914.439
2. Current log-likelihood: -60914.428
Optimizing NNI: done in 2.05525 secs using 398.3% CPU
Optimal log-likelihood: -60914.418
Site proportion and rates:  (0.092,0.051) (0.111,0.191) (0.188,0.400) (0.245,0.720) (0.142,1.089) (0.122,1.761) (0.074,2.621) (0.025,6.266)
Parameters optimization took 2 rounds (1.133 sec)
BEST SCORE FOUND : -60914.418
Total tree length: 47.547

Total number of iterations: 481
CPU time used for tree search: 3247.970 sec (0h:54m:7s)
Wall-clock time used for tree search: 818.605 sec (0h:13m:38s)
Total CPU time used: 3320.680 sec (0h:55m:20s)
Total wall-clock time used: 836.839 sec (0h:13m:56s)

===> START BOOTSTRAP REPLICATE NUMBER 95

Creating bootstrap alignment (seed: 67557)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.043 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -60814.219
2. Current log-likelihood: -60273.407
Optimizing NNI: done in 4.57568 secs using 597.4% CPU
3. Current log-likelihood: -60265.200
Optimizing NNI: done in 2.15682 secs using 398.3% CPU
4. Current log-likelihood: -60251.138
5. Current log-likelihood: -60240.668
Optimizing NNI: done in 2.11696 secs using 397.6% CPU
6. Current log-likelihood: -60237.570
7. Current log-likelihood: -60237.232
Optimal log-likelihood: -60237.146
Site proportion and rates:  (0.092,0.057) (0.101,0.195) (0.102,0.387) (0.071,0.408) (0.276,0.703) (0.167,1.254) (0.164,2.274) (0.027,4.776)
Parameters optimization took 7 rounds (5.504 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.86287 secs using 398.6% CPU
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Computing ML distances took 1.063727 sec (of wall-clock time) 4.249768 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000345945 secs using 426.9% CPU
Constructing RapidNJ tree: done in 0.00435901 secs using 385.2% CPU
Computing RapidNJ tree took 0.004759 sec (of wall-clock time) 0.019175 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60261.211
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.33727 secs using 398.4% CPU
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Iteration 250 / LogL: -193113.236 / Time: 0h:20m:7s (0h:4m:16s left)
4.987 second
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Computing log-likelihood of 98 initial trees ... 5.049 seconds
Current best score: -60188.638

Do NNI search on 20 best initial trees
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BETTER TREE FOUND at iteration 142: -104041.263
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Iteration 20 / LogL: -60050.410 / Time: 0h:0m:46s
Finish initializing candidate tree set (20)
Current best tree score: -59954.172 / CPU time: 39.433
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 300 / LogL: -193146.054 / Time: 0h:23m:45s (0h:0m:14s left)
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Iteration 150 / LogL: -59930.584 / Time: 0h:3m:52s (0h:2m:4s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.28954 secs using 399.1% CPU
BETTER TREE FOUND at iteration 236: -104036.724
Optimizing NNI: done in 1.45879 secs using 399% CPU
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Optimizing NNI: done in 1.988 secs using 398.7% CPU
Iteration 240 / LogL: -104056.118 / Time: 0h:10m:19s (0h:4m:8s left)
Optimizing NNI: done in 4.14547 secs using 597.6% CPU
TREE SEARCH COMPLETED AFTER 304 ITERATIONS / Time: 0h:24m:1s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -193106.258
Optimizing NNI: done in 1.37311 secs using 399.3% CPU
2. Current log-likelihood: -193106.227
3. Current log-likelihood: -193106.217
Optimizing NNI: done in 2.0657 secs using 398.7% CPU
Optimizing NNI: done in 1.68974 secs using 399.3% CPU
Iteration 160 / LogL: -59937.393 / Time: 0h:4m:7s (0h:1m:48s left)
Optimal log-likelihood: -193106.205
Site proportion and rates:  (0.019,0.095) (0.046,0.216) (0.002,0.252) (0.122,0.366) (0.319,0.595) (0.201,0.932) (0.164,1.496) (0.127,2.521)
Parameters optimization took 3 rounds (2.134 sec)
BEST SCORE FOUND : -193106.205
Total tree length: 157.126

Total number of iterations: 304
CPU time used for tree search: 8314.867 sec (2h:18m:34s)
Wall-clock time used for tree search: 1417.081 sec (0h:23m:37s)
Total CPU time used: 8473.421 sec (2h:21m:13s)
Total wall-clock time used: 1443.720 sec (0h:24m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 25

Creating bootstrap alignment (seed: 70488)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.351 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194338.315
Optimizing NNI: done in 1.32695 secs using 399% CPU
Optimizing NNI: done in 2.19419 secs using 398.6% CPU
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2. Current log-likelihood: -191565.266
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3. Current log-likelihood: -191528.476
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4. Current log-likelihood: -191526.631
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5. Current log-likelihood: -191525.708
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6. Current log-likelihood: -191524.964
Optimizing NNI: done in 1.43709 secs using 398.8% CPU
Optimizing NNI: done in 2.08634 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
7. Current log-likelihood: -191523.178
BETTER TREE FOUND at iteration 247: -104036.322
Optimizing NNI: done in 1.49812 secs using 398.9% CPU
Iteration 170 / LogL: -59927.405 / Time: 0h:4m:21s (0h:1m:32s left)
8. Current log-likelihood: -191519.255
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9. Current log-likelihood: -191516.704
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10. Current log-likelihood: -191515.918
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Optimizing NNI: done in 2.4199 secs using 398.9% CPU
Iteration 250 / LogL: -104047.105 / Time: 0h:10m:42s (0h:4m:10s left)
Optimizing NNI: done in 1.22946 secs using 399.4% CPU
11. Current log-likelihood: -191515.536
Optimizing NNI: done in 1.16283 secs using 398.8% CPU
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12. Current log-likelihood: -191515.325
Optimizing NNI: done in 1.95442 secs using 398.8% CPU
Optimizing NNI: done in 1.5612 secs using 398.9% CPU
13. Current log-likelihood: -191515.219
Optimizing NNI: done in 1.61736 secs using 399.2% CPU
Optimizing NNI: done in 2.25663 secs using 398.9% CPU
Optimal log-likelihood: -191515.169
Site proportion and rates:  (0.019,0.107) (0.084,0.244) (0.119,0.383) (0.188,0.543) (0.192,0.746) (0.143,1.059) (0.157,1.672) (0.098,2.776)
Parameters optimization took 13 rounds (27.054 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.37272 secs using 398.8% CPU
Iteration 180 / LogL: -59926.798 / Time: 0h:4m:35s (0h:1m:16s left)
Optimizing NNI: done in 2.2016 secs using 398.8% CPU
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BETTER TREE FOUND at iteration 185: -59925.605
Optimizing NNI: done in 2.091 secs using 398.6% CPU
Optimizing NNI: done in 1.33197 secs using 397.9% CPU
Calculating distance matrix: done in 9.70323 secs using 599.9% CPU
Computing ML distances took 9.703856 sec (of wall-clock time) 58.210939 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00126505 secs using 674.6% CPU
Constructing RapidNJ tree: done in 0.022248 secs using 665.2% CPU
Computing RapidNJ tree took 0.023587 sec (of wall-clock time) 0.158344 sec (of CPU time)
Optimizing NNI: done in 2.18848 secs using 398.5% CPU
Optimizing NNI: done in 1.29964 secs using 398.4% CPU
Log-likelihood of RapidNJ tree: -195646.590
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.61122 secs using 399% CPU
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Iteration 190 / LogL: -59942.995 / Time: 0h:4m:49s (0h:2m:25s left)
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Iteration 260 / LogL: -104052.906 / Time: 0h:11m:5s (0h:3m:43s left)
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Iteration 200 / LogL: -59958.774 / Time: 0h:5m:4s (0h:2m:9s left)
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29.664 second
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BETTER TREE FOUND at iteration 210: -59925.604
Iteration 210 / LogL: -59925.604 / Time: 0h:5m:18s (0h:2m:32s left)
Optimizing NNI: done in 1.27201 secs using 398.4% CPU
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Iteration 270 / LogL: -104046.295 / Time: 0h:11m:39s (0h:3m:20s left)
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Optimizing NNI: done in 1.70814 secs using 399% CPU
Computing log-likelihood of 98 initial trees ... 16.501 seconds
Current best score: -191515.169

Do NNI search on 20 best initial trees
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Iteration 220 / LogL: -59970.020 / Time: 0h:5m:33s (0h:2m:17s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -191023.620
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -190931.059
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Iteration 230 / LogL: -59926.298 / Time: 0h:5m:47s (0h:2m:1s left)
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Iteration 280 / LogL: -104042.798 / Time: 0h:12m:3s (0h:2m:53s left)
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Iteration 240 / LogL: -59925.720 / Time: 0h:6m:1s (0h:1m:45s left)
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Iteration 290 / LogL: -104054.546 / Time: 0h:12m:26s (0h:2m:27s left)
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Iteration 10 / LogL: -190999.388 / Time: 0h:2m:14s
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Iteration 260 / LogL: -59927.875 / Time: 0h:6m:30s (0h:1m:15s left)
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Iteration 270 / LogL: -59938.068 / Time: 0h:6m:43s (0h:1m:0s left)
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Iteration 310 / LogL: -104045.304 / Time: 0h:13m:11s (0h:1m:34s left)
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Iteration 280 / LogL: -59926.645 / Time: 0h:6m:58s (0h:0m:44s left)
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BETTER TREE FOUND at iteration 283: -59925.604
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Iteration 20 / LogL: -190985.516 / Time: 0h:2m:59s
Finish initializing candidate tree set (20)
Current best tree score: -190931.059 / CPU time: 140.347
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 300 / LogL: -59927.479 / Time: 0h:7m:26s (0h:2m:3s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 24: -190923.565
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BETTER TREE FOUND at iteration 25: -190894.162
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Iteration 330 / LogL: -104043.388 / Time: 0h:13m:54s (0h:0m:43s left)
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Iteration 330 / LogL: -60046.003 / Time: 0h:8m:8s (0h:1m:18s left)
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TREE SEARCH COMPLETED AFTER 348 ITERATIONS / Time: 0h:14m:35s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -104036.322
Optimizing NNI: done in 4.23211 secs using 597.7% CPU
2. Current log-likelihood: -104036.308
Optimizing NNI: done in 1.21838 secs using 398.7% CPU
Iteration 340 / LogL: -59927.416 / Time: 0h:8m:22s (0h:1m:3s left)
3. Current log-likelihood: -104036.294
4. Current log-likelihood: -104036.277
Optimizing NNI: done in 1.46497 secs using 398.5% CPU
5. Current log-likelihood: -104036.262
6. Current log-likelihood: -104036.247
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7. Current log-likelihood: -104036.233
Optimizing NNI: done in 4.33641 secs using 597.2% CPU
8. Current log-likelihood: -104036.219
Optimizing NNI: done in 1.17281 secs using 398.8% CPU
9. Current log-likelihood: -104036.204
Optimizing NNI: done in 1.16624 secs using 399.2% CPU
10. Current log-likelihood: -104036.188
11. Current log-likelihood: -104036.178
Optimizing NNI: done in 1.66065 secs using 398.3% CPU
12. Current log-likelihood: -104036.165
13. Current log-likelihood: -104036.152
Optimizing NNI: done in 4.59554 secs using 596.9% CPU
14. Current log-likelihood: -104036.140
Optimizing NNI: done in 1.68356 secs using 398.5% CPU
15. Current log-likelihood: -104036.128
16. Current log-likelihood: -104036.116
Optimizing NNI: done in 1.46785 secs using 398.6% CPU
17. Current log-likelihood: -104036.105
18. Current log-likelihood: -104036.094
Optimizing NNI: done in 1.54085 secs using 398.7% CPU
Optimal log-likelihood: -104036.082
Proportion of invariable sites: 0.034
Site proportion and rates:  (0.092,0.040) (0.044,0.104) (0.075,0.185) (0.106,0.298) (0.094,0.455) (0.142,0.684) (0.139,1.047) (0.201,1.818) (0.072,4.084)
Parameters optimization took 18 rounds (13.260 sec)
BEST SCORE FOUND : -104036.082
Total tree length: 172.920

Total number of iterations: 348
CPU time used for tree search: 3402.136 sec (0h:56m:42s)
Wall-clock time used for tree search: 861.928 sec (0h:14m:21s)
Total CPU time used: 3509.755 sec (0h:58m:29s)
Total wall-clock time used: 888.909 sec (0h:14m:48s)

===> START BOOTSTRAP REPLICATE NUMBER 42

Creating bootstrap alignment (seed: 68224)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.089 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 101 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -109896.351
Optimizing NNI: done in 4.47593 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.28021 secs using 398.6% CPU
2. Current log-likelihood: -107839.618
Optimizing NNI: done in 1.3335 secs using 399.1% CPU
Iteration 350 / LogL: -59935.323 / Time: 0h:8m:36s (0h:0m:48s left)
BETTER TREE FOUND at iteration 37: -190883.147
3. Current log-likelihood: -107749.244
Optimizing NNI: done in 1.62239 secs using 399.1% CPU
4. Current log-likelihood: -107744.241
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5. Current log-likelihood: -107743.854
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6. Current log-likelihood: -107743.613
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7. Current log-likelihood: -107743.510
Optimizing NNI: done in 1.30726 secs using 398.4% CPU
Optimal log-likelihood: -107743.390
Proportion of invariable sites: 0.026
Site proportion and rates:  (0.097,0.037) (0.056,0.116) (0.060,0.198) (0.154,0.325) (0.072,0.493) (0.138,0.746) (0.163,1.180) (0.164,1.865) (0.069,4.201)
Parameters optimization took 7 rounds (10.561 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 4.63955 secs using 399.8% CPU
Computing ML distances took 4.639956 sec (of wall-clock time) 18.548287 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000808001 secs using 421.2% CPU
Constructing RapidNJ tree: done in 0.008605 secs using 390.9% CPU
Computing RapidNJ tree took 0.009478 sec (of wall-clock time) 0.038492 sec (of CPU time)
Optimizing NNI: done in 4.23686 secs using 596.9% CPU
Iteration 40 / LogL: -190949.205 / Time: 0h:4m:43s (0h:11m:43s left)
Log-likelihood of RapidNJ tree: -107793.627
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.28904 secs using 397.5% CPU
Iteration 360 / LogL: -59926.320 / Time: 0h:8m:50s (0h:0m:33s left)
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11.090 second
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Iteration 370 / LogL: -59925.797 / Time: 0h:9m:4s (0h:0m:19s left)
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Computing log-likelihood of 98 initial trees ... 9.802 seconds
Current best score: -107743.390

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 376: -59921.305
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 380: -59921.173
Iteration 380 / LogL: -59921.173 / Time: 0h:9m:20s (0h:2m:27s left)
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Iteration 390 / LogL: -59921.237 / Time: 0h:9m:33s (0h:2m:12s left)
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BETTER TREE FOUND at iteration 1: -107064.065
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Iteration 400 / LogL: -59927.039 / Time: 0h:9m:47s (0h:1m:57s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 50 / LogL: -191109.383 / Time: 0h:5m:49s (0h:10m:20s left)
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Iteration 410 / LogL: -59929.779 / Time: 0h:10m:1s (0h:1m:42s left)
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Iteration 10 / LogL: -107130.130 / Time: 0h:1m:37s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 429: -59920.275
BETTER TREE FOUND at iteration 16: -106987.594
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Iteration 430 / LogL: -59952.319 / Time: 0h:10m:31s (0h:2m:25s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 435: -59920.151
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Iteration 20 / LogL: -107180.852 / Time: 0h:2m:5s
Finish initializing candidate tree set (20)
Current best tree score: -106987.594 / CPU time: 109.615
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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TREE SEARCH COMPLETED AFTER 572 ITERATIONS / Time: 0h:14m:0s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59920.150
Optimal log-likelihood: -59920.147
Site proportion and rates:  (0.085,0.055) (0.108,0.194) (0.097,0.395) (0.068,0.395) (0.270,0.704) (0.175,1.204) (0.165,2.229) (0.032,4.450)
Parameters optimization took 1 rounds (0.351 sec)
BEST SCORE FOUND : -59920.147
Total tree length: 42.873

Total number of iterations: 572
CPU time used for tree search: 3310.482 sec (0h:55m:10s)
Wall-clock time used for tree search: 833.937 sec (0h:13m:53s)
Total CPU time used: 3339.501 sec (0h:55m:39s)
Total wall-clock time used: 841.194 sec (0h:14m:1s)

===> START BOOTSTRAP REPLICATE NUMBER 96

Creating bootstrap alignment (seed: 67558)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.058 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61620.498
Optimizing NNI: done in 2.26957 secs using 398.8% CPU
2. Current log-likelihood: -61020.170
3. Current log-likelihood: -60988.270
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4. Current log-likelihood: -60967.167
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5. Current log-likelihood: -60965.091
Optimizing NNI: done in 1.88062 secs using 399.1% CPU
Optimal log-likelihood: -60965.011
Site proportion and rates:  (0.113,0.068) (0.093,0.184) (0.118,0.368) (0.078,0.428) (0.242,0.737) (0.156,1.281) (0.172,2.126) (0.029,5.351)
Parameters optimization took 5 rounds (4.592 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.1001 secs using 399.7% CPU
Computing ML distances took 1.100267 sec (of wall-clock time) 4.397456 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000375032 secs using 138.1% CPU
Constructing RapidNJ tree: done in 0.00440407 secs using 311.6% CPU
Computing RapidNJ tree took 0.004836 sec (of wall-clock time) 0.016402 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60986.916
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.4975 secs using 399% CPU
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5.066 second
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Iteration 110 / LogL: -106954.348 / Time: 0h:5m:41s (0h:3m:54s left)
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Computing log-likelihood of 98 initial trees ... 5.173 seconds
Current best score: -60932.923

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -60733.091
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Optimizing NNI: done in 1.02034 secs using 399.1% CPU
Iteration 20 / LogL: -60776.255 / Time: 0h:0m:40s
Finish initializing candidate tree set (20)
Current best tree score: -60733.091 / CPU time: 34.359
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 21: -60722.435
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BETTER TREE FOUND at iteration 125: -106943.126
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BETTER TREE FOUND at iteration 113: -190872.527
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Iteration 30 / LogL: -60729.081 / Time: 0h:0m:54s (0h:2m:50s left)
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Iteration 130 / LogL: -106971.740 / Time: 0h:6m:27s (0h:4m:45s left)
BETTER TREE FOUND at iteration 34: -60710.077
Optimizing NNI: done in 4.57957 secs using 597.8% CPU
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BETTER TREE FOUND at iteration 36: -60699.366
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BETTER TREE FOUND at iteration 40: -60692.402
Iteration 40 / LogL: -60692.402 / Time: 0h:1m:13s (0h:3m:8s left)
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Optimizing NNI: done in 2.59184 secs using 398.7% CPU
Iteration 140 / LogL: -106988.475 / Time: 0h:6m:49s (0h:4m:10s left)
BETTER TREE FOUND at iteration 46: -60692.192
Optimizing NNI: done in 4.85047 secs using 597.5% CPU
Iteration 120 / LogL: -190895.493 / Time: 0h:11m:18s (0h:8m:49s left)
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Iteration 150 / LogL: -106961.234 / Time: 0h:7m:11s (0h:3m:37s left)
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Iteration 60 / LogL: -60723.779 / Time: 0h:1m:44s (0h:2m:32s left)
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Iteration 70 / LogL: -60718.907 / Time: 0h:2m:1s (0h:2m:13s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.25367 secs using 398.4% CPU
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BETTER TREE FOUND at iteration 128: -190870.241
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Iteration 160 / LogL: -106960.147 / Time: 0h:7m:34s (0h:3m:5s left)
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Iteration 130 / LogL: -190924.414 / Time: 0h:12m:7s (0h:9m:12s left)
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Iteration 80 / LogL: -60694.785 / Time: 0h:2m:17s (0h:1m:54s left)
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Iteration 170 / LogL: -106962.279 / Time: 0h:7m:57s (0h:2m:35s left)
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Iteration 90 / LogL: -60699.774 / Time: 0h:2m:32s (0h:1m:36s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.11287 secs using 399% CPU
BETTER TREE FOUND at iteration 91: -60687.681
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Iteration 100 / LogL: -60699.640 / Time: 0h:2m:49s (0h:2m:35s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 101: -60687.373
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Iteration 180 / LogL: -106949.546 / Time: 0h:8m:20s (0h:2m:5s left)
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Iteration 140 / LogL: -190871.618 / Time: 0h:12m:54s (0h:8m:10s left)
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Iteration 110 / LogL: -60699.926 / Time: 0h:3m:5s (0h:2m:35s left)
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Iteration 190 / LogL: -106989.928 / Time: 0h:8m:42s (0h:1m:36s left)
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Iteration 120 / LogL: -60740.382 / Time: 0h:3m:20s (0h:2m:16s left)
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Iteration 130 / LogL: -60687.374 / Time: 0h:3m:34s (0h:1m:58s left)
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Iteration 200 / LogL: -106964.155 / Time: 0h:9m:5s (0h:1m:8s left)
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Iteration 150 / LogL: -190948.436 / Time: 0h:13m:40s (0h:7m:9s left)
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Iteration 140 / LogL: -60688.264 / Time: 0h:3m:49s (0h:1m:40s left)
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Iteration 210 / LogL: -107012.529 / Time: 0h:9m:28s (0h:0m:40s left)
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Iteration 150 / LogL: -60691.833 / Time: 0h:4m:4s (0h:1m:23s left)
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Iteration 160 / LogL: -60694.717 / Time: 0h:4m:18s (0h:1m:6s left)
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Iteration 220 / LogL: -106954.621 / Time: 0h:9m:50s (0h:0m:13s left)
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Optimizing NNI: done in 1.98204 secs using 398.1% CPU
Optimizing NNI: done in 1.65698 secs using 399.6% CPU
Optimizing NNI: done in 4.34137 secs using 597.3% CPU
Iteration 160 / LogL: -190890.387 / Time: 0h:14m:27s (0h:6m:10s left)
Optimizing NNI: done in 2.26834 secs using 398.5% CPU
Optimizing NNI: done in 1.44621 secs using 399.3% CPU
Iteration 170 / LogL: -60687.374 / Time: 0h:4m:34s (0h:0m:50s left)
Optimizing NNI: done in 1.38273 secs using 398% CPU
Optimizing NNI: done in 1.92531 secs using 398.4% CPU
TREE SEARCH COMPLETED AFTER 226 ITERATIONS / Time: 0h:10m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106943.126
Optimizing NNI: done in 1.41724 secs using 399.4% CPU
2. Current log-likelihood: -106943.098
3. Current log-likelihood: -106943.061
Optimizing NNI: done in 1.36585 secs using 399.3% CPU
4. Current log-likelihood: -106943.024
Optimizing NNI: done in 1.35726 secs using 398.6% CPU
5. Current log-likelihood: -106942.991
Optimizing NNI: done in 6.96255 secs using 597.4% CPU
6. Current log-likelihood: -106942.971
Optimizing NNI: done in 1.61957 secs using 399.4% CPU
7. Current log-likelihood: -106942.938
Optimizing NNI: done in 1.2107 secs using 399.3% CPU
8. Current log-likelihood: -106942.919
9. Current log-likelihood: -106942.890
Optimizing NNI: done in 1.47289 secs using 399.1% CPU
10. Current log-likelihood: -106942.873
Optimizing NNI: done in 4.38955 secs using 597.3% CPU
Optimizing NNI: done in 1.48229 secs using 399.1% CPU
11. Current log-likelihood: -106942.854
12. Current log-likelihood: -106942.837
13. Current log-likelihood: -106942.821
Optimizing NNI: done in 1.38773 secs using 398.8% CPU
14. Current log-likelihood: -106942.805
15. Current log-likelihood: -106942.789
Optimizing NNI: done in 1.69453 secs using 398.8% CPU
Iteration 180 / LogL: -60688.473 / Time: 0h:4m:48s (0h:0m:33s left)
16. Current log-likelihood: -106942.774
17. Current log-likelihood: -106942.759
Optimizing NNI: done in 4.81155 secs using 597.9% CPU
Optimizing NNI: done in 1.27441 secs using 398.8% CPU
18. Current log-likelihood: -106942.744
19. Current log-likelihood: -106942.729
Optimizing NNI: done in 1.63816 secs using 399.3% CPU
20. Current log-likelihood: -106942.715
21. Current log-likelihood: -106942.701
Optimizing NNI: done in 1.30992 secs using 399.2% CPU
22. Current log-likelihood: -106942.688
Optimizing NNI: done in 4.05821 secs using 597.4% CPU
23. Current log-likelihood: -106942.675
Optimizing NNI: done in 1.49817 secs using 399.5% CPU
24. Current log-likelihood: -106942.662
Optimal log-likelihood: -106942.648
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.089,0.029) (0.058,0.091) (0.077,0.190) (0.177,0.343) (0.088,0.575) (0.123,0.832) (0.141,1.242) (0.152,1.835) (0.071,4.387)
Parameters optimization took 24 rounds (19.333 sec)
BEST SCORE FOUND : -106942.648
Total tree length: 175.247

Total number of iterations: 226
CPU time used for tree search: 2305.659 sec (0h:38m:25s)
Wall-clock time used for tree search: 586.883 sec (0h:9m:46s)
Total CPU time used: 2447.893 sec (0h:40m:47s)
Total wall-clock time used: 622.565 sec (0h:10m:22s)

===> START BOOTSTRAP REPLICATE NUMBER 43

Creating bootstrap alignment (seed: 68225)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.088 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -100348.060
Optimizing NNI: done in 1.53313 secs using 399.1% CPU
2. Current log-likelihood: -98447.945
Optimizing NNI: done in 1.37381 secs using 398.7% CPU
Optimizing NNI: done in 4.05845 secs using 597.2% CPU
Optimizing NNI: done in 1.30151 secs using 399.4% CPU
3. Current log-likelihood: -98356.297
Optimizing NNI: done in 1.4752 secs using 398.6% CPU
4. Current log-likelihood: -98345.024
Optimizing NNI: done in 1.34464 secs using 398.7% CPU
5. Current log-likelihood: -98344.322
Optimizing NNI: done in 4.52723 secs using 597.7% CPU
Optimizing NNI: done in 1.5907 secs using 399.2% CPU
Iteration 190 / LogL: -61548.981 / Time: 0h:5m:3s (0h:0m:17s left)
6. Current log-likelihood: -98344.151
Optimizing NNI: done in 1.69315 secs using 399.2% CPU
7. Current log-likelihood: -98344.035
Optimizing NNI: done in 1.63066 secs using 398.7% CPU
Optimal log-likelihood: -98343.903
Proportion of invariable sites: 0.043
Site proportion and rates:  (0.102,0.040) (0.097,0.133) (0.077,0.239) (0.115,0.354) (0.093,0.548) (0.112,0.858) (0.166,1.404) (0.142,2.112) (0.053,4.644)
Parameters optimization took 7 rounds (11.423 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.64201 secs using 398.8% CPU
Optimizing NNI: done in 5.89867 secs using 597.6% CPU
Optimizing NNI: done in 1.23103 secs using 399.3% CPU
Optimizing NNI: done in 1.75241 secs using 399.2% CPU
Calculating distance matrix: done in 4.56721 secs using 399.9% CPU
Computing ML distances took 4.567580 sec (of wall-clock time) 18.264900 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000702858 secs using 182.8% CPU
Constructing RapidNJ tree: done in 0.00859594 secs using 402.9% CPU
Computing RapidNJ tree took 0.009362 sec (of wall-clock time) 0.036125 sec (of CPU time)
Log-likelihood of RapidNJ tree: -98754.863
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.66381 secs using 398.9% CPU
Optimizing NNI: done in 4.37061 secs using 597.6% CPU
Optimizing NNI: done in 1.5049 secs using 399.2% CPU
Optimizing NNI: done in 1.69022 secs using 399.5% CPU
Optimizing NNI: done in 4.33219 secs using 597.4% CPU
Optimizing NNI: done in 1.32314 secs using 398.7% CPU
Optimizing NNI: done in 1.52848 secs using 399.1% CPU
Iteration 200 / LogL: -60696.608 / Time: 0h:5m:19s (0h:0m:1s left)
Optimizing NNI: done in 1.26601 secs using 398.8% CPU
Optimizing NNI: done in 1.35895 secs using 399.4% CPU
TREE SEARCH COMPLETED AFTER 202 ITERATIONS / Time: 0h:5m:21s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -60687.373
Optimizing NNI: done in 4.53473 secs using 597.3% CPU
Iteration 170 / LogL: -191003.183 / Time: 0h:15m:15s (0h:5m:14s left)
Optimal log-likelihood: -60687.373
Site proportion and rates:  (0.128,0.072) (0.082,0.194) (0.105,0.374) (0.064,0.385) (0.254,0.704) (0.152,1.235) (0.185,2.092) (0.030,5.290)
Parameters optimization took 1 rounds (0.248 sec)
BEST SCORE FOUND : -60687.373
Total tree length: 46.046

Total number of iterations: 202
CPU time used for tree search: 1244.565 sec (0h:20m:44s)
Wall-clock time used for tree search: 315.634 sec (0h:5m:15s)
Total CPU time used: 1270.300 sec (0h:21m:10s)
Total wall-clock time used: 322.052 sec (0h:5m:22s)

===> START BOOTSTRAP REPLICATE NUMBER 97

Creating bootstrap alignment (seed: 67559)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.058 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59335.330
2. Current log-likelihood: -58727.046
10.551 second
3. Current log-likelihood: -58720.181
4. Current log-likelihood: -58719.789
5. Current log-likelihood: -58719.465
6. Current log-likelihood: -58719.180
Optimizing NNI: done in 4.49974 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
7. Current log-likelihood: -58718.924
8. Current log-likelihood: -58718.653
9. Current log-likelihood: -58718.273
10. Current log-likelihood: -58717.351
BETTER TREE FOUND at iteration 171: -190861.873
11. Current log-likelihood: -58708.646
12. Current log-likelihood: -58693.454
13. Current log-likelihood: -58688.885
14. Current log-likelihood: -58688.439
15. Current log-likelihood: -58688.273
Optimizing NNI: done in 4.41674 secs using 597.8% CPU
16. Current log-likelihood: -58688.126
Computing log-likelihood of 98 initial trees ... 10.299 seconds
Current best score: -98343.903

Do NNI search on 20 best initial trees
17. Current log-likelihood: -58687.976
18. Current log-likelihood: -58687.818
19. Current log-likelihood: -58687.654
Optimizing NNI: done in 2.17411 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
20. Current log-likelihood: -58687.483
21. Current log-likelihood: -58687.313
Optimizing NNI: done in 3.98382 secs using 598.5% CPU
22. Current log-likelihood: -58687.151
23. Current log-likelihood: -58687.002
24. Current log-likelihood: -58686.873
25. Current log-likelihood: -58686.767
Optimal log-likelihood: -58686.683
Site proportion and rates:  (0.117,0.065) (0.110,0.190) (0.181,0.435) (0.207,0.690) (0.139,0.996) (0.142,1.710) (0.083,2.723) (0.021,6.838)
Parameters optimization took 25 rounds (18.121 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.09381 secs using 399.9% CPU
Computing ML distances took 1.093999 sec (of wall-clock time) 4.374212 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000338078 secs using 252.3% CPU
Constructing RapidNJ tree: done in 0.00435901 secs using 333.7% CPU
Computing RapidNJ tree took 0.004752 sec (of wall-clock time) 0.017051 sec (of CPU time)
Optimizing NNI: done in 4.14394 secs using 598.2% CPU
Log-likelihood of RapidNJ tree: -58685.879
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.3639 secs using 597.5% CPU
5.083 second
Optimizing NNI: done in 5.12991 secs using 598.3% CPU
Computing log-likelihood of 98 initial trees ... 5.090 seconds
Current best score: -58618.084

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.37879 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -58418.101
Optimizing NNI: done in 1.48723 secs using 398.5% CPU
Optimizing NNI: done in 5.22601 secs using 597.9% CPU
Optimizing NNI: done in 1.25133 secs using 399% CPU
Optimizing NNI: done in 1.60702 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.27515 secs using 596.3% CPU
BETTER TREE FOUND at iteration 4: -58406.357
BETTER TREE FOUND at iteration 1: -97918.161
Optimizing NNI: done in 1.30397 secs using 398.7% CPU
Optimizing NNI: done in 1.22232 secs using 399.2% CPU
Optimizing NNI: done in 2.24212 secs using 398.4% CPU
Optimizing NNI: done in 1.49857 secs using 399.3% CPU
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Optimizing NNI: done in 2.29591 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.47761 secs using 398.8% CPU
Iteration 10 / LogL: -58419.379 / Time: 0h:0m:47s
Optimizing NNI: done in 4.34835 secs using 597.9% CPU
Iteration 180 / LogL: -190866.798 / Time: 0h:16m:3s (0h:8m:9s left)
Optimizing NNI: done in 1.39819 secs using 399.1% CPU
Optimizing NNI: done in 1.394 secs using 398.8% CPU
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Optimizing NNI: done in 1.62879 secs using 398.7% CPU
Optimizing NNI: done in 0.910959 secs using 398.3% CPU
BETTER TREE FOUND at iteration 4: -97900.097
Optimizing NNI: done in 3.99415 secs using 597.7% CPU
Optimizing NNI: done in 1.51864 secs using 398.9% CPU
Optimizing NNI: done in 2.14454 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.58012 secs using 398.9% CPU
Optimizing NNI: done in 0.947157 secs using 399.5% CPU
Optimizing NNI: done in 1.22085 secs using 399% CPU
Iteration 20 / LogL: -58441.985 / Time: 0h:1m:0s
Finish initializing candidate tree set (20)
Current best tree score: -58406.357 / CPU time: 40.957
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.0537 secs using 597.5% CPU
Optimizing NNI: done in 1.42272 secs using 399% CPU
Optimizing NNI: done in 1.41481 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -58384.872
Optimizing NNI: done in 1.43038 secs using 398.9% CPU
Optimizing NNI: done in 4.93685 secs using 597.8% CPU
Optimizing NNI: done in 1.47225 secs using 399.4% CPU
BETTER TREE FOUND at iteration 5: -97848.893
Optimizing NNI: done in 1.53002 secs using 399.2% CPU
Optimizing NNI: done in 1.34618 secs using 399.2% CPU
Optimizing NNI: done in 2.19811 secs using 398.2% CPU
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Iteration 30 / LogL: -58400.502 / Time: 0h:1m:15s (0h:4m:0s left)
Optimizing NNI: done in 1.48247 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.68662 secs using 398% CPU
BETTER TREE FOUND at iteration 31: -58377.933
Optimizing NNI: done in 1.44934 secs using 398.7% CPU
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Iteration 10 / LogL: -97867.440 / Time: 0h:1m:46s
Optimizing NNI: done in 4.99262 secs using 598.1% CPU
Optimizing NNI: done in 1.27841 secs using 399.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.46084 secs using 397.8% CPU
BETTER TREE FOUND at iteration 34: -58376.309
Optimizing NNI: done in 1.38287 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.30862 secs using 399.4% CPU
Optimizing NNI: done in 4.37539 secs using 597.7% CPU
BETTER TREE FOUND at iteration 13: -97841.771
Optimizing NNI: done in 1.20895 secs using 399.5% CPU
Optimizing NNI: done in 1.38248 secs using 399.3% CPU
Iteration 40 / LogL: -58383.165 / Time: 0h:1m:31s (0h:3m:40s left)
Optimizing NNI: done in 2.56855 secs using 398.8% CPU
Optimizing NNI: done in 1.63386 secs using 398.4% CPU
Optimizing NNI: done in 5.00466 secs using 597.2% CPU
Iteration 190 / LogL: -190914.632 / Time: 0h:16m:50s (0h:7m:12s left)
Optimizing NNI: done in 1.35651 secs using 399% CPU
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Optimizing NNI: done in 1.28079 secs using 399.1% CPU
Iteration 50 / LogL: -58377.519 / Time: 0h:1m:45s (0h:3m:1s left)
Optimizing NNI: done in 1.17026 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -58376.016
Optimizing NNI: done in 2.44761 secs using 398.4% CPU
Iteration 20 / LogL: -97902.411 / Time: 0h:2m:14s
Finish initializing candidate tree set (20)
Current best tree score: -97841.771 / CPU time: 117.428
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.23594 secs using 597.8% CPU
Optimizing NNI: done in 1.4257 secs using 399.2% CPU
Optimizing NNI: done in 1.40442 secs using 399.2% CPU
Optimizing NNI: done in 2.46077 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.29297 secs using 399% CPU
Optimizing NNI: done in 3.90293 secs using 597.8% CPU
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Optimizing NNI: done in 1.49303 secs using 398.5% CPU
BETTER TREE FOUND at iteration 21: -97840.259
Optimizing NNI: done in 1.2765 secs using 398.8% CPU
Optimizing NNI: done in 1.08284 secs using 399% CPU
Optimizing NNI: done in 4.7015 secs using 597.6% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.21086 secs using 399.2% CPU
Optimizing NNI: done in 1.26176 secs using 399.1% CPU
Iteration 60 / LogL: -58382.186 / Time: 0h:1m:59s (0h:3m:4s left)
BETTER TREE FOUND at iteration 22: -97832.104
Optimizing NNI: done in 1.66314 secs using 399% CPU
Optimizing NNI: done in 2.03124 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.1615 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.33348 secs using 399.5% CPU
Optimizing NNI: done in 1.29528 secs using 399.1% CPU
BETTER TREE FOUND at iteration 23: -97826.704
BETTER TREE FOUND at iteration 196: -190859.512
Optimizing NNI: done in 1.28005 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.30683 secs using 399.3% CPU
Optimizing NNI: done in 5.12049 secs using 596.2% CPU
BETTER TREE FOUND at iteration 25: -97807.522
Optimizing NNI: done in 1.3678 secs using 398.7% CPU
Optimizing NNI: done in 1.5227 secs using 398.5% CPU
Optimizing NNI: done in 2.26147 secs using 398.6% CPU
Optimizing NNI: done in 0.924447 secs using 399% CPU
Iteration 70 / LogL: -58397.620 / Time: 0h:2m:13s (0h:2m:36s left)
Optimizing NNI: done in 4.79261 secs using 598.1% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.1 secs using 398.6% CPU
Iteration 30 / LogL: -97821.411 / Time: 0h:2m:48s (0h:9m:10s left)
BETTER TREE FOUND at iteration 75: -58375.865
Optimizing NNI: done in 4.03808 secs using 597.8% CPU
Iteration 200 / LogL: -190881.648 / Time: 0h:17m:38s (0h:8m:30s left)
Optimizing NNI: done in 1.39335 secs using 399% CPU
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Iteration 80 / LogL: -58383.781 / Time: 0h:2m:28s (0h:2m:58s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.93111 secs using 398.7% CPU
BETTER TREE FOUND at iteration 83: -58375.728
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BETTER TREE FOUND at iteration 36: -97789.343
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Iteration 90 / LogL: -58379.141 / Time: 0h:2m:43s (0h:2m:50s left)
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Iteration 40 / LogL: -97817.749 / Time: 0h:3m:13s (0h:7m:55s left)
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Iteration 100 / LogL: -58379.341 / Time: 0h:2m:57s (0h:2m:28s left)
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Optimizing NNI: done in 4.92833 secs using 597.3% CPU
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BETTER TREE FOUND at iteration 45: -97786.203
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Iteration 210 / LogL: -190903.968 / Time: 0h:18m:23s (0h:7m:34s left)
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Iteration 50 / LogL: -97809.359 / Time: 0h:3m:37s (0h:7m:1s left)
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Iteration 110 / LogL: -58386.511 / Time: 0h:3m:11s (0h:2m:7s left)
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Iteration 120 / LogL: -58398.215 / Time: 0h:3m:25s (0h:1m:48s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 59: -97785.071
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Iteration 60 / LogL: -97798.848 / Time: 0h:4m:1s (0h:6m:44s left)
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Iteration 130 / LogL: -58376.866 / Time: 0h:3m:39s (0h:1m:30s left)
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Iteration 140 / LogL: -58388.935 / Time: 0h:3m:53s (0h:1m:12s left)
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Iteration 220 / LogL: -190877.092 / Time: 0h:19m:9s (0h:6m:38s left)
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Iteration 70 / LogL: -97786.383 / Time: 0h:4m:23s (0h:5m:39s left)
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Iteration 150 / LogL: -58378.251 / Time: 0h:4m:6s (0h:0m:54s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 158: -58374.814
Optimizing NNI: done in 2.2036 secs using 398.4% CPU
Iteration 80 / LogL: -97829.626 / Time: 0h:4m:45s (0h:4m:45s left)
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Iteration 160 / LogL: -58385.216 / Time: 0h:4m:22s (0h:2m:41s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 161: -58374.028
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 168: -58374.027
BETTER TREE FOUND at iteration 86: -97784.004
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Iteration 170 / LogL: -58374.698 / Time: 0h:4m:36s (0h:2m:40s left)
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Iteration 230 / LogL: -190891.787 / Time: 0h:19m:55s (0h:5m:44s left)
BETTER TREE FOUND at iteration 88: -97782.836
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Iteration 90 / LogL: -97803.971 / Time: 0h:5m:11s (0h:5m:42s left)
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Iteration 180 / LogL: -58412.907 / Time: 0h:4m:50s (0h:2m:22s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 190 / LogL: -58374.288 / Time: 0h:5m:4s (0h:2m:5s left)
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BETTER TREE FOUND at iteration 235: -190854.303
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Iteration 100 / LogL: -97847.245 / Time: 0h:5m:32s (0h:4m:55s left)
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Iteration 200 / LogL: -58374.050 / Time: 0h:5m:17s (0h:1m:48s left)
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Iteration 110 / LogL: -97845.490 / Time: 0h:5m:54s (0h:4m:13s left)
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Iteration 240 / LogL: -191084.635 / Time: 0h:20m:45s (0h:8m:15s left)
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Iteration 210 / LogL: -58610.049 / Time: 0h:5m:31s (0h:1m:32s left)
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Iteration 220 / LogL: -58374.028 / Time: 0h:5m:45s (0h:1m:15s left)
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Iteration 120 / LogL: -97793.540 / Time: 0h:6m:16s (0h:3m:34s left)
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Iteration 230 / LogL: -58409.907 / Time: 0h:5m:58s (0h:0m:59s left)
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Iteration 130 / LogL: -97797.031 / Time: 0h:6m:36s (0h:2m:58s left)
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Iteration 240 / LogL: -58377.187 / Time: 0h:6m:13s (0h:0m:43s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 132: -97781.977
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Iteration 250 / LogL: -190865.030 / Time: 0h:21m:36s (0h:7m:22s left)
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Iteration 250 / LogL: -58374.292 / Time: 0h:6m:26s (0h:0m:27s left)
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Iteration 140 / LogL: -97815.489 / Time: 0h:7m:0s (0h:4m:38s left)
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Iteration 260 / LogL: -58383.767 / Time: 0h:6m:40s (0h:0m:12s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 145: -97776.502
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Optimizing NNI: done in 1.07818 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 269 ITERATIONS / Time: 0h:6m:52s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58374.027
Optimal log-likelihood: -58374.021
Site proportion and rates:  (0.152,0.077) (0.071,0.220) (0.157,0.399) (0.235,0.678) (0.152,1.024) (0.133,1.762) (0.080,2.741) (0.021,6.775)
Parameters optimization took 1 rounds (0.350 sec)
BEST SCORE FOUND : -58374.021
Total tree length: 44.118

Total number of iterations: 269
CPU time used for tree search: 1551.988 sec (0h:25m:51s)
Wall-clock time used for tree search: 392.705 sec (0h:6m:32s)
Total CPU time used: 1631.513 sec (0h:27m:11s)
Total wall-clock time used: 412.640 sec (0h:6m:52s)

===> START BOOTSTRAP REPLICATE NUMBER 98

Creating bootstrap alignment (seed: 67560)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.049 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59748.970
2. Current log-likelihood: -59186.120
Optimizing NNI: done in 2.47193 secs using 398.4% CPU
3. Current log-likelihood: -59161.097
4. Current log-likelihood: -59154.666
5. Current log-likelihood: -59151.974
Optimizing NNI: done in 2.71189 secs using 398.7% CPU
6. Current log-likelihood: -59149.481
7. Current log-likelihood: -59147.335
8. Current log-likelihood: -59146.426
Optimizing NNI: done in 2.13555 secs using 398.4% CPU
Iteration 150 / LogL: -97929.564 / Time: 0h:7m:25s (0h:4m:43s left)
9. Current log-likelihood: -59146.063
Optimizing NNI: done in 8.1617 secs using 597.7% CPU
10. Current log-likelihood: -59145.871
11. Current log-likelihood: -59145.741
Optimizing NNI: done in 2.46473 secs using 398.4% CPU
Optimal log-likelihood: -59145.597
Site proportion and rates:  (0.101,0.062) (0.111,0.193) (0.182,0.402) (0.162,0.627) (0.200,0.985) (0.125,1.588) (0.086,2.526) (0.032,5.798)
Parameters optimization took 11 rounds (8.854 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.08881 secs using 400% CPU
Computing ML distances took 1.088983 sec (of wall-clock time) 4.355301 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000375986 secs using 416% CPU
Constructing RapidNJ tree: done in 0.00438881 secs using 318.2% CPU
Computing RapidNJ tree took 0.004814 sec (of wall-clock time) 0.018299 sec (of CPU time)
Log-likelihood of RapidNJ tree: -59194.412
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.11758 secs using 398.7% CPU
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5.171 second
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Computing log-likelihood of 98 initial trees ... 5.119 seconds
Current best score: -59045.964

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -58861.693
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 258: -190853.566
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Iteration 160 / LogL: -97810.018 / Time: 0h:7m:48s (0h:4m:10s left)
BETTER TREE FOUND at iteration 2: -58858.291
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 5: -58823.164
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Iteration 260 / LogL: -190860.494 / Time: 0h:22m:45s (0h:8m:36s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 165: -97775.944
BETTER TREE FOUND at iteration 8: -58814.638
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Iteration 10 / LogL: -58866.652 / Time: 0h:0m:45s
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Iteration 170 / LogL: -97833.662 / Time: 0h:8m:12s (0h:4m:36s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 19: -58790.384
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Iteration 20 / LogL: -58871.299 / Time: 0h:1m:3s
Finish initializing candidate tree set (20)
Current best tree score: -58790.384 / CPU time: 52.476
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 269: -190849.106
BETTER TREE FOUND at iteration 182: -97775.174
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 69: -58783.110
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BETTER TREE FOUND at iteration 106: -58781.303
Optimizing NNI: done in 4.70232 secs using 597% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.49519 secs using 398.9% CPU
BETTER TREE FOUND at iteration 230: -97768.805
Iteration 230 / LogL: -97768.805 / Time: 0h:10m:31s (0h:4m:35s left)
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Iteration 110 / LogL: -58783.131 / Time: 0h:3m:16s (0h:2m:52s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 118: -58780.883
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Iteration 120 / LogL: -58787.066 / Time: 0h:3m:31s (0h:2m:54s left)
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Iteration 240 / LogL: -98011.669 / Time: 0h:10m:54s (0h:4m:6s left)
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Iteration 130 / LogL: -58784.236 / Time: 0h:3m:45s (0h:2m:34s left)
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Iteration 300 / LogL: -190858.062 / Time: 0h:25m:56s (0h:5m:59s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.43514 secs using 398.4% CPU
BETTER TREE FOUND at iteration 135: -58780.462
Optimizing NNI: done in 1.35251 secs using 399.1% CPU
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Iteration 250 / LogL: -97789.660 / Time: 0h:11m:16s (0h:3m:37s left)
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Iteration 140 / LogL: -58798.053 / Time: 0h:4m:1s (0h:2m:45s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 143: -58780.394
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -58780.328
Optimizing NNI: done in 2.25881 secs using 398.5% CPU
Optimizing NNI: done in 5.78306 secs using 596.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.6577 secs using 398.7% CPU
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BETTER TREE FOUND at iteration 305: -190848.408
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Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -58780.267
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Iteration 150 / LogL: -58782.277 / Time: 0h:4m:19s (0h:2m:41s left)
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Iteration 260 / LogL: -97773.408 / Time: 0h:11m:39s (0h:3m:9s left)
Optimizing NNI: done in 1.4364 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 152: -58780.208
Optimizing NNI: done in 4.09923 secs using 597.5% CPU
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Iteration 160 / LogL: -58804.862 / Time: 0h:4m:34s (0h:2m:38s left)
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Iteration 310 / LogL: -190878.505 / Time: 0h:26m:44s (0h:8m:13s left)
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Iteration 270 / LogL: -97794.687 / Time: 0h:12m:3s (0h:2m:41s left)
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Iteration 170 / LogL: -58780.943 / Time: 0h:4m:48s (0h:2m:19s left)
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Iteration 180 / LogL: -58797.094 / Time: 0h:5m:3s (0h:2m:1s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 182: -58776.983
Optimizing NNI: done in 2.52188 secs using 398.5% CPU
Iteration 280 / LogL: -97770.174 / Time: 0h:12m:27s (0h:2m:13s left)
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Iteration 190 / LogL: -58782.266 / Time: 0h:5m:20s (0h:2m:35s left)
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Iteration 320 / LogL: -190881.301 / Time: 0h:27m:30s (0h:7m:19s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 192: -58775.267
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Iteration 290 / LogL: -97852.151 / Time: 0h:12m:51s (0h:1m:46s left)
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Iteration 200 / LogL: -58793.358 / Time: 0h:5m:34s (0h:2m:34s left)
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Iteration 210 / LogL: -58809.606 / Time: 0h:5m:49s (0h:2m:17s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.53504 secs using 398.1% CPU
BETTER TREE FOUND at iteration 214: -58775.205
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Iteration 300 / LogL: -97844.607 / Time: 0h:13m:15s (0h:1m:19s left)
Optimizing NNI: done in 1.61918 secs using 399% CPU
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Optimizing NNI: done in 1.57369 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -58775.146
Optimizing NNI: done in 4.55915 secs using 596.8% CPU
Optimizing NNI: done in 2.64071 secs using 398.3% CPU
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Iteration 220 / LogL: -58802.448 / Time: 0h:6m:4s (0h:2m:36s left)
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Iteration 330 / LogL: -190870.720 / Time: 0h:28m:19s (0h:6m:27s left)
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Iteration 230 / LogL: -58778.982 / Time: 0h:6m:18s (0h:2m:18s left)
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Iteration 310 / LogL: -97837.419 / Time: 0h:13m:38s (0h:0m:52s left)
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Iteration 240 / LogL: -58776.212 / Time: 0h:6m:32s (0h:2m:1s left)
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Iteration 320 / LogL: -97773.216 / Time: 0h:14m:3s (0h:0m:26s left)
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Iteration 250 / LogL: -58813.791 / Time: 0h:6m:46s (0h:1m:44s left)
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Iteration 340 / LogL: -190920.711 / Time: 0h:29m:7s (0h:5m:34s left)
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Optimizing NNI: done in 2.196 secs using 398.8% CPU
Optimizing NNI: done in 1.75059 secs using 398.6% CPU
Iteration 260 / LogL: -58828.218 / Time: 0h:7m:0s (0h:1m:27s left)
Optimizing NNI: done in 2.97036 secs using 398.5% CPU
Optimizing NNI: done in 1.74878 secs using 398.8% CPU
Optimizing NNI: done in 5.0012 secs using 597.7% CPU
Optimizing NNI: done in 1.42901 secs using 399.1% CPU
Optimizing NNI: done in 2.22964 secs using 398.7% CPU
Optimizing NNI: done in 1.71611 secs using 398.6% CPU
Optimizing NNI: done in 2.08118 secs using 398.9% CPU
Iteration 330 / LogL: -97809.454 / Time: 0h:14m:25s (0h:0m:0s left)
Optimizing NNI: done in 1.56029 secs using 398.5% CPU
Optimizing NNI: done in 4.12077 secs using 596.9% CPU
Optimizing NNI: done in 1.41593 secs using 398.8% CPU
Optimizing NNI: done in 2.08474 secs using 398.2% CPU
TREE SEARCH COMPLETED AFTER 331 ITERATIONS / Time: 0h:14m:27s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -97768.805
2. Current log-likelihood: -97768.758
Optimizing NNI: done in 1.38473 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -58775.091
3. Current log-likelihood: -97768.707
4. Current log-likelihood: -97768.662
Optimizing NNI: done in 1.46542 secs using 398.4% CPU
Optimizing NNI: done in 5.00637 secs using 596.9% CPU
5. Current log-likelihood: -97768.622
Optimizing NNI: done in 1.56327 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
6. Current log-likelihood: -97768.585
BETTER TREE FOUND at iteration 268: -58775.035
7. Current log-likelihood: -97768.551
Optimizing NNI: done in 1.46832 secs using 399% CPU
8. Current log-likelihood: -97768.517
Optimizing NNI: done in 1.38121 secs using 399% CPU
Iteration 270 / LogL: -58788.102 / Time: 0h:7m:17s (0h:2m:39s left)
9. Current log-likelihood: -97768.486
Optimizing NNI: done in 5.24791 secs using 597.3% CPU
10. Current log-likelihood: -97768.469
Optimizing NNI: done in 1.21446 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 271: -58774.975
11. Current log-likelihood: -97768.448
12. Current log-likelihood: -97768.419
Optimizing NNI: done in 1.31608 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -58774.921
13. Current log-likelihood: -97768.400
14. Current log-likelihood: -97768.371
Optimizing NNI: done in 4.9069 secs using 597.2% CPU
Optimizing NNI: done in 1.65759 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
15. Current log-likelihood: -97768.355
BETTER TREE FOUND at iteration 273: -58774.477
16. Current log-likelihood: -97768.336
17. Current log-likelihood: -97768.309
Optimizing NNI: done in 1.59856 secs using 398.5% CPU
18. Current log-likelihood: -97768.293
Optimizing NNI: done in 4.14798 secs using 597.1% CPU
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19. Current log-likelihood: -97768.275
Optimizing NNI: done in 1.06538 secs using 399% CPU
20. Current log-likelihood: -97768.248
21. Current log-likelihood: -97768.233
Optimizing NNI: done in 1.38143 secs using 399.2% CPU
22. Current log-likelihood: -97768.215
23. Current log-likelihood: -97768.199
Optimizing NNI: done in 1.37601 secs using 398.9% CPU
Optimizing NNI: done in 4.35906 secs using 596.8% CPU
24. Current log-likelihood: -97768.183
25. Current log-likelihood: -97768.167
Optimizing NNI: done in 1.32456 secs using 399.3% CPU
26. Current log-likelihood: -97768.152
27. Current log-likelihood: -97768.137
Optimizing NNI: done in 1.4826 secs using 398.8% CPU
Iteration 280 / LogL: -58779.299 / Time: 0h:7m:34s (0h:2m:31s left)
28. Current log-likelihood: -97768.122
29. Current log-likelihood: -97768.108
Optimizing NNI: done in 1.30593 secs using 399.3% CPU
30. Current log-likelihood: -97768.094
31. Current log-likelihood: -97768.080
Optimizing NNI: done in 5.12764 secs using 597.6% CPU
Optimizing NNI: done in 1.55007 secs using 398.6% CPU
32. Current log-likelihood: -97768.066
33. Current log-likelihood: -97768.052
Optimizing NNI: done in 1.40846 secs using 399.1% CPU
34. Current log-likelihood: -97768.038
35. Current log-likelihood: -97768.025
Optimizing NNI: done in 1.36021 secs using 398.8% CPU
36. Current log-likelihood: -97768.011
37. Current log-likelihood: -97767.998
Optimizing NNI: done in 1.25406 secs using 398.8% CPU
Optimizing NNI: done in 4.50438 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
38. Current log-likelihood: -97767.985
39. Current log-likelihood: -97767.971
Optimizing NNI: done in 1.45459 secs using 399.2% CPU
40. Current log-likelihood: -97767.958
BETTER TREE FOUND at iteration 349: -190845.732
41. Current log-likelihood: -97767.945
Optimizing NNI: done in 1.39395 secs using 399.1% CPU
42. Current log-likelihood: -97767.933
43. Current log-likelihood: -97767.920
44. Current log-likelihood: -97767.907
Optimizing NNI: done in 1.56022 secs using 399.1% CPU
45. Current log-likelihood: -97767.895
46. Current log-likelihood: -97767.883
Optimizing NNI: done in 1.85858 secs using 398.6% CPU
47. Current log-likelihood: -97767.870
Optimizing NNI: done in 4.4725 secs using 597.7% CPU
Iteration 350 / LogL: -190860.648 / Time: 0h:29m:56s (0h:8m:29s left)
48. Current log-likelihood: -97767.858
Optimizing NNI: done in 1.31104 secs using 399.2% CPU
Iteration 290 / LogL: -58800.556 / Time: 0h:7m:48s (0h:2m:14s left)
49. Current log-likelihood: -97767.846
50. Current log-likelihood: -97767.834
51. Current log-likelihood: -97767.822
Optimizing NNI: done in 1.53104 secs using 399.7% CPU
52. Current log-likelihood: -97767.810
Optimizing NNI: done in 3.80365 secs using 597.8% CPU
Optimizing NNI: done in 1.37276 secs using 399% CPU
53. Current log-likelihood: -97767.798
54. Current log-likelihood: -97767.787
Optimizing NNI: done in 1.17412 secs using 399.6% CPU
55. Current log-likelihood: -97767.775
56. Current log-likelihood: -97767.765
Optimizing NNI: done in 1.32425 secs using 399.4% CPU
Optimal log-likelihood: -97767.751
Proportion of invariable sites: 0.041
Site proportion and rates:  (0.088,0.028) (0.105,0.110) (0.080,0.216) (0.126,0.347) (0.106,0.566) (0.104,0.900) (0.160,1.412) (0.139,2.110) (0.052,4.842)
Parameters optimization took 56 rounds (45.751 sec)
BEST SCORE FOUND : -97767.751
Total tree length: 151.628

Total number of iterations: 331
CPU time used for tree search: 3358.322 sec (0h:55m:58s)
Wall-clock time used for tree search: 850.614 sec (0h:14m:10s)
Total CPU time used: 3609.674 sec (1h:0m:9s)
Total wall-clock time used: 913.700 sec (0h:15m:13s)

===> START BOOTSTRAP REPLICATE NUMBER 44

Creating bootstrap alignment (seed: 68226)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -111674.256
Optimizing NNI: done in 1.4634 secs using 398.6% CPU
Optimizing NNI: done in 4.30083 secs using 597.9% CPU
2. Current log-likelihood: -109728.716
Optimizing NNI: done in 1.603 secs using 398.7% CPU
3. Current log-likelihood: -109679.638
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4. Current log-likelihood: -109670.159
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Optimizing NNI: done in 1.34293 secs using 398.3% CPU
5. Current log-likelihood: -109669.132
Optimizing NNI: done in 1.30863 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
6. Current log-likelihood: -109668.618
BETTER TREE FOUND at iteration 300: -58774.147
Iteration 300 / LogL: -58774.147 / Time: 0h:8m:3s (0h:2m:41s left)
7. Current log-likelihood: -109668.123
Optimizing NNI: done in 1.35877 secs using 398.3% CPU
Optimizing NNI: done in 4.65685 secs using 597% CPU
8. Current log-likelihood: -109667.655
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9. Current log-likelihood: -109667.227
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10. Current log-likelihood: -109666.795
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11. Current log-likelihood: -109666.393
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12. Current log-likelihood: -109666.008
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13. Current log-likelihood: -109665.638
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14. Current log-likelihood: -109665.284
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15. Current log-likelihood: -109664.941
Optimizing NNI: done in 1.39487 secs using 398% CPU
Iteration 310 / LogL: -58800.667 / Time: 0h:8m:17s (0h:2m:24s left)
Optimizing NNI: done in 4.84014 secs using 597.1% CPU
16. Current log-likelihood: -109664.613
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17. Current log-likelihood: -109664.293
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18. Current log-likelihood: -109663.981
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19. Current log-likelihood: -109663.684
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20. Current log-likelihood: -109663.392
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21. Current log-likelihood: -109663.108
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22. Current log-likelihood: -109662.834
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23. Current log-likelihood: -109662.564
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24. Current log-likelihood: -109662.302
Optimizing NNI: done in 1.62144 secs using 398.8% CPU
Iteration 320 / LogL: -58784.141 / Time: 0h:8m:32s (0h:2m:8s left)
25. Current log-likelihood: -109662.046
Optimizing NNI: done in 1.49667 secs using 399.3% CPU
Optimizing NNI: done in 5.07819 secs using 597.4% CPU
Iteration 360 / LogL: -190866.761 / Time: 0h:30m:42s (0h:7m:36s left)
26. Current log-likelihood: -109661.880
Optimizing NNI: done in 1.26759 secs using 399% CPU
27. Current log-likelihood: -109661.616
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28. Current log-likelihood: -109661.459
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29. Current log-likelihood: -109661.298
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30. Current log-likelihood: -109661.049
Optimizing NNI: done in 1.30981 secs using 398.7% CPU
Optimizing NNI: done in 1.42252 secs using 399% CPU
31. Current log-likelihood: -109660.903
Optimizing NNI: done in 4.58717 secs using 598% CPU
Optimizing NNI: done in 1.42044 secs using 398.5% CPU
BETTER TREE FOUND at iteration 328: -58774.139
32. Current log-likelihood: -109660.752
Optimizing NNI: done in 1.21621 secs using 399.5% CPU
33. Current log-likelihood: -109660.518
Optimizing NNI: done in 1.30696 secs using 398.9% CPU
Iteration 330 / LogL: -58775.559 / Time: 0h:8m:46s (0h:2m:36s left)
34. Current log-likelihood: -109660.373
Optimizing NNI: done in 1.5638 secs using 398.7% CPU
35. Current log-likelihood: -109660.221
Optimizing NNI: done in 4.69984 secs using 596.8% CPU
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36. Current log-likelihood: -109660.046
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37. Current log-likelihood: -109659.743
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38. Current log-likelihood: -109658.115
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39. Current log-likelihood: -109652.551
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40. Current log-likelihood: -109649.755
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41. Current log-likelihood: -109649.041
Optimizing NNI: done in 4.68105 secs using 597.5% CPU
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42. Current log-likelihood: -109648.781
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43. Current log-likelihood: -109648.602
Optimizing NNI: done in 1.28805 secs using 399% CPU
Iteration 340 / LogL: -58776.573 / Time: 0h:9m:0s (0h:2m:20s left)
Optimizing NNI: done in 1.39549 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
44. Current log-likelihood: -109648.453
Optimizing NNI: done in 4.94057 secs using 597.1% CPU
BETTER TREE FOUND at iteration 341: -58773.779
45. Current log-likelihood: -109648.310
Optimizing NNI: done in 1.43828 secs using 398.8% CPU
46. Current log-likelihood: -109648.173
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47. Current log-likelihood: -109648.041
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Optimizing NNI: done in 4.20387 secs using 597.1% CPU
48. Current log-likelihood: -109647.912
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49. Current log-likelihood: -109647.786
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50. Current log-likelihood: -109647.665
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51. Current log-likelihood: -109647.547
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Optimizing NNI: done in 1.2622 secs using 399.3% CPU
52. Current log-likelihood: -109647.430
53. Current log-likelihood: -109647.325
Optimizing NNI: done in 1.32483 secs using 398.9% CPU
Iteration 350 / LogL: -58774.237 / Time: 0h:9m:15s (0h:2m:24s left)
Optimizing NNI: done in 4.31562 secs using 596.5% CPU
54. Current log-likelihood: -109647.221
Optimizing NNI: done in 1.61777 secs using 399.2% CPU
55. Current log-likelihood: -109647.119
Optimizing NNI: done in 1.67312 secs using 399.5% CPU
56. Current log-likelihood: -109647.017
Optimizing NNI: done in 1.47749 secs using 399.1% CPU
57. Current log-likelihood: -109646.913
Optimizing NNI: done in 4.60361 secs using 597.5% CPU
Iteration 370 / LogL: -190855.422 / Time: 0h:31m:29s (0h:6m:44s left)
Optimizing NNI: done in 1.41585 secs using 399.4% CPU
Optimal log-likelihood: -109646.762
Proportion of invariable sites: 0.014
Site proportion and rates:  (0.058,0.028) (0.088,0.089) (0.092,0.187) (0.118,0.305) (0.113,0.511) (0.128,0.872) (0.132,1.302) (0.190,1.861) (0.068,3.570)
Parameters optimization took 57 rounds (86.738 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.71844 secs using 398.9% CPU
Optimizing NNI: done in 1.6389 secs using 398.3% CPU
Optimizing NNI: done in 4.33656 secs using 597.8% CPU
Calculating distance matrix: done in 4.69112 secs using 400% CPU
Computing ML distances took 4.691410 sec (of wall-clock time) 18.763460 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000720978 secs using 262.7% CPU
Constructing RapidNJ tree: done in 0.00867796 secs using 354.9% CPU
Computing RapidNJ tree took 0.009461 sec (of wall-clock time) 0.035798 sec (of CPU time)
Optimizing NNI: done in 1.55239 secs using 397.9% CPU
Log-likelihood of RapidNJ tree: -109972.906
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.29015 secs using 399% CPU
Optimizing NNI: done in 1.65836 secs using 398.7% CPU
Optimizing NNI: done in 5.03641 secs using 597.5% CPU
Optimizing NNI: done in 1.49182 secs using 398.2% CPU
Iteration 360 / LogL: -58781.290 / Time: 0h:9m:30s (0h:2m:8s left)
Optimizing NNI: done in 1.44295 secs using 397.2% CPU
Optimizing NNI: done in 1.59707 secs using 398.4% CPU
Optimizing NNI: done in 1.74991 secs using 398.8% CPU
Optimizing NNI: done in 6.38232 secs using 597.5% CPU
Optimizing NNI: done in 1.53842 secs using 399.2% CPU
10.390 second
Optimizing NNI: done in 1.47418 secs using 399.1% CPU
Optimizing NNI: done in 1.51103 secs using 399.3% CPU
Optimizing NNI: done in 1.47121 secs using 399.4% CPU
Optimizing NNI: done in 5.27214 secs using 597.5% CPU
Optimizing NNI: done in 1.54652 secs using 398.8% CPU
Optimizing NNI: done in 1.71759 secs using 398.9% CPU
Optimizing NNI: done in 1.40888 secs using 398.8% CPU
Iteration 370 / LogL: -58782.210 / Time: 0h:9m:46s (0h:1m:52s left)
Optimizing NNI: done in 5.05752 secs using 597.2% CPU
Computing log-likelihood of 98 initial trees ... 10.065 seconds
Current best score: -109646.762

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.5208 secs using 398.2% CPU
Optimizing NNI: done in 1.56808 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.43368 secs using 398.9% CPU
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Optimizing NNI: done in 4.78666 secs using 597.4% CPU
Optimizing NNI: done in 1.6867 secs using 399.1% CPU
Iteration 380 / LogL: -58789.346 / Time: 0h:10m:1s (0h:1m:36s left)
Optimizing NNI: done in 1.67368 secs using 399.1% CPU
BETTER TREE FOUND at iteration 1: -109234.822
Optimizing NNI: done in 1.90469 secs using 399% CPU
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Optimizing NNI: done in 1.45444 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.50095 secs using 398.4% CPU
Optimizing NNI: done in 1.24239 secs using 399.4% CPU
Optimizing NNI: done in 4.18476 secs using 598% CPU
Iteration 380 / LogL: -190891.766 / Time: 0h:32m:18s (0h:5m:52s left)
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Optimizing NNI: done in 0.922705 secs using 398.9% CPU
BETTER TREE FOUND at iteration 2: -109228.447
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Optimizing NNI: done in 1.47418 secs using 399.2% CPU
Iteration 390 / LogL: -58774.922 / Time: 0h:10m:15s (0h:1m:20s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 4: -109212.197
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Iteration 400 / LogL: -58774.128 / Time: 0h:10m:28s (0h:1m:4s left)
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Iteration 10 / LogL: -109297.086 / Time: 0h:2m:41s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 386: -190845.483
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Iteration 410 / LogL: -58777.031 / Time: 0h:10m:42s (0h:0m:48s left)
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Iteration 20 / LogL: -109273.412 / Time: 0h:3m:2s
Finish initializing candidate tree set (20)
Current best tree score: -109212.197 / CPU time: 89.800
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 420 / LogL: -58780.367 / Time: 0h:10m:57s (0h:0m:32s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -109182.852
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BETTER TREE FOUND at iteration 27: -109180.877
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BETTER TREE FOUND at iteration 29: -109173.128
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Iteration 30 / LogL: -109211.559 / Time: 0h:3m:29s (0h:11m:54s left)
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Iteration 440 / LogL: -59157.092 / Time: 0h:11m:26s (0h:0m:1s left)
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TREE SEARCH COMPLETED AFTER 442 ITERATIONS / Time: 0h:11m:29s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -58773.779
Optimizing NNI: done in 2.02997 secs using 398.9% CPU
2. Current log-likelihood: -58773.759
3. Current log-likelihood: -58773.744
4. Current log-likelihood: -58773.730
5. Current log-likelihood: -58773.716
6. Current log-likelihood: -58773.700
Optimizing NNI: done in 1.82067 secs using 398.8% CPU
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7. Current log-likelihood: -58773.687
8. Current log-likelihood: -58773.670
9. Current log-likelihood: -58773.657
10. Current log-likelihood: -58773.644
11. Current log-likelihood: -58773.630
Optimizing NNI: done in 2.2597 secs using 398.4% CPU
12. Current log-likelihood: -58773.618
13. Current log-likelihood: -58773.605
14. Current log-likelihood: -58773.594
15. Current log-likelihood: -58773.583
Optimizing NNI: done in 1.81458 secs using 397.9% CPU
16. Current log-likelihood: -58773.572
17. Current log-likelihood: -58773.562
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18. Current log-likelihood: -58773.549
19. Current log-likelihood: -58773.539
Optimizing NNI: done in 1.85088 secs using 398.5% CPU
20. Current log-likelihood: -58773.529
Optimal log-likelihood: -58773.514
Site proportion and rates:  (0.081,0.054) (0.118,0.162) (0.183,0.389) (0.185,0.637) (0.213,1.013) (0.128,1.755) (0.062,2.739) (0.030,5.939)
Parameters optimization took 20 rounds (8.978 sec)
BEST SCORE FOUND : -58773.514
Total tree length: 44.038

Total number of iterations: 442
CPU time used for tree search: 2690.951 sec (0h:44m:50s)
Wall-clock time used for tree search: 678.624 sec (0h:11m:18s)
Total CPU time used: 2768.864 sec (0h:46m:8s)
Total wall-clock time used: 698.159 sec (0h:11m:38s)

===> START BOOTSTRAP REPLICATE NUMBER 99

Creating bootstrap alignment (seed: 67561)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.052 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -61112.758
2. Current log-likelihood: -60555.173
Optimizing NNI: done in 2.03968 secs using 399% CPU
3. Current log-likelihood: -60534.892
4. Current log-likelihood: -60533.428
Optimizing NNI: done in 1.90954 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
5. Current log-likelihood: -60533.069
Optimizing NNI: done in 4.97528 secs using 597.4% CPU
6. Current log-likelihood: -60532.866
7. Current log-likelihood: -60532.737
Optimal log-likelihood: -60532.655
Site proportion and rates:  (0.138,0.085) (0.041,0.179) (0.174,0.347) (0.057,0.575) (0.143,0.659) (0.208,1.096) (0.177,1.992) (0.061,3.467)
Parameters optimization took 7 rounds (5.813 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
BETTER TREE FOUND at iteration 39: -109166.316
Calculating distance matrix: done in 1.08297 secs using 399.9% CPU
Computing ML distances took 1.083154 sec (of wall-clock time) 4.330979 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000344038 secs using 421.2% CPU
Constructing RapidNJ tree: done in 0.00423598 secs using 389.2% CPU
Computing RapidNJ tree took 0.004639 sec (of wall-clock time) 0.018655 sec (of CPU time)
Log-likelihood of RapidNJ tree: -60375.988
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.55331 secs using 597.6% CPU
Iteration 400 / LogL: -190859.780 / Time: 0h:33m:55s (0h:7m:18s left)
Optimizing NNI: done in 1.99191 secs using 398.2% CPU
Iteration 40 / LogL: -109172.866 / Time: 0h:3m:52s (0h:9m:48s left)
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4.980 second
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Computing log-likelihood of 98 initial trees ... 5.105 seconds
Current best score: -60299.388

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -60088.391
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Estimate model parameters (epsilon = 0.100)
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Iteration 50 / LogL: -109236.555 / Time: 0h:4m:12s (0h:7m:38s left)
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Iteration 10 / LogL: -60167.225 / Time: 0h:0m:44s
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Estimate model parameters (epsilon = 0.100)
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Iteration 60 / LogL: -109191.649 / Time: 0h:4m:32s (0h:6m:4s left)
BETTER TREE FOUND at iteration 12: -60048.992
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 64: -109159.907
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Iteration 20 / LogL: -60130.383 / Time: 0h:1m:14s
Finish initializing candidate tree set (20)
Current best tree score: -60032.475 / CPU time: 66.443
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Iteration 110 / LogL: -109162.834 / Time: 0h:6m:18s (0h:4m:47s left)
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Iteration 70 / LogL: -60001.900 / Time: 0h:2m:38s (0h:3m:15s left)
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Iteration 80 / LogL: -59989.713 / Time: 0h:2m:53s (0h:2m:44s left)
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Iteration 120 / LogL: -109174.201 / Time: 0h:6m:38s (0h:4m:4s left)
Optimizing NNI: done in 1.25639 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.0696 secs using 597.9% CPU
BETTER TREE FOUND at iteration 81: -59985.055
Optimizing NNI: done in 1.81238 secs using 399.2% CPU
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Iteration 90 / LogL: -60005.967 / Time: 0h:3m:10s (0h:3m:14s left)
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Iteration 130 / LogL: -109183.397 / Time: 0h:6m:58s (0h:3m:24s left)
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Iteration 440 / LogL: -190861.756 / Time: 0h:37m:6s (0h:3m:53s left)
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Iteration 100 / LogL: -59986.427 / Time: 0h:3m:25s (0h:2m:48s left)
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Iteration 140 / LogL: -109164.156 / Time: 0h:7m:18s (0h:2m:47s left)
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Iteration 110 / LogL: -59986.512 / Time: 0h:3m:40s (0h:2m:23s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.6472 secs using 398.9% CPU
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Iteration 120 / LogL: -59998.045 / Time: 0h:3m:55s (0h:2m:0s left)
BETTER TREE FOUND at iteration 148: -109158.545
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Iteration 150 / LogL: -109175.169 / Time: 0h:7m:43s (0h:5m:4s left)
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Iteration 450 / LogL: -190922.631 / Time: 0h:37m:51s (0h:3m:2s left)
BETTER TREE FOUND at iteration 126: -59984.194
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BETTER TREE FOUND at iteration 130: -59982.156
Iteration 130 / LogL: -59982.156 / Time: 0h:4m:12s (0h:3m:15s left)
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Iteration 160 / LogL: -109163.300 / Time: 0h:8m:2s (0h:4m:27s left)
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Iteration 140 / LogL: -60001.193 / Time: 0h:4m:27s (0h:2m:52s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 455: -190845.047
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Iteration 170 / LogL: -109187.172 / Time: 0h:8m:23s (0h:3m:52s left)
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Iteration 150 / LogL: -59986.071 / Time: 0h:4m:41s (0h:2m:31s left)
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Iteration 460 / LogL: -190885.902 / Time: 0h:38m:39s (0h:8m:0s left)
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Iteration 160 / LogL: -59994.598 / Time: 0h:4m:57s (0h:2m:10s left)
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Iteration 180 / LogL: -109180.268 / Time: 0h:8m:43s (0h:3m:18s left)
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Iteration 170 / LogL: -59991.650 / Time: 0h:5m:12s (0h:1m:50s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 190 / LogL: -109161.147 / Time: 0h:9m:2s (0h:2m:46s left)
BETTER TREE FOUND at iteration 174: -59981.283
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Iteration 180 / LogL: -60003.943 / Time: 0h:5m:27s (0h:2m:52s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 186: -59978.430
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Iteration 470 / LogL: -190917.051 / Time: 0h:39m:25s (0h:7m:8s left)
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BETTER TREE FOUND at iteration 199: -109156.811
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Iteration 190 / LogL: -59984.339 / Time: 0h:5m:42s (0h:2m:54s left)
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BETTER TREE FOUND at iteration 191: -59977.994
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Iteration 200 / LogL: -59978.057 / Time: 0h:5m:58s (0h:2m:44s left)
BETTER TREE FOUND at iteration 208: -109156.012
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Iteration 210 / LogL: -109187.313 / Time: 0h:9m:47s (0h:4m:35s left)
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Iteration 210 / LogL: -60004.219 / Time: 0h:6m:14s (0h:2m:24s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 226: -109155.003
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Iteration 290 / LogL: -59979.465 / Time: 0h:8m:12s (0h:0m:1s left)
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TREE SEARCH COMPLETED AFTER 292 ITERATIONS / Time: 0h:8m:15s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59977.994
Optimizing NNI: done in 1.98556 secs using 398.7% CPU
Optimal log-likelihood: -59977.986
Site proportion and rates:  (0.158,0.090) (0.079,0.271) (0.155,0.387) (0.170,0.665) (0.203,1.072) (0.158,1.903) (0.054,2.917) (0.022,5.210)
Parameters optimization took 1 rounds (0.730 sec)
BEST SCORE FOUND : -59977.986
Total tree length: 44.571

Total number of iterations: 292
CPU time used for tree search: 1933.002 sec (0h:32m:13s)
Wall-clock time used for tree search: 488.379 sec (0h:8m:8s)
Total CPU time used: 1966.338 sec (0h:32m:46s)
Total wall-clock time used: 496.716 sec (0h:8m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 100

Creating bootstrap alignment (seed: 67562)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.051 seconds

NOTE: 62 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -58200.332
2. Current log-likelihood: -57593.171
Optimizing NNI: done in 1.93566 secs using 398.6% CPU
Optimizing NNI: done in 4.89701 secs using 598.3% CPU
3. Current log-likelihood: -57583.116
4. Current log-likelihood: -57580.562
5. Current log-likelihood: -57576.641
Optimizing NNI: done in 2.17557 secs using 398.6% CPU
6. Current log-likelihood: -57574.309
7. Current log-likelihood: -57571.401
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8. Current log-likelihood: -57560.496
9. Current log-likelihood: -57556.756
Optimizing NNI: done in 5.55387 secs using 597.3% CPU
10. Current log-likelihood: -57556.408
Optimizing NNI: done in 1.86485 secs using 398.7% CPU
Optimal log-likelihood: -57556.322
Site proportion and rates:  (0.101,0.058) (0.127,0.179) (0.140,0.376) (0.083,0.378) (0.252,0.729) (0.142,1.499) (0.126,2.506) (0.030,5.877)
Parameters optimization took 10 rounds (7.978 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10002 secs using 399.6% CPU
Computing ML distances took 1.100193 sec (of wall-clock time) 4.396067 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000374079 secs using 426.1% CPU
Constructing RapidNJ tree: done in 0.00431991 secs using 358.2% CPU
Computing RapidNJ tree took 0.004743 sec (of wall-clock time) 0.018026 sec (of CPU time)
Optimizing NNI: done in 2.01858 secs using 398.6% CPU
Log-likelihood of RapidNJ tree: -57689.113
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.63387 secs using 597.6% CPU
Optimizing NNI: done in 2.43 secs using 398.6% CPU
Iteration 280 / LogL: -109185.567 / Time: 0h:12m:12s (0h:2m:0s left)
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5.139 second
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Computing log-likelihood of 98 initial trees ... 5.154 seconds
Current best score: -57496.400

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -57360.550
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Iteration 290 / LogL: -109176.220 / Time: 0h:12m:32s (0h:1m:33s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 510 / LogL: -190867.601 / Time: 0h:42m:38s (0h:3m:46s left)
BETTER TREE FOUND at iteration 9: -57326.546
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Iteration 10 / LogL: -57363.803 / Time: 0h:0m:35s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 16: -57316.154
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Iteration 20 / LogL: -57380.527 / Time: 0h:0m:49s
Finish initializing candidate tree set (20)
Current best tree score: -57316.154 / CPU time: 39.580
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Iteration 300 / LogL: -109166.336 / Time: 0h:12m:52s (0h:1m:7s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -57299.562
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 43: -57299.459
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Optimizing NNI: done in 1.51525 secs using 398.8% CPU
Optimizing NNI: done in 2.18038 secs using 399.1% CPU
Iteration 320 / LogL: -109170.543 / Time: 0h:13m:33s (0h:0m:15s left)
Optimizing NNI: done in 1.35368 secs using 399.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 47: -57299.339
Optimizing NNI: done in 1.92449 secs using 398.6% CPU
Optimizing NNI: done in 4.65748 secs using 597.6% CPU
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Optimizing NNI: done in 1.78107 secs using 399.3% CPU
Iteration 50 / LogL: -57313.674 / Time: 0h:1m:39s (0h:3m:17s left)
Optimizing NNI: done in 2.60143 secs using 398.3% CPU
Optimizing NNI: done in 4.91605 secs using 597.8% CPU
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Optimizing NNI: done in 1.26459 secs using 399.4% CPU
Optimizing NNI: done in 1.30805 secs using 399% CPU
BETTER TREE FOUND at iteration 53: -57299.335
Optimizing NNI: done in 2.06909 secs using 398.9% CPU
Optimizing NNI: done in 1.17935 secs using 398.6% CPU
Optimizing NNI: done in 5.0422 secs using 597.2% CPU
Optimizing NNI: done in 2.04439 secs using 398.5% CPU
Optimizing NNI: done in 1.376 secs using 398.9% CPU
Optimizing NNI: done in 1.79829 secs using 398.6% CPU
TREE SEARCH COMPLETED AFTER 327 ITERATIONS / Time: 0h:13m:48s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -109155.003
Optimizing NNI: done in 1.72063 secs using 399.4% CPU
Optimizing NNI: done in 1.54348 secs using 398.8% CPU
2. Current log-likelihood: -109154.936
Optimizing NNI: done in 4.94553 secs using 597.4% CPU
Optimizing NNI: done in 1.64546 secs using 398.9% CPU
3. Current log-likelihood: -109154.857
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4. Current log-likelihood: -109154.807
5. Current log-likelihood: -109154.762
Optimizing NNI: done in 1.43451 secs using 399.1% CPU
Iteration 60 / LogL: -57304.806 / Time: 0h:1m:53s (0h:2m:59s left)
6. Current log-likelihood: -109154.718
Optimizing NNI: done in 4.25762 secs using 597.2% CPU
Optimizing NNI: done in 1.51648 secs using 398.6% CPU
7. Current log-likelihood: -109154.680
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8. Current log-likelihood: -109154.640
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9. Current log-likelihood: -109154.603
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Optimizing NNI: done in 1.60764 secs using 398.3% CPU
10. Current log-likelihood: -109154.571
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11. Current log-likelihood: -109154.535
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12. Current log-likelihood: -109154.515
13. Current log-likelihood: -109154.482
Optimizing NNI: done in 4.40661 secs using 597.7% CPU
Optimizing NNI: done in 1.6333 secs using 398.1% CPU
BETTER TREE FOUND at iteration 67: -57299.329
14. Current log-likelihood: -109154.453
15. Current log-likelihood: -109154.435
Optimizing NNI: done in 1.4549 secs using 398.7% CPU
16. Current log-likelihood: -109154.410
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17. Current log-likelihood: -109154.378
Optimizing NNI: done in 4.29295 secs using 597.1% CPU
Iteration 530 / LogL: -190854.754 / Time: 0h:44m:11s (0h:2m:5s left)
18. Current log-likelihood: -109154.360
Optimizing NNI: done in 1.64306 secs using 398.8% CPU
Iteration 70 / LogL: -57494.274 / Time: 0h:2m:8s (0h:3m:1s left)
19. Current log-likelihood: -109154.327
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20. Current log-likelihood: -109154.309
21. Current log-likelihood: -109154.290
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22. Current log-likelihood: -109154.256
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23. Current log-likelihood: -109154.238
24. Current log-likelihood: -109154.219
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25. Current log-likelihood: -109154.190
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26. Current log-likelihood: -109154.168
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27. Current log-likelihood: -109154.135
28. Current log-likelihood: -109154.118
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31. Current log-likelihood: -109154.064
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33. Current log-likelihood: -109154.029
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34. Current log-likelihood: -109154.012
Optimizing NNI: done in 1.13539 secs using 398.9% CPU
Iteration 80 / LogL: -57320.819 / Time: 0h:2m:23s (0h:2m:38s left)
35. Current log-likelihood: -109153.994
36. Current log-likelihood: -109153.977
Optimizing NNI: done in 1.56281 secs using 399.3% CPU
37. Current log-likelihood: -109153.959
38. Current log-likelihood: -109153.942
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39. Current log-likelihood: -109153.924
40. Current log-likelihood: -109153.907
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41. Current log-likelihood: -109153.890
42. Current log-likelihood: -109153.873
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43. Current log-likelihood: -109153.856
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44. Current log-likelihood: -109153.840
45. Current log-likelihood: -109153.824
Optimizing NNI: done in 1.52852 secs using 399.4% CPU
46. Current log-likelihood: -109153.808
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47. Current log-likelihood: -109153.792
48. Current log-likelihood: -109153.777
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49. Current log-likelihood: -109153.761
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50. Current log-likelihood: -109153.746
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51. Current log-likelihood: -109153.730
Optimizing NNI: done in 1.37947 secs using 399.3% CPU
Iteration 90 / LogL: -57306.254 / Time: 0h:2m:38s (0h:2m:16s left)
52. Current log-likelihood: -109153.715
53. Current log-likelihood: -109153.700
Optimizing NNI: done in 1.28628 secs using 399.1% CPU
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54. Current log-likelihood: -109153.684
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56. Current log-likelihood: -109153.654
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58. Current log-likelihood: -109153.624
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59. Current log-likelihood: -109153.610
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61. Current log-likelihood: -109153.580
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65. Current log-likelihood: -109153.523
66. Current log-likelihood: -109153.509
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67. Current log-likelihood: -109153.494
68. Current log-likelihood: -109153.480
Optimizing NNI: done in 1.58759 secs using 399.5% CPU
Iteration 100 / LogL: -57299.411 / Time: 0h:2m:52s (0h:1m:56s left)
69. Current log-likelihood: -109153.466
70. Current log-likelihood: -109153.452
Optimizing NNI: done in 1.43463 secs using 399.3% CPU
Optimizing NNI: done in 4.85628 secs using 597.6% CPU
Iteration 540 / LogL: -190851.850 / Time: 0h:44m:57s (0h:1m:15s left)
71. Current log-likelihood: -109153.439
72. Current log-likelihood: -109153.425
Optimizing NNI: done in 1.62837 secs using 399.4% CPU
73. Current log-likelihood: -109153.411
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75. Current log-likelihood: -109153.384
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76. Current log-likelihood: -109153.370
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77. Current log-likelihood: -109153.356
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80. Current log-likelihood: -109153.316
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81. Current log-likelihood: -109153.305
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82. Current log-likelihood: -109153.292
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83. Current log-likelihood: -109153.278
84. Current log-likelihood: -109153.265
Optimizing NNI: done in 1.57381 secs using 398.6% CPU
Iteration 110 / LogL: -57531.975 / Time: 0h:3m:6s (0h:1m:37s left)
85. Current log-likelihood: -109153.252
Optimizing NNI: done in 1.37231 secs using 398.7% CPU
Optimizing NNI: done in 4.687 secs using 597.9% CPU
86. Current log-likelihood: -109153.239
Optimizing NNI: done in 1.1928 secs using 399.3% CPU
Optimal log-likelihood: -109153.226
Proportion of invariable sites: 0.013
Site proportion and rates:  (0.052,0.022) (0.086,0.080) (0.116,0.190) (0.110,0.317) (0.109,0.529) (0.123,0.874) (0.145,1.328) (0.174,1.901) (0.071,3.471)
Parameters optimization took 86 rounds (81.543 sec)
BEST SCORE FOUND : -109153.226
Total tree length: 174.807

Total number of iterations: 327
CPU time used for tree search: 2902.040 sec (0h:48m:22s)
Wall-clock time used for tree search: 735.707 sec (0h:12m:15s)
Total CPU time used: 3596.194 sec (0h:59m:56s)
Total wall-clock time used: 910.045 sec (0h:15m:10s)

===> START BOOTSTRAP REPLICATE NUMBER 45

Creating bootstrap alignment (seed: 68227)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.075 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105462.786
Optimizing NNI: done in 1.32399 secs using 398.9% CPU
2. Current log-likelihood: -103446.273
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Optimizing NNI: done in 4.59278 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
3. Current log-likelihood: -103369.706
Optimizing NNI: done in 1.56791 secs using 399.4% CPU
BETTER TREE FOUND at iteration 544: -190842.935
4. Current log-likelihood: -103365.423
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5. Current log-likelihood: -103364.171
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6. Current log-likelihood: -103363.385
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7. Current log-likelihood: -103362.702
Optimizing NNI: done in 1.6295 secs using 399.1% CPU
Iteration 120 / LogL: -57299.487 / Time: 0h:3m:21s (0h:1m:19s left)
8. Current log-likelihood: -103362.226
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9. Current log-likelihood: -103361.789
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10. Current log-likelihood: -103361.491
11. Current log-likelihood: -103361.331
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13. Current log-likelihood: -103361.039
Optimizing NNI: done in 4.47664 secs using 597.8% CPU
14. Current log-likelihood: -103360.873
Optimizing NNI: done in 1.52324 secs using 399.3% CPU
Optimal log-likelihood: -103360.761
Proportion of invariable sites: 0.030
Site proportion and rates:  (0.106,0.036) (0.079,0.114) (0.071,0.207) (0.069,0.311) (0.110,0.441) (0.133,0.689) (0.132,1.115) (0.206,1.857) (0.064,4.379)
Parameters optimization took 14 rounds (20.273 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.74615 secs using 398.3% CPU
Optimizing NNI: done in 1.52915 secs using 399.1% CPU
Optimizing NNI: done in 4.57284 secs using 597% CPU
Optimizing NNI: done in 1.39145 secs using 398.6% CPU
Calculating distance matrix: done in 4.70492 secs using 399.9% CPU
Computing ML distances took 4.705201 sec (of wall-clock time) 18.815854 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000699997 secs using 395.7% CPU
Constructing RapidNJ tree: done in 0.0085721 secs using 380.6% CPU
Computing RapidNJ tree took 0.009345 sec (of wall-clock time) 0.037408 sec (of CPU time)
Optimizing NNI: done in 1.60162 secs using 398.9% CPU
Log-likelihood of RapidNJ tree: -103666.169
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.27698 secs using 398.7% CPU
Iteration 130 / LogL: -57304.349 / Time: 0h:3m:36s (0h:1m:2s left)
Optimizing NNI: done in 4.78066 secs using 597.8% CPU
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Iteration 550 / LogL: -191030.543 / Time: 0h:45m:46s (0h:7m:50s left)
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10.645 second
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Iteration 140 / LogL: -57301.038 / Time: 0h:3m:51s (0h:0m:44s left)
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Optimizing NNI: done in 5.13706 secs using 597% CPU
Computing log-likelihood of 98 initial trees ... 10.111 seconds
Current best score: -103360.761

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 150 / LogL: -57299.332 / Time: 0h:4m:6s (0h:0m:28s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 154: -57296.712
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BETTER TREE FOUND at iteration 1: -102819.877
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Estimate model parameters (epsilon = 0.100)
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Iteration 160 / LogL: -57299.753 / Time: 0h:4m:22s (0h:2m:35s left)
BETTER TREE FOUND at iteration 2: -102791.773
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 4: -102747.559
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Iteration 560 / LogL: -190872.691 / Time: 0h:46m:33s (0h:6m:59s left)
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Iteration 170 / LogL: -57298.003 / Time: 0h:4m:36s (0h:2m:17s left)
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Iteration 10 / LogL: -102816.941 / Time: 0h:1m:32s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 174: -57295.513
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Iteration 180 / LogL: -57297.392 / Time: 0h:4m:52s (0h:2m:33s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 17: -102736.050
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Iteration 20 / LogL: -102763.714 / Time: 0h:1m:55s
Finish initializing candidate tree set (20)
Current best tree score: -102736.050 / CPU time: 89.702
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.48502 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.32121 secs using 597.1% CPU
BETTER TREE FOUND at iteration 190: -57294.067
Iteration 190 / LogL: -57294.067 / Time: 0h:5m:7s (0h:2m:42s left)
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BETTER TREE FOUND at iteration 195: -57294.060
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Iteration 570 / LogL: -190879.486 / Time: 0h:47m:20s (0h:6m:9s left)
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Iteration 200 / LogL: -57295.805 / Time: 0h:5m:21s (0h:2m:33s left)
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Iteration 30 / LogL: -102775.971 / Time: 0h:2m:18s (0h:6m:55s left)
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Optimizing NNI: done in 5.07661 secs using 597.2% CPU
BETTER TREE FOUND at iteration 206: -57293.129
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Iteration 210 / LogL: -57296.399 / Time: 0h:5m:37s (0h:2m:34s left)
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BETTER TREE FOUND at iteration 36: -102735.061
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Iteration 220 / LogL: -57357.112 / Time: 0h:5m:50s (0h:2m:17s left)
Optimizing NNI: done in 2.2789 secs using 398.5% CPU
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BETTER TREE FOUND at iteration 39: -102730.549
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Optimizing NNI: done in 1.32059 secs using 399.1% CPU
Optimizing NNI: done in 4.18715 secs using 597.7% CPU
BETTER TREE FOUND at iteration 40: -102727.813
Iteration 40 / LogL: -102727.813 / Time: 0h:2m:46s (0h:7m:6s left)
Optimizing NNI: done in 1.66997 secs using 398.8% CPU
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BETTER TREE FOUND at iteration 229: -57293.125
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Iteration 580 / LogL: -190869.661 / Time: 0h:48m:8s (0h:5m:19s left)
Optimizing NNI: done in 1.57275 secs using 399.3% CPU
Iteration 230 / LogL: -57300.392 / Time: 0h:6m:4s (0h:2m:37s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.71616 secs using 398.7% CPU
Optimizing NNI: done in 1.32394 secs using 399.3% CPU
BETTER TREE FOUND at iteration 49: -102727.086
Optimizing NNI: done in 1.36469 secs using 399.4% CPU
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Iteration 240 / LogL: -57299.518 / Time: 0h:6m:19s (0h:2m:21s left)
Optimizing NNI: done in 5.47313 secs using 597.8% CPU
Optimizing NNI: done in 2.28829 secs using 399% CPU
Iteration 50 / LogL: -102737.034 / Time: 0h:3m:10s (0h:6m:23s left)
Optimizing NNI: done in 1.66678 secs using 398.6% CPU
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Iteration 250 / LogL: -57308.189 / Time: 0h:6m:33s (0h:2m:4s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.89067 secs using 399.1% CPU
BETTER TREE FOUND at iteration 252: -57293.123
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BETTER TREE FOUND at iteration 57: -102722.575
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BETTER TREE FOUND at iteration 256: -57293.121
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Iteration 60 / LogL: -102736.721 / Time: 0h:3m:35s (0h:5m:54s left)
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Iteration 260 / LogL: -57302.326 / Time: 0h:6m:49s (0h:2m:31s left)
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Iteration 590 / LogL: -190883.095 / Time: 0h:48m:55s (0h:4m:29s left)
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Iteration 270 / LogL: -57301.355 / Time: 0h:7m:2s (0h:2m:15s left)
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Iteration 70 / LogL: -102738.905 / Time: 0h:3m:58s (0h:5m:0s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.46079 secs using 399% CPU
Iteration 280 / LogL: -57303.870 / Time: 0h:7m:16s (0h:1m:58s left)
BETTER TREE FOUND at iteration 73: -102722.107
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Iteration 290 / LogL: -57293.180 / Time: 0h:7m:29s (0h:1m:42s left)
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Iteration 80 / LogL: -102738.030 / Time: 0h:4m:23s (0h:5m:10s left)
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Iteration 600 / LogL: -190881.696 / Time: 0h:49m:42s (0h:3m:39s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.48515 secs using 398.7% CPU
Iteration 300 / LogL: -57296.083 / Time: 0h:7m:44s (0h:1m:26s left)
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BETTER TREE FOUND at iteration 85: -102720.382
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Iteration 90 / LogL: -102721.704 / Time: 0h:4m:46s (0h:5m:6s left)
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Iteration 310 / LogL: -57319.962 / Time: 0h:7m:57s (0h:1m:11s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 91: -102715.102
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Iteration 320 / LogL: -57297.981 / Time: 0h:8m:11s (0h:0m:55s left)
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Iteration 100 / LogL: -102758.189 / Time: 0h:5m:10s (0h:4m:45s left)
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Iteration 340 / LogL: -57422.647 / Time: 0h:8m:40s (0h:0m:24s left)
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Iteration 110 / LogL: -102732.293 / Time: 0h:5m:32s (0h:4m:6s left)
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Optimizing NNI: done in 1.36752 secs using 398.8% CPU
Optimizing NNI: done in 4.40401 secs using 597.9% CPU
Optimizing NNI: done in 1.92635 secs using 398.5% CPU
Optimizing NNI: done in 1.40249 secs using 399.4% CPU
Optimizing NNI: done in 1.02283 secs using 398.4% CPU
Iteration 350 / LogL: -57296.092 / Time: 0h:8m:53s (0h:0m:9s left)
Optimizing NNI: done in 1.31662 secs using 399.1% CPU
Optimizing NNI: done in 2.41211 secs using 398.6% CPU
Optimizing NNI: done in 4.02419 secs using 598% CPU
Optimizing NNI: done in 1.36911 secs using 399.1% CPU
Optimizing NNI: done in 2.45684 secs using 398.6% CPU
Optimizing NNI: done in 1.40555 secs using 398.9% CPU
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Optimizing NNI: done in 2.24723 secs using 398.4% CPU
Optimizing NNI: done in 4.20773 secs using 597.8% CPU
Optimizing NNI: done in 1.48486 secs using 398.5% CPU
Optimizing NNI: done in 1.85644 secs using 399.1% CPU
Optimizing NNI: done in 1.28048 secs using 399.1% CPU
Optimizing NNI: done in 1.28832 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 357 ITERATIONS / Time: 0h:9m:2s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -57293.121
Optimizing NNI: done in 1.95356 secs using 398.3% CPU
Iteration 120 / LogL: -102784.715 / Time: 0h:5m:53s (0h:3m:30s left)
2. Current log-likelihood: -57293.107
Optimal log-likelihood: -57293.093
Site proportion and rates:  (0.091,0.054) (0.125,0.165) (0.148,0.377) (0.087,0.378) (0.247,0.730) (0.153,1.516) (0.117,2.524) (0.030,5.797)
Parameters optimization took 2 rounds (1.013 sec)
BEST SCORE FOUND : -57293.093
Total tree length: 44.745

Total number of iterations: 357
CPU time used for tree search: 2112.572 sec (0h:35m:12s)
Wall-clock time used for tree search: 533.295 sec (0h:8m:53s)
Total CPU time used: 2154.914 sec (0h:35m:54s)
Total wall-clock time used: 543.894 sec (0h:9m:3s)

===> COMPUTE CONSENSUS TREE FROM 100 BOOTSTRAP TREES

Reading tree(s) file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.boottrees ...
100 tree(s) loaded (0 rooted and 100 unrooted)
0 split(s) discarded because frequency <= -1.000
1535 splits found
Consensus tree written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.contree

===> START ANALYSIS ON THE ORIGINAL ALIGNMENT


NOTE: 96 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -59438.897
Optimizing NNI: done in 4.65254 secs using 597.4% CPU
2. Current log-likelihood: -59416.189
Optimizing NNI: done in 2.16468 secs using 398.5% CPU
3. Current log-likelihood: -59404.119
Optimizing NNI: done in 2.06873 secs using 398.7% CPU
4. Current log-likelihood: -59402.681
5. Current log-likelihood: -59401.809
Optimizing NNI: done in 2.11325 secs using 398.6% CPU
Optimizing NNI: done in 5.17649 secs using 596.9% CPU
Iteration 620 / LogL: -190853.152 / Time: 0h:51m:13s (0h:1m:59s left)
6. Current log-likelihood: -59400.852
7. Current log-likelihood: -59400.113
Optimizing NNI: done in 2.14375 secs using 398.2% CPU
8. Current log-likelihood: -59399.653
9. Current log-likelihood: -59399.388
Optimizing NNI: done in 2.34836 secs using 398.3% CPU
10. Current log-likelihood: -59399.221
Optimizing NNI: done in 5.04197 secs using 597.3% CPU
11. Current log-likelihood: -59399.099
Optimizing NNI: done in 2.15844 secs using 398.8% CPU
Optimal log-likelihood: -59398.993
Site proportion and rates:  (0.120,0.069) (0.120,0.222) (0.157,0.403) (0.215,0.689) (0.143,1.089) (0.105,1.674) (0.113,2.425) (0.027,5.505)
Parameters optimization took 11 rounds (13.032 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 1.10319 secs using 400% CPU
Computing ML distances took 1.103367 sec (of wall-clock time) 4.412952 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000343084 secs using 420% CPU
Constructing RapidNJ tree: done in 0.00433397 secs using 371.3% CPU
Computing RapidNJ tree took 0.004729 sec (of wall-clock time) 0.017964 sec (of CPU time)
Optimizing NNI: done in 2.16943 secs using 398.7% CPU
Log-likelihood of RapidNJ tree: -59605.988
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.37199 secs using 596.7% CPU
Optimizing NNI: done in 1.99327 secs using 398.8% CPU
Optimizing NNI: done in 1.89849 secs using 398.7% CPU
5.073 second
Optimizing NNI: done in 4.5366 secs using 598.2% CPU
Optimizing NNI: done in 2.4957 secs using 398.8% CPU
Iteration 130 / LogL: -102726.276 / Time: 0h:6m:15s (0h:2m:57s left)
Optimizing NNI: done in 2.28061 secs using 398.6% CPU
Optimizing NNI: done in 4.90661 secs using 597.4% CPU
Optimizing NNI: done in 2.03257 secs using 398.8% CPU
Computing log-likelihood of 98 initial trees ... 7.397 seconds
Current best score: -59398.993

Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.440984 secs using 400.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.26114 secs using 398.9% CPU
BETTER TREE FOUND at iteration 1: -59398.888
Optimizing NNI: done in 2.05067 secs using 398.5% CPU
Optimizing NNI: done in 5.12971 secs using 598.1% CPU
Optimizing NNI: done in 1.79926 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.84667 secs using 398.6% CPU
BETTER TREE FOUND at iteration 2: -59382.919
Optimizing NNI: done in 1.62228 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.44806 secs using 398.5% CPU
Optimizing NNI: done in 3.95656 secs using 598.7% CPU
BETTER TREE FOUND at iteration 3: -59377.450
Optimizing NNI: done in 2.02136 secs using 398.6% CPU
Optimizing NNI: done in 1.73938 secs using 398.6% CPU
Optimizing NNI: done in 1.73711 secs using 398.6% CPU
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Optimizing NNI: done in 1.45795 secs using 399.4% CPU
Optimizing NNI: done in 2.19033 secs using 398.6% CPU
Iteration 140 / LogL: -102721.188 / Time: 0h:6m:36s (0h:2m:25s left)
Optimizing NNI: done in 1.91245 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.77647 secs using 398.4% CPU
Optimizing NNI: done in 4.85484 secs using 597.7% CPU
BETTER TREE FOUND at iteration 7: -59376.488
Optimizing NNI: done in 2.1391 secs using 399% CPU
Optimizing NNI: done in 2.35282 secs using 399.2% CPU
Optimizing NNI: done in 1.87243 secs using 398.5% CPU
Optimizing NNI: done in 1.71891 secs using 399.2% CPU
Optimizing NNI: done in 4.50622 secs using 597.6% CPU
Optimizing NNI: done in 2.2862 secs using 398.7% CPU
Optimizing NNI: done in 2.04118 secs using 399.1% CPU
Iteration 10 / LogL: -59377.612 / Time: 0h:0m:50s
Optimizing NNI: done in 1.8881 secs using 398.2% CPU
Optimizing NNI: done in 1.77979 secs using 398.7% CPU
Optimizing NNI: done in 4.40077 secs using 597.2% CPU
Iteration 630 / LogL: -190876.261 / Time: 0h:52m:0s (0h:1m:9s left)
Optimizing NNI: done in 1.76008 secs using 399.1% CPU
Optimizing NNI: done in 1.8039 secs using 398.8% CPU
Optimizing NNI: done in 1.94082 secs using 399.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.21174 secs using 398.7% CPU
Optimizing NNI: done in 4.82155 secs using 598.1% CPU
BETTER TREE FOUND at iteration 13: -59374.677
Optimizing NNI: done in 1.90044 secs using 398.9% CPU
Optimizing NNI: done in 1.70086 secs using 399% CPU
Optimizing NNI: done in 2.65021 secs using 398.6% CPU
Optimizing NNI: done in 1.67747 secs using 399.1% CPU
Optimizing NNI: done in 4.03846 secs using 598% CPU
Optimizing NNI: done in 2.12174 secs using 398.8% CPU
Iteration 150 / LogL: -102945.304 / Time: 0h:6m:57s (0h:1m:54s left)
Optimizing NNI: done in 1.86704 secs using 399.2% CPU
Optimizing NNI: done in 1.79786 secs using 399.3% CPU
Optimizing NNI: done in 2.58691 secs using 398.5% CPU
Optimizing NNI: done in 4.74445 secs using 596.9% CPU
Optimizing NNI: done in 1.89603 secs using 399.3% CPU
Optimizing NNI: done in 1.9163 secs using 398.9% CPU
Optimizing NNI: done in 1.47896 secs using 399.3% CPU
Optimizing NNI: done in 1.97602 secs using 398.8% CPU
Optimizing NNI: done in 1.85131 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 20: -59371.662
Iteration 20 / LogL: -59371.662 / Time: 0h:1m:11s
Finish initializing candidate tree set (20)
Current best tree score: -59371.662 / CPU time: 56.654
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.64516 secs using 597.1% CPU
Optimizing NNI: done in 2.03381 secs using 398.9% CPU
Optimizing NNI: done in 1.99015 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.07521 secs using 398.7% CPU
Optimizing NNI: done in 2.12707 secs using 398.2% CPU
BETTER TREE FOUND at iteration 21: -59367.264
Optimizing NNI: done in 4.63266 secs using 598.2% CPU
Optimizing NNI: done in 1.97657 secs using 398.8% CPU
Optimizing NNI: done in 2.16663 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -59367.112
Optimizing NNI: done in 2.63632 secs using 398.2% CPU
Optimizing NNI: done in 4.6939 secs using 597.6% CPU
Optimizing NNI: done in 1.94424 secs using 399.4% CPU
Optimizing NNI: done in 2.18657 secs using 398.8% CPU
Optimizing NNI: done in 2.52842 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.0476 secs using 398.1% CPU
Iteration 160 / LogL: -102718.082 / Time: 0h:7m:19s (0h:1m:25s left)
Optimizing NNI: done in 4.32445 secs using 597.7% CPU
BETTER TREE FOUND at iteration 24: -59363.523
Optimizing NNI: done in 2.30048 secs using 398.5% CPU
Optimizing NNI: done in 1.81462 secs using 399.5% CPU
Optimizing NNI: done in 1.95298 secs using 398.7% CPU
Optimizing NNI: done in 4.83937 secs using 597.3% CPU
Optimizing NNI: done in 2.31071 secs using 398.8% CPU
Optimizing NNI: done in 2.30533 secs using 398.3% CPU
Optimizing NNI: done in 2.18654 secs using 399% CPU
Optimizing NNI: done in 1.99927 secs using 398.9% CPU
Optimizing NNI: done in 4.78993 secs using 597.3% CPU
Optimizing NNI: done in 1.98679 secs using 398.6% CPU
Optimizing NNI: done in 2.87386 secs using 399.1% CPU
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Optimizing NNI: done in 2.50629 secs using 399.2% CPU
Optimizing NNI: done in 4.46936 secs using 597.7% CPU
Iteration 640 / LogL: -190882.124 / Time: 0h:52m:47s (0h:0m:19s left)
Optimizing NNI: done in 2.09064 secs using 398.6% CPU
Optimizing NNI: done in 2.61688 secs using 399.1% CPU
Iteration 30 / LogL: -59370.267 / Time: 0h:1m:41s (0h:5m:29s left)
Optimizing NNI: done in 2.27249 secs using 399.2% CPU
Optimizing NNI: done in 2.17988 secs using 399.6% CPU
Optimizing NNI: done in 4.44456 secs using 597.5% CPU
Optimizing NNI: done in 2.09013 secs using 399.1% CPU
Optimizing NNI: done in 2.60688 secs using 399% CPU
Optimizing NNI: done in 1.82629 secs using 398.7% CPU
Iteration 170 / LogL: -102749.725 / Time: 0h:7m:41s (0h:0m:57s left)
Optimizing NNI: done in 2.39141 secs using 399.4% CPU
Optimizing NNI: done in 4.41703 secs using 597.9% CPU
Optimizing NNI: done in 2.19263 secs using 399.2% CPU
Optimizing NNI: done in 2.00245 secs using 398.9% CPU
Optimizing NNI: done in 2.09288 secs using 398.4% CPU
Optimizing NNI: done in 1.83078 secs using 399.1% CPU
Optimizing NNI: done in 4.72283 secs using 597.9% CPU
Optimizing NNI: done in 2.29433 secs using 398.5% CPU
Optimizing NNI: done in 2.46968 secs using 398.9% CPU
Optimizing NNI: done in 1.87372 secs using 398.4% CPU
Optimizing NNI: done in 2.12276 secs using 399.3% CPU
Optimizing NNI: done in 2.41045 secs using 398.7% CPU
Optimizing NNI: done in 5.03455 secs using 596.8% CPU
Optimizing NNI: done in 2.12267 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.13922 secs using 398.6% CPU
BETTER TREE FOUND at iteration 38: -59359.166
Optimizing NNI: done in 2.12421 secs using 397.9% CPU
Optimizing NNI: done in 2.12619 secs using 399.3% CPU
Optimizing NNI: done in 5.05577 secs using 597.5% CPU
TREE SEARCH COMPLETED AFTER 645 ITERATIONS / Time: 0h:53m:11s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -190842.935
Optimizing NNI: done in 1.93867 secs using 398.3% CPU
Optimal log-likelihood: -190842.931
Site proportion and rates:  (0.019,0.107) (0.091,0.255) (0.118,0.387) (0.212,0.561) (0.173,0.777) (0.137,1.080) (0.152,1.681) (0.098,2.784)
Parameters optimization took 1 rounds (1.023 sec)
BEST SCORE FOUND : -190842.931
Total tree length: 153.370

Total number of iterations: 645
CPU time used for tree search: 18681.139 sec (5h:11m:21s)
Wall-clock time used for tree search: 3152.211 sec (0h:52m:32s)
Total CPU time used: 18920.837 sec (5h:15m:20s)
Total wall-clock time used: 3192.477 sec (0h:53m:12s)

===> START BOOTSTRAP REPLICATE NUMBER 26

Creating bootstrap alignment (seed: 70489)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.380 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -198657.357
Optimizing NNI: done in 2.74666 secs using 399.2% CPU
Iteration 40 / LogL: -59378.026 / Time: 0h:2m:5s (0h:5m:15s left)
Optimizing NNI: done in 2.37927 secs using 398.3% CPU
Optimizing NNI: done in 2.39739 secs using 398.6% CPU
2. Current log-likelihood: -196084.059
Optimizing NNI: done in 1.7264 secs using 398.3% CPU
Iteration 180 / LogL: -102730.459 / Time: 0h:8m:3s (0h:0m:29s left)
Optimizing NNI: done in 2.44901 secs using 399.2% CPU
3. Current log-likelihood: -196009.175
Optimizing NNI: done in 2.11317 secs using 398.5% CPU
Optimizing NNI: done in 1.75701 secs using 399.3% CPU
4. Current log-likelihood: -196004.284
Optimizing NNI: done in 2.33775 secs using 398.3% CPU
Optimizing NNI: done in 2.48139 secs using 398.8% CPU
Optimizing NNI: done in 1.77707 secs using 399% CPU
5. Current log-likelihood: -196003.916
Optimizing NNI: done in 2.09111 secs using 399.1% CPU
Optimizing NNI: done in 1.90001 secs using 398.5% CPU
Optimal log-likelihood: -196003.846
Site proportion and rates:  (0.006,0.122) (0.060,0.225) (0.103,0.351) (0.215,0.519) (0.168,0.723) (0.164,1.030) (0.194,1.615) (0.090,2.592)
Parameters optimization took 5 rounds (12.143 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.08315 secs using 399.2% CPU
Optimizing NNI: done in 1.95092 secs using 398.3% CPU
Optimizing NNI: done in 2.21898 secs using 398.6% CPU
Optimizing NNI: done in 2.36592 secs using 399.2% CPU
Optimizing NNI: done in 1.88035 secs using 398.3% CPU
Optimizing NNI: done in 2.05767 secs using 399.2% CPU
Optimizing NNI: done in 2.30719 secs using 398.3% CPU
Optimizing NNI: done in 2.79754 secs using 399.1% CPU
Calculating distance matrix: done in 9.62842 secs using 599.9% CPU
Computing ML distances took 9.628952 sec (of wall-clock time) 57.764313 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00131798 secs using 521.7% CPU
Constructing RapidNJ tree: done in 0.0228782 secs using 677.1% CPU
Computing RapidNJ tree took 0.024266 sec (of wall-clock time) 0.163400 sec (of CPU time)
Optimizing NNI: done in 2.2436 secs using 398.6% CPU
Optimizing NNI: done in 2.13744 secs using 399% CPU
Iteration 50 / LogL: -59364.251 / Time: 0h:2m:28s (0h:4m:26s left)
Log-likelihood of RapidNJ tree: -200022.965
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.00042 secs using 398.5% CPU
Iteration 190 / LogL: -102729.401 / Time: 0h:8m:24s (0h:0m:2s left)
Optimizing NNI: done in 2.27888 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -59358.930
Optimizing NNI: done in 2.69879 secs using 398.3% CPU
Optimizing NNI: done in 1.93011 secs using 398.5% CPU
TREE SEARCH COMPLETED AFTER 192 ITERATIONS / Time: 0h:8m:28s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102715.102
Optimizing NNI: done in 2.85354 secs using 398.4% CPU
2. Current log-likelihood: -102715.090
3. Current log-likelihood: -102715.079
4. Current log-likelihood: -102715.069
Optimal log-likelihood: -102715.055
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.104,0.032) (0.074,0.101) (0.083,0.200) (0.078,0.318) (0.107,0.453) (0.117,0.695) (0.140,1.087) (0.204,1.854) (0.063,4.533)
Parameters optimization took 4 rounds (3.527 sec)
BEST SCORE FOUND : -102715.055
Total tree length: 167.837

Total number of iterations: 192
CPU time used for tree search: 1891.749 sec (0h:31m:31s)
Wall-clock time used for tree search: 482.613 sec (0h:8m:2s)
Total CPU time used: 2010.193 sec (0h:33m:30s)
Total wall-clock time used: 512.310 sec (0h:8m:32s)

===> START BOOTSTRAP REPLICATE NUMBER 46

Creating bootstrap alignment (seed: 68228)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.089 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -103949.447
Optimizing NNI: done in 3.44579 secs using 398.4% CPU
2. Current log-likelihood: -101613.856
Optimizing NNI: done in 3.25107 secs using 398% CPU
3. Current log-likelihood: -101535.583
4. Current log-likelihood: -101534.811
Optimal log-likelihood: -101534.765
Proportion of invariable sites: 0.015
Site proportion and rates:  (0.099,0.036) (0.093,0.115) (0.078,0.210) (0.092,0.287) (0.124,0.421) (0.115,0.672) (0.114,1.101) (0.188,1.791) (0.082,4.259)
Parameters optimization took 4 rounds (6.723 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 3.63045 secs using 398.4% CPU
Optimizing NNI: done in 3.43583 secs using 398% CPU
Calculating distance matrix: done in 4.75117 secs using 399.9% CPU
Computing ML distances took 4.751442 sec (of wall-clock time) 19.000428 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000695944 secs using 325.7% CPU
Constructing RapidNJ tree: done in 0.00879812 secs using 385% CPU
Computing RapidNJ tree took 0.009557 sec (of wall-clock time) 0.036162 sec (of CPU time)
Log-likelihood of RapidNJ tree: -101609.363
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 3.00274 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 57: -59357.122
Optimizing NNI: done in 3.09357 secs using 398.6% CPU
30.115 second
Optimizing NNI: done in 3.52959 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 59: -59356.739
10.337 second
Optimizing NNI: done in 2.38192 secs using 399.1% CPU
Iteration 60 / LogL: -59364.510 / Time: 0h:3m:3s (0h:5m:7s left)
Optimizing NNI: done in 2.15512 secs using 398.8% CPU
Optimizing NNI: done in 2.04094 secs using 399% CPU
Optimizing NNI: done in 2.07209 secs using 399.4% CPU
Computing log-likelihood of 98 initial trees ... 9.861 seconds
Current best score: -101534.765

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.55452 secs using 399.3% CPU
Optimizing NNI: done in 2.30656 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.11202 secs using 399.2% CPU
Computing log-likelihood of 98 initial trees ... 16.485 seconds
Current best score: -196003.846

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.52111 secs using 398.7% CPU
Optimizing NNI: done in 3.29092 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.00329 secs using 399.2% CPU
Optimizing NNI: done in 2.30349 secs using 399.1% CPU
BETTER TREE FOUND at iteration 1: -195384.606
Optimizing NNI: done in 2.18387 secs using 399.2% CPU
Optimizing NNI: done in 2.26874 secs using 399.2% CPU
Iteration 70 / LogL: -59373.819 / Time: 0h:3m:25s (0h:4m:25s left)
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BETTER TREE FOUND at iteration 2: -195271.066
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Iteration 80 / LogL: -59361.769 / Time: 0h:3m:47s (0h:3m:47s left)
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BETTER TREE FOUND at iteration 3: -100813.811
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BETTER TREE FOUND at iteration 6: -195267.673
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BETTER TREE FOUND at iteration 87: -59356.689
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Iteration 90 / LogL: -59569.853 / Time: 0h:4m:11s (0h:4m:36s left)
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BETTER TREE FOUND at iteration 98: -59356.592
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Iteration 100 / LogL: -59366.505 / Time: 0h:4m:33s (0h:4m:30s left)
BETTER TREE FOUND at iteration 20: -100810.325
Iteration 20 / LogL: -100810.325 / Time: 0h:1m:57s
Finish initializing candidate tree set (20)
Current best tree score: -100810.325 / CPU time: 104.252
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 21: -100790.354
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Iteration 110 / LogL: -59359.276 / Time: 0h:4m:54s (0h:3m:57s left)
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Iteration 20 / LogL: -195390.480 / Time: 0h:2m:49s
Finish initializing candidate tree set (20)
Current best tree score: -195267.673 / CPU time: 145.411
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 30: -100777.275
Iteration 30 / LogL: -100777.275 / Time: 0h:2m:22s (0h:8m:9s left)
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BETTER TREE FOUND at iteration 23: -195242.016
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Iteration 130 / LogL: -59357.399 / Time: 0h:5m:36s (0h:2m:57s left)
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BETTER TREE FOUND at iteration 29: -195234.036
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BETTER TREE FOUND at iteration 49: -100763.363
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Iteration 30 / LogL: -195292.120 / Time: 0h:3m:42s (0h:12m:39s left)
BETTER TREE FOUND at iteration 135: -59356.539
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BETTER TREE FOUND at iteration 33: -195219.384
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Iteration 60 / LogL: -100763.851 / Time: 0h:3m:33s (0h:5m:22s left)
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Iteration 150 / LogL: -59357.023 / Time: 0h:6m:20s (0h:3m:37s left)
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Iteration 70 / LogL: -100769.629 / Time: 0h:3m:56s (0h:4m:30s left)
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Iteration 160 / LogL: -59357.189 / Time: 0h:6m:43s (0h:3m:10s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 42: -195213.254
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BETTER TREE FOUND at iteration 43: -195189.804
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Iteration 80 / LogL: -100790.735 / Time: 0h:4m:18s (0h:3m:45s left)
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Iteration 170 / LogL: -59373.291 / Time: 0h:7m:3s (0h:2m:43s left)
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BETTER TREE FOUND at iteration 90: -100762.924
Iteration 90 / LogL: -100762.924 / Time: 0h:4m:41s (0h:5m:16s left)
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Iteration 100 / LogL: -100831.751 / Time: 0h:5m:4s (0h:4m:36s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 57: -195187.746
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Iteration 110 / LogL: -100789.613 / Time: 0h:5m:26s (0h:3m:59s left)
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Iteration 200 / LogL: -59368.124 / Time: 0h:8m:7s (0h:1m:25s left)
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Iteration 60 / LogL: -195211.945 / Time: 0h:6m:10s (0h:10m:8s left)
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Iteration 120 / LogL: -100807.208 / Time: 0h:5m:48s (0h:3m:24s left)
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Iteration 210 / LogL: -59378.244 / Time: 0h:8m:29s (0h:1m:0s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.39166 secs using 399.2% CPU
BETTER TREE FOUND at iteration 130: -100762.411
Iteration 130 / LogL: -100762.411 / Time: 0h:6m:11s (0h:4m:47s left)
Optimizing NNI: done in 4.74815 secs using 597.2% CPU
Optimizing NNI: done in 2.8691 secs using 399.4% CPU
Iteration 220 / LogL: -59381.036 / Time: 0h:8m:51s (0h:0m:36s left)
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Iteration 70 / LogL: -195260.947 / Time: 0h:6m:55s (0h:8m:43s left)
Optimizing NNI: done in 2.40169 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.26106 secs using 398.9% CPU
BETTER TREE FOUND at iteration 230: -59356.531
Iteration 230 / LogL: -59356.531 / Time: 0h:9m:12s (0h:4m:1s left)
BETTER TREE FOUND at iteration 140: -100761.588
Iteration 140 / LogL: -100761.588 / Time: 0h:6m:34s (0h:4m:44s left)
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Iteration 240 / LogL: -59357.340 / Time: 0h:9m:33s (0h:3m:35s left)
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Iteration 150 / LogL: -100769.203 / Time: 0h:6m:56s (0h:4m:11s left)
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Iteration 80 / LogL: -195189.297 / Time: 0h:7m:40s (0h:7m:28s left)
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Iteration 250 / LogL: -59362.213 / Time: 0h:9m:54s (0h:3m:11s left)
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Iteration 160 / LogL: -100789.276 / Time: 0h:7m:18s (0h:3m:40s left)
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Iteration 260 / LogL: -59372.838 / Time: 0h:10m:15s (0h:2m:46s left)
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Iteration 170 / LogL: -100770.380 / Time: 0h:7m:41s (0h:3m:11s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.56044 secs using 399.1% CPU
BETTER TREE FOUND at iteration 174: -100759.450
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Iteration 90 / LogL: -195210.027 / Time: 0h:8m:27s (0h:6m:21s left)
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Iteration 270 / LogL: -59358.377 / Time: 0h:10m:37s (0h:2m:22s left)
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Iteration 180 / LogL: -100898.521 / Time: 0h:8m:5s (0h:4m:15s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 184: -100759.179
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Iteration 280 / LogL: -59385.785 / Time: 0h:10m:57s (0h:1m:57s left)
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BETTER TREE FOUND at iteration 186: -100757.899
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Iteration 190 / LogL: -100767.327 / Time: 0h:8m:32s (0h:4m:20s left)
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Iteration 100 / LogL: -195205.379 / Time: 0h:9m:12s (0h:5m:17s left)
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Iteration 290 / LogL: -59357.886 / Time: 0h:11m:19s (0h:1m:34s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 101: -195186.228
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BETTER TREE FOUND at iteration 295: -59356.525
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Iteration 200 / LogL: -100794.122 / Time: 0h:8m:53s (0h:3m:50s left)
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Iteration 300 / LogL: -59356.958 / Time: 0h:11m:40s (0h:3m:42s left)
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Iteration 210 / LogL: -100880.130 / Time: 0h:9m:14s (0h:3m:21s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 213: -100755.871
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Iteration 310 / LogL: -59374.230 / Time: 0h:12m:2s (0h:3m:18s left)
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Iteration 110 / LogL: -195295.545 / Time: 0h:10m:3s (0h:8m:23s left)
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Iteration 220 / LogL: -100765.691 / Time: 0h:9m:38s (0h:4m:5s left)
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Iteration 320 / LogL: -59356.608 / Time: 0h:12m:24s (0h:2m:55s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 115: -195184.035
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TREE SEARCH COMPLETED AFTER 396 ITERATIONS / Time: 0h:15m:13s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -59356.525
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3. Current log-likelihood: -59356.486
4. Current log-likelihood: -59356.473
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Estimate model parameters (epsilon = 0.100)
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23. Current log-likelihood: -59356.223
Optimal log-likelihood: -59356.207
Site proportion and rates:  (0.102,0.060) (0.116,0.191) (0.171,0.388) (0.218,0.683) (0.150,1.077) (0.103,1.690) (0.112,2.431) (0.028,5.350)
Parameters optimization took 23 rounds (18.924 sec)
BEST SCORE FOUND : -59356.207
Total tree length: 44.567

Total number of iterations: 396
CPU time used for tree search: 3572.380 sec (0h:59m:32s)
Wall-clock time used for tree search: 898.836 sec (0h:14m:58s)
Total CPU time used: 3706.925 sec (1h:1m:46s)
Total wall-clock time used: 932.541 sec (0h:15m:32s)
Reading input trees file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.contree
BETTER TREE FOUND at iteration 307: -100754.833
Log-likelihood of consensus tree: -59369.021

===> ASSIGN BOOTSTRAP SUPPORTS TO THE TREE FROM ORIGINAL ALIGNMENT

Reading tree /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.treefile ...
unrooted tree detected
Reading tree(s) file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.boottrees ...
100 tree(s) loaded (0 rooted and 100 unrooted)
Rescaling split weights by 1.000
1535 splits found
Creating bootstrap support values...
Tree with assigned support written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.treefile

Analysis results written to: 
  IQ-TREE report:                /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.iqtree
  Maximum-likelihood tree:       /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.treefile
  Likelihood distances:          /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.mldist
  Screen log file:               /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.log

Performing transfer bootstrap expectation...
TBE tree written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.tbe.tree
TBE statistic written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.tbe.stat

Total CPU time for bootstrap: 170238.035 seconds.
Total wall-clock time for bootstrap: 43123.837 seconds.

Non-parametric bootstrap results written to:
  Bootstrap trees:          /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.boottrees
  Consensus tree:           /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/biosynthesis.contree

Date and Time: Tue Jul  8 04:01:58 2025
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Estimate model parameters (epsilon = 0.100)
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Iteration 360 / LogL: -100884.138 / Time: 0h:14m:47s (0h:3m:27s left)
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Iteration 180 / LogL: -195206.150 / Time: 0h:15m:36s (0h:7m:45s left)
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Iteration 370 / LogL: -100756.149 / Time: 0h:15m:9s (0h:3m:2s left)
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Iteration 380 / LogL: -100785.335 / Time: 0h:15m:30s (0h:2m:37s left)
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Iteration 200 / LogL: -195203.735 / Time: 0h:17m:12s (0h:5m:57s left)
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Iteration 420 / LogL: -100755.293 / Time: 0h:16m:57s (0h:0m:58s left)
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Iteration 430 / LogL: -100767.495 / Time: 0h:17m:18s (0h:0m:33s left)
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Iteration 210 / LogL: -195240.708 / Time: 0h:18m:1s (0h:5m:5s left)
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Iteration 440 / LogL: -100766.567 / Time: 0h:17m:41s (0h:0m:9s left)
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TREE SEARCH COMPLETED AFTER 445 ITERATIONS / Time: 0h:17m:52s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -100753.888
Optimal log-likelihood: -100753.876
Proportion of invariable sites: 0.014
Site proportion and rates:  (0.089,0.029) (0.096,0.090) (0.087,0.196) (0.083,0.271) (0.130,0.391) (0.118,0.649) (0.113,1.077) (0.190,1.751) (0.078,4.689)
Parameters optimization took 1 rounds (0.764 sec)
BEST SCORE FOUND : -100753.876
Total tree length: 188.141

Total number of iterations: 445
CPU time used for tree search: 4191.447 sec (1h:9m:51s)
Wall-clock time used for tree search: 1059.570 sec (0h:17m:39s)
Total CPU time used: 4245.574 sec (1h:10m:45s)
Total wall-clock time used: 1073.114 sec (0h:17m:53s)

===> START BOOTSTRAP REPLICATE NUMBER 47

Creating bootstrap alignment (seed: 68229)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105403.183
2. Current log-likelihood: -103313.087
Optimizing NNI: done in 4.92356 secs using 597.8% CPU
3. Current log-likelihood: -103205.382
4. Current log-likelihood: -103197.684
5. Current log-likelihood: -103197.330
Optimizing NNI: done in 4.49087 secs using 596.9% CPU
Optimal log-likelihood: -103197.174
Proportion of invariable sites: 0.041
Site proportion and rates:  (0.096,0.045) (0.101,0.133) (0.049,0.230) (0.115,0.328) (0.075,0.509) (0.140,0.742) (0.178,1.288) (0.140,2.044) (0.066,4.166)
Parameters optimization took 5 rounds (8.539 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.68151 secs using 598% CPU
Calculating distance matrix: done in 4.6415 secs using 399.9% CPU
Computing ML distances took 4.641793 sec (of wall-clock time) 18.562351 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000721931 secs using 92.81% CPU
Constructing RapidNJ tree: done in 0.008636 secs using 390% CPU
Computing RapidNJ tree took 0.009419 sec (of wall-clock time) 0.035222 sec (of CPU time)
Log-likelihood of RapidNJ tree: -103471.858
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.6632 secs using 597.1% CPU
Optimizing NNI: done in 4.68771 secs using 597.7% CPU
Iteration 220 / LogL: -195259.460 / Time: 0h:18m:48s (0h:4m:12s left)
10.440 second
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Optimizing NNI: done in 4.11945 secs using 597% CPU
Computing log-likelihood of 98 initial trees ... 10.033 seconds
Current best score: -103197.174

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -102696.432
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -102694.075
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Estimate model parameters (epsilon = 0.100)
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Iteration 230 / LogL: -195216.322 / Time: 0h:19m:34s (0h:3m:19s left)
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BETTER TREE FOUND at iteration 4: -102651.567
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -102641.261
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 7: -102614.164
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Iteration 10 / LogL: -102633.661 / Time: 0h:1m:44s
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Iteration 240 / LogL: -195207.381 / Time: 0h:20m:19s (0h:2m:27s left)
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Iteration 20 / LogL: -102663.734 / Time: 0h:2m:7s
Finish initializing candidate tree set (20)
Current best tree score: -102614.164 / CPU time: 113.654
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 24: -102603.292
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -102585.461
Iteration 30 / LogL: -102585.461 / Time: 0h:2m:35s (0h:8m:56s left)
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Iteration 250 / LogL: -195172.774 / Time: 0h:21m:9s (0h:1m:36s left)
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Iteration 40 / LogL: -102602.958 / Time: 0h:2m:56s (0h:6m:47s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 47: -102584.678
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Iteration 50 / LogL: -102591.983 / Time: 0h:3m:21s (0h:6m:39s left)
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Iteration 260 / LogL: -195178.092 / Time: 0h:21m:55s (0h:0m:45s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.73929 secs using 597.2% CPU
BETTER TREE FOUND at iteration 55: -102584.340
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Iteration 60 / LogL: -102639.338 / Time: 0h:3m:48s (0h:6m:7s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 62: -102574.908
Optimizing NNI: done in 4.65326 secs using 597.4% CPU
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Iteration 70 / LogL: -102634.916 / Time: 0h:4m:13s (0h:5m:38s left)
Optimizing NNI: done in 4.41738 secs using 597.5% CPU
Iteration 270 / LogL: -195178.842 / Time: 0h:22m:41s (0h:0m:-6s left)
TREE SEARCH COMPLETED AFTER 270 ITERATIONS / Time: 0h:22m:41s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -195170.486
Optimizing NNI: done in 2.11006 secs using 397.8% CPU
Optimal log-likelihood: -195170.480
Site proportion and rates:  (0.006,0.122) (0.061,0.228) (0.113,0.360) (0.214,0.527) (0.168,0.738) (0.160,1.041) (0.189,1.623) (0.090,2.624)
Parameters optimization took 1 rounds (1.177 sec)
BEST SCORE FOUND : -195170.480
Total tree length: 153.055

Total number of iterations: 270
CPU time used for tree search: 7837.305 sec (2h:10m:37s)
Wall-clock time used for tree search: 1336.973 sec (0h:22m:16s)
Total CPU time used: 7987.840 sec (2h:13m:7s)
Total wall-clock time used: 1362.309 sec (0h:22m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 27

Creating bootstrap alignment (seed: 70490)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.291 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -193213.847
Optimizing NNI: done in 2.18773 secs using 398.3% CPU
2. Current log-likelihood: -190598.767
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3. Current log-likelihood: -190573.127
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Estimate model parameters (epsilon = 0.100)
4. Current log-likelihood: -190571.685
BETTER TREE FOUND at iteration 74: -102571.106
5. Current log-likelihood: -190570.684
6. Current log-likelihood: -190570.038
Optimizing NNI: done in 2.35172 secs using 399% CPU
7. Current log-likelihood: -190569.594
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8. Current log-likelihood: -190569.270
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9. Current log-likelihood: -190569.023
10. Current log-likelihood: -190568.801
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11. Current log-likelihood: -190568.596
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12. Current log-likelihood: -190568.406
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Iteration 80 / LogL: -102592.582 / Time: 0h:4m:38s (0h:5m:31s left)
13. Current log-likelihood: -190568.236
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14. Current log-likelihood: -190568.074
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15. Current log-likelihood: -190567.933
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16. Current log-likelihood: -190567.805
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17. Current log-likelihood: -190567.703
Optimizing NNI: done in 2.39478 secs using 398.5% CPU
Optimal log-likelihood: -190567.608
Site proportion and rates:  (0.016,0.095) (0.078,0.260) (0.105,0.391) (0.169,0.534) (0.194,0.732) (0.168,0.969) (0.136,1.506) (0.132,2.540)
Parameters optimization took 17 rounds (33.202 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 9.98273 secs using 599.9% CPU
Computing ML distances took 9.983277 sec (of wall-clock time) 59.889816 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00116086 secs using 584.3% CPU
Constructing RapidNJ tree: done in 0.0220799 secs using 677.7% CPU
Computing RapidNJ tree took 0.023291 sec (of wall-clock time) 0.157776 sec (of CPU time)
Optimizing NNI: done in 2.27372 secs using 398.6% CPU
Iteration 90 / LogL: -102631.029 / Time: 0h:5m:0s (0h:4m:43s left)
Log-likelihood of RapidNJ tree: -195253.910
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 3.00748 secs using 398.2% CPU
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Iteration 100 / LogL: -102609.471 / Time: 0h:5m:29s (0h:4m:5s left)
29.815 second
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Computing log-likelihood of 98 initial trees ... 16.049 seconds
Current best score: -190567.608

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 110 / LogL: -102620.308 / Time: 0h:5m:50s (0h:3m:25s left)
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BETTER TREE FOUND at iteration 1: -189893.143
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Iteration 20 / LogL: -189842.745 / Time: 0h:3m:5s
Finish initializing candidate tree set (20)
Current best tree score: -189753.180 / CPU time: 140.274
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 4.52318 secs using 597.6% CPU
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Optimizing NNI: done in 2.09541 secs using 398.1% CPU
Optimizing NNI: done in 1.92881 secs using 398% CPU
Optimizing NNI: done in 4.25835 secs using 597.4% CPU
Optimizing NNI: done in 2.38839 secs using 398.5% CPU
Iteration 260 / LogL: -102564.138 / Time: 0h:11m:49s (0h:3m:58s left)
Optimizing NNI: done in 4.20769 secs using 597.6% CPU
Optimizing NNI: done in 2.15442 secs using 398.7% CPU
Optimizing NNI: done in 2.74179 secs using 398.4% CPU
Optimizing NNI: done in 4.64114 secs using 596.8% CPU
Optimizing NNI: done in 2.23115 secs using 397.9% CPU
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Optimizing NNI: done in 4.66218 secs using 597.7% CPU
Optimizing NNI: done in 2.44173 secs using 398.5% CPU
Optimizing NNI: done in 1.95835 secs using 398.3% CPU
Optimizing NNI: done in 4.0778 secs using 597.7% CPU
Iteration 80 / LogL: -189722.517 / Time: 0h:7m:49s (0h:8m:36s left)
Optimizing NNI: done in 2.18201 secs using 398.6% CPU
Optimizing NNI: done in 2.02402 secs using 398.1% CPU
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Optimizing NNI: done in 2.42916 secs using 398.1% CPU
Optimizing NNI: done in 1.95592 secs using 398.9% CPU
Iteration 270 / LogL: -102573.813 / Time: 0h:12m:12s (0h:3m:29s left)
Optimizing NNI: done in 4.45116 secs using 597.9% CPU
Optimizing NNI: done in 2.47814 secs using 398.1% CPU
Optimizing NNI: done in 2.25507 secs using 398.2% CPU
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Optimizing NNI: done in 2.49284 secs using 398.5% CPU
Optimizing NNI: done in 2.33527 secs using 398.3% CPU
Optimizing NNI: done in 4.20759 secs using 598.2% CPU
Optimizing NNI: done in 1.98226 secs using 398% CPU
Optimizing NNI: done in 2.21489 secs using 398.7% CPU
Optimizing NNI: done in 4.32532 secs using 597.6% CPU
Optimizing NNI: done in 1.81909 secs using 398.7% CPU
Optimizing NNI: done in 2.12856 secs using 398.4% CPU
Optimizing NNI: done in 3.90087 secs using 597% CPU
Optimizing NNI: done in 2.52422 secs using 398.5% CPU
Optimizing NNI: done in 2.13591 secs using 398.2% CPU
Iteration 280 / LogL: -102657.148 / Time: 0h:12m:35s (0h:3m:1s left)
Optimizing NNI: done in 4.4656 secs using 597.8% CPU
Optimizing NNI: done in 2.10954 secs using 398.4% CPU
Optimizing NNI: done in 2.35573 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 282: -102558.073
Optimizing NNI: done in 4.77486 secs using 596.7% CPU
Optimizing NNI: done in 2.51012 secs using 398% CPU
Optimizing NNI: done in 2.10651 secs using 398.8% CPU
Optimizing NNI: done in 4.81516 secs using 597.6% CPU
Optimizing NNI: done in 2.29032 secs using 398.3% CPU
Optimizing NNI: done in 1.80794 secs using 398.6% CPU
Optimizing NNI: done in 4.57756 secs using 597.6% CPU
Iteration 90 / LogL: -189701.277 / Time: 0h:8m:34s (0h:7m:24s left)
Optimizing NNI: done in 2.27908 secs using 398.2% CPU
Optimizing NNI: done in 2.52674 secs using 397.9% CPU
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Optimizing NNI: done in 2.3068 secs using 398.3% CPU
Optimizing NNI: done in 2.27168 secs using 398% CPU
Iteration 290 / LogL: -102576.312 / Time: 0h:12m:58s (0h:4m:7s left)
Optimizing NNI: done in 4.70434 secs using 597.6% CPU
Optimizing NNI: done in 1.90435 secs using 398.1% CPU
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Iteration 300 / LogL: -102578.867 / Time: 0h:13m:21s (0h:3m:39s left)
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Optimizing NNI: done in 2.08681 secs using 398.7% CPU
Optimizing NNI: done in 4.3801 secs using 597.2% CPU
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Optimizing NNI: done in 2.33961 secs using 398.5% CPU
Optimizing NNI: done in 4.29208 secs using 597.5% CPU
Iteration 100 / LogL: -189717.711 / Time: 0h:9m:17s (0h:6m:17s left)
Optimizing NNI: done in 2.31271 secs using 398.6% CPU
Optimizing NNI: done in 2.31537 secs using 398% CPU
Optimizing NNI: done in 5.11182 secs using 598.5% CPU
Optimizing NNI: done in 2.04652 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 308: -102557.918
Optimizing NNI: done in 2.08708 secs using 398.2% CPU
Optimizing NNI: done in 3.99664 secs using 597.5% CPU
Optimizing NNI: done in 2.22807 secs using 398.3% CPU
Iteration 310 / LogL: -102585.214 / Time: 0h:13m:45s (0h:4m:21s left)
Optimizing NNI: done in 3.61627 secs using 597.9% CPU
Optimizing NNI: done in 2.04112 secs using 398% CPU
Optimizing NNI: done in 2.28022 secs using 399.1% CPU
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Optimizing NNI: done in 2.00123 secs using 398.4% CPU
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Optimizing NNI: done in 2.58637 secs using 397.7% CPU
Iteration 320 / LogL: -102598.098 / Time: 0h:14m:9s (0h:3m:54s left)
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Iteration 110 / LogL: -189769.900 / Time: 0h:9m:59s (0h:5m:13s left)
Optimizing NNI: done in 2.60204 secs using 398.7% CPU
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Iteration 330 / LogL: -102563.132 / Time: 0h:14m:32s (0h:3m:26s left)
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Optimizing NNI: done in 2.36904 secs using 398.4% CPU
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Optimizing NNI: done in 5.53235 secs using 597.9% CPU
Optimizing NNI: done in 1.99405 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 334: -102556.093
Optimizing NNI: done in 4.14477 secs using 597.5% CPU
Optimizing NNI: done in 2.03459 secs using 398.7% CPU
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Iteration 340 / LogL: -102572.253 / Time: 0h:14m:56s (0h:4m:8s left)
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Optimizing NNI: done in 4.77731 secs using 597.7% CPU
Iteration 120 / LogL: -189689.416 / Time: 0h:10m:45s (0h:4m:14s left)
Optimizing NNI: done in 2.37691 secs using 399% CPU
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Iteration 350 / LogL: -102592.478 / Time: 0h:15m:18s (0h:3m:41s left)
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Iteration 360 / LogL: -102651.498 / Time: 0h:15m:41s (0h:3m:14s left)
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Iteration 370 / LogL: -102567.398 / Time: 0h:16m:4s (0h:2m:47s left)
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Optimizing NNI: done in 7.90788 secs using 597.9% CPU
Iteration 130 / LogL: -189766.169 / Time: 0h:11m:52s (0h:3m:24s left)
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Iteration 380 / LogL: -102626.840 / Time: 0h:16m:26s (0h:2m:20s left)
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Optimizing NNI: done in 2.1818 secs using 398.6% CPU
Iteration 390 / LogL: -102556.335 / Time: 0h:16m:48s (0h:1m:54s left)
Optimizing NNI: done in 3.86073 secs using 598% CPU
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Optimizing NNI: done in 2.71855 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 393: -102555.651
Optimizing NNI: done in 4.81921 secs using 595.1% CPU
Iteration 140 / LogL: -189694.123 / Time: 0h:12m:42s (0h:2m:28s left)
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Iteration 400 / LogL: -102559.361 / Time: 0h:17m:11s (0h:4m:0s left)
Optimizing NNI: done in 4.17481 secs using 597% CPU
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Iteration 410 / LogL: -102629.771 / Time: 0h:17m:33s (0h:3m:33s left)
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Iteration 150 / LogL: -189697.922 / Time: 0h:13m:25s (0h:1m:31s left)
Optimizing NNI: done in 2.52317 secs using 398.5% CPU
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Iteration 420 / LogL: -102615.325 / Time: 0h:17m:54s (0h:3m:7s left)
Optimizing NNI: done in 2.0618 secs using 398.1% CPU
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Iteration 430 / LogL: -102643.831 / Time: 0h:18m:17s (0h:2m:41s left)
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Iteration 160 / LogL: -189709.525 / Time: 0h:14m:10s (0h:0m:37s left)
Optimizing NNI: done in 2.36235 secs using 398.2% CPU
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Optimizing NNI: done in 2.1599 secs using 398.6% CPU
Iteration 440 / LogL: -102585.386 / Time: 0h:18m:39s (0h:2m:15s left)
Optimizing NNI: done in 4.33041 secs using 597.7% CPU
Optimizing NNI: done in 2.16264 secs using 398.3% CPU
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Optimizing NNI: done in 4.70135 secs using 597.3% CPU
TREE SEARCH COMPLETED AFTER 168 ITERATIONS / Time: 0h:14m:44s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -189684.004
Optimizing NNI: done in 1.88395 secs using 398.2% CPU
Iteration 450 / LogL: -102718.202 / Time: 0h:19m:1s (0h:1m:49s left)
Optimal log-likelihood: -189684.002
Site proportion and rates:  (0.016,0.096) (0.082,0.266) (0.113,0.397) (0.182,0.551) (0.188,0.755) (0.152,0.995) (0.139,1.528) (0.126,2.570)
Parameters optimization took 1 rounds (0.712 sec)
BEST SCORE FOUND : -189684.002
Total tree length: 154.275

Total number of iterations: 168
CPU time used for tree search: 4868.672 sec (1h:21m:8s)
Wall-clock time used for tree search: 839.681 sec (0h:13m:59s)
Total CPU time used: 5143.177 sec (1h:25m:43s)
Total wall-clock time used: 885.712 sec (0h:14m:45s)

===> START BOOTSTRAP REPLICATE NUMBER 28

Creating bootstrap alignment (seed: 70491)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.286 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -197206.650
Optimizing NNI: done in 2.0556 secs using 398.2% CPU
2. Current log-likelihood: -194416.633
Optimizing NNI: done in 2.2878 secs using 398.3% CPU
3. Current log-likelihood: -194384.646
Optimizing NNI: done in 2.34476 secs using 398.4% CPU
4. Current log-likelihood: -194383.238
Optimizing NNI: done in 2.50967 secs using 398.4% CPU
5. Current log-likelihood: -194382.343
Optimizing NNI: done in 2.42655 secs using 398.1% CPU
6. Current log-likelihood: -194381.627
Optimizing NNI: done in 2.10518 secs using 398.7% CPU
7. Current log-likelihood: -194381.016
Optimizing NNI: done in 2.21141 secs using 399.1% CPU
8. Current log-likelihood: -194380.477
Optimizing NNI: done in 1.90487 secs using 398.4% CPU
9. Current log-likelihood: -194379.965
Optimizing NNI: done in 2.20397 secs using 398% CPU
10. Current log-likelihood: -194379.487
Optimizing NNI: done in 1.83704 secs using 398.6% CPU
Iteration 460 / LogL: -102746.039 / Time: 0h:19m:23s (0h:1m:23s left)
11. Current log-likelihood: -194379.074
Optimizing NNI: done in 1.86025 secs using 397.9% CPU
12. Current log-likelihood: -194378.761
13. Current log-likelihood: -194378.566
Optimizing NNI: done in 2.63294 secs using 398.5% CPU
Optimal log-likelihood: -194378.461
Site proportion and rates:  (0.009,0.065) (0.094,0.233) (0.139,0.374) (0.172,0.565) (0.169,0.785) (0.148,1.039) (0.166,1.592) (0.103,2.685)
Parameters optimization took 13 rounds (28.282 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.09038 secs using 398.2% CPU
Optimizing NNI: done in 2.02849 secs using 398.2% CPU
Optimizing NNI: done in 2.01255 secs using 398.6% CPU
Optimizing NNI: done in 2.28438 secs using 398.2% CPU
Optimizing NNI: done in 2.03217 secs using 398.8% CPU
Optimizing NNI: done in 1.86378 secs using 398.5% CPU
Calculating distance matrix: done in 10.584 secs using 599.8% CPU
Computing ML distances took 10.584631 sec (of wall-clock time) 63.488636 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00144887 secs using 709.2% CPU
Constructing RapidNJ tree: done in 0.0226779 secs using 672.9% CPU
Computing RapidNJ tree took 0.024213 sec (of wall-clock time) 0.162954 sec (of CPU time)
Optimizing NNI: done in 1.74097 secs using 398.5% CPU
Optimizing NNI: done in 2.02336 secs using 398% CPU
Iteration 470 / LogL: -102633.239 / Time: 0h:19m:44s (0h:0m:58s left)
Log-likelihood of RapidNJ tree: -198057.330
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|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.2372 secs using 398.5% CPU
Optimizing NNI: done in 2.29924 secs using 399.1% CPU
Optimizing NNI: done in 1.88049 secs using 398.8% CPU
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Optimizing NNI: done in 2.12397 secs using 398.6% CPU
Iteration 480 / LogL: -102557.957 / Time: 0h:20m:6s (0h:0m:32s left)
Optimizing NNI: done in 2.35692 secs using 398.1% CPU
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Optimizing NNI: done in 2.25587 secs using 399% CPU
30.489 second
Optimizing NNI: done in 1.89412 secs using 398.8% CPU
Optimizing NNI: done in 2.28957 secs using 398.9% CPU
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Optimizing NNI: done in 2.11469 secs using 398.3% CPU
Optimizing NNI: done in 2.19328 secs using 398.7% CPU
Iteration 490 / LogL: -102561.406 / Time: 0h:20m:27s (0h:0m:7s left)
Optimizing NNI: done in 2.15154 secs using 398.3% CPU
Optimizing NNI: done in 2.21621 secs using 398.6% CPU
Computing log-likelihood of 98 initial trees ... 16.276 seconds
Current best score: -194378.461

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.19 secs using 398.1% CPU
Optimizing NNI: done in 1.99024 secs using 398.3% CPU
TREE SEARCH COMPLETED AFTER 494 ITERATIONS / Time: 0h:20m:36s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102555.651
Optimal log-likelihood: -102555.639
Proportion of invariable sites: 0.040
Site proportion and rates:  (0.080,0.036) (0.107,0.105) (0.053,0.200) (0.117,0.308) (0.076,0.470) (0.146,0.710) (0.172,1.261) (0.144,1.979) (0.064,4.636)
Parameters optimization took 1 rounds (0.779 sec)
BEST SCORE FOUND : -102555.639
Total tree length: 169.963

Total number of iterations: 494
CPU time used for tree search: 4836.129 sec (1h:20m:36s)
Wall-clock time used for tree search: 1221.854 sec (0h:20m:21s)
Total CPU time used: 4896.432 sec (1h:21m:36s)
Total wall-clock time used: 1236.953 sec (0h:20m:36s)

===> START BOOTSTRAP REPLICATE NUMBER 48

Creating bootstrap alignment (seed: 68230)...

Optimizing NNI: done in 3.62063 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.103 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -109577.603
2. Current log-likelihood: -107652.892
3. Current log-likelihood: -107536.863
BETTER TREE FOUND at iteration 1: -193692.715
4. Current log-likelihood: -107524.997
5. Current log-likelihood: -107523.689
Optimizing NNI: done in 3.44511 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
6. Current log-likelihood: -107523.169
7. Current log-likelihood: -107522.716
8. Current log-likelihood: -107522.407
9. Current log-likelihood: -107522.203
10. Current log-likelihood: -107522.039
BETTER TREE FOUND at iteration 2: -193626.796
11. Current log-likelihood: -107521.860
Optimal log-likelihood: -107521.716
Proportion of invariable sites: 0.026
Site proportion and rates:  (0.094,0.038) (0.091,0.121) (0.062,0.243) (0.050,0.274) (0.137,0.459) (0.171,0.776) (0.137,1.290) (0.167,1.949) (0.066,3.928)
Parameters optimization took 11 rounds (15.045 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.34927 secs using 596.7% CPU
Calculating distance matrix: done in 4.62647 secs using 399.9% CPU
Computing ML distances took 4.626731 sec (of wall-clock time) 18.504100 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000740051 secs using 53.24% CPU
Constructing RapidNJ tree: done in 0.00852609 secs using 393.9% CPU
Computing RapidNJ tree took 0.009324 sec (of wall-clock time) 0.034773 sec (of CPU time)
Log-likelihood of RapidNJ tree: -107413.003
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.88724 secs using 596.9% CPU
Optimizing NNI: done in 6.43373 secs using 597% CPU
10.684 second
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Optimizing NNI: done in 4.34725 secs using 596.9% CPU
Computing log-likelihood of 98 initial trees ... 9.842 seconds
Current best score: -107413.003

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.01774 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.93249 secs using 596.3% CPU
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Optimizing NNI: done in 4.64205 secs using 596.5% CPU
Iteration 10 / LogL: -193674.054 / Time: 0h:2m:29s
BETTER TREE FOUND at iteration 1: -106678.131
Optimizing NNI: done in 2.81627 secs using 398.5% CPU
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 5: -106658.374
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.14227 secs using 597.3% CPU
BETTER TREE FOUND at iteration 10: -106629.677
Iteration 10 / LogL: -106629.677 / Time: 0h:1m:27s
Optimizing NNI: done in 4.47713 secs using 597.7% CPU
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Iteration 20 / LogL: -193655.593 / Time: 0h:3m:18s
Finish initializing candidate tree set (20)
Current best tree score: -193626.796 / CPU time: 153.920
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 2.24276 secs using 398.4% CPU
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Iteration 20 / LogL: -106648.317 / Time: 0h:1m:53s
Finish initializing candidate tree set (20)
Current best tree score: -106629.677 / CPU time: 92.768
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -106604.841
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -106603.384
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Iteration 30 / LogL: -106746.911 / Time: 0h:2m:19s (0h:7m:38s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 30: -193602.483
Iteration 30 / LogL: -193602.483 / Time: 0h:4m:12s (0h:14m:29s left)
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Iteration 40 / LogL: -106624.027 / Time: 0h:2m:41s (0h:5m:51s left)
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Iteration 50 / LogL: -106657.754 / Time: 0h:3m:1s (0h:4m:37s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 53: -106602.570
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 57: -106600.073
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Iteration 40 / LogL: -193793.472 / Time: 0h:5m:7s (0h:12m:50s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 80 / LogL: -106742.212 / Time: 0h:4m:6s (0h:4m:0s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.84016 secs using 398.7% CPU
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Iteration 50 / LogL: -193685.300 / Time: 0h:6m:0s (0h:11m:52s left)
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Iteration 100 / LogL: -106601.587 / Time: 0h:4m:46s (0h:2m:44s left)
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Iteration 110 / LogL: -106632.197 / Time: 0h:5m:4s (0h:2m:11s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 60: -193569.236
Iteration 60 / LogL: -193569.236 / Time: 0h:6m:53s (0h:11m:40s left)
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Iteration 120 / LogL: -106605.414 / Time: 0h:5m:25s (0h:1m:41s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 123: -106598.296
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BETTER TREE FOUND at iteration 116: -193561.951
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Iteration 280 / LogL: -106627.586 / Time: 0h:10m:59s (0h:0m:7s left)
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TREE SEARCH COMPLETED AFTER 284 ITERATIONS / Time: 0h:11m:7s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106596.212
Optimizing NNI: done in 5.0548 secs using 597.3% CPU
2. Current log-likelihood: -106596.167
3. Current log-likelihood: -106596.099
4. Current log-likelihood: -106596.034
5. Current log-likelihood: -106595.983
6. Current log-likelihood: -106595.934
Optimizing NNI: done in 4.93518 secs using 598.1% CPU
7. Current log-likelihood: -106595.893
8. Current log-likelihood: -106595.857
9. Current log-likelihood: -106595.826
10. Current log-likelihood: -106595.807
11. Current log-likelihood: -106595.787
12. Current log-likelihood: -106595.768
13. Current log-likelihood: -106595.749
14. Current log-likelihood: -106595.730
Optimizing NNI: done in 6.35139 secs using 596.9% CPU
15. Current log-likelihood: -106595.712
16. Current log-likelihood: -106595.694
17. Current log-likelihood: -106595.676
18. Current log-likelihood: -106595.659
19. Current log-likelihood: -106595.642
20. Current log-likelihood: -106595.625
21. Current log-likelihood: -106595.609
22. Current log-likelihood: -106595.593
23. Current log-likelihood: -106595.578
Optimizing NNI: done in 5.86659 secs using 597.4% CPU
Iteration 130 / LogL: -193633.358 / Time: 0h:13m:0s (0h:8m:40s left)
24. Current log-likelihood: -106595.563
25. Current log-likelihood: -106595.548
26. Current log-likelihood: -106595.533
27. Current log-likelihood: -106595.519
28. Current log-likelihood: -106595.505
29. Current log-likelihood: -106595.490
30. Current log-likelihood: -106595.476
31. Current log-likelihood: -106595.463
32. Current log-likelihood: -106595.449
Optimizing NNI: done in 6.31737 secs using 597.3% CPU
33. Current log-likelihood: -106595.436
34. Current log-likelihood: -106595.423
35. Current log-likelihood: -106595.411
36. Current log-likelihood: -106595.398
37. Current log-likelihood: -106595.386
38. Current log-likelihood: -106595.373
39. Current log-likelihood: -106595.362
Optimizing NNI: done in 4.81115 secs using 596.8% CPU
40. Current log-likelihood: -106595.351
41. Current log-likelihood: -106595.340
42. Current log-likelihood: -106595.329
Optimal log-likelihood: -106595.315
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.095,0.033) (0.085,0.114) (0.105,0.239) (0.026,0.305) (0.136,0.476) (0.163,0.806) (0.142,1.312) (0.157,1.962) (0.065,4.034)
Parameters optimization took 42 rounds (31.273 sec)
BEST SCORE FOUND : -106595.315
Total tree length: 162.769

Total number of iterations: 284
CPU time used for tree search: 2547.145 sec (0h:42m:27s)
Wall-clock time used for tree search: 646.758 sec (0h:10m:46s)
Total CPU time used: 2754.562 sec (0h:45m:54s)
Total wall-clock time used: 698.800 sec (0h:11m:38s)

===> START BOOTSTRAP REPLICATE NUMBER 49

Creating bootstrap alignment (seed: 68231)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.114 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -102323.578
2. Current log-likelihood: -100291.821
Optimizing NNI: done in 5.35331 secs using 597.1% CPU
3. Current log-likelihood: -100213.408
4. Current log-likelihood: -100210.325
5. Current log-likelihood: -100209.809
6. Current log-likelihood: -100209.529
Optimizing NNI: done in 5.37755 secs using 597.7% CPU
7. Current log-likelihood: -100209.405
Optimal log-likelihood: -100209.252
Proportion of invariable sites: 0.023
Site proportion and rates:  (0.125,0.040) (0.109,0.127) (0.079,0.224) (0.105,0.351) (0.099,0.524) (0.122,0.845) (0.111,1.290) (0.156,2.042) (0.071,4.333)
Parameters optimization took 7 rounds (11.332 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 5.30572 secs using 597.2% CPU
Calculating distance matrix: done in 4.64541 secs using 399.9% CPU
Computing ML distances took 4.645775 sec (of wall-clock time) 18.580227 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000703096 secs using 396.1% CPU
Constructing RapidNJ tree: done in 0.00887108 secs using 344.9% CPU
Computing RapidNJ tree took 0.009633 sec (of wall-clock time) 0.035744 sec (of CPU time)
Log-likelihood of RapidNJ tree: -100519.051
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.6787 secs using 597.2% CPU
Optimizing NNI: done in 5.82454 secs using 597.4% CPU
10.284 second
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Optimizing NNI: done in 4.27907 secs using 596.4% CPU
Computing log-likelihood of 98 initial trees ... 9.967 seconds
Current best score: -100209.252

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.38582 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
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Iteration 140 / LogL: -193625.525 / Time: 0h:13m:54s (0h:7m:36s left)
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BETTER TREE FOUND at iteration 1: -99823.921
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -99720.391
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -99705.048
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Iteration 10 / LogL: -99719.998 / Time: 0h:1m:31s
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Iteration 20 / LogL: -99758.571 / Time: 0h:1m:50s
Finish initializing candidate tree set (20)
Current best tree score: -99705.048 / CPU time: 93.377
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 171: -193554.841
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Iteration 120 / LogL: -99700.655 / Time: 0h:5m:30s (0h:1m:3s left)
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Iteration 130 / LogL: -99675.330 / Time: 0h:5m:49s (0h:0m:35s left)
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Iteration 200 / LogL: -193614.322 / Time: 0h:19m:8s (0h:6m:49s left)
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Iteration 140 / LogL: -99666.135 / Time: 0h:6m:9s (0h:0m:7s left)
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TREE SEARCH COMPLETED AFTER 144 ITERATIONS / Time: 0h:6m:18s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -99666.043
2. Current log-likelihood: -99666.004
3. Current log-likelihood: -99665.964
4. Current log-likelihood: -99665.931
5. Current log-likelihood: -99665.911
6. Current log-likelihood: -99665.874
Optimizing NNI: done in 7.65065 secs using 597% CPU
7. Current log-likelihood: -99665.844
8. Current log-likelihood: -99665.823
9. Current log-likelihood: -99665.793
10. Current log-likelihood: -99665.772
11. Current log-likelihood: -99665.745
Optimizing NNI: done in 5.65943 secs using 597.3% CPU
12. Current log-likelihood: -99665.726
13. Current log-likelihood: -99665.709
14. Current log-likelihood: -99665.692
15. Current log-likelihood: -99665.675
Optimizing NNI: done in 4.79233 secs using 597.5% CPU
16. Current log-likelihood: -99665.657
17. Current log-likelihood: -99665.641
18. Current log-likelihood: -99665.623
19. Current log-likelihood: -99665.608
20. Current log-likelihood: -99665.592
21. Current log-likelihood: -99665.577
Optimizing NNI: done in 5.3354 secs using 597.8% CPU
22. Current log-likelihood: -99665.563
23. Current log-likelihood: -99665.548
24. Current log-likelihood: -99665.535
25. Current log-likelihood: -99665.523
26. Current log-likelihood: -99665.510
Optimizing NNI: done in 5.15951 secs using 597.4% CPU
27. Current log-likelihood: -99665.495
28. Current log-likelihood: -99665.482
29. Current log-likelihood: -99665.470
30. Current log-likelihood: -99665.459
31. Current log-likelihood: -99665.447
32. Current log-likelihood: -99665.435
Optimizing NNI: done in 5.50956 secs using 597% CPU
Iteration 210 / LogL: -193657.998 / Time: 0h:20m:4s (0h:5m:51s left)
33. Current log-likelihood: -99665.421
Optimal log-likelihood: -99665.406
Proportion of invariable sites: 0.021
Site proportion and rates:  (0.116,0.032) (0.112,0.112) (0.094,0.220) (0.105,0.353) (0.093,0.527) (0.103,0.823) (0.121,1.214) (0.164,2.014) (0.070,4.475)
Parameters optimization took 33 rounds (33.927 sec)
BEST SCORE FOUND : -99665.406
Total tree length: 152.495

Total number of iterations: 144
CPU time used for tree search: 1409.005 sec (0h:23m:29s)
Wall-clock time used for tree search: 361.104 sec (0h:6m:1s)
Total CPU time used: 1612.386 sec (0h:26m:52s)
Total wall-clock time used: 412.143 sec (0h:6m:52s)

===> START BOOTSTRAP REPLICATE NUMBER 50

Creating bootstrap alignment (seed: 68232)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.117 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105408.072
2. Current log-likelihood: -103523.842
3. Current log-likelihood: -103456.928
Optimizing NNI: done in 5.42048 secs using 597.4% CPU
4. Current log-likelihood: -103397.248
5. Current log-likelihood: -103390.170
6. Current log-likelihood: -103388.945
Optimizing NNI: done in 5.34181 secs using 597.3% CPU
7. Current log-likelihood: -103388.141
8. Current log-likelihood: -103387.574
9. Current log-likelihood: -103387.107
Optimizing NNI: done in 4.84603 secs using 597.2% CPU
10. Current log-likelihood: -103386.680
11. Current log-likelihood: -103386.344
12. Current log-likelihood: -103386.183
Optimizing NNI: done in 5.19304 secs using 597.1% CPU
13. Current log-likelihood: -103385.992
14. Current log-likelihood: -103385.846
15. Current log-likelihood: -103385.679
Optimal log-likelihood: -103385.528
Proportion of invariable sites: 0.014
Site proportion and rates:  (0.093,0.040) (0.114,0.120) (0.060,0.213) (0.104,0.315) (0.093,0.488) (0.150,0.760) (0.175,1.306) (0.141,2.114) (0.055,4.552)
Parameters optimization took 15 rounds (23.964 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 5.36079 secs using 597.8% CPU
Calculating distance matrix: done in 4.62986 secs using 399.9% CPU
Computing ML distances took 4.630145 sec (of wall-clock time) 18.517799 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000746965 secs using 325.9% CPU
Constructing RapidNJ tree: done in 0.00872588 secs using 342.1% CPU
Computing RapidNJ tree took 0.009532 sec (of wall-clock time) 0.035156 sec (of CPU time)
Log-likelihood of RapidNJ tree: -103813.969
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 5.54182 secs using 597.2% CPU
Optimizing NNI: done in 7.32954 secs using 597.3% CPU
10.545 second
Optimizing NNI: done in 7.47344 secs using 596.8% CPU
Computing log-likelihood of 98 initial trees ... 10.173 seconds
Current best score: -103385.528

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 220 / LogL: -193605.408 / Time: 0h:21m:2s (0h:4m:53s left)
Optimizing NNI: done in 4.49471 secs using 597.3% CPU
Optimizing NNI: done in 5.14323 secs using 597.7% CPU
BETTER TREE FOUND at iteration 1: -102932.983
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 6: -102916.644
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Iteration 230 / LogL: -193575.129 / Time: 0h:21m:54s (0h:3m:55s left)
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Iteration 10 / LogL: -102981.741 / Time: 0h:1m:52s
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Iteration 20 / LogL: -102952.563 / Time: 0h:2m:23s
Finish initializing candidate tree set (20)
Current best tree score: -102916.644 / CPU time: 113.018
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 2.78538 secs using 398.7% CPU
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Optimizing NNI: done in 2.73571 secs using 398.8% CPU
Optimizing NNI: done in 2.46201 secs using 398.6% CPU
Optimizing NNI: done in 5.0011 secs using 597.3% CPU
Optimizing NNI: done in 2.24513 secs using 398.7% CPU
Optimizing NNI: done in 2.61792 secs using 398.8% CPU
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Optimizing NNI: done in 2.39169 secs using 399% CPU
Optimizing NNI: done in 2.7939 secs using 398.9% CPU
Optimizing NNI: done in 5.26658 secs using 597.3% CPU
Iteration 240 / LogL: -193566.429 / Time: 0h:22m:47s (0h:2m:57s left)
Optimizing NNI: done in 2.74028 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -102908.903
Optimizing NNI: done in 6.47633 secs using 596.9% CPU
Optimizing NNI: done in 2.29992 secs using 399.4% CPU
Optimizing NNI: done in 2.64367 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.72835 secs using 597.5% CPU
BETTER TREE FOUND at iteration 30: -102899.979
Iteration 30 / LogL: -102899.979 / Time: 0h:2m:54s (0h:9m:59s left)
Optimizing NNI: done in 2.53592 secs using 398.2% CPU
Optimizing NNI: done in 5.85326 secs using 597.4% CPU
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Optimizing NNI: done in 5.28989 secs using 597% CPU
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Optimizing NNI: done in 5.82968 secs using 597% CPU
Optimizing NNI: done in 2.7609 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.03298 secs using 596.7% CPU
BETTER TREE FOUND at iteration 36: -102897.686
Optimizing NNI: done in 5.61358 secs using 597.6% CPU
Optimizing NNI: done in 2.63853 secs using 398.6% CPU
Optimizing NNI: done in 3.08029 secs using 398.5% CPU
Optimizing NNI: done in 6.29119 secs using 597.1% CPU
Optimizing NNI: done in 2.67799 secs using 398.5% CPU
Optimizing NNI: done in 2.67699 secs using 398.9% CPU
Iteration 40 / LogL: -102924.176 / Time: 0h:3m:31s (0h:8m:39s left)
Optimizing NNI: done in 4.65936 secs using 596.8% CPU
Optimizing NNI: done in 2.66229 secs using 397.9% CPU
Optimizing NNI: done in 2.42291 secs using 398.4% CPU
Optimizing NNI: done in 4.8922 secs using 597.3% CPU
Iteration 250 / LogL: -193577.308 / Time: 0h:23m:43s (0h:1m:59s left)
Optimizing NNI: done in 2.79029 secs using 398.9% CPU
Optimizing NNI: done in 2.40839 secs using 399% CPU
Optimizing NNI: done in 5.74215 secs using 596.4% CPU
Optimizing NNI: done in 2.17503 secs using 398.8% CPU
Optimizing NNI: done in 2.605 secs using 398.9% CPU
Optimizing NNI: done in 4.92975 secs using 597.5% CPU
Optimizing NNI: done in 2.47824 secs using 398.5% CPU
Optimizing NNI: done in 2.8264 secs using 398.7% CPU
Optimizing NNI: done in 2.37431 secs using 399.2% CPU
Optimizing NNI: done in 7.27989 secs using 597% CPU
Optimizing NNI: done in 2.2837 secs using 398.9% CPU
Iteration 50 / LogL: -102909.207 / Time: 0h:3m:56s (0h:6m:54s left)
Optimizing NNI: done in 3.61317 secs using 597.5% CPU
Optimizing NNI: done in 3.07709 secs using 399% CPU
Optimizing NNI: done in 2.81575 secs using 398.6% CPU
Optimizing NNI: done in 5.6347 secs using 596.7% CPU
Optimizing NNI: done in 2.38245 secs using 398.5% CPU
Optimizing NNI: done in 3.20322 secs using 398.6% CPU
Optimizing NNI: done in 5.53524 secs using 596.8% CPU
Optimizing NNI: done in 2.54004 secs using 398.7% CPU
Optimizing NNI: done in 2.73604 secs using 398.5% CPU
Optimizing NNI: done in 5.17454 secs using 597.5% CPU
Optimizing NNI: done in 2.47295 secs using 398.9% CPU
Optimizing NNI: done in 2.62674 secs using 398.9% CPU
Optimizing NNI: done in 2.47288 secs using 398.8% CPU
Optimizing NNI: done in 5.87956 secs using 596.3% CPU
Optimizing NNI: done in 2.57434 secs using 399% CPU
Iteration 60 / LogL: -102902.690 / Time: 0h:4m:23s (0h:5m:39s left)
Optimizing NNI: done in 4.93044 secs using 596.2% CPU
Optimizing NNI: done in 2.79732 secs using 398.8% CPU
Optimizing NNI: done in 2.32458 secs using 398.7% CPU
Optimizing NNI: done in 2.30812 secs using 398.7% CPU
Optimizing NNI: done in 5.14367 secs using 597.1% CPU
Iteration 260 / LogL: -193566.798 / Time: 0h:24m:37s (0h:1m:2s left)
Optimizing NNI: done in 2.63245 secs using 398.8% CPU
Optimizing NNI: done in 4.97771 secs using 597.6% CPU
Optimizing NNI: done in 2.78328 secs using 398.9% CPU
Optimizing NNI: done in 3.14702 secs using 398.8% CPU
Optimizing NNI: done in 5.83191 secs using 597.9% CPU
Optimizing NNI: done in 2.95102 secs using 398.1% CPU
Optimizing NNI: done in 2.37031 secs using 398.8% CPU
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Optimizing NNI: done in 2.68014 secs using 398.9% CPU
Optimizing NNI: done in 2.61291 secs using 398% CPU
Iteration 70 / LogL: -102904.597 / Time: 0h:4m:50s (0h:4m:37s left)
Optimizing NNI: done in 5.04103 secs using 596.8% CPU
Optimizing NNI: done in 2.70944 secs using 398.4% CPU
Optimizing NNI: done in 2.52938 secs using 398.7% CPU
Optimizing NNI: done in 5.36526 secs using 596.9% CPU
Optimizing NNI: done in 2.93925 secs using 398.7% CPU
Optimizing NNI: done in 2.52549 secs using 398.6% CPU
Optimizing NNI: done in 5.23875 secs using 596.9% CPU
Optimizing NNI: done in 2.74609 secs using 398.4% CPU
Optimizing NNI: done in 2.2683 secs using 398.8% CPU
Optimizing NNI: done in 5.00155 secs using 597.4% CPU
Optimizing NNI: done in 3.064 secs using 398.2% CPU
Optimizing NNI: done in 2.56913 secs using 398.9% CPU
Optimizing NNI: done in 6.0266 secs using 596.9% CPU
Optimizing NNI: done in 2.6742 secs using 398.7% CPU
Optimizing NNI: done in 2.37746 secs using 398.7% CPU
Iteration 80 / LogL: -102913.068 / Time: 0h:5m:17s (0h:3m:44s left)
Optimizing NNI: done in 4.98076 secs using 597.7% CPU
Optimizing NNI: done in 2.54525 secs using 398.3% CPU
Optimizing NNI: done in 3.00885 secs using 398.7% CPU
Optimizing NNI: done in 5.03943 secs using 596.9% CPU
Iteration 270 / LogL: -193646.243 / Time: 0h:25m:30s (0h:0m:5s left)
Optimizing NNI: done in 2.10278 secs using 398.8% CPU
Optimizing NNI: done in 2.58265 secs using 398.8% CPU
Optimizing NNI: done in 4.73906 secs using 597.1% CPU
Optimizing NNI: done in 2.80065 secs using 398.2% CPU
Optimizing NNI: done in 2.53457 secs using 398.6% CPU
Optimizing NNI: done in 5.05338 secs using 597% CPU
TREE SEARCH COMPLETED AFTER 272 ITERATIONS / Time: 0h:25m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -193554.841
Optimal log-likelihood: -193554.836
Site proportion and rates:  (0.009,0.067) (0.096,0.236) (0.132,0.368) (0.181,0.555) (0.167,0.787) (0.147,1.038) (0.166,1.602) (0.102,2.721)
Parameters optimization took 1 rounds (1.483 sec)
BEST SCORE FOUND : -193554.836
Total tree length: 158.184

Total number of iterations: 272
CPU time used for tree search: 8776.524 sec (2h:26m:16s)
Wall-clock time used for tree search: 1495.154 sec (0h:24m:55s)
Total CPU time used: 9052.356 sec (2h:30m:52s)
Total wall-clock time used: 1541.428 sec (0h:25m:41s)

===> START BOOTSTRAP REPLICATE NUMBER 29

Creating bootstrap alignment (seed: 70492)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.317 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194037.289
Optimizing NNI: done in 2.91125 secs using 398.5% CPU
2. Current log-likelihood: -191447.743
Optimizing NNI: done in 2.82294 secs using 398.5% CPU
3. Current log-likelihood: -191412.530
Optimizing NNI: done in 2.59106 secs using 398.6% CPU
4. Current log-likelihood: -191410.764
Optimizing NNI: done in 2.29196 secs using 398.4% CPU
Iteration 90 / LogL: -102897.906 / Time: 0h:5m:43s (0h:2m:57s left)
5. Current log-likelihood: -191409.956
Optimizing NNI: done in 2.18703 secs using 398.9% CPU
6. Current log-likelihood: -191409.443
Optimizing NNI: done in 2.23672 secs using 398.7% CPU
7. Current log-likelihood: -191409.072
Optimizing NNI: done in 2.23501 secs using 398.8% CPU
8. Current log-likelihood: -191408.797
9. Current log-likelihood: -191408.588
Optimizing NNI: done in 2.6728 secs using 398.2% CPU
10. Current log-likelihood: -191408.429
Optimizing NNI: done in 2.48666 secs using 399.2% CPU
11. Current log-likelihood: -191408.319
Optimizing NNI: done in 2.65094 secs using 398.4% CPU
Optimal log-likelihood: -191408.246
Site proportion and rates:  (0.020,0.083) (0.058,0.227) (0.104,0.370) (0.194,0.506) (0.125,0.687) (0.219,0.987) (0.173,1.555) (0.106,2.603)
Parameters optimization took 11 rounds (22.676 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.6068 secs using 398.6% CPU
Optimizing NNI: done in 2.79402 secs using 398.6% CPU
Optimizing NNI: done in 2.75093 secs using 399% CPU
Calculating distance matrix: done in 9.6086 secs using 599.8% CPU
Computing ML distances took 9.609144 sec (of wall-clock time) 57.633814 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.0014801 secs using 624.9% CPU
Constructing RapidNJ tree: done in 0.0220251 secs using 684.4% CPU
Computing RapidNJ tree took 0.023577 sec (of wall-clock time) 0.160662 sec (of CPU time)
Optimizing NNI: done in 2.26932 secs using 398.9% CPU
Iteration 100 / LogL: -102911.410 / Time: 0h:6m:8s (0h:2m:14s left)
Log-likelihood of RapidNJ tree: -194590.633
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.32069 secs using 398.9% CPU
Optimizing NNI: done in 2.65805 secs using 398.9% CPU
Optimizing NNI: done in 2.55214 secs using 398.6% CPU
Optimizing NNI: done in 2.96128 secs using 398.7% CPU
Optimizing NNI: done in 2.50153 secs using 399.1% CPU
Optimizing NNI: done in 2.49497 secs using 398.6% CPU
Optimizing NNI: done in 2.49342 secs using 398.9% CPU
Optimizing NNI: done in 2.60542 secs using 399% CPU
Optimizing NNI: done in 2.68252 secs using 398.7% CPU
Optimizing NNI: done in 2.3203 secs using 398.5% CPU
Iteration 110 / LogL: -102900.111 / Time: 0h:6m:34s (0h:1m:34s left)
Optimizing NNI: done in 2.00657 secs using 398.8% CPU
Optimizing NNI: done in 2.84363 secs using 398.5% CPU
30.190 second
Optimizing NNI: done in 2.53955 secs using 398.8% CPU
Optimizing NNI: done in 2.4537 secs using 399% CPU
Optimizing NNI: done in 2.66078 secs using 398.4% CPU
Optimizing NNI: done in 2.56565 secs using 398.5% CPU
Optimizing NNI: done in 2.62261 secs using 398.5% CPU
Optimizing NNI: done in 2.82911 secs using 398.6% CPU
Computing log-likelihood of 98 initial trees ... 16.146 seconds
Current best score: -191408.246

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.77809 secs using 398.5% CPU
Optimizing NNI: done in 2.95255 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.73508 secs using 398.7% CPU
Iteration 120 / LogL: -102909.774 / Time: 0h:7m:0s (0h:0m:56s left)
BETTER TREE FOUND at iteration 1: -190831.067
Optimizing NNI: done in 2.56422 secs using 397.9% CPU
Optimizing NNI: done in 2.47003 secs using 398.8% CPU
Optimizing NNI: done in 4.43209 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.28 secs using 397.6% CPU
Optimizing NNI: done in 2.28728 secs using 398.7% CPU
Optimizing NNI: done in 2.43248 secs using 398.4% CPU
Optimizing NNI: done in 2.28424 secs using 399% CPU
Optimizing NNI: done in 2.40228 secs using 398.3% CPU
BETTER TREE FOUND at iteration 2: -190739.442
Optimizing NNI: done in 2.73353 secs using 398.8% CPU
Optimizing NNI: done in 4.24692 secs using 597.2% CPU
Optimizing NNI: done in 2.418 secs using 399.1% CPU
Optimizing NNI: done in 2.77782 secs using 398.3% CPU
Iteration 130 / LogL: -102921.382 / Time: 0h:7m:25s (0h:0m:20s left)
Optimizing NNI: done in 4.3246 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.72183 secs using 398.5% CPU
Optimizing NNI: done in 2.32883 secs using 398.8% CPU
Optimizing NNI: done in 2.13765 secs using 398.8% CPU
BETTER TREE FOUND at iteration 4: -190715.764
Optimizing NNI: done in 2.53121 secs using 398.6% CPU
Optimizing NNI: done in 4.1378 secs using 596.7% CPU
Optimizing NNI: done in 2.30782 secs using 398.7% CPU
Optimizing NNI: done in 2.49055 secs using 398.4% CPU
Optimizing NNI: done in 4.18883 secs using 598.3% CPU
Optimizing NNI: done in 3.12095 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 137 ITERATIONS / Time: 0h:7m:43s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102897.686
2. Current log-likelihood: -102897.667
3. Current log-likelihood: -102897.648
Optimizing NNI: done in 4.24461 secs using 597.7% CPU
4. Current log-likelihood: -102897.631
5. Current log-likelihood: -102897.615
6. Current log-likelihood: -102897.600
Optimal log-likelihood: -102897.585
Proportion of invariable sites: 0.013
Site proportion and rates:  (0.088,0.034) (0.107,0.101) (0.075,0.200) (0.118,0.325) (0.114,0.540) (0.121,0.810) (0.160,1.293) (0.149,2.071) (0.054,4.751)
Parameters optimization took 6 rounds (5.778 sec)
BEST SCORE FOUND : -102897.585
Total tree length: 164.300

Total number of iterations: 137
CPU time used for tree search: 1695.877 sec (0h:28m:15s)
Wall-clock time used for tree search: 433.300 sec (0h:7m:13s)
Total CPU time used: 1839.939 sec (0h:30m:39s)
Total wall-clock time used: 469.431 sec (0h:7m:49s)

===> START BOOTSTRAP REPLICATE NUMBER 51

Creating bootstrap alignment (seed: 68233)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.118 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104301.964
Optimizing NNI: done in 4.38798 secs using 596.9% CPU
Estimate model parameters (epsilon = 0.100)
2. Current log-likelihood: -102438.943
3. Current log-likelihood: -102373.903
BETTER TREE FOUND at iteration 8: -190691.276
4. Current log-likelihood: -102370.301
5. Current log-likelihood: -102368.913
6. Current log-likelihood: -102360.998
Optimizing NNI: done in 4.06779 secs using 596.6% CPU
7. Current log-likelihood: -102350.571
8. Current log-likelihood: -102349.764
9. Current log-likelihood: -102349.481
Optimizing NNI: done in 4.20918 secs using 598% CPU
Iteration 10 / LogL: -190811.888 / Time: 0h:2m:27s
10. Current log-likelihood: -102349.356
Optimal log-likelihood: -102349.206
Proportion of invariable sites: 0.016
Site proportion and rates:  (0.104,0.041) (0.122,0.141) (0.096,0.249) (0.086,0.394) (0.127,0.610) (0.121,0.978) (0.146,1.538) (0.135,2.182) (0.047,4.364)
Parameters optimization took 10 rounds (15.779 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.24787 secs using 597.4% CPU
Calculating distance matrix: done in 4.58434 secs using 399.9% CPU
Computing ML distances took 4.584608 sec (of wall-clock time) 18.333492 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000693083 secs using 414.5% CPU
Constructing RapidNJ tree: done in 0.00876784 secs using 356.3% CPU
Computing RapidNJ tree took 0.009513 sec (of wall-clock time) 0.036990 sec (of CPU time)
Log-likelihood of RapidNJ tree: -102491.221
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.59521 secs using 596.8% CPU
Optimizing NNI: done in 5.75644 secs using 597.5% CPU
10.512 second
Optimizing NNI: done in 5.11756 secs using 597.4% CPU
Optimizing NNI: done in 4.19477 secs using 597.5% CPU
Optimizing NNI: done in 4.07715 secs using 597.3% CPU
Computing log-likelihood of 98 initial trees ... 9.692 seconds
Current best score: -102349.206

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.71639 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.48746 secs using 596.9% CPU
Optimizing NNI: done in 4.56203 secs using 597.1% CPU
Optimizing NNI: done in 3.96154 secs using 597.5% CPU
Optimizing NNI: done in 4.24495 secs using 597.1% CPU
Iteration 20 / LogL: -190703.316 / Time: 0h:3m:12s
Finish initializing candidate tree set (20)
Current best tree score: -190691.276 / CPU time: 158.444
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 3.77725 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -101864.013
BETTER TREE FOUND at iteration 21: -190664.941
Optimizing NNI: done in 2.29184 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.1441 secs using 598.1% CPU
Optimizing NNI: done in 4.69757 secs using 597.7% CPU
BETTER TREE FOUND at iteration 2: -101699.737
Optimizing NNI: done in 4.65739 secs using 597.9% CPU
Optimizing NNI: done in 2.48292 secs using 398.9% CPU
Optimizing NNI: done in 2.54535 secs using 398.4% CPU
Optimizing NNI: done in 4.36269 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.56448 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -101694.802
BETTER TREE FOUND at iteration 25: -190663.199
Optimizing NNI: done in 2.00407 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.72959 secs using 597% CPU
BETTER TREE FOUND at iteration 6: -101649.866
Optimizing NNI: done in 2.41377 secs using 398.4% CPU
Optimizing NNI: done in 4.79701 secs using 597.8% CPU
Optimizing NNI: done in 2.79849 secs using 398.3% CPU
Optimizing NNI: done in 4.46786 secs using 597.8% CPU
Optimizing NNI: done in 2.55391 secs using 398.9% CPU
Optimizing NNI: done in 2.95011 secs using 398.7% CPU
Iteration 10 / LogL: -101718.957 / Time: 0h:1m:45s
Optimizing NNI: done in 4.56477 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.43859 secs using 399.3% CPU
Optimizing NNI: done in 2.45823 secs using 398.1% CPU
BETTER TREE FOUND at iteration 29: -190640.633
Optimizing NNI: done in 2.3811 secs using 398.6% CPU
Optimizing NNI: done in 4.36718 secs using 597.5% CPU
Iteration 30 / LogL: -190738.359 / Time: 0h:4m:9s (0h:14m:11s left)
Optimizing NNI: done in 2.93714 secs using 398.6% CPU
Optimizing NNI: done in 2.56337 secs using 398.4% CPU
Optimizing NNI: done in 4.40694 secs using 597.7% CPU
Optimizing NNI: done in 2.46487 secs using 398.4% CPU
Optimizing NNI: done in 2.75164 secs using 398.5% CPU
Optimizing NNI: done in 4.23946 secs using 597.9% CPU
Optimizing NNI: done in 2.49452 secs using 398.9% CPU
Optimizing NNI: done in 4.33021 secs using 597.9% CPU
Optimizing NNI: done in 2.62488 secs using 398.4% CPU
Optimizing NNI: done in 2.95301 secs using 398.3% CPU
Iteration 20 / LogL: -101697.077 / Time: 0h:2m:12s
Finish initializing candidate tree set (20)
Current best tree score: -101649.866 / CPU time: 110.457
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.24337 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.99711 secs using 398.9% CPU
Optimizing NNI: done in 2.17118 secs using 399.2% CPU
BETTER TREE FOUND at iteration 34: -190636.607
Optimizing NNI: done in 2.05188 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -101636.917
Optimizing NNI: done in 4.67428 secs using 597.5% CPU
Optimizing NNI: done in 1.98504 secs using 398.6% CPU
Optimizing NNI: done in 2.07317 secs using 399.2% CPU
Optimizing NNI: done in 4.76874 secs using 597.7% CPU
Optimizing NNI: done in 2.49077 secs using 398.7% CPU
Optimizing NNI: done in 2.47525 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.46639 secs using 597.1% CPU
BETTER TREE FOUND at iteration 27: -101602.064
Optimizing NNI: done in 2.13134 secs using 398.6% CPU
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Iteration 30 / LogL: -101602.237 / Time: 0h:2m:38s (0h:8m:50s left)
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Iteration 40 / LogL: -190699.683 / Time: 0h:4m:59s (0h:12m:0s left)
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BETTER TREE FOUND at iteration 41: -190618.258
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BETTER TREE FOUND at iteration 39: -101589.016
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Iteration 40 / LogL: -101599.027 / Time: 0h:3m:2s (0h:7m:43s left)
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BETTER TREE FOUND at iteration 45: -190610.284
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BETTER TREE FOUND at iteration 48: -101581.139
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Iteration 50 / LogL: -101612.406 / Time: 0h:3m:26s (0h:6m:52s left)
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Iteration 50 / LogL: -190624.475 / Time: 0h:5m:50s (0h:11m:18s left)
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BETTER TREE FOUND at iteration 58: -101576.706
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Iteration 60 / LogL: -101599.126 / Time: 0h:3m:50s (0h:6m:22s left)
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BETTER TREE FOUND at iteration 55: -190606.313
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BETTER TREE FOUND at iteration 57: -190602.515
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Iteration 70 / LogL: -101581.138 / Time: 0h:4m:11s (0h:5m:20s left)
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Iteration 60 / LogL: -190763.585 / Time: 0h:6m:38s (0h:10m:54s left)
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Iteration 80 / LogL: -101605.960 / Time: 0h:4m:33s (0h:4m:29s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 87: -101571.145
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Iteration 90 / LogL: -101577.543 / Time: 0h:4m:56s (0h:5m:23s left)
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Iteration 70 / LogL: -190634.118 / Time: 0h:7m:23s (0h:9m:19s left)
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Iteration 100 / LogL: -101612.956 / Time: 0h:5m:18s (0h:4m:39s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 106: -101568.265
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Iteration 110 / LogL: -101570.843 / Time: 0h:5m:42s (0h:5m:1s left)
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Iteration 80 / LogL: -190621.551 / Time: 0h:8m:9s (0h:7m:56s left)
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Iteration 120 / LogL: -101588.643 / Time: 0h:6m:3s (0h:4m:22s left)
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Iteration 130 / LogL: -101617.733 / Time: 0h:6m:24s (0h:3m:46s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 89: -190600.157
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Iteration 90 / LogL: -190702.778 / Time: 0h:8m:57s (0h:9m:57s left)
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Iteration 140 / LogL: -101589.336 / Time: 0h:6m:46s (0h:3m:12s left)
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Iteration 150 / LogL: -101571.675 / Time: 0h:7m:8s (0h:2m:40s left)
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Iteration 100 / LogL: -190620.539 / Time: 0h:9m:42s (0h:8m:43s left)
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Iteration 160 / LogL: -101571.279 / Time: 0h:7m:30s (0h:2m:10s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 163: -101567.842
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Estimate model parameters (epsilon = 0.100)
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Iteration 170 / LogL: -101581.740 / Time: 0h:7m:54s (0h:4m:21s left)
BETTER TREE FOUND at iteration 106: -190589.080
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Iteration 110 / LogL: -190730.857 / Time: 0h:10m:27s (0h:9m:12s left)
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Iteration 180 / LogL: -101614.708 / Time: 0h:8m:16s (0h:3m:50s left)
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Iteration 190 / LogL: -101586.393 / Time: 0h:8m:39s (0h:3m:20s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 116: -190583.041
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Iteration 120 / LogL: -190785.119 / Time: 0h:11m:14s (0h:9m:3s left)
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Iteration 210 / LogL: -101570.028 / Time: 0h:9m:23s (0h:2m:22s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 211: -101566.901
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Iteration 130 / LogL: -190650.940 / Time: 0h:11m:58s (0h:7m:58s left)
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Optimizing NNI: done in 2.46471 secs using 399.2% CPU
Iteration 230 / LogL: -101593.663 / Time: 0h:10m:10s (0h:3m:35s left)
Optimizing NNI: done in 4.61669 secs using 597.3% CPU
Optimizing NNI: done in 2.32248 secs using 398.3% CPU
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Optimizing NNI: done in 2.24431 secs using 398.6% CPU
Optimizing NNI: done in 4.90836 secs using 597.1% CPU
Iteration 140 / LogL: -190646.966 / Time: 0h:12m:44s (0h:6m:57s left)
Optimizing NNI: done in 1.87378 secs using 398.3% CPU
Optimizing NNI: done in 1.93719 secs using 398.9% CPU
Iteration 240 / LogL: -101569.443 / Time: 0h:10m:32s (0h:3m:7s left)
Optimizing NNI: done in 4.15347 secs using 598% CPU
Optimizing NNI: done in 2.01416 secs using 398.4% CPU
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Optimizing NNI: done in 2.41723 secs using 399.3% CPU
Optimizing NNI: done in 4.25649 secs using 598% CPU
Optimizing NNI: done in 2.2369 secs using 398.3% CPU
Optimizing NNI: done in 2.53769 secs using 398.7% CPU
Optimizing NNI: done in 4.13566 secs using 597.4% CPU
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Optimizing NNI: done in 2.10162 secs using 398.6% CPU
Optimizing NNI: done in 4.17767 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 145: -190574.402
Optimizing NNI: done in 2.07138 secs using 399.1% CPU
Optimizing NNI: done in 2.28307 secs using 398.6% CPU
Iteration 250 / LogL: -101573.397 / Time: 0h:10m:55s (0h:2m:40s left)
Optimizing NNI: done in 4.12486 secs using 597.6% CPU
Optimizing NNI: done in 2.28598 secs using 398.8% CPU
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Iteration 150 / LogL: -190613.646 / Time: 0h:13m:29s (0h:8m:35s left)
Optimizing NNI: done in 2.49735 secs using 399.1% CPU
Iteration 260 / LogL: -101572.447 / Time: 0h:11m:17s (0h:2m:13s left)
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Iteration 270 / LogL: -101577.909 / Time: 0h:11m:38s (0h:1m:46s left)
Optimizing NNI: done in 1.98753 secs using 398.3% CPU
Optimizing NNI: done in 2.07096 secs using 399% CPU
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Optimizing NNI: done in 4.49433 secs using 597.5% CPU
Iteration 160 / LogL: -190596.640 / Time: 0h:14m:13s (0h:7m:36s left)
Optimizing NNI: done in 2.06646 secs using 398.7% CPU
Iteration 280 / LogL: -101588.927 / Time: 0h:11m:59s (0h:1m:19s left)
Optimizing NNI: done in 1.93404 secs using 398.7% CPU
Optimizing NNI: done in 2.10301 secs using 398.7% CPU
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Optimizing NNI: done in 4.54783 secs using 598% CPU
Optimizing NNI: done in 1.95679 secs using 398.7% CPU
Optimizing NNI: done in 2.14959 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.21511 secs using 597.4% CPU
BETTER TREE FOUND at iteration 286: -101566.665
Optimizing NNI: done in 2.04127 secs using 398.9% CPU
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Iteration 290 / LogL: -101599.464 / Time: 0h:12m:22s (0h:4m:6s left)
Optimizing NNI: done in 2.17249 secs using 398.8% CPU
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Iteration 170 / LogL: -190729.318 / Time: 0h:14m:58s (0h:6m:38s left)
Optimizing NNI: done in 1.98392 secs using 399% CPU
Iteration 300 / LogL: -101582.298 / Time: 0h:12m:44s (0h:3m:39s left)
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Iteration 310 / LogL: -101592.082 / Time: 0h:13m:5s (0h:3m:13s left)
Optimizing NNI: done in 5.53278 secs using 597.5% CPU
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Optimizing NNI: done in 2.38312 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 316: -101566.526
Optimizing NNI: done in 4.6003 secs using 597.3% CPU
Optimizing NNI: done in 2.19675 secs using 399.1% CPU
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Iteration 320 / LogL: -101577.884 / Time: 0h:13m:28s (0h:4m:3s left)
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Iteration 180 / LogL: -190611.542 / Time: 0h:15m:43s (0h:5m:42s left)
Optimizing NNI: done in 1.88553 secs using 399% CPU
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Iteration 330 / LogL: -101572.507 / Time: 0h:13m:49s (0h:3m:36s left)
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Iteration 340 / LogL: -101576.020 / Time: 0h:14m:10s (0h:3m:10s left)
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Iteration 190 / LogL: -190700.227 / Time: 0h:16m:27s (0h:4m:47s left)
Optimizing NNI: done in 2.08945 secs using 398.6% CPU
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Iteration 350 / LogL: -101572.286 / Time: 0h:14m:32s (0h:2m:45s left)
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Iteration 360 / LogL: -101603.862 / Time: 0h:14m:55s (0h:2m:19s left)
Optimizing NNI: done in 1.87349 secs using 398.9% CPU
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Iteration 200 / LogL: -190645.034 / Time: 0h:17m:11s (0h:3m:53s left)
Optimizing NNI: done in 2.29868 secs using 399.1% CPU
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Iteration 370 / LogL: -101587.113 / Time: 0h:15m:17s (0h:1m:54s left)
Optimizing NNI: done in 2.13439 secs using 398.4% CPU
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Iteration 380 / LogL: -101598.560 / Time: 0h:15m:40s (0h:1m:29s left)
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Iteration 210 / LogL: -190601.697 / Time: 0h:17m:54s (0h:2m:59s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.3367 secs using 597.4% CPU
BETTER TREE FOUND at iteration 382: -101565.928
Optimizing NNI: done in 2.37182 secs using 399.6% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 215: -190565.754
Optimizing NNI: done in 2.04285 secs using 398.4% CPU
Iteration 390 / LogL: -101811.913 / Time: 0h:16m:3s (0h:3m:47s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 398: -101564.861
Optimizing NNI: done in 4.00694 secs using 597% CPU
Iteration 220 / LogL: -190622.009 / Time: 0h:18m:38s (0h:8m:4s left)
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Iteration 400 / LogL: -101609.947 / Time: 0h:16m:26s (0h:4m:2s left)
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Iteration 410 / LogL: -101634.553 / Time: 0h:16m:48s (0h:3m:36s left)
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Iteration 230 / LogL: -190606.207 / Time: 0h:19m:21s (0h:7m:11s left)
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Iteration 420 / LogL: -101610.363 / Time: 0h:17m:10s (0h:3m:11s left)
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Iteration 430 / LogL: -101577.036 / Time: 0h:17m:32s (0h:2m:46s left)
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Iteration 450 / LogL: -101612.555 / Time: 0h:18m:15s (0h:1m:57s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 460 / LogL: -101584.680 / Time: 0h:18m:37s (0h:1m:32s left)
BETTER TREE FOUND at iteration 250: -190565.017
Iteration 250 / LogL: -190565.017 / Time: 0h:20m:51s (0h:8m:22s left)
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Iteration 490 / LogL: -101574.686 / Time: 0h:19m:43s (0h:0m:19s left)
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Optimizing NNI: done in 2.28644 secs using 399.2% CPU
TREE SEARCH COMPLETED AFTER 499 ITERATIONS / Time: 0h:20m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101564.861
2. Current log-likelihood: -101564.848
Optimal log-likelihood: -101564.834
Proportion of invariable sites: 0.014
Site proportion and rates:  (0.097,0.031) (0.097,0.108) (0.116,0.208) (0.091,0.363) (0.139,0.586) (0.123,0.981) (0.118,1.479) (0.157,2.112) (0.048,4.642)
Parameters optimization took 2 rounds (1.436 sec)
BEST SCORE FOUND : -101564.834
Total tree length: 149.254

Total number of iterations: 499
CPU time used for tree search: 4679.812 sec (1h:17m:59s)
Wall-clock time used for tree search: 1181.607 sec (0h:19m:41s)
Total CPU time used: 4772.443 sec (1h:19m:32s)
Total wall-clock time used: 1204.812 sec (0h:20m:4s)

===> START BOOTSTRAP REPLICATE NUMBER 52

Creating bootstrap alignment (seed: 68234)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.101 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -107419.454
2. Current log-likelihood: -105293.190
Optimizing NNI: done in 4.75093 secs using 597.6% CPU
Iteration 270 / LogL: -190579.466 / Time: 0h:22m:21s (0h:6m:38s left)
3. Current log-likelihood: -105203.515
4. Current log-likelihood: -105195.175
Optimizing NNI: done in 4.36683 secs using 597.6% CPU
5. Current log-likelihood: -105194.390
6. Current log-likelihood: -105194.021
7. Current log-likelihood: -105193.780
8. Current log-likelihood: -105193.678
Optimizing NNI: done in 5.36557 secs using 597.7% CPU
9. Current log-likelihood: -105193.566
Optimal log-likelihood: -105193.440
Proportion of invariable sites: 0.023
Site proportion and rates:  (0.106,0.038) (0.077,0.115) (0.089,0.195) (0.073,0.303) (0.086,0.444) (0.135,0.730) (0.169,1.247) (0.177,1.907) (0.064,4.082)
Parameters optimization took 9 rounds (13.502 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.32526 secs using 597.6% CPU
Calculating distance matrix: done in 4.74274 secs using 399.9% CPU
Computing ML distances took 4.743127 sec (of wall-clock time) 18.965671 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000696898 secs using 111.5% CPU
Constructing RapidNJ tree: done in 0.00852489 secs using 402.9% CPU
Computing RapidNJ tree took 0.009290 sec (of wall-clock time) 0.035749 sec (of CPU time)
Log-likelihood of RapidNJ tree: -105329.599
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.23295 secs using 596.9% CPU
Optimizing NNI: done in 6.45708 secs using 597.6% CPU
11.000 second
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Optimizing NNI: done in 5.13946 secs using 597.5% CPU
Computing log-likelihood of 98 initial trees ... 9.940 seconds
Current best score: -105193.440

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 280 / LogL: -190624.570 / Time: 0h:23m:12s (0h:5m:49s left)
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BETTER TREE FOUND at iteration 1: -104801.166
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 282: -190563.739
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BETTER TREE FOUND at iteration 2: -104682.553
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Iteration 10 / LogL: -104707.886 / Time: 0h:1m:38s
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Iteration 290 / LogL: -190580.314 / Time: 0h:24m:21s (0h:7m:45s left)
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Iteration 20 / LogL: -104785.028 / Time: 0h:2m:5s
Finish initializing candidate tree set (20)
Current best tree score: -104682.553 / CPU time: 106.260
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 27: -104662.482
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -104654.912
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Iteration 30 / LogL: -104692.663 / Time: 0h:2m:38s (0h:8m:55s left)
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Iteration 300 / LogL: -190687.835 / Time: 0h:25m:8s (0h:6m:53s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -104652.536
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 41: -104642.704
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 62: -104634.845
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 74: -104630.733
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 91: -104630.199
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Iteration 110 / LogL: -104661.288 / Time: 0h:5m:34s (0h:4m:8s left)
Optimizing NNI: done in 4.33925 secs using 596.5% CPU
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Iteration 340 / LogL: -190687.728 / Time: 0h:28m:8s (0h:3m:29s left)
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Iteration 120 / LogL: -104677.800 / Time: 0h:5m:55s (0h:3m:31s left)
Optimizing NNI: done in 2.36291 secs using 398.4% CPU
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Iteration 130 / LogL: -104669.432 / Time: 0h:6m:15s (0h:2m:57s left)
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Iteration 350 / LogL: -190607.840 / Time: 0h:28m:53s (0h:2m:38s left)
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Iteration 140 / LogL: -104630.987 / Time: 0h:6m:36s (0h:2m:25s left)
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Optimizing NNI: done in 4.84638 secs using 597.2% CPU
BETTER TREE FOUND at iteration 146: -104625.771
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Optimizing NNI: done in 2.18141 secs using 397.6% CPU
BETTER TREE FOUND at iteration 355: -190563.512
Optimizing NNI: done in 2.18429 secs using 396.8% CPU
Iteration 150 / LogL: -104653.028 / Time: 0h:7m:0s (0h:4m:30s left)
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Iteration 160 / LogL: -104665.873 / Time: 0h:7m:19s (0h:3m:57s left)
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Iteration 360 / LogL: -190583.731 / Time: 0h:29m:39s (0h:7m:50s left)
Optimizing NNI: done in 1.88964 secs using 398% CPU
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Optimizing NNI: done in 4.41523 secs using 597.6% CPU
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BETTER TREE FOUND at iteration 162: -104618.183
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Iteration 170 / LogL: -104638.616 / Time: 0h:7m:48s (0h:4m:14s left)
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Optimizing NNI: done in 4.30841 secs using 597.4% CPU
BETTER TREE FOUND at iteration 173: -104611.729
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Iteration 370 / LogL: -190567.918 / Time: 0h:30m:24s (0h:7m:0s left)
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Iteration 180 / LogL: -104637.498 / Time: 0h:8m:11s (0h:4m:15s left)
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Iteration 190 / LogL: -104775.981 / Time: 0h:8m:32s (0h:3m:45s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 197: -104610.360
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Iteration 380 / LogL: -190611.477 / Time: 0h:31m:9s (0h:6m:9s left)
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Iteration 200 / LogL: -104661.822 / Time: 0h:8m:54s (0h:4m:20s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 201: -104609.694
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Iteration 210 / LogL: -104633.363 / Time: 0h:9m:15s (0h:4m:1s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.0582 secs using 597.3% CPU
BETTER TREE FOUND at iteration 212: -104608.265
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Iteration 390 / LogL: -190575.077 / Time: 0h:31m:54s (0h:5m:19s left)
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Iteration 220 / LogL: -104610.635 / Time: 0h:9m:38s (0h:4m:2s left)
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Iteration 230 / LogL: -104633.552 / Time: 0h:9m:58s (0h:3m:34s left)
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Iteration 240 / LogL: -104626.297 / Time: 0h:10m:18s (0h:3m:6s left)
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Iteration 400 / LogL: -190612.293 / Time: 0h:32m:40s (0h:4m:30s left)
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Iteration 250 / LogL: -104658.020 / Time: 0h:10m:39s (0h:2m:39s left)
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Iteration 260 / LogL: -104625.580 / Time: 0h:10m:59s (0h:2m:12s left)
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Iteration 410 / LogL: -190568.596 / Time: 0h:33m:28s (0h:3m:40s left)
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Iteration 270 / LogL: -104618.567 / Time: 0h:11m:19s (0h:1m:46s left)
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Iteration 280 / LogL: -104611.565 / Time: 0h:11m:39s (0h:1m:20s left)
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Iteration 420 / LogL: -190601.966 / Time: 0h:34m:13s (0h:2m:51s left)
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Iteration 290 / LogL: -104634.091 / Time: 0h:12m:0s (0h:0m:54s left)
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Iteration 300 / LogL: -104610.740 / Time: 0h:12m:21s (0h:0m:29s left)
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Iteration 430 / LogL: -190599.754 / Time: 0h:34m:59s (0h:2m:2s left)
Optimizing NNI: done in 2.17433 secs using 398.8% CPU
Iteration 310 / LogL: -104644.623 / Time: 0h:12m:41s (0h:0m:4s left)
Optimizing NNI: done in 1.93956 secs using 398.7% CPU
Optimizing NNI: done in 4.14393 secs using 597.6% CPU
Optimizing NNI: done in 1.91454 secs using 398.5% CPU
Optimizing NNI: done in 2.02478 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 313 ITERATIONS / Time: 0h:12m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -104608.265
2. Current log-likelihood: -104608.241
3. Current log-likelihood: -104608.211
Optimizing NNI: done in 4.41084 secs using 598.1% CPU
4. Current log-likelihood: -104608.195
5. Current log-likelihood: -104608.180
6. Current log-likelihood: -104608.166
7. Current log-likelihood: -104608.152
8. Current log-likelihood: -104608.140
9. Current log-likelihood: -104608.129
10. Current log-likelihood: -104608.118
11. Current log-likelihood: -104608.108
Optimizing NNI: done in 4.02762 secs using 598.3% CPU
Optimal log-likelihood: -104608.093
Proportion of invariable sites: 0.023
Site proportion and rates:  (0.092,0.033) (0.082,0.090) (0.096,0.184) (0.075,0.287) (0.101,0.451) (0.127,0.748) (0.181,1.281) (0.160,1.914) (0.063,4.296)
Parameters optimization took 11 rounds (6.627 sec)
BEST SCORE FOUND : -104608.093
Total tree length: 178.426

Total number of iterations: 313
CPU time used for tree search: 2947.908 sec (0h:49m:7s)
Wall-clock time used for tree search: 747.926 sec (0h:12m:27s)
Total CPU time used: 3052.130 sec (0h:50m:52s)
Total wall-clock time used: 774.059 sec (0h:12m:54s)

===> START BOOTSTRAP REPLICATE NUMBER 53

Creating bootstrap alignment (seed: 68235)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.113 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 110 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -103267.872
2. Current log-likelihood: -101525.830
3. Current log-likelihood: -101470.005
Optimizing NNI: done in 4.69971 secs using 597.4% CPU
4. Current log-likelihood: -101437.058
5. Current log-likelihood: -101426.670
Optimizing NNI: done in 4.52005 secs using 598% CPU
6. Current log-likelihood: -101426.149
Optimal log-likelihood: -101426.103
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.104,0.041) (0.089,0.131) (0.097,0.230) (0.115,0.370) (0.120,0.584) (0.113,0.901) (0.122,1.418) (0.170,2.261) (0.044,4.324)
Parameters optimization took 6 rounds (9.829 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.21443 secs using 597.8% CPU
Calculating distance matrix: done in 4.67618 secs using 399.9% CPU
Computing ML distances took 4.676430 sec (of wall-clock time) 18.699351 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000701904 secs using 241.9% CPU
Constructing RapidNJ tree: done in 0.00853205 secs using 356.6% CPU
Computing RapidNJ tree took 0.009288 sec (of wall-clock time) 0.034819 sec (of CPU time)
Log-likelihood of RapidNJ tree: -102116.267
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.10041 secs using 597.6% CPU
Optimizing NNI: done in 6.71898 secs using 597.6% CPU
10.552 second
Optimizing NNI: done in 5.26125 secs using 597.2% CPU
Optimizing NNI: done in 4.79763 secs using 596.8% CPU
Iteration 440 / LogL: -190611.944 / Time: 0h:35m:48s (0h:1m:13s left)
Computing log-likelihood of 98 initial trees ... 10.309 seconds
Current best score: -101426.103

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.56834 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.23799 secs using 596.9% CPU
Optimizing NNI: done in 4.51764 secs using 597.6% CPU
Optimizing NNI: done in 4.28024 secs using 597.2% CPU
Optimizing NNI: done in 4.58072 secs using 597.8% CPU
Optimizing NNI: done in 4.79399 secs using 597.1% CPU
BETTER TREE FOUND at iteration 1: -101112.584
Optimizing NNI: done in 1.85447 secs using 398% CPU
Optimizing NNI: done in 4.56271 secs using 597.4% CPU
Optimizing NNI: done in 2.16252 secs using 398.4% CPU
Optimizing NNI: done in 2.52941 secs using 398.2% CPU
Optimizing NNI: done in 3.92274 secs using 597.8% CPU
Optimizing NNI: done in 2.24664 secs using 398.4% CPU
Optimizing NNI: done in 1.57766 secs using 397.8% CPU
Optimizing NNI: done in 1.76343 secs using 398.5% CPU
Optimizing NNI: done in 4.43432 secs using 596.7% CPU
Optimizing NNI: done in 3.49001 secs using 398.7% CPU
Optimizing NNI: done in 4.19151 secs using 597.8% CPU
Optimizing NNI: done in 2.65393 secs using 398.3% CPU
Optimizing NNI: done in 4.16588 secs using 597.4% CPU
Iteration 450 / LogL: -190655.438 / Time: 0h:36m:33s (0h:0m:24s left)
Optimizing NNI: done in 2.58362 secs using 398% CPU
Iteration 10 / LogL: -101122.031 / Time: 0h:1m:20s
Optimizing NNI: done in 2.40195 secs using 398.6% CPU
Optimizing NNI: done in 4.62848 secs using 598% CPU
Optimizing NNI: done in 2.48225 secs using 398.8% CPU
Optimizing NNI: done in 2.38249 secs using 398.9% CPU
Optimizing NNI: done in 4.09881 secs using 597.8% CPU
Optimizing NNI: done in 2.80944 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.16119 secs using 597% CPU
BETTER TREE FOUND at iteration 14: -101094.273
Optimizing NNI: done in 2.1078 secs using 398.9% CPU
Optimizing NNI: done in 4.93147 secs using 597.1% CPU
Optimizing NNI: done in 3.19624 secs using 398.2% CPU
Optimizing NNI: done in 3.11791 secs using 398.8% CPU
Optimizing NNI: done in 4.82674 secs using 597.5% CPU
Optimizing NNI: done in 2.12818 secs using 398.5% CPU
Optimizing NNI: done in 4.57856 secs using 597.2% CPU
TREE SEARCH COMPLETED AFTER 456 ITERATIONS / Time: 0h:37m:0s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -190563.512
Optimizing NNI: done in 3.35313 secs using 398.1% CPU
Optimal log-likelihood: -190563.508
Site proportion and rates:  (0.020,0.088) (0.068,0.243) (0.125,0.388) (0.207,0.538) (0.088,0.737) (0.212,0.993) (0.171,1.561) (0.109,2.572)
Parameters optimization took 1 rounds (0.947 sec)
BEST SCORE FOUND : -190563.508
Total tree length: 156.345

Total number of iterations: 456
CPU time used for tree search: 12910.975 sec (3h:35m:10s)
Wall-clock time used for tree search: 2186.400 sec (0h:36m:26s)
Total CPU time used: 13121.872 sec (3h:38m:41s)
Total wall-clock time used: 2221.810 sec (0h:37m:1s)

===> START BOOTSTRAP REPLICATE NUMBER 30

Creating bootstrap alignment (seed: 70493)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.316 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -201133.499
Optimizing NNI: done in 2.59277 secs using 398% CPU
Iteration 20 / LogL: -101161.356 / Time: 0h:1m:51s
Finish initializing candidate tree set (20)
Current best tree score: -101094.273 / CPU time: 95.377
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
2. Current log-likelihood: -198594.532
Optimizing NNI: done in 2.74681 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
3. Current log-likelihood: -198568.368
4. Current log-likelihood: -198559.914
5. Current log-likelihood: -198543.824
BETTER TREE FOUND at iteration 21: -101079.520
Optimizing NNI: done in 1.97066 secs using 398.4% CPU
6. Current log-likelihood: -198540.697
7. Current log-likelihood: -198540.560
Optimizing NNI: done in 2.4092 secs using 398% CPU
Optimal log-likelihood: -198540.552
Site proportion and rates:  (0.009,0.077) (0.040,0.244) (0.150,0.367) (0.170,0.535) (0.209,0.764) (0.185,1.036) (0.124,1.612) (0.114,2.575)
Parameters optimization took 7 rounds (14.402 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.20232 secs using 399% CPU
Optimizing NNI: done in 1.98246 secs using 398.3% CPU
Optimizing NNI: done in 1.96865 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Calculating distance matrix: done in 10.1376 secs using 599.8% CPU
Computing ML distances took 10.138085 sec (of wall-clock time) 60.809932 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00128293 secs using 440.8% CPU
Constructing RapidNJ tree: done in 0.022207 secs using 685.2% CPU
Computing RapidNJ tree took 0.023556 sec (of wall-clock time) 0.159124 sec (of CPU time)
BETTER TREE FOUND at iteration 26: -101076.464
Log-likelihood of RapidNJ tree: -203274.384
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.756 secs using 398.5% CPU
Optimizing NNI: done in 2.36591 secs using 398.9% CPU
Optimizing NNI: done in 1.84226 secs using 398.3% CPU
Optimizing NNI: done in 2.88753 secs using 398.1% CPU
Iteration 30 / LogL: -101133.585 / Time: 0h:2m:27s (0h:8m:6s left)
Optimizing NNI: done in 3.54673 secs using 398.4% CPU
Optimizing NNI: done in 2.94552 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -101073.932
Optimizing NNI: done in 2.67368 secs using 398.5% CPU
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30.233 second
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 39: -101063.314
Optimizing NNI: done in 2.22289 secs using 398.7% CPU
Iteration 40 / LogL: -101085.763 / Time: 0h:2m:58s (0h:7m:33s left)
Optimizing NNI: done in 2.31477 secs using 398.9% CPU
Optimizing NNI: done in 2.44812 secs using 397.8% CPU
Computing log-likelihood of 98 initial trees ... 16.560 seconds
Current best score: -198540.552

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.4007 secs using 398.6% CPU
Optimizing NNI: done in 3.08086 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.24256 secs using 398.4% CPU
Optimizing NNI: done in 2.26931 secs using 398.9% CPU
BETTER TREE FOUND at iteration 1: -197917.097
Optimizing NNI: done in 2.53268 secs using 398.4% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.92865 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 47: -101057.591
BETTER TREE FOUND at iteration 2: -197714.031
Optimizing NNI: done in 2.64342 secs using 398.5% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.20851 secs using 398.9% CPU
Iteration 50 / LogL: -101204.487 / Time: 0h:3m:25s (0h:6m:46s left)
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BETTER TREE FOUND at iteration 3: -197684.291
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Iteration 60 / LogL: -101069.138 / Time: 0h:3m:49s (0h:5m:38s left)
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Iteration 10 / LogL: -197733.058 / Time: 0h:2m:8s
Optimizing NNI: done in 2.19481 secs using 398.4% CPU
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Iteration 70 / LogL: -101077.274 / Time: 0h:4m:12s (0h:4m:41s left)
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Iteration 80 / LogL: -101081.315 / Time: 0h:4m:36s (0h:3m:54s left)
Optimizing NNI: done in 2.93803 secs using 398.2% CPU
Optimizing NNI: done in 4.26869 secs using 596.8% CPU
Iteration 20 / LogL: -197758.313 / Time: 0h:2m:51s
Finish initializing candidate tree set (20)
Current best tree score: -197684.291 / CPU time: 142.645
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.67885 secs using 398.2% CPU
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Iteration 90 / LogL: -101069.081 / Time: 0h:5m:0s (0h:3m:12s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.45168 secs using 398.3% CPU
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BETTER TREE FOUND at iteration 26: -197674.388
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.83701 secs using 398.7% CPU
Optimizing NNI: done in 2.26824 secs using 398% CPU
Iteration 100 / LogL: -101083.269 / Time: 0h:5m:24s (0h:2m:34s left)
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BETTER TREE FOUND at iteration 27: -197666.260
Optimizing NNI: done in 2.31939 secs using 398.6% CPU
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Iteration 30 / LogL: -197806.920 / Time: 0h:3m:56s (0h:13m:9s left)
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Optimizing NNI: done in 2.35287 secs using 398.5% CPU
Iteration 110 / LogL: -101083.205 / Time: 0h:5m:48s (0h:1m:58s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.88458 secs using 399.3% CPU
Iteration 120 / LogL: -101058.944 / Time: 0h:6m:11s (0h:1m:24s left)
BETTER TREE FOUND at iteration 35: -197658.864
Optimizing NNI: done in 2.44384 secs using 398.2% CPU
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Iteration 130 / LogL: -101219.687 / Time: 0h:6m:35s (0h:0m:52s left)
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Iteration 40 / LogL: -197697.866 / Time: 0h:4m:48s (0h:11m:43s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 137: -101057.185
Optimizing NNI: done in 5.61716 secs using 597.2% CPU
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Iteration 140 / LogL: -101073.689 / Time: 0h:7m:0s (0h:4m:53s left)
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Iteration 60 / LogL: -197657.536 / Time: 0h:6m:38s (0h:11m:14s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 93: -197646.459
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TREE SEARCH COMPLETED AFTER 284 ITERATIONS / Time: 0h:12m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101056.799
2. Current log-likelihood: -101056.774
3. Current log-likelihood: -101056.756
4. Current log-likelihood: -101056.741
5. Current log-likelihood: -101056.725
Optimizing NNI: done in 5.29806 secs using 597% CPU
6. Current log-likelihood: -101056.712
7. Current log-likelihood: -101056.700
8. Current log-likelihood: -101056.688
9. Current log-likelihood: -101056.677
10. Current log-likelihood: -101056.664
Optimal log-likelihood: -101056.653
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.096,0.034) (0.085,0.107) (0.104,0.216) (0.120,0.360) (0.126,0.579) (0.121,0.920) (0.124,1.477) (0.160,2.295) (0.038,4.951)
Parameters optimization took 10 rounds (9.149 sec)
BEST SCORE FOUND : -101056.653
Total tree length: 154.319

Total number of iterations: 284
CPU time used for tree search: 2929.777 sec (0h:48m:49s)
Wall-clock time used for tree search: 743.306 sec (0h:12m:23s)
Total CPU time used: 3030.321 sec (0h:50m:30s)
Total wall-clock time used: 768.506 sec (0h:12m:48s)

===> START BOOTSTRAP REPLICATE NUMBER 54

Creating bootstrap alignment (seed: 68236)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.100 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104308.040
Optimizing NNI: done in 4.89981 secs using 597.1% CPU
2. Current log-likelihood: -102165.375
3. Current log-likelihood: -102106.698
4. Current log-likelihood: -102093.394
Optimizing NNI: done in 4.96575 secs using 597.4% CPU
5. Current log-likelihood: -102089.234
6. Current log-likelihood: -102088.936
Optimal log-likelihood: -102088.841
Proportion of invariable sites: 0.043
Site proportion and rates:  (0.122,0.041) (0.067,0.128) (0.063,0.218) (0.105,0.334) (0.118,0.516) (0.101,0.823) (0.185,1.377) (0.127,2.002) (0.071,4.010)
Parameters optimization took 6 rounds (9.041 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 110 / LogL: -197704.164 / Time: 0h:11m:10s (0h:9m:0s left)
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Computing ML distances took 4.685568 sec (of wall-clock time) 18.738107 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000797033 secs using 380.2% CPU
Constructing RapidNJ tree: done in 0.00843287 secs using 429.5% CPU
Computing RapidNJ tree took 0.009280 sec (of wall-clock time) 0.040934 sec (of CPU time)
Optimizing NNI: done in 3.9274 secs using 598% CPU
Log-likelihood of RapidNJ tree: -102616.621
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 8.3293 secs using 596.8% CPU
10.472 second
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Computing log-likelihood of 98 initial trees ... 10.041 seconds
Current best score: -102088.841

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 127: -197642.515
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 10: -101578.910
Iteration 10 / LogL: -101578.910 / Time: 0h:1m:52s
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Iteration 130 / LogL: -197670.410 / Time: 0h:13m:0s (0h:9m:46s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 15: -101572.180
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Iteration 20 / LogL: -101670.011 / Time: 0h:2m:27s
Finish initializing candidate tree set (20)
Current best tree score: -101572.180 / CPU time: 132.025
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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BETTER TREE FOUND at iteration 26: -101565.074
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -101556.752
Optimizing NNI: done in 5.43117 secs using 596.2% CPU
Iteration 140 / LogL: -197699.518 / Time: 0h:13m:53s (0h:8m:41s left)
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BETTER TREE FOUND at iteration 28: -101555.658
Optimizing NNI: done in 5.33455 secs using 597.4% CPU
Optimizing NNI: done in 2.37946 secs using 397.2% CPU
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BETTER TREE FOUND at iteration 29: -101554.202
Optimizing NNI: done in 5.06806 secs using 597.4% CPU
Optimizing NNI: done in 2.44521 secs using 396.9% CPU
Iteration 30 / LogL: -101566.925 / Time: 0h:3m:4s (0h:10m:28s left)
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Iteration 40 / LogL: -101577.172 / Time: 0h:3m:29s (0h:7m:57s left)
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Iteration 150 / LogL: -197736.745 / Time: 0h:14m:45s (0h:7m:37s left)
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Iteration 50 / LogL: -101560.346 / Time: 0h:3m:53s (0h:6m:16s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -101551.738
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Iteration 60 / LogL: -101577.894 / Time: 0h:4m:19s (0h:6m:40s left)
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BETTER TREE FOUND at iteration 62: -101550.388
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Iteration 160 / LogL: -197670.774 / Time: 0h:15m:38s (0h:6m:35s left)
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Iteration 70 / LogL: -101554.213 / Time: 0h:4m:47s (0h:6m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 78: -101544.808
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Iteration 80 / LogL: -101566.787 / Time: 0h:5m:13s (0h:6m:29s left)
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Iteration 170 / LogL: -197653.772 / Time: 0h:16m:29s (0h:5m:33s left)
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Iteration 90 / LogL: -101569.600 / Time: 0h:5m:37s (0h:5m:33s left)
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Iteration 100 / LogL: -101551.982 / Time: 0h:6m:1s (0h:4m:44s left)
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Iteration 180 / LogL: -197810.065 / Time: 0h:17m:22s (0h:4m:33s left)
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Iteration 110 / LogL: -101702.022 / Time: 0h:6m:24s (0h:3m:59s left)
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Iteration 120 / LogL: -101660.536 / Time: 0h:6m:46s (0h:3m:17s left)
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Iteration 130 / LogL: -101566.170 / Time: 0h:7m:11s (0h:2m:40s left)
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Iteration 190 / LogL: -197646.008 / Time: 0h:18m:11s (0h:3m:33s left)
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Iteration 140 / LogL: -101560.867 / Time: 0h:7m:33s (0h:2m:4s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 146: -101537.388
Optimizing NNI: done in 2.28201 secs using 398.1% CPU
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Iteration 150 / LogL: -101564.943 / Time: 0h:7m:59s (0h:5m:8s left)
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Iteration 200 / LogL: -197770.826 / Time: 0h:19m:1s (0h:2m:34s left)
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Iteration 160 / LogL: -101552.572 / Time: 0h:8m:22s (0h:4m:31s left)
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Iteration 170 / LogL: -101561.295 / Time: 0h:8m:44s (0h:3m:55s left)
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Iteration 210 / LogL: -197766.423 / Time: 0h:19m:52s (0h:1m:36s left)
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Iteration 180 / LogL: -101555.512 / Time: 0h:9m:7s (0h:3m:21s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 213: -197635.549
BETTER TREE FOUND at iteration 181: -101529.201
Optimizing NNI: done in 2.19899 secs using 398% CPU
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Iteration 190 / LogL: -101543.578 / Time: 0h:9m:32s (0h:4m:35s left)
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Iteration 220 / LogL: -197654.880 / Time: 0h:20m:49s (0h:8m:50s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 229: -197634.335
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 218: -101528.459
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Iteration 230 / LogL: -197649.481 / Time: 0h:21m:44s (0h:9m:23s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 221: -101526.498
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Iteration 230 / LogL: -101534.450 / Time: 0h:11m:17s (0h:4m:29s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 298: -101525.068
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Iteration 390 / LogL: -101554.520 / Time: 0h:17m:19s (0h:0m:21s left)
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TREE SEARCH COMPLETED AFTER 399 ITERATIONS / Time: 0h:17m:40s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101525.068
2. Current log-likelihood: -101525.053
Optimizing NNI: done in 5.017 secs using 596.9% CPU
Iteration 310 / LogL: -197679.242 / Time: 0h:28m:40s (0h:1m:45s left)
3. Current log-likelihood: -101525.039
4. Current log-likelihood: -101525.027
5. Current log-likelihood: -101525.015
6. Current log-likelihood: -101525.003
7. Current log-likelihood: -101524.992
8. Current log-likelihood: -101524.982
9. Current log-likelihood: -101524.972
Optimizing NNI: done in 5.30656 secs using 597.5% CPU
Optimal log-likelihood: -101524.961
Proportion of invariable sites: 0.041
Site proportion and rates:  (0.085,0.025) (0.083,0.081) (0.075,0.180) (0.115,0.317) (0.128,0.509) (0.092,0.816) (0.189,1.341) (0.129,2.022) (0.063,4.548)
Parameters optimization took 9 rounds (6.374 sec)
BEST SCORE FOUND : -101524.961
Total tree length: 169.654

Total number of iterations: 399
CPU time used for tree search: 4126.307 sec (1h:8m:46s)
Wall-clock time used for tree search: 1044.662 sec (0h:17m:24s)
Total CPU time used: 4213.018 sec (1h:10m:13s)
Total wall-clock time used: 1066.403 sec (0h:17m:46s)

===> START BOOTSTRAP REPLICATE NUMBER 55

Creating bootstrap alignment (seed: 68237)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.116 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 101 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -115602.902
2. Current log-likelihood: -113793.268
3. Current log-likelihood: -113695.456
Optimizing NNI: done in 5.05597 secs using 597.3% CPU
4. Current log-likelihood: -113691.054
5. Current log-likelihood: -113690.705
6. Current log-likelihood: -113690.556
7. Current log-likelihood: -113690.425
Optimizing NNI: done in 4.98135 secs using 596.6% CPU
8. Current log-likelihood: -113690.307
9. Current log-likelihood: -113690.202
Optimal log-likelihood: -113690.053
Proportion of invariable sites: 0.023
Site proportion and rates:  (0.077,0.038) (0.076,0.122) (0.035,0.219) (0.085,0.303) (0.138,0.430) (0.148,0.664) (0.137,1.004) (0.209,1.796) (0.071,3.998)
Parameters optimization took 9 rounds (13.335 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 5.54438 secs using 597% CPU
Calculating distance matrix: done in 4.7163 secs using 399.6% CPU
Computing ML distances took 4.716698 sec (of wall-clock time) 18.847760 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000793219 secs using 115.6% CPU
Constructing RapidNJ tree: done in 0.0086751 secs using 367.3% CPU
Computing RapidNJ tree took 0.009525 sec (of wall-clock time) 0.033798 sec (of CPU time)
Log-likelihood of RapidNJ tree: -114062.444
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.503 secs using 596.4% CPU
Optimizing NNI: done in 6.09398 secs using 597.3% CPU
10.614 second
Optimizing NNI: done in 5.67415 secs using 597.2% CPU
Computing log-likelihood of 98 initial trees ... 9.690 seconds
Current best score: -113690.053

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -113229.486
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Estimate model parameters (epsilon = 0.100)
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Iteration 320 / LogL: -197649.428 / Time: 0h:29m:37s (0h:0m:50s left)
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BETTER TREE FOUND at iteration 2: -113133.424
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Iteration 10 / LogL: -113190.937 / Time: 0h:1m:18s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 13: -113099.297
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Optimizing NNI: done in 1.65655 secs using 398.7% CPU
Iteration 20 / LogL: -113500.087 / Time: 0h:1m:43s
Finish initializing candidate tree set (20)
Current best tree score: -113099.297 / CPU time: 84.778
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 4.90221 secs using 596.9% CPU
Iteration 330 / LogL: -197664.621 / Time: 0h:30m:30s (0h:0m:-6s left)
TREE SEARCH COMPLETED AFTER 330 ITERATIONS / Time: 0h:30m:30s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -197634.335
Optimal log-likelihood: -197634.330
Site proportion and rates:  (0.009,0.078) (0.047,0.253) (0.162,0.377) (0.195,0.574) (0.199,0.813) (0.161,1.071) (0.139,1.712) (0.089,2.728)
Parameters optimization took 1 rounds (0.490 sec)
BEST SCORE FOUND : -197634.330
Total tree length: 153.202

Total number of iterations: 330
CPU time used for tree search: 10608.141 sec (2h:56m:48s)
Wall-clock time used for tree search: 1801.599 sec (0h:30m:1s)
Total CPU time used: 10781.628 sec (2h:59m:41s)
Total wall-clock time used: 1830.737 sec (0h:30m:30s)

===> START BOOTSTRAP REPLICATE NUMBER 31

Creating bootstrap alignment (seed: 70494)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.341 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -191833.696
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2. Current log-likelihood: -189132.835
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Estimate model parameters (epsilon = 0.100)
3. Current log-likelihood: -189092.781
4. Current log-likelihood: -189087.094
BETTER TREE FOUND at iteration 23: -113057.535
5. Current log-likelihood: -189081.672
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6. Current log-likelihood: -189077.390
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7. Current log-likelihood: -189075.866
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8. Current log-likelihood: -189075.446
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9. Current log-likelihood: -189075.337
Optimizing NNI: done in 2.21439 secs using 399.2% CPU
Optimal log-likelihood: -189075.311
Site proportion and rates:  (0.010,0.099) (0.060,0.258) (0.110,0.394) (0.247,0.556) (0.173,0.767) (0.155,1.062) (0.135,1.620) (0.109,2.618)
Parameters optimization took 9 rounds (20.620 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Optimizing NNI: done in 1.65797 secs using 398.9% CPU
Iteration 30 / LogL: -113100.292 / Time: 0h:2m:8s (0h:6m:50s left)
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Calculating distance matrix: done in 9.56419 secs using 599.9% CPU
Computing ML distances took 9.564735 sec (of wall-clock time) 57.376964 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00134706 secs using 460.9% CPU
Constructing RapidNJ tree: done in 0.0227768 secs using 687.4% CPU
Computing RapidNJ tree took 0.024185 sec (of wall-clock time) 0.164134 sec (of CPU time)
Optimizing NNI: done in 2.02447 secs using 398.8% CPU
Log-likelihood of RapidNJ tree: -192799.555
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.87586 secs using 398.4% CPU
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Iteration 40 / LogL: -113134.148 / Time: 0h:2m:27s (0h:5m:14s left)
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29.411 second
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Iteration 50 / LogL: -113148.991 / Time: 0h:2m:48s (0h:4m:10s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 52: -113048.361
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Optimizing NNI: done in 2.03386 secs using 398.4% CPU
Computing log-likelihood of 98 initial trees ... 16.069 seconds
Current best score: -189075.311

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -188399.011
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Iteration 60 / LogL: -113093.477 / Time: 0h:3m:12s (0h:4m:59s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -188270.377
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 5: -188252.486
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Iteration 70 / LogL: -113058.602 / Time: 0h:3m:31s (0h:4m:11s left)
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Iteration 90 / LogL: -113048.554 / Time: 0h:4m:10s (0h:2m:54s left)
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Iteration 100 / LogL: -113061.504 / Time: 0h:4m:29s (0h:2m:21s left)
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Iteration 20 / LogL: -188355.930 / Time: 0h:2m:45s
Finish initializing candidate tree set (20)
Current best tree score: -188252.486 / CPU time: 133.236
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 21: -188228.514
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 210 / LogL: -113073.841 / Time: 0h:7m:53s (0h:1m:23s left)
Optimizing NNI: done in 4.83912 secs using 597.8% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.74787 secs using 399.2% CPU
Optimizing NNI: done in 1.73024 secs using 399.1% CPU
BETTER TREE FOUND at iteration 63: -188205.140
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Iteration 220 / LogL: -113113.181 / Time: 0h:8m:10s (0h:1m:0s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.57467 secs using 399% CPU
BETTER TREE FOUND at iteration 65: -188176.140
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Iteration 230 / LogL: -113064.736 / Time: 0h:8m:29s (0h:0m:37s left)
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Iteration 70 / LogL: -188201.816 / Time: 0h:6m:53s (0h:9m:28s left)
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Iteration 240 / LogL: -113064.725 / Time: 0h:8m:48s (0h:0m:15s left)
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Optimizing NNI: done in 1.83809 secs using 399.1% CPU
TREE SEARCH COMPLETED AFTER 248 ITERATIONS / Time: 0h:9m:2s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -113047.407
2. Current log-likelihood: -113047.375
3. Current log-likelihood: -113047.330
Optimizing NNI: done in 4.33592 secs using 597.6% CPU
4. Current log-likelihood: -113047.290
5. Current log-likelihood: -113047.253
6. Current log-likelihood: -113047.223
7. Current log-likelihood: -113047.201
8. Current log-likelihood: -113047.171
Optimizing NNI: done in 4.07801 secs using 597.9% CPU
9. Current log-likelihood: -113047.145
10. Current log-likelihood: -113047.128
11. Current log-likelihood: -113047.110
12. Current log-likelihood: -113047.094
13. Current log-likelihood: -113047.078
14. Current log-likelihood: -113047.063
15. Current log-likelihood: -113047.049
Optimizing NNI: done in 4.78115 secs using 596.2% CPU
16. Current log-likelihood: -113047.036
17. Current log-likelihood: -113047.022
18. Current log-likelihood: -113047.012
Optimal log-likelihood: -113046.997
Proportion of invariable sites: 0.023
Site proportion and rates:  (0.075,0.034) (0.077,0.109) (0.057,0.236) (0.061,0.310) (0.140,0.423) (0.146,0.662) (0.137,0.996) (0.212,1.800) (0.071,3.985)
Parameters optimization took 18 rounds (13.809 sec)
BEST SCORE FOUND : -113046.997
Total tree length: 164.338

Total number of iterations: 248
CPU time used for tree search: 2056.384 sec (0h:34m:16s)
Wall-clock time used for tree search: 523.762 sec (0h:8m:43s)
Total CPU time used: 2187.075 sec (0h:36m:27s)
Total wall-clock time used: 556.567 sec (0h:9m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 56

Creating bootstrap alignment (seed: 68238)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -113613.210
Optimizing NNI: done in 4.0788 secs using 596.2% CPU
2. Current log-likelihood: -111664.723
3. Current log-likelihood: -111556.034
4. Current log-likelihood: -111549.682
Optimizing NNI: done in 4.59966 secs using 598.3% CPU
Iteration 80 / LogL: -188189.861 / Time: 0h:7m:38s (0h:8m:12s left)
5. Current log-likelihood: -111549.198
6. Current log-likelihood: -111548.817
7. Current log-likelihood: -111548.447
Optimizing NNI: done in 3.99369 secs using 597.7% CPU
8. Current log-likelihood: -111548.077
9. Current log-likelihood: -111547.709
10. Current log-likelihood: -111547.349
Optimizing NNI: done in 4.86117 secs using 598.1% CPU
11. Current log-likelihood: -111546.997
12. Current log-likelihood: -111546.651
Optimizing NNI: done in 4.08143 secs using 596.8% CPU
13. Current log-likelihood: -111546.325
14. Current log-likelihood: -111546.033
15. Current log-likelihood: -111545.776
Optimizing NNI: done in 4.34995 secs using 597.1% CPU
16. Current log-likelihood: -111545.639
17. Current log-likelihood: -111545.526
18. Current log-likelihood: -111545.396
Optimizing NNI: done in 4.65541 secs using 597.9% CPU
Optimal log-likelihood: -111545.256
Proportion of invariable sites: 0.028
Site proportion and rates:  (0.071,0.035) (0.074,0.109) (0.055,0.185) (0.109,0.278) (0.116,0.439) (0.139,0.703) (0.164,1.165) (0.180,1.801) (0.064,4.458)
Parameters optimization took 18 rounds (28.670 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.10847 secs using 598% CPU
Calculating distance matrix: done in 4.75573 secs using 399.9% CPU
Computing ML distances took 4.755983 sec (of wall-clock time) 19.019065 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000735044 secs using 142.7% CPU
Constructing RapidNJ tree: done in 0.00858998 secs using 357.2% CPU
Computing RapidNJ tree took 0.009379 sec (of wall-clock time) 0.032180 sec (of CPU time)
Log-likelihood of RapidNJ tree: -111844.275
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.57716 secs using 597.6% CPU
Optimizing NNI: done in 6.69314 secs using 597.1% CPU
10.914 second
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Optimizing NNI: done in 4.65619 secs using 597.3% CPU
Iteration 90 / LogL: -188219.523 / Time: 0h:8m:26s (0h:7m:6s left)
Computing log-likelihood of 98 initial trees ... 10.471 seconds
Current best score: -111545.256

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.89327 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -111072.830
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -111011.268
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Iteration 10 / LogL: -111104.132 / Time: 0h:1m:35s
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Iteration 100 / LogL: -188206.150 / Time: 0h:9m:13s (0h:6m:3s left)
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Iteration 20 / LogL: -111075.974 / Time: 0h:1m:57s
Finish initializing candidate tree set (20)
Current best tree score: -111011.268 / CPU time: 82.594
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.66339 secs using 597% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -110988.686
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -110974.930
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Iteration 30 / LogL: -110995.873 / Time: 0h:2m:26s (0h:7m:44s left)
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Iteration 110 / LogL: -188183.332 / Time: 0h:10m:2s (0h:8m:50s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 111: -188171.265
BETTER TREE FOUND at iteration 32: -110969.222
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Iteration 40 / LogL: -110987.227 / Time: 0h:2m:57s (0h:6m:58s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 120 / LogL: -188386.569 / Time: 0h:10m:47s (0h:8m:15s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 50: -110963.370
Iteration 50 / LogL: -110963.370 / Time: 0h:3m:23s (0h:6m:54s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 52: -110961.445
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 92: -110959.863
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Iteration 120 / LogL: -110962.816 / Time: 0h:5m:52s (0h:3m:33s left)
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Iteration 140 / LogL: -110978.957 / Time: 0h:6m:34s (0h:2m:27s left)
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Iteration 150 / LogL: -110961.661 / Time: 0h:6m:54s (0h:1m:56s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 151: -110957.587
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Iteration 170 / LogL: -188185.973 / Time: 0h:14m:30s (0h:5m:50s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 154: -110956.925
Optimizing NNI: done in 4.70251 secs using 597.7% CPU
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Iteration 160 / LogL: -110999.280 / Time: 0h:7m:18s (0h:4m:19s left)
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Iteration 170 / LogL: -111221.681 / Time: 0h:7m:39s (0h:3m:48s left)
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Iteration 180 / LogL: -188226.314 / Time: 0h:15m:19s (0h:4m:57s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 190 / LogL: -110971.553 / Time: 0h:8m:19s (0h:2m:49s left)
BETTER TREE FOUND at iteration 187: -188167.694
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Iteration 190 / LogL: -188232.840 / Time: 0h:16m:6s (0h:8m:15s left)
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Iteration 210 / LogL: -110960.482 / Time: 0h:9m:2s (0h:1m:54s left)
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Iteration 200 / LogL: -188175.136 / Time: 0h:16m:51s (0h:7m:22s left)
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Optimizing NNI: done in 2.24082 secs using 398.8% CPU
Iteration 220 / LogL: -110972.745 / Time: 0h:9m:23s (0h:1m:27s left)
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Iteration 230 / LogL: -110982.835 / Time: 0h:9m:44s (0h:1m:1s left)
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Iteration 210 / LogL: -188198.279 / Time: 0h:17m:35s (0h:6m:28s left)
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Iteration 240 / LogL: -110969.981 / Time: 0h:10m:4s (0h:0m:35s left)
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Iteration 250 / LogL: -110960.602 / Time: 0h:10m:24s (0h:0m:10s left)
Optimizing NNI: done in 1.89592 secs using 398.6% CPU
Optimizing NNI: done in 5.92484 secs using 597.6% CPU
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Optimizing NNI: done in 4.45807 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.36395 secs using 398.5% CPU
BETTER TREE FOUND at iteration 216: -188166.745
Optimizing NNI: done in 1.80714 secs using 398.2% CPU
TREE SEARCH COMPLETED AFTER 255 ITERATIONS / Time: 0h:10m:34s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -110956.925
2. Current log-likelihood: -110956.881
3. Current log-likelihood: -110956.815
4. Current log-likelihood: -110956.752
Optimizing NNI: done in 4.24375 secs using 597% CPU
5. Current log-likelihood: -110956.687
6. Current log-likelihood: -110956.629
7. Current log-likelihood: -110956.573
8. Current log-likelihood: -110956.518
Optimizing NNI: done in 4.32596 secs using 597.4% CPU
9. Current log-likelihood: -110956.463
10. Current log-likelihood: -110956.411
11. Current log-likelihood: -110956.358
12. Current log-likelihood: -110956.307
Optimizing NNI: done in 4.50722 secs using 597% CPU
13. Current log-likelihood: -110956.257
14. Current log-likelihood: -110956.208
15. Current log-likelihood: -110956.159
16. Current log-likelihood: -110956.112
Optimizing NNI: done in 4.06621 secs using 597.5% CPU
Iteration 220 / LogL: -188185.270 / Time: 0h:18m:22s (0h:8m:3s left)
17. Current log-likelihood: -110956.065
18. Current log-likelihood: -110956.019
19. Current log-likelihood: -110955.973
20. Current log-likelihood: -110955.930
Optimizing NNI: done in 4.38543 secs using 596.8% CPU
21. Current log-likelihood: -110955.887
22. Current log-likelihood: -110955.845
23. Current log-likelihood: -110955.804
24. Current log-likelihood: -110955.762
Optimizing NNI: done in 4.32164 secs using 597.2% CPU
25. Current log-likelihood: -110955.723
26. Current log-likelihood: -110955.682
27. Current log-likelihood: -110955.643
28. Current log-likelihood: -110955.604
Optimizing NNI: done in 4.38724 secs using 597.1% CPU
29. Current log-likelihood: -110955.566
30. Current log-likelihood: -110955.528
31. Current log-likelihood: -110955.491
32. Current log-likelihood: -110955.453
33. Current log-likelihood: -110955.417
Optimizing NNI: done in 4.53971 secs using 597.6% CPU
34. Current log-likelihood: -110955.383
35. Current log-likelihood: -110955.349
36. Current log-likelihood: -110955.316
37. Current log-likelihood: -110955.283
38. Current log-likelihood: -110955.251
Optimizing NNI: done in 4.50658 secs using 598.2% CPU
Estimate model parameters (epsilon = 0.100)
39. Current log-likelihood: -110955.219
BETTER TREE FOUND at iteration 225: -188163.601
40. Current log-likelihood: -110955.187
41. Current log-likelihood: -110955.155
42. Current log-likelihood: -110955.125
43. Current log-likelihood: -110955.106
44. Current log-likelihood: -110955.074
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Optimizing NNI: done in 4.74992 secs using 597% CPU
46. Current log-likelihood: -110955.025
47. Current log-likelihood: -110954.996
48. Current log-likelihood: -110954.979
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Optimizing NNI: done in 4.41097 secs using 597% CPU
51. Current log-likelihood: -110954.923
52. Current log-likelihood: -110954.904
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55. Current log-likelihood: -110954.838
Optimizing NNI: done in 4.36164 secs using 597.4% CPU
56. Current log-likelihood: -110954.822
57. Current log-likelihood: -110954.804
58. Current log-likelihood: -110954.785
59. Current log-likelihood: -110954.757
60. Current log-likelihood: -110954.741
61. Current log-likelihood: -110954.723
Optimizing NNI: done in 4.30913 secs using 597.1% CPU
62. Current log-likelihood: -110954.705
63. Current log-likelihood: -110954.678
64. Current log-likelihood: -110954.662
65. Current log-likelihood: -110954.645
66. Current log-likelihood: -110954.628
67. Current log-likelihood: -110954.612
68. Current log-likelihood: -110954.594
Optimizing NNI: done in 5.53821 secs using 597.3% CPU
Iteration 230 / LogL: -188206.470 / Time: 0h:19m:10s (0h:7m:57s left)
69. Current log-likelihood: -110954.578
70. Current log-likelihood: -110954.561
71. Current log-likelihood: -110954.546
72. Current log-likelihood: -110954.528
Optimizing NNI: done in 4.21305 secs using 597.7% CPU
73. Current log-likelihood: -110954.502
74. Current log-likelihood: -110954.487
75. Current log-likelihood: -110954.471
76. Current log-likelihood: -110954.455
77. Current log-likelihood: -110954.440
78. Current log-likelihood: -110954.425
79. Current log-likelihood: -110954.410
80. Current log-likelihood: -110954.394
81. Current log-likelihood: -110954.379
Optimizing NNI: done in 4.82365 secs using 597% CPU
82. Current log-likelihood: -110954.365
83. Current log-likelihood: -110954.350
84. Current log-likelihood: -110954.336
85. Current log-likelihood: -110954.321
86. Current log-likelihood: -110954.307
87. Current log-likelihood: -110954.293
88. Current log-likelihood: -110954.279
Optimizing NNI: done in 4.5713 secs using 597.6% CPU
89. Current log-likelihood: -110954.265
90. Current log-likelihood: -110954.251
91. Current log-likelihood: -110954.237
92. Current log-likelihood: -110954.223
93. Current log-likelihood: -110954.210
94. Current log-likelihood: -110954.196
95. Current log-likelihood: -110954.183
96. Current log-likelihood: -110954.170
Optimizing NNI: done in 4.52348 secs using 598% CPU
97. Current log-likelihood: -110954.156
98. Current log-likelihood: -110954.143
99. Current log-likelihood: -110954.129
Optimal log-likelihood: -110954.129
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.058,0.027) (0.061,0.080) (0.083,0.165) (0.122,0.277) (0.116,0.454) (0.117,0.708) (0.168,1.130) (0.185,1.794) (0.062,4.652)
Parameters optimization took 99 rounds (84.431 sec)
BEST SCORE FOUND : -110954.129
Total tree length: 185.210

Total number of iterations: 255
CPU time used for tree search: 2356.083 sec (0h:39m:16s)
Wall-clock time used for tree search: 599.491 sec (0h:9m:59s)
Total CPU time used: 2831.763 sec (0h:47m:11s)
Total wall-clock time used: 718.935 sec (0h:11m:58s)

===> START BOOTSTRAP REPLICATE NUMBER 57

Creating bootstrap alignment (seed: 68239)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.127 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104642.278
2. Current log-likelihood: -102603.761
Optimizing NNI: done in 4.55924 secs using 597.3% CPU
3. Current log-likelihood: -102548.775
4. Current log-likelihood: -102545.385
5. Current log-likelihood: -102541.592
Optimizing NNI: done in 4.82774 secs using 597% CPU
6. Current log-likelihood: -102539.132
7. Current log-likelihood: -102538.192
Optimizing NNI: done in 3.82339 secs using 597.7% CPU
8. Current log-likelihood: -102537.800
9. Current log-likelihood: -102537.531
10. Current log-likelihood: -102537.415
Optimizing NNI: done in 4.22602 secs using 596.7% CPU
Optimal log-likelihood: -102537.261
Proportion of invariable sites: 0.021
Site proportion and rates:  (0.078,0.037) (0.086,0.116) (0.115,0.210) (0.129,0.337) (0.101,0.556) (0.137,0.845) (0.121,1.386) (0.142,2.011) (0.070,4.221)
Parameters optimization took 10 rounds (15.981 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Computing ML distances took 4.645334 sec (of wall-clock time) 18.577385 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000736952 secs using 414.5% CPU
Constructing RapidNJ tree: done in 0.00876713 secs using 375.7% CPU
Computing RapidNJ tree took 0.009557 sec (of wall-clock time) 0.038480 sec (of CPU time)
Log-likelihood of RapidNJ tree: -102881.520
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 4.88096 secs using 597.7% CPU
Iteration 240 / LogL: -188339.681 / Time: 0h:19m:56s (0h:7m:5s left)
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10.703 second
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Computing log-likelihood of 98 initial trees ... 10.107 seconds
Current best score: -102537.261

Do NNI search on 20 best initial trees
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Iteration 20 / LogL: -102166.509 / Time: 0h:2m:1s
Finish initializing candidate tree set (20)
Current best tree score: -102032.220 / CPU time: 99.600
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 191: -102007.635
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Iteration 290 / LogL: -102021.597 / Time: 0h:12m:4s (0h:0m:22s left)
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Iteration 400 / LogL: -188368.865 / Time: 0h:31m:53s (0h:3m:21s left)
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Iteration 300 / LogL: -102077.965 / Time: 0h:12m:24s (0h:0m:-3s left)
TREE SEARCH COMPLETED AFTER 300 ITERATIONS / Time: 0h:12m:24s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102003.120
2. Current log-likelihood: -102003.102
3. Current log-likelihood: -102003.086
4. Current log-likelihood: -102003.070
Optimizing NNI: done in 4.53384 secs using 597.3% CPU
5. Current log-likelihood: -102003.054
6. Current log-likelihood: -102003.038
7. Current log-likelihood: -102003.022
8. Current log-likelihood: -102003.006
9. Current log-likelihood: -102002.990
10. Current log-likelihood: -102002.974
11. Current log-likelihood: -102002.958
Optimizing NNI: done in 4.66632 secs using 596.9% CPU
12. Current log-likelihood: -102002.943
13. Current log-likelihood: -102002.928
14. Current log-likelihood: -102002.913
15. Current log-likelihood: -102002.899
16. Current log-likelihood: -102002.884
17. Current log-likelihood: -102002.870
18. Current log-likelihood: -102002.855
Optimizing NNI: done in 4.58865 secs using 596.9% CPU
19. Current log-likelihood: -102002.841
20. Current log-likelihood: -102002.827
21. Current log-likelihood: -102002.813
22. Current log-likelihood: -102002.799
23. Current log-likelihood: -102002.785
24. Current log-likelihood: -102002.772
Optimizing NNI: done in 4.43881 secs using 596.7% CPU
25. Current log-likelihood: -102002.758
26. Current log-likelihood: -102002.744
27. Current log-likelihood: -102002.731
28. Current log-likelihood: -102002.717
29. Current log-likelihood: -102002.704
30. Current log-likelihood: -102002.691
31. Current log-likelihood: -102002.678
Optimizing NNI: done in 4.39483 secs using 597.4% CPU
32. Current log-likelihood: -102002.666
33. Current log-likelihood: -102002.653
34. Current log-likelihood: -102002.641
35. Current log-likelihood: -102002.629
36. Current log-likelihood: -102002.616
37. Current log-likelihood: -102002.604
Optimizing NNI: done in 4.64766 secs using 596.8% CPU
38. Current log-likelihood: -102002.591
39. Current log-likelihood: -102002.578
40. Current log-likelihood: -102002.566
41. Current log-likelihood: -102002.554
42. Current log-likelihood: -102002.542
43. Current log-likelihood: -102002.530
44. Current log-likelihood: -102002.518
45. Current log-likelihood: -102002.506
46. Current log-likelihood: -102002.494
Optimizing NNI: done in 5.96045 secs using 596.4% CPU
Optimal log-likelihood: -102002.479
Proportion of invariable sites: 0.020
Site proportion and rates:  (0.067,0.026) (0.093,0.092) (0.120,0.200) (0.125,0.327) (0.112,0.544) (0.129,0.829) (0.140,1.391) (0.126,2.046) (0.069,4.440)
Parameters optimization took 46 rounds (31.978 sec)
BEST SCORE FOUND : -102002.479
Total tree length: 164.208

Total number of iterations: 300
CPU time used for tree search: 2848.015 sec (0h:47m:28s)
Wall-clock time used for tree search: 722.464 sec (0h:12m:2s)
Total CPU time used: 3063.102 sec (0h:51m:3s)
Total wall-clock time used: 776.450 sec (0h:12m:56s)

===> START BOOTSTRAP REPLICATE NUMBER 58

Creating bootstrap alignment (seed: 68240)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.116 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104046.884
2. Current log-likelihood: -102087.369
Optimizing NNI: done in 4.20256 secs using 597.8% CPU
3. Current log-likelihood: -102003.741
4. Current log-likelihood: -101997.659
5. Current log-likelihood: -101996.934
Optimizing NNI: done in 4.31894 secs using 597.7% CPU
6. Current log-likelihood: -101996.714
7. Current log-likelihood: -101996.579
Optimal log-likelihood: -101996.459
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.092,0.040) (0.104,0.127) (0.091,0.212) (0.111,0.386) (0.131,0.562) (0.090,0.856) (0.136,1.346) (0.158,1.979) (0.061,4.520)
Parameters optimization took 7 rounds (11.493 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 3.95079 secs using 597.2% CPU
Iteration 410 / LogL: -188167.842 / Time: 0h:32m:39s (0h:2m:33s left)
Calculating distance matrix: done in 4.61046 secs using 399.9% CPU
Computing ML distances took 4.610729 sec (of wall-clock time) 18.438013 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000720024 secs using 134% CPU
Constructing RapidNJ tree: done in 0.00854301 secs using 448% CPU
Computing RapidNJ tree took 0.009323 sec (of wall-clock time) 0.039598 sec (of CPU time)
Optimizing NNI: done in 4.08498 secs using 597.2% CPU
Log-likelihood of RapidNJ tree: -102211.751
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.11253 secs using 597.2% CPU
10.547 second
Optimizing NNI: done in 6.637 secs using 597.6% CPU
Optimizing NNI: done in 5.63241 secs using 597.9% CPU
Computing log-likelihood of 98 initial trees ... 10.042 seconds
Current best score: -101996.459

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.78457 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 6.41414 secs using 597.8% CPU
Optimizing NNI: done in 7.43778 secs using 597.7% CPU
BETTER TREE FOUND at iteration 1: -101467.042
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.54355 secs using 597.6% CPU
BETTER TREE FOUND at iteration 4: -101443.201
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Iteration 420 / LogL: -188334.998 / Time: 0h:33m:32s (0h:1m:45s left)
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Iteration 10 / LogL: -101497.007 / Time: 0h:1m:15s
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Iteration 20 / LogL: -101476.794 / Time: 0h:1m:38s
Finish initializing candidate tree set (20)
Current best tree score: -101443.201 / CPU time: 81.389
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.28764 secs using 597% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.91994 secs using 597% CPU
BETTER TREE FOUND at iteration 22: -101418.269
Optimizing NNI: done in 2.03199 secs using 398.5% CPU
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Iteration 430 / LogL: -188196.277 / Time: 0h:34m:16s (0h:0m:57s left)
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Iteration 30 / LogL: -101430.960 / Time: 0h:2m:4s (0h:6m:33s left)
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BETTER TREE FOUND at iteration 39: -101408.514
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Iteration 440 / LogL: -188185.406 / Time: 0h:35m:1s (0h:0m:9s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 43: -101406.458
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Estimate model parameters (epsilon = 0.100)
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TREE SEARCH COMPLETED AFTER 443 ITERATIONS / Time: 0h:35m:15s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -188158.765
BETTER TREE FOUND at iteration 47: -101405.067
Optimal log-likelihood: -188158.764
Site proportion and rates:  (0.010,0.099) (0.067,0.257) (0.101,0.388) (0.240,0.552) (0.187,0.757) (0.165,1.091) (0.126,1.667) (0.105,2.662)
Parameters optimization took 1 rounds (0.712 sec)
BEST SCORE FOUND : -188158.764
Total tree length: 148.886

Total number of iterations: 443
CPU time used for tree search: 12293.935 sec (3h:24m:53s)
Wall-clock time used for tree search: 2082.595 sec (0h:34m:42s)
Total CPU time used: 12492.702 sec (3h:28m:12s)
Total wall-clock time used: 2115.991 sec (0h:35m:15s)

===> START BOOTSTRAP REPLICATE NUMBER 32

Creating bootstrap alignment (seed: 70495)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.258 seconds

NOTE: 242 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196989.251
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2. Current log-likelihood: -194311.494
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3. Current log-likelihood: -194285.626
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Iteration 50 / LogL: -101456.506 / Time: 0h:2m:55s (0h:5m:46s left)
4. Current log-likelihood: -194282.049
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5. Current log-likelihood: -194277.560
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6. Current log-likelihood: -194272.826
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7. Current log-likelihood: -194269.610
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Estimate model parameters (epsilon = 0.100)
8. Current log-likelihood: -194268.887
BETTER TREE FOUND at iteration 54: -101397.147
Optimal log-likelihood: -194268.801
Site proportion and rates:  (0.012,0.099) (0.030,0.195) (0.158,0.346) (0.202,0.548) (0.173,0.758) (0.151,1.027) (0.176,1.599) (0.098,2.665)
Parameters optimization took 8 rounds (19.717 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 9.82493 secs using 599.9% CPU
Computing ML distances took 9.825471 sec (of wall-clock time) 58.946330 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00134182 secs using 191.7% CPU
Constructing RapidNJ tree: done in 0.022903 secs using 676.7% CPU
Computing RapidNJ tree took 0.024314 sec (of wall-clock time) 0.157873 sec (of CPU time)
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Iteration 60 / LogL: -101412.802 / Time: 0h:3m:20s (0h:5m:19s left)
Log-likelihood of RapidNJ tree: -197969.790
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.17473 secs using 398.9% CPU
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30.429 second
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Computing log-likelihood of 98 initial trees ... 16.643 seconds
Current best score: -194268.801

Do NNI search on 20 best initial trees
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Iteration 80 / LogL: -101411.152 / Time: 0h:4m:9s (0h:3m:53s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -193845.235 / Time: 0h:2m:53s
Finish initializing candidate tree set (20)
Current best tree score: -193676.691 / CPU time: 139.603
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 82: -193607.865
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BETTER TREE FOUND at iteration 89: -193605.876
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TREE SEARCH COMPLETED AFTER 312 ITERATIONS / Time: 0h:13m:5s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101388.467
2. Current log-likelihood: -101388.452
3. Current log-likelihood: -101388.440
Optimizing NNI: done in 5.39613 secs using 596.6% CPU
4. Current log-likelihood: -101388.429
Optimal log-likelihood: -101388.416
Proportion of invariable sites: 0.026
Site proportion and rates:  (0.092,0.036) (0.108,0.123) (0.085,0.199) (0.133,0.384) (0.132,0.586) (0.076,0.920) (0.132,1.352) (0.156,1.960) (0.060,4.765)
Parameters optimization took 4 rounds (2.526 sec)
BEST SCORE FOUND : -101388.416
Total tree length: 158.291

Total number of iterations: 312
CPU time used for tree search: 3031.744 sec (0h:50m:31s)
Wall-clock time used for tree search: 768.480 sec (0h:12m:48s)
Total CPU time used: 3111.256 sec (0h:51m:51s)
Total wall-clock time used: 788.401 sec (0h:13m:8s)

===> START BOOTSTRAP REPLICATE NUMBER 59

Creating bootstrap alignment (seed: 68241)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.145 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -108322.505
2. Current log-likelihood: -106329.772
3. Current log-likelihood: -106276.526
Optimizing NNI: done in 4.77768 secs using 597.2% CPU
4. Current log-likelihood: -106275.454
5. Current log-likelihood: -106275.090
6. Current log-likelihood: -106274.854
Optimizing NNI: done in 5.40913 secs using 598% CPU
7. Current log-likelihood: -106274.752
Optimal log-likelihood: -106274.619
Proportion of invariable sites: 0.021
Site proportion and rates:  (0.085,0.039) (0.087,0.121) (0.052,0.207) (0.113,0.308) (0.115,0.472) (0.111,0.696) (0.128,1.048) (0.215,1.762) (0.072,4.082)
Parameters optimization took 7 rounds (11.212 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 5.15734 secs using 598% CPU
Calculating distance matrix: done in 4.59267 secs using 400% CPU
Computing ML distances took 4.592956 sec (of wall-clock time) 18.370070 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000705957 secs using 411.8% CPU
Constructing RapidNJ tree: done in 0.00834894 secs using 395.7% CPU
Computing RapidNJ tree took 0.009106 sec (of wall-clock time) 0.036678 sec (of CPU time)
Log-likelihood of RapidNJ tree: -106517.625
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 7.47664 secs using 596.7% CPU
10.507 second
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Computing log-likelihood of 98 initial trees ... 10.086 seconds
Current best score: -106274.619

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 110 / LogL: -193720.830 / Time: 0h:11m:20s (0h:8m:31s left)
BETTER TREE FOUND at iteration 1: -105893.834
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -105796.133
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 7: -105752.806
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 12: -105733.299
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Iteration 120 / LogL: -193610.372 / Time: 0h:12m:14s (0h:7m:24s left)
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Iteration 20 / LogL: -105842.950 / Time: 0h:2m:15s
Finish initializing candidate tree set (20)
Current best tree score: -105733.299 / CPU time: 118.409
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 130: -193590.246
Iteration 130 / LogL: -193590.246 / Time: 0h:13m:8s (0h:10m:11s left)
BETTER TREE FOUND at iteration 33: -105732.611
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 41: -105717.079
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Iteration 80 / LogL: -105712.009 / Time: 0h:5m:3s (0h:4m:32s left)
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Iteration 160 / LogL: -193609.355 / Time: 0h:15m:43s (0h:6m:55s left)
Optimizing NNI: done in 2.30678 secs using 397.8% CPU
Optimizing NNI: done in 2.36196 secs using 397.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.77126 secs using 596.9% CPU
BETTER TREE FOUND at iteration 90: -105703.103
Iteration 90 / LogL: -105703.103 / Time: 0h:5m:30s (0h:6m:11s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.45826 secs using 597.2% CPU
BETTER TREE FOUND at iteration 98: -105702.640
Optimizing NNI: done in 2.1899 secs using 397.3% CPU
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Iteration 100 / LogL: -105715.703 / Time: 0h:5m:57s (0h:5m:53s left)
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Iteration 170 / LogL: -193622.119 / Time: 0h:16m:35s (0h:5m:53s left)
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Iteration 110 / LogL: -105729.565 / Time: 0h:6m:21s (0h:5m:8s left)
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Optimizing NNI: done in 4.72686 secs using 597.5% CPU
BETTER TREE FOUND at iteration 116: -105702.245
Optimizing NNI: done in 2.33789 secs using 397.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 120: -105701.424
Iteration 120 / LogL: -105701.424 / Time: 0h:6m:48s (0h:5m:43s left)
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Iteration 180 / LogL: -193593.863 / Time: 0h:17m:26s (0h:4m:52s left)
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Iteration 130 / LogL: -105729.255 / Time: 0h:7m:12s (0h:5m:1s left)
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Iteration 140 / LogL: -105703.875 / Time: 0h:7m:38s (0h:4m:23s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 147: -105700.125
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Iteration 190 / LogL: -193691.780 / Time: 0h:18m:17s (0h:3m:52s left)
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Iteration 150 / LogL: -105728.606 / Time: 0h:8m:4s (0h:5m:15s left)
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Iteration 160 / LogL: -105770.077 / Time: 0h:8m:27s (0h:4m:37s left)
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Iteration 200 / LogL: -193614.206 / Time: 0h:19m:8s (0h:2m:53s left)
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Iteration 170 / LogL: -105700.351 / Time: 0h:8m:52s (0h:4m:2s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 171: -105698.896
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 179: -105698.545
Optimizing NNI: done in 4.39828 secs using 598.1% CPU
Estimate model parameters (epsilon = 0.100)
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Iteration 180 / LogL: -105705.287 / Time: 0h:9m:20s (0h:5m:9s left)
BETTER TREE FOUND at iteration 206: -193589.519
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Iteration 210 / LogL: -193606.873 / Time: 0h:20m:0s (0h:9m:11s left)
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Iteration 190 / LogL: -106024.742 / Time: 0h:9m:45s (0h:4m:35s left)
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Iteration 200 / LogL: -105705.678 / Time: 0h:10m:11s (0h:4m:2s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 205: -105697.262
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Iteration 220 / LogL: -193608.054 / Time: 0h:20m:50s (0h:8m:10s left)
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Iteration 210 / LogL: -105712.133 / Time: 0h:10m:37s (0h:4m:49s left)
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Iteration 220 / LogL: -105710.748 / Time: 0h:11m:0s (0h:4m:16s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 226: -193580.255
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Iteration 230 / LogL: -105777.259 / Time: 0h:11m:23s (0h:3m:43s left)
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Iteration 230 / LogL: -193590.826 / Time: 0h:21m:45s (0h:9m:7s left)
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Iteration 240 / LogL: -105725.454 / Time: 0h:11m:47s (0h:3m:12s left)
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Iteration 250 / LogL: -105744.774 / Time: 0h:12m:12s (0h:2m:41s left)
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Iteration 240 / LogL: -193641.591 / Time: 0h:22m:36s (0h:8m:8s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 254: -105697.143
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Iteration 260 / LogL: -105735.040 / Time: 0h:12m:37s (0h:4m:34s left)
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Iteration 270 / LogL: -105709.030 / Time: 0h:13m:2s (0h:4m:4s left)
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Iteration 250 / LogL: -193599.400 / Time: 0h:23m:31s (0h:7m:10s left)
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BETTER TREE FOUND at iteration 324: -105696.622
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 359: -105696.517
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Iteration 460 / LogL: -105738.902 / Time: 0h:20m:52s (0h:0m:-3s left)
TREE SEARCH COMPLETED AFTER 460 ITERATIONS / Time: 0h:20m:52s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -105696.517
Optimal log-likelihood: -105696.517
Proportion of invariable sites: 0.021
Site proportion and rates:  (0.086,0.035) (0.094,0.115) (0.135,0.257) (0.127,0.423) (0.104,0.646) (0.112,0.929) (0.188,1.493) (0.073,2.227) (0.061,4.645)
Parameters optimization took 1 rounds (0.338 sec)
BEST SCORE FOUND : -105696.517
Total tree length: 171.385

Total number of iterations: 460
CPU time used for tree search: 4885.414 sec (1h:21m:25s)
Wall-clock time used for tree search: 1235.924 sec (0h:20m:35s)
Total CPU time used: 4954.553 sec (1h:22m:34s)
Total wall-clock time used: 1253.235 sec (0h:20m:53s)

===> START BOOTSTRAP REPLICATE NUMBER 60

Creating bootstrap alignment (seed: 68242)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.089 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105063.120
2. Current log-likelihood: -103142.568
Optimizing NNI: done in 5.15019 secs using 598% CPU
3. Current log-likelihood: -103080.831
4. Current log-likelihood: -103078.874
Optimal log-likelihood: -103078.837
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.082,0.038) (0.101,0.120) (0.060,0.204) (0.102,0.320) (0.091,0.453) (0.134,0.680) (0.110,1.067) (0.229,1.831) (0.062,4.369)
Parameters optimization took 4 rounds (6.161 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.81235 secs using 596.8% CPU
Calculating distance matrix: done in 4.75309 secs using 399.9% CPU
Computing ML distances took 4.753353 sec (of wall-clock time) 19.006400 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000720024 secs using 417.1% CPU
Constructing RapidNJ tree: done in 0.00848889 secs using 375.5% CPU
Computing RapidNJ tree took 0.009268 sec (of wall-clock time) 0.036320 sec (of CPU time)
Log-likelihood of RapidNJ tree: -103361.759
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 6.05193 secs using 596.8% CPU
Optimizing NNI: done in 7.74451 secs using 597% CPU
10.614 second
Optimizing NNI: done in 7.21018 secs using 597.3% CPU
Computing log-likelihood of 98 initial trees ... 9.954 seconds
Current best score: -103078.837

Do NNI search on 20 best initial trees
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Iteration 350 / LogL: -193608.338 / Time: 0h:31m:46s (0h:2m:27s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -102630.782
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -102604.394
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 5: -102602.869
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Iteration 360 / LogL: -193587.612 / Time: 0h:32m:35s (0h:1m:32s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 9: -102571.017
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Iteration 10 / LogL: -102866.666 / Time: 0h:1m:33s
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Iteration 20 / LogL: -102932.457 / Time: 0h:1m:55s
Finish initializing candidate tree set (20)
Current best tree score: -102571.017 / CPU time: 103.522
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 23: -102568.699
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 24: -102547.806
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -102546.403
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Iteration 370 / LogL: -194117.954 / Time: 0h:33m:26s (0h:0m:38s left)
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Iteration 30 / LogL: -102579.855 / Time: 0h:2m:22s (0h:7m:47s left)
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Iteration 40 / LogL: -102578.171 / Time: 0h:2m:44s (0h:5m:57s left)
Optimizing NNI: done in 4.2121 secs using 597.6% CPU
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TREE SEARCH COMPLETED AFTER 378 ITERATIONS / Time: 0h:34m:2s

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|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -193576.257
Optimal log-likelihood: -193576.257
Site proportion and rates:  (0.017,0.113) (0.024,0.201) (0.165,0.340) (0.182,0.543) (0.178,0.742) (0.160,1.016) (0.179,1.606) (0.095,2.691)
Parameters optimization took 1 rounds (0.519 sec)
BEST SCORE FOUND : -193576.257
Total tree length: 155.567

Total number of iterations: 378
CPU time used for tree search: 11849.006 sec (3h:17m:29s)
Wall-clock time used for tree search: 2009.232 sec (0h:33m:29s)
Total CPU time used: 12052.581 sec (3h:20m:52s)
Total wall-clock time used: 2043.356 sec (0h:34m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 33

Creating bootstrap alignment (seed: 70496)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.286 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -195912.878
Optimizing NNI: done in 2.18823 secs using 398.7% CPU
Optimizing NNI: done in 1.85755 secs using 398.6% CPU
2. Current log-likelihood: -193465.581
Optimizing NNI: done in 2.25994 secs using 398.4% CPU
3. Current log-likelihood: -193421.112
Optimizing NNI: done in 2.18482 secs using 398.7% CPU
4. Current log-likelihood: -193418.205
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5. Current log-likelihood: -193417.340
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6. Current log-likelihood: -193416.677
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7. Current log-likelihood: -193416.134
Optimizing NNI: done in 2.33277 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
8. Current log-likelihood: -193415.744
BETTER TREE FOUND at iteration 50: -102543.951
Iteration 50 / LogL: -102543.951 / Time: 0h:3m:8s (0h:6m:24s left)
9. Current log-likelihood: -193415.499
Optimizing NNI: done in 1.94225 secs using 398.6% CPU
10. Current log-likelihood: -193415.369
Optimizing NNI: done in 2.35933 secs using 398% CPU
Optimal log-likelihood: -193415.315
Site proportion and rates:  (0.023,0.108) (0.003,0.155) (0.151,0.326) (0.186,0.524) (0.140,0.697) (0.260,1.010) (0.120,1.581) (0.119,2.538)
Parameters optimization took 10 rounds (22.166 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 10.1033 secs using 599.9% CPU
Computing ML distances took 10.103837 sec (of wall-clock time) 60.608005 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00128698 secs using 274.7% CPU
Constructing RapidNJ tree: done in 0.0225172 secs using 676.5% CPU
Computing RapidNJ tree took 0.023885 sec (of wall-clock time) 0.156908 sec (of CPU time)
Optimizing NNI: done in 1.95831 secs using 399.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 57: -102542.618
Log-likelihood of RapidNJ tree: -198865.554
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.78095 secs using 399.1% CPU
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Iteration 60 / LogL: -102635.697 / Time: 0h:3m:30s (0h:5m:45s left)
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Iteration 70 / LogL: -102602.224 / Time: 0h:3m:49s (0h:4m:49s left)
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30.073 second
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 78: -102541.016
Optimizing NNI: done in 2.05733 secs using 398.7% CPU
Computing log-likelihood of 98 initial trees ... 16.239 seconds
Current best score: -193415.315

Do NNI search on 20 best initial trees
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Iteration 80 / LogL: -102550.198 / Time: 0h:4m:12s (0h:5m:12s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -192882.719
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Iteration 90 / LogL: -102546.925 / Time: 0h:4m:32s (0h:4m:28s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 92: -102539.270
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Estimate model parameters (epsilon = 0.100)
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Iteration 100 / LogL: -102539.629 / Time: 0h:4m:56s (0h:4m:56s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 10: -192880.615
Iteration 10 / LogL: -192880.615 / Time: 0h:2m:20s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 17: -192860.645
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Iteration 20 / LogL: -192888.128 / Time: 0h:3m:6s
Finish initializing candidate tree set (20)
Current best tree score: -192860.645 / CPU time: 152.103
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 130: -102536.264
Iteration 130 / LogL: -102536.264 / Time: 0h:5m:59s (0h:4m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 152: -102531.950
BETTER TREE FOUND at iteration 28: -192815.891
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Iteration 40 / LogL: -192882.420 / Time: 0h:5m:10s (0h:11m:39s left)
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Iteration 190 / LogL: -102561.751 / Time: 0h:8m:1s (0h:2m:37s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 198: -102531.675
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Iteration 200 / LogL: -102589.990 / Time: 0h:8m:23s (0h:4m:8s left)
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Iteration 210 / LogL: -102539.429 / Time: 0h:8m:42s (0h:3m:39s left)
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Iteration 50 / LogL: -192844.299 / Time: 0h:5m:58s (0h:9m:29s left)
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Iteration 220 / LogL: -102540.189 / Time: 0h:9m:1s (0h:3m:12s left)
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Iteration 230 / LogL: -102570.347 / Time: 0h:9m:22s (0h:2m:47s left)
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Iteration 60 / LogL: -192834.479 / Time: 0h:6m:45s (0h:7m:46s left)
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Iteration 240 / LogL: -102535.105 / Time: 0h:9m:43s (0h:2m:21s left)
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Iteration 250 / LogL: -102536.099 / Time: 0h:10m:3s (0h:1m:56s left)
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Iteration 70 / LogL: -192838.843 / Time: 0h:7m:31s (0h:6m:19s left)
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Iteration 260 / LogL: -102536.211 / Time: 0h:10m:22s (0h:1m:31s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 72: -192814.304
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Iteration 270 / LogL: -102572.568 / Time: 0h:10m:44s (0h:1m:7s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 274: -102531.210
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Iteration 280 / LogL: -102540.812 / Time: 0h:11m:5s (0h:3m:44s left)
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Iteration 290 / LogL: -102562.161 / Time: 0h:11m:26s (0h:3m:19s left)
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Iteration 320 / LogL: -102549.343 / Time: 0h:12m:27s (0h:2m:6s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.81833 secs using 398.7% CPU
Optimizing NNI: done in 1.95351 secs using 398.7% CPU
Iteration 330 / LogL: -102543.964 / Time: 0h:12m:45s (0h:1m:42s left)
BETTER TREE FOUND at iteration 100: -192804.933
Iteration 100 / LogL: -192804.933 / Time: 0h:9m:56s (0h:10m:2s left)
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Iteration 340 / LogL: -102551.191 / Time: 0h:13m:6s (0h:1m:18s left)
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Iteration 350 / LogL: -102540.310 / Time: 0h:13m:26s (0h:0m:55s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 109: -192800.191
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Iteration 110 / LogL: -192809.479 / Time: 0h:10m:47s (0h:9m:47s left)
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Iteration 360 / LogL: -102540.496 / Time: 0h:13m:47s (0h:0m:32s left)
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Iteration 370 / LogL: -102563.751 / Time: 0h:14m:7s (0h:0m:9s left)
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Optimizing NNI: done in 1.97425 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 375 ITERATIONS / Time: 0h:14m:18s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102531.210
Optimal log-likelihood: -102531.206
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.074,0.032) (0.098,0.102) (0.073,0.195) (0.153,0.346) (0.133,0.577) (0.083,0.844) (0.097,1.238) (0.200,1.878) (0.060,4.592)
Parameters optimization took 1 rounds (0.915 sec)
BEST SCORE FOUND : -102531.206
Total tree length: 165.267

Total number of iterations: 375
CPU time used for tree search: 3340.391 sec (0h:55m:40s)
Wall-clock time used for tree search: 846.084 sec (0h:14m:6s)
Total CPU time used: 3392.367 sec (0h:56m:32s)
Total wall-clock time used: 859.078 sec (0h:14m:19s)

===> START BOOTSTRAP REPLICATE NUMBER 61

Creating bootstrap alignment (seed: 68243)...

Optimizing NNI: done in 4.37664 secs using 597% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.133 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106236.160
2. Current log-likelihood: -104128.938
3. Current log-likelihood: -104031.644
Optimizing NNI: done in 4.70909 secs using 597.3% CPU
Iteration 120 / LogL: -192875.107 / Time: 0h:11m:33s (0h:8m:38s left)
4. Current log-likelihood: -104027.471
5. Current log-likelihood: -104026.775
6. Current log-likelihood: -104026.165
Optimizing NNI: done in 4.92955 secs using 597.3% CPU
7. Current log-likelihood: -104025.593
8. Current log-likelihood: -104025.054
9. Current log-likelihood: -104024.549
Optimizing NNI: done in 4.47395 secs using 597.2% CPU
10. Current log-likelihood: -104024.083
11. Current log-likelihood: -104023.652
12. Current log-likelihood: -104023.260
13. Current log-likelihood: -104022.909
14. Current log-likelihood: -104022.588
Optimizing NNI: done in 5.99298 secs using 597.1% CPU
15. Current log-likelihood: -104022.287
16. Current log-likelihood: -104022.020
17. Current log-likelihood: -104021.872
Optimizing NNI: done in 4.87764 secs using 598% CPU
18. Current log-likelihood: -104021.723
19. Current log-likelihood: -104021.591
20. Current log-likelihood: -104021.465
Optimal log-likelihood: -104021.327
Proportion of invariable sites: 0.038
Site proportion and rates:  (0.090,0.038) (0.089,0.112) (0.086,0.194) (0.115,0.316) (0.070,0.428) (0.123,0.696) (0.111,1.173) (0.204,1.852) (0.073,4.253)
Parameters optimization took 20 rounds (29.974 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Computing ML distances took 4.614208 sec (of wall-clock time) 18.453886 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00068903 secs using 485.5% CPU
Constructing RapidNJ tree: done in 0.00869608 secs using 357.1% CPU
Computing RapidNJ tree took 0.009451 sec (of wall-clock time) 0.034455 sec (of CPU time)
Optimizing NNI: done in 4.62455 secs using 597.4% CPU
Log-likelihood of RapidNJ tree: -104703.545
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 6.41472 secs using 597.2% CPU
10.574 second
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Optimizing NNI: done in 6.60192 secs using 598.2% CPU
Computing log-likelihood of 98 initial trees ... 10.197 seconds
Current best score: -104021.327

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 20 / LogL: -103825.881 / Time: 0h:1m:53s
Finish initializing candidate tree set (20)
Current best tree score: -103596.136 / CPU time: 77.890
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 5.08409 secs using 597.5% CPU
Optimizing NNI: done in 2.19722 secs using 398.1% CPU
Optimizing NNI: done in 2.45395 secs using 398.8% CPU
Optimizing NNI: done in 4.35885 secs using 597.8% CPU
Optimizing NNI: done in 2.59585 secs using 398.5% CPU
Optimizing NNI: done in 2.27244 secs using 398.6% CPU
Optimizing NNI: done in 4.56527 secs using 597.6% CPU
Optimizing NNI: done in 2.17568 secs using 398.5% CPU
Iteration 190 / LogL: -103549.582 / Time: 0h:8m:44s (0h:1m:56s left)
Optimizing NNI: done in 2.43844 secs using 398.6% CPU
Optimizing NNI: done in 4.99925 secs using 597.7% CPU
Optimizing NNI: done in 2.11885 secs using 398.7% CPU
Optimizing NNI: done in 2.09707 secs using 398.7% CPU
Optimizing NNI: done in 2.39012 secs using 398.5% CPU
Optimizing NNI: done in 4.97305 secs using 596.9% CPU
Optimizing NNI: done in 2.35327 secs using 398.4% CPU
Optimizing NNI: done in 4.35778 secs using 597.1% CPU
Iteration 230 / LogL: -192813.217 / Time: 0h:20m:27s (0h:2m:35s left)
Optimizing NNI: done in 3.08426 secs using 398.1% CPU
Optimizing NNI: done in 1.84246 secs using 398.4% CPU
Optimizing NNI: done in 4.27261 secs using 597.8% CPU
Optimizing NNI: done in 2.27325 secs using 398.8% CPU
Optimizing NNI: done in 2.30325 secs using 398.2% CPU
Optimizing NNI: done in 4.25404 secs using 598.1% CPU
Optimizing NNI: done in 2.47503 secs using 399% CPU
Iteration 200 / LogL: -103588.349 / Time: 0h:9m:8s (0h:1m:28s left)
Optimizing NNI: done in 2.1694 secs using 398.3% CPU
Optimizing NNI: done in 4.60182 secs using 597.3% CPU
Optimizing NNI: done in 1.83276 secs using 398.5% CPU
Optimizing NNI: done in 2.07702 secs using 398.8% CPU
Optimizing NNI: done in 3.99639 secs using 597.5% CPU
Optimizing NNI: done in 2.40666 secs using 398.8% CPU
Optimizing NNI: done in 3.00294 secs using 397.7% CPU
Optimizing NNI: done in 4.53609 secs using 597.8% CPU
Optimizing NNI: done in 2.14051 secs using 398.3% CPU
Optimizing NNI: done in 1.98281 secs using 398.2% CPU
Optimizing NNI: done in 4.69839 secs using 597.6% CPU
Optimizing NNI: done in 2.55419 secs using 398.4% CPU
Optimizing NNI: done in 2.33185 secs using 398.5% CPU
Optimizing NNI: done in 4.50215 secs using 597.5% CPU
Optimizing NNI: done in 2.09893 secs using 398.2% CPU
Iteration 210 / LogL: -103849.611 / Time: 0h:9m:31s (0h:1m:0s left)
Optimizing NNI: done in 2.15037 secs using 398.6% CPU
Optimizing NNI: done in 4.29378 secs using 596.7% CPU
Optimizing NNI: done in 2.1548 secs using 398.3% CPU
Optimizing NNI: done in 2.07834 secs using 398.2% CPU
Optimizing NNI: done in 4.63885 secs using 597.5% CPU
Optimizing NNI: done in 2.12287 secs using 398.3% CPU
Optimizing NNI: done in 2.52743 secs using 397.9% CPU
Optimizing NNI: done in 4.40048 secs using 597.7% CPU
Iteration 240 / LogL: -192824.395 / Time: 0h:21m:11s (0h:1m:41s left)
Optimizing NNI: done in 2.32769 secs using 398.4% CPU
Optimizing NNI: done in 2.19076 secs using 398.1% CPU
Optimizing NNI: done in 4.40101 secs using 598.2% CPU
Optimizing NNI: done in 2.49914 secs using 398.5% CPU
Optimizing NNI: done in 2.33211 secs using 398.3% CPU
Optimizing NNI: done in 4.45998 secs using 597.4% CPU
Optimizing NNI: done in 2.05065 secs using 398.8% CPU
Iteration 220 / LogL: -103609.927 / Time: 0h:9m:54s (0h:0m:32s left)
Optimizing NNI: done in 2.01421 secs using 398.6% CPU
Optimizing NNI: done in 4.29691 secs using 597.8% CPU
Optimizing NNI: done in 2.26648 secs using 398.4% CPU
Optimizing NNI: done in 3.04506 secs using 398.4% CPU
Optimizing NNI: done in 5.85869 secs using 597.1% CPU
Optimizing NNI: done in 2.22072 secs using 398.3% CPU
Optimizing NNI: done in 2.07378 secs using 398.2% CPU
Optimizing NNI: done in 5.07029 secs using 597.4% CPU
Optimizing NNI: done in 2.15036 secs using 398.2% CPU
Optimizing NNI: done in 2.67248 secs using 398% CPU
Optimizing NNI: done in 4.32678 secs using 597.4% CPU
Optimizing NNI: done in 2.39212 secs using 398.9% CPU
Optimizing NNI: done in 1.96022 secs using 398.1% CPU
Optimizing NNI: done in 2.05115 secs using 397.8% CPU
Iteration 230 / LogL: -103537.649 / Time: 0h:10m:17s (0h:0m:5s left)
Optimizing NNI: done in 5.50286 secs using 597.2% CPU
Optimizing NNI: done in 2.05277 secs using 398.5% CPU
Optimizing NNI: done in 2.21704 secs using 398.2% CPU
Optimizing NNI: done in 4.41963 secs using 597.4% CPU
Optimizing NNI: done in 2.22533 secs using 398% CPU
TREE SEARCH COMPLETED AFTER 233 ITERATIONS / Time: 0h:10m:23s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -103535.208
2. Current log-likelihood: -103535.178
3. Current log-likelihood: -103535.134
Optimizing NNI: done in 4.91548 secs using 597.4% CPU
4. Current log-likelihood: -103535.092
5. Current log-likelihood: -103535.052
6. Current log-likelihood: -103535.012
7. Current log-likelihood: -103534.974
Optimizing NNI: done in 4.62617 secs using 597.5% CPU
Iteration 250 / LogL: -192817.205 / Time: 0h:22m:0s (0h:0m:47s left)
8. Current log-likelihood: -103534.937
9. Current log-likelihood: -103534.902
10. Current log-likelihood: -103534.869
11. Current log-likelihood: -103534.837
12. Current log-likelihood: -103534.804
Optimizing NNI: done in 4.38493 secs using 598.3% CPU
13. Current log-likelihood: -103534.773
14. Current log-likelihood: -103534.743
15. Current log-likelihood: -103534.724
16. Current log-likelihood: -103534.694
Optimizing NNI: done in 5.19573 secs using 597.9% CPU
17. Current log-likelihood: -103534.666
18. Current log-likelihood: -103534.640
19. Current log-likelihood: -103534.623
20. Current log-likelihood: -103534.605
21. Current log-likelihood: -103534.578
22. Current log-likelihood: -103534.562
Optimizing NNI: done in 4.60761 secs using 597.5% CPU
23. Current log-likelihood: -103534.544
24. Current log-likelihood: -103534.527
25. Current log-likelihood: -103534.511
26. Current log-likelihood: -103534.495
27. Current log-likelihood: -103534.479
28. Current log-likelihood: -103534.464
Optimizing NNI: done in 4.32499 secs using 597.5% CPU
29. Current log-likelihood: -103534.448
30. Current log-likelihood: -103534.433
31. Current log-likelihood: -103534.419
32. Current log-likelihood: -103534.404
33. Current log-likelihood: -103534.390
34. Current log-likelihood: -103534.376
35. Current log-likelihood: -103534.363
Optimizing NNI: done in 4.77513 secs using 597.7% CPU
36. Current log-likelihood: -103534.349
37. Current log-likelihood: -103534.337
38. Current log-likelihood: -103534.323
39. Current log-likelihood: -103534.311
40. Current log-likelihood: -103534.298
41. Current log-likelihood: -103534.286
Optimizing NNI: done in 4.17879 secs using 597.9% CPU
42. Current log-likelihood: -103534.274
43. Current log-likelihood: -103534.262
44. Current log-likelihood: -103534.250
45. Current log-likelihood: -103534.239
46. Current log-likelihood: -103534.227
47. Current log-likelihood: -103534.215
Optimizing NNI: done in 4.0574 secs using 597.8% CPU
48. Current log-likelihood: -103534.204
Optimal log-likelihood: -103534.191
Proportion of invariable sites: 0.038
Site proportion and rates:  (0.084,0.034) (0.082,0.094) (0.102,0.184) (0.130,0.318) (0.071,0.467) (0.108,0.721) (0.111,1.163) (0.200,1.855) (0.073,4.355)
Parameters optimization took 48 rounds (40.844 sec)
BEST SCORE FOUND : -103534.191
Total tree length: 178.022

Total number of iterations: 233
CPU time used for tree search: 2311.275 sec (0h:38m:31s)
Wall-clock time used for tree search: 587.997 sec (0h:9m:47s)
Total CPU time used: 2616.443 sec (0h:43m:36s)
Total wall-clock time used: 664.619 sec (0h:11m:4s)

===> START BOOTSTRAP REPLICATE NUMBER 62

Creating bootstrap alignment (seed: 68244)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.104 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -110210.299
2. Current log-likelihood: -108131.474
Optimizing NNI: done in 4.66843 secs using 597.2% CPU
3. Current log-likelihood: -108057.398
4. Current log-likelihood: -108056.766
Optimal log-likelihood: -108056.721
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.108,0.038) (0.080,0.122) (0.086,0.213) (0.080,0.322) (0.069,0.460) (0.156,0.683) (0.141,1.120) (0.170,1.773) (0.085,4.063)
Parameters optimization took 4 rounds (6.038 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.27369 secs using 597.6% CPU
Calculating distance matrix: done in 4.693 secs using 399.8% CPU
Computing ML distances took 4.693289 sec (of wall-clock time) 18.764964 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000693798 secs using 441.8% CPU
Constructing RapidNJ tree: done in 0.00837803 secs using 348.1% CPU
Computing RapidNJ tree took 0.009138 sec (of wall-clock time) 0.032292 sec (of CPU time)
Log-likelihood of RapidNJ tree: -108240.565
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.51629 secs using 597.2% CPU
Iteration 260 / LogL: -192856.884 / Time: 0h:22m:45s (0h:0m:-6s left)
TREE SEARCH COMPLETED AFTER 260 ITERATIONS / Time: 0h:22m:45s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192775.691
Optimal log-likelihood: -192775.687
Site proportion and rates:  (0.024,0.109) (0.082,0.289) (0.090,0.381) (0.192,0.543) (0.118,0.722) (0.263,1.018) (0.109,1.610) (0.121,2.531)
Parameters optimization took 1 rounds (1.121 sec)
BEST SCORE FOUND : -192775.687
Total tree length: 152.548

Total number of iterations: 260
CPU time used for tree search: 7804.613 sec (2h:10m:4s)
Wall-clock time used for tree search: 1331.778 sec (0h:22m:11s)
Total CPU time used: 8014.232 sec (2h:13m:34s)
Total wall-clock time used: 1366.944 sec (0h:22m:46s)

===> START BOOTSTRAP REPLICATE NUMBER 34

Creating bootstrap alignment (seed: 70497)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.316 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196478.857
2. Current log-likelihood: -193652.769
3. Current log-likelihood: -193620.141
4. Current log-likelihood: -193614.358
10.858 second
5. Current log-likelihood: -193608.321
6. Current log-likelihood: -193605.469
7. Current log-likelihood: -193604.850
8. Current log-likelihood: -193604.728
Optimal log-likelihood: -193604.714
Site proportion and rates:  (0.013,0.072) (0.067,0.224) (0.105,0.353) (0.225,0.539) (0.134,0.736) (0.201,1.003) (0.151,1.617) (0.104,2.711)
Parameters optimization took 8 rounds (15.881 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Computing log-likelihood of 98 initial trees ... 9.958 seconds
Current best score: -108056.721

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.03453 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Calculating distance matrix: done in 10.1167 secs using 599.9% CPU
Computing ML distances took 10.117267 sec (of wall-clock time) 60.693053 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00145698 secs using 526.6% CPU
Constructing RapidNJ tree: done in 0.022378 secs using 666.3% CPU
Computing RapidNJ tree took 0.023904 sec (of wall-clock time) 0.159247 sec (of CPU time)
Log-likelihood of RapidNJ tree: -197998.315
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... BETTER TREE FOUND at iteration 1: -107509.177
Optimizing NNI: done in 2.15808 secs using 398% CPU
30.444 second
Optimizing NNI: done in 3.64171 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -107481.467
Optimizing NNI: done in 2.4803 secs using 398.6% CPU
Optimizing NNI: done in 2.38729 secs using 398.1% CPU
Optimizing NNI: done in 2.68949 secs using 398.7% CPU
Optimizing NNI: done in 2.20044 secs using 398.8% CPU
Computing log-likelihood of 98 initial trees ... 16.175 seconds
Current best score: -193604.714

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.57283 secs using 398.9% CPU
Optimizing NNI: done in 2.77075 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.43182 secs using 398.7% CPU
Optimizing NNI: done in 2.4243 secs using 399% CPU
Iteration 10 / LogL: -107488.279 / Time: 0h:1m:33s
BETTER TREE FOUND at iteration 1: -193006.660
Optimizing NNI: done in 2.59347 secs using 398.7% CPU
Optimizing NNI: done in 2.21655 secs using 399.2% CPU
Optimizing NNI: done in 4.00982 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.7049 secs using 398.9% CPU
BETTER TREE FOUND at iteration 2: -192897.101
Optimizing NNI: done in 2.43278 secs using 398.9% CPU
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Optimizing NNI: done in 4.09529 secs using 596.9% CPU
Optimizing NNI: done in 2.08138 secs using 398.5% CPU
Optimizing NNI: done in 2.13593 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.05401 secs using 598.1% CPU
BETTER TREE FOUND at iteration 17: -107471.976
Optimizing NNI: done in 4.32454 secs using 596.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.93766 secs using 398% CPU
BETTER TREE FOUND at iteration 5: -192864.794
Optimizing NNI: done in 2.43723 secs using 398.6% CPU
Optimizing NNI: done in 2.66701 secs using 398.7% CPU
Iteration 20 / LogL: -107545.389 / Time: 0h:2m:2s
Finish initializing candidate tree set (20)
Current best tree score: -107471.976 / CPU time: 110.363
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.06584 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.14061 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -192858.931
BETTER TREE FOUND at iteration 21: -107469.811
Optimizing NNI: done in 4.38371 secs using 597.8% CPU
Optimizing NNI: done in 2.38881 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -107459.120
Optimizing NNI: done in 3.94402 secs using 597.3% CPU
Optimizing NNI: done in 2.22145 secs using 399% CPU
Optimizing NNI: done in 2.28549 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.82701 secs using 597.3% CPU
BETTER TREE FOUND at iteration 24: -107438.520
Optimizing NNI: done in 3.9491 secs using 597.9% CPU
Iteration 10 / LogL: -192884.111 / Time: 0h:2m:8s
Optimizing NNI: done in 1.83206 secs using 398.4% CPU
Optimizing NNI: done in 1.77111 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.02243 secs using 596.8% CPU
BETTER TREE FOUND at iteration 26: -107437.469
Optimizing NNI: done in 2.05895 secs using 398.4% CPU
Optimizing NNI: done in 3.71531 secs using 597.8% CPU
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Optimizing NNI: done in 4.21514 secs using 597.5% CPU
Optimizing NNI: done in 1.89701 secs using 398.4% CPU
Iteration 30 / LogL: -107469.348 / Time: 0h:2m:35s (0h:8m:33s left)
Optimizing NNI: done in 1.97608 secs using 398.7% CPU
Optimizing NNI: done in 3.31156 secs using 597.7% CPU
Optimizing NNI: done in 1.85669 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -107431.471
Optimizing NNI: done in 4.29552 secs using 597.6% CPU
Optimizing NNI: done in 2.03263 secs using 398.9% CPU
Optimizing NNI: done in 1.84355 secs using 398.5% CPU
Optimizing NNI: done in 3.9275 secs using 597.4% CPU
Optimizing NNI: done in 1.95676 secs using 398% CPU
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Optimizing NNI: done in 1.99423 secs using 398% CPU
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Optimizing NNI: done in 2.45194 secs using 398.6% CPU
Optimizing NNI: done in 2.3826 secs using 398.4% CPU
Iteration 40 / LogL: -107454.785 / Time: 0h:2m:58s (0h:7m:1s left)
Optimizing NNI: done in 4.35563 secs using 597% CPU
Optimizing NNI: done in 2.31221 secs using 398.6% CPU
Optimizing NNI: done in 4.19388 secs using 597.8% CPU
Iteration 20 / LogL: -192939.074 / Time: 0h:2m:49s
Optimizing NNI: done in 1.93589 secs using 398.5% CPU
Finish initializing candidate tree set (20)
Current best tree score: -192858.931 / CPU time: 141.210
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.94339 secs using 398.8% CPU
Optimizing NNI: done in 2.13243 secs using 399% CPU
Optimizing NNI: done in 4.45362 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.84586 secs using 398.8% CPU
BETTER TREE FOUND at iteration 21: -192840.649
Optimizing NNI: done in 1.9832 secs using 398.8% CPU
Optimizing NNI: done in 1.84534 secs using 398.5% CPU
Optimizing NNI: done in 4.51349 secs using 596.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.04038 secs using 398.8% CPU
BETTER TREE FOUND at iteration 22: -192811.077
Optimizing NNI: done in 2.24458 secs using 398.4% CPU
Optimizing NNI: done in 2.08108 secs using 397.8% CPU
Iteration 50 / LogL: -107448.459 / Time: 0h:3m:19s (0h:5m:33s left)
Optimizing NNI: done in 2.27182 secs using 398.3% CPU
Optimizing NNI: done in 5.49744 secs using 596.7% CPU
Optimizing NNI: done in 2.18454 secs using 398.4% CPU
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Optimizing NNI: done in 3.99159 secs using 597.8% CPU
Optimizing NNI: done in 2.62871 secs using 398.5% CPU
Optimizing NNI: done in 4.23879 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.33183 secs using 398.1% CPU
BETTER TREE FOUND at iteration 26: -192798.751
Optimizing NNI: done in 1.83637 secs using 398.9% CPU
Optimizing NNI: done in 2.0127 secs using 398.4% CPU
Optimizing NNI: done in 4.22124 secs using 596.2% CPU
Optimizing NNI: done in 1.88758 secs using 398.7% CPU
Iteration 60 / LogL: -107457.674 / Time: 0h:3m:41s (0h:4m:29s left)
Optimizing NNI: done in 1.82177 secs using 398.2% CPU
Optimizing NNI: done in 1.88578 secs using 398.1% CPU
Optimizing NNI: done in 4.54324 secs using 596.7% CPU
Optimizing NNI: done in 2.03235 secs using 398.7% CPU
Optimizing NNI: done in 1.82126 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.16251 secs using 597.1% CPU
BETTER TREE FOUND at iteration 64: -107430.984
Optimizing NNI: done in 2.14234 secs using 398.7% CPU
Optimizing NNI: done in 2.08407 secs using 398.4% CPU
Optimizing NNI: done in 5.18546 secs using 597% CPU
Iteration 30 / LogL: -192872.545 / Time: 0h:3m:41s (0h:12m:13s left)
Optimizing NNI: done in 2.08607 secs using 398.9% CPU
Optimizing NNI: done in 1.99132 secs using 398.5% CPU
Optimizing NNI: done in 4.38636 secs using 596.7% CPU
Optimizing NNI: done in 1.93746 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 69: -107429.755
Optimizing NNI: done in 4.64509 secs using 597.5% CPU
Optimizing NNI: done in 2.33513 secs using 398.5% CPU
Iteration 70 / LogL: -107464.558 / Time: 0h:4m:5s (0h:5m:52s left)
Optimizing NNI: done in 2.1446 secs using 398.2% CPU
Optimizing NNI: done in 4.40356 secs using 597.3% CPU
Optimizing NNI: done in 1.96561 secs using 398.6% CPU
Optimizing NNI: done in 2.06695 secs using 396.5% CPU
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Iteration 80 / LogL: -107436.747 / Time: 0h:4m:26s (0h:5m:0s left)
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Iteration 40 / LogL: -192820.663 / Time: 0h:4m:27s (0h:9m:48s left)
Optimizing NNI: done in 1.96591 secs using 398.2% CPU
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Iteration 90 / LogL: -107434.009 / Time: 0h:4m:48s (0h:4m:15s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.87811 secs using 597.3% CPU
BETTER TREE FOUND at iteration 100: -107428.021
Iteration 100 / LogL: -107428.021 / Time: 0h:5m:11s (0h:5m:14s left)
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Optimizing NNI: done in 4.48123 secs using 596.5% CPU
Iteration 50 / LogL: -192806.953 / Time: 0h:5m:11s (0h:8m:2s left)
BETTER TREE FOUND at iteration 106: -107424.397
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Iteration 110 / LogL: -107431.551 / Time: 0h:5m:35s (0h:4m:55s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 117: -107423.420
Optimizing NNI: done in 4.5154 secs using 597.8% CPU
Optimizing NNI: done in 2.71795 secs using 398.8% CPU
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Iteration 120 / LogL: -107424.070 / Time: 0h:5m:57s (0h:4m:51s left)
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Iteration 60 / LogL: -192826.974 / Time: 0h:5m:55s (0h:6m:37s left)
BETTER TREE FOUND at iteration 125: -107422.876
Optimizing NNI: done in 2.16042 secs using 399.2% CPU
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Iteration 130 / LogL: -107455.697 / Time: 0h:6m:19s (0h:4m:39s left)
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Iteration 70 / LogL: -192865.112 / Time: 0h:6m:40s (0h:5m:24s left)
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Iteration 150 / LogL: -107444.488 / Time: 0h:7m:1s (0h:3m:31s left)
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BETTER TREE FOUND at iteration 152: -107422.875
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 158: -107422.452
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Iteration 160 / LogL: -107440.651 / Time: 0h:7m:24s (0h:4m:33s left)
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Iteration 80 / LogL: -192807.185 / Time: 0h:7m:25s (0h:4m:19s left)
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Iteration 180 / LogL: -107468.335 / Time: 0h:8m:6s (0h:3m:32s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.94944 secs using 398.3% CPU
BETTER TREE FOUND at iteration 90: -192796.065
Iteration 90 / LogL: -192796.065 / Time: 0h:8m:11s (0h:9m:11s left)
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Iteration 190 / LogL: -107440.181 / Time: 0h:8m:29s (0h:3m:3s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 92: -192794.196
Optimizing NNI: done in 2.2692 secs using 399.2% CPU
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Iteration 210 / LogL: -107427.605 / Time: 0h:9m:11s (0h:2m:6s left)
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Iteration 100 / LogL: -192900.656 / Time: 0h:8m:58s (0h:8m:19s left)
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Iteration 220 / LogL: -107426.579 / Time: 0h:9m:33s (0h:1m:39s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.06251 secs using 398.4% CPU
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BETTER TREE FOUND at iteration 106: -192790.875
Optimizing NNI: done in 1.76816 secs using 399% CPU
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Iteration 230 / LogL: -107458.492 / Time: 0h:9m:53s (0h:1m:12s left)
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Iteration 110 / LogL: -192806.141 / Time: 0h:9m:45s (0h:8m:35s left)
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Iteration 240 / LogL: -107424.634 / Time: 0h:10m:14s (0h:0m:46s left)
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Iteration 250 / LogL: -107459.430 / Time: 0h:10m:35s (0h:0m:20s left)
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Iteration 120 / LogL: -192868.400 / Time: 0h:10m:32s (0h:7m:36s left)
Optimizing NNI: done in 2.05397 secs using 397.9% CPU
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Optimizing NNI: done in 2.21726 secs using 398.6% CPU
Optimizing NNI: done in 1.96222 secs using 398.5% CPU
TREE SEARCH COMPLETED AFTER 259 ITERATIONS / Time: 0h:10m:53s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -107422.452
2. Current log-likelihood: -107422.439
Optimizing NNI: done in 4.67611 secs using 597.6% CPU
3. Current log-likelihood: -107422.427
4. Current log-likelihood: -107422.416
5. Current log-likelihood: -107422.405
6. Current log-likelihood: -107422.395
7. Current log-likelihood: -107422.384
Optimal log-likelihood: -107422.371
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.101,0.033) (0.068,0.097) (0.097,0.185) (0.089,0.309) (0.087,0.469) (0.138,0.697) (0.143,1.092) (0.168,1.755) (0.084,4.237)
Parameters optimization took 7 rounds (4.745 sec)
BEST SCORE FOUND : -107422.371
Total tree length: 177.408

Total number of iterations: 259
CPU time used for tree search: 2526.110 sec (0h:42m:6s)
Wall-clock time used for tree search: 641.997 sec (0h:10m:41s)
Total CPU time used: 2592.743 sec (0h:43m:12s)
Total wall-clock time used: 658.674 sec (0h:10m:58s)

===> START BOOTSTRAP REPLICATE NUMBER 63

Creating bootstrap alignment (seed: 68245)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105282.085
Optimizing NNI: done in 4.40587 secs using 597.5% CPU
2. Current log-likelihood: -103260.104
3. Current log-likelihood: -103181.871
Optimizing NNI: done in 4.1596 secs using 598% CPU
4. Current log-likelihood: -103177.144
5. Current log-likelihood: -103176.228
6. Current log-likelihood: -103175.510
Optimizing NNI: done in 4.10735 secs using 596.7% CPU
7. Current log-likelihood: -103174.979
8. Current log-likelihood: -103174.496
9. Current log-likelihood: -103174.052
Optimizing NNI: done in 5.08029 secs using 597.7% CPU
10. Current log-likelihood: -103173.629
11. Current log-likelihood: -103173.236
12. Current log-likelihood: -103172.870
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13. Current log-likelihood: -103172.530
14. Current log-likelihood: -103172.228
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15. Current log-likelihood: -103171.951
16. Current log-likelihood: -103171.690
17. Current log-likelihood: -103171.528
18. Current log-likelihood: -103171.275
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19. Current log-likelihood: -103171.126
20. Current log-likelihood: -103170.977
21. Current log-likelihood: -103170.835
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Iteration 130 / LogL: -192862.654 / Time: 0h:11m:15s (0h:6m:38s left)
22. Current log-likelihood: -103170.695
23. Current log-likelihood: -103170.563
24. Current log-likelihood: -103170.435
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25. Current log-likelihood: -103170.315
26. Current log-likelihood: -103170.195
27. Current log-likelihood: -103170.078
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28. Current log-likelihood: -103169.967
29. Current log-likelihood: -103169.857
30. Current log-likelihood: -103169.753
Optimizing NNI: done in 4.47714 secs using 597.8% CPU
31. Current log-likelihood: -103169.650
Optimal log-likelihood: -103169.488
Proportion of invariable sites: 0.021
Site proportion and rates:  (0.089,0.034) (0.094,0.106) (0.082,0.199) (0.091,0.305) (0.074,0.431) (0.155,0.664) (0.109,1.096) (0.214,1.888) (0.070,4.064)
Parameters optimization took 31 rounds (45.595 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 4.75347 secs using 399.9% CPU
Computing ML distances took 4.753763 sec (of wall-clock time) 19.011088 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000731945 secs using 281.3% CPU
Constructing RapidNJ tree: done in 0.00846577 secs using 403.2% CPU
Computing RapidNJ tree took 0.009264 sec (of wall-clock time) 0.036627 sec (of CPU time)
Log-likelihood of RapidNJ tree: -103496.075
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 3.99914 secs using 597.1% CPU
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10.585 second
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Optimizing NNI: done in 4.40787 secs using 597.6% CPU
Computing log-likelihood of 98 initial trees ... 9.929 seconds
Current best score: -103169.488

Do NNI search on 20 best initial trees
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Iteration 140 / LogL: -192888.971 / Time: 0h:11m:58s (0h:5m:41s left)
BETTER TREE FOUND at iteration 1: -102669.219
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Iteration 20 / LogL: -102654.692 / Time: 0h:2m:10s
Finish initializing candidate tree set (20)
Current best tree score: -102646.570 / CPU time: 78.935
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 170 / LogL: -102613.095 / Time: 0h:7m:37s (0h:2m:7s left)
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Iteration 230 / LogL: -192934.336 / Time: 0h:18m:36s (0h:5m:2s left)
Optimizing NNI: done in 2.12619 secs using 398.2% CPU
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Iteration 180 / LogL: -102623.279 / Time: 0h:7m:57s (0h:1m:38s left)
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Iteration 190 / LogL: -102616.912 / Time: 0h:8m:18s (0h:1m:11s left)
Optimizing NNI: done in 5.02178 secs using 597.2% CPU
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Iteration 240 / LogL: -193054.944 / Time: 0h:19m:21s (0h:4m:12s left)
Optimizing NNI: done in 1.8484 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 199: -102589.756
Optimizing NNI: done in 4.21186 secs using 597.1% CPU
Optimizing NNI: done in 2.12201 secs using 398.5% CPU
Iteration 200 / LogL: -102592.739 / Time: 0h:8m:41s (0h:4m:19s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.86704 secs using 399.1% CPU
Optimizing NNI: done in 1.88751 secs using 398.6% CPU
BETTER TREE FOUND at iteration 243: -192786.557
Optimizing NNI: done in 1.74535 secs using 398.9% CPU
Optimizing NNI: done in 2.09037 secs using 399% CPU
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Optimizing NNI: done in 4.82798 secs using 597.6% CPU
BETTER TREE FOUND at iteration 210: -102589.479
Iteration 210 / LogL: -102589.479 / Time: 0h:9m:2s (0h:4m:19s left)
Optimizing NNI: done in 2.23264 secs using 398.6% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.47676 secs using 597.3% CPU
Iteration 250 / LogL: -192805.095 / Time: 0h:20m:7s (0h:7m:30s left)
BETTER TREE FOUND at iteration 220: -102587.371
Iteration 220 / LogL: -102587.371 / Time: 0h:9m:23s (0h:4m:17s left)
Optimizing NNI: done in 2.01538 secs using 398.6% CPU
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Iteration 230 / LogL: -102625.126 / Time: 0h:9m:43s (0h:3m:49s left)
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Iteration 240 / LogL: -102588.351 / Time: 0h:10m:2s (0h:3m:21s left)
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Iteration 260 / LogL: -192826.241 / Time: 0h:20m:53s (0h:6m:41s left)
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Iteration 250 / LogL: -102605.354 / Time: 0h:10m:23s (0h:2m:55s left)
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Iteration 260 / LogL: -102603.343 / Time: 0h:10m:42s (0h:2m:28s left)
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Iteration 270 / LogL: -192966.696 / Time: 0h:21m:35s (0h:5m:51s left)
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Iteration 270 / LogL: -102622.021 / Time: 0h:11m:4s (0h:2m:3s left)
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Iteration 280 / LogL: -102604.558 / Time: 0h:11m:24s (0h:1m:38s left)
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Iteration 280 / LogL: -192880.272 / Time: 0h:22m:18s (0h:5m:2s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 290 / LogL: -102597.344 / Time: 0h:11m:44s (0h:1m:13s left)
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BETTER TREE FOUND at iteration 282: -192782.779
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Iteration 300 / LogL: -102684.394 / Time: 0h:12m:3s (0h:0m:48s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.89444 secs using 596.9% CPU
Iteration 290 / LogL: -192806.385 / Time: 0h:23m:6s (0h:7m:21s left)
BETTER TREE FOUND at iteration 309: -102586.706
Optimizing NNI: done in 2.75962 secs using 398.1% CPU
Iteration 310 / LogL: -102614.436 / Time: 0h:12m:26s (0h:3m:59s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.59618 secs using 597.8% CPU
BETTER TREE FOUND at iteration 312: -102584.810
Optimizing NNI: done in 2.06544 secs using 398.9% CPU
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Iteration 320 / LogL: -102593.919 / Time: 0h:12m:47s (0h:3m:41s left)
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Iteration 300 / LogL: -192821.705 / Time: 0h:23m:51s (0h:6m:32s left)
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Iteration 330 / LogL: -102599.181 / Time: 0h:13m:6s (0h:3m:16s left)
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Iteration 340 / LogL: -102591.452 / Time: 0h:13m:26s (0h:2m:51s left)
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Iteration 350 / LogL: -102607.399 / Time: 0h:13m:45s (0h:2m:26s left)
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Iteration 310 / LogL: -192841.703 / Time: 0h:24m:35s (0h:5m:43s left)
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Iteration 360 / LogL: -102679.186 / Time: 0h:14m:4s (0h:2m:2s left)
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Iteration 370 / LogL: -102608.903 / Time: 0h:14m:23s (0h:1m:38s left)
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Iteration 320 / LogL: -192829.344 / Time: 0h:25m:18s (0h:4m:55s left)
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Iteration 380 / LogL: -102589.593 / Time: 0h:14m:43s (0h:1m:14s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 323: -192780.936
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Iteration 390 / LogL: -102593.156 / Time: 0h:15m:3s (0h:0m:51s left)
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Iteration 330 / LogL: -192817.747 / Time: 0h:26m:5s (0h:7m:22s left)
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Iteration 400 / LogL: -102587.191 / Time: 0h:15m:22s (0h:0m:27s left)
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Iteration 410 / LogL: -102595.319 / Time: 0h:15m:42s (0h:0m:4s left)
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TREE SEARCH COMPLETED AFTER 413 ITERATIONS / Time: 0h:15m:48s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102584.810
Optimal log-likelihood: -102584.804
Proportion of invariable sites: 0.021
Site proportion and rates:  (0.090,0.033) (0.097,0.104) (0.090,0.202) (0.078,0.312) (0.070,0.414) (0.160,0.657) (0.116,1.126) (0.206,1.916) (0.071,4.010)
Parameters optimization took 1 rounds (0.604 sec)
BEST SCORE FOUND : -102584.804
Total tree length: 168.371

Total number of iterations: 413
CPU time used for tree search: 3543.612 sec (0h:59m:3s)
Wall-clock time used for tree search: 896.826 sec (0h:14m:56s)
Total CPU time used: 3752.334 sec (1h:2m:32s)
Total wall-clock time used: 949.189 sec (0h:15m:49s)

===> START BOOTSTRAP REPLICATE NUMBER 64

Creating bootstrap alignment (seed: 68246)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.128 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106737.557
Optimizing NNI: done in 3.81999 secs using 598.4% CPU
2. Current log-likelihood: -104744.091
3. Current log-likelihood: -104668.380
4. Current log-likelihood: -104665.988
Optimizing NNI: done in 4.3833 secs using 597.2% CPU
Optimal log-likelihood: -104665.971
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.078,0.036) (0.072,0.115) (0.079,0.215) (0.103,0.288) (0.061,0.449) (0.130,0.633) (0.109,0.996) (0.271,1.695) (0.065,4.097)
Parameters optimization took 4 rounds (6.618 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.37178 secs using 597.3% CPU
Calculating distance matrix: done in 4.64231 secs using 399.9% CPU
Computing ML distances took 4.642664 sec (of wall-clock time) 18.567509 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000696898 secs using 352.1% CPU
Constructing RapidNJ tree: done in 0.00847101 secs using 348.7% CPU
Computing RapidNJ tree took 0.009222 sec (of wall-clock time) 0.033888 sec (of CPU time)
Log-likelihood of RapidNJ tree: -104632.154
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 3.94701 secs using 597.5% CPU
Iteration 340 / LogL: -192796.563 / Time: 0h:26m:48s (0h:6m:33s left)
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10.724 second
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Optimizing NNI: done in 4.07121 secs using 597.5% CPU
Computing log-likelihood of 98 initial trees ... 9.961 seconds
Current best score: -104632.154

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 350 / LogL: -192791.758 / Time: 0h:27m:30s (0h:5m:45s left)
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BETTER TREE FOUND at iteration 1: -103926.255
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Iteration 10 / LogL: -103983.965 / Time: 0h:1m:31s
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 365: -192775.019
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BETTER TREE FOUND at iteration 16: -103896.857
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 17: -103895.427
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Iteration 370 / LogL: -192922.370 / Time: 0h:28m:58s (0h:7m:27s left)
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Iteration 20 / LogL: -103987.630 / Time: 0h:2m:31s
Finish initializing candidate tree set (20)
Current best tree score: -103895.427 / CPU time: 138.706
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -103893.413
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Iteration 390 / LogL: -192863.721 / Time: 0h:30m:25s (0h:5m:51s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 75: -103843.442
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BETTER TREE FOUND at iteration 93: -103842.162
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BETTER TREE FOUND at iteration 108: -103841.215
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Estimate model parameters (epsilon = 0.100)
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Iteration 270 / LogL: -103844.517 / Time: 0h:12m:19s (0h:1m:22s left)
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TREE SEARCH COMPLETED AFTER 509 ITERATIONS / Time: 0h:39m:2s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192762.819
Optimal log-likelihood: -192762.817
Site proportion and rates:  (0.014,0.076) (0.080,0.237) (0.101,0.370) (0.227,0.547) (0.122,0.746) (0.200,0.992) (0.151,1.598) (0.105,2.733)
Parameters optimization took 1 rounds (1.240 sec)
BEST SCORE FOUND : -192762.817
Total tree length: 158.161

Total number of iterations: 509
CPU time used for tree search: 13673.209 sec (3h:47m:53s)
Wall-clock time used for tree search: 2314.340 sec (0h:38m:34s)
Total CPU time used: 13848.206 sec (3h:50m:48s)
Total wall-clock time used: 2343.720 sec (0h:39m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 35

Creating bootstrap alignment (seed: 70498)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.280 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -197825.799
Optimizing NNI: done in 2.44985 secs using 399.2% CPU
2. Current log-likelihood: -195186.712
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Estimate model parameters (epsilon = 0.100)
3. Current log-likelihood: -195130.256
BETTER TREE FOUND at iteration 277: -103826.789
4. Current log-likelihood: -195128.426
Optimizing NNI: done in 2.43897 secs using 398.7% CPU
5. Current log-likelihood: -195127.787
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6. Current log-likelihood: -195127.406
7. Current log-likelihood: -195127.179
Optimizing NNI: done in 2.31999 secs using 398.9% CPU
Iteration 280 / LogL: -103837.250 / Time: 0h:12m:43s (0h:4m:25s left)
8. Current log-likelihood: -195127.047
Optimizing NNI: done in 2.10025 secs using 398.1% CPU
Optimal log-likelihood: -195126.974
Site proportion and rates:  (0.023,0.097) (0.047,0.233) (0.110,0.355) (0.160,0.516) (0.201,0.701) (0.208,1.029) (0.146,1.602) (0.105,2.637)
Parameters optimization took 8 rounds (16.895 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 9.72266 secs using 599.9% CPU
Computing ML distances took 9.723222 sec (of wall-clock time) 58.329938 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00119305 secs using 682.8% CPU
Constructing RapidNJ tree: done in 0.0226231 secs using 687.1% CPU
Computing RapidNJ tree took 0.023888 sec (of wall-clock time) 0.165183 sec (of CPU time)
Log-likelihood of RapidNJ tree: -198773.843
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.3206 secs using 398.5% CPU
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Iteration 290 / LogL: -103835.240 / Time: 0h:13m:4s (0h:3m:56s left)
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Iteration 300 / LogL: -103869.979 / Time: 0h:13m:26s (0h:3m:27s left)
29.460 second
Optimizing NNI: done in 2.44925 secs using 398.6% CPU
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Optimizing NNI: done in 2.24439 secs using 398.7% CPU
Computing log-likelihood of 98 initial trees ... 15.927 seconds
Current best score: -195126.974

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 310 / LogL: -103830.418 / Time: 0h:13m:49s (0h:2m:59s left)
BETTER TREE FOUND at iteration 1: -194563.793
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -194455.167
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Iteration 320 / LogL: -103853.823 / Time: 0h:14m:11s (0h:2m:32s left)
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Iteration 10 / LogL: -194526.184 / Time: 0h:2m:2s
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Iteration 20 / LogL: -194629.847 / Time: 0h:2m:43s
Finish initializing candidate tree set (20)
Current best tree score: -194455.167 / CPU time: 134.423
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 25: -194439.751
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 365: -103826.108
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Iteration 370 / LogL: -103829.688 / Time: 0h:16m:4s (0h:4m:8s left)
BETTER TREE FOUND at iteration 26: -194427.893
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 35: -194405.220
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Iteration 40 / LogL: -194519.262 / Time: 0h:4m:48s (0h:11m:41s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 42: -194397.230
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Iteration 420 / LogL: -103877.411 / Time: 0h:17m:56s (0h:1m:55s left)
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Iteration 50 / LogL: -194417.043 / Time: 0h:5m:35s (0h:10m:29s left)
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Iteration 430 / LogL: -103835.401 / Time: 0h:18m:19s (0h:1m:29s left)
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Iteration 440 / LogL: -103846.846 / Time: 0h:18m:40s (0h:1m:3s left)
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Iteration 60 / LogL: -194406.467 / Time: 0h:6m:19s (0h:8m:47s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 61: -194380.166
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Iteration 450 / LogL: -103832.940 / Time: 0h:19m:2s (0h:0m:38s left)
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Iteration 460 / LogL: -103835.329 / Time: 0h:19m:25s (0h:0m:12s left)
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Iteration 70 / LogL: -194459.667 / Time: 0h:7m:8s (0h:9m:24s left)
Optimizing NNI: done in 2.25204 secs using 398.4% CPU
TREE SEARCH COMPLETED AFTER 466 ITERATIONS / Time: 0h:19m:38s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -103826.108
2. Current log-likelihood: -103826.095
3. Current log-likelihood: -103826.084
4. Current log-likelihood: -103826.073
5. Current log-likelihood: -103826.062
6. Current log-likelihood: -103826.051
Optimizing NNI: done in 4.61863 secs using 597.9% CPU
7. Current log-likelihood: -103826.039
8. Current log-likelihood: -103826.027
Optimal log-likelihood: -103826.014
Proportion of invariable sites: 0.032
Site proportion and rates:  (0.067,0.028) (0.076,0.090) (0.083,0.194) (0.121,0.286) (0.142,0.524) (0.109,0.838) (0.172,1.372) (0.142,1.948) (0.055,4.730)
Parameters optimization took 8 rounds (5.455 sec)
BEST SCORE FOUND : -103826.014
Total tree length: 174.871

Total number of iterations: 466
CPU time used for tree search: 4616.713 sec (1h:16m:56s)
Wall-clock time used for tree search: 1166.515 sec (0h:19m:26s)
Total CPU time used: 4688.245 sec (1h:18m:8s)
Total wall-clock time used: 1184.425 sec (0h:19m:44s)

===> START BOOTSTRAP REPLICATE NUMBER 65

Creating bootstrap alignment (seed: 68247)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.116 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -107558.018
Optimizing NNI: done in 3.98479 secs using 597.6% CPU
2. Current log-likelihood: -105626.732
3. Current log-likelihood: -105544.349
4. Current log-likelihood: -105540.243
Optimizing NNI: done in 3.85835 secs using 597.3% CPU
5. Current log-likelihood: -105539.079
6. Current log-likelihood: -105538.139
7. Current log-likelihood: -105537.265
Optimizing NNI: done in 4.58004 secs using 597.1% CPU
8. Current log-likelihood: -105536.559
9. Current log-likelihood: -105535.907
Optimizing NNI: done in 4.12517 secs using 598% CPU
10. Current log-likelihood: -105535.319
11. Current log-likelihood: -105534.810
12. Current log-likelihood: -105534.364
13. Current log-likelihood: -105533.972
Optimizing NNI: done in 4.72916 secs using 598.1% CPU
14. Current log-likelihood: -105533.628
15. Current log-likelihood: -105533.315
16. Current log-likelihood: -105533.003
Optimizing NNI: done in 4.80897 secs using 597.5% CPU
17. Current log-likelihood: -105532.703
18. Current log-likelihood: -105532.407
19. Current log-likelihood: -105532.143
Optimizing NNI: done in 4.63691 secs using 597.9% CPU
20. Current log-likelihood: -105531.987
21. Current log-likelihood: -105531.834
22. Current log-likelihood: -105531.676
23. Current log-likelihood: -105531.537
Optimizing NNI: done in 4.37884 secs using 598.5% CPU
24. Current log-likelihood: -105531.391
25. Current log-likelihood: -105531.262
26. Current log-likelihood: -105531.129
27. Current log-likelihood: -105531.024
Optimizing NNI: done in 5.11549 secs using 597.6% CPU
Iteration 80 / LogL: -194423.837 / Time: 0h:7m:53s (0h:8m:5s left)
28. Current log-likelihood: -105530.888
Optimal log-likelihood: -105530.740
Proportion of invariable sites: 0.024
Site proportion and rates:  (0.089,0.035) (0.056,0.108) (0.093,0.194) (0.101,0.317) (0.150,0.448) (0.096,0.704) (0.134,1.125) (0.194,1.929) (0.064,4.432)
Parameters optimization took 28 rounds (40.048 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.61543 secs using 597.3% CPU
Calculating distance matrix: done in 4.62089 secs using 400% CPU
Computing ML distances took 4.621253 sec (of wall-clock time) 18.482653 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000728846 secs using 75.87% CPU
Constructing RapidNJ tree: done in 0.00848413 secs using 371.7% CPU
Computing RapidNJ tree took 0.009269 sec (of wall-clock time) 0.032591 sec (of CPU time)
Log-likelihood of RapidNJ tree: -105898.501
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 4.64217 secs using 597.1% CPU
Optimizing NNI: done in 7.02193 secs using 597.7% CPU
11.212 second
Optimizing NNI: done in 6.48875 secs using 597.7% CPU
Computing log-likelihood of 98 initial trees ... 10.400 seconds
Current best score: -105530.740

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.77961 secs using 597.8% CPU
Optimizing NNI: done in 1.74663 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
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Iteration 90 / LogL: -194398.563 / Time: 0h:8m:46s (0h:6m:59s left)
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BETTER TREE FOUND at iteration 1: -105171.963
Optimizing NNI: done in 4.1125 secs using 598.4% CPU
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 4.49596 secs using 597.5% CPU
BETTER TREE FOUND at iteration 2: -105054.975
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Iteration 100 / LogL: -194459.562 / Time: 0h:9m:32s (0h:5m:52s left)
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BETTER TREE FOUND at iteration 8: -105024.205
Optimizing NNI: done in 4.68424 secs using 597.3% CPU
Optimizing NNI: done in 2.85676 secs using 398% CPU
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Iteration 10 / LogL: -105119.994 / Time: 0h:2m:30s
Optimizing NNI: done in 4.50897 secs using 595.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.62665 secs using 597.4% CPU
BETTER TREE FOUND at iteration 19: -104996.751
Optimizing NNI: done in 1.67107 secs using 398% CPU
Iteration 20 / LogL: -105311.957 / Time: 0h:2m:56s
Finish initializing candidate tree set (20)
Current best tree score: -104996.751 / CPU time: 130.773
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.24025 secs using 597.5% CPU
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Iteration 110 / LogL: -194399.477 / Time: 0h:10m:16s (0h:4m:48s left)
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BETTER TREE FOUND at iteration 25: -104970.521
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -104944.661
Optimizing NNI: done in 4.8146 secs using 597.8% CPU
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Iteration 30 / LogL: -104984.990 / Time: 0h:3m:22s (0h:11m:29s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.95506 secs using 597.2% CPU
BETTER TREE FOUND at iteration 40: -104942.797
Iteration 40 / LogL: -104942.797 / Time: 0h:3m:45s (0h:9m:38s left)
Optimizing NNI: done in 2.59576 secs using 398.7% CPU
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Iteration 120 / LogL: -194404.502 / Time: 0h:11m:3s (0h:3m:48s left)
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Iteration 50 / LogL: -104959.791 / Time: 0h:4m:8s (0h:7m:35s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.17791 secs using 597.7% CPU
BETTER TREE FOUND at iteration 51: -104941.514
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Iteration 60 / LogL: -104943.097 / Time: 0h:4m:30s (0h:6m:56s left)
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Iteration 130 / LogL: -194384.103 / Time: 0h:11m:48s (0h:2m:50s left)
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Iteration 70 / LogL: -104956.888 / Time: 0h:4m:51s (0h:5m:42s left)
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Optimizing NNI: done in 4.36482 secs using 597.5% CPU
BETTER TREE FOUND at iteration 72: -104938.009
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Optimizing NNI: done in 2.40146 secs using 398.8% CPU
Iteration 80 / LogL: -104947.058 / Time: 0h:5m:15s (0h:6m:7s left)
BETTER TREE FOUND at iteration 139: -194370.580
Optimizing NNI: done in 2.21489 secs using 398.6% CPU
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Iteration 140 / LogL: -194417.986 / Time: 0h:12m:35s (0h:8m:57s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 87: -104934.336
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Iteration 90 / LogL: -104936.690 / Time: 0h:5m:39s (0h:6m:9s left)
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Iteration 100 / LogL: -104935.375 / Time: 0h:6m:0s (0h:5m:16s left)
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Iteration 150 / LogL: -194446.075 / Time: 0h:13m:19s (0h:7m:57s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 109: -104933.943
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Iteration 110 / LogL: -104935.166 / Time: 0h:6m:24s (0h:5m:49s left)
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Iteration 120 / LogL: -104938.489 / Time: 0h:6m:46s (0h:5m:4s left)
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Iteration 160 / LogL: -194459.117 / Time: 0h:14m:3s (0h:6m:58s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 125: -104932.686
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Iteration 130 / LogL: -104959.114 / Time: 0h:7m:9s (0h:5m:16s left)
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Iteration 140 / LogL: -104962.805 / Time: 0h:7m:31s (0h:4m:35s left)
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Iteration 170 / LogL: -194398.262 / Time: 0h:14m:47s (0h:6m:2s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 144: -104931.843
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Iteration 150 / LogL: -104935.491 / Time: 0h:7m:54s (0h:4m:59s left)
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Iteration 160 / LogL: -104948.467 / Time: 0h:8m:16s (0h:4m:22s left)
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Iteration 180 / LogL: -194413.004 / Time: 0h:15m:35s (0h:5m:8s left)
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Iteration 170 / LogL: -104944.713 / Time: 0h:8m:37s (0h:3m:46s left)
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Iteration 180 / LogL: -104992.233 / Time: 0h:9m:0s (0h:3m:13s left)
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Iteration 190 / LogL: -194464.916 / Time: 0h:16m:21s (0h:4m:14s left)
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Iteration 190 / LogL: -104978.197 / Time: 0h:9m:30s (0h:2m:42s left)
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Iteration 200 / LogL: -194405.963 / Time: 0h:17m:6s (0h:3m:21s left)
Optimizing NNI: done in 3.32016 secs using 398.4% CPU
Optimizing NNI: done in 4.55058 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.94526 secs using 397.9% CPU
BETTER TREE FOUND at iteration 201: -194365.172
Optimizing NNI: done in 2.82479 secs using 397.9% CPU
Iteration 200 / LogL: -104937.431 / Time: 0h:10m:0s (0h:2m:12s left)
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Iteration 210 / LogL: -104946.605 / Time: 0h:10m:32s (0h:1m:42s left)
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Iteration 210 / LogL: -194416.946 / Time: 0h:17m:58s (0h:7m:49s left)
Optimizing NNI: done in 2.2112 secs using 398.7% CPU
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Iteration 220 / LogL: -104971.400 / Time: 0h:10m:55s (0h:1m:11s left)
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Iteration 230 / LogL: -104964.049 / Time: 0h:11m:16s (0h:0m:41s left)
Optimizing NNI: done in 2.05436 secs using 398.6% CPU
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Optimizing NNI: done in 2.86553 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 233: -104931.190
Optimizing NNI: done in 4.46651 secs using 596.3% CPU
Optimizing NNI: done in 2.08366 secs using 399.2% CPU
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Optimizing NNI: done in 4.38232 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.39786 secs using 398.5% CPU
BETTER TREE FOUND at iteration 220: -194363.635
Iteration 220 / LogL: -194363.635 / Time: 0h:18m:48s (0h:8m:34s left)
Optimizing NNI: done in 2.01574 secs using 398.7% CPU
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Iteration 240 / LogL: -104934.967 / Time: 0h:11m:40s (0h:4m:32s left)
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Iteration 250 / LogL: -104940.385 / Time: 0h:12m:1s (0h:4m:0s left)
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Optimizing NNI: done in 2.34104 secs using 399.1% CPU
UPDATE BEST LOG-LIKELIHOOD: -104931.186
Optimizing NNI: done in 4.36373 secs using 596.8% CPU
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Iteration 230 / LogL: -194417.705 / Time: 0h:19m:33s (0h:7m:40s left)
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Iteration 260 / LogL: -104946.005 / Time: 0h:12m:25s (0h:3m:30s left)
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Iteration 270 / LogL: -104948.060 / Time: 0h:12m:46s (0h:2m:59s left)
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Iteration 240 / LogL: -194400.336 / Time: 0h:20m:18s (0h:6m:47s left)
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Iteration 280 / LogL: -104931.843 / Time: 0h:13m:7s (0h:2m:29s left)
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Iteration 290 / LogL: -104933.676 / Time: 0h:13m:29s (0h:2m:0s left)
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Iteration 250 / LogL: -194407.376 / Time: 0h:21m:3s (0h:5m:55s left)
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Iteration 300 / LogL: -105082.013 / Time: 0h:13m:51s (0h:1m:31s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.07678 secs using 398.9% CPU
Iteration 310 / LogL: -104932.477 / Time: 0h:14m:13s (0h:1m:3s left)
BETTER TREE FOUND at iteration 255: -194354.534
Optimizing NNI: done in 2.27112 secs using 398% CPU
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BETTER TREE FOUND at iteration 314: -104931.177
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Iteration 320 / LogL: -104958.493 / Time: 0h:14m:34s (0h:4m:17s left)
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Iteration 260 / LogL: -194423.015 / Time: 0h:21m:52s (0h:8m:1s left)
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Iteration 330 / LogL: -104968.948 / Time: 0h:14m:57s (0h:3m:48s left)
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Iteration 340 / LogL: -104964.019 / Time: 0h:15m:19s (0h:3m:20s left)
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Iteration 270 / LogL: -194446.518 / Time: 0h:22m:37s (0h:7m:8s left)
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Iteration 350 / LogL: -104936.137 / Time: 0h:15m:41s (0h:2m:52s left)
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Iteration 360 / LogL: -104935.957 / Time: 0h:16m:3s (0h:2m:24s left)
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Iteration 280 / LogL: -194373.535 / Time: 0h:23m:21s (0h:6m:16s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 369: -104930.769
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Iteration 370 / LogL: -104950.460 / Time: 0h:16m:25s (0h:4m:24s left)
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Iteration 380 / LogL: -104962.902 / Time: 0h:16m:47s (0h:3m:56s left)
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Iteration 290 / LogL: -194371.751 / Time: 0h:24m:6s (0h:5m:25s left)
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Iteration 390 / LogL: -104945.732 / Time: 0h:17m:9s (0h:3m:29s left)
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Iteration 400 / LogL: -104949.658 / Time: 0h:17m:30s (0h:3m:1s left)
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Iteration 420 / LogL: -104932.010 / Time: 0h:18m:13s (0h:2m:7s left)
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Iteration 460 / LogL: -104957.018 / Time: 0h:19m:41s (0h:0m:23s left)
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Iteration 330 / LogL: -194395.208 / Time: 0h:27m:12s (0h:2m:4s left)
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Iteration 470 / LogL: -104942.829 / Time: 0h:20m:2s (0h:0m:-3s left)
TREE SEARCH COMPLETED AFTER 470 ITERATIONS / Time: 0h:20m:2s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -104930.769
2. Current log-likelihood: -104930.753
3. Current log-likelihood: -104930.733
4. Current log-likelihood: -104930.704
5. Current log-likelihood: -104930.687
Optimizing NNI: done in 4.3263 secs using 597.3% CPU
6. Current log-likelihood: -104930.662
7. Current log-likelihood: -104930.647
8. Current log-likelihood: -104930.631
9. Current log-likelihood: -104930.616
10. Current log-likelihood: -104930.601
Optimizing NNI: done in 4.17189 secs using 598% CPU
11. Current log-likelihood: -104930.586
12. Current log-likelihood: -104930.572
13. Current log-likelihood: -104930.558
14. Current log-likelihood: -104930.545
15. Current log-likelihood: -104930.532
16. Current log-likelihood: -104930.519
Optimizing NNI: done in 4.80967 secs using 597.7% CPU
17. Current log-likelihood: -104930.506
18. Current log-likelihood: -104930.493
19. Current log-likelihood: -104930.481
20. Current log-likelihood: -104930.469
21. Current log-likelihood: -104930.457
22. Current log-likelihood: -104930.445
Optimizing NNI: done in 4.51779 secs using 597.9% CPU
23. Current log-likelihood: -104930.432
24. Current log-likelihood: -104930.420
25. Current log-likelihood: -104930.410
26. Current log-likelihood: -104930.399
27. Current log-likelihood: -104930.389
28. Current log-likelihood: -104930.377
29. Current log-likelihood: -104930.365
Optimizing NNI: done in 4.6277 secs using 597.9% CPU
30. Current log-likelihood: -104930.353
31. Current log-likelihood: -104930.341
32. Current log-likelihood: -104930.329
33. Current log-likelihood: -104930.317
34. Current log-likelihood: -104930.305
35. Current log-likelihood: -104930.293
36. Current log-likelihood: -104930.282
37. Current log-likelihood: -104930.271
Optimizing NNI: done in 4.95702 secs using 597.8% CPU
38. Current log-likelihood: -104930.259
39. Current log-likelihood: -104930.247
40. Current log-likelihood: -104930.237
Optimal log-likelihood: -104930.225
Proportion of invariable sites: 0.022
Site proportion and rates:  (0.062,0.025) (0.083,0.079) (0.093,0.190) (0.098,0.305) (0.156,0.440) (0.090,0.684) (0.135,1.107) (0.195,1.918) (0.067,4.352)
Parameters optimization took 40 rounds (29.834 sec)
BEST SCORE FOUND : -104930.225
Total tree length: 160.011

Total number of iterations: 470
CPU time used for tree search: 4577.286 sec (1h:16m:17s)
Wall-clock time used for tree search: 1156.964 sec (0h:19m:16s)
Total CPU time used: 4878.032 sec (1h:21m:18s)
Total wall-clock time used: 1232.443 sec (0h:20m:32s)

===> START BOOTSTRAP REPLICATE NUMBER 66

Creating bootstrap alignment (seed: 68248)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.118 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 101 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104553.789
2. Current log-likelihood: -102692.257
Optimizing NNI: done in 4.20506 secs using 598.2% CPU
3. Current log-likelihood: -102568.546
4. Current log-likelihood: -102561.581
Optimizing NNI: done in 4.20703 secs using 597.7% CPU
Optimal log-likelihood: -102561.488
Proportion of invariable sites: 0.016
Site proportion and rates:  (0.112,0.040) (0.096,0.127) (0.059,0.233) (0.102,0.324) (0.086,0.463) (0.111,0.723) (0.150,1.172) (0.217,1.959) (0.052,4.160)
Parameters optimization took 4 rounds (6.540 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.74155 secs using 597.8% CPU
Iteration 340 / LogL: -194423.680 / Time: 0h:27m:58s (0h:1m:14s left)
Calculating distance matrix: done in 4.6521 secs using 399.9% CPU
Computing ML distances took 4.652490 sec (of wall-clock time) 18.603974 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000709057 secs using 396.2% CPU
Constructing RapidNJ tree: done in 0.00853086 secs using 381.2% CPU
Computing RapidNJ tree took 0.009306 sec (of wall-clock time) 0.037246 sec (of CPU time)
Log-likelihood of RapidNJ tree: -102670.342
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.3064 secs using 597.8% CPU
Optimizing NNI: done in 5.26387 secs using 597.7% CPU
10.700 second
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Optimizing NNI: done in 4.99024 secs using 597.9% CPU
Computing log-likelihood of 98 initial trees ... 9.777 seconds
Current best score: -102561.488

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 346: -194352.273
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Iteration 350 / LogL: -194375.075 / Time: 0h:28m:47s (0h:7m:54s left)
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BETTER TREE FOUND at iteration 1: -102161.963
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -102016.756
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Iteration 10 / LogL: -102129.845 / Time: 0h:1m:29s
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Iteration 360 / LogL: -194410.309 / Time: 0h:29m:31s (0h:7m:4s left)
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Iteration 20 / LogL: -102084.340 / Time: 0h:1m:52s
Finish initializing candidate tree set (20)
Current best tree score: -102016.756 / CPU time: 100.068
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -102004.780
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -102002.773
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 30: -102000.250
Iteration 30 / LogL: -102000.250 / Time: 0h:2m:25s (0h:8m:21s left)
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Iteration 370 / LogL: -194447.965 / Time: 0h:30m:15s (0h:6m:13s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 32: -101985.723
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Iteration 40 / LogL: -101987.458 / Time: 0h:2m:53s (0h:6m:48s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 41: -101970.805
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Iteration 390 / LogL: -194384.776 / Time: 0h:31m:45s (0h:4m:34s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 74: -101970.154
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 78: -101969.019
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 122: -101967.101
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BETTER TREE FOUND at iteration 126: -101966.418
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 143: -101964.336
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 153: -101963.618
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TREE SEARCH COMPLETED AFTER 447 ITERATIONS / Time: 0h:36m:0s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -194352.273
2. Current log-likelihood: -194352.256
Optimizing NNI: done in 2.62188 secs using 398.2% CPU
Optimal log-likelihood: -194352.246
Site proportion and rates:  (0.028,0.109) (0.085,0.280) (0.147,0.429) (0.183,0.615) (0.117,0.769) (0.194,1.048) (0.144,1.632) (0.101,2.665)
Parameters optimization took 2 rounds (2.483 sec)
BEST SCORE FOUND : -194352.246
Total tree length: 157.236

Total number of iterations: 447
CPU time used for tree search: 12589.375 sec (3h:29m:49s)
Wall-clock time used for tree search: 2131.592 sec (0h:35m:31s)
Total CPU time used: 12775.393 sec (3h:32m:55s)
Total wall-clock time used: 2162.794 sec (0h:36m:2s)

===> START BOOTSTRAP REPLICATE NUMBER 36

Creating bootstrap alignment (seed: 70499)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.283 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -192651.231
Optimizing NNI: done in 1.94612 secs using 398.9% CPU
2. Current log-likelihood: -189732.385
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Iteration 180 / LogL: -101969.756 / Time: 0h:8m:19s (0h:3m:23s left)
3. Current log-likelihood: -189660.680
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4. Current log-likelihood: -189641.398
Optimizing NNI: done in 2.16421 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 182: -101962.780
5. Current log-likelihood: -189640.225
Optimal log-likelihood: -189640.196
Site proportion and rates:  (0.011,0.110) (0.054,0.216) (0.131,0.340) (0.209,0.532) (0.191,0.780) (0.168,1.099) (0.152,1.689) (0.083,2.887)
Parameters optimization took 5 rounds (11.182 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 10.2977 secs using 599.9% CPU
Computing ML distances took 10.298193 sec (of wall-clock time) 61.776987 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00128722 secs using 363.2% CPU
Constructing RapidNJ tree: done in 0.0232651 secs using 696% CPU
Computing RapidNJ tree took 0.024610 sec (of wall-clock time) 0.167704 sec (of CPU time)
Optimizing NNI: done in 2.18556 secs using 398.3% CPU
Log-likelihood of RapidNJ tree: -193368.858
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.87656 secs using 398.9% CPU
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Iteration 190 / LogL: -101981.075 / Time: 0h:8m:42s (0h:4m:14s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 196: -101961.222
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Iteration 200 / LogL: -101966.418 / Time: 0h:9m:6s (0h:4m:23s left)
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30.137 second
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Computing log-likelihood of 98 initial trees ... 16.549 seconds
Current best score: -189611.742

Do NNI search on 20 best initial trees
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Iteration 210 / LogL: -101963.794 / Time: 0h:9m:29s (0h:3m:54s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -188813.404
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -188794.281
BETTER TREE FOUND at iteration 225: -101959.764
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Iteration 230 / LogL: -101978.003 / Time: 0h:10m:15s (0h:4m:15s left)
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Iteration 10 / LogL: -188818.319 / Time: 0h:2m:0s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 13: -188765.433
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Iteration 240 / LogL: -102006.296 / Time: 0h:10m:39s (0h:3m:47s left)
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Iteration 250 / LogL: -102029.747 / Time: 0h:11m:2s (0h:3m:19s left)
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Iteration 20 / LogL: -188858.085 / Time: 0h:2m:48s
Finish initializing candidate tree set (20)
Current best tree score: -188765.433 / CPU time: 144.890
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 21: -188763.527
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Estimate model parameters (epsilon = 0.100)
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Iteration 260 / LogL: -101976.112 / Time: 0h:11m:24s (0h:2m:51s left)
BETTER TREE FOUND at iteration 23: -188735.395
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Optimizing NNI: done in 2.52664 secs using 398% CPU
TREE SEARCH COMPLETED AFTER 326 ITERATIONS / Time: 0h:13m:53s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101959.764
Optimizing NNI: done in 5.18481 secs using 597.7% CPU
Iteration 50 / LogL: -188659.524 / Time: 0h:5m:38s (0h:10m:34s left)
2. Current log-likelihood: -101959.747
3. Current log-likelihood: -101959.720
4. Current log-likelihood: -101959.704
5. Current log-likelihood: -101959.687
6. Current log-likelihood: -101959.670
7. Current log-likelihood: -101959.653
8. Current log-likelihood: -101959.637
Optimizing NNI: done in 4.52779 secs using 597.1% CPU
9. Current log-likelihood: -101959.622
10. Current log-likelihood: -101959.607
11. Current log-likelihood: -101959.592
12. Current log-likelihood: -101959.578
13. Current log-likelihood: -101959.563
14. Current log-likelihood: -101959.548
15. Current log-likelihood: -101959.534
Optimizing NNI: done in 4.70186 secs using 598% CPU
16. Current log-likelihood: -101959.520
17. Current log-likelihood: -101959.506
18. Current log-likelihood: -101959.493
19. Current log-likelihood: -101959.479
20. Current log-likelihood: -101959.467
21. Current log-likelihood: -101959.454
22. Current log-likelihood: -101959.441
23. Current log-likelihood: -101959.428
24. Current log-likelihood: -101959.416
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25. Current log-likelihood: -101959.403
26. Current log-likelihood: -101959.390
27. Current log-likelihood: -101959.378
28. Current log-likelihood: -101959.365
29. Current log-likelihood: -101959.353
30. Current log-likelihood: -101959.342
Optimizing NNI: done in 4.92366 secs using 597.1% CPU
31. Current log-likelihood: -101959.330
32. Current log-likelihood: -101959.319
33. Current log-likelihood: -101959.307
34. Current log-likelihood: -101959.296
35. Current log-likelihood: -101959.285
Optimal log-likelihood: -101959.270
Proportion of invariable sites: 0.014
Site proportion and rates:  (0.100,0.030) (0.104,0.104) (0.067,0.215) (0.086,0.299) (0.099,0.435) (0.105,0.681) (0.157,1.121) (0.221,1.949) (0.048,4.719)
Parameters optimization took 35 rounds (24.159 sec)
BEST SCORE FOUND : -101959.270
Total tree length: 166.874

Total number of iterations: 326
CPU time used for tree search: 3238.907 sec (0h:53m:58s)
Wall-clock time used for tree search: 821.260 sec (0h:13m:41s)
Total CPU time used: 3384.518 sec (0h:56m:24s)
Total wall-clock time used: 857.791 sec (0h:14m:17s)

===> START BOOTSTRAP REPLICATE NUMBER 67

Creating bootstrap alignment (seed: 68249)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -111570.798
Optimizing NNI: done in 5.80067 secs using 597.1% CPU
2. Current log-likelihood: -109430.627
3. Current log-likelihood: -109381.680
4. Current log-likelihood: -109378.499
Optimizing NNI: done in 4.80252 secs using 597.3% CPU
5. Current log-likelihood: -109378.052
6. Current log-likelihood: -109377.697
7. Current log-likelihood: -109377.298
8. Current log-likelihood: -109376.846
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9. Current log-likelihood: -109376.333
10. Current log-likelihood: -109375.766
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12. Current log-likelihood: -109374.230
13. Current log-likelihood: -109373.377
14. Current log-likelihood: -109372.492
15. Current log-likelihood: -109371.594
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16. Current log-likelihood: -109370.670
17. Current log-likelihood: -109369.730
18. Current log-likelihood: -109368.791
Optimizing NNI: done in 4.78524 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
19. Current log-likelihood: -109367.859
BETTER TREE FOUND at iteration 60: -188637.889
Iteration 60 / LogL: -188637.889 / Time: 0h:6m:31s (0h:11m:3s left)
20. Current log-likelihood: -109366.930
21. Current log-likelihood: -109366.024
22. Current log-likelihood: -109365.150
Optimizing NNI: done in 5.29387 secs using 596.8% CPU
23. Current log-likelihood: -109364.319
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25. Current log-likelihood: -109362.908
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Optimizing NNI: done in 5.08419 secs using 597.4% CPU
27. Current log-likelihood: -109361.741
28. Current log-likelihood: -109361.214
29. Current log-likelihood: -109360.725
Optimizing NNI: done in 5.72944 secs using 597.4% CPU
30. Current log-likelihood: -109360.283
31. Current log-likelihood: -109359.872
32. Current log-likelihood: -109359.481
Optimizing NNI: done in 4.44034 secs using 597.7% CPU
33. Current log-likelihood: -109359.120
34. Current log-likelihood: -109358.796
35. Current log-likelihood: -109358.540
36. Current log-likelihood: -109358.414
37. Current log-likelihood: -109358.282
Optimizing NNI: done in 5.37767 secs using 597% CPU
Optimal log-likelihood: -109358.144
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.074,0.031) (0.083,0.090) (0.052,0.178) (0.094,0.291) (0.112,0.448) (0.138,0.689) (0.173,1.146) (0.166,1.858) (0.080,3.778)
Parameters optimization took 37 rounds (56.755 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.66308 secs using 597.4% CPU
Calculating distance matrix: done in 4.686 secs using 400% CPU
Computing ML distances took 4.686252 sec (of wall-clock time) 18.742740 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000699997 secs using 100.3% CPU
Constructing RapidNJ tree: done in 0.00856018 secs using 380% CPU
Computing RapidNJ tree took 0.009316 sec (of wall-clock time) 0.033744 sec (of CPU time)
Log-likelihood of RapidNJ tree: -109898.018
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.62534 secs using 597.1% CPU
Optimizing NNI: done in 7.18601 secs using 597.3% CPU
10.827 second
Optimizing NNI: done in 6.96529 secs using 597.1% CPU
Computing log-likelihood of 98 initial trees ... 10.214 seconds
Current best score: -109358.144

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.37399 secs using 597.2% CPU
Iteration 70 / LogL: -188647.827 / Time: 0h:7m:27s (0h:9m:43s left)
BETTER TREE FOUND at iteration 1: -108962.748
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BETTER TREE FOUND at iteration 3: -108832.131
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -108827.994
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Iteration 80 / LogL: -188690.985 / Time: 0h:8m:17s (0h:8m:23s left)
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Iteration 20 / LogL: -108874.320 / Time: 0h:2m:18s
Finish initializing candidate tree set (20)
Current best tree score: -108827.994 / CPU time: 75.521
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -108821.847
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -108808.243
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.1055 secs using 398.3% CPU
BETTER TREE FOUND at iteration 100: -188632.827
Iteration 100 / LogL: -188632.827 / Time: 0h:10m:2s (0h:10m:8s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 103: -188630.936
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TREE SEARCH COMPLETED AFTER 227 ITERATIONS / Time: 0h:9m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -108799.758
Optimal log-likelihood: -108799.744
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.072,0.029) (0.089,0.087) (0.058,0.190) (0.084,0.299) (0.116,0.453) (0.118,0.679) (0.182,1.105) (0.176,1.854) (0.078,3.769)
Parameters optimization took 1 rounds (0.748 sec)
BEST SCORE FOUND : -108799.744
Total tree length: 164.762

Total number of iterations: 227
CPU time used for tree search: 2059.416 sec (0h:34m:19s)
Wall-clock time used for tree search: 524.694 sec (0h:8m:44s)
Total CPU time used: 2312.092 sec (0h:38m:32s)
Total wall-clock time used: 588.080 sec (0h:9m:48s)

===> START BOOTSTRAP REPLICATE NUMBER 68

Creating bootstrap alignment (seed: 68250)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.089 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 100 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104547.890
Optimizing NNI: done in 5.13677 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
2. Current log-likelihood: -102756.855
BETTER TREE FOUND at iteration 167: -188621.760
3. Current log-likelihood: -102649.114
4. Current log-likelihood: -102638.532
Optimizing NNI: done in 4.26352 secs using 598.1% CPU
5. Current log-likelihood: -102637.151
6. Current log-likelihood: -102636.130
7. Current log-likelihood: -102635.442
8. Current log-likelihood: -102634.906
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9. Current log-likelihood: -102634.455
10. Current log-likelihood: -102634.133
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Iteration 170 / LogL: -188654.739 / Time: 0h:16m:5s (0h:9m:14s left)
11. Current log-likelihood: -102633.916
12. Current log-likelihood: -102633.767
13. Current log-likelihood: -102633.603
14. Current log-likelihood: -102633.486
Optimizing NNI: done in 5.4196 secs using 598.1% CPU
15. Current log-likelihood: -102633.360
Optimal log-likelihood: -102633.249
Proportion of invariable sites: 0.037
Site proportion and rates:  (0.081,0.038) (0.096,0.121) (0.068,0.225) (0.139,0.348) (0.137,0.550) (0.106,0.858) (0.117,1.352) (0.168,2.134) (0.050,4.800)
Parameters optimization took 15 rounds (23.079 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Computing ML distances took 4.616049 sec (of wall-clock time) 18.456985 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000693083 secs using 416.8% CPU
Constructing RapidNJ tree: done in 0.00867105 secs using 365.1% CPU
Computing RapidNJ tree took 0.009421 sec (of wall-clock time) 0.036767 sec (of CPU time)
Log-likelihood of RapidNJ tree: -102918.706
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.9611 secs using 597.6% CPU
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10.443 second
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Computing log-likelihood of 98 initial trees ... 9.516 seconds
Current best score: -102633.249

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -102054.834
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Iteration 10 / LogL: -102138.887 / Time: 0h:1m:17s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 17: -102041.207
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Iteration 20 / LogL: -102376.202 / Time: 0h:1m:45s
Finish initializing candidate tree set (20)
Current best tree score: -102041.207 / CPU time: 76.216
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -102028.713
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BETTER TREE FOUND at iteration 158: -102000.554
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 186: -102000.102
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TREE SEARCH COMPLETED AFTER 268 ITERATIONS / Time: 0h:24m:36s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -188621.760
Optimizing NNI: done in 1.97659 secs using 398.6% CPU
Iteration 210 / LogL: -102024.159 / Time: 0h:8m:46s (0h:3m:11s left)
Optimal log-likelihood: -188621.747
Site proportion and rates:  (0.012,0.109) (0.056,0.221) (0.133,0.342) (0.208,0.538) (0.180,0.785) (0.167,1.090) (0.158,1.659) (0.084,2.883)
Parameters optimization took 1 rounds (1.183 sec)
BEST SCORE FOUND : -188621.747
Total tree length: 153.309

Total number of iterations: 268
CPU time used for tree search: 8528.739 sec (2h:22m:8s)
Wall-clock time used for tree search: 1453.227 sec (0h:24m:13s)
Total CPU time used: 8676.728 sec (2h:24m:36s)
Total wall-clock time used: 1478.049 sec (0h:24m:38s)

===> START BOOTSTRAP REPLICATE NUMBER 37

Creating bootstrap alignment (seed: 70500)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.306 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -195370.106
Optimizing NNI: done in 2.28889 secs using 398.7% CPU
2. Current log-likelihood: -192682.336
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3. Current log-likelihood: -192651.748
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4. Current log-likelihood: -192646.072
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5. Current log-likelihood: -192644.277
Optimizing NNI: done in 2.15992 secs using 398% CPU
6. Current log-likelihood: -192643.963
Optimizing NNI: done in 1.73535 secs using 398.1% CPU
Optimal log-likelihood: -192643.898
Site proportion and rates:  (0.014,0.084) (0.069,0.237) (0.092,0.351) (0.210,0.515) (0.156,0.733) (0.192,0.986) (0.165,1.573) (0.103,2.720)
Parameters optimization took 6 rounds (13.091 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 220 / LogL: -102018.746 / Time: 0h:9m:6s (0h:2m:44s left)
Optimizing NNI: done in 2.25686 secs using 398.3% CPU
Calculating distance matrix: done in 9.45595 secs using 599.8% CPU
Computing ML distances took 9.456500 sec (of wall-clock time) 56.720950 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00123811 secs using 410.2% CPU
Constructing RapidNJ tree: done in 0.021898 secs using 666.8% CPU
Computing RapidNJ tree took 0.023208 sec (of wall-clock time) 0.151686 sec (of CPU time)
Optimizing NNI: done in 1.77702 secs using 398.7% CPU
Log-likelihood of RapidNJ tree: -197193.197
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.10143 secs using 398.3% CPU
Optimizing NNI: done in 2.05294 secs using 398.5% CPU
Optimizing NNI: done in 1.64623 secs using 397.4% CPU
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Optimizing NNI: done in 1.92452 secs using 398.3% CPU
Optimizing NNI: done in 1.73826 secs using 397.8% CPU
Iteration 230 / LogL: -102140.880 / Time: 0h:9m:27s (0h:2m:18s left)
Optimizing NNI: done in 2.24166 secs using 398.5% CPU
Optimizing NNI: done in 2.05649 secs using 398.4% CPU
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Optimizing NNI: done in 2.29149 secs using 398.6% CPU
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29.776 second
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Optimizing NNI: done in 1.68608 secs using 398.5% CPU
Optimizing NNI: done in 2.07758 secs using 398.5% CPU
Iteration 240 / LogL: -102001.361 / Time: 0h:9m:48s (0h:1m:53s left)
Optimizing NNI: done in 2.08347 secs using 398.8% CPU
Optimizing NNI: done in 1.88841 secs using 398% CPU
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Optimizing NNI: done in 2.06325 secs using 398.1% CPU
Optimizing NNI: done in 2.10383 secs using 398.8% CPU
Computing log-likelihood of 98 initial trees ... 19.798 seconds
Current best score: -192643.898

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.8382 secs using 398.7% CPU
Optimizing NNI: done in 1.96547 secs using 397.9% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.18578 secs using 398.5% CPU
BETTER TREE FOUND at iteration 1: -192048.552
Optimizing NNI: done in 2.48126 secs using 399% CPU
Iteration 250 / LogL: -102245.192 / Time: 0h:10m:9s (0h:1m:28s left)
Optimizing NNI: done in 1.85844 secs using 398.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.63647 secs using 399.1% CPU
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BETTER TREE FOUND at iteration 2: -191867.409
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -191859.550
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Iteration 260 / LogL: -102030.394 / Time: 0h:10m:28s (0h:1m:3s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 8: -191854.739
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Iteration 270 / LogL: -102006.380 / Time: 0h:10m:49s (0h:0m:38s left)
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Iteration 10 / LogL: -191897.643 / Time: 0h:2m:5s
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Iteration 280 / LogL: -102018.244 / Time: 0h:11m:10s (0h:0m:14s left)
Optimizing NNI: done in 4.26531 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.9341 secs using 398.6% CPU
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BETTER TREE FOUND at iteration 14: -191839.670
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Optimizing NNI: done in 2.24055 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 287 ITERATIONS / Time: 0h:11m:24s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102000.102
2. Current log-likelihood: -102000.092
3. Current log-likelihood: -102000.081
Optimizing NNI: done in 4.0147 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimal log-likelihood: -102000.070
Proportion of invariable sites: 0.036
Site proportion and rates:  (0.079,0.034) (0.095,0.112) (0.084,0.219) (0.125,0.348) (0.152,0.561) (0.099,0.897) (0.107,1.361) (0.171,2.075) (0.050,4.956)
Parameters optimization took 3 rounds (2.469 sec)
BEST SCORE FOUND : -102000.070
Total tree length: 155.520

Total number of iterations: 287
CPU time used for tree search: 2581.951 sec (0h:43m:1s)
Wall-clock time used for tree search: 655.772 sec (0h:10m:55s)
Total CPU time used: 2707.875 sec (0h:45m:7s)
Total wall-clock time used: 687.350 sec (0h:11m:27s)

===> START BOOTSTRAP REPLICATE NUMBER 69

Creating bootstrap alignment (seed: 68251)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -111262.655
2. Current log-likelihood: -109316.552
BETTER TREE FOUND at iteration 17: -191836.126
3. Current log-likelihood: -109272.189
4. Current log-likelihood: -109270.522
5. Current log-likelihood: -109269.883
Optimizing NNI: done in 3.92395 secs using 597.8% CPU
6. Current log-likelihood: -109268.424
7. Current log-likelihood: -109266.186
Optimizing NNI: done in 4.09672 secs using 597.5% CPU
8. Current log-likelihood: -109265.961
Optimal log-likelihood: -109265.902
Proportion of invariable sites: 0.016
Site proportion and rates:  (0.091,0.040) (0.068,0.121) (0.098,0.208) (0.065,0.317) (0.125,0.434) (0.156,0.747) (0.121,1.207) (0.187,1.816) (0.073,4.009)
Parameters optimization took 8 rounds (12.086 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 3.98003 secs using 597.5% CPU
Iteration 20 / LogL: -191838.330 / Time: 0h:2m:54s
Finish initializing candidate tree set (20)
Current best tree score: -191836.126 / CPU time: 150.148
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Calculating distance matrix: done in 4.75051 secs using 399.9% CPU
Computing ML distances took 4.750744 sec (of wall-clock time) 18.998565 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000738144 secs using 76.68% CPU
Constructing RapidNJ tree: done in 0.00838113 secs using 386.7% CPU
Computing RapidNJ tree took 0.009179 sec (of wall-clock time) 0.033185 sec (of CPU time)
Log-likelihood of RapidNJ tree: -109700.794
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 4.99684 secs using 598% CPU
Optimizing NNI: done in 6.20829 secs using 597.8% CPU
10.960 second
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Estimate model parameters (epsilon = 0.100)
Computing log-likelihood of 98 initial trees ... 9.843 seconds
Current best score: -109265.902

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -191828.855
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BETTER TREE FOUND at iteration 1: -108812.207
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 27: -191817.120
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 10: -108779.318
Iteration 10 / LogL: -108779.318 / Time: 0h:1m:14s
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Iteration 30 / LogL: -191851.439 / Time: 0h:3m:54s (0h:13m:3s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 15: -108767.250
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 33: -191811.045
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 19: -108760.779
BETTER TREE FOUND at iteration 34: -191796.627
Optimizing NNI: done in 1.87631 secs using 398.9% CPU
Iteration 20 / LogL: -108869.963 / Time: 0h:1m:43s
Finish initializing candidate tree set (20)
Current best tree score: -108760.779 / CPU time: 85.330
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 23: -108730.317
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Iteration 40 / LogL: -191866.136 / Time: 0h:4m:50s (0h:11m:38s left)
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BETTER TREE FOUND at iteration 30: -108716.890
Iteration 30 / LogL: -108716.890 / Time: 0h:2m:15s (0h:7m:48s left)
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Iteration 40 / LogL: -108737.851 / Time: 0h:2m:36s (0h:6m:1s left)
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Iteration 50 / LogL: -191810.439 / Time: 0h:5m:38s (0h:11m:16s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 60: -108714.047
Iteration 60 / LogL: -108714.047 / Time: 0h:3m:18s (0h:5m:35s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 91: -108712.891
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 70: -191775.363
Iteration 70 / LogL: -191775.363 / Time: 0h:7m:10s (0h:10m:23s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 98: -108710.104
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 109: -108707.995
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 89: -191767.016
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Iteration 110 / LogL: -191804.126 / Time: 0h:10m:13s (0h:7m:24s left)
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Iteration 200 / LogL: -108716.665 / Time: 0h:7m:56s (0h:0m:21s left)
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Iteration 210 / LogL: -108715.370 / Time: 0h:8m:16s (0h:0m:-3s left)
TREE SEARCH COMPLETED AFTER 210 ITERATIONS / Time: 0h:8m:16s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -108707.995
2. Current log-likelihood: -108707.973
3. Current log-likelihood: -108707.939
Optimizing NNI: done in 5.03065 secs using 597.6% CPU
Iteration 120 / LogL: -191806.961 / Time: 0h:10m:58s (0h:6m:21s left)
4. Current log-likelihood: -108707.918
5. Current log-likelihood: -108707.888
6. Current log-likelihood: -108707.858
7. Current log-likelihood: -108707.842
8. Current log-likelihood: -108707.824
9. Current log-likelihood: -108707.807
Optimizing NNI: done in 4.36712 secs using 597.5% CPU
10. Current log-likelihood: -108707.790
11. Current log-likelihood: -108707.773
12. Current log-likelihood: -108707.757
13. Current log-likelihood: -108707.741
14. Current log-likelihood: -108707.726
15. Current log-likelihood: -108707.711
16. Current log-likelihood: -108707.697
Optimizing NNI: done in 4.71316 secs using 596.9% CPU
17. Current log-likelihood: -108707.683
18. Current log-likelihood: -108707.669
19. Current log-likelihood: -108707.656
20. Current log-likelihood: -108707.643
21. Current log-likelihood: -108707.631
22. Current log-likelihood: -108707.618
23. Current log-likelihood: -108707.608
Optimizing NNI: done in 4.4729 secs using 597.5% CPU
24. Current log-likelihood: -108707.597
25. Current log-likelihood: -108707.587
26. Current log-likelihood: -108707.576
Optimal log-likelihood: -108707.564
Proportion of invariable sites: 0.016
Site proportion and rates:  (0.087,0.036) (0.064,0.103) (0.120,0.199) (0.159,0.386) (0.099,0.613) (0.104,0.891) (0.099,1.279) (0.174,1.784) (0.077,4.079)
Parameters optimization took 26 rounds (18.966 sec)
BEST SCORE FOUND : -108707.564
Total tree length: 172.842

Total number of iterations: 210
CPU time used for tree search: 1874.156 sec (0h:31m:14s)
Wall-clock time used for tree search: 478.337 sec (0h:7m:58s)
Total CPU time used: 2023.057 sec (0h:33m:43s)
Total wall-clock time used: 515.678 sec (0h:8m:35s)

===> START BOOTSTRAP REPLICATE NUMBER 70

Creating bootstrap alignment (seed: 68252)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.104 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105831.050
Optimizing NNI: done in 4.54773 secs using 596.9% CPU
2. Current log-likelihood: -103791.676
3. Current log-likelihood: -103709.260
4. Current log-likelihood: -103703.815
Optimizing NNI: done in 4.3295 secs using 597.4% CPU
5. Current log-likelihood: -103702.824
6. Current log-likelihood: -103702.219
7. Current log-likelihood: -103701.727
Optimizing NNI: done in 3.99356 secs using 598.2% CPU
8. Current log-likelihood: -103701.321
9. Current log-likelihood: -103700.980
10. Current log-likelihood: -103700.700
Optimizing NNI: done in 4.54878 secs using 597.2% CPU
11. Current log-likelihood: -103700.537
12. Current log-likelihood: -103700.387
Optimizing NNI: done in 3.95079 secs using 597.8% CPU
13. Current log-likelihood: -103700.255
14. Current log-likelihood: -103700.135
15. Current log-likelihood: -103700.029
Optimizing NNI: done in 4.05691 secs using 598.1% CPU
Optimal log-likelihood: -103699.874
Proportion of invariable sites: 0.035
Site proportion and rates:  (0.082,0.036) (0.108,0.118) (0.088,0.211) (0.082,0.327) (0.055,0.470) (0.144,0.698) (0.129,1.160) (0.214,1.892) (0.063,4.110)
Parameters optimization took 15 rounds (23.320 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.06836 secs using 596.3% CPU
Iteration 130 / LogL: -191786.852 / Time: 0h:11m:42s (0h:5m:21s left)
Calculating distance matrix: done in 4.61058 secs using 399.9% CPU
Computing ML distances took 4.610820 sec (of wall-clock time) 18.440388 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00068903 secs using 381.4% CPU
Constructing RapidNJ tree: done in 0.00838089 secs using 340% CPU
Computing RapidNJ tree took 0.009135 sec (of wall-clock time) 0.032600 sec (of CPU time)
Log-likelihood of RapidNJ tree: -103991.220
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.82549 secs using 598.1% CPU
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10.588 second
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Optimizing NNI: done in 4.57771 secs using 597.3% CPU
Computing log-likelihood of 98 initial trees ... 10.288 seconds
Current best score: -103699.874

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -103248.694
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -103231.968
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BETTER TREE FOUND at iteration 6: -103216.073
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 11: -103210.639
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Iteration 150 / LogL: -191809.788 / Time: 0h:13m:13s (0h:3m:27s left)
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Iteration 20 / LogL: -103221.006 / Time: 0h:2m:4s
Finish initializing candidate tree set (20)
Current best tree score: -103210.639 / CPU time: 95.366
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -103182.257
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -103174.697
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Iteration 40 / LogL: -103190.288 / Time: 0h:2m:57s (0h:6m:57s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 43: -103168.936
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Iteration 50 / LogL: -103172.253 / Time: 0h:3m:22s (0h:6m:23s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 53: -103158.965
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 69: -103153.762
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Iteration 70 / LogL: -103171.967 / Time: 0h:4m:11s (0h:6m:1s left)
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Iteration 90 / LogL: -103187.409 / Time: 0h:4m:56s (0h:4m:22s left)
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Iteration 190 / LogL: -192032.840 / Time: 0h:16m:18s (0h:0m:-6s left)
TREE SEARCH COMPLETED AFTER 190 ITERATIONS / Time: 0h:16m:18s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -191767.016
Optimizing NNI: done in 1.89764 secs using 398.7% CPU
Optimal log-likelihood: -191767.014
Site proportion and rates:  (0.014,0.083) (0.084,0.247) (0.098,0.380) (0.190,0.523) (0.157,0.730) (0.186,0.989) (0.165,1.565) (0.105,2.703)
Parameters optimization took 1 rounds (0.762 sec)
BEST SCORE FOUND : -191767.014
Total tree length: 151.018

Total number of iterations: 190
CPU time used for tree search: 5548.603 sec (1h:32m:28s)
Wall-clock time used for tree search: 953.598 sec (0h:15m:53s)
Total CPU time used: 5699.525 sec (1h:34m:59s)
Total wall-clock time used: 978.954 sec (0h:16m:18s)

===> START BOOTSTRAP REPLICATE NUMBER 38

Creating bootstrap alignment (seed: 70501)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.316 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -197475.437
Optimizing NNI: done in 2.10454 secs using 398.8% CPU
2. Current log-likelihood: -194858.817
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3. Current log-likelihood: -194815.761
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4. Current log-likelihood: -194800.260
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5. Current log-likelihood: -194789.340
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6. Current log-likelihood: -194787.345
Optimizing NNI: done in 2.30321 secs using 398.4% CPU
7. Current log-likelihood: -194787.217
Optimal log-likelihood: -194787.213
Site proportion and rates:  (0.021,0.105) (0.041,0.239) (0.123,0.369) (0.206,0.533) (0.178,0.731) (0.165,1.030) (0.161,1.593) (0.106,2.610)
Parameters optimization took 7 rounds (14.742 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 100 / LogL: -103161.264 / Time: 0h:5m:19s (0h:3m:42s left)
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Calculating distance matrix: done in 10.0129 secs using 599.9% CPU
Computing ML distances took 10.013384 sec (of wall-clock time) 60.070067 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00131583 secs using 595.1% CPU
Constructing RapidNJ tree: done in 0.0230401 secs using 679.1% CPU
Computing RapidNJ tree took 0.024415 sec (of wall-clock time) 0.166303 sec (of CPU time)
Log-likelihood of RapidNJ tree: -200317.185
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.51613 secs using 398.5% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 107: -103153.433
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 110: -103152.738
Iteration 110 / LogL: -103152.738 / Time: 0h:5m:48s (0h:5m:19s left)
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30.901 second
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Iteration 120 / LogL: -103167.522 / Time: 0h:6m:10s (0h:4m:40s left)
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Computing log-likelihood of 98 initial trees ... 16.207 seconds
Current best score: -194787.213

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -194009.320
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Iteration 130 / LogL: -103153.364 / Time: 0h:6m:33s (0h:4m:4s left)
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Iteration 140 / LogL: -103170.844 / Time: 0h:6m:56s (0h:3m:29s left)
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Iteration 10 / LogL: -194079.289 / Time: 0h:1m:56s
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Iteration 150 / LogL: -103181.689 / Time: 0h:7m:19s (0h:2m:57s left)
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Iteration 20 / LogL: -194204.734 / Time: 0h:2m:37s
Finish initializing candidate tree set (20)
Current best tree score: -194009.320 / CPU time: 130.602
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 175: -103151.918
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 178: -103151.625
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 232: -103145.562
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BETTER TREE FOUND at iteration 58: -193958.764
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Iteration 60 / LogL: -193995.195 / Time: 0h:5m:51s (0h:9m:43s left)
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Iteration 240 / LogL: -103157.062 / Time: 0h:10m:55s (0h:4m:12s left)
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BETTER TREE FOUND at iteration 62: -193955.904
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Iteration 250 / LogL: -103150.514 / Time: 0h:11m:18s (0h:3m:43s left)
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BETTER TREE FOUND at iteration 255: -103145.372
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Iteration 70 / LogL: -193961.644 / Time: 0h:6m:38s (0h:8m:50s left)
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Iteration 270 / LogL: -103203.076 / Time: 0h:12m:7s (0h:3m:49s left)
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BETTER TREE FOUND at iteration 83: -193953.550
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Iteration 290 / LogL: -103174.226 / Time: 0h:12m:52s (0h:2m:53s left)
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Iteration 300 / LogL: -103164.973 / Time: 0h:13m:15s (0h:2m:26s left)
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Iteration 90 / LogL: -194079.150 / Time: 0h:8m:12s (0h:8m:34s left)
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Iteration 310 / LogL: -103150.584 / Time: 0h:13m:38s (0h:1m:59s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 316: -103144.756
BETTER TREE FOUND at iteration 98: -193947.647
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Iteration 320 / LogL: -103152.850 / Time: 0h:14m:3s (0h:4m:13s left)
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Iteration 100 / LogL: -193966.774 / Time: 0h:9m:1s (0h:8m:55s left)
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Iteration 330 / LogL: -103173.237 / Time: 0h:14m:25s (0h:3m:46s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 332: -103144.215
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BETTER TREE FOUND at iteration 109: -193947.307
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Iteration 110 / LogL: -194014.225 / Time: 0h:9m:49s (0h:8m:54s left)
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BETTER TREE FOUND at iteration 342: -103144.175
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 111: -193946.352
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Iteration 350 / LogL: -103159.211 / Time: 0h:15m:13s (0h:4m:0s left)
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Iteration 360 / LogL: -103168.607 / Time: 0h:15m:34s (0h:3m:33s left)
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Iteration 120 / LogL: -194033.550 / Time: 0h:10m:33s (0h:8m:4s left)
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BETTER TREE FOUND at iteration 121: -193941.438
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BETTER TREE FOUND at iteration 369: -103143.947
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Iteration 390 / LogL: -103157.147 / Time: 0h:16m:45s (0h:3m:24s left)
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BETTER TREE FOUND at iteration 139: -193939.969
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Iteration 420 / LogL: -103174.355 / Time: 0h:17m:52s (0h:2m:5s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 150: -193937.287
Iteration 150 / LogL: -193937.287 / Time: 0h:12m:54s (0h:8m:39s left)
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Iteration 430 / LogL: -103272.000 / Time: 0h:18m:16s (0h:1m:39s left)
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Iteration 440 / LogL: -103148.488 / Time: 0h:18m:39s (0h:1m:13s left)
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Iteration 160 / LogL: -194003.579 / Time: 0h:13m:41s (0h:7m:44s left)
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Iteration 450 / LogL: -103146.309 / Time: 0h:19m:1s (0h:0m:48s left)
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Iteration 460 / LogL: -103153.187 / Time: 0h:19m:25s (0h:0m:22s left)
Optimizing NNI: done in 4.15144 secs using 596.7% CPU
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Iteration 170 / LogL: -194029.154 / Time: 0h:14m:26s (0h:6m:50s left)
Optimizing NNI: done in 2.62405 secs using 398.5% CPU
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Optimizing NNI: done in 2.37099 secs using 398.6% CPU
Iteration 470 / LogL: -103234.044 / Time: 0h:19m:48s (0h:0m:-3s left)
TREE SEARCH COMPLETED AFTER 470 ITERATIONS / Time: 0h:19m:48s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -103143.947
Optimal log-likelihood: -103143.936
Proportion of invariable sites: 0.034
Site proportion and rates:  (0.079,0.032) (0.102,0.108) (0.098,0.197) (0.082,0.321) (0.064,0.475) (0.139,0.707) (0.133,1.178) (0.209,1.915) (0.061,4.195)
Parameters optimization took 1 rounds (0.778 sec)
BEST SCORE FOUND : -103143.936
Total tree length: 167.906

Total number of iterations: 470
CPU time used for tree search: 4587.668 sec (1h:16m:27s)
Wall-clock time used for tree search: 1159.046 sec (0h:19m:19s)
Total CPU time used: 4707.491 sec (1h:18m:27s)
Total wall-clock time used: 1189.103 sec (0h:19m:49s)

===> START BOOTSTRAP REPLICATE NUMBER 71

Creating bootstrap alignment (seed: 68253)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.114 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105642.530
2. Current log-likelihood: -103398.365
Optimizing NNI: done in 4.50419 secs using 596.9% CPU
3. Current log-likelihood: -103304.899
4. Current log-likelihood: -103301.325
5. Current log-likelihood: -103299.649
Optimizing NNI: done in 4.20144 secs using 597.3% CPU
6. Current log-likelihood: -103298.364
7. Current log-likelihood: -103297.482
8. Current log-likelihood: -103296.880
Optimizing NNI: done in 4.56545 secs using 597.5% CPU
9. Current log-likelihood: -103296.416
10. Current log-likelihood: -103296.019
Optimizing NNI: done in 4.32795 secs using 598% CPU
11. Current log-likelihood: -103295.674
12. Current log-likelihood: -103295.370
13. Current log-likelihood: -103295.107
14. Current log-likelihood: -103294.969
Optimizing NNI: done in 4.82487 secs using 597.8% CPU
15. Current log-likelihood: -103294.832
16. Current log-likelihood: -103294.707
17. Current log-likelihood: -103294.591
Optimizing NNI: done in 4.20201 secs using 597.4% CPU
Iteration 180 / LogL: -194118.201 / Time: 0h:15m:11s (0h:5m:56s left)
18. Current log-likelihood: -103294.487
Optimal log-likelihood: -103294.331
Proportion of invariable sites: 0.035
Site proportion and rates:  (0.095,0.034) (0.099,0.109) (0.081,0.229) (0.116,0.342) (0.081,0.536) (0.093,0.759) (0.168,1.198) (0.141,1.832) (0.089,3.945)
Parameters optimization took 18 rounds (28.078 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.2326 secs using 596.8% CPU
Calculating distance matrix: done in 4.90523 secs using 399.9% CPU
Computing ML distances took 4.905480 sec (of wall-clock time) 19.614793 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000698805 secs using 414.3% CPU
Constructing RapidNJ tree: done in 0.00847697 secs using 402.7% CPU
Computing RapidNJ tree took 0.009231 sec (of wall-clock time) 0.037435 sec (of CPU time)
Optimizing NNI: done in 4.2229 secs using 596.9% CPU
Log-likelihood of RapidNJ tree: -103559.371
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.51211 secs using 597.9% CPU
Optimizing NNI: done in 5.50975 secs using 597.2% CPU
11.086 second
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Optimizing NNI: done in 4.36065 secs using 597.3% CPU
Computing log-likelihood of 98 initial trees ... 10.107 seconds
Current best score: -103294.331

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.24282 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.28917 secs using 597.6% CPU
BETTER TREE FOUND at iteration 1: -102785.043
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Estimate model parameters (epsilon = 0.100)
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Iteration 190 / LogL: -193958.502 / Time: 0h:15m:56s (0h:5m:3s left)
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BETTER TREE FOUND at iteration 4: -102770.147
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Iteration 10 / LogL: -102794.774 / Time: 0h:1m:35s
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Iteration 200 / LogL: -193945.779 / Time: 0h:16m:41s (0h:4m:11s left)
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Iteration 20 / LogL: -102837.815 / Time: 0h:2m:5s
Finish initializing candidate tree set (20)
Current best tree score: -102770.147 / CPU time: 91.067
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -102767.451
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -102762.438
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -102736.273
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -102729.722
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 37: -102717.745
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Iteration 40 / LogL: -102857.178 / Time: 0h:3m:8s (0h:7m:48s left)
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Iteration 220 / LogL: -193984.596 / Time: 0h:18m:7s (0h:2m:28s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 48: -102713.306
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Iteration 50 / LogL: -102729.016 / Time: 0h:3m:32s (0h:7m:4s left)
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Iteration 60 / LogL: -102745.949 / Time: 0h:3m:54s (0h:5m:49s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -102712.135
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Iteration 100 / LogL: -102729.410 / Time: 0h:5m:18s (0h:3m:29s left)
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Iteration 250 / LogL: -193958.054 / Time: 0h:20m:22s (0h:0m:0s left)
Optimizing NNI: done in 2.31966 secs using 398.5% CPU
Optimizing NNI: done in 2.12613 secs using 398.8% CPU
Iteration 110 / LogL: -102756.818 / Time: 0h:5m:40s (0h:2m:51s left)
Optimizing NNI: done in 2.1086 secs using 398.3% CPU
Optimizing NNI: done in 6.25395 secs using 596.5% CPU
TREE SEARCH COMPLETED AFTER 251 ITERATIONS / Time: 0h:20m:29s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -193937.287
Optimal log-likelihood: -193937.281
Site proportion and rates:  (0.021,0.109) (0.041,0.238) (0.132,0.371) (0.201,0.537) (0.165,0.730) (0.169,1.017) (0.168,1.599) (0.103,2.627)
Parameters optimization took 1 rounds (0.951 sec)
BEST SCORE FOUND : -193937.281
Total tree length: 156.397

Total number of iterations: 251
CPU time used for tree search: 7027.490 sec (1h:57m:7s)
Wall-clock time used for tree search: 1202.236 sec (0h:20m:2s)
Total CPU time used: 7193.911 sec (1h:59m:53s)
Total wall-clock time used: 1230.183 sec (0h:20m:30s)

===> START BOOTSTRAP REPLICATE NUMBER 39

Creating bootstrap alignment (seed: 70502)...

Optimizing NNI: done in 1.85543 secs using 398.6% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.285 seconds

NOTE: 230 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -197305.023
Optimizing NNI: done in 1.96014 secs using 398.3% CPU
2. Current log-likelihood: -194697.293
Optimizing NNI: done in 2.11761 secs using 398.8% CPU
3. Current log-likelihood: -194667.992
Optimizing NNI: done in 1.79619 secs using 398.5% CPU
4. Current log-likelihood: -194666.867
Optimizing NNI: done in 1.66896 secs using 398.8% CPU
5. Current log-likelihood: -194666.343
Optimizing NNI: done in 2.28695 secs using 398.8% CPU
6. Current log-likelihood: -194665.881
Optimizing NNI: done in 2.15265 secs using 399.1% CPU
7. Current log-likelihood: -194665.432
8. Current log-likelihood: -194665.019
Optimizing NNI: done in 2.03132 secs using 398.7% CPU
9. Current log-likelihood: -194664.652
Optimizing NNI: done in 1.93846 secs using 398.5% CPU
Iteration 120 / LogL: -102719.798 / Time: 0h:6m:1s (0h:2m:16s left)
10. Current log-likelihood: -194664.351
Optimizing NNI: done in 1.82269 secs using 398.5% CPU
11. Current log-likelihood: -194664.118
Optimizing NNI: done in 1.75956 secs using 397.6% CPU
12. Current log-likelihood: -194663.930
Optimizing NNI: done in 1.78547 secs using 399% CPU
13. Current log-likelihood: -194663.803
Optimizing NNI: done in 2.09202 secs using 399% CPU
14. Current log-likelihood: -194663.696
Optimizing NNI: done in 2.16884 secs using 398.5% CPU
Optimal log-likelihood: -194663.604
Site proportion and rates:  (0.017,0.097) (0.084,0.263) (0.082,0.377) (0.218,0.545) (0.161,0.765) (0.199,1.030) (0.136,1.616) (0.104,2.680)
Parameters optimization took 14 rounds (26.599 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.28631 secs using 399% CPU
Optimizing NNI: done in 2.27518 secs using 398.4% CPU
Optimizing NNI: done in 2.12026 secs using 399% CPU
Optimizing NNI: done in 2.60779 secs using 398.9% CPU
Calculating distance matrix: done in 9.83642 secs using 599.6% CPU
Computing ML distances took 9.836973 sec (of wall-clock time) 58.985163 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00135589 secs using 524% CPU
Constructing RapidNJ tree: done in 0.0224931 secs using 675.9% CPU
Computing RapidNJ tree took 0.023916 sec (of wall-clock time) 0.160360 sec (of CPU time)
Optimizing NNI: done in 2.47605 secs using 399.1% CPU
Iteration 130 / LogL: -102777.809 / Time: 0h:6m:22s (0h:1m:43s left)
Log-likelihood of RapidNJ tree: -200005.138
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.15256 secs using 398.4% CPU
Optimizing NNI: done in 1.83327 secs using 398.3% CPU
Optimizing NNI: done in 2.4846 secs using 398.4% CPU
Optimizing NNI: done in 1.93931 secs using 398.7% CPU
Optimizing NNI: done in 2.08539 secs using 398.5% CPU
Optimizing NNI: done in 2.50001 secs using 398.8% CPU
Optimizing NNI: done in 2.05457 secs using 398.9% CPU
Optimizing NNI: done in 1.83003 secs using 398.8% CPU
Optimizing NNI: done in 2.45705 secs using 398.6% CPU
Optimizing NNI: done in 2.02401 secs using 398.4% CPU
Iteration 140 / LogL: -102776.838 / Time: 0h:6m:44s (0h:1m:12s left)
Optimizing NNI: done in 1.96866 secs using 398.7% CPU
Optimizing NNI: done in 2.1469 secs using 399.1% CPU
Optimizing NNI: done in 2.13742 secs using 398.9% CPU
Optimizing NNI: done in 2.0761 secs using 398.6% CPU
30.111 second
Optimizing NNI: done in 2.15314 secs using 398.7% CPU
Optimizing NNI: done in 1.908 secs using 398.4% CPU
Optimizing NNI: done in 2.41944 secs using 398% CPU
Optimizing NNI: done in 1.93976 secs using 398.9% CPU
Optimizing NNI: done in 1.98159 secs using 398.9% CPU
Optimizing NNI: done in 1.8766 secs using 398.7% CPU
Iteration 150 / LogL: -102730.699 / Time: 0h:7m:5s (0h:0m:42s left)
Optimizing NNI: done in 2.51631 secs using 398.8% CPU
Computing log-likelihood of 98 initial trees ... 15.822 seconds
Current best score: -194663.604

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.28586 secs using 398.2% CPU
Optimizing NNI: done in 2.45389 secs using 398.6% CPU
Optimizing NNI: done in 3.47658 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.93179 secs using 398.5% CPU
Optimizing NNI: done in 1.92277 secs using 398.9% CPU
BETTER TREE FOUND at iteration 1: -194030.311
Optimizing NNI: done in 2.01046 secs using 398.7% CPU
Optimizing NNI: done in 3.76575 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.97678 secs using 398.9% CPU
Optimizing NNI: done in 2.14023 secs using 398.9% CPU
BETTER TREE FOUND at iteration 2: -193991.249
Optimizing NNI: done in 1.7978 secs using 398.6% CPU
Optimizing NNI: done in 1.81968 secs using 398.8% CPU
Iteration 160 / LogL: -102765.487 / Time: 0h:7m:26s (0h:0m:14s left)
Optimizing NNI: done in 4.49566 secs using 596.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.47709 secs using 398.9% CPU
BETTER TREE FOUND at iteration 3: -193960.152
Optimizing NNI: done in 2.01077 secs using 398.2% CPU
Optimizing NNI: done in 2.17562 secs using 399% CPU
Optimizing NNI: done in 4.38029 secs using 596.9% CPU
Optimizing NNI: done in 1.87316 secs using 398.6% CPU
Optimizing NNI: done in 2.46622 secs using 398.7% CPU
Optimizing NNI: done in 4.4438 secs using 597.2% CPU
Optimizing NNI: done in 2.15389 secs using 398.5% CPU
TREE SEARCH COMPLETED AFTER 166 ITERATIONS / Time: 0h:7m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102712.135
2. Current log-likelihood: -102712.118
3. Current log-likelihood: -102712.107
Optimizing NNI: done in 3.01515 secs using 597.6% CPU
4. Current log-likelihood: -102712.092
5. Current log-likelihood: -102712.077
6. Current log-likelihood: -102712.064
7. Current log-likelihood: -102712.050
8. Current log-likelihood: -102712.034
Optimizing NNI: done in 4.42203 secs using 596.4% CPU
9. Current log-likelihood: -102712.020
10. Current log-likelihood: -102712.007
11. Current log-likelihood: -102711.993
12. Current log-likelihood: -102711.980
Optimizing NNI: done in 4.75877 secs using 596.4% CPU
13. Current log-likelihood: -102711.966
14. Current log-likelihood: -102711.954
15. Current log-likelihood: -102711.941
16. Current log-likelihood: -102711.929
17. Current log-likelihood: -102711.916
Optimizing NNI: done in 5.35872 secs using 596.8% CPU
18. Current log-likelihood: -102711.904
19. Current log-likelihood: -102711.893
20. Current log-likelihood: -102711.882
21. Current log-likelihood: -102711.871
Optimizing NNI: done in 4.62719 secs using 597.3% CPU
Iteration 10 / LogL: -194051.606 / Time: 0h:2m:16s
Optimal log-likelihood: -102711.856
Proportion of invariable sites: 0.035
Site proportion and rates:  (0.093,0.030) (0.104,0.109) (0.098,0.237) (0.086,0.342) (0.088,0.524) (0.092,0.769) (0.165,1.175) (0.146,1.812) (0.092,3.864)
Parameters optimization took 21 rounds (21.958 sec)
BEST SCORE FOUND : -102711.856
Total tree length: 177.522

Total number of iterations: 166
CPU time used for tree search: 1662.027 sec (0h:27m:42s)
Wall-clock time used for tree search: 425.203 sec (0h:7m:5s)
Total CPU time used: 1886.405 sec (0h:31m:26s)
Total wall-clock time used: 481.520 sec (0h:8m:1s)

===> START BOOTSTRAP REPLICATE NUMBER 72

Creating bootstrap alignment (seed: 68254)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.087 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105986.762
2. Current log-likelihood: -104075.761
3. Current log-likelihood: -103995.315
Optimizing NNI: done in 4.73796 secs using 597% CPU
4. Current log-likelihood: -103976.729
5. Current log-likelihood: -103974.732
Optimal log-likelihood: -103974.651
Proportion of invariable sites: 0.019
Site proportion and rates:  (0.097,0.042) (0.078,0.130) (0.096,0.237) (0.123,0.356) (0.102,0.544) (0.132,0.869) (0.157,1.384) (0.138,2.087) (0.059,4.151)
Parameters optimization took 5 rounds (8.417 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.94391 secs using 596.7% CPU
Calculating distance matrix: done in 4.63802 secs using 400% CPU
Computing ML distances took 4.638298 sec (of wall-clock time) 18.550147 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000778198 secs using 403% CPU
Constructing RapidNJ tree: done in 0.00848699 secs using 316.5% CPU
Computing RapidNJ tree took 0.009317 sec (of wall-clock time) 0.031516 sec (of CPU time)
Optimizing NNI: done in 5.01188 secs using 596.8% CPU
Log-likelihood of RapidNJ tree: -104509.245
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 6.34242 secs using 597% CPU
10.451 second
Optimizing NNI: done in 5.0389 secs using 597.5% CPU
Optimizing NNI: done in 7.1107 secs using 597% CPU
Computing log-likelihood of 98 initial trees ... 9.883 seconds
Current best score: -103974.651

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.76106 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 6.56487 secs using 597.3% CPU
Optimizing NNI: done in 6.71834 secs using 597% CPU
Optimizing NNI: done in 7.05063 secs using 596.9% CPU
Optimizing NNI: done in 4.85298 secs using 596.9% CPU
Iteration 20 / LogL: -193998.147 / Time: 0h:3m:14s
Finish initializing candidate tree set (20)
Current best tree score: -193960.152 / CPU time: 156.408
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
BETTER TREE FOUND at iteration 1: -103590.675
Optimizing NNI: done in 2.00004 secs using 398.4% CPU
Optimizing NNI: done in 2.40025 secs using 398.8% CPU
Optimizing NNI: done in 5.77318 secs using 596.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.96667 secs using 398.6% CPU
BETTER TREE FOUND at iteration 21: -193868.849
Optimizing NNI: done in 2.80681 secs using 398% CPU
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Iteration 10 / LogL: -103732.714 / Time: 0h:1m:20s
Optimizing NNI: done in 5.12771 secs using 597.4% CPU
Optimizing NNI: done in 3.11503 secs using 398.7% CPU
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Optimizing NNI: done in 2.13089 secs using 397.9% CPU
Optimizing NNI: done in 1.98034 secs using 398.5% CPU
Iteration 20 / LogL: -103673.504 / Time: 0h:1m:46s
Finish initializing candidate tree set (20)
Current best tree score: -103590.675 / CPU time: 91.955
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.45028 secs using 398% CPU
Optimizing NNI: done in 5.82285 secs using 596.9% CPU
Optimizing NNI: done in 2.43079 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -103577.545
Optimizing NNI: done in 5.32657 secs using 597.3% CPU
Iteration 30 / LogL: -193976.873 / Time: 0h:4m:11s (0h:13m:7s left)
Optimizing NNI: done in 2.71963 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.28752 secs using 596.8% CPU
BETTER TREE FOUND at iteration 23: -103563.815
Optimizing NNI: done in 2.43124 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.64047 secs using 398.5% CPU
Optimizing NNI: done in 2.29169 secs using 398.7% CPU
Iteration 30 / LogL: -103572.839 / Time: 0h:2m:16s (0h:7m:18s left)
Optimizing NNI: done in 2.2315 secs using 398% CPU
Optimizing NNI: done in 2.27376 secs using 398.2% CPU
Optimizing NNI: done in 2.02011 secs using 398.5% CPU
Optimizing NNI: done in 1.93292 secs using 398.8% CPU
BETTER TREE FOUND at iteration 34: -193852.978
Optimizing NNI: done in 2.01209 secs using 398.8% CPU
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Optimizing NNI: done in 4.64558 secs using 597.5% CPU
Optimizing NNI: done in 2.03758 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 37: -103553.933
Optimizing NNI: done in 4.93802 secs using 596.5% CPU
Optimizing NNI: done in 2.83322 secs using 398.7% CPU
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Optimizing NNI: done in 2.61665 secs using 398.7% CPU
Iteration 40 / LogL: -103573.752 / Time: 0h:2m:44s (0h:6m:48s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.09196 secs using 398.8% CPU
Optimizing NNI: done in 1.81657 secs using 398.7% CPU
BETTER TREE FOUND at iteration 38: -193850.180
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Iteration 40 / LogL: -193855.270 / Time: 0h:5m:14s (0h:13m:9s left)
Optimizing NNI: done in 2.4368 secs using 398.7% CPU
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Iteration 50 / LogL: -103562.844 / Time: 0h:3m:6s (0h:5m:31s left)
Optimizing NNI: done in 4.63625 secs using 597.2% CPU
Optimizing NNI: done in 2.45299 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.31251 secs using 398.5% CPU
Optimizing NNI: done in 2.44911 secs using 398.6% CPU
BETTER TREE FOUND at iteration 45: -193836.977
Optimizing NNI: done in 2.77252 secs using 398.9% CPU
Iteration 60 / LogL: -103603.935 / Time: 0h:3m:29s (0h:4m:33s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 64: -103551.805
Optimizing NNI: done in 1.99157 secs using 398.6% CPU
Optimizing NNI: done in 7.57674 secs using 597.4% CPU
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Iteration 70 / LogL: -103649.043 / Time: 0h:3m:55s (0h:5m:20s left)
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Iteration 50 / LogL: -193861.368 / Time: 0h:6m:23s (0h:12m:23s left)
Optimizing NNI: done in 2.41981 secs using 398.9% CPU
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Iteration 80 / LogL: -103589.503 / Time: 0h:4m:19s (0h:4m:35s left)
Optimizing NNI: done in 6.49024 secs using 597.2% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 88: -103548.767
Optimizing NNI: done in 5.99754 secs using 596.6% CPU
Optimizing NNI: done in 2.69834 secs using 398.3% CPU
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Iteration 90 / LogL: -103563.591 / Time: 0h:4m:46s (0h:5m:15s left)
Optimizing NNI: done in 4.46093 secs using 597.3% CPU
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Iteration 60 / LogL: -193858.178 / Time: 0h:7m:19s (0h:10m:32s left)
Optimizing NNI: done in 2.49815 secs using 398.2% CPU
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Iteration 100 / LogL: -103570.774 / Time: 0h:5m:9s (0h:4m:35s left)
Optimizing NNI: done in 5.00112 secs using 597.7% CPU
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Iteration 110 / LogL: -103554.074 / Time: 0h:5m:32s (0h:3m:58s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.48197 secs using 597.2% CPU
BETTER TREE FOUND at iteration 113: -103546.585
Optimizing NNI: done in 2.65608 secs using 398.5% CPU
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Iteration 70 / LogL: -193848.250 / Time: 0h:8m:11s (0h:8m:53s left)
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Iteration 120 / LogL: -103638.880 / Time: 0h:6m:0s (0h:4m:41s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 123: -103545.906
Optimizing NNI: done in 6.11049 secs using 596.7% CPU
Optimizing NNI: done in 2.13649 secs using 398.2% CPU
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Iteration 130 / LogL: -103590.310 / Time: 0h:6m:25s (0h:4m:37s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 76: -193835.227
Optimizing NNI: done in 2.39969 secs using 398.5% CPU
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Optimizing NNI: done in 3.89173 secs using 597.1% CPU
BETTER TREE FOUND at iteration 134: -103542.255
Optimizing NNI: done in 2.22351 secs using 399% CPU
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Iteration 80 / LogL: -193917.433 / Time: 0h:9m:6s (0h:11m:4s left)
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Iteration 140 / LogL: -103918.625 / Time: 0h:6m:50s (0h:4m:37s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 148: -103542.045
Optimizing NNI: done in 2.13925 secs using 398.6% CPU
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Iteration 150 / LogL: -103546.401 / Time: 0h:7m:12s (0h:4m:44s left)
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Iteration 160 / LogL: -103566.515 / Time: 0h:7m:36s (0h:4m:12s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.70275 secs using 398.6% CPU
BETTER TREE FOUND at iteration 90: -193834.260
Iteration 90 / LogL: -193834.260 / Time: 0h:10m:2s (0h:11m:17s left)
Optimizing NNI: done in 2.3064 secs using 398.3% CPU
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Iteration 170 / LogL: -103623.026 / Time: 0h:7m:59s (0h:3m:41s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 174: -103541.254
Optimizing NNI: done in 4.82364 secs using 597.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.22703 secs using 398.3% CPU
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BETTER TREE FOUND at iteration 96: -193830.531
Optimizing NNI: done in 2.50426 secs using 398.3% CPU
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Iteration 180 / LogL: -103588.059 / Time: 0h:8m:25s (0h:4m:25s left)
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Iteration 100 / LogL: -193872.705 / Time: 0h:10m:56s (0h:10m:36s left)
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Iteration 190 / LogL: -103566.445 / Time: 0h:8m:49s (0h:3m:55s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.22022 secs using 398.7% CPU
BETTER TREE FOUND at iteration 104: -193810.125
Optimizing NNI: done in 2.31996 secs using 398.4% CPU
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Iteration 200 / LogL: -103593.691 / Time: 0h:9m:12s (0h:3m:25s left)
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Iteration 110 / LogL: -193855.975 / Time: 0h:11m:49s (0h:10m:11s left)
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Iteration 210 / LogL: -103545.399 / Time: 0h:9m:35s (0h:2m:56s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.15765 secs using 399% CPU
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BETTER TREE FOUND at iteration 113: -193802.277
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Iteration 220 / LogL: -103552.504 / Time: 0h:9m:58s (0h:2m:27s left)
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Iteration 230 / LogL: -103554.868 / Time: 0h:10m:20s (0h:1m:59s left)
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Iteration 120 / LogL: -193858.666 / Time: 0h:12m:45s (0h:9m:57s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.07098 secs using 597.2% CPU
BETTER TREE FOUND at iteration 236: -103541.006
Optimizing NNI: done in 2.56317 secs using 398.6% CPU
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Iteration 240 / LogL: -103581.032 / Time: 0h:10m:44s (0h:4m:18s left)
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Iteration 250 / LogL: -103551.329 / Time: 0h:11m:7s (0h:3m:50s left)
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Iteration 130 / LogL: -193839.613 / Time: 0h:13m:33s (0h:8m:42s left)
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Iteration 260 / LogL: -103551.848 / Time: 0h:11m:32s (0h:3m:23s left)
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Iteration 270 / LogL: -103561.836 / Time: 0h:11m:55s (0h:2m:55s left)
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Iteration 140 / LogL: -193840.547 / Time: 0h:14m:18s (0h:7m:30s left)
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Iteration 280 / LogL: -103545.701 / Time: 0h:12m:17s (0h:2m:28s left)
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Iteration 290 / LogL: -103550.672 / Time: 0h:12m:42s (0h:2m:1s left)
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Iteration 150 / LogL: -193835.280 / Time: 0h:15m:6s (0h:6m:23s left)
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Iteration 300 / LogL: -103563.905 / Time: 0h:13m:6s (0h:1m:34s left)
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Iteration 310 / LogL: -103579.809 / Time: 0h:13m:29s (0h:1m:8s left)
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Optimizing NNI: done in 2.09614 secs using 398.6% CPU
Optimizing NNI: done in 4.62653 secs using 597.3% CPU
Iteration 160 / LogL: -193825.639 / Time: 0h:15m:57s (0h:5m:19s left)
Optimizing NNI: done in 1.88329 secs using 399.2% CPU
Optimizing NNI: done in 3.06871 secs using 398.7% CPU
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Optimizing NNI: done in 2.26123 secs using 398.7% CPU
Iteration 320 / LogL: -103613.442 / Time: 0h:13m:52s (0h:0m:41s left)
Optimizing NNI: done in 4.86895 secs using 597.1% CPU
Optimizing NNI: done in 2.43771 secs using 398.7% CPU
Optimizing NNI: done in 2.22517 secs using 398.5% CPU
Optimizing NNI: done in 2.43473 secs using 398.6% CPU
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Optimizing NNI: done in 3.7572 secs using 597.6% CPU
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Optimizing NNI: done in 2.47708 secs using 398.5% CPU
Optimizing NNI: done in 4.67292 secs using 596.6% CPU
Optimizing NNI: done in 2.4425 secs using 399% CPU
Optimizing NNI: done in 2.26034 secs using 398.4% CPU
Optimizing NNI: done in 5.33332 secs using 596.8% CPU
Optimizing NNI: done in 2.59175 secs using 398.4% CPU
Optimizing NNI: done in 2.25709 secs using 398.6% CPU
Iteration 330 / LogL: -103543.318 / Time: 0h:14m:17s (0h:0m:15s left)
Optimizing NNI: done in 4.4862 secs using 596.7% CPU
Optimizing NNI: done in 2.19428 secs using 399.1% CPU
Optimizing NNI: done in 2.30306 secs using 398.5% CPU
Optimizing NNI: done in 4.78842 secs using 597.7% CPU
Optimizing NNI: done in 1.77719 secs using 398.4% CPU
Optimizing NNI: done in 2.37542 secs using 398.6% CPU
Optimizing NNI: done in 4.69902 secs using 596.9% CPU
Iteration 170 / LogL: -193845.308 / Time: 0h:16m:44s (0h:4m:15s left)
Optimizing NNI: done in 2.38761 secs using 398.5% CPU
Optimizing NNI: done in 2.41092 secs using 399% CPU
Optimizing NNI: done in 4.75833 secs using 597.7% CPU
Optimizing NNI: done in 2.48186 secs using 398.7% CPU
TREE SEARCH COMPLETED AFTER 337 ITERATIONS / Time: 0h:14m:33s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -103541.006
Optimal log-likelihood: -103540.994
Proportion of invariable sites: 0.018
Site proportion and rates:  (0.084,0.035) (0.088,0.110) (0.100,0.230) (0.135,0.359) (0.094,0.558) (0.117,0.855) (0.168,1.353) (0.139,2.074) (0.057,4.386)
Parameters optimization took 1 rounds (1.064 sec)
BEST SCORE FOUND : -103540.994
Total tree length: 163.092

Total number of iterations: 337
CPU time used for tree search: 3392.050 sec (0h:56m:32s)
Wall-clock time used for tree search: 858.942 sec (0h:14m:18s)
Total CPU time used: 3453.735 sec (0h:57m:33s)
Total wall-clock time used: 874.386 sec (0h:14m:34s)

===> START BOOTSTRAP REPLICATE NUMBER 73

Creating bootstrap alignment (seed: 68255)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.103 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -111447.566
2. Current log-likelihood: -109518.728
3. Current log-likelihood: -109408.818
Optimizing NNI: done in 5.40197 secs using 597.2% CPU
4. Current log-likelihood: -109396.427
5. Current log-likelihood: -109394.661
Optimizing NNI: done in 3.91296 secs using 598.2% CPU
6. Current log-likelihood: -109393.477
7. Current log-likelihood: -109392.497
8. Current log-likelihood: -109391.693
Optimizing NNI: done in 4.57595 secs using 596.7% CPU
9. Current log-likelihood: -109391.123
10. Current log-likelihood: -109390.618
11. Current log-likelihood: -109390.181
Optimizing NNI: done in 4.81881 secs using 597.2% CPU
12. Current log-likelihood: -109389.801
13. Current log-likelihood: -109389.483
14. Current log-likelihood: -109389.207
Optimizing NNI: done in 4.63455 secs using 597.9% CPU
15. Current log-likelihood: -109388.964
16. Current log-likelihood: -109388.830
17. Current log-likelihood: -109388.698
18. Current log-likelihood: -109388.577
19. Current log-likelihood: -109388.467
Optimizing NNI: done in 6.14788 secs using 596.8% CPU
20. Current log-likelihood: -109388.367
Optimal log-likelihood: -109388.214
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.072,0.035) (0.091,0.114) (0.082,0.208) (0.120,0.335) (0.101,0.537) (0.110,0.842) (0.141,1.205) (0.197,1.873) (0.058,4.249)
Parameters optimization took 20 rounds (30.105 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.46926 secs using 597% CPU
Calculating distance matrix: done in 4.67429 secs using 399.9% CPU
Computing ML distances took 4.674644 sec (of wall-clock time) 18.693144 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000682831 secs using 127.9% CPU
Constructing RapidNJ tree: done in 0.00839806 secs using 349.7% CPU
Computing RapidNJ tree took 0.009142 sec (of wall-clock time) 0.033115 sec (of CPU time)
Log-likelihood of RapidNJ tree: -109581.210
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.89526 secs using 597% CPU
Optimizing NNI: done in 6.66678 secs using 597.3% CPU
Iteration 180 / LogL: -193861.837 / Time: 0h:17m:36s (0h:3m:14s left)
10.513 second
Optimizing NNI: done in 5.31054 secs using 597.7% CPU
Optimizing NNI: done in 4.58691 secs using 597.6% CPU
Computing log-likelihood of 98 initial trees ... 10.206 seconds
Current best score: -109388.214

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.23751 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.46633 secs using 596.9% CPU
Optimizing NNI: done in 4.85837 secs using 597.2% CPU
BETTER TREE FOUND at iteration 1: -108774.675
Optimizing NNI: done in 1.82897 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.87703 secs using 597.2% CPU
BETTER TREE FOUND at iteration 2: -108760.522
Optimizing NNI: done in 5.25744 secs using 596.9% CPU
Optimizing NNI: done in 2.01364 secs using 398.2% CPU
Optimizing NNI: done in 1.82257 secs using 399% CPU
Optimizing NNI: done in 1.91509 secs using 397.9% CPU
Optimizing NNI: done in 5.90223 secs using 596.6% CPU
Optimizing NNI: done in 2.22107 secs using 398.5% CPU
Optimizing NNI: done in 2.03547 secs using 398.1% CPU
Optimizing NNI: done in 4.41251 secs using 597.1% CPU
Optimizing NNI: done in 2.94824 secs using 398.5% CPU
Optimizing NNI: done in 2.03712 secs using 398.8% CPU
Optimizing NNI: done in 4.70047 secs using 597.3% CPU
Optimizing NNI: done in 1.69769 secs using 398.8% CPU
Iteration 10 / LogL: -109019.151 / Time: 0h:1m:32s
Optimizing NNI: done in 3.53889 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.48983 secs using 597% CPU
Iteration 190 / LogL: -193817.450 / Time: 0h:18m:27s (0h:2m:14s left)
Optimizing NNI: done in 4.81866 secs using 596.8% CPU
BETTER TREE FOUND at iteration 11: -108735.840
Optimizing NNI: done in 2.64128 secs using 398.2% CPU
Optimizing NNI: done in 2.27867 secs using 398.7% CPU
Optimizing NNI: done in 6.3265 secs using 596.6% CPU
Optimizing NNI: done in 1.79506 secs using 398% CPU
Optimizing NNI: done in 2.66389 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.98997 secs using 597.4% CPU
Optimizing NNI: done in 4.7206 secs using 597.5% CPU
Optimizing NNI: done in 4.85413 secs using 596.7% CPU
BETTER TREE FOUND at iteration 15: -108729.052
Optimizing NNI: done in 1.65443 secs using 397.9% CPU
Optimizing NNI: done in 4.61979 secs using 597.5% CPU
Optimizing NNI: done in 3.15676 secs using 398.1% CPU
Optimizing NNI: done in 1.83284 secs using 398.5% CPU
Optimizing NNI: done in 4.33698 secs using 597% CPU
Optimizing NNI: done in 2.70105 secs using 398.8% CPU
Optimizing NNI: done in 2.26043 secs using 398.4% CPU
Iteration 20 / LogL: -108880.126 / Time: 0h:2m:13s
Finish initializing candidate tree set (20)
Current best tree score: -108729.052 / CPU time: 97.714
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.01151 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.66478 secs using 598% CPU
BETTER TREE FOUND at iteration 21: -108726.812
Optimizing NNI: done in 1.99677 secs using 398.8% CPU
Optimizing NNI: done in 4.39963 secs using 596.6% CPU
Optimizing NNI: done in 1.84831 secs using 398% CPU
Optimizing NNI: done in 2.69764 secs using 398.2% CPU
Optimizing NNI: done in 4.85689 secs using 597.7% CPU
Iteration 200 / LogL: -193881.071 / Time: 0h:19m:17s (0h:1m:15s left)
Optimizing NNI: done in 2.06254 secs using 397.9% CPU
Optimizing NNI: done in 2.21664 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.99142 secs using 597.3% CPU
BETTER TREE FOUND at iteration 26: -108710.563
Optimizing NNI: done in 2.10626 secs using 398.7% CPU
Optimizing NNI: done in 4.70467 secs using 597% CPU
Optimizing NNI: done in 1.99318 secs using 398.8% CPU
Optimizing NNI: done in 2.46592 secs using 398.7% CPU
Optimizing NNI: done in 3.70098 secs using 598.2% CPU
Optimizing NNI: done in 2.43927 secs using 398.7% CPU
Iteration 30 / LogL: -108756.762 / Time: 0h:2m:41s (0h:8m:53s left)
Optimizing NNI: done in 2.13242 secs using 398.6% CPU
Optimizing NNI: done in 5.70978 secs using 597% CPU
Optimizing NNI: done in 2.3427 secs using 399% CPU
Optimizing NNI: done in 1.80853 secs using 398.8% CPU
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Optimizing NNI: done in 1.78102 secs using 398.6% CPU
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Optimizing NNI: done in 1.71623 secs using 398.9% CPU
Optimizing NNI: done in 2.23638 secs using 398.8% CPU
Optimizing NNI: done in 5.33687 secs using 596.7% CPU
Optimizing NNI: done in 2.20798 secs using 398.4% CPU
Iteration 40 / LogL: -108729.750 / Time: 0h:3m:1s (0h:6m:40s left)
Optimizing NNI: done in 1.86575 secs using 398.3% CPU
Optimizing NNI: done in 4.87704 secs using 596.9% CPU
Optimizing NNI: done in 2.26584 secs using 398.7% CPU
Optimizing NNI: done in 1.80356 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.83565 secs using 596.9% CPU
BETTER TREE FOUND at iteration 43: -108706.258
Optimizing NNI: done in 1.89454 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -108704.378
Optimizing NNI: done in 4.85141 secs using 597.3% CPU
Iteration 210 / LogL: -193860.302 / Time: 0h:20m:6s (0h:0m:17s left)
Optimizing NNI: done in 2.01317 secs using 398.9% CPU
Optimizing NNI: done in 2.10605 secs using 398% CPU
Optimizing NNI: done in 1.69496 secs using 398.3% CPU
Optimizing NNI: done in 5.97808 secs using 596.7% CPU
Optimizing NNI: done in 1.78646 secs using 398.6% CPU
Optimizing NNI: done in 2.29506 secs using 398.7% CPU
Optimizing NNI: done in 4.909 secs using 597.3% CPU
Optimizing NNI: done in 1.81251 secs using 399.1% CPU
Iteration 50 / LogL: -108710.989 / Time: 0h:3m:26s (0h:6m:35s left)
Optimizing NNI: done in 1.83009 secs using 398.4% CPU
Optimizing NNI: done in 2.03607 secs using 398.4% CPU
Optimizing NNI: done in 5.16331 secs using 597.1% CPU
Optimizing NNI: done in 1.99897 secs using 398.6% CPU
Optimizing NNI: done in 1.97738 secs using 398.9% CPU
Optimizing NNI: done in 4.73979 secs using 597.8% CPU
TREE SEARCH COMPLETED AFTER 214 ITERATIONS / Time: 0h:20m:27s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -193802.277
Optimizing NNI: done in 2.17845 secs using 398.1% CPU
Optimal log-likelihood: -193802.263
Site proportion and rates:  (0.017,0.100) (0.107,0.281) (0.118,0.438) (0.180,0.578) (0.154,0.781) (0.190,1.054) (0.128,1.619) (0.106,2.693)
Parameters optimization took 1 rounds (1.203 sec)
BEST SCORE FOUND : -193802.263
Total tree length: 151.896

Total number of iterations: 214
CPU time used for tree search: 6947.239 sec (1h:55m:47s)
Wall-clock time used for tree search: 1188.577 sec (0h:19m:48s)
Total CPU time used: 7184.071 sec (1h:59m:44s)
Total wall-clock time used: 1228.322 sec (0h:20m:28s)

===> START BOOTSTRAP REPLICATE NUMBER 40

Creating bootstrap alignment (seed: 70503)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.317 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -192649.576
Optimizing NNI: done in 2.16974 secs using 398.7% CPU
2. Current log-likelihood: -189995.249
Optimizing NNI: done in 2.16996 secs using 398.6% CPU
3. Current log-likelihood: -189969.157
Optimizing NNI: done in 1.78854 secs using 398.3% CPU
4. Current log-likelihood: -189966.863
Optimizing NNI: done in 1.77193 secs using 398.7% CPU
Optimizing NNI: done in 1.94605 secs using 398.1% CPU
Iteration 60 / LogL: -108711.823 / Time: 0h:3m:46s (0h:5m:22s left)
5. Current log-likelihood: -189965.097
Optimizing NNI: done in 1.7219 secs using 398.8% CPU
6. Current log-likelihood: -189963.516
Optimizing NNI: done in 2.0407 secs using 398.4% CPU
7. Current log-likelihood: -189962.294
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8. Current log-likelihood: -189961.481
9. Current log-likelihood: -189960.851
Optimizing NNI: done in 2.42536 secs using 398.3% CPU
10. Current log-likelihood: -189960.322
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11. Current log-likelihood: -189959.838
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12. Current log-likelihood: -189959.386
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13. Current log-likelihood: -189958.927
Optimizing NNI: done in 1.91741 secs using 398.7% CPU
14. Current log-likelihood: -189958.374
Optimizing NNI: done in 1.89559 secs using 397.7% CPU
Estimate model parameters (epsilon = 0.100)
15. Current log-likelihood: -189957.461
BETTER TREE FOUND at iteration 69: -108700.499
16. Current log-likelihood: -189954.577
Optimizing NNI: done in 1.92716 secs using 398.8% CPU
Iteration 70 / LogL: -108720.985 / Time: 0h:4m:9s (0h:5m:57s left)
17. Current log-likelihood: -189945.540
Optimizing NNI: done in 1.59764 secs using 398.3% CPU
Optimizing NNI: done in 1.84099 secs using 398.5% CPU
18. Current log-likelihood: -189942.319
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19. Current log-likelihood: -189939.439
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20. Current log-likelihood: -189939.037
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21. Current log-likelihood: -189938.651
Optimizing NNI: done in 2.13341 secs using 398.5% CPU
22. Current log-likelihood: -189938.119
23. Current log-likelihood: -189937.506
Optimizing NNI: done in 2.0377 secs using 399% CPU
Optimizing NNI: done in 1.8316 secs using 398.8% CPU
24. Current log-likelihood: -189937.015
Optimizing NNI: done in 1.67308 secs using 398.2% CPU
25. Current log-likelihood: -189936.691
26. Current log-likelihood: -189936.468
Optimizing NNI: done in 2.14603 secs using 398.6% CPU
Iteration 80 / LogL: -108748.496 / Time: 0h:4m:28s (0h:5m:2s left)
Optimizing NNI: done in 1.74396 secs using 399% CPU
27. Current log-likelihood: -189936.296
Optimizing NNI: done in 1.60949 secs using 398.6% CPU
28. Current log-likelihood: -189936.143
Optimizing NNI: done in 2.10345 secs using 398.6% CPU
29. Current log-likelihood: -189935.998
Optimizing NNI: done in 1.6141 secs using 398.7% CPU
30. Current log-likelihood: -189935.831
31. Current log-likelihood: -189935.604
Optimizing NNI: done in 2.33438 secs using 398.8% CPU
32. Current log-likelihood: -189935.208
Optimizing NNI: done in 2.42644 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
33. Current log-likelihood: -189934.572
BETTER TREE FOUND at iteration 86: -108689.585
34. Current log-likelihood: -189933.801
Optimizing NNI: done in 2.22735 secs using 398.1% CPU
35. Current log-likelihood: -189933.165
Optimizing NNI: done in 1.80482 secs using 398.7% CPU
36. Current log-likelihood: -189932.490
Optimizing NNI: done in 2.02596 secs using 398.7% CPU
37. Current log-likelihood: -189932.298
Optimizing NNI: done in 2.0189 secs using 398.6% CPU
Iteration 90 / LogL: -108705.357 / Time: 0h:4m:51s (0h:5m:14s left)
Optimal log-likelihood: -189932.208
Site proportion and rates:  (0.030,0.110) (0.162,0.329) (0.205,0.537) (0.175,0.758) (0.166,1.013) (0.145,1.537) (0.098,2.414) (0.019,3.882)
Parameters optimization took 37 rounds (74.093 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.26171 secs using 397.7% CPU
Optimizing NNI: done in 2.00874 secs using 398.5% CPU
Optimizing NNI: done in 1.93694 secs using 398.7% CPU
Optimizing NNI: done in 2.11658 secs using 398.4% CPU
Calculating distance matrix: done in 9.47964 secs using 599.8% CPU
Computing ML distances took 9.480254 sec (of wall-clock time) 56.865002 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00129104 secs using 888.2% CPU
Constructing RapidNJ tree: done in 0.022747 secs using 666.8% CPU
Computing RapidNJ tree took 0.024110 sec (of wall-clock time) 0.168203 sec (of CPU time)
Optimizing NNI: done in 1.81616 secs using 398.6% CPU
Log-likelihood of RapidNJ tree: -193508.463
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.78507 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 96: -108688.916
Optimizing NNI: done in 1.85441 secs using 398.8% CPU
Optimizing NNI: done in 1.9442 secs using 398.6% CPU
Optimizing NNI: done in 1.79665 secs using 398.3% CPU
Optimizing NNI: done in 2.1208 secs using 398.3% CPU
Iteration 100 / LogL: -108689.202 / Time: 0h:5m:14s (0h:5m:4s left)
Optimizing NNI: done in 1.9679 secs using 398.6% CPU
Optimizing NNI: done in 2.11372 secs using 398% CPU
Optimizing NNI: done in 2.18466 secs using 398.3% CPU
Optimizing NNI: done in 1.93644 secs using 398.3% CPU
Optimizing NNI: done in 2.03979 secs using 398.6% CPU
Optimizing NNI: done in 2.26395 secs using 398.4% CPU
Optimizing NNI: done in 2.07904 secs using 398.3% CPU
Optimizing NNI: done in 2.1241 secs using 398.4% CPU
30.512 second
Optimizing NNI: done in 2.04659 secs using 398.8% CPU
Optimizing NNI: done in 1.89173 secs using 398.9% CPU
Iteration 110 / LogL: -108725.622 / Time: 0h:5m:35s (0h:4m:24s left)
Optimizing NNI: done in 1.73049 secs using 398.9% CPU
Optimizing NNI: done in 2.08801 secs using 397.8% CPU
Optimizing NNI: done in 1.87856 secs using 398.5% CPU
Optimizing NNI: done in 1.90047 secs using 398.6% CPU
Optimizing NNI: done in 1.71029 secs using 398.7% CPU
Optimizing NNI: done in 1.72516 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 116: -108688.231
Computing log-likelihood of 98 initial trees ... 16.312 seconds
Current best score: -189932.208

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.07579 secs using 398.1% CPU
Optimizing NNI: done in 2.31831 secs using 397.8% CPU
Optimizing NNI: done in 3.39808 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.9999 secs using 398% CPU
Optimizing NNI: done in 2.15465 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -189425.297
BETTER TREE FOUND at iteration 120: -108686.842
Iteration 120 / LogL: -108686.842 / Time: 0h:5m:58s (0h:5m:1s left)
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BETTER TREE FOUND at iteration 123: -108682.786
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Iteration 10 / LogL: -189315.325 / Time: 0h:3m:25s
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Iteration 20 / LogL: -189372.831 / Time: 0h:4m:23s
Finish initializing candidate tree set (20)
Current best tree score: -189315.325 / CPU time: 177.882
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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BETTER TREE FOUND at iteration 27: -189275.875
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 50: -189263.857
Iteration 50 / LogL: -189263.857 / Time: 0h:7m:2s (0h:14m:20s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 61: -189250.429
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Iteration 280 / LogL: -108684.826 / Time: 0h:11m:38s (0h:0m:30s left)
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Iteration 290 / LogL: -108683.221 / Time: 0h:11m:57s (0h:0m:4s left)
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TREE SEARCH COMPLETED AFTER 293 ITERATIONS / Time: 0h:12m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -108680.384
Optimizing NNI: done in 4.20341 secs using 597.7% CPU
2. Current log-likelihood: -108680.367
3. Current log-likelihood: -108680.352
4. Current log-likelihood: -108680.335
5. Current log-likelihood: -108680.320
6. Current log-likelihood: -108680.304
7. Current log-likelihood: -108680.288
8. Current log-likelihood: -108680.274
Optimizing NNI: done in 4.76851 secs using 597.3% CPU
9. Current log-likelihood: -108680.259
10. Current log-likelihood: -108680.246
11. Current log-likelihood: -108680.232
12. Current log-likelihood: -108680.219
13. Current log-likelihood: -108680.207
14. Current log-likelihood: -108680.195
Optimal log-likelihood: -108680.181
Proportion of invariable sites: 0.028
Site proportion and rates:  (0.070,0.030) (0.091,0.110) (0.093,0.210) (0.108,0.335) (0.114,0.540) (0.137,0.903) (0.117,1.296) (0.186,1.906) (0.056,4.331)
Parameters optimization took 14 rounds (9.777 sec)
BEST SCORE FOUND : -108680.181
Total tree length: 170.639

Total number of iterations: 293
CPU time used for tree search: 2708.623 sec (0h:45m:8s)
Wall-clock time used for tree search: 687.590 sec (0h:11m:27s)
Total CPU time used: 2891.439 sec (0h:48m:11s)
Total wall-clock time used: 733.464 sec (0h:12m:13s)

===> START BOOTSTRAP REPLICATE NUMBER 74

Creating bootstrap alignment (seed: 68256)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.119 seconds
Optimizing NNI: done in 4.55475 secs using 597.3% CPU
Iteration 70 / LogL: -189318.460 / Time: 0h:8m:36s (0h:11m:20s left)
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -109247.579
2. Current log-likelihood: -107326.876
3. Current log-likelihood: -107200.034
Optimizing NNI: done in 4.69145 secs using 597.1% CPU
4. Current log-likelihood: -107187.026
5. Current log-likelihood: -107186.555
Optimal log-likelihood: -107186.486
Proportion of invariable sites: 0.037
Site proportion and rates:  (0.083,0.038) (0.080,0.120) (0.076,0.207) (0.091,0.335) (0.068,0.487) (0.144,0.723) (0.195,1.240) (0.178,1.946) (0.047,4.585)
Parameters optimization took 5 rounds (7.849 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.61601 secs using 597.8% CPU
Calculating distance matrix: done in 4.62994 secs using 399.9% CPU
Computing ML distances took 4.630184 sec (of wall-clock time) 18.514814 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000793934 secs using 169% CPU
Constructing RapidNJ tree: done in 0.00864697 secs using 403.5% CPU
Computing RapidNJ tree took 0.009494 sec (of wall-clock time) 0.036490 sec (of CPU time)
Log-likelihood of RapidNJ tree: -107454.865
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.98318 secs using 597.3% CPU
Optimizing NNI: done in 5.37172 secs using 597.2% CPU
11.301 second
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Optimizing NNI: done in 6.05957 secs using 597.3% CPU
Computing log-likelihood of 98 initial trees ... 10.150 seconds
Current best score: -107186.486

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 80 / LogL: -189263.439 / Time: 0h:9m:25s (0h:9m:39s left)
Optimizing NNI: done in 4.25446 secs using 597.7% CPU
Optimizing NNI: done in 4.11175 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -106627.767
BETTER TREE FOUND at iteration 82: -189248.769
Optimizing NNI: done in 2.13363 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 83: -189239.407
Optimizing NNI: done in 4.89297 secs using 596.9% CPU
BETTER TREE FOUND at iteration 2: -106566.746
Optimizing NNI: done in 2.21014 secs using 399% CPU
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Optimizing NNI: done in 1.98651 secs using 398.5% CPU
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BETTER TREE FOUND at iteration 86: -189236.102
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BETTER TREE FOUND at iteration 9: -106554.937
Optimizing NNI: done in 4.58993 secs using 597.5% CPU
Optimizing NNI: done in 2.20693 secs using 398.4% CPU
Iteration 10 / LogL: -106629.665 / Time: 0h:1m:36s
Optimizing NNI: done in 2.07453 secs using 398.5% CPU
Optimizing NNI: done in 4.64851 secs using 597.2% CPU
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Optimizing NNI: done in 3.66375 secs using 597.7% CPU
Iteration 90 / LogL: -189275.080 / Time: 0h:10m:19s (0h:11m:7s left)
Optimizing NNI: done in 2.7549 secs using 398.5% CPU
Optimizing NNI: done in 2.13256 secs using 398% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.98267 secs using 597.5% CPU
BETTER TREE FOUND at iteration 16: -106542.184
Optimizing NNI: done in 2.38133 secs using 398.2% CPU
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Optimizing NNI: done in 2.95222 secs using 398.3% CPU
Iteration 20 / LogL: -106598.590 / Time: 0h:2m:4s
Finish initializing candidate tree set (20)
Current best tree score: -106542.184 / CPU time: 110.622
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.68151 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.4979 secs using 597.2% CPU
BETTER TREE FOUND at iteration 21: -106526.002
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Iteration 30 / LogL: -106542.464 / Time: 0h:2m:30s (0h:7m:50s left)
Optimizing NNI: done in 4.75521 secs using 598.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.16561 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -106525.729
BETTER TREE FOUND at iteration 100: -189230.682
Iteration 100 / LogL: -189230.682 / Time: 0h:11m:10s (0h:11m:16s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.95217 secs using 597.6% CPU
BETTER TREE FOUND at iteration 36: -106515.429
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Iteration 40 / LogL: -106626.305 / Time: 0h:2m:58s (0h:7m:20s left)
Optimizing NNI: done in 2.18076 secs using 398% CPU
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Iteration 110 / LogL: -189371.104 / Time: 0h:11m:56s (0h:9m:50s left)
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Iteration 50 / LogL: -106544.783 / Time: 0h:3m:21s (0h:5m:52s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 52: -106507.443
Optimizing NNI: done in 4.88683 secs using 597.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.95766 secs using 398.1% CPU
Optimizing NNI: done in 2.45689 secs using 398.6% CPU
Iteration 60 / LogL: -106541.682 / Time: 0h:3m:46s (0h:5m:53s left)
BETTER TREE FOUND at iteration 115: -189224.526
Optimizing NNI: done in 2.14325 secs using 398.3% CPU
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Iteration 70 / LogL: -106532.917 / Time: 0h:4m:9s (0h:4m:56s left)
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Iteration 120 / LogL: -189235.008 / Time: 0h:12m:48s (0h:10m:13s left)
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Iteration 80 / LogL: -106570.577 / Time: 0h:4m:32s (0h:4m:8s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 85: -106503.176
Optimizing NNI: done in 4.28359 secs using 596.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.43347 secs using 397.9% CPU
Iteration 90 / LogL: -106516.645 / Time: 0h:4m:57s (0h:5m:17s left)
BETTER TREE FOUND at iteration 129: -189207.671
Optimizing NNI: done in 2.07042 secs using 398.3% CPU
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Iteration 130 / LogL: -189238.534 / Time: 0h:13m:38s (0h:10m:28s left)
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Iteration 100 / LogL: -106508.247 / Time: 0h:5m:19s (0h:4m:34s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 107: -106501.955
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 108: -106501.254
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Iteration 110 / LogL: -106545.379 / Time: 0h:5m:47s (0h:5m:12s left)
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Iteration 140 / LogL: -189253.777 / Time: 0h:14m:24s (0h:9m:13s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 141: -189196.644
Optimizing NNI: done in 2.46707 secs using 398.4% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.41846 secs using 597.5% CPU
BETTER TREE FOUND at iteration 120: -106499.901
Iteration 120 / LogL: -106499.901 / Time: 0h:6m:14s (0h:5m:14s left)
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BETTER TREE FOUND at iteration 123: -106496.630
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BETTER TREE FOUND at iteration 126: -106495.829
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Iteration 150 / LogL: -189204.827 / Time: 0h:15m:11s (0h:9m:16s left)
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Iteration 130 / LogL: -106551.996 / Time: 0h:6m:40s (0h:4m:58s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 140 / LogL: -106611.857 / Time: 0h:7m:5s (0h:4m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 156: -189194.234
BETTER TREE FOUND at iteration 141: -106494.489
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Iteration 160 / LogL: -189204.590 / Time: 0h:16m:2s (0h:9m:40s left)
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Iteration 150 / LogL: -106521.669 / Time: 0h:7m:29s (0h:4m:34s left)
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Iteration 160 / LogL: -106500.102 / Time: 0h:7m:52s (0h:4m:0s left)
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Iteration 170 / LogL: -189223.952 / Time: 0h:16m:48s (0h:8m:32s left)
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Iteration 170 / LogL: -106527.818 / Time: 0h:8m:16s (0h:3m:28s left)
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Iteration 180 / LogL: -106497.545 / Time: 0h:8m:40s (0h:2m:57s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 185: -106493.991
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Iteration 180 / LogL: -189226.925 / Time: 0h:17m:33s (0h:7m:27s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 253: -106493.250
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 223: -189187.015
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Iteration 340 / LogL: -106499.107 / Time: 0h:15m:1s (0h:0m:34s left)
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Iteration 260 / LogL: -189279.853 / Time: 0h:23m:51s (0h:5m:48s left)
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Iteration 350 / LogL: -106505.733 / Time: 0h:15m:25s (0h:0m:7s left)
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TREE SEARCH COMPLETED AFTER 354 ITERATIONS / Time: 0h:15m:35s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106493.250
2. Current log-likelihood: -106493.239
3. Current log-likelihood: -106493.228
Optimizing NNI: done in 4.49549 secs using 597.6% CPU
4. Current log-likelihood: -106493.216
5. Current log-likelihood: -106493.205
6. Current log-likelihood: -106493.193
7. Current log-likelihood: -106493.182
8. Current log-likelihood: -106493.172
Optimal log-likelihood: -106493.157
Proportion of invariable sites: 0.036
Site proportion and rates:  (0.075,0.030) (0.080,0.095) (0.091,0.199) (0.078,0.321) (0.076,0.470) (0.142,0.707) (0.185,1.207) (0.191,1.895) (0.046,4.890)
Parameters optimization took 8 rounds (6.512 sec)
BEST SCORE FOUND : -106493.157
Total tree length: 163.137

Total number of iterations: 354
CPU time used for tree search: 3638.474 sec (1h:0m:38s)
Wall-clock time used for tree search: 921.981 sec (0h:15m:21s)
Total CPU time used: 3719.355 sec (1h:1m:59s)
Total wall-clock time used: 942.263 sec (0h:15m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 75

Creating bootstrap alignment (seed: 68257)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -107367.622
Optimizing NNI: done in 5.15935 secs using 596.9% CPU
2. Current log-likelihood: -105400.974
3. Current log-likelihood: -105340.295
Optimizing NNI: done in 3.3341 secs using 597.9% CPU
4. Current log-likelihood: -105330.220
5. Current log-likelihood: -105316.594
Optimizing NNI: done in 4.54406 secs using 597.6% CPU
6. Current log-likelihood: -105307.170
7. Current log-likelihood: -105306.833
Optimal log-likelihood: -105306.821
Proportion of invariable sites: 0.041
Site proportion and rates:  (0.092,0.043) (0.112,0.136) (0.059,0.246) (0.126,0.369) (0.096,0.614) (0.131,0.884) (0.102,1.333) (0.175,1.997) (0.066,3.954)
Parameters optimization took 7 rounds (10.715 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.72181 secs using 597.4% CPU
Calculating distance matrix: done in 4.74138 secs using 399.9% CPU
Computing ML distances took 4.741772 sec (of wall-clock time) 18.964286 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00071907 secs using 415.3% CPU
Constructing RapidNJ tree: done in 0.00862908 secs using 380.3% CPU
Computing RapidNJ tree took 0.009401 sec (of wall-clock time) 0.038529 sec (of CPU time)
Log-likelihood of RapidNJ tree: -105600.800
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.56219 secs using 596.3% CPU
Iteration 270 / LogL: -189213.884 / Time: 0h:24m:36s (0h:4m:50s left)
Optimizing NNI: done in 5.31372 secs using 598% CPU
10.583 second
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Optimizing NNI: done in 4.33468 secs using 597.4% CPU
Computing log-likelihood of 98 initial trees ... 9.644 seconds
Current best score: -105306.821

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -104650.230
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.51037 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 278: -189186.240
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Optimizing NNI: done in 4.9828 secs using 597.6% CPU
Iteration 280 / LogL: -189243.164 / Time: 0h:25m:28s (0h:8m:56s left)
BETTER TREE FOUND at iteration 2: -104536.715
Optimizing NNI: done in 2.6618 secs using 398.1% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.01598 secs using 597.8% CPU
BETTER TREE FOUND at iteration 7: -104471.359
Optimizing NNI: done in 1.71168 secs using 399.2% CPU
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Optimizing NNI: done in 4.71158 secs using 597.1% CPU
Optimizing NNI: done in 1.75668 secs using 399.2% CPU
Iteration 10 / LogL: -104674.804 / Time: 0h:1m:35s
Optimizing NNI: done in 1.72628 secs using 398.7% CPU
Optimizing NNI: done in 2.45238 secs using 398.5% CPU
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Optimizing NNI: done in 3.07467 secs using 398.2% CPU
Iteration 20 / LogL: -104521.132 / Time: 0h:1m:58s
Finish initializing candidate tree set (20)
Current best tree score: -104471.359 / CPU time: 101.625
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.33326 secs using 597.6% CPU
Iteration 290 / LogL: -189240.286 / Time: 0h:26m:17s (0h:8m:0s left)
Optimizing NNI: done in 1.9061 secs using 398.2% CPU
Optimizing NNI: done in 1.761 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.07562 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -104461.509
Optimizing NNI: done in 1.97213 secs using 397.9% CPU
BETTER TREE FOUND at iteration 291: -189184.356
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Iteration 30 / LogL: -104472.129 / Time: 0h:2m:21s (0h:7m:28s left)
Optimizing NNI: done in 4.74087 secs using 596.9% CPU
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Optimizing NNI: done in 2.35279 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -104440.745
Optimizing NNI: done in 4.31265 secs using 598% CPU
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Optimizing NNI: done in 5.18444 secs using 597.5% CPU
BETTER TREE FOUND at iteration 37: -104439.117
Optimizing NNI: done in 2.13039 secs using 398.7% CPU
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Iteration 40 / LogL: -104476.485 / Time: 0h:2m:48s (0h:6m:58s left)
Optimizing NNI: done in 1.95855 secs using 398.2% CPU
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Iteration 300 / LogL: -189186.205 / Time: 0h:27m:9s (0h:8m:15s left)
Optimizing NNI: done in 1.94876 secs using 398.1% CPU
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Iteration 50 / LogL: -104447.722 / Time: 0h:3m:8s (0h:5m:35s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.79793 secs using 597.6% CPU
BETTER TREE FOUND at iteration 58: -104438.410
Optimizing NNI: done in 2.24234 secs using 398.8% CPU
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Iteration 60 / LogL: -104479.691 / Time: 0h:3m:31s (0h:5m:50s left)
Optimizing NNI: done in 4.77665 secs using 596.8% CPU
Optimizing NNI: done in 2.17406 secs using 398.8% CPU
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Iteration 310 / LogL: -189205.971 / Time: 0h:27m:55s (0h:7m:19s left)
Optimizing NNI: done in 2.33751 secs using 398.4% CPU
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Iteration 70 / LogL: -104444.919 / Time: 0h:3m:53s (0h:4m:57s left)
Optimizing NNI: done in 4.68755 secs using 597.5% CPU
Optimizing NNI: done in 1.94575 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 71: -104436.487
Optimizing NNI: done in 4.83467 secs using 596.4% CPU
Optimizing NNI: done in 1.57134 secs using 399% CPU
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Iteration 80 / LogL: -104442.755 / Time: 0h:4m:16s (0h:4m:55s left)
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Iteration 320 / LogL: -189214.481 / Time: 0h:28m:40s (0h:6m:22s left)
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Iteration 90 / LogL: -104467.810 / Time: 0h:4m:37s (0h:4m:12s left)
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Iteration 100 / LogL: -104455.325 / Time: 0h:4m:56s (0h:3m:32s left)
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Iteration 330 / LogL: -189199.652 / Time: 0h:29m:26s (0h:5m:27s left)
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Iteration 110 / LogL: -104438.624 / Time: 0h:5m:17s (0h:2m:57s left)
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Iteration 120 / LogL: -104458.326 / Time: 0h:5m:38s (0h:2m:24s left)
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Iteration 340 / LogL: -189353.647 / Time: 0h:30m:13s (0h:4m:32s left)
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Iteration 130 / LogL: -104536.497 / Time: 0h:5m:59s (0h:1m:54s left)
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Iteration 140 / LogL: -104456.456 / Time: 0h:6m:20s (0h:1m:24s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 142: -104436.230
Optimizing NNI: done in 4.55278 secs using 597.6% CPU
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Iteration 350 / LogL: -189328.341 / Time: 0h:31m:0s (0h:3m:38s left)
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Iteration 150 / LogL: -104537.259 / Time: 0h:6m:43s (0h:4m:8s left)
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Iteration 160 / LogL: -104465.882 / Time: 0h:7m:3s (0h:3m:38s left)
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Iteration 170 / LogL: -104461.898 / Time: 0h:7m:24s (0h:3m:9s left)
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Iteration 360 / LogL: -189205.049 / Time: 0h:31m:47s (0h:2m:44s left)
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Iteration 180 / LogL: -104442.396 / Time: 0h:7m:44s (0h:2m:40s left)
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Iteration 190 / LogL: -104446.094 / Time: 0h:8m:5s (0h:2m:13s left)
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Iteration 370 / LogL: -189234.891 / Time: 0h:32m:36s (0h:1m:51s left)
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Iteration 200 / LogL: -104442.255 / Time: 0h:8m:25s (0h:1m:46s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 210: -104433.176
Iteration 210 / LogL: -104433.176 / Time: 0h:8m:48s (0h:4m:12s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 267: -104432.642
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BETTER TREE FOUND at iteration 408: -189176.160
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Iteration 360 / LogL: -104514.812 / Time: 0h:13m:58s (0h:0m:16s left)
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TREE SEARCH COMPLETED AFTER 368 ITERATIONS / Time: 0h:14m:15s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -104432.642
2. Current log-likelihood: -104432.623
3. Current log-likelihood: -104432.597
4. Current log-likelihood: -104432.581
5. Current log-likelihood: -104432.568
Optimizing NNI: done in 5.28154 secs using 597.5% CPU
6. Current log-likelihood: -104432.555
7. Current log-likelihood: -104432.542
8. Current log-likelihood: -104432.531
9. Current log-likelihood: -104432.521
Optimal log-likelihood: -104432.506
Proportion of invariable sites: 0.041
Site proportion and rates:  (0.084,0.035) (0.101,0.110) (0.077,0.211) (0.128,0.355) (0.092,0.575) (0.137,0.847) (0.105,1.302) (0.178,1.994) (0.058,4.539)
Parameters optimization took 9 rounds (6.980 sec)
BEST SCORE FOUND : -104432.506
Total tree length: 168.582

Total number of iterations: 368
CPU time used for tree search: 3311.461 sec (0h:55m:11s)
Wall-clock time used for tree search: 838.808 sec (0h:13m:58s)
Total CPU time used: 3406.811 sec (0h:56m:46s)
Total wall-clock time used: 862.704 sec (0h:14m:22s)

===> START BOOTSTRAP REPLICATE NUMBER 76

Creating bootstrap alignment (seed: 68258)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.118 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -111581.940
Optimizing NNI: done in 4.54889 secs using 597.5% CPU
2. Current log-likelihood: -109574.683
3. Current log-likelihood: -109496.419
Optimizing NNI: done in 4.26898 secs using 597.8% CPU
4. Current log-likelihood: -109489.754
5. Current log-likelihood: -109484.793
6. Current log-likelihood: -109483.705
Optimizing NNI: done in 4.28845 secs using 596.7% CPU
Iteration 450 / LogL: -189197.709 / Time: 0h:38m:51s (0h:5m:1s left)
7. Current log-likelihood: -109483.490
8. Current log-likelihood: -109483.363
9. Current log-likelihood: -109483.262
Optimizing NNI: done in 4.57242 secs using 597.5% CPU
Optimal log-likelihood: -109483.140
Proportion of invariable sites: 0.028
Site proportion and rates:  (0.067,0.041) (0.099,0.114) (0.063,0.193) (0.164,0.336) (0.106,0.535) (0.086,0.767) (0.172,1.209) (0.132,1.773) (0.084,4.244)
Parameters optimization took 9 rounds (14.640 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.39536 secs using 596.9% CPU
Calculating distance matrix: done in 4.73885 secs using 399.9% CPU
Computing ML distances took 4.739217 sec (of wall-clock time) 18.950976 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000696182 secs using 419.7% CPU
Constructing RapidNJ tree: done in 0.00855398 secs using 371.2% CPU
Computing RapidNJ tree took 0.009303 sec (of wall-clock time) 0.035641 sec (of CPU time)
Log-likelihood of RapidNJ tree: -109843.452
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.37299 secs using 597.6% CPU
Optimizing NNI: done in 4.51436 secs using 596.8% CPU
10.899 second
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Optimizing NNI: done in 4.65754 secs using 597% CPU
Computing log-likelihood of 98 initial trees ... 10.023 seconds
Current best score: -109483.140

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 460 / LogL: -189242.200 / Time: 0h:39m:38s (0h:4m:8s left)
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BETTER TREE FOUND at iteration 1: -109087.182
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 4: -109041.918
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Iteration 10 / LogL: -109099.848 / Time: 0h:1m:38s
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Estimate model parameters (epsilon = 0.100)
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Iteration 470 / LogL: -189215.766 / Time: 0h:40m:24s (0h:3m:16s left)
BETTER TREE FOUND at iteration 11: -109034.750
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Iteration 20 / LogL: -109059.131 / Time: 0h:2m:8s
Finish initializing candidate tree set (20)
Current best tree score: -109034.750 / CPU time: 107.927
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 23: -109006.384
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Iteration 480 / LogL: -189180.542 / Time: 0h:41m:9s (0h:2m:24s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -109004.451
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Estimate model parameters (epsilon = 0.100)
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Iteration 490 / LogL: -189212.458 / Time: 0h:41m:53s (0h:1m:32s left)
BETTER TREE FOUND at iteration 41: -109002.049
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BETTER TREE FOUND at iteration 53: -109000.551
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 54: -108998.986
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Iteration 500 / LogL: -189261.792 / Time: 0h:42m:39s (0h:0m:41s left)
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Iteration 60 / LogL: -109008.710 / Time: 0h:4m:9s (0h:6m:37s left)
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Iteration 70 / LogL: -109005.144 / Time: 0h:4m:35s (0h:5m:34s left)
Optimizing NNI: done in 2.33617 secs using 396.9% CPU
Optimizing NNI: done in 4.71247 secs using 597% CPU
TREE SEARCH COMPLETED AFTER 509 ITERATIONS / Time: 0h:43m:19s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -189176.160
Optimizing NNI: done in 2.46822 secs using 397.1% CPU
Optimal log-likelihood: -189176.155
Site proportion and rates:  (0.029,0.112) (0.167,0.329) (0.198,0.539) (0.188,0.758) (0.156,1.027) (0.127,1.486) (0.104,2.259) (0.032,3.466)
Parameters optimization took 1 rounds (1.471 sec)
BEST SCORE FOUND : -189176.155
Total tree length: 148.272

Total number of iterations: 509
CPU time used for tree search: 14862.939 sec (4h:7m:42s)
Wall-clock time used for tree search: 2514.052 sec (0h:41m:54s)
Total CPU time used: 15382.981 sec (4h:16m:22s)
Total wall-clock time used: 2601.278 sec (0h:43m:21s)

===> START BOOTSTRAP REPLICATE NUMBER 41

Creating bootstrap alignment (seed: 70504)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.289 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -191147.700
Optimizing NNI: done in 2.45869 secs using 397.7% CPU
2. Current log-likelihood: -188675.323
Optimizing NNI: done in 2.79238 secs using 397.2% CPU
3. Current log-likelihood: -188628.349
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4. Current log-likelihood: -188626.169
5. Current log-likelihood: -188625.634
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6. Current log-likelihood: -188625.359
Optimizing NNI: done in 2.88804 secs using 397.8% CPU
7. Current log-likelihood: -188625.151
8. Current log-likelihood: -188625.002
Optimizing NNI: done in 2.81618 secs using 397.6% CPU
9. Current log-likelihood: -188624.901
Optimizing NNI: done in 2.73268 secs using 397.2% CPU
Optimal log-likelihood: -188624.842
Site proportion and rates:  (0.013,0.081) (0.047,0.245) (0.077,0.334) (0.169,0.513) (0.203,0.646) (0.242,1.013) (0.177,1.670) (0.073,2.786)
Parameters optimization took 9 rounds (19.084 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.78581 secs using 397.5% CPU
Iteration 80 / LogL: -109012.208 / Time: 0h:5m:1s (0h:4m:42s left)
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Optimizing NNI: done in 2.7894 secs using 397.4% CPU
Estimate model parameters (epsilon = 0.100)
Calculating distance matrix: done in 9.53368 secs using 599.9% CPU
Computing ML distances took 9.534227 sec (of wall-clock time) 57.193642 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00130701 secs using 673.4% CPU
Constructing RapidNJ tree: done in 0.02302 secs using 669.5% CPU
Computing RapidNJ tree took 0.024396 sec (of wall-clock time) 0.164456 sec (of CPU time)
BETTER TREE FOUND at iteration 82: -108991.067
Log-likelihood of RapidNJ tree: -193567.571
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.55578 secs using 397.1% CPU
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Iteration 90 / LogL: -109007.107 / Time: 0h:5m:37s (0h:5m:48s left)
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30.154 second
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Optimizing NNI: done in 2.96518 secs using 397.3% CPU
Computing log-likelihood of 98 initial trees ... 16.633 seconds
Current best score: -188624.842

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -188135.566
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Iteration 100 / LogL: -109024.755 / Time: 0h:6m:6s (0h:5m:3s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 101: -108990.602
BETTER TREE FOUND at iteration 2: -188123.508
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 5: -188121.951
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 9: -188104.622
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Iteration 10 / LogL: -188232.703 / Time: 0h:2m:17s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 119: -108990.543
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Iteration 120 / LogL: -108991.963 / Time: 0h:7m:4s (0h:5m:52s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 126: -108989.770
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Iteration 130 / LogL: -108999.031 / Time: 0h:7m:33s (0h:5m:37s left)
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Iteration 20 / LogL: -188194.394 / Time: 0h:3m:14s
Finish initializing candidate tree set (20)
Current best tree score: -188104.622 / CPU time: 163.100
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 30 / LogL: -188274.975 / Time: 0h:4m:5s (0h:13m:15s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 170: -108988.270
Iteration 170 / LogL: -108988.270 / Time: 0h:9m:24s (0h:5m:34s left)
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Iteration 180 / LogL: -108990.470 / Time: 0h:9m:53s (0h:4m:58s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 132: -188033.705
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Iteration 340 / LogL: -109023.109 / Time: 0h:17m:24s (0h:0m:-4s left)
TREE SEARCH COMPLETED AFTER 340 ITERATIONS / Time: 0h:17m:24s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -108987.892
Optimizing NNI: done in 4.01958 secs using 597.2% CPU
2. Current log-likelihood: -108987.882
Optimal log-likelihood: -108987.868
Proportion of invariable sites: 0.028
Site proportion and rates:  (0.058,0.036) (0.097,0.095) (0.076,0.183) (0.168,0.331) (0.124,0.548) (0.113,0.880) (0.196,1.376) (0.075,2.160) (0.065,4.921)
Parameters optimization took 2 rounds (1.527 sec)
BEST SCORE FOUND : -108987.868
Total tree length: 187.399

Total number of iterations: 340
CPU time used for tree search: 4035.688 sec (1h:7m:15s)
Wall-clock time used for tree search: 1023.800 sec (0h:17m:3s)
Total CPU time used: 4125.020 sec (1h:8m:45s)
Total wall-clock time used: 1046.194 sec (0h:17m:26s)

===> START BOOTSTRAP REPLICATE NUMBER 77

Creating bootstrap alignment (seed: 68259)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.116 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105516.009
2. Current log-likelihood: -103526.914
Optimizing NNI: done in 4.16374 secs using 597.8% CPU
3. Current log-likelihood: -103477.096
4. Current log-likelihood: -103475.180
5. Current log-likelihood: -103473.836
Optimizing NNI: done in 4.54637 secs using 597.1% CPU
6. Current log-likelihood: -103472.164
7. Current log-likelihood: -103471.435
8. Current log-likelihood: -103471.168
Optimizing NNI: done in 4.2902 secs using 597.2% CPU
9. Current log-likelihood: -103471.002
10. Current log-likelihood: -103470.884
11. Current log-likelihood: -103470.671
Optimizing NNI: done in 4.01714 secs using 597.4% CPU
Optimal log-likelihood: -103470.570
Proportion of invariable sites: 0.018
Site proportion and rates:  (0.099,0.037) (0.125,0.117) (0.062,0.206) (0.076,0.316) (0.143,0.505) (0.108,0.817) (0.123,1.287) (0.176,1.906) (0.070,4.183)
Parameters optimization took 11 rounds (17.112 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.67482 secs using 597.3% CPU
Calculating distance matrix: done in 4.69975 secs using 399.8% CPU
Computing ML distances took 4.700120 sec (of wall-clock time) 18.792704 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000777006 secs using 404.4% CPU
Constructing RapidNJ tree: done in 0.00859594 secs using 328.4% CPU
Computing RapidNJ tree took 0.009429 sec (of wall-clock time) 0.033003 sec (of CPU time)
Log-likelihood of RapidNJ tree: -103942.906
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.04586 secs using 598% CPU
Optimizing NNI: done in 5.94135 secs using 597.4% CPU
10.495 second
Optimizing NNI: done in 5.83494 secs using 598% CPU
Iteration 150 / LogL: -188064.872 / Time: 0h:13m:23s (0h:7m:21s left)
Optimizing NNI: done in 4.95769 secs using 596.9% CPU
Computing log-likelihood of 98 initial trees ... 10.188 seconds
Current best score: -103470.570

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.78591 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.19356 secs using 596.6% CPU
Optimizing NNI: done in 3.89347 secs using 597.1% CPU
Optimizing NNI: done in 4.57541 secs using 596.6% CPU
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Optimizing NNI: done in 4.6908 secs using 596.9% CPU
Optimizing NNI: done in 4.35204 secs using 598.3% CPU
BETTER TREE FOUND at iteration 1: -103099.708
Optimizing NNI: done in 2.41099 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.14571 secs using 597.3% CPU
BETTER TREE FOUND at iteration 2: -103067.465
Optimizing NNI: done in 2.52258 secs using 397.8% CPU
Optimizing NNI: done in 4.4563 secs using 597% CPU
Optimizing NNI: done in 2.6297 secs using 397.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -103057.186
Optimizing NNI: done in 4.45353 secs using 596.7% CPU
Iteration 160 / LogL: -188107.389 / Time: 0h:14m:9s (0h:6m:24s left)
Optimizing NNI: done in 2.28662 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -103055.477
Optimizing NNI: done in 5.12562 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 161: -188022.545
Optimizing NNI: done in 2.60827 secs using 397.7% CPU
Optimizing NNI: done in 1.94947 secs using 398.4% CPU
Optimizing NNI: done in 4.37443 secs using 597.2% CPU
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Optimizing NNI: done in 2.7954 secs using 398.5% CPU
Iteration 10 / LogL: -103088.241 / Time: 0h:1m:40s
Optimizing NNI: done in 1.93706 secs using 398.3% CPU
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Optimizing NNI: done in 2.64835 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.42017 secs using 597.9% CPU
BETTER TREE FOUND at iteration 17: -103047.473
Optimizing NNI: done in 4.38612 secs using 597.5% CPU
Optimizing NNI: done in 2.61294 secs using 398.5% CPU
Optimizing NNI: done in 2.64026 secs using 398.1% CPU
Optimizing NNI: done in 4.43733 secs using 597.2% CPU
Optimizing NNI: done in 2.05733 secs using 397% CPU
Iteration 20 / LogL: -103104.617 / Time: 0h:2m:6s
Finish initializing candidate tree set (20)
Current best tree score: -103047.473 / CPU time: 103.473
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 2.57629 secs using 397.9% CPU
Optimizing NNI: done in 4.07163 secs using 597.9% CPU
Iteration 170 / LogL: -188277.974 / Time: 0h:14m:55s (0h:8m:2s left)
Optimizing NNI: done in 2.42175 secs using 398.5% CPU
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Optimizing NNI: done in 2.46135 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -103041.843
Iteration 30 / LogL: -103041.843 / Time: 0h:2m:33s (0h:8m:49s left)
Optimizing NNI: done in 5.51478 secs using 597.5% CPU
Optimizing NNI: done in 2.18444 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.77905 secs using 597.2% CPU
BETTER TREE FOUND at iteration 31: -103040.980
Optimizing NNI: done in 2.04702 secs using 398.4% CPU
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Optimizing NNI: done in 4.26131 secs using 597.7% CPU
Optimizing NNI: done in 1.76394 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 34: -103035.363
Optimizing NNI: done in 4.64122 secs using 597.1% CPU
Optimizing NNI: done in 1.82255 secs using 398.5% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.72677 secs using 597.2% CPU
Iteration 180 / LogL: -188078.842 / Time: 0h:15m:42s (0h:7m:6s left)
BETTER TREE FOUND at iteration 38: -103017.060
Optimizing NNI: done in 2.34145 secs using 398.6% CPU
Optimizing NNI: done in 4.28949 secs using 597.1% CPU
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Iteration 40 / LogL: -103037.971 / Time: 0h:3m:1s (0h:7m:36s left)
Optimizing NNI: done in 2.43839 secs using 398.6% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.53051 secs using 398.3% CPU
BETTER TREE FOUND at iteration 183: -188020.763
Optimizing NNI: done in 2.3707 secs using 398.3% CPU
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Iteration 50 / LogL: -103029.987 / Time: 0h:3m:25s (0h:6m:8s left)
Optimizing NNI: done in 4.39685 secs using 597.3% CPU
Optimizing NNI: done in 2.53252 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.75464 secs using 597.7% CPU
BETTER TREE FOUND at iteration 51: -103010.443
Optimizing NNI: done in 2.07549 secs using 398.8% CPU
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Iteration 190 / LogL: -188032.472 / Time: 0h:16m:30s (0h:8m:7s left)
Optimizing NNI: done in 2.32939 secs using 398% CPU
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Optimizing NNI: done in 2.74857 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.68098 secs using 597.3% CPU
BETTER TREE FOUND at iteration 59: -103009.797
Optimizing NNI: done in 2.45777 secs using 398.6% CPU
Iteration 60 / LogL: -103034.623 / Time: 0h:3m:56s (0h:6m:35s left)
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Iteration 70 / LogL: -103025.369 / Time: 0h:4m:19s (0h:5m:34s left)
Optimizing NNI: done in 2.19319 secs using 398.6% CPU
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Optimizing NNI: done in 2.2898 secs using 398.1% CPU
Optimizing NNI: done in 1.94866 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 73: -103006.848
Optimizing NNI: done in 4.14542 secs using 597.5% CPU
Iteration 200 / LogL: -188032.391 / Time: 0h:17m:13s (0h:7m:10s left)
Optimizing NNI: done in 2.29126 secs using 398.5% CPU
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Iteration 80 / LogL: -103052.741 / Time: 0h:4m:44s (0h:5m:34s left)
Optimizing NNI: done in 4.14834 secs using 597.5% CPU
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Iteration 90 / LogL: -103049.850 / Time: 0h:5m:8s (0h:4m:47s left)
Optimizing NNI: done in 2.14813 secs using 398.4% CPU
Optimizing NNI: done in 4.08221 secs using 598.1% CPU
Iteration 210 / LogL: -188067.742 / Time: 0h:17m:56s (0h:6m:15s left)
Optimizing NNI: done in 2.48502 secs using 398.9% CPU
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Iteration 100 / LogL: -103067.613 / Time: 0h:5m:29s (0h:4m:2s left)
Optimizing NNI: done in 2.09192 secs using 398.3% CPU
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Iteration 110 / LogL: -103020.111 / Time: 0h:5m:51s (0h:3m:23s left)
Optimizing NNI: done in 2.24732 secs using 398.8% CPU
Optimizing NNI: done in 4.8765 secs using 597.5% CPU
Iteration 220 / LogL: -188102.190 / Time: 0h:18m:41s (0h:5m:22s left)
Optimizing NNI: done in 2.06804 secs using 398.7% CPU
Optimizing NNI: done in 2.13145 secs using 399% CPU
Optimizing NNI: done in 4.15165 secs using 597.9% CPU
Optimizing NNI: done in 2.27973 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 114: -103005.326
Optimizing NNI: done in 4.51015 secs using 597.4% CPU
Optimizing NNI: done in 2.53205 secs using 398.9% CPU
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Iteration 120 / LogL: -103026.339 / Time: 0h:6m:15s (0h:4m:56s left)
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Iteration 130 / LogL: -103122.574 / Time: 0h:6m:38s (0h:4m:19s left)
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Iteration 230 / LogL: -188044.596 / Time: 0h:19m:25s (0h:4m:29s left)
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Iteration 140 / LogL: -103029.003 / Time: 0h:7m:1s (0h:3m:44s left)
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Iteration 240 / LogL: -188041.539 / Time: 0h:20m:10s (0h:3m:37s left)
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Iteration 150 / LogL: -103020.871 / Time: 0h:7m:24s (0h:3m:11s left)
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Iteration 160 / LogL: -103016.596 / Time: 0h:7m:48s (0h:2m:39s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 164: -103005.161
Optimizing NNI: done in 2.19431 secs using 398.8% CPU
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Iteration 250 / LogL: -188157.515 / Time: 0h:20m:55s (0h:2m:46s left)
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Iteration 170 / LogL: -103032.061 / Time: 0h:8m:12s (0h:4m:33s left)
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Iteration 180 / LogL: -103006.201 / Time: 0h:8m:36s (0h:4m:2s left)
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Iteration 280 / LogL: -188071.168 / Time: 0h:23m:8s (0h:0m:14s left)
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Iteration 230 / LogL: -103073.566 / Time: 0h:10m:30s (0h:1m:33s left)
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TREE SEARCH COMPLETED AFTER 284 ITERATIONS / Time: 0h:23m:26s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -188020.763
Optimal log-likelihood: -188020.762
Site proportion and rates:  (0.013,0.082) (0.057,0.264) (0.066,0.336) (0.208,0.524) (0.174,0.668) (0.232,1.028) (0.172,1.656) (0.078,2.736)
Parameters optimization took 1 rounds (0.483 sec)
BEST SCORE FOUND : -188020.762
Total tree length: 146.234

Total number of iterations: 284
CPU time used for tree search: 8063.986 sec (2h:14m:23s)
Wall-clock time used for tree search: 1375.095 sec (0h:22m:55s)
Total CPU time used: 8255.905 sec (2h:17m:35s)
Total wall-clock time used: 1407.305 sec (0h:23m:27s)

===> START BOOTSTRAP REPLICATE NUMBER 42

Creating bootstrap alignment (seed: 70505)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.259 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199067.732
Optimizing NNI: done in 2.38696 secs using 398.8% CPU
2. Current log-likelihood: -196509.386
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3. Current log-likelihood: -196426.721
Optimizing NNI: done in 2.34483 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 237: -103004.905
4. Current log-likelihood: -196418.164
Optimizing NNI: done in 2.08347 secs using 398.4% CPU
5. Current log-likelihood: -196414.754
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6. Current log-likelihood: -196413.464
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Iteration 240 / LogL: -103008.662 / Time: 0h:10m:54s (0h:4m:25s left)
7. Current log-likelihood: -196413.102
Optimizing NNI: done in 2.63141 secs using 398.1% CPU
Optimal log-likelihood: -196413.002
Site proportion and rates:  (0.009,0.067) (0.060,0.245) (0.107,0.381) (0.200,0.553) (0.172,0.742) (0.203,1.054) (0.150,1.617) (0.097,2.550)
Parameters optimization took 7 rounds (16.609 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 9.50503 secs using 599.8% CPU
Computing ML distances took 9.505563 sec (of wall-clock time) 57.011284 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00135899 secs using 391% CPU
Constructing RapidNJ tree: done in 0.0233641 secs using 657.6% CPU
Computing RapidNJ tree took 0.024780 sec (of wall-clock time) 0.159640 sec (of CPU time)
Optimizing NNI: done in 2.22605 secs using 398% CPU
Log-likelihood of RapidNJ tree: -199792.155
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.33797 secs using 398.6% CPU
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Iteration 250 / LogL: -103092.650 / Time: 0h:11m:17s (0h:3m:56s left)
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29.695 second
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Iteration 260 / LogL: -103140.948 / Time: 0h:11m:40s (0h:3m:28s left)
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Computing log-likelihood of 98 initial trees ... 16.347 seconds
Current best score: -196413.002

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -195853.188
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 8: -195785.442
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Iteration 290 / LogL: -103028.895 / Time: 0h:12m:49s (0h:2m:5s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 295: -103003.744
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Iteration 20 / LogL: -195838.403 / Time: 0h:2m:55s
Finish initializing candidate tree set (20)
Current best tree score: -195785.442 / CPU time: 147.492
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 30 / LogL: -195780.728 / Time: 0h:3m:50s (0h:12m:57s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 355: -103003.643
BETTER TREE FOUND at iteration 40: -195725.456
Iteration 40 / LogL: -195725.456 / Time: 0h:4m:39s (0h:11m:55s left)
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Iteration 50 / LogL: -195732.441 / Time: 0h:5m:25s (0h:9m:56s left)
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TREE SEARCH COMPLETED AFTER 456 ITERATIONS / Time: 0h:19m:12s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -103003.643
Optimal log-likelihood: -103003.643
Proportion of invariable sites: 0.017
Site proportion and rates:  (0.093,0.032) (0.125,0.100) (0.068,0.193) (0.087,0.315) (0.151,0.515) (0.105,0.868) (0.109,1.291) (0.177,1.879) (0.069,4.393)
Parameters optimization took 1 rounds (0.459 sec)
BEST SCORE FOUND : -103003.643
Total tree length: 164.775

Total number of iterations: 456
CPU time used for tree search: 4470.450 sec (1h:14m:30s)
Wall-clock time used for tree search: 1129.889 sec (0h:18m:49s)
Total CPU time used: 4564.097 sec (1h:16m:4s)
Total wall-clock time used: 1153.364 sec (0h:19m:13s)

===> START BOOTSTRAP REPLICATE NUMBER 78

Creating bootstrap alignment (seed: 68260)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.104 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -108460.851
Optimizing NNI: done in 4.62674 secs using 597.4% CPU
2. Current log-likelihood: -106310.202
3. Current log-likelihood: -106260.257
4. Current log-likelihood: -106256.351
Optimizing NNI: done in 4.4418 secs using 597.8% CPU
Iteration 90 / LogL: -195727.867 / Time: 0h:8m:38s (0h:8m:14s left)
5. Current log-likelihood: -106256.238
Optimal log-likelihood: -106256.148
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.114,0.042) (0.069,0.122) (0.081,0.208) (0.108,0.308) (0.106,0.493) (0.097,0.759) (0.126,1.170) (0.194,1.807) (0.080,3.906)
Parameters optimization took 5 rounds (7.598 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Computing ML distances took 4.635587 sec (of wall-clock time) 18.534051 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000705957 secs using 216.9% CPU
Constructing RapidNJ tree: done in 0.00854301 secs using 411.9% CPU
Computing RapidNJ tree took 0.009296 sec (of wall-clock time) 0.039555 sec (of CPU time)
Log-likelihood of RapidNJ tree: -106300.826
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.33743 secs using 597.6% CPU
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10.919 second
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Computing log-likelihood of 98 initial trees ... 9.733 seconds
Current best score: -106256.148

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 100 / LogL: -195713.589 / Time: 0h:9m:22s (0h:7m:5s left)
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Iteration 110 / LogL: -195716.522 / Time: 0h:10m:6s (0h:6m:1s left)
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BETTER TREE FOUND at iteration 10: -105661.971
Iteration 10 / LogL: -105661.971 / Time: 0h:2m:10s
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Iteration 20 / LogL: -105671.581 / Time: 0h:2m:37s
Finish initializing candidate tree set (20)
Current best tree score: -105661.971 / CPU time: 143.922
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 80 / LogL: -105639.980 / Time: 0h:5m:0s (0h:5m:46s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.73409 secs using 597.2% CPU
BETTER TREE FOUND at iteration 86: -105606.114
Optimizing NNI: done in 1.58349 secs using 398.9% CPU
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Optimizing NNI: done in 1.91049 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.63869 secs using 596.2% CPU
Iteration 160 / LogL: -195763.143 / Time: 0h:13m:54s (0h:1m:18s left)
BETTER TREE FOUND at iteration 90: -105601.035
Iteration 90 / LogL: -105601.035 / Time: 0h:5m:22s (0h:6m:2s left)
Optimizing NNI: done in 2.12862 secs using 399% CPU
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Iteration 100 / LogL: -105604.685 / Time: 0h:5m:43s (0h:5m:12s left)
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Optimizing NNI: done in 4.53356 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 168: -195696.347
Optimizing NNI: done in 2.07899 secs using 397.9% CPU
Optimizing NNI: done in 2.3712 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.67268 secs using 598.2% CPU
BETTER TREE FOUND at iteration 110: -105596.500
Iteration 110 / LogL: -105596.500 / Time: 0h:6m:8s (0h:5m:37s left)
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Iteration 170 / LogL: -195723.348 / Time: 0h:14m:44s (0h:8m:32s left)
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Iteration 120 / LogL: -105604.264 / Time: 0h:6m:28s (0h:4m:53s left)
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Iteration 130 / LogL: -105631.882 / Time: 0h:6m:50s (0h:4m:14s left)
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Iteration 180 / LogL: -195743.418 / Time: 0h:15m:29s (0h:7m:36s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 138: -105594.603
Optimizing NNI: done in 5.0247 secs using 597.2% CPU
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Iteration 140 / LogL: -105617.462 / Time: 0h:7m:13s (0h:5m:5s left)
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Iteration 150 / LogL: -105594.929 / Time: 0h:7m:35s (0h:4m:29s left)
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Iteration 190 / LogL: -195714.205 / Time: 0h:16m:14s (0h:6m:42s left)
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Iteration 160 / LogL: -105612.075 / Time: 0h:7m:57s (0h:3m:54s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 194: -195687.074
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Iteration 170 / LogL: -105601.735 / Time: 0h:8m:18s (0h:3m:20s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 175: -105593.863
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Iteration 200 / LogL: -195730.093 / Time: 0h:17m:2s (0h:8m:3s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 5.55971 secs using 596.5% CPU
BETTER TREE FOUND at iteration 177: -105590.868
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Iteration 180 / LogL: -105617.358 / Time: 0h:8m:43s (0h:4m:43s left)
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Iteration 190 / LogL: -105608.457 / Time: 0h:9m:4s (0h:4m:10s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.25136 secs using 398.5% CPU
BETTER TREE FOUND at iteration 209: -195686.044
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Iteration 210 / LogL: -195699.682 / Time: 0h:17m:50s (0h:8m:27s left)
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Iteration 200 / LogL: -105869.160 / Time: 0h:9m:26s (0h:3m:39s left)
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Iteration 210 / LogL: -105595.690 / Time: 0h:9m:47s (0h:3m:8s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.34272 secs using 399% CPU
BETTER TREE FOUND at iteration 219: -195683.304
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Iteration 220 / LogL: -195704.148 / Time: 0h:18m:38s (0h:8m:25s left)
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Iteration 220 / LogL: -105638.677 / Time: 0h:10m:9s (0h:2m:38s left)
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Iteration 230 / LogL: -105611.874 / Time: 0h:10m:32s (0h:2m:9s left)
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Iteration 240 / LogL: -105644.397 / Time: 0h:10m:53s (0h:1m:41s left)
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Iteration 230 / LogL: -195696.957 / Time: 0h:19m:26s (0h:7m:33s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 243: -105590.073
Optimizing NNI: done in 2.39473 secs using 398.4% CPU
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Iteration 250 / LogL: -105658.245 / Time: 0h:11m:15s (0h:4m:12s left)
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Iteration 260 / LogL: -105606.761 / Time: 0h:11m:37s (0h:3m:43s left)
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Iteration 240 / LogL: -195715.493 / Time: 0h:20m:13s (0h:6m:40s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.00877 secs using 398.6% CPU
BETTER TREE FOUND at iteration 241: -195681.937
Optimizing NNI: done in 2.4787 secs using 398% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.42623 secs using 597% CPU
BETTER TREE FOUND at iteration 270: -105588.657
Iteration 270 / LogL: -105588.657 / Time: 0h:12m:1s (0h:4m:28s left)
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Iteration 280 / LogL: -105720.560 / Time: 0h:12m:24s (0h:4m:0s left)
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Iteration 250 / LogL: -195728.856 / Time: 0h:21m:0s (0h:7m:40s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 260: -195681.101
Iteration 260 / LogL: -195681.101 / Time: 0h:21m:49s (0h:8m:25s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 343: -105588.383
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BETTER TREE FOUND at iteration 294: -195680.249
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Iteration 440 / LogL: -105592.286 / Time: 0h:18m:14s (0h:0m:7s left)
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TREE SEARCH COMPLETED AFTER 444 ITERATIONS / Time: 0h:18m:24s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -105588.383
2. Current log-likelihood: -105588.373
Optimal log-likelihood: -105588.360
Proportion of invariable sites: 0.024
Site proportion and rates:  (0.066,0.028) (0.104,0.081) (0.101,0.188) (0.103,0.310) (0.115,0.481) (0.098,0.783) (0.125,1.169) (0.188,1.794) (0.077,4.210)
Parameters optimization took 2 rounds (1.280 sec)
BEST SCORE FOUND : -105588.360
Total tree length: 172.176

Total number of iterations: 444
CPU time used for tree search: 4314.235 sec (1h:11m:54s)
Wall-clock time used for tree search: 1090.830 sec (0h:18m:10s)
Total CPU time used: 4372.647 sec (1h:12m:52s)
Total wall-clock time used: 1105.449 sec (0h:18m:25s)

===> START BOOTSTRAP REPLICATE NUMBER 79

Creating bootstrap alignment (seed: 68261)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.158 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 104 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -103013.695
2. Current log-likelihood: -101089.412
Optimizing NNI: done in 4.77188 secs using 596.7% CPU
3. Current log-likelihood: -101018.163
4. Current log-likelihood: -101008.399
Optimizing NNI: done in 4.21523 secs using 597% CPU
5. Current log-likelihood: -101007.102
6. Current log-likelihood: -101006.539
7. Current log-likelihood: -101006.056
Optimizing NNI: done in 4.44655 secs using 598.1% CPU
Iteration 330 / LogL: -195702.776 / Time: 0h:27m:8s (0h:5m:16s left)
8. Current log-likelihood: -101004.074
9. Current log-likelihood: -100998.517
10. Current log-likelihood: -100996.712
Optimizing NNI: done in 4.5758 secs using 597.6% CPU
Optimal log-likelihood: -100996.633
Proportion of invariable sites: 0.017
Site proportion and rates:  (0.112,0.045) (0.115,0.143) (0.105,0.263) (0.132,0.415) (0.100,0.672) (0.072,0.930) (0.114,1.440) (0.170,2.083) (0.060,3.999)
Parameters optimization took 10 rounds (16.536 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.56323 secs using 597.4% CPU
Calculating distance matrix: done in 4.6465 secs using 399.9% CPU
Computing ML distances took 4.646866 sec (of wall-clock time) 18.580942 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000818968 secs using 302.6% CPU
Constructing RapidNJ tree: done in 0.00861406 secs using 400.6% CPU
Computing RapidNJ tree took 0.009494 sec (of wall-clock time) 0.039660 sec (of CPU time)
Log-likelihood of RapidNJ tree: -101221.943
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.78261 secs using 596.8% CPU
Optimizing NNI: done in 5.63812 secs using 596.3% CPU
10.608 second
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Optimizing NNI: done in 4.86889 secs using 596.5% CPU
Computing log-likelihood of 98 initial trees ... 9.950 seconds
Current best score: -100996.633

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 340 / LogL: -195724.822 / Time: 0h:27m:57s (0h:4m:27s left)
BETTER TREE FOUND at iteration 1: -100563.950
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -100520.665
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Iteration 350 / LogL: -195688.637 / Time: 0h:28m:42s (0h:3m:37s left)
Optimizing NNI: done in 3.10579 secs using 398.1% CPU
Iteration 10 / LogL: -100614.783 / Time: 0h:1m:47s
Optimizing NNI: done in 4.04293 secs using 597.7% CPU
Optimizing NNI: done in 3.42806 secs using 398% CPU
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Optimizing NNI: done in 3.21296 secs using 398.1% CPU
Iteration 20 / LogL: -100542.492 / Time: 0h:2m:13s
Finish initializing candidate tree set (20)
Current best tree score: -100520.665 / CPU time: 111.160
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.17739 secs using 398.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.50858 secs using 597.7% CPU
BETTER TREE FOUND at iteration 21: -100505.013
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Optimizing NNI: done in 4.48389 secs using 597.3% CPU
BETTER TREE FOUND at iteration 24: -100497.308
Optimizing NNI: done in 4.50504 secs using 596.6% CPU
Iteration 360 / LogL: -195755.801 / Time: 0h:29m:27s (0h:2m:47s left)
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Iteration 30 / LogL: -100552.571 / Time: 0h:2m:42s (0h:8m:46s left)
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Optimizing NNI: done in 4.24314 secs using 597.2% CPU
BETTER TREE FOUND at iteration 33: -100495.790
Optimizing NNI: done in 2.19696 secs using 398.3% CPU
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Iteration 40 / LogL: -100506.786 / Time: 0h:3m:10s (0h:7m:33s left)
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Iteration 370 / LogL: -195689.073 / Time: 0h:30m:12s (0h:1m:57s left)
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Iteration 50 / LogL: -100514.915 / Time: 0h:3m:31s (0h:5m:58s left)
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Optimizing NNI: done in 1.68396 secs using 398.4% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 52: -100482.090
Optimizing NNI: done in 4.92778 secs using 597.7% CPU
Optimizing NNI: done in 1.95021 secs using 397.4% CPU
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Iteration 60 / LogL: -100559.392 / Time: 0h:3m:55s (0h:6m:6s left)
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Iteration 380 / LogL: -195684.712 / Time: 0h:30m:58s (0h:1m:8s left)
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Iteration 70 / LogL: -100484.911 / Time: 0h:4m:16s (0h:5m:4s left)
Optimizing NNI: done in 1.98142 secs using 398.5% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.0218 secs using 398.4% CPU
BETTER TREE FOUND at iteration 385: -195677.768
Optimizing NNI: done in 2.24322 secs using 397.9% CPU
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Iteration 80 / LogL: -100497.859 / Time: 0h:4m:38s (0h:4m:13s left)
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Iteration 390 / LogL: -195701.463 / Time: 0h:31m:45s (0h:7m:45s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 85: -100478.059
Optimizing NNI: done in 4.37038 secs using 597.5% CPU
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Iteration 90 / LogL: -100487.862 / Time: 0h:5m:2s (0h:5m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 95: -100477.200
Optimizing NNI: done in 4.82332 secs using 598.1% CPU
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Iteration 100 / LogL: -100510.084 / Time: 0h:5m:26s (0h:5m:12s left)
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Iteration 400 / LogL: -195689.203 / Time: 0h:32m:32s (0h:6m:55s left)
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Iteration 110 / LogL: -100483.561 / Time: 0h:5m:47s (0h:4m:30s left)
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Iteration 120 / LogL: -100482.272 / Time: 0h:6m:9s (0h:3m:52s left)
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Iteration 410 / LogL: -196004.695 / Time: 0h:33m:17s (0h:6m:6s left)
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Iteration 130 / LogL: -100513.032 / Time: 0h:6m:30s (0h:3m:16s left)
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Optimizing NNI: done in 1.81646 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 135: -100476.881
Optimizing NNI: done in 4.37573 secs using 597.6% CPU
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Iteration 140 / LogL: -100478.165 / Time: 0h:6m:53s (0h:4m:42s left)
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Iteration 420 / LogL: -195697.909 / Time: 0h:34m:2s (0h:5m:16s left)
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Iteration 150 / LogL: -100497.306 / Time: 0h:7m:14s (0h:4m:7s left)
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Iteration 160 / LogL: -100528.103 / Time: 0h:7m:34s (0h:3m:34s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.30991 secs using 597.5% CPU
BETTER TREE FOUND at iteration 162: -100476.644
Optimizing NNI: done in 2.00623 secs using 398.5% CPU
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Iteration 430 / LogL: -195723.620 / Time: 0h:34m:47s (0h:4m:27s left)
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Iteration 170 / LogL: -100480.311 / Time: 0h:7m:57s (0h:4m:19s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.09096 secs using 398.4% CPU
BETTER TREE FOUND at iteration 434: -195677.232
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Iteration 180 / LogL: -100476.809 / Time: 0h:8m:18s (0h:3m:48s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 183: -100476.084
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Iteration 440 / LogL: -195731.915 / Time: 0h:35m:33s (0h:7m:36s left)
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Iteration 190 / LogL: -100516.730 / Time: 0h:8m:43s (0h:4m:17s left)
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Iteration 200 / LogL: -100519.223 / Time: 0h:9m:3s (0h:3m:46s left)
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Iteration 450 / LogL: -195690.243 / Time: 0h:36m:16s (0h:6m:47s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 464: -195675.576
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Iteration 480 / LogL: -196397.961 / Time: 0h:38m:45s (0h:6m:47s left)
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Iteration 280 / LogL: -100481.350 / Time: 0h:11m:53s (0h:0m:7s left)
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TREE SEARCH COMPLETED AFTER 284 ITERATIONS / Time: 0h:12m:2s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -100476.084
Optimizing NNI: done in 6.35195 secs using 597.4% CPU
2. Current log-likelihood: -100476.057
3. Current log-likelihood: -100476.019
4. Current log-likelihood: -100475.983
5. Current log-likelihood: -100475.964
6. Current log-likelihood: -100475.945
7. Current log-likelihood: -100475.927
8. Current log-likelihood: -100475.907
Optimizing NNI: done in 6.17963 secs using 597.9% CPU
9. Current log-likelihood: -100475.889
10. Current log-likelihood: -100475.872
11. Current log-likelihood: -100475.856
12. Current log-likelihood: -100475.840
13. Current log-likelihood: -100475.824
14. Current log-likelihood: -100475.810
15. Current log-likelihood: -100475.795
16. Current log-likelihood: -100475.781
Optimizing NNI: done in 5.67286 secs using 597.1% CPU
17. Current log-likelihood: -100475.767
18. Current log-likelihood: -100475.753
19. Current log-likelihood: -100475.740
20. Current log-likelihood: -100475.727
21. Current log-likelihood: -100475.714
22. Current log-likelihood: -100475.702
Optimizing NNI: done in 4.11483 secs using 597.2% CPU
23. Current log-likelihood: -100475.690
24. Current log-likelihood: -100475.679
25. Current log-likelihood: -100475.669
Optimal log-likelihood: -100475.658
Proportion of invariable sites: 0.016
Site proportion and rates:  (0.102,0.033) (0.103,0.112) (0.120,0.224) (0.137,0.386) (0.108,0.634) (0.072,0.906) (0.141,1.440) (0.143,2.097) (0.058,4.666)
Parameters optimization took 25 rounds (19.389 sec)
BEST SCORE FOUND : -100475.658
Total tree length: 165.383

Total number of iterations: 284
CPU time used for tree search: 2754.335 sec (0h:45m:54s)
Wall-clock time used for tree search: 699.431 sec (0h:11m:39s)
Total CPU time used: 2921.964 sec (0h:48m:41s)
Total wall-clock time used: 741.478 sec (0h:12m:21s)

===> START BOOTSTRAP REPLICATE NUMBER 80

Creating bootstrap alignment (seed: 68262)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 109 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -110486.819
2. Current log-likelihood: -108339.283
Optimizing NNI: done in 4.75671 secs using 597.7% CPU
3. Current log-likelihood: -108286.180
4. Current log-likelihood: -108284.385
Optimizing NNI: done in 4.40496 secs using 596.6% CPU
5. Current log-likelihood: -108283.699
6. Current log-likelihood: -108283.076
7. Current log-likelihood: -108282.490
Optimizing NNI: done in 4.59694 secs using 597.4% CPU
8. Current log-likelihood: -108281.939
9. Current log-likelihood: -108281.419
10. Current log-likelihood: -108280.976
Optimizing NNI: done in 4.21807 secs using 597.6% CPU
Iteration 490 / LogL: -195681.174 / Time: 0h:39m:34s (0h:5m:59s left)
11. Current log-likelihood: -108280.587
12. Current log-likelihood: -108280.278
13. Current log-likelihood: -108280.109
Optimizing NNI: done in 4.58364 secs using 597.5% CPU
14. Current log-likelihood: -108279.927
15. Current log-likelihood: -108279.787
16. Current log-likelihood: -108279.636
Optimal log-likelihood: -108279.496
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.094,0.035) (0.103,0.112) (0.031,0.200) (0.102,0.296) (0.088,0.444) (0.107,0.689) (0.165,1.095) (0.207,1.762) (0.070,4.152)
Parameters optimization took 16 rounds (23.992 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 5.25507 secs using 597.2% CPU
Calculating distance matrix: done in 4.71999 secs using 399.8% CPU
Computing ML distances took 4.720262 sec (of wall-clock time) 18.873075 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000729084 secs using 330.6% CPU
Constructing RapidNJ tree: done in 0.00845599 secs using 384.2% CPU
Computing RapidNJ tree took 0.009241 sec (of wall-clock time) 0.036912 sec (of CPU time)
Log-likelihood of RapidNJ tree: -108712.698
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.31758 secs using 597.1% CPU
Optimizing NNI: done in 5.09718 secs using 596.8% CPU
Optimizing NNI: done in 5.08025 secs using 597.6% CPU
10.996 second
Optimizing NNI: done in 6.44826 secs using 597.3% CPU
Computing log-likelihood of 98 initial trees ... 10.314 seconds
Current best score: -108279.496

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 500 / LogL: -195726.595 / Time: 0h:40m:24s (0h:5m:10s left)
BETTER TREE FOUND at iteration 1: -107809.375
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -107751.440
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -107737.643
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Iteration 10 / LogL: -107799.440 / Time: 0h:1m:31s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 17: -107704.863
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Iteration 510 / LogL: -195706.165 / Time: 0h:41m:10s (0h:4m:22s left)
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Optimizing NNI: done in 2.32603 secs using 398.7% CPU
Iteration 20 / LogL: -107784.600 / Time: 0h:1m:55s
Finish initializing candidate tree set (20)
Current best tree score: -107704.863 / CPU time: 85.880
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.5876 secs using 595.9% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -107695.600
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -107684.771
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -107679.987
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Iteration 30 / LogL: -107706.623 / Time: 0h:2m:22s (0h:8m:2s left)
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Iteration 520 / LogL: -195698.327 / Time: 0h:41m:56s (0h:3m:33s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 37: -107677.743
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 59: -107669.510
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 68: -107668.779
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 73: -107667.379
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Iteration 540 / LogL: -195687.868 / Time: 0h:43m:26s (0h:1m:56s left)
Optimizing NNI: done in 2.01651 secs using 398.8% CPU
Optimizing NNI: done in 1.77452 secs using 398.8% CPU
Optimizing NNI: done in 4.31709 secs using 597.4% CPU
Optimizing NNI: done in 2.11964 secs using 398.7% CPU
Iteration 80 / LogL: -107703.870 / Time: 0h:4m:13s (0h:4m:57s left)
Optimizing NNI: done in 1.94034 secs using 399.2% CPU
Optimizing NNI: done in 4.65923 secs using 596.9% CPU
Optimizing NNI: done in 2.31363 secs using 398.4% CPU
Optimizing NNI: done in 1.82609 secs using 398.8% CPU
BETTER TREE FOUND at iteration 83: -107667.378
Optimizing NNI: done in 2.01743 secs using 398.7% CPU
Optimizing NNI: done in 4.57413 secs using 597.1% CPU
Optimizing NNI: done in 1.8366 secs using 398.8% CPU
Optimizing NNI: done in 1.99499 secs using 398.7% CPU
Optimizing NNI: done in 4.58541 secs using 598% CPU
Optimizing NNI: done in 1.81682 secs using 398.9% CPU
Optimizing NNI: done in 1.84618 secs using 398.8% CPU
Optimizing NNI: done in 4.23978 secs using 596.2% CPU
Optimizing NNI: done in 2.14699 secs using 398.4% CPU
Optimizing NNI: done in 2.11808 secs using 398.5% CPU
Iteration 90 / LogL: -107680.989 / Time: 0h:4m:33s (0h:4m:45s left)
Optimizing NNI: done in 4.70061 secs using 597.9% CPU
Optimizing NNI: done in 2.09064 secs using 398.5% CPU
Optimizing NNI: done in 1.98821 secs using 398.7% CPU
Optimizing NNI: done in 4.26806 secs using 597.4% CPU
Optimizing NNI: done in 2.1478 secs using 398.7% CPU
Optimizing NNI: done in 2.05239 secs using 398.8% CPU
Optimizing NNI: done in 4.09221 secs using 597.4% CPU
Optimizing NNI: done in 2.04535 secs using 397.6% CPU
Optimizing NNI: done in 1.80755 secs using 398.7% CPU
Optimizing NNI: done in 1.6954 secs using 398.8% CPU
Optimizing NNI: done in 4.90537 secs using 597.4% CPU
Optimizing NNI: done in 1.98972 secs using 398.2% CPU
Optimizing NNI: done in 2.1803 secs using 398.7% CPU
Optimizing NNI: done in 4.41512 secs using 598.1% CPU
Iteration 550 / LogL: -195694.752 / Time: 0h:44m:12s (0h:1m:7s left)
Optimizing NNI: done in 1.91725 secs using 399.1% CPU
Iteration 100 / LogL: -107687.608 / Time: 0h:4m:53s (0h:4m:5s left)
Optimizing NNI: done in 2.12671 secs using 398.7% CPU
Optimizing NNI: done in 2.01492 secs using 398.4% CPU
Optimizing NNI: done in 4.68519 secs using 597.4% CPU
Optimizing NNI: done in 1.71974 secs using 398.6% CPU
Optimizing NNI: done in 1.9683 secs using 398.6% CPU
Optimizing NNI: done in 4.48651 secs using 597.7% CPU
Optimizing NNI: done in 1.98571 secs using 398.7% CPU
Optimizing NNI: done in 2.00365 secs using 398.7% CPU
Optimizing NNI: done in 4.55181 secs using 597.9% CPU
Optimizing NNI: done in 2.01926 secs using 398.9% CPU
Optimizing NNI: done in 1.73363 secs using 399% CPU
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Optimizing NNI: done in 4.5531 secs using 596.6% CPU
Optimizing NNI: done in 2.0091 secs using 398.9% CPU
Iteration 110 / LogL: -107682.179 / Time: 0h:5m:13s (0h:3m:29s left)
Optimizing NNI: done in 1.85546 secs using 398.4% CPU
Optimizing NNI: done in 3.99699 secs using 597.9% CPU
Optimizing NNI: done in 2.10897 secs using 398.7% CPU
Optimizing NNI: done in 2.04988 secs using 398.3% CPU
Optimizing NNI: done in 4.40771 secs using 598% CPU
Optimizing NNI: done in 1.92126 secs using 398.7% CPU
Optimizing NNI: done in 2.03974 secs using 398.4% CPU
Optimizing NNI: done in 4.55555 secs using 597.8% CPU
Optimizing NNI: done in 1.85968 secs using 398.3% CPU
Optimizing NNI: done in 2.14885 secs using 398.8% CPU
Optimizing NNI: done in 4.17016 secs using 597.4% CPU
Optimizing NNI: done in 2.18552 secs using 398.5% CPU
Optimizing NNI: done in 1.88166 secs using 398.6% CPU
Optimizing NNI: done in 3.85979 secs using 598.1% CPU
Optimizing NNI: done in 1.88572 secs using 398.9% CPU
Iteration 120 / LogL: -107670.281 / Time: 0h:5m:33s (0h:2m:56s left)
Optimizing NNI: done in 1.8609 secs using 398.8% CPU
Optimizing NNI: done in 1.71892 secs using 399% CPU
Optimizing NNI: done in 4.87572 secs using 597.4% CPU
Iteration 560 / LogL: -195716.855 / Time: 0h:44m:56s (0h:0m:19s left)
Optimizing NNI: done in 1.7638 secs using 398.7% CPU
Optimizing NNI: done in 1.8375 secs using 398.7% CPU
Optimizing NNI: done in 4.16097 secs using 597.2% CPU
Optimizing NNI: done in 1.45971 secs using 398.9% CPU
Optimizing NNI: done in 1.71042 secs using 398.8% CPU
Optimizing NNI: done in 3.81613 secs using 597.7% CPU
Optimizing NNI: done in 2.21174 secs using 398.8% CPU
Optimizing NNI: done in 2.13596 secs using 398.7% CPU
Optimizing NNI: done in 4.36711 secs using 597.4% CPU
Optimizing NNI: done in 1.88299 secs using 398.8% CPU
Optimizing NNI: done in 1.62968 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 130: -107666.808
Iteration 130 / LogL: -107666.808 / Time: 0h:5m:53s (0h:4m:33s left)
Optimizing NNI: done in 4.29552 secs using 597.3% CPU
Optimizing NNI: done in 2.30978 secs using 398.9% CPU
Optimizing NNI: done in 2.24758 secs using 398.6% CPU
Optimizing NNI: done in 4.84666 secs using 596.2% CPU
TREE SEARCH COMPLETED AFTER 565 ITERATIONS / Time: 0h:45m:18s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -195675.576
Optimizing NNI: done in 1.78427 secs using 398.7% CPU
Optimal log-likelihood: -195675.574
Site proportion and rates:  (0.009,0.066) (0.063,0.248) (0.127,0.395) (0.183,0.565) (0.164,0.737) (0.207,1.045) (0.154,1.623) (0.094,2.588)
Parameters optimization took 1 rounds (0.707 sec)
BEST SCORE FOUND : -195675.574
Total tree length: 152.276

Total number of iterations: 565
CPU time used for tree search: 15920.083 sec (4h:25m:20s)
Wall-clock time used for tree search: 2690.497 sec (0h:44m:50s)
Total CPU time used: 16091.153 sec (4h:28m:11s)
Total wall-clock time used: 2719.183 sec (0h:45m:19s)

===> START BOOTSTRAP REPLICATE NUMBER 43

Creating bootstrap alignment (seed: 70506)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.282 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -190985.942
Optimizing NNI: done in 1.87934 secs using 398.5% CPU
2. Current log-likelihood: -188363.890
Optimizing NNI: done in 2.20518 secs using 398.7% CPU
Optimizing NNI: done in 1.7836 secs using 398.2% CPU
3. Current log-likelihood: -188337.330
Optimizing NNI: done in 1.5922 secs using 398.2% CPU
4. Current log-likelihood: -188335.679
Optimizing NNI: done in 1.82987 secs using 399% CPU
5. Current log-likelihood: -188334.715
Optimizing NNI: done in 2.18831 secs using 398.5% CPU
6. Current log-likelihood: -188334.054
Optimizing NNI: done in 2.16955 secs using 397.8% CPU
Iteration 140 / LogL: -107700.724 / Time: 0h:6m:13s (0h:4m:1s left)
7. Current log-likelihood: -188333.614
Optimizing NNI: done in 1.71358 secs using 398.4% CPU
8. Current log-likelihood: -188333.264
Optimizing NNI: done in 1.85451 secs using 399.4% CPU
9. Current log-likelihood: -188332.938
Optimizing NNI: done in 1.90809 secs using 399% CPU
10. Current log-likelihood: -188332.580
Optimizing NNI: done in 1.94556 secs using 398.8% CPU
11. Current log-likelihood: -188332.131
Optimizing NNI: done in 2.21585 secs using 398.4% CPU
Optimizing NNI: done in 1.83101 secs using 398.4% CPU
12. Current log-likelihood: -188331.509
Optimizing NNI: done in 2.06111 secs using 398.5% CPU
13. Current log-likelihood: -188330.618
Optimizing NNI: done in 1.89473 secs using 398.7% CPU
14. Current log-likelihood: -188329.545
Optimizing NNI: done in 2.09829 secs using 398.1% CPU
15. Current log-likelihood: -188328.639
Optimizing NNI: done in 2.35073 secs using 398.9% CPU
Iteration 150 / LogL: -107667.746 / Time: 0h:6m:33s (0h:3m:31s left)
16. Current log-likelihood: -188328.086
Optimizing NNI: done in 1.94162 secs using 398.2% CPU
17. Current log-likelihood: -188327.807
Optimizing NNI: done in 1.98332 secs using 398.7% CPU
18. Current log-likelihood: -188327.681
Optimizing NNI: done in 2.44239 secs using 398.3% CPU
Optimal log-likelihood: -188327.628
Site proportion and rates:  (0.010,0.073) (0.068,0.263) (0.155,0.391) (0.242,0.594) (0.146,0.847) (0.148,1.119) (0.133,1.653) (0.098,2.734)
Parameters optimization took 18 rounds (39.776 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.65564 secs using 398.8% CPU
Optimizing NNI: done in 2.0061 secs using 398.4% CPU
Optimizing NNI: done in 2.00445 secs using 398.8% CPU
Optimizing NNI: done in 1.89054 secs using 398.7% CPU
Optimizing NNI: done in 2.01198 secs using 398.7% CPU
Calculating distance matrix: done in 10.3736 secs using 599.9% CPU
Computing ML distances took 10.374231 sec (of wall-clock time) 62.232507 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00133514 secs using 457% CPU
Constructing RapidNJ tree: done in 0.023057 secs using 683% CPU
Computing RapidNJ tree took 0.024453 sec (of wall-clock time) 0.164692 sec (of CPU time)
Optimizing NNI: done in 2.05704 secs using 398.8% CPU
Log-likelihood of RapidNJ tree: -193146.480
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.93968 secs using 398.8% CPU
Iteration 160 / LogL: -107668.653 / Time: 0h:6m:53s (0h:3m:2s left)
Optimizing NNI: done in 2.18648 secs using 398% CPU
Optimizing NNI: done in 1.99777 secs using 398.9% CPU
Optimizing NNI: done in 1.81591 secs using 398.8% CPU
Optimizing NNI: done in 2.02453 secs using 398.3% CPU
Optimizing NNI: done in 1.85088 secs using 398.8% CPU
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Optimizing NNI: done in 2.13457 secs using 399% CPU
Optimizing NNI: done in 2.19143 secs using 398.3% CPU
Optimizing NNI: done in 2.0617 secs using 398.5% CPU
Optimizing NNI: done in 2.29806 secs using 398.5% CPU
Iteration 170 / LogL: -107676.393 / Time: 0h:7m:14s (0h:2m:34s left)
Optimizing NNI: done in 1.98306 secs using 398.8% CPU
Optimizing NNI: done in 2.06186 secs using 398.7% CPU
Optimizing NNI: done in 1.78964 secs using 398.3% CPU
30.058 second
Optimizing NNI: done in 2.13647 secs using 399% CPU
Optimizing NNI: done in 2.04015 secs using 398.3% CPU
Optimizing NNI: done in 1.88503 secs using 398.6% CPU
Optimizing NNI: done in 2.19637 secs using 399% CPU
Optimizing NNI: done in 2.09456 secs using 398% CPU
Optimizing NNI: done in 1.92861 secs using 398.7% CPU
Optimizing NNI: done in 2.09356 secs using 398.9% CPU
Iteration 180 / LogL: -107676.569 / Time: 0h:7m:34s (0h:2m:7s left)
Optimizing NNI: done in 2.10419 secs using 398.8% CPU
Computing log-likelihood of 98 initial trees ... 16.314 seconds
Current best score: -188327.628

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.85495 secs using 398.5% CPU
Optimizing NNI: done in 2.17868 secs using 398.9% CPU
Optimizing NNI: done in 2.75268 secs using 598.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.76543 secs using 398.8% CPU
Optimizing NNI: done in 1.69065 secs using 398.7% CPU
Optimizing NNI: done in 2.02511 secs using 397.2% CPU
BETTER TREE FOUND at iteration 1: -187789.360
Optimizing NNI: done in 2.21629 secs using 398.3% CPU
Optimizing NNI: done in 1.8389 secs using 398.8% CPU
Optimizing NNI: done in 4.41109 secs using 597.8% CPU
Optimizing NNI: done in 2.09884 secs using 398.7% CPU
Optimizing NNI: done in 1.81416 secs using 398.1% CPU
Iteration 190 / LogL: -107666.984 / Time: 0h:7m:54s (0h:1m:40s left)
Optimizing NNI: done in 3.8934 secs using 596.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.84701 secs using 398.6% CPU
Optimizing NNI: done in 1.90402 secs using 398.7% CPU
BETTER TREE FOUND at iteration 3: -187656.350
Optimizing NNI: done in 1.8389 secs using 398.1% CPU
Optimizing NNI: done in 2.06991 secs using 398.5% CPU
Optimizing NNI: done in 1.5948 secs using 399% CPU
Optimizing NNI: done in 5.03196 secs using 597.1% CPU
Optimizing NNI: done in 1.86853 secs using 398.3% CPU
Optimizing NNI: done in 1.76418 secs using 398.2% CPU
Optimizing NNI: done in 4.22975 secs using 597.1% CPU
Optimizing NNI: done in 2.10391 secs using 398.7% CPU
Optimizing NNI: done in 1.77322 secs using 398.1% CPU
Optimizing NNI: done in 4.84696 secs using 596.9% CPU
Optimizing NNI: done in 1.94074 secs using 399% CPU
Iteration 200 / LogL: -107680.271 / Time: 0h:8m:13s (0h:1m:14s left)
Optimizing NNI: done in 2.00041 secs using 398.6% CPU
Optimizing NNI: done in 1.78069 secs using 398.9% CPU
Optimizing NNI: done in 4.37926 secs using 597.4% CPU
Optimizing NNI: done in 1.85154 secs using 398.6% CPU
Optimizing NNI: done in 1.80002 secs using 398.5% CPU
Optimizing NNI: done in 4.77569 secs using 596.9% CPU
Optimizing NNI: done in 2.25126 secs using 398.7% CPU
Optimizing NNI: done in 1.94614 secs using 398.3% CPU
Optimizing NNI: done in 1.96548 secs using 398.6% CPU
Optimizing NNI: done in 4.95192 secs using 597.1% CPU
Optimizing NNI: done in 1.76368 secs using 398.9% CPU
Optimizing NNI: done in 2.17498 secs using 398.8% CPU
Optimizing NNI: done in 4.22572 secs using 596.6% CPU
Iteration 10 / LogL: -187782.259 / Time: 0h:2m:31s
Optimizing NNI: done in 1.8648 secs using 398.7% CPU
Iteration 210 / LogL: -107678.756 / Time: 0h:8m:33s (0h:0m:49s left)
Optimizing NNI: done in 2.03325 secs using 398.8% CPU
Optimizing NNI: done in 4.30838 secs using 597.1% CPU
Optimizing NNI: done in 2.15795 secs using 398.8% CPU
Optimizing NNI: done in 2.05454 secs using 398.9% CPU
Optimizing NNI: done in 4.83842 secs using 597.2% CPU
Optimizing NNI: done in 1.80814 secs using 399.5% CPU
Optimizing NNI: done in 1.78089 secs using 398.7% CPU
Optimizing NNI: done in 3.57819 secs using 597.5% CPU
Optimizing NNI: done in 1.92116 secs using 398.4% CPU
Optimizing NNI: done in 1.98289 secs using 398.4% CPU
Optimizing NNI: done in 4.51475 secs using 597% CPU
Optimizing NNI: done in 2.18347 secs using 398.4% CPU
Optimizing NNI: done in 1.88314 secs using 398.9% CPU
Optimizing NNI: done in 3.32996 secs using 597.7% CPU
Optimizing NNI: done in 2.00119 secs using 398.8% CPU
Iteration 220 / LogL: -107669.646 / Time: 0h:8m:53s (0h:0m:24s left)
Optimizing NNI: done in 1.94178 secs using 398.8% CPU
Optimizing NNI: done in 2.03914 secs using 398.8% CPU
Optimizing NNI: done in 4.97263 secs using 596.8% CPU
Optimizing NNI: done in 2.05304 secs using 398.3% CPU
Optimizing NNI: done in 3.48095 secs using 597% CPU
Optimizing NNI: done in 1.58233 secs using 398.8% CPU
Optimizing NNI: done in 2.07081 secs using 398.6% CPU
Optimizing NNI: done in 2.0027 secs using 398.6% CPU
Optimizing NNI: done in 4.78085 secs using 597.9% CPU
Optimizing NNI: done in 1.79936 secs using 398.4% CPU
Optimizing NNI: done in 1.98749 secs using 399.2% CPU
Optimizing NNI: done in 4.70393 secs using 597% CPU
Optimizing NNI: done in 2.1651 secs using 398.6% CPU
Optimizing NNI: done in 2.09719 secs using 398.3% CPU
Iteration 230 / LogL: -107675.495 / Time: 0h:9m:13s (0h:0m:0s left)
Optimizing NNI: done in 4.75674 secs using 596.3% CPU
Iteration 20 / LogL: -187768.545 / Time: 0h:3m:15s
Finish initializing candidate tree set (20)
Current best tree score: -187656.350 / CPU time: 143.300
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.23021 secs using 398.1% CPU
TREE SEARCH COMPLETED AFTER 231 ITERATIONS / Time: 0h:9m:15s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -107666.808
Optimal log-likelihood: -107666.795
Proportion of invariable sites: 0.033
Site proportion and rates:  (0.096,0.035) (0.099,0.102) (0.040,0.197) (0.098,0.295) (0.095,0.458) (0.103,0.701) (0.166,1.104) (0.201,1.757) (0.070,4.259)
Parameters optimization took 1 rounds (1.080 sec)
BEST SCORE FOUND : -107666.795
Total tree length: 169.838

Total number of iterations: 231
CPU time used for tree search: 2063.365 sec (0h:34m:23s)
Wall-clock time used for tree search: 525.841 sec (0h:8m:45s)
Total CPU time used: 2186.706 sec (0h:36m:26s)
Total wall-clock time used: 556.763 sec (0h:9m:16s)

===> START BOOTSTRAP REPLICATE NUMBER 81

Creating bootstrap alignment (seed: 68263)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.132 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105297.325
2. Current log-likelihood: -103211.095
3. Current log-likelihood: -103122.187
Optimizing NNI: done in 5.83707 secs using 596.9% CPU
4. Current log-likelihood: -103117.441
5. Current log-likelihood: -103116.222
6. Current log-likelihood: -103115.222
Optimizing NNI: done in 4.27774 secs using 597.8% CPU
7. Current log-likelihood: -103114.367
8. Current log-likelihood: -103113.644
9. Current log-likelihood: -103113.026
Optimizing NNI: done in 4.5042 secs using 597.6% CPU
10. Current log-likelihood: -103112.494
11. Current log-likelihood: -103112.041
Optimizing NNI: done in 3.99452 secs using 597.5% CPU
12. Current log-likelihood: -103111.660
13. Current log-likelihood: -103111.342
14. Current log-likelihood: -103111.110
Optimizing NNI: done in 4.15445 secs using 598.2% CPU
15. Current log-likelihood: -103110.971
16. Current log-likelihood: -103110.865
17. Current log-likelihood: -103110.752
Optimal log-likelihood: -103110.650
Proportion of invariable sites: 0.051
Site proportion and rates:  (0.103,0.035) (0.086,0.112) (0.074,0.213) (0.076,0.305) (0.116,0.457) (0.094,0.740) (0.116,1.082) (0.204,1.840) (0.079,4.087)
Parameters optimization took 17 rounds (24.729 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.95958 secs using 596.6% CPU
Calculating distance matrix: done in 4.69837 secs using 399.9% CPU
Computing ML distances took 4.698805 sec (of wall-clock time) 18.789576 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00068903 secs using 308.5% CPU
Constructing RapidNJ tree: done in 0.00852013 secs using 465.4% CPU
Computing RapidNJ tree took 0.009275 sec (of wall-clock time) 0.044620 sec (of CPU time)
Log-likelihood of RapidNJ tree: -103627.089
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.54003 secs using 596.8% CPU
Optimizing NNI: done in 4.6256 secs using 597.2% CPU
Optimizing NNI: done in 4.7129 secs using 598.2% CPU
10.831 second
Optimizing NNI: done in 4.93251 secs using 597.4% CPU
Iteration 30 / LogL: -187692.312 / Time: 0h:4m:2s (0h:10m:9s left)
Optimizing NNI: done in 4.62119 secs using 597.9% CPU
Computing log-likelihood of 98 initial trees ... 9.885 seconds
Current best score: -103110.650

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.57677 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.47641 secs using 597.6% CPU
Optimizing NNI: done in 4.14325 secs using 597.3% CPU
BETTER TREE FOUND at iteration 1: -102689.281
Optimizing NNI: done in 3.97244 secs using 596.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.97031 secs using 398.6% CPU
Optimizing NNI: done in 1.59213 secs using 398.5% CPU
BETTER TREE FOUND at iteration 34: -187652.525
Optimizing NNI: done in 1.95672 secs using 398.5% CPU
Optimizing NNI: done in 2.84223 secs using 398.6% CPU
Optimizing NNI: done in 4.41363 secs using 598.2% CPU
Optimizing NNI: done in 1.63102 secs using 398.5% CPU
Optimizing NNI: done in 1.97695 secs using 398.5% CPU
Optimizing NNI: done in 4.71271 secs using 597.1% CPU
Optimizing NNI: done in 2.12374 secs using 397.9% CPU
Optimizing NNI: done in 2.77646 secs using 398.1% CPU
Optimizing NNI: done in 4.73795 secs using 597% CPU
Optimizing NNI: done in 2.22889 secs using 398.9% CPU
Iteration 10 / LogL: -102697.672 / Time: 0h:1m:22s
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Iteration 40 / LogL: -187686.013 / Time: 0h:4m:51s (0h:11m:40s left)
Optimizing NNI: done in 3.41933 secs using 398.6% CPU
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Optimizing NNI: done in 1.85284 secs using 398.7% CPU
Iteration 20 / LogL: -102885.855 / Time: 0h:1m:45s
Finish initializing candidate tree set (20)
Current best tree score: -102689.281 / CPU time: 74.800
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.38051 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.80072 secs using 597.4% CPU
Optimizing NNI: done in 4.41985 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -102634.295
BETTER TREE FOUND at iteration 44: -187644.870
Optimizing NNI: done in 2.22216 secs using 398.5% CPU
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Iteration 30 / LogL: -102635.308 / Time: 0h:2m:14s (0h:7m:0s left)
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BETTER TREE FOUND at iteration 33: -102625.087
Optimizing NNI: done in 4.28638 secs using 597.4% CPU
Iteration 50 / LogL: -187786.098 / Time: 0h:5m:40s (0h:10m:52s left)
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Iteration 40 / LogL: -102652.771 / Time: 0h:2m:37s (0h:6m:14s left)
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BETTER TREE FOUND at iteration 41: -102622.984
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Iteration 50 / LogL: -102626.752 / Time: 0h:3m:0s (0h:5m:35s left)
Optimizing NNI: done in 2.03551 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -102621.087
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Iteration 60 / LogL: -187753.151 / Time: 0h:6m:26s (0h:9m:9s left)
BETTER TREE FOUND at iteration 53: -102619.233
Optimizing NNI: done in 1.99788 secs using 398.1% CPU
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BETTER TREE FOUND at iteration 57: -102616.176
Optimizing NNI: done in 4.51476 secs using 596.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 58: -102614.366
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 69: -102607.887
Optimizing NNI: done in 2.02157 secs using 398.8% CPU
Iteration 70 / LogL: -102624.875 / Time: 0h:3m:52s (0h:5m:33s left)
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Iteration 70 / LogL: -187765.528 / Time: 0h:7m:11s (0h:7m:41s left)
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Iteration 80 / LogL: -102614.090 / Time: 0h:4m:12s (0h:4m:44s left)
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Iteration 90 / LogL: -102618.150 / Time: 0h:4m:32s (0h:4m:1s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 93: -102605.778
BETTER TREE FOUND at iteration 80: -187642.127
Iteration 80 / LogL: -187642.127 / Time: 0h:8m:0s (0h:10m:8s left)
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BETTER TREE FOUND at iteration 99: -102601.059
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Iteration 100 / LogL: -102701.922 / Time: 0h:4m:58s (0h:4m:58s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 105: -102600.328
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 86: -187630.761
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Iteration 110 / LogL: -102610.282 / Time: 0h:5m:19s (0h:4m:38s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 89: -187628.530
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Iteration 90 / LogL: -187660.950 / Time: 0h:8m:53s (0h:9m:52s left)
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Iteration 120 / LogL: -102644.552 / Time: 0h:5m:40s (0h:4m:2s left)
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Iteration 130 / LogL: -102605.643 / Time: 0h:6m:0s (0h:3m:29s left)
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Iteration 140 / LogL: -102617.030 / Time: 0h:6m:19s (0h:2m:57s left)
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Iteration 100 / LogL: -187678.897 / Time: 0h:9m:37s (0h:8m:39s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 146: -102594.285
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Iteration 150 / LogL: -102601.772 / Time: 0h:6m:40s (0h:4m:17s left)
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Iteration 160 / LogL: -102651.677 / Time: 0h:7m:0s (0h:3m:47s left)
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Iteration 110 / LogL: -187714.092 / Time: 0h:10m:27s (0h:7m:34s left)
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Iteration 170 / LogL: -102602.983 / Time: 0h:7m:20s (0h:3m:18s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.22141 secs using 398.6% CPU
BETTER TREE FOUND at iteration 113: -187618.028
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Iteration 180 / LogL: -102606.051 / Time: 0h:7m:40s (0h:2m:49s left)
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Iteration 190 / LogL: -102600.542 / Time: 0h:8m:1s (0h:2m:22s left)
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Iteration 120 / LogL: -187687.453 / Time: 0h:11m:18s (0h:8m:49s left)
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Iteration 200 / LogL: -102629.829 / Time: 0h:8m:22s (0h:1m:56s left)
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Iteration 210 / LogL: -102631.757 / Time: 0h:8m:42s (0h:1m:29s left)
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Iteration 220 / LogL: -102606.182 / Time: 0h:9m:2s (0h:1m:4s left)
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Iteration 230 / LogL: -102607.680 / Time: 0h:9m:24s (0h:0m:39s left)
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Iteration 140 / LogL: -187665.032 / Time: 0h:12m:53s (0h:6m:45s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.56307 secs using 399.4% CPU
BETTER TREE FOUND at iteration 141: -187604.242
Optimizing NNI: done in 2.07192 secs using 399% CPU
Iteration 240 / LogL: -102632.177 / Time: 0h:9m:43s (0h:0m:14s left)
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TREE SEARCH COMPLETED AFTER 247 ITERATIONS / Time: 0h:9m:57s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102594.285
Optimizing NNI: done in 5.43032 secs using 596.9% CPU
2. Current log-likelihood: -102594.263
3. Current log-likelihood: -102594.232
4. Current log-likelihood: -102594.205
5. Current log-likelihood: -102594.189
6. Current log-likelihood: -102594.173
7. Current log-likelihood: -102594.158
Optimizing NNI: done in 4.12508 secs using 597.2% CPU
8. Current log-likelihood: -102594.143
9. Current log-likelihood: -102594.130
10. Current log-likelihood: -102594.118
11. Current log-likelihood: -102594.106
12. Current log-likelihood: -102594.094
13. Current log-likelihood: -102594.083
Optimizing NNI: done in 4.43119 secs using 597.5% CPU
14. Current log-likelihood: -102594.072
Optimal log-likelihood: -102594.060
Proportion of invariable sites: 0.050
Site proportion and rates:  (0.102,0.031) (0.086,0.106) (0.074,0.206) (0.080,0.292) (0.124,0.468) (0.115,0.798) (0.092,1.178) (0.199,1.855) (0.076,4.218)
Parameters optimization took 14 rounds (9.791 sec)
BEST SCORE FOUND : -102594.060
Total tree length: 175.046

Total number of iterations: 247
CPU time used for tree search: 2227.204 sec (0h:37m:7s)
Wall-clock time used for tree search: 566.741 sec (0h:9m:26s)
Total CPU time used: 2388.261 sec (0h:39m:48s)
Total wall-clock time used: 607.144 sec (0h:10m:7s)

===> START BOOTSTRAP REPLICATE NUMBER 82

Creating bootstrap alignment (seed: 68264)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.103 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104841.758
2. Current log-likelihood: -102556.912
Optimizing NNI: done in 4.19974 secs using 597.8% CPU
3. Current log-likelihood: -102505.834
4. Current log-likelihood: -102505.719
Optimal log-likelihood: -102505.644
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.079,0.036) (0.136,0.119) (0.052,0.197) (0.078,0.308) (0.089,0.440) (0.095,0.641) (0.156,1.002) (0.208,1.772) (0.078,4.138)
Parameters optimization took 4 rounds (5.777 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.76094 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
Calculating distance matrix: done in 4.71566 secs using 399.9% CPU
Computing ML distances took 4.716039 sec (of wall-clock time) 18.860381 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000725985 secs using 396.2% CPU
Constructing RapidNJ tree: done in 0.00872993 secs using 363.9% CPU
Computing RapidNJ tree took 0.009521 sec (of wall-clock time) 0.037158 sec (of CPU time)
Log-likelihood of RapidNJ tree: -102961.674
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... BETTER TREE FOUND at iteration 148: -187594.877
Optimizing NNI: done in 6.94656 secs using 598.2% CPU
10.553 second
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Iteration 150 / LogL: -187713.587 / Time: 0h:13m:48s (0h:9m:4s left)
Optimizing NNI: done in 4.7933 secs using 597.7% CPU
Computing log-likelihood of 98 initial trees ... 9.859 seconds
Current best score: -102505.644

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -102020.293
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 4: -101988.773
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -101976.734
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Iteration 10 / LogL: -102269.429 / Time: 0h:1m:4s
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Iteration 160 / LogL: -187626.606 / Time: 0h:14m:35s (0h:8m:4s left)
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Iteration 20 / LogL: -102269.363 / Time: 0h:1m:22s
Finish initializing candidate tree set (20)
Current best tree score: -101976.734 / CPU time: 71.284
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 21: -101976.297
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -101958.627
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Iteration 30 / LogL: -101971.405 / Time: 0h:1m:49s (0h:6m:12s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 87: -101954.610
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 90: -101951.316
Iteration 90 / LogL: -101951.316 / Time: 0h:3m:52s (0h:4m:20s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 210: -187591.146
Iteration 210 / LogL: -187591.146 / Time: 0h:18m:39s (0h:8m:55s left)
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Iteration 140 / LogL: -102068.063 / Time: 0h:5m:30s (0h:1m:58s left)
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BETTER TREE FOUND at iteration 143: -101949.625
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Iteration 150 / LogL: -101951.352 / Time: 0h:5m:53s (0h:3m:40s left)
BETTER TREE FOUND at iteration 218: -187589.554
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Iteration 220 / LogL: -187636.324 / Time: 0h:19m:27s (0h:8m:42s left)
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Iteration 160 / LogL: -101964.815 / Time: 0h:6m:13s (0h:3m:14s left)
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BETTER TREE FOUND at iteration 161: -101947.718
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Iteration 230 / LogL: -187621.244 / Time: 0h:20m:15s (0h:7m:47s left)
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Iteration 190 / LogL: -101971.065 / Time: 0h:7m:13s (0h:2m:42s left)
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Iteration 200 / LogL: -101970.517 / Time: 0h:7m:32s (0h:2m:18s left)
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Iteration 210 / LogL: -101959.285 / Time: 0h:7m:52s (0h:1m:55s left)
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Iteration 220 / LogL: -101991.409 / Time: 0h:8m:11s (0h:1m:32s left)
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Iteration 250 / LogL: -187805.688 / Time: 0h:21m:49s (0h:5m:57s left)
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Iteration 230 / LogL: -101953.440 / Time: 0h:8m:31s (0h:1m:9s left)
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Iteration 240 / LogL: -101950.159 / Time: 0h:8m:50s (0h:0m:46s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 245: -101947.354
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Iteration 250 / LogL: -101966.261 / Time: 0h:9m:11s (0h:3m:30s left)
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Iteration 260 / LogL: -101986.458 / Time: 0h:9m:30s (0h:3m:7s left)
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Iteration 270 / LogL: -101949.265 / Time: 0h:9m:48s (0h:2m:44s left)
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Iteration 270 / LogL: -187673.125 / Time: 0h:23m:25s (0h:4m:10s left)
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Iteration 280 / LogL: -187620.098 / Time: 0h:24m:11s (0h:3m:17s left)
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Iteration 310 / LogL: -101956.271 / Time: 0h:11m:4s (0h:1m:15s left)
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Iteration 320 / LogL: -101952.465 / Time: 0h:11m:24s (0h:0m:53s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.87256 secs using 398.9% CPU
BETTER TREE FOUND at iteration 289: -187587.068
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Iteration 290 / LogL: -187647.310 / Time: 0h:24m:58s (0h:8m:33s left)
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Iteration 330 / LogL: -101996.220 / Time: 0h:11m:43s (0h:0m:32s left)
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Iteration 340 / LogL: -101954.633 / Time: 0h:12m:3s (0h:0m:10s left)
Optimizing NNI: done in 1.65273 secs using 398.1% CPU
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Optimizing NNI: done in 1.938 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 346 ITERATIONS / Time: 0h:12m:14s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -101947.354
Optimizing NNI: done in 5.32371 secs using 596.9% CPU
2. Current log-likelihood: -101947.344
3. Current log-likelihood: -101947.333
4. Current log-likelihood: -101947.323
Optimal log-likelihood: -101947.306
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.078,0.034) (0.133,0.112) (0.060,0.190) (0.070,0.293) (0.090,0.418) (0.098,0.611) (0.165,0.997) (0.204,1.801) (0.074,4.352)
Parameters optimization took 4 rounds (2.302 sec)
BEST SCORE FOUND : -101947.306
Total tree length: 175.807

Total number of iterations: 346
CPU time used for tree search: 2851.460 sec (0h:47m:31s)
Wall-clock time used for tree search: 723.277 sec (0h:12m:3s)
Total CPU time used: 2906.716 sec (0h:48m:26s)
Total wall-clock time used: 737.097 sec (0h:12m:17s)

===> START BOOTSTRAP REPLICATE NUMBER 83

Creating bootstrap alignment (seed: 68265)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.102 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -108897.848
2. Current log-likelihood: -106942.613
3. Current log-likelihood: -106878.263
Optimizing NNI: done in 6.2616 secs using 597.4% CPU
Iteration 300 / LogL: -187740.613 / Time: 0h:25m:45s (0h:7m:39s left)
4. Current log-likelihood: -106875.146
5. Current log-likelihood: -106874.863
6. Current log-likelihood: -106874.750
Optimal log-likelihood: -106874.600
Proportion of invariable sites: 0.036
Site proportion and rates:  (0.085,0.037) (0.081,0.125) (0.101,0.231) (0.070,0.320) (0.079,0.455) (0.119,0.675) (0.140,1.061) (0.229,1.776) (0.060,4.470)
Parameters optimization took 6 rounds (9.757 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 6.63722 secs using 597.3% CPU
Calculating distance matrix: done in 4.64698 secs using 399.9% CPU
Computing ML distances took 4.647323 sec (of wall-clock time) 18.582648 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000741005 secs using 275.7% CPU
Constructing RapidNJ tree: done in 0.00858593 secs using 334% CPU
Computing RapidNJ tree took 0.009386 sec (of wall-clock time) 0.033434 sec (of CPU time)
Log-likelihood of RapidNJ tree: -107026.451
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 6.14149 secs using 597.2% CPU
Optimizing NNI: done in 5.70171 secs using 596.3% CPU
10.686 second
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Optimizing NNI: done in 4.12985 secs using 595.9% CPU
Computing log-likelihood of 98 initial trees ... 10.232 seconds
Current best score: -106874.600

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 4.31912 secs using 597% CPU
BETTER TREE FOUND at iteration 1: -106145.514
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.94573 secs using 597.7% CPU
Iteration 310 / LogL: -187634.695 / Time: 0h:26m:33s (0h:6m:47s left)
BETTER TREE FOUND at iteration 2: -106110.488
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Iteration 10 / LogL: -106121.784 / Time: 0h:1m:11s
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Iteration 20 / LogL: -106179.039 / Time: 0h:1m:32s
Finish initializing candidate tree set (20)
Current best tree score: -106110.488 / CPU time: 77.460
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Iteration 320 / LogL: -187611.520 / Time: 0h:27m:19s (0h:5m:54s left)
BETTER TREE FOUND at iteration 22: -106108.344
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 26: -106099.676
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Iteration 30 / LogL: -106103.264 / Time: 0h:2m:3s (0h:6m:49s left)
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Iteration 40 / LogL: -106185.425 / Time: 0h:2m:25s (0h:5m:21s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 330 / LogL: -187604.314 / Time: 0h:28m:16s (0h:5m:4s left)
BETTER TREE FOUND at iteration 44: -106068.593
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Iteration 50 / LogL: -106094.854 / Time: 0h:2m:49s (0h:5m:24s left)
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Iteration 70 / LogL: -106069.874 / Time: 0h:3m:29s (0h:3m:44s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 74: -106065.511
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Iteration 350 / LogL: -187626.001 / Time: 0h:29m:46s (0h:3m:19s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 95: -106064.385
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Iteration 100 / LogL: -106071.018 / Time: 0h:4m:36s (0h:4m:25s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 121: -106063.012
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Iteration 370 / LogL: -187655.836 / Time: 0h:31m:17s (0h:1m:36s left)
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Iteration 130 / LogL: -106081.299 / Time: 0h:5m:41s (0h:4m:0s left)
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Iteration 140 / LogL: -106075.125 / Time: 0h:6m:0s (0h:3m:30s left)
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Iteration 160 / LogL: -106150.066 / Time: 0h:6m:41s (0h:2m:33s left)
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Iteration 170 / LogL: -106071.109 / Time: 0h:7m:1s (0h:2m:7s left)
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Iteration 390 / LogL: -187680.432 / Time: 0h:32m:50s (0h:0m:-6s left)
TREE SEARCH COMPLETED AFTER 390 ITERATIONS / Time: 0h:32m:50s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -187587.068
Optimal log-likelihood: -187587.068
Site proportion and rates:  (0.010,0.080) (0.077,0.275) (0.163,0.397) (0.265,0.619) (0.141,0.921) (0.117,1.152) (0.136,1.692) (0.092,2.786)
Parameters optimization took 1 rounds (0.478 sec)
BEST SCORE FOUND : -187587.068
Total tree length: 143.233

Total number of iterations: 390
CPU time used for tree search: 11308.664 sec (3h:8m:28s)
Wall-clock time used for tree search: 1918.645 sec (0h:31m:58s)
Total CPU time used: 11621.939 sec (3h:13m:41s)
Total wall-clock time used: 1971.169 sec (0h:32m:51s)

===> START BOOTSTRAP REPLICATE NUMBER 44

Creating bootstrap alignment (seed: 70507)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.318 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194100.753
Optimizing NNI: done in 1.79251 secs using 398.6% CPU
2. Current log-likelihood: -191432.976
Optimizing NNI: done in 1.92853 secs using 398.1% CPU
3. Current log-likelihood: -191396.875
Optimizing NNI: done in 2.22923 secs using 398.4% CPU
Optimizing NNI: done in 1.92615 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
4. Current log-likelihood: -191392.539
BETTER TREE FOUND at iteration 178: -106062.004
5. Current log-likelihood: -191391.270
6. Current log-likelihood: -191390.903
Optimizing NNI: done in 2.48929 secs using 398% CPU
Optimal log-likelihood: -191390.805
Site proportion and rates:  (0.004,0.065) (0.065,0.230) (0.096,0.351) (0.222,0.533) (0.176,0.753) (0.171,1.047) (0.164,1.538) (0.102,2.634)
Parameters optimization took 6 rounds (13.163 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.99686 secs using 398.3% CPU
Iteration 180 / LogL: -106064.163 / Time: 0h:7m:24s (0h:4m:3s left)
Optimizing NNI: done in 2.1333 secs using 398.8% CPU
Optimizing NNI: done in 1.92659 secs using 399.1% CPU
Optimizing NNI: done in 2.28411 secs using 398.4% CPU
Optimizing NNI: done in 2.70368 secs using 398.3% CPU
Calculating distance matrix: done in 9.43349 secs using 599.9% CPU
Computing ML distances took 9.434028 sec (of wall-clock time) 56.592907 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00127292 secs using 376.8% CPU
Constructing RapidNJ tree: done in 0.0227642 secs using 626.3% CPU
Computing RapidNJ tree took 0.024098 sec (of wall-clock time) 0.148237 sec (of CPU time)
Log-likelihood of RapidNJ tree: -194758.264
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.22593 secs using 398.5% CPU
Optimizing NNI: done in 2.06331 secs using 398.3% CPU
Optimizing NNI: done in 2.06048 secs using 398.7% CPU
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Optimizing NNI: done in 1.84612 secs using 398.5% CPU
Optimizing NNI: done in 2.02698 secs using 398.1% CPU
Iteration 190 / LogL: -106093.032 / Time: 0h:7m:45s (0h:3m:36s left)
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Optimizing NNI: done in 2.06382 secs using 398.6% CPU
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29.539 second
Optimizing NNI: done in 2.28795 secs using 398.3% CPU
Optimizing NNI: done in 2.23344 secs using 398.9% CPU
Iteration 200 / LogL: -106096.154 / Time: 0h:8m:9s (0h:3m:11s left)
Optimizing NNI: done in 1.92775 secs using 398.3% CPU
Optimizing NNI: done in 2.5482 secs using 398% CPU
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Optimizing NNI: done in 2.00723 secs using 399% CPU
Optimizing NNI: done in 1.72983 secs using 398.3% CPU
Computing log-likelihood of 98 initial trees ... 16.188 seconds
Current best score: -191390.805

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.93076 secs using 398.3% CPU
Optimizing NNI: done in 1.8656 secs using 398.2% CPU
Optimizing NNI: done in 2.90881 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.19707 secs using 398.4% CPU
BETTER TREE FOUND at iteration 1: -190671.019
Optimizing NNI: done in 2.41567 secs using 398.3% CPU
Optimizing NNI: done in 2.0721 secs using 398% CPU
Iteration 210 / LogL: -106117.195 / Time: 0h:8m:30s (0h:2m:45s left)
Optimizing NNI: done in 3.88299 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.00512 secs using 398.1% CPU
Optimizing NNI: done in 1.8415 secs using 398.3% CPU
BETTER TREE FOUND at iteration 2: -190581.830
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Optimizing NNI: done in 3.9687 secs using 597% CPU
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Optimizing NNI: done in 4.51554 secs using 596.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -190554.168
Optimizing NNI: done in 2.16984 secs using 398.7% CPU
Optimizing NNI: done in 2.50402 secs using 398.3% CPU
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Iteration 220 / LogL: -106168.771 / Time: 0h:8m:50s (0h:2m:20s left)
Optimizing NNI: done in 4.44304 secs using 596.3% CPU
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Iteration 230 / LogL: -106169.401 / Time: 0h:9m:11s (0h:1m:55s left)
Optimizing NNI: done in 4.52158 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.22715 secs using 398.5% CPU
BETTER TREE FOUND at iteration 10: -190515.241
Iteration 10 / LogL: -190515.241 / Time: 0h:2m:3s
Optimizing NNI: done in 2.28252 secs using 397.8% CPU
Optimizing NNI: done in 2.19753 secs using 398.2% CPU
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Optimizing NNI: done in 1.86439 secs using 398.4% CPU
Optimizing NNI: done in 2.33712 secs using 399.1% CPU
Iteration 240 / LogL: -106101.490 / Time: 0h:9m:33s (0h:1m:31s left)
Optimizing NNI: done in 4.42061 secs using 597.5% CPU
Optimizing NNI: done in 2.22797 secs using 398.8% CPU
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Iteration 250 / LogL: -106229.531 / Time: 0h:9m:54s (0h:1m:6s left)
Optimizing NNI: done in 4.24961 secs using 597.4% CPU
Optimizing NNI: done in 2.11841 secs using 398.6% CPU
Iteration 20 / LogL: -190545.313 / Time: 0h:2m:46s
Finish initializing candidate tree set (20)
Current best tree score: -190515.241 / CPU time: 141.544
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 2.21673 secs using 398.2% CPU
Optimizing NNI: done in 4.29797 secs using 596.4% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.04185 secs using 398.3% CPU
Optimizing NNI: done in 2.49821 secs using 398.4% CPU
BETTER TREE FOUND at iteration 22: -190494.593
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.14925 secs using 398.6% CPU
BETTER TREE FOUND at iteration 23: -190472.484
Optimizing NNI: done in 1.92572 secs using 398.4% CPU
Iteration 260 / LogL: -106079.769 / Time: 0h:10m:16s (0h:0m:42s left)
Optimizing NNI: done in 1.91736 secs using 398.8% CPU
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Iteration 270 / LogL: -106067.403 / Time: 0h:10m:37s (0h:0m:18s left)
Optimizing NNI: done in 2.08241 secs using 398.4% CPU
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Optimizing NNI: done in 5.42233 secs using 597.3% CPU
Iteration 30 / LogL: -190487.157 / Time: 0h:3m:41s (0h:11m:50s left)
Optimizing NNI: done in 2.31881 secs using 398.6% CPU
Optimizing NNI: done in 1.77589 secs using 399.1% CPU
Optimizing NNI: done in 1.80246 secs using 398.2% CPU
TREE SEARCH COMPLETED AFTER 279 ITERATIONS / Time: 0h:10m:55s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106062.004
Optimizing NNI: done in 4.57844 secs using 596.3% CPU
Optimal log-likelihood: -106061.991
Proportion of invariable sites: 0.035
Site proportion and rates:  (0.084,0.034) (0.087,0.116) (0.125,0.239) (0.051,0.344) (0.076,0.464) (0.115,0.672) (0.147,1.079) (0.222,1.796) (0.059,4.587)
Parameters optimization took 1 rounds (0.919 sec)
BEST SCORE FOUND : -106061.991
Total tree length: 160.882

Total number of iterations: 279
CPU time used for tree search: 2520.274 sec (0h:42m:0s)
Wall-clock time used for tree search: 640.517 sec (0h:10m:40s)
Total CPU time used: 2585.640 sec (0h:43m:5s)
Total wall-clock time used: 656.889 sec (0h:10m:56s)

===> START BOOTSTRAP REPLICATE NUMBER 84

Creating bootstrap alignment (seed: 68266)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.101 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106907.781
2. Current log-likelihood: -105064.792
3. Current log-likelihood: -105004.153
Optimizing NNI: done in 4.23162 secs using 597.3% CPU
4. Current log-likelihood: -104960.650
5. Current log-likelihood: -104959.263
6. Current log-likelihood: -104958.962
Optimizing NNI: done in 4.90757 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
7. Current log-likelihood: -104958.715
8. Current log-likelihood: -104958.575
BETTER TREE FOUND at iteration 33: -190464.922
9. Current log-likelihood: -104958.440
10. Current log-likelihood: -104958.319
Optimal log-likelihood: -104958.171
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.116,0.042) (0.099,0.127) (0.064,0.234) (0.100,0.327) (0.119,0.514) (0.103,0.820) (0.131,1.265) (0.176,1.942) (0.066,4.246)
Parameters optimization took 10 rounds (14.057 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.59718 secs using 597.9% CPU
Calculating distance matrix: done in 4.70919 secs using 399.8% CPU
Computing ML distances took 4.709573 sec (of wall-clock time) 18.829938 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000756025 secs using 371.4% CPU
Constructing RapidNJ tree: done in 0.00854111 secs using 313.1% CPU
Computing RapidNJ tree took 0.009353 sec (of wall-clock time) 0.031581 sec (of CPU time)
Log-likelihood of RapidNJ tree: -105210.964
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 4.70792 secs using 597.2% CPU
Optimizing NNI: done in 4.35646 secs using 596.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -190457.294
10.558 second
Optimizing NNI: done in 4.23836 secs using 597.6% CPU
Optimizing NNI: done in 5.00437 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -190449.692
Computing log-likelihood of 98 initial trees ... 9.818 seconds
Current best score: -104958.171

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.29347 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.4117 secs using 597.8% CPU
Optimizing NNI: done in 4.24939 secs using 597.2% CPU
Iteration 40 / LogL: -190512.389 / Time: 0h:4m:34s (0h:11m:28s left)
Optimizing NNI: done in 5.33479 secs using 597.8% CPU
BETTER TREE FOUND at iteration 1: -104381.497
Optimizing NNI: done in 2.07754 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -104244.173
Optimizing NNI: done in 4.752 secs using 597.2% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -104226.298
Optimizing NNI: done in 4.50554 secs using 597.8% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.85567 secs using 596.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -104168.719
Optimizing NNI: done in 2.297 secs using 398.4% CPU
BETTER TREE FOUND at iteration 44: -190443.915
Optimizing NNI: done in 2.88077 secs using 398.6% CPU
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Iteration 10 / LogL: -104278.201 / Time: 0h:1m:22s
Optimizing NNI: done in 4.58078 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.71089 secs using 398.7% CPU
BETTER TREE FOUND at iteration 47: -190441.475
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.46273 secs using 398.6% CPU
BETTER TREE FOUND at iteration 50: -190421.737
Iteration 50 / LogL: -190421.737 / Time: 0h:5m:30s (0h:11m:14s left)
Optimizing NNI: done in 2.5352 secs using 398.4% CPU
Optimizing NNI: done in 2.46431 secs using 398.6% CPU
Iteration 20 / LogL: -104246.849 / Time: 0h:1m:47s
Finish initializing candidate tree set (20)
Current best tree score: -104168.719 / CPU time: 87.924
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 5.08627 secs using 597.3% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -104145.255
Optimizing NNI: done in 2.05871 secs using 398.1% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.32129 secs using 398.8% CPU
Iteration 30 / LogL: -104178.841 / Time: 0h:2m:10s (0h:6m:58s left)
BETTER TREE FOUND at iteration 55: -190416.720
Optimizing NNI: done in 1.9325 secs using 398.4% CPU
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Iteration 40 / LogL: -104148.158 / Time: 0h:2m:29s (0h:5m:17s left)
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Iteration 60 / LogL: -190494.289 / Time: 0h:6m:23s (0h:10m:16s left)
Optimizing NNI: done in 1.73789 secs using 398.5% CPU
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Iteration 50 / LogL: -104209.879 / Time: 0h:2m:49s (0h:4m:13s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.9398 secs using 597.7% CPU
BETTER TREE FOUND at iteration 55: -104137.631
Optimizing NNI: done in 2.03771 secs using 398.1% CPU
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Iteration 60 / LogL: -104158.880 / Time: 0h:3m:11s (0h:5m:7s left)
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TREE SEARCH COMPLETED AFTER 206 ITERATIONS / Time: 0h:8m:15s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -104128.524
Optimal log-likelihood: -104128.521
Proportion of invariable sites: 0.024
Site proportion and rates:  (0.117,0.039) (0.088,0.117) (0.068,0.216) (0.109,0.322) (0.119,0.508) (0.102,0.829) (0.131,1.278) (0.177,1.952) (0.066,4.233)
Parameters optimization took 1 rounds (0.457 sec)
BEST SCORE FOUND : -104128.521
Total tree length: 155.205

Total number of iterations: 206
CPU time used for tree search: 1862.241 sec (0h:31m:2s)
Wall-clock time used for tree search: 475.033 sec (0h:7m:55s)
Total CPU time used: 1943.991 sec (0h:32m:23s)
Total wall-clock time used: 495.524 sec (0h:8m:15s)

===> START BOOTSTRAP REPLICATE NUMBER 85

Creating bootstrap alignment (seed: 68267)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.116 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 109 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -108621.150
Optimizing NNI: done in 4.29719 secs using 597.7% CPU
2. Current log-likelihood: -106695.044
3. Current log-likelihood: -106626.122
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4. Current log-likelihood: -106622.372
5. Current log-likelihood: -106622.017
6. Current log-likelihood: -106621.757
Optimizing NNI: done in 5.13257 secs using 597% CPU
Iteration 130 / LogL: -190409.854 / Time: 0h:12m:12s (0h:5m:0s left)
7. Current log-likelihood: -106621.619
8. Current log-likelihood: -106621.488
9. Current log-likelihood: -106621.372
10. Current log-likelihood: -106621.267
Optimizing NNI: done in 4.93053 secs using 597.8% CPU
Optimal log-likelihood: -106621.126
Proportion of invariable sites: 0.039
Site proportion and rates:  (0.075,0.035) (0.088,0.116) (0.054,0.207) (0.116,0.319) (0.072,0.436) (0.121,0.689) (0.124,1.061) (0.246,1.753) (0.063,4.124)
Parameters optimization took 10 rounds (15.684 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 4.58461 secs using 399.9% CPU
Computing ML distances took 4.584878 sec (of wall-clock time) 18.333226 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000748158 secs using 105.9% CPU
Constructing RapidNJ tree: done in 0.00838304 secs using 334.2% CPU
Computing RapidNJ tree took 0.009205 sec (of wall-clock time) 0.032342 sec (of CPU time)
Log-likelihood of RapidNJ tree: -107220.088
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.52493 secs using 597% CPU
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10.647 second
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Computing log-likelihood of 98 initial trees ... 10.161 seconds
Current best score: -106621.126

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -106364.652
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Iteration 140 / LogL: -190455.343 / Time: 0h:13m:1s (0h:4m:1s left)
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BETTER TREE FOUND at iteration 5: -106304.454
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Iteration 10 / LogL: -106361.318 / Time: 0h:1m:43s
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Iteration 150 / LogL: -190490.752 / Time: 0h:13m:49s (0h:3m:3s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 151: -190398.215
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Iteration 20 / LogL: -106328.156 / Time: 0h:2m:9s
Finish initializing candidate tree set (20)
Current best tree score: -106304.454 / CPU time: 108.197
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 23: -106295.167
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 24: -106287.138
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -106271.547
Optimizing NNI: done in 2.57701 secs using 398.4% CPU
Optimizing NNI: done in 5.27275 secs using 596.9% CPU
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Optimizing NNI: done in 4.88732 secs using 597.3% CPU
Iteration 160 / LogL: -190422.257 / Time: 0h:14m:42s (0h:8m:24s left)
Optimizing NNI: done in 2.53438 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -106269.651
Iteration 30 / LogL: -106269.651 / Time: 0h:2m:44s (0h:9m:25s left)
Optimizing NNI: done in 4.88126 secs using 597.5% CPU
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Iteration 40 / LogL: -106374.875 / Time: 0h:3m:9s (0h:7m:17s left)
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Iteration 170 / LogL: -190444.608 / Time: 0h:15m:28s (0h:7m:25s left)
Optimizing NNI: done in 2.52021 secs using 398.4% CPU
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Iteration 50 / LogL: -106276.869 / Time: 0h:3m:34s (0h:5m:49s left)
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Iteration 60 / LogL: -106326.344 / Time: 0h:4m:1s (0h:4m:46s left)
Optimizing NNI: done in 5.29228 secs using 597.1% CPU
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Iteration 180 / LogL: -190408.686 / Time: 0h:16m:19s (0h:6m:28s left)
Optimizing NNI: done in 2.47925 secs using 398.6% CPU
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Iteration 70 / LogL: -106272.168 / Time: 0h:4m:25s (0h:3m:50s left)
Optimizing NNI: done in 3.9 secs using 597.7% CPU
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Iteration 80 / LogL: -106405.235 / Time: 0h:4m:51s (0h:3m:4s left)
Optimizing NNI: done in 2.20685 secs using 398.6% CPU
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Iteration 190 / LogL: -190405.532 / Time: 0h:17m:5s (0h:5m:30s left)
Optimizing NNI: done in 2.65853 secs using 398.5% CPU
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Optimizing NNI: done in 2.89041 secs using 397.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.59421 secs using 598.3% CPU
BETTER TREE FOUND at iteration 90: -106265.961
Iteration 90 / LogL: -106265.961 / Time: 0h:5m:18s (0h:5m:58s left)
Optimizing NNI: done in 4.65721 secs using 597.4% CPU
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Iteration 100 / LogL: -106278.966 / Time: 0h:5m:43s (0h:5m:12s left)
Optimizing NNI: done in 4.80518 secs using 597.3% CPU
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Iteration 200 / LogL: -190406.523 / Time: 0h:17m:51s (0h:4m:34s left)
Optimizing NNI: done in 2.95537 secs using 399% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 106: -106265.666
Optimizing NNI: done in 2.26284 secs using 398.9% CPU
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Iteration 110 / LogL: -106345.923 / Time: 0h:6m:11s (0h:5m:27s left)
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Iteration 120 / LogL: -106268.452 / Time: 0h:6m:36s (0h:4m:46s left)
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Iteration 210 / LogL: -190449.044 / Time: 0h:18m:40s (0h:3m:39s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.69617 secs using 398% CPU
Iteration 130 / LogL: -106284.147 / Time: 0h:7m:2s (0h:4m:8s left)
BETTER TREE FOUND at iteration 215: -190394.274
Optimizing NNI: done in 2.26276 secs using 398.6% CPU
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Iteration 220 / LogL: -190456.392 / Time: 0h:19m:27s (0h:8m:26s left)
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Iteration 140 / LogL: -106316.039 / Time: 0h:7m:28s (0h:3m:32s left)
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Iteration 150 / LogL: -106304.192 / Time: 0h:7m:54s (0h:2m:58s left)
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Iteration 230 / LogL: -190470.886 / Time: 0h:20m:16s (0h:7m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 160: -106265.296
Iteration 160 / LogL: -106265.296 / Time: 0h:8m:21s (0h:5m:15s left)
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Iteration 170 / LogL: -106279.163 / Time: 0h:8m:46s (0h:4m:40s left)
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Iteration 240 / LogL: -190449.405 / Time: 0h:21m:5s (0h:6m:37s left)
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Iteration 180 / LogL: -106269.736 / Time: 0h:9m:9s (0h:4m:5s left)
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Iteration 190 / LogL: -106393.458 / Time: 0h:9m:35s (0h:3m:32s left)
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Iteration 250 / LogL: -190430.425 / Time: 0h:21m:52s (0h:5m:42s left)
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Iteration 200 / LogL: -106283.586 / Time: 0h:9m:59s (0h:3m:0s left)
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Iteration 210 / LogL: -106271.886 / Time: 0h:10m:24s (0h:2m:29s left)
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Iteration 260 / LogL: -190471.115 / Time: 0h:22m:42s (0h:4m:49s left)
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Iteration 220 / LogL: -106273.774 / Time: 0h:10m:48s (0h:1m:58s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 252: -106264.951
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Iteration 320 / LogL: -106280.561 / Time: 0h:15m:6s (0h:1m:30s left)
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Estimate model parameters (epsilon = 0.100)
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TREE SEARCH COMPLETED AFTER 316 ITERATIONS / Time: 0h:27m:14s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -190394.274
Optimal log-likelihood: -190394.264
Site proportion and rates:  (0.004,0.065) (0.068,0.238) (0.101,0.355) (0.206,0.535) (0.195,0.753) (0.172,1.074) (0.151,1.562) (0.102,2.648)
Parameters optimization took 1 rounds (0.481 sec)
BEST SCORE FOUND : -190394.264
Total tree length: 150.611

Total number of iterations: 316
CPU time used for tree search: 9466.094 sec (2h:37m:46s)
Wall-clock time used for tree search: 1609.674 sec (0h:26m:49s)
Total CPU time used: 9616.368 sec (2h:40m:16s)
Total wall-clock time used: 1634.915 sec (0h:27m:14s)

===> START BOOTSTRAP REPLICATE NUMBER 45

Creating bootstrap alignment (seed: 70508)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.281 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196249.441
BETTER TREE FOUND at iteration 322: -106264.608
2. Current log-likelihood: -193449.381
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3. Current log-likelihood: -193415.017
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4. Current log-likelihood: -193411.588
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5. Current log-likelihood: -193409.497
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7. Current log-likelihood: -193407.931
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8. Current log-likelihood: -193407.284
9. Current log-likelihood: -193406.868
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10. Current log-likelihood: -193406.711
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Iteration 330 / LogL: -106311.358 / Time: 0h:15m:33s (0h:4m:20s left)
Optimal log-likelihood: -193406.652
Site proportion and rates:  (0.016,0.089) (0.051,0.241) (0.113,0.361) (0.160,0.531) (0.197,0.720) (0.227,0.975) (0.150,1.689) (0.086,2.845)
Parameters optimization took 10 rounds (21.797 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 9.92171 secs using 599.9% CPU
Computing ML distances took 9.922289 sec (of wall-clock time) 59.519229 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00128317 secs using 517.9% CPU
Constructing RapidNJ tree: done in 0.022867 secs using 691.9% CPU
Computing RapidNJ tree took 0.024233 sec (of wall-clock time) 0.166213 sec (of CPU time)
Optimizing NNI: done in 2.45087 secs using 398.5% CPU
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Log-likelihood of RapidNJ tree: -197333.441
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.18606 secs using 399% CPU
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29.597 second
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Computing log-likelihood of 98 initial trees ... 16.234 seconds
Current best score: -193406.652

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -192880.295
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Iteration 20 / LogL: -192842.250 / Time: 0h:3m:13s
Finish initializing candidate tree set (20)
Current best tree score: -192831.289 / CPU time: 156.864
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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BETTER TREE FOUND at iteration 25: -192771.245
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Optimizing NNI: done in 2.81614 secs using 398.5% CPU
Optimizing NNI: done in 3.0717 secs using 398.8% CPU
Iteration 420 / LogL: -106270.480 / Time: 0h:19m:20s (0h:3m:0s left)
BETTER TREE FOUND at iteration 27: -192730.267
Optimizing NNI: done in 2.6147 secs using 398.6% CPU
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Iteration 30 / LogL: -192794.000 / Time: 0h:4m:22s (0h:14m:38s left)
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Iteration 430 / LogL: -106266.804 / Time: 0h:19m:44s (0h:2m:31s left)
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Iteration 440 / LogL: -106332.785 / Time: 0h:20m:9s (0h:2m:3s left)
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Iteration 40 / LogL: -192807.552 / Time: 0h:5m:6s (0h:11m:23s left)
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Iteration 450 / LogL: -106308.812 / Time: 0h:20m:39s (0h:1m:36s left)
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Iteration 50 / LogL: -192778.086 / Time: 0h:5m:49s (0h:9m:8s left)
Optimizing NNI: done in 3.09865 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 457: -106263.380
Optimizing NNI: done in 5.00745 secs using 597.3% CPU
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Iteration 460 / LogL: -106265.026 / Time: 0h:21m:13s (0h:4m:29s left)
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Iteration 470 / LogL: -106288.363 / Time: 0h:21m:43s (0h:4m:1s left)
Optimizing NNI: done in 2.75811 secs using 398.4% CPU
Optimizing NNI: done in 4.67632 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.28865 secs using 398.7% CPU
Optimizing NNI: done in 2.59661 secs using 399.3% CPU
BETTER TREE FOUND at iteration 60: -192728.821
Iteration 60 / LogL: -192728.821 / Time: 0h:6m:38s (0h:11m:15s left)
Optimizing NNI: done in 2.07769 secs using 398.6% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.43409 secs using 398.5% CPU
BETTER TREE FOUND at iteration 62: -192719.114
Optimizing NNI: done in 2.45399 secs using 398.8% CPU
Optimizing NNI: done in 2.27685 secs using 398.4% CPU
Iteration 480 / LogL: -106267.237 / Time: 0h:22m:7s (0h:3m:33s left)
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Iteration 490 / LogL: -106267.143 / Time: 0h:22m:33s (0h:3m:5s left)
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Iteration 70 / LogL: -192741.568 / Time: 0h:7m:28s (0h:9m:57s left)
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Iteration 500 / LogL: -106272.105 / Time: 0h:22m:58s (0h:2m:37s left)
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Iteration 510 / LogL: -106270.568 / Time: 0h:23m:24s (0h:2m:9s left)
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Iteration 80 / LogL: -192719.558 / Time: 0h:8m:14s (0h:8m:33s left)
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Iteration 520 / LogL: -106271.323 / Time: 0h:23m:49s (0h:1m:41s left)
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Iteration 90 / LogL: -192721.329 / Time: 0h:9m:0s (0h:7m:16s left)
Optimizing NNI: done in 2.22776 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 530: -106262.666
Iteration 530 / LogL: -106262.666 / Time: 0h:24m:14s (0h:4m:34s left)
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Iteration 540 / LogL: -106270.595 / Time: 0h:24m:39s (0h:4m:7s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 99: -192702.096
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Iteration 100 / LogL: -192713.895 / Time: 0h:9m:48s (0h:9m:48s left)
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Iteration 550 / LogL: -106347.031 / Time: 0h:25m:4s (0h:3m:39s left)
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Iteration 560 / LogL: -106280.830 / Time: 0h:25m:27s (0h:3m:11s left)
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Iteration 110 / LogL: -192755.815 / Time: 0h:10m:30s (0h:8m:34s left)
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Iteration 570 / LogL: -106323.914 / Time: 0h:25m:53s (0h:2m:43s left)
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Iteration 580 / LogL: -106291.019 / Time: 0h:26m:18s (0h:2m:16s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.61747 secs using 398.9% CPU
BETTER TREE FOUND at iteration 119: -192697.802
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Iteration 120 / LogL: -192729.165 / Time: 0h:11m:17s (0h:9m:23s left)
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Iteration 590 / LogL: -106391.124 / Time: 0h:26m:44s (0h:1m:48s left)
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Iteration 600 / LogL: -106264.949 / Time: 0h:27m:9s (0h:1m:21s left)
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Iteration 130 / LogL: -192738.873 / Time: 0h:12m:0s (0h:8m:16s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 602: -106261.090
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 145: -192684.414
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Iteration 700 / LogL: -106322.048 / Time: 0h:31m:27s (0h:0m:5s left)
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TREE SEARCH COMPLETED AFTER 703 ITERATIONS / Time: 0h:31m:34s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106261.090
Optimal log-likelihood: -106261.078
Proportion of invariable sites: 0.039
Site proportion and rates:  (0.072,0.032) (0.086,0.104) (0.073,0.203) (0.166,0.360) (0.099,0.628) (0.104,0.906) (0.158,1.409) (0.147,1.971) (0.056,4.384)
Parameters optimization took 1 rounds (0.641 sec)
BEST SCORE FOUND : -106261.078
Total tree length: 171.859

Total number of iterations: 703
CPU time used for tree search: 7433.706 sec (2h:3m:53s)
Wall-clock time used for tree search: 1873.258 sec (0h:31m:13s)
Total CPU time used: 7522.948 sec (2h:5m:22s)
Total wall-clock time used: 1895.630 sec (0h:31m:35s)

===> START BOOTSTRAP REPLICATE NUMBER 86

Creating bootstrap alignment (seed: 68268)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.118 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106599.272
Optimizing NNI: done in 5.23437 secs using 597.8% CPU
2. Current log-likelihood: -104666.755
3. Current log-likelihood: -104541.842
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Iteration 190 / LogL: -192777.983 / Time: 0h:16m:27s (0h:4m:47s left)
4. Current log-likelihood: -104535.988
5. Current log-likelihood: -104534.850
6. Current log-likelihood: -104533.874
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7. Current log-likelihood: -104533.149
8. Current log-likelihood: -104532.519
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9. Current log-likelihood: -104531.987
10. Current log-likelihood: -104531.524
11. Current log-likelihood: -104531.117
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12. Current log-likelihood: -104530.762
13. Current log-likelihood: -104530.445
14. Current log-likelihood: -104530.231
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15. Current log-likelihood: -104530.042
16. Current log-likelihood: -104529.871
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17. Current log-likelihood: -104529.729
18. Current log-likelihood: -104529.593
19. Current log-likelihood: -104529.491
Optimizing NNI: done in 4.14551 secs using 597.1% CPU
Optimal log-likelihood: -104529.365
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.107,0.038) (0.089,0.118) (0.072,0.224) (0.129,0.378) (0.080,0.592) (0.123,0.835) (0.118,1.188) (0.189,1.865) (0.066,4.176)
Parameters optimization took 19 rounds (30.437 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 4.6288 secs using 399.9% CPU
Computing ML distances took 4.629084 sec (of wall-clock time) 18.512193 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00068903 secs using 261.4% CPU
Constructing RapidNJ tree: done in 0.00875401 secs using 413.4% CPU
Computing RapidNJ tree took 0.009494 sec (of wall-clock time) 0.038588 sec (of CPU time)
Log-likelihood of RapidNJ tree: -104672.633
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.59172 secs using 597.4% CPU
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10.300 second
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Iteration 200 / LogL: -192772.438 / Time: 0h:17m:12s (0h:3m:53s left)
Optimizing NNI: done in 4.4675 secs using 598% CPU
Computing log-likelihood of 98 initial trees ... 10.072 seconds
Current best score: -104529.365

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -104099.417
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -104096.808
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -104055.457
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Iteration 210 / LogL: -192699.037 / Time: 0h:17m:57s (0h:3m:0s left)
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Iteration 10 / LogL: -104086.318 / Time: 0h:1m:43s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 11: -104049.714
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Iteration 20 / LogL: -104088.001 / Time: 0h:2m:11s
Finish initializing candidate tree set (20)
Current best tree score: -104049.714 / CPU time: 95.356
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Iteration 240 / LogL: -192733.366 / Time: 0h:20m:8s (0h:0m:25s left)
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Iteration 60 / LogL: -104031.028 / Time: 0h:3m:55s (0h:6m:10s left)
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Optimizing NNI: done in 4.21362 secs using 598.3% CPU
TREE SEARCH COMPLETED AFTER 246 ITERATIONS / Time: 0h:20m:33s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192684.414
Optimal log-likelihood: -192684.412
Site proportion and rates:  (0.021,0.107) (0.086,0.288) (0.078,0.385) (0.147,0.527) (0.190,0.700) (0.236,0.964) (0.154,1.681) (0.086,2.852)
Parameters optimization took 1 rounds (0.698 sec)
BEST SCORE FOUND : -192684.412
Total tree length: 154.867

Total number of iterations: 246
CPU time used for tree search: 7003.948 sec (1h:56m:43s)
Wall-clock time used for tree search: 1197.127 sec (0h:19m:57s)
Total CPU time used: 7227.694 sec (2h:0m:27s)
Total wall-clock time used: 1234.649 sec (0h:20m:34s)

===> START BOOTSTRAP REPLICATE NUMBER 46

Creating bootstrap alignment (seed: 70509)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.255 seconds

NOTE: 247 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
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1. Initial log-likelihood: -195017.442
Optimizing NNI: done in 1.71018 secs using 399% CPU
Iteration 70 / LogL: -104018.287 / Time: 0h:4m:13s (0h:5m:5s left)
2. Current log-likelihood: -192291.308
Optimizing NNI: done in 1.76863 secs using 399.3% CPU
3. Current log-likelihood: -192245.195
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4. Current log-likelihood: -192225.386
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5. Current log-likelihood: -192222.649
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6. Current log-likelihood: -192222.373
Optimizing NNI: done in 2.55115 secs using 398.7% CPU
Optimal log-likelihood: -192222.300
Site proportion and rates:  (0.017,0.085) (0.038,0.223) (0.143,0.360) (0.185,0.543) (0.211,0.765) (0.185,1.085) (0.129,1.710) (0.091,2.785)
Parameters optimization took 6 rounds (14.166 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Iteration 80 / LogL: -104139.625 / Time: 0h:4m:35s (0h:4m:14s left)
Calculating distance matrix: done in 10.2429 secs using 599.8% CPU
Computing ML distances took 10.243467 sec (of wall-clock time) 61.443329 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00127888 secs using 234.5% CPU
Constructing RapidNJ tree: done in 0.0230749 secs using 685.6% CPU
Computing RapidNJ tree took 0.024417 sec (of wall-clock time) 0.161913 sec (of CPU time)
Optimizing NNI: done in 1.80201 secs using 398.2% CPU
Optimizing NNI: done in 1.91785 secs using 398.3% CPU
Log-likelihood of RapidNJ tree: -196757.135
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.15115 secs using 398.6% CPU
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Iteration 90 / LogL: -104034.486 / Time: 0h:4m:58s (0h:3m:31s left)
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30.280 second
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 100: -104014.010
Iteration 100 / LogL: -104014.010 / Time: 0h:5m:21s (0h:5m:24s left)
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Computing log-likelihood of 98 initial trees ... 17.116 seconds
Current best score: -192222.300

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -191692.383
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Estimate model parameters (epsilon = 0.100)
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Iteration 110 / LogL: -104019.287 / Time: 0h:5m:41s (0h:4m:41s left)
BETTER TREE FOUND at iteration 2: -191685.158
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Iteration 150 / LogL: -104060.105 / Time: 0h:7m:2s (0h:2m:21s left)
BETTER TREE FOUND at iteration 14: -191561.717
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Iteration 20 / LogL: -191608.556 / Time: 0h:3m:26s
Finish initializing candidate tree set (20)
Current best tree score: -191561.717 / CPU time: 177.710
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 185: -104012.627
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Iteration 270 / LogL: -104034.251 / Time: 0h:11m:18s (0h:0m:37s left)
Optimizing NNI: done in 4.86143 secs using 597.6% CPU
Optimizing NNI: done in 1.70631 secs using 398.7% CPU
Optimizing NNI: done in 2.28949 secs using 398.7% CPU
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Iteration 60 / LogL: -191548.599 / Time: 0h:7m:11s (0h:7m:48s left)
Optimizing NNI: done in 2.44456 secs using 398.3% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.49491 secs using 398.8% CPU
Iteration 280 / LogL: -104225.207 / Time: 0h:11m:39s (0h:0m:12s left)
BETTER TREE FOUND at iteration 63: -191539.785
Optimizing NNI: done in 2.40904 secs using 398.4% CPU
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Optimizing NNI: done in 2.3361 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 286 ITERATIONS / Time: 0h:11m:51s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -104012.627
Optimizing NNI: done in 5.11756 secs using 597.1% CPU
Optimal log-likelihood: -104012.619
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.105,0.036) (0.084,0.106) (0.081,0.217) (0.124,0.376) (0.082,0.576) (0.112,0.822) (0.130,1.172) (0.188,1.855) (0.067,4.220)
Parameters optimization took 1 rounds (1.104 sec)
BEST SCORE FOUND : -104012.619
Total tree length: 159.077

Total number of iterations: 286
CPU time used for tree search: 2662.253 sec (0h:44m:22s)
Wall-clock time used for tree search: 675.644 sec (0h:11m:15s)
Total CPU time used: 2811.336 sec (0h:46m:51s)
Total wall-clock time used: 713.038 sec (0h:11m:53s)

===> START BOOTSTRAP REPLICATE NUMBER 87

Creating bootstrap alignment (seed: 68269)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.144 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 100 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -113043.305
2. Current log-likelihood: -110831.107
3. Current log-likelihood: -110769.552
Optimizing NNI: done in 4.70208 secs using 597.2% CPU
4. Current log-likelihood: -110766.202
5. Current log-likelihood: -110764.604
6. Current log-likelihood: -110763.259
Optimizing NNI: done in 4.84138 secs using 597.4% CPU
7. Current log-likelihood: -110762.176
8. Current log-likelihood: -110761.198
9. Current log-likelihood: -110760.323
Optimizing NNI: done in 4.86789 secs using 597.5% CPU
10. Current log-likelihood: -110759.548
11. Current log-likelihood: -110758.861
12. Current log-likelihood: -110758.255
13. Current log-likelihood: -110757.740
Optimizing NNI: done in 5.63339 secs using 597.7% CPU
14. Current log-likelihood: -110757.297
15. Current log-likelihood: -110756.899
16. Current log-likelihood: -110756.556
Optimizing NNI: done in 4.69865 secs using 596.6% CPU
Iteration 70 / LogL: -191566.279 / Time: 0h:8m:5s (0h:10m:53s left)
17. Current log-likelihood: -110756.246
18. Current log-likelihood: -110755.976
19. Current log-likelihood: -110755.731
20. Current log-likelihood: -110755.577
21. Current log-likelihood: -110755.434
Optimizing NNI: done in 5.21371 secs using 598% CPU
22. Current log-likelihood: -110755.302
23. Current log-likelihood: -110755.182
24. Current log-likelihood: -110755.068
25. Current log-likelihood: -110754.965
Optimal log-likelihood: -110754.815
Proportion of invariable sites: 0.016
Site proportion and rates:  (0.076,0.030) (0.085,0.096) (0.052,0.184) (0.122,0.294) (0.080,0.421) (0.120,0.613) (0.184,1.047) (0.183,1.685) (0.083,4.029)
Parameters optimization took 25 rounds (34.848 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 5.55314 secs using 597.5% CPU
Calculating distance matrix: done in 4.73949 secs using 399.8% CPU
Computing ML distances took 4.739813 sec (of wall-clock time) 18.950514 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000725031 secs using 447.4% CPU
Constructing RapidNJ tree: done in 0.00858498 secs using 477.8% CPU
Computing RapidNJ tree took 0.009371 sec (of wall-clock time) 0.044321 sec (of CPU time)
Optimizing NNI: done in 4.86192 secs using 597.6% CPU
Log-likelihood of RapidNJ tree: -110734.411
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 6.76032 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 74: -191536.975
10.934 second
Optimizing NNI: done in 5.24355 secs using 597.3% CPU
Optimizing NNI: done in 4.22743 secs using 597.1% CPU
Computing log-likelihood of 98 initial trees ... 9.636 seconds
Current best score: -110734.411

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -109975.628
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -109947.128
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -109944.866
BETTER TREE FOUND at iteration 79: -191529.885
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Iteration 80 / LogL: -191548.153 / Time: 0h:9m:2s (0h:11m:19s left)
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Iteration 10 / LogL: -109967.774 / Time: 0h:1m:30s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 85: -191524.656
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Iteration 20 / LogL: -109979.415 / Time: 0h:1m:52s
Finish initializing candidate tree set (20)
Current best tree score: -109944.866 / CPU time: 71.905
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 4.53686 secs using 598% CPU
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -109914.526
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 88: -191523.003
BETTER TREE FOUND at iteration 24: -109913.677
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Iteration 90 / LogL: -191620.984 / Time: 0h:9m:56s (0h:10m:56s left)
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Iteration 30 / LogL: -109931.408 / Time: 0h:2m:17s (0h:7m:25s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 34: -109906.873
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -109897.251
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Iteration 40 / LogL: -109907.439 / Time: 0h:2m:42s (0h:6m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 52: -109887.937
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Iteration 60 / LogL: -109901.891 / Time: 0h:3m:26s (0h:5m:21s left)
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Iteration 70 / LogL: -109888.379 / Time: 0h:3m:45s (0h:4m:27s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 76: -109882.617
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Estimate model parameters (epsilon = 0.100)
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Iteration 160 / LogL: -109944.259 / Time: 0h:6m:45s (0h:0m:40s left)
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Iteration 150 / LogL: -191696.489 / Time: 0h:14m:57s (0h:6m:55s left)
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TREE SEARCH COMPLETED AFTER 177 ITERATIONS / Time: 0h:7m:18s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -109882.617
Optimal log-likelihood: -109882.605
Proportion of invariable sites: 0.015
Site proportion and rates:  (0.074,0.030) (0.089,0.092) (0.063,0.193) (0.109,0.302) (0.092,0.430) (0.107,0.632) (0.180,1.034) (0.181,1.663) (0.092,3.829)
Parameters optimization took 1 rounds (0.597 sec)
BEST SCORE FOUND : -109882.605
Total tree length: 185.155

Total number of iterations: 177
CPU time used for tree search: 1555.064 sec (0h:25m:55s)
Wall-clock time used for tree search: 398.302 sec (0h:6m:38s)
Total CPU time used: 1719.472 sec (0h:28m:39s)
Total wall-clock time used: 439.556 sec (0h:7m:19s)

===> START BOOTSTRAP REPLICATE NUMBER 88

Creating bootstrap alignment (seed: 68270)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.103 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -108836.948
2. Current log-likelihood: -106992.325
Optimizing NNI: done in 5.81488 secs using 597.3% CPU
3. Current log-likelihood: -106917.434
4. Current log-likelihood: -106894.798
Optimizing NNI: done in 4.74835 secs using 597.6% CPU
5. Current log-likelihood: -106893.910
6. Current log-likelihood: -106893.810
Optimal log-likelihood: -106893.674
Proportion of invariable sites: 0.020
Site proportion and rates:  (0.118,0.047) (0.074,0.128) (0.061,0.218) (0.097,0.333) (0.099,0.487) (0.169,0.801) (0.114,1.324) (0.194,1.989) (0.054,4.073)
Parameters optimization took 6 rounds (9.489 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 5.0708 secs using 597.3% CPU
Calculating distance matrix: done in 4.7067 secs using 399.9% CPU
Computing ML distances took 4.707055 sec (of wall-clock time) 18.821915 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000690937 secs using 559.8% CPU
Constructing RapidNJ tree: done in 0.00854111 secs using 370.4% CPU
Computing RapidNJ tree took 0.009289 sec (of wall-clock time) 0.035559 sec (of CPU time)
Log-likelihood of RapidNJ tree: -107273.889
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.68132 secs using 597.2% CPU
Optimizing NNI: done in 4.67592 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 155: -191514.868
10.725 second
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Optimizing NNI: done in 3.81854 secs using 598.3% CPU
Computing log-likelihood of 98 initial trees ... 9.881 seconds
Current best score: -106893.674

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -106371.739
BETTER TREE FOUND at iteration 158: -191512.667
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Iteration 160 / LogL: -191528.681 / Time: 0h:15m:53s (0h:9m:47s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 8: -106354.845
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Iteration 10 / LogL: -106388.985 / Time: 0h:1m:3s
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BETTER TREE FOUND at iteration 163: -191501.331
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Iteration 20 / LogL: -106474.176 / Time: 0h:1m:26s
Finish initializing candidate tree set (20)
Current best tree score: -106354.845 / CPU time: 70.646
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -106314.559
Iteration 30 / LogL: -106314.559 / Time: 0h:1m:59s (0h:6m:50s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 135: -106300.501
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Iteration 220 / LogL: -191514.730 / Time: 0h:20m:50s (0h:4m:5s left)
Optimizing NNI: done in 1.77779 secs using 398.6% CPU
Iteration 140 / LogL: -106343.249 / Time: 0h:5m:51s (0h:4m:0s left)
Optimizing NNI: done in 1.9808 secs using 398.5% CPU
Optimizing NNI: done in 5.33687 secs using 597.1% CPU
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Iteration 150 / LogL: -106303.783 / Time: 0h:6m:11s (0h:3m:32s left)
Optimizing NNI: done in 1.93196 secs using 398.9% CPU
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Optimizing NNI: done in 5.17723 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.02741 secs using 398.9% CPU
Optimizing NNI: done in 1.72283 secs using 398.6% CPU
BETTER TREE FOUND at iteration 226: -191499.697
Optimizing NNI: done in 1.76717 secs using 398.9% CPU
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Iteration 160 / LogL: -106310.567 / Time: 0h:6m:31s (0h:3m:4s left)
Optimizing NNI: done in 2.321 secs using 398.2% CPU
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Optimizing NNI: done in 4.85939 secs using 597% CPU
Iteration 230 / LogL: -191597.751 / Time: 0h:21m:41s (0h:9m:5s left)
Optimizing NNI: done in 1.84681 secs using 399.1% CPU
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Iteration 170 / LogL: -106320.562 / Time: 0h:6m:51s (0h:2m:38s left)
Optimizing NNI: done in 2.05212 secs using 398.3% CPU
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Iteration 180 / LogL: -106346.578 / Time: 0h:7m:12s (0h:2m:12s left)
Optimizing NNI: done in 1.71249 secs using 398.4% CPU
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Optimizing NNI: done in 2.06148 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.41435 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 188: -106299.838
BETTER TREE FOUND at iteration 240: -191498.744
Iteration 240 / LogL: -191498.744 / Time: 0h:22m:31s (0h:9m:25s left)
Optimizing NNI: done in 1.90338 secs using 399.1% CPU
Optimizing NNI: done in 1.96732 secs using 399% CPU
Iteration 190 / LogL: -106355.006 / Time: 0h:7m:34s (0h:3m:55s left)
Optimizing NNI: done in 4.6574 secs using 597.2% CPU
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Iteration 200 / LogL: -106308.593 / Time: 0h:7m:54s (0h:3m:29s left)
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Iteration 210 / LogL: -106322.105 / Time: 0h:8m:15s (0h:3m:4s left)
Optimizing NNI: done in 4.54319 secs using 597% CPU
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Iteration 250 / LogL: -191541.013 / Time: 0h:23m:22s (0h:8m:26s left)
Optimizing NNI: done in 2.10282 secs using 398.8% CPU
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Iteration 220 / LogL: -106309.323 / Time: 0h:8m:34s (0h:2m:39s left)
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Iteration 230 / LogL: -106313.975 / Time: 0h:8m:54s (0h:2m:15s left)
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Iteration 260 / LogL: -191566.993 / Time: 0h:24m:9s (0h:7m:27s left)
Optimizing NNI: done in 2.26617 secs using 398.9% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.94309 secs using 398.5% CPU
Iteration 240 / LogL: -106301.231 / Time: 0h:9m:14s (0h:1m:51s left)
BETTER TREE FOUND at iteration 261: -191496.642
Optimizing NNI: done in 1.89786 secs using 398.8% CPU
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Iteration 250 / LogL: -106354.716 / Time: 0h:9m:33s (0h:1m:27s left)
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Iteration 260 / LogL: -106314.112 / Time: 0h:9m:54s (0h:1m:4s left)
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Iteration 270 / LogL: -191512.300 / Time: 0h:25m:0s (0h:8m:27s left)
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Iteration 270 / LogL: -106309.864 / Time: 0h:10m:14s (0h:0m:41s left)
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Iteration 280 / LogL: -106306.441 / Time: 0h:10m:34s (0h:0m:18s left)
Optimizing NNI: done in 1.84225 secs using 398.7% CPU
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Iteration 280 / LogL: -191506.548 / Time: 0h:25m:46s (0h:7m:29s left)
Optimizing NNI: done in 1.92145 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 286: -106297.638
Optimizing NNI: done in 2.20621 secs using 398.6% CPU
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Iteration 290 / LogL: -106314.292 / Time: 0h:10m:56s (0h:3m:38s left)
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Iteration 300 / LogL: -106331.695 / Time: 0h:11m:17s (0h:3m:14s left)
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Iteration 290 / LogL: -191531.723 / Time: 0h:26m:34s (0h:6m:31s left)
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Iteration 310 / LogL: -106311.942 / Time: 0h:11m:36s (0h:2m:51s left)
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Iteration 320 / LogL: -106322.220 / Time: 0h:11m:55s (0h:2m:27s left)
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Iteration 330 / LogL: -106341.740 / Time: 0h:12m:16s (0h:2m:5s left)
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Iteration 300 / LogL: -191562.207 / Time: 0h:27m:24s (0h:5m:35s left)
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Iteration 340 / LogL: -106299.648 / Time: 0h:12m:36s (0h:1m:42s left)
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Iteration 350 / LogL: -106304.037 / Time: 0h:12m:56s (0h:1m:20s left)
Optimizing NNI: done in 5.14249 secs using 597% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.4669 secs using 597.1% CPU
BETTER TREE FOUND at iteration 354: -106296.827
Optimizing NNI: done in 2.34649 secs using 398.4% CPU
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Iteration 310 / LogL: -191536.260 / Time: 0h:28m:12s (0h:4m:39s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 346: -191496.456
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Iteration 450 / LogL: -106303.512 / Time: 0h:16m:18s (0h:0m:8s left)
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Iteration 350 / LogL: -191515.524 / Time: 0h:31m:28s (0h:8m:39s left)
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TREE SEARCH COMPLETED AFTER 455 ITERATIONS / Time: 0h:16m:27s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106296.827
2. Current log-likelihood: -106296.807
3. Current log-likelihood: -106296.791
4. Current log-likelihood: -106296.774
5. Current log-likelihood: -106296.759
6. Current log-likelihood: -106296.745
Optimizing NNI: done in 4.64767 secs using 597.1% CPU
7. Current log-likelihood: -106296.732
8. Current log-likelihood: -106296.720
9. Current log-likelihood: -106296.709
Optimal log-likelihood: -106296.698
Proportion of invariable sites: 0.020
Site proportion and rates:  (0.115,0.043) (0.078,0.121) (0.062,0.222) (0.085,0.324) (0.111,0.467) (0.155,0.786) (0.116,1.245) (0.205,1.979) (0.053,4.162)
Parameters optimization took 9 rounds (6.978 sec)
BEST SCORE FOUND : -106296.698
Total tree length: 156.237

Total number of iterations: 455
CPU time used for tree search: 3843.317 sec (1h:4m:3s)
Wall-clock time used for tree search: 972.186 sec (0h:16m:12s)
Total CPU time used: 3933.495 sec (1h:5m:33s)
Total wall-clock time used: 994.788 sec (0h:16m:34s)

===> START BOOTSTRAP REPLICATE NUMBER 89

Creating bootstrap alignment (seed: 68271)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.130 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -100604.524
2. Current log-likelihood: -98466.958
Optimizing NNI: done in 4.55451 secs using 596.7% CPU
3. Current log-likelihood: -98393.647
4. Current log-likelihood: -98393.043
Optimal log-likelihood: -98393.019
Proportion of invariable sites: 0.038
Site proportion and rates:  (0.134,0.039) (0.087,0.125) (0.073,0.211) (0.098,0.327) (0.113,0.491) (0.107,0.742) (0.101,1.196) (0.165,1.949) (0.085,4.243)
Parameters optimization took 4 rounds (5.512 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Optimizing NNI: done in 4.09426 secs using 596.7% CPU
Calculating distance matrix: done in 4.77403 secs using 399.9% CPU
Computing ML distances took 4.774386 sec (of wall-clock time) 19.093554 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000702858 secs using 267.5% CPU
Constructing RapidNJ tree: done in 0.00877309 secs using 384.1% CPU
Computing RapidNJ tree took 0.009534 sec (of wall-clock time) 0.035884 sec (of CPU time)
Log-likelihood of RapidNJ tree: -99088.622
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.99798 secs using 597.4% CPU
Optimizing NNI: done in 6.94715 secs using 596.3% CPU
10.783 second
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Computing log-likelihood of 98 initial trees ... 10.189 seconds
Current best score: -98393.019

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -98056.898
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Iteration 360 / LogL: -191524.293 / Time: 0h:32m:19s (0h:7m:44s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -97988.144
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Iteration 10 / LogL: -98008.397 / Time: 0h:1m:15s
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Iteration 370 / LogL: -191514.965 / Time: 0h:33m:7s (0h:6m:49s left)
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Iteration 20 / LogL: -98070.571 / Time: 0h:1m:35s
Finish initializing candidate tree set (20)
Current best tree score: -97988.144 / CPU time: 84.283
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -97972.694
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -97963.353
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -97956.879
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Iteration 50 / LogL: -97968.324 / Time: 0h:2m:52s (0h:4m:44s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 53: -97954.460
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 127: -97953.430
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 148: -97952.837
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TREE SEARCH COMPLETED AFTER 447 ITERATIONS / Time: 0h:39m:27s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -191496.456
Optimizing NNI: done in 1.92449 secs using 398.6% CPU
Optimal log-likelihood: -191496.448
Site proportion and rates:  (0.020,0.091) (0.044,0.245) (0.147,0.370) (0.184,0.556) (0.226,0.789) (0.170,1.123) (0.119,1.769) (0.090,2.793)
Parameters optimization took 1 rounds (0.528 sec)
BEST SCORE FOUND : -191496.448
Total tree length: 156.431

Total number of iterations: 447
CPU time used for tree search: 13821.111 sec (3h:50m:21s)
Wall-clock time used for tree search: 2339.420 sec (0h:38m:59s)
Total CPU time used: 13993.665 sec (3h:53m:13s)
Total wall-clock time used: 2368.346 sec (0h:39m:28s)

===> START BOOTSTRAP REPLICATE NUMBER 47

Creating bootstrap alignment (seed: 70510)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.286 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -203907.496
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2. Current log-likelihood: -200922.659
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3. Current log-likelihood: -200889.061
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4. Current log-likelihood: -200882.744
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5. Current log-likelihood: -200880.833
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Iteration 190 / LogL: -98020.760 / Time: 0h:8m:3s (0h:2m:28s left)
6. Current log-likelihood: -200880.499
Optimizing NNI: done in 2.15192 secs using 398% CPU
Optimal log-likelihood: -200880.421
Site proportion and rates:  (0.017,0.087) (0.054,0.226) (0.118,0.323) (0.170,0.519) (0.178,0.715) (0.164,0.961) (0.174,1.544) (0.125,2.449)
Parameters optimization took 6 rounds (13.080 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 9.62971 secs using 599.9% CPU
Computing ML distances took 9.630269 sec (of wall-clock time) 57.766980 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00136304 secs using 521.2% CPU
Constructing RapidNJ tree: done in 0.0227919 secs using 657.9% CPU
Computing RapidNJ tree took 0.024232 sec (of wall-clock time) 0.158417 sec (of CPU time)
Optimizing NNI: done in 2.2999 secs using 398.2% CPU
Log-likelihood of RapidNJ tree: -204950.835
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 2.07082 secs using 398.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 207: -97952.534
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29.381 second
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Iteration 210 / LogL: -97959.203 / Time: 0h:8m:49s (0h:4m:5s left)
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Computing log-likelihood of 98 initial trees ... 16.339 seconds
Current best score: -200880.421

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -200287.463
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Iteration 220 / LogL: -97976.710 / Time: 0h:9m:11s (0h:3m:38s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -200082.655
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Iteration 230 / LogL: -97999.584 / Time: 0h:9m:32s (0h:3m:12s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 10: -200068.374
Iteration 10 / LogL: -200068.374 / Time: 0h:1m:59s
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Iteration 250 / LogL: -97959.319 / Time: 0h:10m:15s (0h:2m:20s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 255: -97950.253
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Iteration 20 / LogL: -200153.110 / Time: 0h:2m:42s
Finish initializing candidate tree set (20)
Current best tree score: -200068.374 / CPU time: 137.906
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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TREE SEARCH COMPLETED AFTER 356 ITERATIONS / Time: 0h:14m:14s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -97950.253
2. Current log-likelihood: -97950.218
3. Current log-likelihood: -97950.164
4. Current log-likelihood: -97950.110
5. Current log-likelihood: -97950.058
Optimizing NNI: done in 5.32057 secs using 596.7% CPU
6. Current log-likelihood: -97950.009
7. Current log-likelihood: -97949.961
8. Current log-likelihood: -97949.916
9. Current log-likelihood: -97949.871
10. Current log-likelihood: -97949.828
Optimizing NNI: done in 5.06738 secs using 597.2% CPU
11. Current log-likelihood: -97949.787
12. Current log-likelihood: -97949.751
13. Current log-likelihood: -97949.713
14. Current log-likelihood: -97949.680
15. Current log-likelihood: -97949.648
Optimizing NNI: done in 4.47516 secs using 598.3% CPU
16. Current log-likelihood: -97949.617
17. Current log-likelihood: -97949.596
18. Current log-likelihood: -97949.561
19. Current log-likelihood: -97949.526
Optimizing NNI: done in 4.12268 secs using 597% CPU
20. Current log-likelihood: -97949.495
21. Current log-likelihood: -97949.465
22. Current log-likelihood: -97949.437
23. Current log-likelihood: -97949.419
24. Current log-likelihood: -97949.399
25. Current log-likelihood: -97949.368
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26. Current log-likelihood: -97949.350
27. Current log-likelihood: -97949.320
28. Current log-likelihood: -97949.303
29. Current log-likelihood: -97949.274
30. Current log-likelihood: -97949.257
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31. Current log-likelihood: -97949.229
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36. Current log-likelihood: -97949.133
Optimizing NNI: done in 4.4366 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
37. Current log-likelihood: -97949.117
38. Current log-likelihood: -97949.100
39. Current log-likelihood: -97949.083
BETTER TREE FOUND at iteration 69: -200010.805
40. Current log-likelihood: -97949.067
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42. Current log-likelihood: -97949.036
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Iteration 70 / LogL: -200075.651 / Time: 0h:7m:1s (0h:10m:4s left)
48. Current log-likelihood: -97948.947
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54. Current log-likelihood: -97948.862
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62. Current log-likelihood: -97948.753
Optimizing NNI: done in 5.11993 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
63. Current log-likelihood: -97948.740
64. Current log-likelihood: -97948.726
65. Current log-likelihood: -97948.713
66. Current log-likelihood: -97948.700
67. Current log-likelihood: -97948.688
BETTER TREE FOUND at iteration 72: -200007.187
68. Current log-likelihood: -97948.676
69. Current log-likelihood: -97948.665
70. Current log-likelihood: -97948.653
Optimal log-likelihood: -97948.639
Proportion of invariable sites: 0.036
Site proportion and rates:  (0.108,0.028) (0.093,0.087) (0.091,0.187) (0.100,0.306) (0.120,0.471) (0.099,0.716) (0.106,1.152) (0.167,1.920) (0.082,4.556)
Parameters optimization took 70 rounds (53.108 sec)
BEST SCORE FOUND : -97948.639
Total tree length: 170.941

Total number of iterations: 356
CPU time used for tree search: 3326.196 sec (0h:55m:26s)
Wall-clock time used for tree search: 842.975 sec (0h:14m:2s)
Total CPU time used: 3584.223 sec (0h:59m:44s)
Total wall-clock time used: 907.742 sec (0h:15m:7s)

===> START BOOTSTRAP REPLICATE NUMBER 90

Creating bootstrap alignment (seed: 68272)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.115 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 101 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -109865.498
2. Current log-likelihood: -107603.540
Optimizing NNI: done in 4.92888 secs using 597.5% CPU
3. Current log-likelihood: -107553.885
4. Current log-likelihood: -107552.005
5. Current log-likelihood: -107550.570
Optimizing NNI: done in 4.75158 secs using 597.4% CPU
6. Current log-likelihood: -107549.160
7. Current log-likelihood: -107547.798
8. Current log-likelihood: -107546.502
Optimizing NNI: done in 5.47741 secs using 597.5% CPU
9. Current log-likelihood: -107545.283
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Optimizing NNI: done in 4.16215 secs using 598% CPU
12. Current log-likelihood: -107542.273
13. Current log-likelihood: -107541.590
14. Current log-likelihood: -107540.953
Optimizing NNI: done in 4.42129 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
15. Current log-likelihood: -107540.507
BETTER TREE FOUND at iteration 77: -200006.694
16. Current log-likelihood: -107540.044
17. Current log-likelihood: -107539.767
18. Current log-likelihood: -107539.543
19. Current log-likelihood: -107539.379
Optimizing NNI: done in 4.84321 secs using 597.1% CPU
20. Current log-likelihood: -107539.185
Optimal log-likelihood: -107539.036
Proportion of invariable sites: 0.024
Site proportion and rates:  (0.081,0.031) (0.091,0.098) (0.080,0.201) (0.092,0.308) (0.086,0.434) (0.120,0.668) (0.150,1.023) (0.185,1.764) (0.091,3.795)
Parameters optimization took 20 rounds (31.018 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.23814 secs using 597.9% CPU
Calculating distance matrix: done in 4.70271 secs using 399.8% CPU
Computing ML distances took 4.703091 sec (of wall-clock time) 18.803147 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000782967 secs using 414.6% CPU
Constructing RapidNJ tree: done in 0.00862694 secs using 358.7% CPU
Computing RapidNJ tree took 0.009466 sec (of wall-clock time) 0.036830 sec (of CPU time)
Log-likelihood of RapidNJ tree: -107700.405
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 4.51259 secs using 597.6% CPU
Iteration 80 / LogL: -200112.557 / Time: 0h:7m:52s (0h:9m:40s left)
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10.832 second
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 83: -200003.338
Optimizing NNI: done in 3.84324 secs using 597.9% CPU
Computing log-likelihood of 98 initial trees ... 9.798 seconds
Current best score: -107539.036

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 87: -199995.100
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Iteration 90 / LogL: -200013.014 / Time: 0h:8m:42s (0h:9m:29s left)
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BETTER TREE FOUND at iteration 1: -106939.931
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 92: -199991.846
BETTER TREE FOUND at iteration 2: -106919.003
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Iteration 10 / LogL: -106982.937 / Time: 0h:2m:15s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 100: -199990.150
Iteration 100 / LogL: -199990.150 / Time: 0h:9m:45s (0h:9m:51s left)
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Iteration 20 / LogL: -106921.854 / Time: 0h:2m:40s
Finish initializing candidate tree set (20)
Current best tree score: -106903.964 / CPU time: 123.762
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -106877.017
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -106868.779
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Iteration 110 / LogL: -199998.690 / Time: 0h:10m:35s (0h:8m:44s left)
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BETTER TREE FOUND at iteration 40: -106867.239
Iteration 40 / LogL: -106867.239 / Time: 0h:3m:33s (0h:9m:6s left)
Optimizing NNI: done in 4.48202 secs using 596.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -106860.355
Optimizing NNI: done in 5.07811 secs using 597.3% CPU
Optimizing NNI: done in 1.67647 secs using 398.5% CPU
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Iteration 50 / LogL: -106896.510 / Time: 0h:3m:55s (0h:7m:31s left)
Optimizing NNI: done in 2.03706 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.48674 secs using 597.4% CPU
Iteration 120 / LogL: -200012.049 / Time: 0h:11m:22s (0h:7m:38s left)
BETTER TREE FOUND at iteration 56: -106859.819
Optimizing NNI: done in 1.98984 secs using 398.7% CPU
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Optimizing NNI: done in 5.09302 secs using 597.4% CPU
BETTER TREE FOUND at iteration 60: -106854.279
Iteration 60 / LogL: -106854.279 / Time: 0h:4m:17s (0h:7m:16s left)
Optimizing NNI: done in 1.97071 secs using 398.5% CPU
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Iteration 70 / LogL: -106859.725 / Time: 0h:4m:37s (0h:6m:2s left)
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Iteration 130 / LogL: -200082.884 / Time: 0h:12m:9s (0h:6m:35s left)
Optimizing NNI: done in 2.22831 secs using 398.7% CPU
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Iteration 80 / LogL: -106867.515 / Time: 0h:4m:57s (0h:5m:1s left)
Optimizing NNI: done in 4.7204 secs using 597.1% CPU
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Iteration 90 / LogL: -106864.256 / Time: 0h:5m:17s (0h:4m:9s left)
Optimizing NNI: done in 4.87104 secs using 596.5% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.93422 secs using 399% CPU
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BETTER TREE FOUND at iteration 136: -199984.689
Optimizing NNI: done in 2.30993 secs using 398.8% CPU
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Iteration 100 / LogL: -106944.581 / Time: 0h:5m:37s (0h:3m:24s left)
Optimizing NNI: done in 4.49493 secs using 597.2% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 101: -106853.458
Optimizing NNI: done in 4.36973 secs using 597% CPU
Iteration 140 / LogL: -200058.940 / Time: 0h:12m:58s (0h:8m:57s left)
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Iteration 110 / LogL: -106859.497 / Time: 0h:5m:59s (0h:5m:0s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.31368 secs using 398.9% CPU
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Iteration 120 / LogL: -106973.368 / Time: 0h:6m:20s (0h:4m:18s left)
BETTER TREE FOUND at iteration 147: -199983.711
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Iteration 150 / LogL: -200022.273 / Time: 0h:13m:52s (0h:9m:1s left)
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Iteration 130 / LogL: -106908.797 / Time: 0h:6m:39s (0h:3m:39s left)
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Iteration 140 / LogL: -106857.107 / Time: 0h:6m:57s (0h:3m:3s left)
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Iteration 150 / LogL: -106859.819 / Time: 0h:7m:16s (0h:2m:29s left)
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Iteration 160 / LogL: -106886.645 / Time: 0h:7m:39s (0h:1m:58s left)
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Iteration 160 / LogL: -200008.157 / Time: 0h:14m:55s (0h:8m:9s left)
Optimizing NNI: done in 2.90838 secs using 398.2% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.65036 secs using 596.4% CPU
BETTER TREE FOUND at iteration 165: -106849.823
Optimizing NNI: done in 4.095 secs using 596.6% CPU
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Iteration 170 / LogL: -106854.939 / Time: 0h:8m:11s (0h:4m:36s left)
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Iteration 170 / LogL: -200018.025 / Time: 0h:15m:42s (0h:7m:9s left)
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Iteration 180 / LogL: -106869.407 / Time: 0h:8m:37s (0h:4m:5s left)
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Iteration 190 / LogL: -107049.109 / Time: 0h:9m:5s (0h:3m:36s left)
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Iteration 180 / LogL: -200103.062 / Time: 0h:16m:29s (0h:6m:10s left)
Optimizing NNI: done in 2.62086 secs using 399% CPU
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Iteration 200 / LogL: -106855.883 / Time: 0h:9m:31s (0h:3m:6s left)
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Iteration 210 / LogL: -106878.158 / Time: 0h:9m:59s (0h:2m:37s left)
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Iteration 190 / LogL: -200107.307 / Time: 0h:17m:20s (0h:5m:13s left)
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Iteration 220 / LogL: -106921.271 / Time: 0h:10m:21s (0h:2m:7s left)
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Iteration 230 / LogL: -106962.062 / Time: 0h:10m:41s (0h:1m:38s left)
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Iteration 200 / LogL: -199999.034 / Time: 0h:18m:6s (0h:4m:16s left)
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Iteration 240 / LogL: -106859.325 / Time: 0h:11m:1s (0h:1m:9s left)
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Optimizing NNI: done in 2.02094 secs using 398.3% CPU
Iteration 250 / LogL: -106882.246 / Time: 0h:11m:22s (0h:0m:41s left)
Optimizing NNI: done in 2.04493 secs using 398.5% CPU
Optimizing NNI: done in 4.70741 secs using 598% CPU
Optimizing NNI: done in 2.0686 secs using 398.7% CPU
Optimizing NNI: done in 1.82315 secs using 398.6% CPU
Optimizing NNI: done in 5.31449 secs using 597.8% CPU
Optimizing NNI: done in 2.20399 secs using 398.6% CPU
Optimizing NNI: done in 1.99348 secs using 399.1% CPU
Optimizing NNI: done in 1.68467 secs using 398.5% CPU
Optimizing NNI: done in 5.57496 secs using 597.3% CPU
Optimizing NNI: done in 1.85793 secs using 398.8% CPU
Optimizing NNI: done in 2.27956 secs using 398.6% CPU
Optimizing NNI: done in 2.01392 secs using 398.7% CPU
Optimizing NNI: done in 5.21882 secs using 597.3% CPU
Iteration 210 / LogL: -199991.305 / Time: 0h:18m:55s (0h:3m:20s left)
Optimizing NNI: done in 2.19467 secs using 398.7% CPU
Iteration 260 / LogL: -107096.049 / Time: 0h:11m:42s (0h:0m:13s left)
Optimizing NNI: done in 1.97552 secs using 399% CPU
Optimizing NNI: done in 4.7705 secs using 597.3% CPU
Optimizing NNI: done in 1.97041 secs using 398.5% CPU
Optimizing NNI: done in 2.26486 secs using 398.5% CPU
Optimizing NNI: done in 4.48656 secs using 597% CPU
Optimizing NNI: done in 2.0611 secs using 398.8% CPU
Optimizing NNI: done in 2.01194 secs using 399% CPU
Optimizing NNI: done in 4.38738 secs using 597.1% CPU
Optimizing NNI: done in 1.83071 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 266 ITERATIONS / Time: 0h:11m:54s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106849.823
2. Current log-likelihood: -106849.806
3. Current log-likelihood: -106849.781
4. Current log-likelihood: -106849.767
5. Current log-likelihood: -106849.753
6. Current log-likelihood: -106849.740
Optimizing NNI: done in 4.86611 secs using 597.5% CPU
7. Current log-likelihood: -106849.728
8. Current log-likelihood: -106849.717
9. Current log-likelihood: -106849.707
10. Current log-likelihood: -106849.696
11. Current log-likelihood: -106849.685
Optimal log-likelihood: -106849.677
Proportion of invariable sites: 0.023
Site proportion and rates:  (0.060,0.023) (0.098,0.074) (0.090,0.178) (0.095,0.300) (0.089,0.437) (0.120,0.654) (0.149,1.023) (0.187,1.744) (0.090,3.915)
Parameters optimization took 11 rounds (8.135 sec)
BEST SCORE FOUND : -106849.677
Total tree length: 179.483

Total number of iterations: 266
CPU time used for tree search: 2668.710 sec (0h:44m:28s)
Wall-clock time used for tree search: 677.668 sec (0h:11m:17s)
Total CPU time used: 2849.017 sec (0h:47m:29s)
Total wall-clock time used: 722.910 sec (0h:12m:2s)

===> START BOOTSTRAP REPLICATE NUMBER 91

Creating bootstrap alignment (seed: 68273)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.116 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -113470.525
Optimizing NNI: done in 5.39637 secs using 596.8% CPU
2. Current log-likelihood: -111450.425
3. Current log-likelihood: -111368.133
4. Current log-likelihood: -111364.181
Optimizing NNI: done in 4.51588 secs using 596.7% CPU
5. Current log-likelihood: -111363.402
6. Current log-likelihood: -111362.964
7. Current log-likelihood: -111362.612
Optimizing NNI: done in 4.47281 secs using 597.3% CPU
8. Current log-likelihood: -111362.306
9. Current log-likelihood: -111362.048
10. Current log-likelihood: -111361.892
11. Current log-likelihood: -111361.665
Optimizing NNI: done in 4.77196 secs using 597.4% CPU
12. Current log-likelihood: -111361.539
13. Current log-likelihood: -111361.418
14. Current log-likelihood: -111361.307
15. Current log-likelihood: -111361.207
Optimizing NNI: done in 4.88019 secs using 597.2% CPU
Optimal log-likelihood: -111361.060
Proportion of invariable sites: 0.018
Site proportion and rates:  (0.058,0.043) (0.119,0.115) (0.056,0.228) (0.110,0.306) (0.096,0.434) (0.150,0.689) (0.166,1.201) (0.156,1.889) (0.070,4.251)
Parameters optimization took 15 rounds (21.456 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.41677 secs using 597.7% CPU
Iteration 220 / LogL: -200031.152 / Time: 0h:19m:43s (0h:2m:25s left)
Calculating distance matrix: done in 4.86966 secs using 399.9% CPU
Computing ML distances took 4.870049 sec (of wall-clock time) 19.474160 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000788927 secs using 399.1% CPU
Constructing RapidNJ tree: done in 0.00829196 secs using 388.1% CPU
Computing RapidNJ tree took 0.009133 sec (of wall-clock time) 0.035979 sec (of CPU time)
Log-likelihood of RapidNJ tree: -111746.388
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.44613 secs using 596.7% CPU
Optimizing NNI: done in 6.7825 secs using 597.3% CPU
10.793 second
Optimizing NNI: done in 7.4219 secs using 596.6% CPU
Computing log-likelihood of 98 initial trees ... 9.954 seconds
Current best score: -111361.060

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.09519 secs using 597.6% CPU
Optimizing NNI: done in 2.03846 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.25458 secs using 597.4% CPU
Optimizing NNI: done in 5.62046 secs using 597.4% CPU
Optimizing NNI: done in 4.4614 secs using 597.7% CPU
BETTER TREE FOUND at iteration 1: -110756.501
Optimizing NNI: done in 4.81553 secs using 597.2% CPU
Optimizing NNI: done in 2.0411 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.96867 secs using 597.9% CPU
BETTER TREE FOUND at iteration 2: -110580.599
Optimizing NNI: done in 1.90602 secs using 398.7% CPU
Optimizing NNI: done in 4.47433 secs using 597.1% CPU
Iteration 230 / LogL: -200041.114 / Time: 0h:20m:35s (0h:1m:31s left)
Optimizing NNI: done in 2.51624 secs using 398.9% CPU
Optimizing NNI: done in 2.06899 secs using 398.5% CPU
Optimizing NNI: done in 4.48693 secs using 596.5% CPU
Optimizing NNI: done in 1.95824 secs using 399.1% CPU
Optimizing NNI: done in 2.42099 secs using 398.8% CPU
Optimizing NNI: done in 4.53765 secs using 597.3% CPU
Optimizing NNI: done in 2.34483 secs using 398.9% CPU
Optimizing NNI: done in 2.38166 secs using 398.3% CPU
Optimizing NNI: done in 4.86696 secs using 598.2% CPU
Optimizing NNI: done in 2.62136 secs using 398.6% CPU
Iteration 10 / LogL: -110611.192 / Time: 0h:1m:32s
Optimizing NNI: done in 2.61398 secs using 398.1% CPU
Optimizing NNI: done in 5.54169 secs using 597% CPU
Optimizing NNI: done in 2.29226 secs using 398.3% CPU
Optimizing NNI: done in 2.59805 secs using 398.4% CPU
Optimizing NNI: done in 2.40216 secs using 398.5% CPU
Optimizing NNI: done in 5.57186 secs using 597.3% CPU
Optimizing NNI: done in 1.91943 secs using 398.4% CPU
Optimizing NNI: done in 2.14525 secs using 398.4% CPU
Optimizing NNI: done in 5.38028 secs using 597.4% CPU
Optimizing NNI: done in 2.36279 secs using 398.6% CPU
Optimizing NNI: done in 2.18466 secs using 398.8% CPU
Optimizing NNI: done in 2.1109 secs using 398.4% CPU
Optimizing NNI: done in 5.08934 secs using 597.2% CPU
Optimizing NNI: done in 1.67083 secs using 398.8% CPU
Iteration 20 / LogL: -110751.581 / Time: 0h:1m:55s
Finish initializing candidate tree set (20)
Current best tree score: -110580.599 / CPU time: 87.803
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.9852 secs using 398.9% CPU
Optimizing NNI: done in 4.6613 secs using 597.7% CPU
Optimizing NNI: done in 2.342 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -110573.888
Optimizing NNI: done in 4.88044 secs using 597.5% CPU
Optimizing NNI: done in 1.91587 secs using 399.1% CPU
Optimizing NNI: done in 2.15965 secs using 399.1% CPU
Optimizing NNI: done in 1.70873 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.87779 secs using 597.4% CPU
Iteration 240 / LogL: -199986.391 / Time: 0h:21m:26s (0h:0m:37s left)
Optimizing NNI: done in 6.00459 secs using 596.9% CPU
Optimizing NNI: done in 4.24947 secs using 597.8% CPU
BETTER TREE FOUND at iteration 25: -110544.391
Optimizing NNI: done in 4.65661 secs using 596.4% CPU
Optimizing NNI: done in 2.51232 secs using 398.6% CPU
Optimizing NNI: done in 1.76995 secs using 399% CPU
Optimizing NNI: done in 4.51971 secs using 597.5% CPU
Optimizing NNI: done in 2.35658 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.14633 secs using 597.3% CPU
BETTER TREE FOUND at iteration 28: -110531.912
Optimizing NNI: done in 1.75146 secs using 398.9% CPU
Optimizing NNI: done in 2.13812 secs using 398.8% CPU
Iteration 30 / LogL: -110582.472 / Time: 0h:2m:36s (0h:8m:48s left)
Optimizing NNI: done in 5.07586 secs using 597.4% CPU
Optimizing NNI: done in 1.76336 secs using 398.4% CPU
Optimizing NNI: done in 1.93564 secs using 398.4% CPU
Optimizing NNI: done in 4.42363 secs using 596.8% CPU
Optimizing NNI: done in 2.23676 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -110527.918
Optimizing NNI: done in 4.59288 secs using 597.6% CPU
TREE SEARCH COMPLETED AFTER 248 ITERATIONS / Time: 0h:22m:4s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -199983.711
Optimizing NNI: done in 2.40061 secs using 398.9% CPU
2. Current log-likelihood: -199983.689
Optimizing NNI: done in 1.94409 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimal log-likelihood: -199983.678
Site proportion and rates:  (0.018,0.087) (0.111,0.266) (0.068,0.356) (0.166,0.524) (0.194,0.731) (0.145,0.984) (0.175,1.537) (0.123,2.478)
Parameters optimization took 2 rounds (2.963 sec)
BEST SCORE FOUND : -199983.678
Total tree length: 162.995

Total number of iterations: 248
CPU time used for tree search: 7616.085 sec (2h:6m:56s)
Wall-clock time used for tree search: 1299.749 sec (0h:21m:39s)
Total CPU time used: 7781.025 sec (2h:9m:41s)
Total wall-clock time used: 1327.432 sec (0h:22m:7s)

===> START BOOTSTRAP REPLICATE NUMBER 48

Creating bootstrap alignment (seed: 70511)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.347 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -193993.272
BETTER TREE FOUND at iteration 35: -110519.615
2. Current log-likelihood: -191490.142
Optimizing NNI: done in 1.86246 secs using 398.5% CPU
Optimizing NNI: done in 2.17654 secs using 398.5% CPU
3. Current log-likelihood: -191461.357
Optimizing NNI: done in 1.75754 secs using 399.4% CPU
4. Current log-likelihood: -191460.611
Optimizing NNI: done in 2.12598 secs using 398.2% CPU
5. Current log-likelihood: -191460.479
Optimizing NNI: done in 2.01485 secs using 398.5% CPU
Iteration 40 / LogL: -110524.369 / Time: 0h:3m:1s (0h:7m:21s left)
6. Current log-likelihood: -191460.321
Optimizing NNI: done in 2.12365 secs using 397.1% CPU
7. Current log-likelihood: -191460.108
Optimizing NNI: done in 1.68468 secs using 398.8% CPU
8. Current log-likelihood: -191459.813
Optimizing NNI: done in 1.57737 secs using 399% CPU
9. Current log-likelihood: -191459.441
Optimizing NNI: done in 2.02897 secs using 398.2% CPU
10. Current log-likelihood: -191458.934
Optimizing NNI: done in 2.11426 secs using 398.9% CPU
11. Current log-likelihood: -191458.165
Optimizing NNI: done in 1.73754 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
12. Current log-likelihood: -191457.075
BETTER TREE FOUND at iteration 46: -110518.575
13. Current log-likelihood: -191455.844
Optimizing NNI: done in 2.07225 secs using 398.5% CPU
14. Current log-likelihood: -191454.754
Optimizing NNI: done in 2.07473 secs using 399% CPU
15. Current log-likelihood: -191453.869
Optimizing NNI: done in 1.83169 secs using 398.4% CPU
16. Current log-likelihood: -191453.177
Optimizing NNI: done in 1.81613 secs using 399.3% CPU
Iteration 50 / LogL: -110547.092 / Time: 0h:3m:22s (0h:6m:37s left)
17. Current log-likelihood: -191452.634
Optimizing NNI: done in 1.82634 secs using 398.9% CPU
18. Current log-likelihood: -191452.211
Optimizing NNI: done in 2.04667 secs using 398.8% CPU
19. Current log-likelihood: -191451.870
Optimizing NNI: done in 1.92753 secs using 398.2% CPU
20. Current log-likelihood: -191451.575
Optimizing NNI: done in 2.05295 secs using 398.9% CPU
21. Current log-likelihood: -191451.324
Optimizing NNI: done in 1.84887 secs using 399.1% CPU
Estimate model parameters (epsilon = 0.100)
22. Current log-likelihood: -191451.085
BETTER TREE FOUND at iteration 55: -110518.001
23. Current log-likelihood: -191450.862
Optimizing NNI: done in 2.0428 secs using 398.9% CPU
24. Current log-likelihood: -191450.670
Optimizing NNI: done in 1.83547 secs using 398.6% CPU
25. Current log-likelihood: -191450.503
Optimizing NNI: done in 1.9488 secs using 398.4% CPU
26. Current log-likelihood: -191450.368
Optimizing NNI: done in 2.18115 secs using 399.1% CPU
27. Current log-likelihood: -191450.255
Optimizing NNI: done in 1.93334 secs using 398.8% CPU
Iteration 60 / LogL: -110537.816 / Time: 0h:3m:44s (0h:6m:1s left)
Optimizing NNI: done in 1.88693 secs using 398.3% CPU
Optimal log-likelihood: -191450.171
Site proportion and rates:  (0.018,0.091) (0.063,0.236) (0.143,0.386) (0.226,0.567) (0.145,0.848) (0.158,1.055) (0.138,1.619) (0.109,2.638)
Parameters optimization took 27 rounds (56.785 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.09438 secs using 398.8% CPU
Optimizing NNI: done in 1.75493 secs using 398.6% CPU
Optimizing NNI: done in 2.42473 secs using 398.6% CPU
Optimizing NNI: done in 1.79252 secs using 398.9% CPU
Calculating distance matrix: done in 9.66517 secs using 599.9% CPU
Computing ML distances took 9.665694 sec (of wall-clock time) 57.979253 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00122404 secs using 540.7% CPU
Constructing RapidNJ tree: done in 0.0222869 secs using 640.2% CPU
Computing RapidNJ tree took 0.023594 sec (of wall-clock time) 0.150957 sec (of CPU time)
Optimizing NNI: done in 1.88751 secs using 398% CPU
Log-likelihood of RapidNJ tree: -194979.300
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.82788 secs using 398.4% CPU
Optimizing NNI: done in 1.7408 secs using 397.9% CPU
Optimizing NNI: done in 2.16562 secs using 399.1% CPU
Optimizing NNI: done in 1.98769 secs using 398.4% CPU
Iteration 70 / LogL: -110537.934 / Time: 0h:4m:4s (0h:5m:1s left)
Optimizing NNI: done in 1.75258 secs using 398.5% CPU
Optimizing NNI: done in 1.82959 secs using 398.9% CPU
Optimizing NNI: done in 1.98975 secs using 398.6% CPU
Optimizing NNI: done in 2.15632 secs using 398.9% CPU
Optimizing NNI: done in 2.05332 secs using 398.7% CPU
Optimizing NNI: done in 1.98297 secs using 398.8% CPU
Optimizing NNI: done in 1.94499 secs using 398.2% CPU
Optimizing NNI: done in 1.79757 secs using 398.4% CPU
Optimizing NNI: done in 2.08309 secs using 398.6% CPU
Optimizing NNI: done in 1.91699 secs using 398.6% CPU
Iteration 80 / LogL: -110535.630 / Time: 0h:4m:24s (0h:4m:10s left)
Optimizing NNI: done in 1.70456 secs using 398.6% CPU
29.113 second
Optimizing NNI: done in 2.0482 secs using 398.7% CPU
Optimizing NNI: done in 1.71405 secs using 398.2% CPU
Optimizing NNI: done in 1.75575 secs using 398.5% CPU
Optimizing NNI: done in 1.90442 secs using 398.8% CPU
Optimizing NNI: done in 1.86077 secs using 398.9% CPU
Optimizing NNI: done in 1.89982 secs using 398.5% CPU
Optimizing NNI: done in 1.97263 secs using 398.4% CPU
Optimizing NNI: done in 1.8159 secs using 398.8% CPU
Optimizing NNI: done in 1.88145 secs using 398% CPU
Iteration 90 / LogL: -110520.018 / Time: 0h:4m:43s (0h:3m:26s left)
Computing log-likelihood of 98 initial trees ... 16.401 seconds
Current best score: -191450.171

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.83773 secs using 398.7% CPU
Optimizing NNI: done in 3.15107 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.75318 secs using 398.7% CPU
Optimizing NNI: done in 1.9155 secs using 398.8% CPU
BETTER TREE FOUND at iteration 1: -190751.759
Optimizing NNI: done in 2.09958 secs using 398.9% CPU
Optimizing NNI: done in 2.06569 secs using 398.9% CPU
Optimizing NNI: done in 4.24535 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.01659 secs using 398.8% CPU
Optimizing NNI: done in 1.89021 secs using 399.1% CPU
BETTER TREE FOUND at iteration 2: -190698.105
Optimizing NNI: done in 1.85857 secs using 398.2% CPU
Optimizing NNI: done in 1.81488 secs using 398.7% CPU
Optimizing NNI: done in 4.03819 secs using 596.2% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.76424 secs using 398.5% CPU
Iteration 100 / LogL: -110827.836 / Time: 0h:5m:2s (0h:2m:47s left)
Optimizing NNI: done in 2.0172 secs using 397% CPU
BETTER TREE FOUND at iteration 3: -190664.961
Optimizing NNI: done in 1.79397 secs using 398.9% CPU
Optimizing NNI: done in 1.80513 secs using 398.8% CPU
Optimizing NNI: done in 3.80994 secs using 597.3% CPU
Optimizing NNI: done in 1.91254 secs using 399.2% CPU
Optimizing NNI: done in 1.66035 secs using 398.8% CPU
Optimizing NNI: done in 4.33523 secs using 597.1% CPU
Optimizing NNI: done in 1.95335 secs using 398.6% CPU
Optimizing NNI: done in 2.12577 secs using 398.3% CPU
Optimizing NNI: done in 1.70312 secs using 398.1% CPU
Optimizing NNI: done in 4.74242 secs using 596.8% CPU
Optimizing NNI: done in 1.92391 secs using 398.3% CPU
Optimizing NNI: done in 1.70841 secs using 398.7% CPU
Iteration 110 / LogL: -110545.216 / Time: 0h:5m:21s (0h:2m:12s left)
Optimizing NNI: done in 4.21756 secs using 597.9% CPU
Optimizing NNI: done in 1.92518 secs using 398.1% CPU
Optimizing NNI: done in 1.67275 secs using 398.8% CPU
Optimizing NNI: done in 4.12562 secs using 597.6% CPU
Optimizing NNI: done in 1.86646 secs using 398.5% CPU
Optimizing NNI: done in 1.95474 secs using 399.2% CPU
Optimizing NNI: done in 4.22216 secs using 596.4% CPU
Optimizing NNI: done in 2.16292 secs using 398.8% CPU
Optimizing NNI: done in 1.64401 secs using 399.1% CPU
Optimizing NNI: done in 4.02924 secs using 598% CPU
Iteration 10 / LogL: -190791.167 / Time: 0h:2m:45s
Optimizing NNI: done in 1.9503 secs using 398.8% CPU
Optimizing NNI: done in 1.76518 secs using 399% CPU
Optimizing NNI: done in 1.6822 secs using 398.8% CPU
Optimizing NNI: done in 3.88483 secs using 597.4% CPU
Optimizing NNI: done in 1.55693 secs using 398.9% CPU
Iteration 120 / LogL: -110542.185 / Time: 0h:5m:39s (0h:1m:39s left)
Optimizing NNI: done in 2.03226 secs using 398.2% CPU
Optimizing NNI: done in 4.667 secs using 596.7% CPU
Optimizing NNI: done in 1.6534 secs using 398.9% CPU
Optimizing NNI: done in 2.26835 secs using 398.9% CPU
Optimizing NNI: done in 1.76905 secs using 398.6% CPU
Optimizing NNI: done in 4.35976 secs using 597.1% CPU
Optimizing NNI: done in 1.63854 secs using 398.5% CPU
Optimizing NNI: done in 1.98375 secs using 398.9% CPU
Optimizing NNI: done in 4.35035 secs using 597.1% CPU
Optimizing NNI: done in 1.88202 secs using 398.9% CPU
Optimizing NNI: done in 2.03568 secs using 398.6% CPU
Optimizing NNI: done in 3.87592 secs using 598.2% CPU
Optimizing NNI: done in 1.85714 secs using 398.7% CPU
Optimizing NNI: done in 1.77136 secs using 398.6% CPU
Iteration 130 / LogL: -110522.279 / Time: 0h:5m:58s (0h:1m:9s left)
Optimizing NNI: done in 3.94424 secs using 597.2% CPU
Optimizing NNI: done in 1.78168 secs using 398.5% CPU
Optimizing NNI: done in 2.29825 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 1.80526 secs using 398.8% CPU
Iteration 140 / LogL: -110523.999 / Time: 0h:6m:18s (0h:0m:40s left)
BETTER TREE FOUND at iteration 20: -190627.652
Iteration 20 / LogL: -190627.652 / Time: 0h:3m:30s
Finish initializing candidate tree set (20)
Current best tree score: -190627.652 / CPU time: 142.261
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -190625.076
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Iteration 150 / LogL: -110522.911 / Time: 0h:6m:39s (0h:0m:13s left)
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Optimizing NNI: done in 1.7697 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 156 ITERATIONS / Time: 0h:6m:50s

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|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -110518.001
Optimal log-likelihood: -110518.001
Proportion of invariable sites: 0.018
Site proportion and rates:  (0.069,0.044) (0.114,0.119) (0.140,0.263) (0.106,0.412) (0.118,0.631) (0.090,0.920) (0.153,1.352) (0.122,1.976) (0.069,4.322)
Parameters optimization took 1 rounds (0.463 sec)
BEST SCORE FOUND : -110518.001
Total tree length: 168.794

Total number of iterations: 156
CPU time used for tree search: 1496.382 sec (0h:24m:56s)
Wall-clock time used for tree search: 383.453 sec (0h:6m:23s)
Total CPU time used: 1607.773 sec (0h:26m:47s)
Total wall-clock time used: 411.370 sec (0h:6m:51s)

===> START BOOTSTRAP REPLICATE NUMBER 92

Creating bootstrap alignment (seed: 68274)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.171 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -107410.000
2. Current log-likelihood: -105639.602
Optimizing NNI: done in 4.96994 secs using 597.2% CPU
3. Current log-likelihood: -105524.901
4. Current log-likelihood: -105518.798
5. Current log-likelihood: -105518.696
Optimizing NNI: done in 4.4408 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
6. Current log-likelihood: -105518.593
7. Current log-likelihood: -105518.432
8. Current log-likelihood: -105518.241
BETTER TREE FOUND at iteration 28: -190609.233
9. Current log-likelihood: -105518.107
Optimal log-likelihood: -105518.000
Proportion of invariable sites: 0.032
Site proportion and rates:  (0.085,0.040) (0.081,0.127) (0.075,0.219) (0.114,0.336) (0.091,0.519) (0.136,0.763) (0.135,1.231) (0.205,1.994) (0.046,4.467)
Parameters optimization took 9 rounds (14.141 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.58303 secs using 597% CPU
Calculating distance matrix: done in 4.58448 secs using 399.9% CPU
Computing ML distances took 4.584766 sec (of wall-clock time) 18.333706 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000787973 secs using 255% CPU
Constructing RapidNJ tree: done in 0.00838709 secs using 341.5% CPU
Computing RapidNJ tree took 0.009228 sec (of wall-clock time) 0.032897 sec (of CPU time)
Log-likelihood of RapidNJ tree: -105943.806
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 4.3674 secs using 597.8% CPU
Iteration 30 / LogL: -190693.124 / Time: 0h:4m:22s (0h:14m:46s left)
Optimizing NNI: done in 6.09321 secs using 597.3% CPU
10.686 second
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -190605.203
Optimizing NNI: done in 5.0249 secs using 596.5% CPU
Computing log-likelihood of 98 initial trees ... 10.276 seconds
Current best score: -105518.000

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -105048.193
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -104972.348
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Iteration 40 / LogL: -190645.901 / Time: 0h:5m:14s (0h:12m:21s left)
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Iteration 10 / LogL: -105306.767 / Time: 0h:1m:27s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 17: -104961.059
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Iteration 20 / LogL: -105037.061 / Time: 0h:1m:52s
Finish initializing candidate tree set (20)
Current best tree score: -104961.059 / CPU time: 92.447
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Iteration 50 / LogL: -191165.960 / Time: 0h:6m:1s (0h:10m:4s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -104950.391
BETTER TREE FOUND at iteration 52: -190602.978
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Iteration 30 / LogL: -105000.039 / Time: 0h:2m:24s (0h:7m:46s left)
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Iteration 60 / LogL: -190638.099 / Time: 0h:6m:54s (0h:10m:59s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 90: -190571.464
Iteration 90 / LogL: -190571.464 / Time: 0h:9m:21s (0h:10m:30s left)
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Iteration 100 / LogL: -190607.124 / Time: 0h:10m:6s (0h:9m:10s left)
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TREE SEARCH COMPLETED AFTER 287 ITERATIONS / Time: 0h:12m:8s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -104941.024
2. Current log-likelihood: -104941.010
3. Current log-likelihood: -104940.998
Optimal log-likelihood: -104940.984
Proportion of invariable sites: 0.031
Site proportion and rates:  (0.080,0.035) (0.087,0.111) (0.111,0.233) (0.130,0.396) (0.120,0.650) (0.091,0.938) (0.116,1.324) (0.188,2.017) (0.044,4.850)
Parameters optimization took 3 rounds (2.036 sec)
BEST SCORE FOUND : -104940.984
Total tree length: 158.011

Total number of iterations: 287
CPU time used for tree search: 2791.624 sec (0h:46m:31s)
Wall-clock time used for tree search: 708.504 sec (0h:11m:48s)
Total CPU time used: 2880.802 sec (0h:48m:0s)
Total wall-clock time used: 730.850 sec (0h:12m:10s)

===> START BOOTSTRAP REPLICATE NUMBER 93

Creating bootstrap alignment (seed: 68275)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.088 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -112456.000
Optimizing NNI: done in 3.77919 secs using 598% CPU
Iteration 180 / LogL: -190583.480 / Time: 0h:16m:13s (0h:5m:31s left)
2. Current log-likelihood: -110359.940
3. Current log-likelihood: -110311.170
4. Current log-likelihood: -110310.487
Optimizing NNI: done in 4.36554 secs using 598.1% CPU
5. Current log-likelihood: -110310.345
6. Current log-likelihood: -110310.226
Optimizing NNI: done in 4.23072 secs using 597.6% CPU
7. Current log-likelihood: -110310.112
Optimal log-likelihood: -110309.978
Proportion of invariable sites: 0.030
Site proportion and rates:  (0.068,0.041) (0.073,0.105) (0.076,0.182) (0.093,0.283) (0.076,0.411) (0.127,0.589) (0.126,0.953) (0.245,1.565) (0.086,3.962)
Parameters optimization took 7 rounds (10.605 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 4.69912 secs using 399.9% CPU
Computing ML distances took 4.699412 sec (of wall-clock time) 18.793314 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000728846 secs using 338.1% CPU
Constructing RapidNJ tree: done in 0.00858903 secs using 380.3% CPU
Computing RapidNJ tree took 0.009388 sec (of wall-clock time) 0.035158 sec (of CPU time)
Log-likelihood of RapidNJ tree: -110531.214
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.83748 secs using 597% CPU
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10.904 second
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Computing log-likelihood of 98 initial trees ... 9.938 seconds
Current best score: -110309.978

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Iteration 10 / LogL: -109746.859 / Time: 0h:1m:10s
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BETTER TREE FOUND at iteration 15: -109716.590
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Iteration 20 / LogL: -109800.096 / Time: 0h:1m:33s
Finish initializing candidate tree set (20)
Current best tree score: -109716.590 / CPU time: 77.311
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Iteration 200 / LogL: -190665.261 / Time: 0h:17m:52s (0h:8m:15s left)
BETTER TREE FOUND at iteration 23: -109712.833
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BETTER TREE FOUND at iteration 25: -109704.661
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BETTER TREE FOUND at iteration 29: -109700.828
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BETTER TREE FOUND at iteration 30: -109696.891
Iteration 30 / LogL: -109696.891 / Time: 0h:2m:9s (0h:7m:25s left)
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Iteration 210 / LogL: -190611.262 / Time: 0h:18m:40s (0h:7m:19s left)
BETTER TREE FOUND at iteration 39: -109696.266
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Iteration 40 / LogL: -109730.879 / Time: 0h:2m:32s (0h:6m:26s left)
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BETTER TREE FOUND at iteration 42: -109690.799
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BETTER TREE FOUND at iteration 50: -109688.845
Iteration 50 / LogL: -109688.845 / Time: 0h:2m:55s (0h:5m:58s left)
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Iteration 220 / LogL: -190816.881 / Time: 0h:19m:26s (0h:6m:23s left)
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BETTER TREE FOUND at iteration 59: -109688.027
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Iteration 60 / LogL: -109703.920 / Time: 0h:3m:19s (0h:5m:33s left)
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BETTER TREE FOUND at iteration 64: -109687.566
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BETTER TREE FOUND at iteration 67: -109685.531
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Iteration 70 / LogL: -109774.457 / Time: 0h:3m:42s (0h:5m:12s left)
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Iteration 230 / LogL: -190587.951 / Time: 0h:20m:12s (0h:5m:28s left)
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Iteration 80 / LogL: -109702.954 / Time: 0h:4m:1s (0h:4m:26s left)
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Iteration 90 / LogL: -109690.820 / Time: 0h:4m:22s (0h:3m:46s left)
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BETTER TREE FOUND at iteration 97: -109684.938
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BETTER TREE FOUND at iteration 239: -190555.123
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Iteration 100 / LogL: -109687.307 / Time: 0h:4m:44s (0h:4m:38s left)
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Iteration 240 / LogL: -190584.286 / Time: 0h:21m:0s (0h:8m:41s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 105: -109684.440
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Iteration 110 / LogL: -109701.715 / Time: 0h:5m:6s (0h:4m:27s left)
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Iteration 120 / LogL: -109751.977 / Time: 0h:5m:26s (0h:3m:53s left)
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Iteration 250 / LogL: -190583.396 / Time: 0h:21m:46s (0h:7m:46s left)
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Iteration 130 / LogL: -109701.701 / Time: 0h:5m:46s (0h:3m:21s left)
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Iteration 140 / LogL: -109686.714 / Time: 0h:6m:6s (0h:2m:51s left)
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Iteration 260 / LogL: -190592.286 / Time: 0h:22m:33s (0h:6m:52s left)
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Iteration 150 / LogL: -109695.521 / Time: 0h:6m:27s (0h:2m:23s left)
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Iteration 160 / LogL: -109738.341 / Time: 0h:6m:47s (0h:1m:55s left)
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Iteration 270 / LogL: -190658.425 / Time: 0h:23m:19s (0h:5m:58s left)
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Iteration 170 / LogL: -109699.717 / Time: 0h:7m:14s (0h:1m:29s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.36785 secs using 596% CPU
BETTER TREE FOUND at iteration 177: -109683.664
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Iteration 180 / LogL: -109713.346 / Time: 0h:7m:44s (0h:4m:11s left)
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Iteration 280 / LogL: -190672.738 / Time: 0h:24m:5s (0h:5m:5s left)
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Iteration 190 / LogL: -109812.719 / Time: 0h:8m:9s (0h:3m:45s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 287: -190554.654
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Iteration 200 / LogL: -109684.809 / Time: 0h:8m:30s (0h:3m:17s left)
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Iteration 290 / LogL: -190632.662 / Time: 0h:24m:55s (0h:8m:21s left)
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Iteration 210 / LogL: -109750.334 / Time: 0h:8m:51s (0h:2m:50s left)
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Iteration 220 / LogL: -109708.915 / Time: 0h:9m:12s (0h:2m:23s left)
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Optimizing NNI: done in 1.88149 secs using 397.8% CPU
Optimizing NNI: done in 4.04292 secs using 596.9% CPU
Iteration 300 / LogL: -190643.187 / Time: 0h:25m:41s (0h:7m:28s left)
Optimizing NNI: done in 1.98846 secs using 398.7% CPU
Optimizing NNI: done in 2.38392 secs using 399% CPU
Optimizing NNI: done in 1.93451 secs using 398.6% CPU
Iteration 230 / LogL: -109689.809 / Time: 0h:9m:33s (0h:1m:57s left)
Optimizing NNI: done in 4.74519 secs using 597% CPU
Optimizing NNI: done in 1.84711 secs using 399.2% CPU
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Optimizing NNI: done in 4.64572 secs using 596.2% CPU
Optimizing NNI: done in 1.93495 secs using 398.8% CPU
Optimizing NNI: done in 1.98258 secs using 399% CPU
Optimizing NNI: done in 2.04889 secs using 398.7% CPU
Iteration 240 / LogL: -109716.735 / Time: 0h:9m:52s (0h:1m:31s left)
Optimizing NNI: done in 4.58751 secs using 595.5% CPU
Optimizing NNI: done in 1.96466 secs using 398.9% CPU
Optimizing NNI: done in 2.10374 secs using 398% CPU
Optimizing NNI: done in 4.51993 secs using 596.8% CPU
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Optimizing NNI: done in 4.88815 secs using 596.7% CPU
Optimizing NNI: done in 1.77266 secs using 398.4% CPU
Iteration 250 / LogL: -109686.620 / Time: 0h:10m:13s (0h:1m:6s left)
Optimizing NNI: done in 1.88937 secs using 399% CPU
Optimizing NNI: done in 4.33203 secs using 596.6% CPU
Iteration 310 / LogL: -190588.849 / Time: 0h:26m:28s (0h:6m:35s left)
Optimizing NNI: done in 2.11279 secs using 398.4% CPU
Optimizing NNI: done in 1.8897 secs using 398.2% CPU
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Optimizing NNI: done in 1.90267 secs using 398.3% CPU
Optimizing NNI: done in 2.09737 secs using 398.5% CPU
Iteration 260 / LogL: -109698.606 / Time: 0h:10m:33s (0h:0m:41s left)
Optimizing NNI: done in 4.29389 secs using 597.9% CPU
Optimizing NNI: done in 1.83042 secs using 398.4% CPU
Optimizing NNI: done in 2.24607 secs using 398% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.97288 secs using 597.2% CPU
BETTER TREE FOUND at iteration 262: -109683.184
Optimizing NNI: done in 1.81432 secs using 398.3% CPU
Optimizing NNI: done in 4.57296 secs using 597.6% CPU
Optimizing NNI: done in 1.74524 secs using 398.7% CPU
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Optimizing NNI: done in 2.05636 secs using 398.5% CPU
Iteration 270 / LogL: -109688.714 / Time: 0h:10m:56s (0h:3m:44s left)
Optimizing NNI: done in 4.63484 secs using 597.2% CPU
Optimizing NNI: done in 2.03003 secs using 397.9% CPU
Optimizing NNI: done in 1.69639 secs using 398% CPU
Optimizing NNI: done in 4.17229 secs using 597.9% CPU
Iteration 320 / LogL: -190598.283 / Time: 0h:27m:14s (0h:5m:43s left)
Optimizing NNI: done in 1.98306 secs using 398.7% CPU
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Optimizing NNI: done in 5.50442 secs using 297.3% CPU
Optimizing NNI: done in 9.09845 secs using 473.8% CPU
Optimizing NNI: done in 3.90413 secs using 351.9% CPU
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Iteration 280 / LogL: -109684.051 / Time: 0h:11m:25s (0h:3m:21s left)
Optimizing NNI: done in 5.76533 secs using 597.3% CPU
Optimizing NNI: done in 2.46052 secs using 397.4% CPU
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Iteration 290 / LogL: -110008.854 / Time: 0h:11m:52s (0h:2m:57s left)
Optimizing NNI: done in 1.90553 secs using 398.5% CPU
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Optimizing NNI: done in 6.08886 secs using 597.8% CPU
Iteration 330 / LogL: -190576.785 / Time: 0h:28m:17s (0h:4m:53s left)
Optimizing NNI: done in 2.20025 secs using 397.1% CPU
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Iteration 300 / LogL: -109783.594 / Time: 0h:12m:12s (0h:2m:31s left)
Optimizing NNI: done in 2.44724 secs using 398.5% CPU
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Iteration 310 / LogL: -109728.292 / Time: 0h:12m:33s (0h:2m:6s left)
Optimizing NNI: done in 6.00525 secs using 597.3% CPU
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Iteration 320 / LogL: -109693.542 / Time: 0h:12m:54s (0h:1m:41s left)
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Iteration 340 / LogL: -190641.710 / Time: 0h:29m:16s (0h:4m:3s left)
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Iteration 330 / LogL: -109687.489 / Time: 0h:13m:14s (0h:1m:17s left)
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Iteration 340 / LogL: -109687.272 / Time: 0h:13m:34s (0h:0m:52s left)
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Iteration 350 / LogL: -190576.216 / Time: 0h:30m:1s (0h:3m:10s left)
Optimizing NNI: done in 2.04475 secs using 398.1% CPU
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Iteration 350 / LogL: -109684.391 / Time: 0h:13m:54s (0h:0m:28s left)
Optimizing NNI: done in 2.21979 secs using 398.4% CPU
Optimizing NNI: done in 4.27237 secs using 597.3% CPU
Optimizing NNI: done in 1.64833 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 352: -109682.870
Optimizing NNI: done in 4.13823 secs using 597.4% CPU
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Iteration 360 / LogL: -109685.455 / Time: 0h:14m:16s (0h:3m:39s left)
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Iteration 360 / LogL: -190619.246 / Time: 0h:30m:46s (0h:2m:18s left)
Optimizing NNI: done in 1.78234 secs using 398.6% CPU
Optimizing NNI: done in 1.91442 secs using 397.6% CPU
Iteration 370 / LogL: -109701.633 / Time: 0h:14m:36s (0h:3m:14s left)
Optimizing NNI: done in 2.11623 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.81953 secs using 398.8% CPU
BETTER TREE FOUND at iteration 363: -190553.518
Optimizing NNI: done in 1.88085 secs using 398.7% CPU
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Iteration 380 / LogL: -109954.997 / Time: 0h:14m:57s (0h:2m:50s left)
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Iteration 390 / LogL: -109690.042 / Time: 0h:15m:17s (0h:2m:26s left)
Optimizing NNI: done in 4.99392 secs using 598% CPU
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Iteration 370 / LogL: -190600.064 / Time: 0h:31m:35s (0h:7m:57s left)
Optimizing NNI: done in 1.88381 secs using 398.8% CPU
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Iteration 400 / LogL: -109692.229 / Time: 0h:15m:38s (0h:2m:2s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.34806 secs using 398% CPU
BETTER TREE FOUND at iteration 376: -190553.139
Optimizing NNI: done in 2.36913 secs using 397.8% CPU
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Iteration 410 / LogL: -109691.866 / Time: 0h:15m:59s (0h:1m:38s left)
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Iteration 380 / LogL: -190614.160 / Time: 0h:32m:23s (0h:8m:12s left)
Optimizing NNI: done in 2.03862 secs using 398.3% CPU
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Iteration 420 / LogL: -109702.489 / Time: 0h:16m:20s (0h:1m:14s left)
Optimizing NNI: done in 1.77991 secs using 398.8% CPU
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Iteration 430 / LogL: -109685.647 / Time: 0h:16m:40s (0h:0m:51s left)
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Iteration 390 / LogL: -190612.213 / Time: 0h:33m:7s (0h:7m:19s left)
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Iteration 440 / LogL: -109682.938 / Time: 0h:17m:1s (0h:0m:27s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 444: -109682.271
Optimizing NNI: done in 4.39678 secs using 596.6% CPU
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Iteration 450 / LogL: -109704.560 / Time: 0h:17m:24s (0h:3m:38s left)
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Iteration 400 / LogL: -190562.100 / Time: 0h:33m:53s (0h:6m:27s left)
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Iteration 460 / LogL: -109686.002 / Time: 0h:17m:45s (0h:3m:14s left)
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Iteration 470 / LogL: -109686.238 / Time: 0h:18m:23s (0h:2m:54s left)
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Iteration 480 / LogL: -109691.628 / Time: 0h:19m:27s (0h:2m:35s left)
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Iteration 490 / LogL: -109688.087 / Time: 0h:20m:31s (0h:2m:15s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 7.08711 secs using 286.8% CPU
BETTER TREE FOUND at iteration 417: -190547.507
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Iteration 500 / LogL: -109696.784 / Time: 0h:21m:37s (0h:1m:54s left)
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Iteration 420 / LogL: -190563.449 / Time: 0h:38m:9s (0h:8m:49s left)
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Iteration 510 / LogL: -109731.640 / Time: 0h:22m:38s (0h:1m:30s left)
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Iteration 520 / LogL: -109859.890 / Time: 0h:23m:34s (0h:1m:5s left)
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Iteration 530 / LogL: -109687.528 / Time: 0h:24m:25s (0h:0m:38s left)
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Iteration 430 / LogL: -190570.645 / Time: 0h:40m:39s (0h:8m:14s left)
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Iteration 540 / LogL: -109793.622 / Time: 0h:25m:20s (0h:0m:11s left)
Optimizing NNI: done in 4.14054 secs using 291% CPU
Optimizing NNI: done in 4.24727 secs using 288% CPU
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Optimizing NNI: done in 6.3335 secs using 290.3% CPU
TREE SEARCH COMPLETED AFTER 545 ITERATIONS / Time: 0h:25m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -109682.271
Optimal log-likelihood: -109682.270
Proportion of invariable sites: 0.029
Site proportion and rates:  (0.068,0.041) (0.068,0.092) (0.083,0.178) (0.091,0.280) (0.077,0.409) (0.120,0.574) (0.126,0.930) (0.252,1.554) (0.086,3.955)
Parameters optimization took 1 rounds (0.768 sec)
BEST SCORE FOUND : -109682.270
Total tree length: 184.296

Total number of iterations: 545
CPU time used for tree search: 5537.342 sec (1h:32m:17s)
Wall-clock time used for tree search: 1530.738 sec (0h:25m:30s)
Total CPU time used: 5604.907 sec (1h:33m:24s)
Total wall-clock time used: 1547.875 sec (0h:25m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 94

Creating bootstrap alignment (seed: 68276)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.183 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -107879.734
2. Current log-likelihood: -105672.116
3. Current log-likelihood: -105624.735
Optimizing NNI: done in 15.5482 secs using 431.5% CPU
4. Current log-likelihood: -105623.378
5. Current log-likelihood: -105623.053
6. Current log-likelihood: -105622.781
7. Current log-likelihood: -105622.628
Optimizing NNI: done in 14.7589 secs using 429.5% CPU
8. Current log-likelihood: -105622.398
9. Current log-likelihood: -105622.276
10. Current log-likelihood: -105622.157
11. Current log-likelihood: -105622.048
Optimizing NNI: done in 13.7999 secs using 427.5% CPU
Optimal log-likelihood: -105621.889
Proportion of invariable sites: 0.019
Site proportion and rates:  (0.091,0.035) (0.110,0.109) (0.088,0.187) (0.102,0.305) (0.050,0.438) (0.075,0.658) (0.146,0.994) (0.244,1.725) (0.075,4.003)
Parameters optimization took 11 rounds (43.091 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 9.04254 secs using 296.7% CPU
Computing ML distances took 9.043482 sec (of wall-clock time) 26.829703 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000921011 secs using 71.88% CPU
Constructing RapidNJ tree: done in 0.0336821 secs using 321.6% CPU
Computing RapidNJ tree took 0.034691 sec (of wall-clock time) 0.110069 sec (of CPU time)
Optimizing NNI: done in 12.2535 secs using 424.9% CPU
Log-likelihood of RapidNJ tree: -106143.960
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 12.4956 secs using 438.3% CPU
Iteration 440 / LogL: -190658.855 / Time: 0h:43m:6s (0h:7m:33s left)
18.675 second
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Optimizing NNI: done in 12.7835 secs using 428.8% CPU
Computing log-likelihood of 98 initial trees ... 28.978 seconds
Current best score: -105621.889

Do NNI search on 20 best initial trees
Optimizing NNI: done in 12.7998 secs using 428% CPU
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Estimate model parameters (epsilon = 0.100)
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Optimizing NNI: done in 12.8374 secs using 430.1% CPU
BETTER TREE FOUND at iteration 1: -105198.382
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Iteration 450 / LogL: -190632.042 / Time: 0h:45m:16s (0h:6m:45s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -105195.880
BETTER TREE FOUND at iteration 452: -190546.464
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Iteration 10 / LogL: -105252.285 / Time: 0h:3m:51s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 12: -105194.330
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 12.562 secs using 429.7% CPU
BETTER TREE FOUND at iteration 20: -105155.461
Iteration 20 / LogL: -105155.461 / Time: 0h:5m:20s
Finish initializing candidate tree set (20)
Current best tree score: -105155.461 / CPU time: 265.685
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 460 / LogL: -190617.653 / Time: 0h:47m:30s (0h:9m:31s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 13.6532 secs using 427.4% CPU
BETTER TREE FOUND at iteration 25: -105151.937
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -105112.664
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Iteration 30 / LogL: -105147.759 / Time: 0h:6m:29s (0h:21m:54s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 33: -105110.548
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 34: -105089.116
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Iteration 470 / LogL: -190648.950 / Time: 0h:48m:52s (0h:8m:32s left)
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Iteration 40 / LogL: -105106.026 / Time: 0h:7m:1s (0h:16m:54s left)
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Iteration 50 / LogL: -105093.621 / Time: 0h:7m:24s (0h:12m:41s left)
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Iteration 480 / LogL: -190586.891 / Time: 0h:49m:39s (0h:7m:27s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 60: -105087.611
Iteration 60 / LogL: -105087.611 / Time: 0h:7m:48s (0h:13m:13s left)
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BETTER TREE FOUND at iteration 69: -105087.231
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 70: -105078.831
Iteration 70 / LogL: -105078.831 / Time: 0h:8m:16s (0h:11m:59s left)
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Iteration 490 / LogL: -190554.727 / Time: 0h:50m:24s (0h:6m:23s left)
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Iteration 90 / LogL: -105163.311 / Time: 0h:9m:2s (0h:8m:7s left)
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Iteration 500 / LogL: -190557.171 / Time: 0h:51m:10s (0h:5m:19s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 97: -105076.991
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Iteration 110 / LogL: -105113.156 / Time: 0h:9m:50s (0h:7m:51s left)
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Iteration 510 / LogL: -190708.540 / Time: 0h:51m:57s (0h:4m:17s left)
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Iteration 120 / LogL: -105081.173 / Time: 0h:10m:12s (0h:6m:35s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 127: -105072.218
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Iteration 520 / LogL: -190587.485 / Time: 0h:52m:42s (0h:3m:14s left)
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Iteration 140 / LogL: -105124.197 / Time: 0h:10m:57s (0h:6m:51s left)
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Iteration 150 / LogL: -105121.671 / Time: 0h:11m:19s (0h:5m:51s left)
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Iteration 530 / LogL: -190597.255 / Time: 0h:53m:26s (0h:2m:13s left)
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Iteration 160 / LogL: -105180.012 / Time: 0h:11m:40s (0h:4m:55s left)
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Iteration 170 / LogL: -105076.475 / Time: 0h:12m:1s (0h:4m:3s left)
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Iteration 540 / LogL: -190760.705 / Time: 0h:54m:12s (0h:1m:12s left)
Optimizing NNI: done in 2.45384 secs using 398.6% CPU
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Iteration 180 / LogL: -105076.341 / Time: 0h:12m:24s (0h:3m:15s left)
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Iteration 190 / LogL: -105130.904 / Time: 0h:12m:46s (0h:2m:30s left)
Optimizing NNI: done in 2.01068 secs using 398.6% CPU
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Optimizing NNI: done in 2.163 secs using 398.6% CPU
Optimizing NNI: done in 4.70842 secs using 597.3% CPU
Iteration 550 / LogL: -190608.514 / Time: 0h:54m:58s (0h:0m:12s left)
Optimizing NNI: done in 2.07894 secs using 398.8% CPU
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Optimizing NNI: done in 2.36981 secs using 398.8% CPU
Iteration 200 / LogL: -105086.192 / Time: 0h:13m:8s (0h:1m:46s left)
Optimizing NNI: done in 2.09921 secs using 398% CPU
Optimizing NNI: done in 4.79744 secs using 596.7% CPU
TREE SEARCH COMPLETED AFTER 553 ITERATIONS / Time: 0h:55m:12s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -190546.464
Optimal log-likelihood: -190546.462
Site proportion and rates:  (0.019,0.094) (0.064,0.242) (0.157,0.394) (0.223,0.580) (0.146,0.861) (0.150,1.076) (0.137,1.637) (0.104,2.698)
Parameters optimization took 1 rounds (0.979 sec)
BEST SCORE FOUND : -190546.462
Total tree length: 151.504

Total number of iterations: 553
CPU time used for tree search: 17777.269 sec (4h:56m:17s)
Wall-clock time used for tree search: 3243.794 sec (0h:54m:3s)
Total CPU time used: 18190.856 sec (5h:3m:10s)
Total wall-clock time used: 3313.185 sec (0h:55m:13s)

===> START BOOTSTRAP REPLICATE NUMBER 49

Creating bootstrap alignment (seed: 70512)...

Optimizing NNI: done in 2.00125 secs using 398.8% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.293 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -197493.620
Optimizing NNI: done in 2.17799 secs using 398.3% CPU
2. Current log-likelihood: -194990.655
Optimizing NNI: done in 2.264 secs using 398.6% CPU
3. Current log-likelihood: -194956.020
Optimizing NNI: done in 1.94426 secs using 398.5% CPU
4. Current log-likelihood: -194955.151
Optimizing NNI: done in 1.78483 secs using 398.5% CPU
Optimal log-likelihood: -194955.094
Site proportion and rates:  (0.014,0.108) (0.003,0.228) (0.049,0.245) (0.182,0.399) (0.221,0.617) (0.257,0.948) (0.161,1.561) (0.113,2.491)
Parameters optimization took 4 rounds (9.047 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 2.1756 secs using 398.4% CPU
Optimizing NNI: done in 2.29361 secs using 398.8% CPU
Optimizing NNI: done in 1.88476 secs using 398.7% CPU
Optimizing NNI: done in 2.16629 secs using 398% CPU
Iteration 210 / LogL: -105105.311 / Time: 0h:13m:29s (0h:1m:5s left)
Calculating distance matrix: done in 9.68411 secs using 599.8% CPU
Computing ML distances took 9.684664 sec (of wall-clock time) 58.085959 sec (of CPU time)
Optimizing NNI: done in 1.92338 secs using 398.1% CPU
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00128698 secs using 592.9% CPU
Constructing RapidNJ tree: done in 0.0223582 secs using 664.6% CPU
Computing RapidNJ tree took 0.023715 sec (of wall-clock time) 0.158169 sec (of CPU time)
Optimizing NNI: done in 1.9465 secs using 398.9% CPU
Log-likelihood of RapidNJ tree: -200734.564
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.92687 secs using 398.6% CPU
Optimizing NNI: done in 2.22586 secs using 398.5% CPU
Optimizing NNI: done in 2.05154 secs using 398.8% CPU
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Optimizing NNI: done in 1.87149 secs using 398.8% CPU
Optimizing NNI: done in 1.86302 secs using 398.2% CPU
Iteration 220 / LogL: -105090.897 / Time: 0h:13m:50s (0h:0m:26s left)
Optimizing NNI: done in 2.03372 secs using 398% CPU
Optimizing NNI: done in 2.81578 secs using 398.4% CPU
Optimizing NNI: done in 3.32511 secs using 398.3% CPU
Optimizing NNI: done in 3.06583 secs using 398.2% CPU
Optimizing NNI: done in 2.93143 secs using 398.6% CPU
30.142 second
Optimizing NNI: done in 2.71144 secs using 398% CPU
Optimizing NNI: done in 2.45197 secs using 398.3% CPU
Optimizing NNI: done in 2.09085 secs using 398.3% CPU
TREE SEARCH COMPLETED AFTER 228 ITERATIONS / Time: 0h:14m:12s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -105072.218
2. Current log-likelihood: -105072.207
Optimal log-likelihood: -105072.192
Proportion of invariable sites: 0.018
Site proportion and rates:  (0.085,0.034) (0.109,0.099) (0.108,0.189) (0.133,0.337) (0.071,0.616) (0.132,0.924) (0.192,1.492) (0.095,2.204) (0.057,4.596)
Parameters optimization took 2 rounds (1.326 sec)
BEST SCORE FOUND : -105072.192
Total tree length: 174.864

Total number of iterations: 228
CPU time used for tree search: 2766.700 sec (0h:46m:6s)
Wall-clock time used for tree search: 797.134 sec (0h:13m:17s)
Total CPU time used: 2930.803 sec (0h:48m:50s)
Total wall-clock time used: 853.435 sec (0h:14m:13s)

===> START BOOTSTRAP REPLICATE NUMBER 95

Creating bootstrap alignment (seed: 68277)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.133 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105350.469
2. Current log-likelihood: -103455.822
3. Current log-likelihood: -103322.085
4. Current log-likelihood: -103314.279
5. Current log-likelihood: -103314.146
Computing log-likelihood of 98 initial trees ... 16.021 seconds
Current best score: -194955.094

Do NNI search on 20 best initial trees
Optimal log-likelihood: -103314.042
Proportion of invariable sites: 0.022
Site proportion and rates:  (0.115,0.038) (0.080,0.124) (0.075,0.227) (0.073,0.324) (0.080,0.467) (0.121,0.681) (0.153,1.183) (0.233,1.889) (0.048,4.275)
Parameters optimization took 5 rounds (7.576 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 3.50036 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
Calculating distance matrix: done in 4.60109 secs using 399.9% CPU
Computing ML distances took 4.601583 sec (of wall-clock time) 18.400123 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000802994 secs using 398.1% CPU
Constructing RapidNJ tree: done in 0.00875711 secs using 364.1% CPU
Computing RapidNJ tree took 0.009622 sec (of wall-clock time) 0.036681 sec (of CPU time)
Log-likelihood of RapidNJ tree: -103514.286
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... BETTER TREE FOUND at iteration 1: -194362.575
Optimizing NNI: done in 3.48338 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -194305.765
10.600 second
Optimizing NNI: done in 3.96625 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -194264.082
Optimizing NNI: done in 3.53454 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -194253.405
Computing log-likelihood of 98 initial trees ... 11.947 seconds
Current best score: -103314.042

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.04402 secs using 399% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.70926 secs using 596.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -194239.297
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BETTER TREE FOUND at iteration 1: -102809.599
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Optimizing NNI: done in 3.56238 secs using 597.8% CPU
Iteration 10 / LogL: -194271.342 / Time: 0h:2m:0s
BETTER TREE FOUND at iteration 2: -102807.472
Optimizing NNI: done in 1.71298 secs using 398.5% CPU
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BETTER TREE FOUND at iteration 6: -102738.300
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BETTER TREE FOUND at iteration 15: -194205.913
BETTER TREE FOUND at iteration 9: -102699.477
Optimizing NNI: done in 4.05939 secs using 597.1% CPU
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Iteration 10 / LogL: -102929.341 / Time: 0h:1m:26s
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.83696 secs using 597.1% CPU
BETTER TREE FOUND at iteration 11: -102697.275
Optimizing NNI: done in 2.2776 secs using 399% CPU
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Optimizing NNI: done in 3.67568 secs using 597.3% CPU
Iteration 20 / LogL: -194246.570 / Time: 0h:2m:41s
Finish initializing candidate tree set (20)
Current best tree score: -194205.913 / CPU time: 139.885
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 2.31428 secs using 398.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -194203.841
Optimizing NNI: done in 2.33838 secs using 399% CPU
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Optimizing NNI: done in 2.39427 secs using 398.3% CPU
Iteration 20 / LogL: -102741.080 / Time: 0h:1m:53s
Finish initializing candidate tree set (20)
Current best tree score: -102697.275 / CPU time: 99.988
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 2.25259 secs using 398.6% CPU
BETTER TREE FOUND at iteration 24: -194194.127
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BETTER TREE FOUND at iteration 25: -194184.690
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BETTER TREE FOUND at iteration 28: -102694.056
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Optimizing NNI: done in 4.44653 secs using 598% CPU
BETTER TREE FOUND at iteration 30: -102684.604
Iteration 30 / LogL: -102684.604 / Time: 0h:2m:18s (0h:7m:56s left)
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Iteration 30 / LogL: -194213.611 / Time: 0h:3m:31s (0h:11m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -102678.768
Iteration 40 / LogL: -102678.768 / Time: 0h:2m:39s (0h:6m:48s left)
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Optimizing NNI: done in 1.82824 secs using 399.1% CPU
BETTER TREE FOUND at iteration 33: -194181.923
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Iteration 50 / LogL: -102687.771 / Time: 0h:2m:58s (0h:5m:27s left)
Optimizing NNI: done in 4.53486 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -194177.718
BETTER TREE FOUND at iteration 51: -102677.180
Optimizing NNI: done in 1.84856 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 39: -194158.522
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Iteration 60 / LogL: -102696.871 / Time: 0h:3m:21s (0h:5m:10s left)
Optimizing NNI: done in 4.95939 secs using 598% CPU
Iteration 40 / LogL: -194171.977 / Time: 0h:4m:22s (0h:11m:5s left)
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Iteration 70 / LogL: -102687.785 / Time: 0h:3m:41s (0h:4m:20s left)
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Iteration 80 / LogL: -102688.170 / Time: 0h:4m:1s (0h:3m:37s left)
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Iteration 50 / LogL: -194238.630 / Time: 0h:5m:9s (0h:9m:22s left)
Optimizing NNI: done in 2.02535 secs using 398.7% CPU
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Optimizing NNI: done in 1.87414 secs using 399.4% CPU
Iteration 90 / LogL: -102688.735 / Time: 0h:4m:21s (0h:2m:59s left)
Optimizing NNI: done in 4.73287 secs using 597.9% CPU
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Optimizing NNI: done in 4.36993 secs using 598.1% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.87257 secs using 398.6% CPU
BETTER TREE FOUND at iteration 55: -194153.197
Optimizing NNI: done in 1.74979 secs using 399.3% CPU
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Optimizing NNI: done in 2.29625 secs using 398.8% CPU
Iteration 100 / LogL: -102768.962 / Time: 0h:4m:41s (0h:2m:24s left)
Optimizing NNI: done in 4.04202 secs using 597.7% CPU
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Optimizing NNI: done in 1.72299 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 106: -102676.791
Optimizing NNI: done in 4.60652 secs using 596.9% CPU
Iteration 60 / LogL: -194307.339 / Time: 0h:5m:57s (0h:9m:34s left)
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Iteration 110 / LogL: -102820.239 / Time: 0h:5m:3s (0h:4m:27s left)
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Iteration 120 / LogL: -102693.964 / Time: 0h:5m:23s (0h:3m:53s left)
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Iteration 70 / LogL: -194211.828 / Time: 0h:6m:41s (0h:8m:13s left)
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Iteration 130 / LogL: -102691.368 / Time: 0h:5m:43s (0h:3m:22s left)
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Iteration 140 / LogL: -102692.373 / Time: 0h:6m:3s (0h:2m:52s left)
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Iteration 150 / LogL: -102708.628 / Time: 0h:6m:23s (0h:2m:24s left)
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Iteration 80 / LogL: -194189.826 / Time: 0h:7m:28s (0h:7m:5s left)
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Iteration 160 / LogL: -102691.481 / Time: 0h:6m:42s (0h:1m:56s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.45701 secs using 597.5% CPU
BETTER TREE FOUND at iteration 168: -102673.899
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Iteration 170 / LogL: -102677.577 / Time: 0h:7m:3s (0h:4m:5s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.52241 secs using 596.5% CPU
Iteration 90 / LogL: -194159.380 / Time: 0h:8m:14s (0h:6m:1s left)
BETTER TREE FOUND at iteration 175: -102673.385
Optimizing NNI: done in 1.70457 secs using 398.5% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.80762 secs using 398.7% CPU
Iteration 180 / LogL: -102688.388 / Time: 0h:7m:24s (0h:3m:56s left)
BETTER TREE FOUND at iteration 92: -194148.034
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Iteration 190 / LogL: -102685.932 / Time: 0h:7m:44s (0h:3m:28s left)
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Iteration 100 / LogL: -194200.623 / Time: 0h:9m:2s (0h:8m:23s left)
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Iteration 130 / LogL: -194195.189 / Time: 0h:11m:17s (0h:5m:25s left)
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Iteration 270 / LogL: -102693.936 / Time: 0h:10m:19s (0h:0m:11s left)
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TREE SEARCH COMPLETED AFTER 276 ITERATIONS / Time: 0h:10m:31s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102673.385
2. Current log-likelihood: -102673.370
3. Current log-likelihood: -102673.355
4. Current log-likelihood: -102673.339
5. Current log-likelihood: -102673.324
6. Current log-likelihood: -102673.309
Optimizing NNI: done in 4.46518 secs using 597.8% CPU
7. Current log-likelihood: -102673.295
8. Current log-likelihood: -102673.281
9. Current log-likelihood: -102673.268
10. Current log-likelihood: -102673.255
11. Current log-likelihood: -102673.243
12. Current log-likelihood: -102673.231
13. Current log-likelihood: -102673.220
Optimizing NNI: done in 4.40557 secs using 597.7% CPU
14. Current log-likelihood: -102673.209
15. Current log-likelihood: -102673.198
16. Current log-likelihood: -102673.188
17. Current log-likelihood: -102673.177
Optimal log-likelihood: -102673.162
Proportion of invariable sites: 0.021
Site proportion and rates:  (0.107,0.032) (0.084,0.111) (0.083,0.223) (0.066,0.308) (0.084,0.460) (0.119,0.661) (0.154,1.174) (0.236,1.883) (0.047,4.440)
Parameters optimization took 17 rounds (11.436 sec)
BEST SCORE FOUND : -102673.162
Total tree length: 157.191

Total number of iterations: 276
CPU time used for tree search: 2432.258 sec (0h:40m:32s)
Wall-clock time used for tree search: 617.955 sec (0h:10m:17s)
Total CPU time used: 2530.596 sec (0h:42m:10s)
Total wall-clock time used: 642.614 sec (0h:10m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 96

Creating bootstrap alignment (seed: 68278)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.089 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -111361.437
Optimizing NNI: done in 4.05902 secs using 595.7% CPU
2. Current log-likelihood: -109303.508
3. Current log-likelihood: -109220.601
Optimizing NNI: done in 4.62944 secs using 597.4% CPU
4. Current log-likelihood: -109214.376
5. Current log-likelihood: -109214.274
Optimal log-likelihood: -109214.224
Proportion of invariable sites: 0.032
Site proportion and rates:  (0.086,0.043) (0.069,0.122) (0.081,0.208) (0.075,0.301) (0.088,0.422) (0.146,0.705) (0.164,1.186) (0.169,1.809) (0.091,3.398)
Parameters optimization took 5 rounds (7.600 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.11979 secs using 597.2% CPU
Calculating distance matrix: done in 4.6515 secs using 399.9% CPU
Computing ML distances took 4.651784 sec (of wall-clock time) 18.601364 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000742912 secs using 122.4% CPU
Constructing RapidNJ tree: done in 0.00847721 secs using 407.4% CPU
Computing RapidNJ tree took 0.009280 sec (of wall-clock time) 0.035748 sec (of CPU time)
Log-likelihood of RapidNJ tree: -109566.053
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.0216 secs using 597.3% CPU
Optimizing NNI: done in 3.74095 secs using 598.6% CPU
Iteration 140 / LogL: -194233.314 / Time: 0h:12m:0s (0h:4m:29s left)
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10.878 second
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Computing log-likelihood of 98 initial trees ... 10.021 seconds
Current best score: -109214.224

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 146: -194145.997
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Iteration 150 / LogL: -194172.944 / Time: 0h:12m:47s (0h:8m:14s left)
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BETTER TREE FOUND at iteration 1: -108711.562
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -108643.801
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 10: -108642.355
Iteration 10 / LogL: -108642.355 / Time: 0h:1m:37s
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Iteration 160 / LogL: -194295.215 / Time: 0h:13m:33s (0h:7m:19s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 162: -194141.821
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Iteration 20 / LogL: -108801.932 / Time: 0h:2m:0s
Finish initializing candidate tree set (20)
Current best tree score: -108642.355 / CPU time: 106.995
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -108581.210
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -108570.203
Iteration 30 / LogL: -108570.203 / Time: 0h:2m:45s (0h:9m:29s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 180 / LogL: -194152.828 / Time: 0h:15m:9s (0h:8m:2s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 76: -108533.860
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Iteration 80 / LogL: -108539.210 / Time: 0h:4m:42s (0h:5m:43s left)
Optimizing NNI: done in 2.35235 secs using 398.6% CPU
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Iteration 200 / LogL: -194164.507 / Time: 0h:16m:42s (0h:6m:17s left)
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Iteration 90 / LogL: -108563.669 / Time: 0h:5m:4s (0h:4m:54s left)
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Optimizing NNI: done in 2.37888 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 98: -108531.965
Optimizing NNI: done in 4.29385 secs using 597.7% CPU
Optimizing NNI: done in 2.17909 secs using 399% CPU
Optimizing NNI: done in 1.92135 secs using 398.5% CPU
Iteration 100 / LogL: -108623.409 / Time: 0h:5m:28s (0h:5m:25s left)
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Iteration 210 / LogL: -194169.276 / Time: 0h:17m:28s (0h:5m:26s left)
Optimizing NNI: done in 1.901 secs using 398.4% CPU
Optimizing NNI: done in 1.9541 secs using 398.8% CPU
Iteration 110 / LogL: -108576.922 / Time: 0h:5m:49s (0h:4m:41s left)
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Iteration 120 / LogL: -108565.887 / Time: 0h:6m:9s (0h:4m:2s left)
Optimizing NNI: done in 2.37846 secs using 399% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.33679 secs using 597.3% CPU
BETTER TREE FOUND at iteration 125: -108528.563
Optimizing NNI: done in 1.95209 secs using 398.8% CPU
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Optimizing NNI: done in 5.15531 secs using 596.5% CPU
Iteration 220 / LogL: -194153.857 / Time: 0h:18m:15s (0h:4m:34s left)
BETTER TREE FOUND at iteration 128: -108527.952
Optimizing NNI: done in 2.07273 secs using 398.6% CPU
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Iteration 130 / LogL: -108550.645 / Time: 0h:6m:36s (0h:5m:1s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.83379 secs using 399.3% CPU
BETTER TREE FOUND at iteration 222: -194128.578
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Iteration 140 / LogL: -108543.323 / Time: 0h:6m:57s (0h:4m:24s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.93884 secs using 597.3% CPU
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BETTER TREE FOUND at iteration 142: -108521.884
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Iteration 230 / LogL: -194361.936 / Time: 0h:19m:2s (0h:7m:38s left)
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Iteration 150 / LogL: -108536.923 / Time: 0h:7m:31s (0h:4m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 234: -194126.618
Optimizing NNI: done in 2.71751 secs using 398.6% CPU
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Iteration 160 / LogL: -108555.434 / Time: 0h:7m:52s (0h:4m:3s left)
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Iteration 240 / LogL: -194172.570 / Time: 0h:19m:48s (0h:7m:47s left)
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Iteration 170 / LogL: -108550.461 / Time: 0h:8m:14s (0h:3m:30s left)
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Iteration 180 / LogL: -108559.862 / Time: 0h:8m:34s (0h:2m:58s left)
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Iteration 250 / LogL: -194147.925 / Time: 0h:20m:33s (0h:6m:56s left)
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Iteration 190 / LogL: -108525.527 / Time: 0h:8m:55s (0h:2m:27s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 2.33011 secs using 398.9% CPU
BETTER TREE FOUND at iteration 252: -194124.970
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Iteration 200 / LogL: -108536.866 / Time: 0h:9m:16s (0h:1m:57s left)
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Iteration 260 / LogL: -194193.546 / Time: 0h:21m:19s (0h:7m:34s left)
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Iteration 210 / LogL: -108532.236 / Time: 0h:9m:36s (0h:1m:28s left)
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Iteration 220 / LogL: -108529.245 / Time: 0h:9m:57s (0h:0m:59s left)
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Iteration 230 / LogL: -108582.250 / Time: 0h:10m:17s (0h:0m:32s left)
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Iteration 270 / LogL: -194286.018 / Time: 0h:22m:4s (0h:6m:43s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 232: -108521.531
Optimizing NNI: done in 3.92875 secs using 597% CPU
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Iteration 240 / LogL: -108536.968 / Time: 0h:10m:40s (0h:4m:6s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 246: -108520.469
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Iteration 250 / LogL: -108522.080 / Time: 0h:11m:3s (0h:4m:15s left)
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Iteration 280 / LogL: -194176.471 / Time: 0h:22m:47s (0h:5m:52s left)
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Iteration 260 / LogL: -108583.692 / Time: 0h:11m:23s (0h:3m:46s left)
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Iteration 270 / LogL: -108653.215 / Time: 0h:11m:42s (0h:3m:18s left)
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Iteration 290 / LogL: -194137.878 / Time: 0h:23m:32s (0h:5m:3s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 315: -108519.012
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Iteration 320 / LogL: -108542.560 / Time: 0h:13m:26s (0h:4m:0s left)
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Iteration 350 / LogL: -194248.522 / Time: 0h:27m:58s (0h:4m:58s left)
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Iteration 410 / LogL: -108531.339 / Time: 0h:16m:29s (0h:0m:12s left)
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TREE SEARCH COMPLETED AFTER 416 ITERATIONS / Time: 0h:16m:41s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -108519.012
Optimizing NNI: done in 4.57729 secs using 597.3% CPU
Optimal log-likelihood: -108519.002
Proportion of invariable sites: 0.031
Site proportion and rates:  (0.071,0.035) (0.072,0.095) (0.116,0.202) (0.119,0.355) (0.084,0.557) (0.102,0.783) (0.151,1.186) (0.167,1.794) (0.089,3.614)
Parameters optimization took 1 rounds (0.780 sec)
BEST SCORE FOUND : -108519.002
Total tree length: 179.832

Total number of iterations: 416
CPU time used for tree search: 3905.849 sec (1h:5m:5s)
Wall-clock time used for tree search: 988.116 sec (0h:16m:28s)
Total CPU time used: 3962.701 sec (1h:6m:2s)
Total wall-clock time used: 1002.344 sec (0h:16m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 97

Creating bootstrap alignment (seed: 68279)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.130 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 103 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -106080.570
2. Current log-likelihood: -104491.488
3. Current log-likelihood: -104447.589
Optimizing NNI: done in 4.09321 secs using 597.7% CPU
4. Current log-likelihood: -104422.164
5. Current log-likelihood: -104388.065
6. Current log-likelihood: -104386.378
Optimizing NNI: done in 4.55883 secs using 596.8% CPU
7. Current log-likelihood: -104386.259
Optimal log-likelihood: -104386.106
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.085,0.045) (0.073,0.133) (0.103,0.237) (0.104,0.369) (0.116,0.539) (0.172,0.862) (0.111,1.398) (0.170,2.191) (0.041,4.521)
Parameters optimization took 7 rounds (10.344 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 4.59811 secs using 399.9% CPU
Computing ML distances took 4.598438 sec (of wall-clock time) 18.387415 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.00074482 secs using 415.4% CPU
Constructing RapidNJ tree: done in 0.00866795 secs using 480.2% CPU
Computing RapidNJ tree took 0.009472 sec (of wall-clock time) 0.046875 sec (of CPU time)
Log-likelihood of RapidNJ tree: -104758.806
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.4031 secs using 597.7% CPU
Iteration 360 / LogL: -194220.443 / Time: 0h:28m:43s (0h:4m:9s left)
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10.237 second
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Optimizing NNI: done in 4.2616 secs using 597.7% CPU
Computing log-likelihood of 98 initial trees ... 9.535 seconds
Current best score: -104386.106

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -103905.296
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -103854.047
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -103835.734
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Estimate model parameters (epsilon = 0.100)
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Iteration 370 / LogL: -194140.415 / Time: 0h:29m:32s (0h:3m:21s left)
BETTER TREE FOUND at iteration 9: -103822.023
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Iteration 10 / LogL: -103913.708 / Time: 0h:1m:11s
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Iteration 20 / LogL: -103961.418 / Time: 0h:1m:35s
Finish initializing candidate tree set (20)
Current best tree score: -103822.023 / CPU time: 79.063
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -103819.435
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Iteration 380 / LogL: -194155.528 / Time: 0h:30m:16s (0h:2m:33s left)
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Iteration 30 / LogL: -103840.834 / Time: 0h:1m:57s (0h:6m:12s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -103815.127
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Iteration 40 / LogL: -103827.873 / Time: 0h:2m:18s (0h:5m:26s left)
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Iteration 390 / LogL: -194151.688 / Time: 0h:31m:0s (0h:1m:45s left)
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Iteration 50 / LogL: -103831.278 / Time: 0h:2m:38s (0h:4m:25s left)
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Iteration 60 / LogL: -103848.486 / Time: 0h:2m:59s (0h:3m:38s left)
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Iteration 80 / LogL: -103815.476 / Time: 0h:3m:39s (0h:2m:24s left)
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Iteration 90 / LogL: -104012.333 / Time: 0h:3m:58s (0h:1m:52s left)
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Iteration 410 / LogL: -194197.877 / Time: 0h:32m:30s (0h:0m:9s left)
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Optimizing NNI: done in 2.11222 secs using 398.6% CPU
Optimizing NNI: done in 4.93926 secs using 597.5% CPU
TREE SEARCH COMPLETED AFTER 413 ITERATIONS / Time: 0h:32m:43s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -194119.574
Optimizing NNI: done in 1.81104 secs using 399.2% CPU
Iteration 100 / LogL: -103840.657 / Time: 0h:4m:18s (0h:1m:23s left)
Optimal log-likelihood: -194119.574
Site proportion and rates:  (0.015,0.112) (0.005,0.235) (0.039,0.242) (0.178,0.387) (0.230,0.604) (0.260,0.946) (0.158,1.559) (0.116,2.487)
Parameters optimization took 1 rounds (0.516 sec)
BEST SCORE FOUND : -194119.574
Total tree length: 150.530

Total number of iterations: 413
CPU time used for tree search: 11446.386 sec (3h:10m:46s)
Wall-clock time used for tree search: 1941.207 sec (0h:32m:21s)
Total CPU time used: 11581.203 sec (3h:13m:1s)
Total wall-clock time used: 1963.851 sec (0h:32m:43s)

===> START BOOTSTRAP REPLICATE NUMBER 50

Creating bootstrap alignment (seed: 70513)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.262 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -197637.157
Optimizing NNI: done in 2.20343 secs using 398.4% CPU
2. Current log-likelihood: -195141.550
Optimizing NNI: done in 2.00572 secs using 398.7% CPU
3. Current log-likelihood: -195084.327
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4. Current log-likelihood: -195080.189
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5. Current log-likelihood: -195078.663
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6. Current log-likelihood: -195077.879
Optimizing NNI: done in 1.915 secs using 397.3% CPU
7. Current log-likelihood: -195077.383
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8. Current log-likelihood: -195076.975
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9. Current log-likelihood: -195076.596
Optimizing NNI: done in 1.85547 secs using 398.6% CPU
Optimizing NNI: done in 1.81359 secs using 398.9% CPU
Iteration 110 / LogL: -103820.813 / Time: 0h:4m:38s (0h:0m:56s left)
10. Current log-likelihood: -195076.229
Optimizing NNI: done in 1.79821 secs using 398.7% CPU
11. Current log-likelihood: -195075.898
Optimizing NNI: done in 1.73093 secs using 398.8% CPU
Estimate model parameters (epsilon = 0.100)
12. Current log-likelihood: -195075.642
BETTER TREE FOUND at iteration 112: -103814.651
13. Current log-likelihood: -195075.472
Optimizing NNI: done in 1.99971 secs using 398.9% CPU
Optimal log-likelihood: -195075.380
Site proportion and rates:  (0.015,0.133) (0.062,0.274) (0.099,0.406) (0.196,0.576) (0.173,0.786) (0.222,1.057) (0.151,1.639) (0.082,2.549)
Parameters optimization took 13 rounds (27.768 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.93846 secs using 398.8% CPU
Optimizing NNI: done in 1.85196 secs using 398.7% CPU
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Optimizing NNI: done in 1.97062 secs using 398.8% CPU
Calculating distance matrix: done in 10.0844 secs using 599.9% CPU
Computing ML distances took 10.084899 sec (of wall-clock time) 60.495977 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00117087 secs using 636.8% CPU
Constructing RapidNJ tree: done in 0.022243 secs using 677.9% CPU
Computing RapidNJ tree took 0.023483 sec (of wall-clock time) 0.160683 sec (of CPU time)
Optimizing NNI: done in 2.09694 secs using 398.9% CPU
Optimizing NNI: done in 2.27143 secs using 398.6% CPU
Iteration 120 / LogL: -103971.950 / Time: 0h:4m:59s (0h:3m:51s left)
Optimizing NNI: done in 2.1909 secs using 398.3% CPU
Log-likelihood of RapidNJ tree: -197952.547
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 1.92937 secs using 399.4% CPU
Optimizing NNI: done in 1.83334 secs using 398.5% CPU
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Iteration 130 / LogL: -103815.282 / Time: 0h:5m:17s (0h:3m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 135: -103813.717
Optimizing NNI: done in 1.86452 secs using 399.2% CPU
30.051 second
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Iteration 140 / LogL: -103814.852 / Time: 0h:5m:38s (0h:3m:51s left)
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Optimizing NNI: done in 1.93528 secs using 398.3% CPU
Computing log-likelihood of 98 initial trees ... 16.262 seconds
Current best score: -195075.380

Do NNI search on 20 best initial trees
Optimizing NNI: done in 1.72522 secs using 399.1% CPU
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Estimate model parameters (epsilon = 0.100)
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Iteration 150 / LogL: -103814.074 / Time: 0h:5m:58s (0h:3m:24s left)
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BETTER TREE FOUND at iteration 1: -194391.880
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 2: -194260.920
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Estimate model parameters (epsilon = 0.100)
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Iteration 160 / LogL: -103822.651 / Time: 0h:6m:17s (0h:2m:58s left)
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BETTER TREE FOUND at iteration 3: -194231.775
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 6: -194226.307
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Iteration 170 / LogL: -103829.032 / Time: 0h:6m:38s (0h:2m:33s left)
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Iteration 180 / LogL: -103880.425 / Time: 0h:6m:57s (0h:2m:8s left)
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Iteration 10 / LogL: -194278.040 / Time: 0h:2m:42s
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 11: -194223.121
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Iteration 190 / LogL: -103860.088 / Time: 0h:7m:16s (0h:1m:43s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 12: -194215.472
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Iteration 200 / LogL: -103832.672 / Time: 0h:7m:36s (0h:1m:20s left)
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Iteration 210 / LogL: -103816.813 / Time: 0h:7m:55s (0h:0m:56s left)
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Iteration 20 / LogL: -194345.573 / Time: 0h:3m:51s
Finish initializing candidate tree set (20)
Current best tree score: -194215.472 / CPU time: 187.695
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 2.04666 secs using 398.3% CPU
Optimizing NNI: done in 1.76136 secs using 398.7% CPU
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Iteration 220 / LogL: -103815.131 / Time: 0h:8m:15s (0h:0m:33s left)
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.8586 secs using 398.6% CPU
BETTER TREE FOUND at iteration 22: -194186.469
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Iteration 230 / LogL: -103814.140 / Time: 0h:8m:35s (0h:0m:11s left)
Optimizing NNI: done in 6.05597 secs using 597.9% CPU
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Optimizing NNI: done in 2.11901 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 236 ITERATIONS / Time: 0h:8m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -103813.717
2. Current log-likelihood: -103813.693
Optimizing NNI: done in 5.33065 secs using 597.7% CPU
3. Current log-likelihood: -103813.664
4. Current log-likelihood: -103813.647
5. Current log-likelihood: -103813.629
6. Current log-likelihood: -103813.613
7. Current log-likelihood: -103813.598
8. Current log-likelihood: -103813.584
9. Current log-likelihood: -103813.570
10. Current log-likelihood: -103813.557
11. Current log-likelihood: -103813.544
Optimizing NNI: done in 6.41314 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
12. Current log-likelihood: -103813.531
13. Current log-likelihood: -103813.519
14. Current log-likelihood: -103813.506
15. Current log-likelihood: -103813.495
BETTER TREE FOUND at iteration 27: -194170.110
16. Current log-likelihood: -103813.483
Optimal log-likelihood: -103813.470
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.084,0.041) (0.068,0.123) (0.101,0.228) (0.117,0.363) (0.118,0.551) (0.161,0.870) (0.104,1.368) (0.179,2.163) (0.042,4.465)
Parameters optimization took 16 rounds (11.875 sec)
BEST SCORE FOUND : -103813.470
Total tree length: 139.874

Total number of iterations: 236
CPU time used for tree search: 2007.802 sec (0h:33m:27s)
Wall-clock time used for tree search: 511.187 sec (0h:8m:31s)
Total CPU time used: 2119.477 sec (0h:35m:19s)
Total wall-clock time used: 539.192 sec (0h:8m:59s)

===> START BOOTSTRAP REPLICATE NUMBER 98

Creating bootstrap alignment (seed: 68280)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.116 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 106 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -104849.642
2. Current log-likelihood: -102832.191
3. Current log-likelihood: -102692.145
Optimizing NNI: done in 5.98787 secs using 597.6% CPU
4. Current log-likelihood: -102684.245
5. Current log-likelihood: -102682.661
6. Current log-likelihood: -102681.356
7. Current log-likelihood: -102680.223
Optimizing NNI: done in 5.85386 secs using 597.4% CPU
8. Current log-likelihood: -102679.253
9. Current log-likelihood: -102678.565
10. Current log-likelihood: -102677.966
Optimizing NNI: done in 5.62652 secs using 597.6% CPU
Iteration 30 / LogL: -194356.008 / Time: 0h:4m:57s (0h:16m:33s left)
11. Current log-likelihood: -102677.472
12. Current log-likelihood: -102677.062
13. Current log-likelihood: -102676.712
14. Current log-likelihood: -102676.392
15. Current log-likelihood: -102676.105
Optimizing NNI: done in 5.96268 secs using 597.4% CPU
16. Current log-likelihood: -102675.843
17. Current log-likelihood: -102675.602
18. Current log-likelihood: -102675.459
19. Current log-likelihood: -102675.322
20. Current log-likelihood: -102675.189
Optimizing NNI: done in 6.12444 secs using 597.6% CPU
21. Current log-likelihood: -102675.065
22. Current log-likelihood: -102674.948
23. Current log-likelihood: -102674.837
24. Current log-likelihood: -102674.735
Optimal log-likelihood: -102674.585
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.093,0.035) (0.072,0.112) (0.111,0.201) (0.110,0.295) (0.090,0.459) (0.111,0.708) (0.133,1.186) (0.184,1.936) (0.071,4.246)
Parameters optimization took 24 rounds (34.014 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 6.56081 secs using 597.5% CPU
Calculating distance matrix: done in 4.67908 secs using 399.9% CPU
Computing ML distances took 4.679439 sec (of wall-clock time) 18.712939 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000699997 secs using 219.7% CPU
Constructing RapidNJ tree: done in 0.00864196 secs using 401.1% CPU
Computing RapidNJ tree took 0.009397 sec (of wall-clock time) 0.036336 sec (of CPU time)
Log-likelihood of RapidNJ tree: -103006.994
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 6.29474 secs using 597.7% CPU
Optimizing NNI: done in 6.08508 secs using 597.5% CPU
10.816 second
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Optimizing NNI: done in 4.10031 secs using 597% CPU
Optimizing NNI: done in 4.47257 secs using 597.8% CPU
Computing log-likelihood of 98 initial trees ... 10.479 seconds
Current best score: -102674.585

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -102233.938
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Iteration 40 / LogL: -194192.676 / Time: 0h:5m:50s (0h:13m:1s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -102109.492
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -102081.282
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BETTER TREE FOUND at iteration 18: -102075.303
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Iteration 50 / LogL: -194199.846 / Time: 0h:6m:35s (0h:10m:20s left)
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Iteration 20 / LogL: -102082.279 / Time: 0h:1m:54s
Finish initializing candidate tree set (20)
Current best tree score: -102075.303 / CPU time: 74.259
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 93: -102032.560
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Iteration 120 / LogL: -194207.239 / Time: 0h:12m:6s (0h:0m:42s left)
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Iteration 180 / LogL: -102052.691 / Time: 0h:7m:28s (0h:2m:7s left)
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Iteration 190 / LogL: -102042.211 / Time: 0h:7m:49s (0h:1m:41s left)
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BETTER TREE FOUND at iteration 125: -194167.479
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Iteration 200 / LogL: -102045.393 / Time: 0h:8m:9s (0h:1m:16s left)
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Iteration 130 / LogL: -194208.822 / Time: 0h:12m:57s (0h:9m:32s left)
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Iteration 210 / LogL: -102038.373 / Time: 0h:8m:29s (0h:0m:51s left)
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Iteration 220 / LogL: -102043.578 / Time: 0h:8m:49s (0h:0m:26s left)
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BETTER TREE FOUND at iteration 138: -194167.116
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Iteration 140 / LogL: -194224.909 / Time: 0h:13m:44s (0h:9m:41s left)
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BETTER TREE FOUND at iteration 232: -102030.808
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BETTER TREE FOUND at iteration 143: -194163.304
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BETTER TREE FOUND at iteration 238: -102019.997
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BETTER TREE FOUND at iteration 148: -194163.029
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BETTER TREE FOUND at iteration 249: -102015.888
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BETTER TREE FOUND at iteration 254: -102014.908
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BETTER TREE FOUND at iteration 269: -102010.692
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Iteration 280 / LogL: -102019.826 / Time: 0h:10m:59s (0h:3m:30s left)
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Iteration 290 / LogL: -102019.010 / Time: 0h:11m:19s (0h:3m:5s left)
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Iteration 170 / LogL: -194370.453 / Time: 0h:16m:8s (0h:7m:27s left)
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Iteration 300 / LogL: -102033.725 / Time: 0h:11m:40s (0h:2m:41s left)
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Iteration 310 / LogL: -102013.256 / Time: 0h:12m:0s (0h:2m:17s left)
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Iteration 180 / LogL: -194184.593 / Time: 0h:16m:55s (0h:6m:25s left)
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Iteration 320 / LogL: -102032.119 / Time: 0h:12m:20s (0h:1m:53s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 324: -102010.187
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BETTER TREE FOUND at iteration 328: -102008.305
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Iteration 330 / LogL: -102017.724 / Time: 0h:12m:45s (0h:3m:47s left)
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BETTER TREE FOUND at iteration 189: -194154.335
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Iteration 190 / LogL: -194156.283 / Time: 0h:17m:43s (0h:9m:16s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 348: -102007.705
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Iteration 360 / LogL: -102020.611 / Time: 0h:13m:45s (0h:3m:22s left)
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Iteration 200 / LogL: -194277.254 / Time: 0h:18m:29s (0h:8m:16s left)
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Iteration 370 / LogL: -102017.049 / Time: 0h:14m:5s (0h:2m:58s left)
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Optimizing NNI: done in 2.01562 secs using 398.5% CPU
Iteration 380 / LogL: -102011.675 / Time: 0h:14m:25s (0h:2m:35s left)
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Optimizing NNI: done in 4.82131 secs using 597% CPU
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Optimizing NNI: done in 4.45899 secs using 597.1% CPU
Iteration 210 / LogL: -194249.575 / Time: 0h:19m:15s (0h:7m:16s left)
Optimizing NNI: done in 1.95257 secs using 398.9% CPU
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Iteration 390 / LogL: -102012.340 / Time: 0h:14m:45s (0h:2m:12s left)
Optimizing NNI: done in 1.91668 secs using 398.8% CPU
Optimizing NNI: done in 1.71764 secs using 398.5% CPU
Optimizing NNI: done in 4.99775 secs using 596.8% CPU
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Optimizing NNI: done in 1.9558 secs using 398.8% CPU
Optimizing NNI: done in 4.69719 secs using 597.1% CPU
Optimizing NNI: done in 1.93465 secs using 399% CPU
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Iteration 400 / LogL: -102073.196 / Time: 0h:15m:5s (0h:1m:48s left)
Optimizing NNI: done in 2.07446 secs using 399% CPU
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Iteration 220 / LogL: -194186.314 / Time: 0h:20m:2s (0h:6m:18s left)
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Iteration 410 / LogL: -102015.979 / Time: 0h:15m:25s (0h:1m:25s left)
Optimizing NNI: done in 1.82063 secs using 398.6% CPU
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Iteration 420 / LogL: -102008.376 / Time: 0h:15m:44s (0h:1m:3s left)
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Optimizing NNI: done in 1.69005 secs using 399% CPU
Optimizing NNI: done in 4.24471 secs using 598% CPU
Optimizing NNI: done in 1.8847 secs using 398.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 429: -102006.808
Optimizing NNI: done in 4.43422 secs using 596.7% CPU
Iteration 230 / LogL: -194167.598 / Time: 0h:20m:46s (0h:5m:20s left)
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Iteration 430 / LogL: -102024.911 / Time: 0h:16m:5s (0h:3m:42s left)
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Iteration 440 / LogL: -102124.987 / Time: 0h:16m:24s (0h:3m:19s left)
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Iteration 450 / LogL: -102039.613 / Time: 0h:16m:44s (0h:2m:56s left)
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Iteration 240 / LogL: -194250.828 / Time: 0h:21m:30s (0h:4m:24s left)
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Iteration 460 / LogL: -102033.442 / Time: 0h:17m:3s (0h:2m:33s left)
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Optimizing NNI: done in 1.84778 secs using 398.9% CPU
Iteration 470 / LogL: -102038.221 / Time: 0h:17m:23s (0h:2m:11s left)
Optimizing NNI: done in 1.629 secs using 398.3% CPU
Optimizing NNI: done in 4.69257 secs using 598.1% CPU
Optimizing NNI: done in 1.79246 secs using 398.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 472: -102005.579
Optimizing NNI: done in 1.65709 secs using 398.6% CPU
Optimizing NNI: done in 5.12138 secs using 597.5% CPU
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Iteration 250 / LogL: -194191.160 / Time: 0h:22m:16s (0h:3m:29s left)
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Iteration 480 / LogL: -102049.387 / Time: 0h:17m:42s (0h:3m:24s left)
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Iteration 490 / LogL: -102037.263 / Time: 0h:18m:1s (0h:3m:1s left)
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Iteration 260 / LogL: -194174.514 / Time: 0h:23m:0s (0h:2m:34s left)
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Iteration 500 / LogL: -102032.480 / Time: 0h:18m:21s (0h:2m:38s left)
Optimizing NNI: done in 4.08507 secs using 597.3% CPU
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Optimizing NNI: done in 1.89128 secs using 397% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 506: -102005.339
Optimizing NNI: done in 2.08435 secs using 398.6% CPU
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Iteration 510 / LogL: -102048.694 / Time: 0h:18m:42s (0h:3m:31s left)
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Iteration 520 / LogL: -102014.830 / Time: 0h:19m:2s (0h:3m:9s left)
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Iteration 270 / LogL: -194163.575 / Time: 0h:23m:44s (0h:1m:40s left)
Optimizing NNI: done in 1.84583 secs using 398.7% CPU
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Iteration 530 / LogL: -102013.291 / Time: 0h:19m:22s (0h:2m:46s left)
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Iteration 540 / LogL: -102009.760 / Time: 0h:19m:41s (0h:2m:24s left)
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Iteration 280 / LogL: -194274.751 / Time: 0h:24m:30s (0h:0m:47s left)
Optimizing NNI: done in 2.03819 secs using 399% CPU
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Iteration 550 / LogL: -102278.450 / Time: 0h:20m:1s (0h:2m:2s left)
Optimizing NNI: done in 4.53756 secs using 597.7% CPU
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Iteration 560 / LogL: -102043.764 / Time: 0h:20m:20s (0h:1m:40s left)
Optimizing NNI: done in 1.89362 secs using 398.9% CPU
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Optimizing NNI: done in 4.60687 secs using 596.5% CPU
Iteration 290 / LogL: -194184.373 / Time: 0h:25m:13s (0h:0m:-6s left)
TREE SEARCH COMPLETED AFTER 290 ITERATIONS / Time: 0h:25m:13s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -194154.335
Optimal log-likelihood: -194154.330
Site proportion and rates:  (0.023,0.157) (0.090,0.315) (0.095,0.448) (0.193,0.605) (0.163,0.800) (0.203,1.073) (0.147,1.634) (0.086,2.556)
Parameters optimization took 1 rounds (1.143 sec)
BEST SCORE FOUND : -194154.330
Total tree length: 146.976

Total number of iterations: 290
CPU time used for tree search: 8628.635 sec (2h:23m:48s)
Wall-clock time used for tree search: 1469.677 sec (0h:24m:29s)
Total CPU time used: 8897.326 sec (2h:28m:17s)
Total wall-clock time used: 1514.707 sec (0h:25m:14s)

===> START BOOTSTRAP REPLICATE NUMBER 51

Creating bootstrap alignment (seed: 70514)...

Optimizing NNI: done in 1.95241 secs using 398.4% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.314 seconds

NOTE: 230 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196278.210
Optimizing NNI: done in 1.83092 secs using 398.9% CPU
2. Current log-likelihood: -193642.053
Optimizing NNI: done in 1.89039 secs using 398.3% CPU
3. Current log-likelihood: -193619.817
Optimizing NNI: done in 2.029 secs using 398.8% CPU
Iteration 570 / LogL: -102043.036 / Time: 0h:20m:39s (0h:1m:18s left)
4. Current log-likelihood: -193617.972
Optimizing NNI: done in 1.74161 secs using 398.4% CPU
Optimizing NNI: done in 1.82022 secs using 399.4% CPU
5. Current log-likelihood: -193616.785
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6. Current log-likelihood: -193615.380
Optimizing NNI: done in 1.84827 secs using 398.7% CPU
7. Current log-likelihood: -193613.631
Optimizing NNI: done in 2.22781 secs using 398.4% CPU
8. Current log-likelihood: -193611.563
Optimizing NNI: done in 1.85135 secs using 398.9% CPU
9. Current log-likelihood: -193609.707
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10. Current log-likelihood: -193608.199
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11. Current log-likelihood: -193607.311
Optimizing NNI: done in 1.75367 secs using 398.9% CPU
12. Current log-likelihood: -193606.930
Optimizing NNI: done in 2.07881 secs using 398.4% CPU
Iteration 580 / LogL: -102062.965 / Time: 0h:20m:58s (0h:0m:56s left)
13. Current log-likelihood: -193606.823
Optimizing NNI: done in 2.23106 secs using 398.7% CPU
Optimal log-likelihood: -193606.802
Site proportion and rates:  (0.011,0.102) (0.050,0.221) (0.098,0.355) (0.300,0.569) (0.159,0.816) (0.134,1.066) (0.153,1.655) (0.094,2.709)
Parameters optimization took 13 rounds (28.004 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 1.96713 secs using 398.1% CPU
Optimizing NNI: done in 2.1798 secs using 398.5% CPU
Optimizing NNI: done in 1.76255 secs using 398.6% CPU
Optimizing NNI: done in 1.87462 secs using 398.7% CPU
Optimizing NNI: done in 2.31474 secs using 398.6% CPU
Calculating distance matrix: done in 9.80368 secs using 599.8% CPU
Computing ML distances took 9.804233 sec (of wall-clock time) 58.811194 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00126791 secs using 453.7% CPU
Constructing RapidNJ tree: done in 0.0224872 secs using 695.5% CPU
Computing RapidNJ tree took 0.023821 sec (of wall-clock time) 0.162968 sec (of CPU time)
Optimizing NNI: done in 1.83757 secs using 399.1% CPU
Optimizing NNI: done in 1.94828 secs using 398.3% CPU
Log-likelihood of RapidNJ tree: -198980.968
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.52537 secs using 397.9% CPU
Optimizing NNI: done in 3.1219 secs using 398.2% CPU
Iteration 590 / LogL: -102066.609 / Time: 0h:21m:20s (0h:0m:34s left)
Optimizing NNI: done in 3.06938 secs using 398% CPU
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29.832 second
Optimizing NNI: done in 2.80783 secs using 398% CPU
Optimizing NNI: done in 3.15075 secs using 398% CPU
Iteration 600 / LogL: -102046.810 / Time: 0h:21m:50s (0h:0m:13s left)
Optimizing NNI: done in 2.74891 secs using 397.8% CPU
Optimizing NNI: done in 2.79705 secs using 398.5% CPU
Optimizing NNI: done in 2.57969 secs using 397.6% CPU
Computing log-likelihood of 98 initial trees ... 15.936 seconds
Current best score: -193606.802

Do NNI search on 20 best initial trees
Optimizing NNI: done in 2.72477 secs using 398% CPU
Optimizing NNI: done in 2.73983 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 3.07186 secs using 397.8% CPU
Optimizing NNI: done in 2.3951 secs using 398.7% CPU
BETTER TREE FOUND at iteration 1: -193076.570
Optimizing NNI: done in 2.84166 secs using 398% CPU
TREE SEARCH COMPLETED AFTER 607 ITERATIONS / Time: 0h:22m:9s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -102005.339
2. Current log-likelihood: -102005.317
Optimizing NNI: done in 4.48324 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
3. Current log-likelihood: -102005.290
4. Current log-likelihood: -102005.276
5. Current log-likelihood: -102005.263
6. Current log-likelihood: -102005.251
7. Current log-likelihood: -102005.239
8. Current log-likelihood: -102005.229
BETTER TREE FOUND at iteration 2: -193039.457
9. Current log-likelihood: -102005.219
10. Current log-likelihood: -102005.208
11. Current log-likelihood: -102005.198
Optimal log-likelihood: -102005.185
Proportion of invariable sites: 0.025
Site proportion and rates:  (0.087,0.033) (0.060,0.095) (0.124,0.184) (0.116,0.298) (0.089,0.461) (0.106,0.691) (0.140,1.175) (0.176,1.915) (0.076,4.172)
Parameters optimization took 11 rounds (9.334 sec)
BEST SCORE FOUND : -102005.185
Total tree length: 166.373

Total number of iterations: 607
CPU time used for tree search: 5109.538 sec (1h:25m:9s)
Wall-clock time used for tree search: 1290.094 sec (0h:21m:30s)
Total CPU time used: 5305.327 sec (1h:28m:25s)
Total wall-clock time used: 1339.261 sec (0h:22m:19s)

===> START BOOTSTRAP REPLICATE NUMBER 99

Creating bootstrap alignment (seed: 68281)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.116 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 109 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -109424.597
Optimizing NNI: done in 4.24275 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
2. Current log-likelihood: -107438.925
BETTER TREE FOUND at iteration 3: -193026.376
3. Current log-likelihood: -107375.663
4. Current log-likelihood: -107369.304
5. Current log-likelihood: -107364.519
Optimizing NNI: done in 4.73931 secs using 597.7% CPU
6. Current log-likelihood: -107363.510
7. Current log-likelihood: -107363.174
8. Current log-likelihood: -107362.871
Optimizing NNI: done in 4.53938 secs using 596.8% CPU
9. Current log-likelihood: -107362.444
10. Current log-likelihood: -107361.674
Optimizing NNI: done in 4.03396 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
11. Current log-likelihood: -107360.945
12. Current log-likelihood: -107360.717
BETTER TREE FOUND at iteration 6: -193015.983
Optimal log-likelihood: -107360.562
Proportion of invariable sites: 0.024
Site proportion and rates:  (0.099,0.038) (0.080,0.125) (0.117,0.226) (0.132,0.399) (0.069,0.586) (0.101,0.876) (0.170,1.303) (0.134,1.861) (0.074,4.137)
Parameters optimization took 12 rounds (20.337 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.26369 secs using 596.7% CPU
Calculating distance matrix: done in 4.75833 secs using 399.8% CPU
Computing ML distances took 4.758940 sec (of wall-clock time) 19.025002 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000741005 secs using 349.9% CPU
Constructing RapidNJ tree: done in 0.00843692 secs using 326.9% CPU
Computing RapidNJ tree took 0.009239 sec (of wall-clock time) 0.030196 sec (of CPU time)
Log-likelihood of RapidNJ tree: -107669.765
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 4.26527 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 8: -192984.420
Optimizing NNI: done in 4.26234 secs using 597% CPU
10.841 second
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Iteration 10 / LogL: -193066.549 / Time: 0h:2m:25s
Optimizing NNI: done in 4.28478 secs using 596.8% CPU
Computing log-likelihood of 98 initial trees ... 10.350 seconds
Current best score: -107360.562

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -106989.842
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 3: -106969.331
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 5: -106933.379
Optimizing NNI: done in 4.69309 secs using 597.1% CPU
Iteration 20 / LogL: -193051.923 / Time: 0h:3m:9s
Finish initializing candidate tree set (20)
Current best tree score: -192984.420 / CPU time: 147.406
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Optimizing NNI: done in 1.97848 secs using 399.2% CPU
Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 6: -106921.907
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 1.96367 secs using 398.5% CPU
Iteration 10 / LogL: -106962.555 / Time: 0h:1m:39s
BETTER TREE FOUND at iteration 23: -192971.566
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Iteration 20 / LogL: -106970.766 / Time: 0h:1m:59s
Finish initializing candidate tree set (20)
Current best tree score: -106921.907 / CPU time: 92.913
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 1.97349 secs using 398.4% CPU
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Estimate model parameters (epsilon = 0.100)
Optimizing NNI: done in 4.59255 secs using 597.1% CPU
Iteration 30 / LogL: -193033.760 / Time: 0h:3m:57s (0h:12m:40s left)
BETTER TREE FOUND at iteration 26: -106919.550
Optimizing NNI: done in 4.93844 secs using 596.7% CPU
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Iteration 30 / LogL: -106926.235 / Time: 0h:2m:23s (0h:7m:56s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -192970.841
BETTER TREE FOUND at iteration 32: -106913.595
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Iteration 40 / LogL: -106925.628 / Time: 0h:2m:46s (0h:6m:32s left)
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Iteration 40 / LogL: -192982.969 / Time: 0h:4m:46s (0h:11m:22s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -192947.569
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Iteration 60 / LogL: -106938.404 / Time: 0h:3m:39s (0h:5m:42s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 50 / LogL: -192972.575 / Time: 0h:5m:38s (0h:11m:23s left)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 75: -106899.668
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 83: -106897.206
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 90: -106895.924
Iteration 90 / LogL: -106895.924 / Time: 0h:4m:50s (0h:5m:25s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 116: -106894.218
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 78: -192916.876
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TREE SEARCH COMPLETED AFTER 217 ITERATIONS / Time: 0h:9m:18s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -106894.218
Optimal log-likelihood: -106894.206
Proportion of invariable sites: 0.024
Site proportion and rates:  (0.099,0.035) (0.072,0.116) (0.115,0.212) (0.114,0.374) (0.097,0.547) (0.134,0.915) (0.218,1.475) (0.065,2.239) (0.065,4.321)
Parameters optimization took 1 rounds (0.790 sec)
BEST SCORE FOUND : -106894.206
Total tree length: 165.441

Total number of iterations: 217
CPU time used for tree search: 2088.429 sec (0h:34m:48s)
Wall-clock time used for tree search: 532.124 sec (0h:8m:52s)
Total CPU time used: 2197.011 sec (0h:36m:37s)
Total wall-clock time used: 559.370 sec (0h:9m:19s)

===> START BOOTSTRAP REPLICATE NUMBER 100

Creating bootstrap alignment (seed: 68282)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.101 seconds
WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 107 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -108799.509
Optimizing NNI: done in 4.5233 secs using 598% CPU
2. Current log-likelihood: -106527.405
3. Current log-likelihood: -106450.765
Optimizing NNI: done in 4.18428 secs using 597.3% CPU
4. Current log-likelihood: -106450.456
Optimal log-likelihood: -106450.447
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.102,0.037) (0.076,0.115) (0.085,0.196) (0.107,0.316) (0.058,0.427) (0.131,0.630) (0.166,1.051) (0.166,1.797) (0.081,4.414)
Parameters optimization took 4 rounds (5.526 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Computing ML distances took 4.857912 sec (of wall-clock time) 19.426589 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000715971 secs using 381.6% CPU
Constructing RapidNJ tree: done in 0.00852418 secs using 335.4% CPU
Computing RapidNJ tree took 0.009298 sec (of wall-clock time) 0.033247 sec (of CPU time)
Log-likelihood of RapidNJ tree: -106634.320
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 4.13156 secs using 597.2% CPU
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10.466 second
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Computing log-likelihood of 98 initial trees ... 10.103 seconds
Current best score: -106450.447

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 133: -192912.613
BETTER TREE FOUND at iteration 1: -105729.821
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BETTER TREE FOUND at iteration 6: -105710.023
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Iteration 20 / LogL: -105756.139 / Time: 0h:2m:1s
Finish initializing candidate tree set (20)
Current best tree score: -105710.023 / CPU time: 110.069
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 150 / LogL: -192927.418 / Time: 0h:13m:17s (0h:7m:24s left)
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Iteration 160 / LogL: -193310.711 / Time: 0h:13m:59s (0h:6m:25s left)
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 68: -105678.263
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Iteration 210 / LogL: -105808.710 / Time: 0h:11m:36s (0h:0m:-4s left)
TREE SEARCH COMPLETED AFTER 210 ITERATIONS / Time: 0h:11m:36s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -105668.541
2. Current log-likelihood: -105668.513
3. Current log-likelihood: -105668.471
4. Current log-likelihood: -105668.440
5. Current log-likelihood: -105668.425
Optimizing NNI: done in 4.20569 secs using 596.8% CPU
Iteration 260 / LogL: -193025.415 / Time: 0h:22m:45s (0h:5m:21s left)
6. Current log-likelihood: -105668.410
7. Current log-likelihood: -105668.396
8. Current log-likelihood: -105668.381
9. Current log-likelihood: -105668.366
10. Current log-likelihood: -105668.352
11. Current log-likelihood: -105668.339
Optimizing NNI: done in 4.17003 secs using 597.3% CPU
12. Current log-likelihood: -105668.326
13. Current log-likelihood: -105668.313
14. Current log-likelihood: -105668.300
15. Current log-likelihood: -105668.290
16. Current log-likelihood: -105668.278
17. Current log-likelihood: -105668.266
Optimizing NNI: done in 4.11031 secs using 597.3% CPU
Optimal log-likelihood: -105668.250
Proportion of invariable sites: 0.026
Site proportion and rates:  (0.083,0.029) (0.085,0.087) (0.100,0.183) (0.144,0.325) (0.133,0.578) (0.122,0.922) (0.128,1.390) (0.105,1.956) (0.073,4.805)
Parameters optimization took 17 rounds (12.602 sec)
BEST SCORE FOUND : -105668.250
Total tree length: 179.602

Total number of iterations: 210
CPU time used for tree search: 2558.109 sec (0h:42m:38s)
Wall-clock time used for tree search: 684.783 sec (0h:11m:24s)
Total CPU time used: 2654.528 sec (0h:44m:14s)
Total wall-clock time used: 708.963 sec (0h:11m:48s)

===> COMPUTE CONSENSUS TREE FROM 100 BOOTSTRAP TREES

Reading tree(s) file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.boottrees ...
100 tree(s) loaded (0 rooted and 100 unrooted)
0 split(s) discarded because frequency <= -1.000
1728 splits found
Consensus tree written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.contree

===> START ANALYSIS ON THE ORIGINAL ALIGNMENT

WARNING: Normalizing state frequencies so that sum of them equals to 1

NOTE: 161 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -105229.794
2. Current log-likelihood: -105187.330
Optimizing NNI: done in 4.15374 secs using 597.1% CPU
3. Current log-likelihood: -105181.970
4. Current log-likelihood: -105179.892
Optimizing NNI: done in 4.57877 secs using 597.3% CPU
5. Current log-likelihood: -105178.217
6. Current log-likelihood: -105176.815
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7. Current log-likelihood: -105175.640
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8. Current log-likelihood: -105174.629
9. Current log-likelihood: -105173.740
Optimizing NNI: done in 4.73735 secs using 598% CPU
10. Current log-likelihood: -105172.931
11. Current log-likelihood: -105172.164
Optimizing NNI: done in 3.9912 secs using 596.2% CPU
12. Current log-likelihood: -105171.411
13. Current log-likelihood: -105170.634
Optimizing NNI: done in 4.58715 secs using 597.2% CPU
14. Current log-likelihood: -105169.799
15. Current log-likelihood: -105168.869
Optimizing NNI: done in 5.06687 secs using 597.3% CPU
Iteration 270 / LogL: -192918.538 / Time: 0h:23m:29s (0h:4m:27s left)
16. Current log-likelihood: -105167.815
17. Current log-likelihood: -105166.609
Optimizing NNI: done in 4.37979 secs using 598.1% CPU
18. Current log-likelihood: -105165.245
19. Current log-likelihood: -105163.748
Optimizing NNI: done in 4.43048 secs using 597.7% CPU
20. Current log-likelihood: -105162.173
21. Current log-likelihood: -105160.586
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23. Current log-likelihood: -105157.647
24. Current log-likelihood: -105156.349
Optimizing NNI: done in 3.85681 secs using 596.9% CPU
25. Current log-likelihood: -105155.186
26. Current log-likelihood: -105154.154
Optimizing NNI: done in 4.3204 secs using 597% CPU
27. Current log-likelihood: -105153.250
28. Current log-likelihood: -105152.458
Optimizing NNI: done in 4.36049 secs using 596.6% CPU
29. Current log-likelihood: -105151.772
30. Current log-likelihood: -105151.301
Optimizing NNI: done in 4.03334 secs using 597.7% CPU
31. Current log-likelihood: -105150.902
32. Current log-likelihood: -105150.601
Optimizing NNI: done in 4.64878 secs using 597% CPU
33. Current log-likelihood: -105150.447
34. Current log-likelihood: -105150.318
Optimizing NNI: done in 4.2722 secs using 598.2% CPU
Iteration 280 / LogL: -193009.214 / Time: 0h:24m:12s (0h:3m:33s left)
35. Current log-likelihood: -105150.191
Optimal log-likelihood: -105150.058
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.091,0.037) (0.093,0.117) (0.112,0.231) (0.128,0.398) (0.116,0.642) (0.107,0.975) (0.126,1.424) (0.134,2.028) (0.066,4.251)
Parameters optimization took 35 rounds (81.971 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Optimizing NNI: done in 4.0316 secs using 597.2% CPU
Calculating distance matrix: done in 4.68959 secs using 399.9% CPU
Computing ML distances took 4.689903 sec (of wall-clock time) 18.756450 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 0.000788927 secs using 297% CPU
Constructing RapidNJ tree: done in 0.00862885 secs using 369.1% CPU
Computing RapidNJ tree took 0.009474 sec (of wall-clock time) 0.034733 sec (of CPU time)
Optimizing NNI: done in 4.87904 secs using 597.1% CPU
Log-likelihood of RapidNJ tree: -105745.688
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... Optimizing NNI: done in 5.53336 secs using 597.3% CPU
10.095 second
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Computing log-likelihood of 98 initial trees ... 14.467 seconds
Current best score: -105150.058

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -105139.826
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Iteration 290 / LogL: -193015.272 / Time: 0h:25m:1s (0h:2m:41s left)
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Iteration 10 / LogL: -105182.964 / Time: 0h:2m:24s
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Iteration 20 / LogL: -105173.288 / Time: 0h:2m:48s
Finish initializing candidate tree set (20)
Current best tree score: -105139.826 / CPU time: 79.394
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 22: -105138.149
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -105135.621
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 40: -105133.918
Iteration 40 / LogL: -105133.918 / Time: 0h:3m:57s (0h:10m:9s left)
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BETTER TREE FOUND at iteration 41: -105132.858
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 44: -105130.214
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Iteration 320 / LogL: -192978.605 / Time: 0h:27m:10s (0h:0m:5s left)
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Optimizing NNI: done in 4.45613 secs using 597.2% CPU
TREE SEARCH COMPLETED AFTER 322 ITERATIONS / Time: 0h:27m:19s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192905.152
Optimizing NNI: done in 2.23867 secs using 398.6% CPU
2. Current log-likelihood: -192905.141
Optimal log-likelihood: -192905.133
Site proportion and rates:  (0.010,0.101) (0.051,0.217) (0.099,0.353) (0.302,0.572) (0.155,0.823) (0.137,1.070) (0.144,1.643) (0.102,2.643)
Parameters optimization took 2 rounds (1.805 sec)
BEST SCORE FOUND : -192905.133
Total tree length: 152.194

Total number of iterations: 322
CPU time used for tree search: 9184.365 sec (2h:33m:4s)
Wall-clock time used for tree search: 1597.405 sec (0h:26m:37s)
Total CPU time used: 9443.354 sec (2h:37m:23s)
Total wall-clock time used: 1640.897 sec (0h:27m:20s)

===> START BOOTSTRAP REPLICATE NUMBER 52

Creating bootstrap alignment (seed: 70515)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.323 seconds

NOTE: 244 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -202761.419
Optimizing NNI: done in 2.47215 secs using 398.9% CPU
2. Current log-likelihood: -200112.998
Optimizing NNI: done in 3.28273 secs using 398.7% CPU
Iteration 50 / LogL: -105135.411 / Time: 0h:4m:31s (0h:8m:40s left)
3. Current log-likelihood: -200086.409
Optimizing NNI: done in 2.37442 secs using 398.9% CPU
4. Current log-likelihood: -200085.686
Optimal log-likelihood: -200085.646
Site proportion and rates:  (0.010,0.083) (0.005,0.162) (0.061,0.256) (0.176,0.440) (0.228,0.625) (0.263,0.954) (0.141,1.566) (0.117,2.491)
Parameters optimization took 4 rounds (7.758 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
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Calculating distance matrix: done in 9.75232 secs using 599.9% CPU
Computing ML distances took 9.752838 sec (of wall-clock time) 58.503681 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00132704 secs using 369.2% CPU
Constructing RapidNJ tree: done in 0.022661 secs using 650% CPU
Computing RapidNJ tree took 0.024066 sec (of wall-clock time) 0.154072 sec (of CPU time)
Optimizing NNI: done in 2.67901 secs using 398.7% CPU
Optimizing NNI: done in 3.13267 secs using 398.7% CPU
Log-likelihood of RapidNJ tree: -203995.712
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... Optimizing NNI: done in 2.90644 secs using 398.8% CPU
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Iteration 60 / LogL: -105137.134 / Time: 0h:4m:59s (0h:7m:5s left)
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30.014 second
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Iteration 70 / LogL: -105132.476 / Time: 0h:5m:26s (0h:5m:50s left)
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Computing log-likelihood of 98 initial trees ... 16.814 seconds
Current best score: -200085.646

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 1: -199428.272
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BETTER TREE FOUND at iteration 2: -199263.474
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Iteration 80 / LogL: -105138.113 / Time: 0h:5m:52s (0h:4m:45s left)
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Estimate model parameters (epsilon = 0.100)
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Iteration 90 / LogL: -105130.460 / Time: 0h:6m:19s (0h:3m:50s left)
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Iteration 10 / LogL: -199295.275 / Time: 0h:1m:57s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 92: -105129.884
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Estimate model parameters (epsilon = 0.100)
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Iteration 100 / LogL: -105156.911 / Time: 0h:6m:48s (0h:6m:19s left)
BETTER TREE FOUND at iteration 16: -199204.330
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Iteration 20 / LogL: -199312.186 / Time: 0h:2m:38s
Finish initializing candidate tree set (20)
Current best tree score: -199204.330 / CPU time: 136.776
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
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Iteration 130 / LogL: -105165.172 / Time: 0h:8m:9s (0h:3m:55s left)
BETTER TREE FOUND at iteration 33: -199190.433
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -199177.219
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Iteration 180 / LogL: -105135.049 / Time: 0h:10m:25s (0h:0m:41s left)
BETTER TREE FOUND at iteration 61: -199170.819
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TREE SEARCH COMPLETED AFTER 193 ITERATIONS / Time: 0h:10m:59s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -105129.884
Optimal log-likelihood: -105129.874
Proportion of invariable sites: 0.027
Site proportion and rates:  (0.089,0.034) (0.090,0.108) (0.116,0.228) (0.130,0.396) (0.111,0.635) (0.102,0.952) (0.113,1.356) (0.153,1.950) (0.068,4.229)
Parameters optimization took 1 rounds (1.127 sec)
BEST SCORE FOUND : -105129.874
Total tree length: 168.001

Total number of iterations: 193
CPU time used for tree search: 2247.929 sec (0h:37m:27s)
Wall-clock time used for tree search: 571.274 sec (0h:9m:31s)
Total CPU time used: 2605.724 sec (0h:43m:25s)
Total wall-clock time used: 661.040 sec (0h:11m:1s)
Reading input trees file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.contree
Log-likelihood of consensus tree: -105141.833

===> ASSIGN BOOTSTRAP SUPPORTS TO THE TREE FROM ORIGINAL ALIGNMENT

Reading tree /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.treefile ...
unrooted tree detected
Reading tree(s) file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.boottrees ...
100 tree(s) loaded (0 rooted and 100 unrooted)
Rescaling split weights by 1.000
1728 splits found
Creating bootstrap support values...
Tree with assigned support written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.treefile

Analysis results written to: 
  IQ-TREE report:                /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.iqtree
  Maximum-likelihood tree:       /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.treefile
  Likelihood distances:          /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.mldist
  Screen log file:               /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.log

Performing transfer bootstrap expectation...
TBE tree written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.tbe.tree
TBE statistic written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.tbe.stat

Total CPU time for bootstrap: 350688.454 seconds.
Total wall-clock time for bootstrap: 89199.650 seconds.

Non-parametric bootstrap results written to:
  Bootstrap trees:          /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.boottrees
  Consensus tree:           /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/cdhit_phobius_tm_RECEPTORS.contree

Date and Time: Tue Jul  8 16:49:53 2025
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Iteration 290 / LogL: -199132.520 / Time: 0h:33m:2s (0h:4m:34s left)
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Iteration 300 / LogL: -199155.538 / Time: 0h:34m:19s (0h:3m:26s left)
Optimizing NNI: done in 7.74849 secs using 596% CPU
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Iteration 310 / LogL: -199144.286 / Time: 0h:35m:30s (0h:2m:17s left)
Optimizing NNI: done in 6.68212 secs using 597.9% CPU
Optimizing NNI: done in 6.41106 secs using 597.6% CPU
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Optimizing NNI: done in 6.78328 secs using 598.3% CPU
Iteration 320 / LogL: -199163.991 / Time: 0h:36m:36s (0h:1m:8s left)
Optimizing NNI: done in 6.94236 secs using 597.5% CPU
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Optimizing NNI: done in 7.31452 secs using 597% CPU
Iteration 330 / LogL: -199126.612 / Time: 0h:37m:48s (0h:0m:0s left)
Optimizing NNI: done in 6.07701 secs using 598.3% CPU
TREE SEARCH COMPLETED AFTER 331 ITERATIONS / Time: 0h:37m:54s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -199109.413
2. Current log-likelihood: -199109.402
Optimal log-likelihood: -199109.394
Site proportion and rates:  (0.014,0.106) (0.050,0.259) (0.112,0.390) (0.192,0.543) (0.167,0.721) (0.212,1.007) (0.138,1.578) (0.115,2.485)
Parameters optimization took 2 rounds (2.336 sec)
BEST SCORE FOUND : -199109.394
Total tree length: 155.670

Total number of iterations: 331
CPU time used for tree search: 13307.700 sec (3h:41m:47s)
Wall-clock time used for tree search: 2252.737 sec (0h:37m:32s)
Total CPU time used: 13449.478 sec (3h:44m:9s)
Total wall-clock time used: 2276.562 sec (0h:37m:56s)

===> START BOOTSTRAP REPLICATE NUMBER 53

Creating bootstrap alignment (seed: 70516)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.284 seconds

NOTE: 242 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -200402.600
2. Current log-likelihood: -197815.455
3. Current log-likelihood: -197792.651
4. Current log-likelihood: -197791.483
5. Current log-likelihood: -197790.869
6. Current log-likelihood: -197790.329
7. Current log-likelihood: -197789.791
8. Current log-likelihood: -197789.259
9. Current log-likelihood: -197788.783
10. Current log-likelihood: -197788.422
11. Current log-likelihood: -197788.179
12. Current log-likelihood: -197788.027
Optimal log-likelihood: -197787.937
Site proportion and rates:  (0.012,0.082) (0.036,0.213) (0.125,0.352) (0.195,0.520) (0.132,0.696) (0.231,0.955) (0.146,1.550) (0.123,2.488)
Parameters optimization took 12 rounds (30.279 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 18.2713 secs using 599.9% CPU
Computing ML distances took 18.271907 sec (of wall-clock time) 109.612319 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00152111 secs using 349.5% CPU
Constructing RapidNJ tree: done in 0.0426219 secs using 683.9% CPU
Computing RapidNJ tree took 0.044236 sec (of wall-clock time) 0.297496 sec (of CPU time)
Log-likelihood of RapidNJ tree: -201135.489
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.966 second
Computing log-likelihood of 98 initial trees ... 23.635 seconds
Current best score: -197787.937

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.01325 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -197242.293
Optimizing NNI: done in 6.02485 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -197209.625
Optimizing NNI: done in 6.40706 secs using 596.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -197175.716
Optimizing NNI: done in 7.16891 secs using 597.3% CPU
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Optimizing NNI: done in 7.12222 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -197105.214
Optimizing NNI: done in 5.83235 secs using 596.9% CPU
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Iteration 10 / LogL: -197224.550 / Time: 0h:3m:5s
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Iteration 20 / LogL: -197150.387 / Time: 0h:4m:8s
Finish initializing candidate tree set (20)
Current best tree score: -197105.214 / CPU time: 197.208
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 8.05833 secs using 597.6% CPU
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Iteration 30 / LogL: -197132.291 / Time: 0h:5m:34s (0h:14m:35s left)
Optimizing NNI: done in 7.86531 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -197085.729
Optimizing NNI: done in 6.94537 secs using 596.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 34: -197075.599
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Iteration 40 / LogL: -197111.213 / Time: 0h:7m:1s (0h:16m:55s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 46: -197059.176
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Iteration 50 / LogL: -197077.638 / Time: 0h:8m:25s (0h:16m:30s left)
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Iteration 60 / LogL: -197060.964 / Time: 0h:9m:44s (0h:14m:12s left)
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Iteration 70 / LogL: -197082.447 / Time: 0h:11m:3s (0h:12m:10s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 74: -197052.454
Optimizing NNI: done in 7.96496 secs using 597.4% CPU
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Iteration 80 / LogL: -197055.660 / Time: 0h:12m:28s (0h:14m:49s left)
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Iteration 90 / LogL: -197072.956 / Time: 0h:13m:49s (0h:13m:2s left)
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Iteration 100 / LogL: -197077.325 / Time: 0h:15m:9s (0h:11m:19s left)
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Iteration 110 / LogL: -197071.382 / Time: 0h:16m:32s (0h:9m:42s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 116: -197042.412
Optimizing NNI: done in 7.52285 secs using 597.5% CPU
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Iteration 120 / LogL: -197137.109 / Time: 0h:17m:54s (0h:14m:26s left)
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Iteration 130 / LogL: -197186.477 / Time: 0h:19m:13s (0h:12m:49s left)
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Iteration 140 / LogL: -197084.429 / Time: 0h:20m:38s (0h:11m:16s left)
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Iteration 150 / LogL: -197251.036 / Time: 0h:21m:56s (0h:9m:43s left)
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Iteration 160 / LogL: -197094.004 / Time: 0h:23m:7s (0h:8m:8s left)
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Iteration 180 / LogL: -197058.177 / Time: 0h:25m:32s (0h:5m:8s left)
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Iteration 190 / LogL: -197047.793 / Time: 0h:26m:44s (0h:3m:40s left)
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Iteration 200 / LogL: -197109.813 / Time: 0h:27m:54s (0h:2m:14s left)
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Iteration 210 / LogL: -197126.187 / Time: 0h:29m:7s (0h:0m:50s left)
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Optimizing NNI: done in 7.3986 secs using 597.4% CPU
TREE SEARCH COMPLETED AFTER 217 ITERATIONS / Time: 0h:30m:1s

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|                    FINALIZING TREE SEARCH                        |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -197042.412
Optimal log-likelihood: -197042.401
Site proportion and rates:  (0.012,0.088) (0.040,0.222) (0.141,0.370) (0.216,0.548) (0.122,0.752) (0.204,0.978) (0.148,1.573) (0.117,2.523)
Parameters optimization took 1 rounds (0.955 sec)
BEST SCORE FOUND : -197042.401
Total tree length: 161.087

Total number of iterations: 217
CPU time used for tree search: 10298.420 sec (2h:51m:38s)
Wall-clock time used for tree search: 1750.040 sec (0h:29m:10s)
Total CPU time used: 10608.417 sec (2h:56m:48s)
Total wall-clock time used: 1802.004 sec (0h:30m:2s)

===> START BOOTSTRAP REPLICATE NUMBER 54

Creating bootstrap alignment (seed: 70517)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.316 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196210.068
2. Current log-likelihood: -193430.657
3. Current log-likelihood: -193406.149
4. Current log-likelihood: -193405.769
5. Current log-likelihood: -193405.556
6. Current log-likelihood: -193405.437
Optimal log-likelihood: -193405.355
Site proportion and rates:  (0.011,0.096) (0.039,0.225) (0.103,0.322) (0.143,0.450) (0.187,0.637) (0.235,0.932) (0.148,1.483) (0.134,2.505)
Parameters optimization took 6 rounds (16.787 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 11.4009 secs using 599.9% CPU
Computing ML distances took 11.401620 sec (of wall-clock time) 68.397901 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00190806 secs using 609.2% CPU
Constructing RapidNJ tree: done in 0.0461631 secs using 679.7% CPU
Computing RapidNJ tree took 0.048147 sec (of wall-clock time) 0.325822 sec (of CPU time)
Log-likelihood of RapidNJ tree: -197056.625
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... 29.979 second
Computing log-likelihood of 98 initial trees ... 20.681 seconds
Current best score: -193405.355

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.27554 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -192756.105
Optimizing NNI: done in 6.20917 secs using 597.4% CPU
Optimizing NNI: done in 7.38634 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -192754.839
Optimizing NNI: done in 5.82855 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -192723.025
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Iteration 10 / LogL: -192738.861 / Time: 0h:2m:47s
Optimizing NNI: done in 6.53003 secs using 596.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 11: -192722.206
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Optimizing NNI: done in 7.02888 secs using 596.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 13: -192715.889
Optimizing NNI: done in 8.47671 secs using 597.6% CPU
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Iteration 20 / LogL: -192802.767 / Time: 0h:4m:2s
Finish initializing candidate tree set (20)
Current best tree score: -192715.889 / CPU time: 211.723
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.78318 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -192687.757
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Iteration 30 / LogL: -192694.734 / Time: 0h:5m:19s (0h:16m:41s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -192676.950
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Iteration 40 / LogL: -192685.334 / Time: 0h:6m:35s (0h:16m:11s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 46: -192665.978
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Iteration 50 / LogL: -192696.145 / Time: 0h:7m:49s (0h:15m:18s left)
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Iteration 60 / LogL: -192726.457 / Time: 0h:8m:57s (0h:13m:3s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 61: -192651.522
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 70: -192629.712
Iteration 70 / LogL: -192629.712 / Time: 0h:10m:11s (0h:14m:46s left)
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Iteration 100 / LogL: -192664.379 / Time: 0h:13m:34s (0h:9m:35s left)
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Iteration 110 / LogL: -192643.406 / Time: 0h:14m:42s (0h:8m:5s left)
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Iteration 120 / LogL: -192870.338 / Time: 0h:15m:49s (0h:6m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 127: -192628.168
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 137: -192623.101
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Iteration 150 / LogL: -192638.409 / Time: 0h:19m:19s (0h:11m:16s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 164: -192620.839
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 170: -192619.041
Iteration 170 / LogL: -192619.041 / Time: 0h:21m:40s (0h:12m:49s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 176: -192614.871
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 215: -192614.102
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Iteration 240 / LogL: -192649.384 / Time: 0h:29m:42s (0h:9m:19s left)
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Iteration 250 / LogL: -192620.317 / Time: 0h:30m:49s (0h:8m:2s left)
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Iteration 260 / LogL: -192626.483 / Time: 0h:31m:58s (0h:6m:47s left)
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Iteration 270 / LogL: -192624.591 / Time: 0h:33m:7s (0h:5m:32s left)
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Iteration 280 / LogL: -192666.546 / Time: 0h:34m:14s (0h:4m:17s left)
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Iteration 290 / LogL: -192615.266 / Time: 0h:35m:20s (0h:3m:3s left)
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Iteration 300 / LogL: -192617.233 / Time: 0h:36m:28s (0h:1m:49s left)
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Iteration 310 / LogL: -192637.618 / Time: 0h:37m:37s (0h:0m:36s left)
Optimizing NNI: done in 7.24498 secs using 597.1% CPU
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Optimizing NNI: done in 6.76138 secs using 597% CPU
TREE SEARCH COMPLETED AFTER 316 ITERATIONS / Time: 0h:38m:19s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192614.102
Optimal log-likelihood: -192614.102
Site proportion and rates:  (0.013,0.105) (0.076,0.256) (0.135,0.377) (0.158,0.543) (0.129,0.706) (0.212,0.965) (0.143,1.484) (0.133,2.517)
Parameters optimization took 1 rounds (0.598 sec)
BEST SCORE FOUND : -192614.102
Total tree length: 155.877

Total number of iterations: 316
CPU time used for tree search: 13400.985 sec (3h:43m:20s)
Wall-clock time used for tree search: 2268.356 sec (0h:37m:48s)
Total CPU time used: 13588.824 sec (3h:46m:28s)
Total wall-clock time used: 2299.903 sec (0h:38m:19s)

===> START BOOTSTRAP REPLICATE NUMBER 55

Creating bootstrap alignment (seed: 70518)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.254 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -193834.738
2. Current log-likelihood: -190925.108
3. Current log-likelihood: -190898.832
4. Current log-likelihood: -190898.550
5. Current log-likelihood: -190898.399
Optimal log-likelihood: -190898.291
Site proportion and rates:  (0.015,0.087) (0.021,0.167) (0.111,0.300) (0.164,0.478) (0.211,0.657) (0.250,0.988) (0.131,1.634) (0.096,2.940)
Parameters optimization took 5 rounds (13.227 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 11.7707 secs using 599.9% CPU
Computing ML distances took 11.771346 sec (of wall-clock time) 70.614287 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00176811 secs using 422.7% CPU
Constructing RapidNJ tree: done in 0.0450451 secs using 686% CPU
Computing RapidNJ tree took 0.046900 sec (of wall-clock time) 0.318046 sec (of CPU time)
Log-likelihood of RapidNJ tree: -194059.920
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.467 second
Computing log-likelihood of 98 initial trees ... 22.021 seconds
Current best score: -190898.291

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.38579 secs using 596.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -190271.215
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -190192.332
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -190165.789
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Iteration 10 / LogL: -190312.696 / Time: 0h:2m:44s
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Iteration 20 / LogL: -190258.910 / Time: 0h:3m:46s
Finish initializing candidate tree set (20)
Current best tree score: -190165.789 / CPU time: 197.746
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Iteration 30 / LogL: -190174.258 / Time: 0h:4m:53s (0h:12m:28s left)
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BETTER TREE FOUND at iteration 33: -190161.780
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BETTER TREE FOUND at iteration 34: -190112.004
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BETTER TREE FOUND at iteration 48: -190105.022
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Iteration 50 / LogL: -190122.594 / Time: 0h:7m:19s (0h:14m:37s left)
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BETTER TREE FOUND at iteration 53: -190079.421
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 67: -190069.761
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 79: -190061.662
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BETTER TREE FOUND at iteration 84: -190056.522
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Iteration 90 / LogL: -190118.675 / Time: 0h:12m:6s (0h:12m:46s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 91: -190050.264
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Iteration 140 / LogL: -190085.825 / Time: 0h:18m:4s (0h:6m:37s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 145: -190043.625
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 158: -190043.073
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Iteration 200 / LogL: -190083.868 / Time: 0h:24m:57s (0h:7m:16s left)
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Iteration 210 / LogL: -190080.618 / Time: 0h:26m:3s (0h:5m:59s left)
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Optimizing NNI: done in 6.79167 secs using 597.7% CPU
Iteration 220 / LogL: -190102.485 / Time: 0h:27m:9s (0h:4m:42s left)
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Iteration 230 / LogL: -190080.006 / Time: 0h:28m:16s (0h:3m:27s left)
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Optimizing NNI: done in 6.75039 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 237: -190037.824
Optimizing NNI: done in 6.1209 secs using 597.1% CPU
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Iteration 240 / LogL: -190089.516 / Time: 0h:29m:27s (0h:11m:57s left)
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Iteration 250 / LogL: -190121.953 / Time: 0h:30m:33s (0h:10m:40s left)
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Iteration 260 / LogL: -190045.408 / Time: 0h:31m:41s (0h:9m:25s left)
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Iteration 270 / LogL: -190052.697 / Time: 0h:32m:47s (0h:8m:10s left)
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Iteration 280 / LogL: -190096.009 / Time: 0h:33m:55s (0h:6m:55s left)
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Iteration 290 / LogL: -190408.172 / Time: 0h:35m:3s (0h:5m:42s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 298: -190035.314
Optimizing NNI: done in 6.23744 secs using 598.1% CPU
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Iteration 300 / LogL: -190054.505 / Time: 0h:36m:12s (0h:11m:52s left)
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Iteration 310 / LogL: -190162.468 / Time: 0h:37m:17s (0h:10m:37s left)
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Iteration 320 / LogL: -190070.314 / Time: 0h:38m:26s (0h:9m:23s left)
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Iteration 330 / LogL: -190040.911 / Time: 0h:39m:31s (0h:8m:10s left)
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Iteration 340 / LogL: -190136.193 / Time: 0h:40m:42s (0h:6m:57s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 349: -190034.612
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Iteration 350 / LogL: -190270.449 / Time: 0h:41m:52s (0h:11m:52s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 355: -190031.585
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Iteration 360 / LogL: -190169.518 / Time: 0h:43m:4s (0h:11m:23s left)
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Iteration 370 / LogL: -190075.566 / Time: 0h:44m:14s (0h:10m:11s left)
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Iteration 380 / LogL: -190082.468 / Time: 0h:45m:14s (0h:8m:57s left)
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Iteration 390 / LogL: -190165.445 / Time: 0h:46m:23s (0h:7m:45s left)
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Iteration 400 / LogL: -190052.831 / Time: 0h:47m:32s (0h:6m:33s left)
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Iteration 410 / LogL: -190071.923 / Time: 0h:48m:40s (0h:5m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 419: -190031.379
Optimizing NNI: done in 6.65057 secs using 597.5% CPU
Iteration 420 / LogL: -190061.572 / Time: 0h:49m:50s (0h:11m:46s left)
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Iteration 430 / LogL: -190124.860 / Time: 0h:51m:1s (0h:10m:35s left)
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Iteration 440 / LogL: -190070.114 / Time: 0h:52m:12s (0h:9m:23s left)
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Iteration 450 / LogL: -190120.332 / Time: 0h:53m:22s (0h:8m:12s left)
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Iteration 460 / LogL: -190078.815 / Time: 0h:54m:33s (0h:7m:0s left)
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Iteration 470 / LogL: -190039.014 / Time: 0h:55m:47s (0h:5m:49s left)
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Iteration 480 / LogL: -190092.799 / Time: 0h:56m:59s (0h:4m:38s left)
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Iteration 490 / LogL: -190041.449 / Time: 0h:58m:13s (0h:3m:27s left)
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Optimizing NNI: done in 6.86616 secs using 597.6% CPU
Optimizing NNI: done in 6.78874 secs using 597.4% CPU
Optimizing NNI: done in 6.49635 secs using 597.9% CPU
Iteration 500 / LogL: -190060.735 / Time: 0h:59m:23s (0h:2m:15s left)
Optimizing NNI: done in 7.49263 secs using 597.7% CPU
Optimizing NNI: done in 7.17661 secs using 597.7% CPU
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Optimizing NNI: done in 7.13997 secs using 597% CPU
Optimizing NNI: done in 7.72843 secs using 597.3% CPU
Iteration 510 / LogL: -190229.564 / Time: 1h:0m:36s (0h:1m:4s left)
Optimizing NNI: done in 6.8147 secs using 597.4% CPU
Optimizing NNI: done in 7.21863 secs using 597.3% CPU
Optimizing NNI: done in 6.909 secs using 597.6% CPU
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Optimizing NNI: done in 6.88089 secs using 597.4% CPU
Optimizing NNI: done in 7.48113 secs using 597.6% CPU
Optimizing NNI: done in 7.6148 secs using 596.2% CPU
Iteration 520 / LogL: -190049.896 / Time: 1h:1m:47s (0h:0m:-8s left)
TREE SEARCH COMPLETED AFTER 520 ITERATIONS / Time: 1h:1m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -190031.379
Optimal log-likelihood: -190031.376
Site proportion and rates:  (0.017,0.092) (0.023,0.185) (0.123,0.316) (0.238,0.525) (0.166,0.744) (0.207,1.028) (0.128,1.640) (0.098,2.913)
Parameters optimization took 1 rounds (0.572 sec)
BEST SCORE FOUND : -190031.376
Total tree length: 150.052

Total number of iterations: 520
CPU time used for tree search: 21830.229 sec (6h:3m:50s)
Wall-clock time used for tree search: 3678.065 sec (1h:1m:18s)
Total CPU time used: 22006.812 sec (6h:6m:46s)
Total wall-clock time used: 3707.665 sec (1h:1m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 56

Creating bootstrap alignment (seed: 70519)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.255 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199557.722
2. Current log-likelihood: -197130.713
3. Current log-likelihood: -197043.111
4. Current log-likelihood: -197040.617
5. Current log-likelihood: -197040.251
6. Current log-likelihood: -197039.672
7. Current log-likelihood: -197039.196
8. Current log-likelihood: -197038.922
9. Current log-likelihood: -197038.734
10. Current log-likelihood: -197038.579
11. Current log-likelihood: -197038.442
12. Current log-likelihood: -197038.312
13. Current log-likelihood: -197038.175
14. Current log-likelihood: -197038.021
15. Current log-likelihood: -197037.830
16. Current log-likelihood: -197037.581
17. Current log-likelihood: -197037.233
18. Current log-likelihood: -197036.763
19. Current log-likelihood: -197036.134
20. Current log-likelihood: -197035.266
21. Current log-likelihood: -197034.061
22. Current log-likelihood: -197032.617
23. Current log-likelihood: -197031.454
24. Current log-likelihood: -197030.872
25. Current log-likelihood: -197030.653
Optimal log-likelihood: -197030.575
Site proportion and rates:  (0.014,0.101) (0.050,0.245) (0.144,0.406) (0.253,0.599) (0.116,0.822) (0.212,1.090) (0.115,1.654) (0.095,2.726)
Parameters optimization took 25 rounds (54.583 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 11.1345 secs using 599.9% CPU
Computing ML distances took 11.135383 sec (of wall-clock time) 66.801070 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00152802 secs using 548.8% CPU
Constructing RapidNJ tree: done in 0.04126 secs using 686.7% CPU
Computing RapidNJ tree took 0.042867 sec (of wall-clock time) 0.292269 sec (of CPU time)
Log-likelihood of RapidNJ tree: -203304.874
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.244 second
Computing log-likelihood of 98 initial trees ... 20.300 seconds
Current best score: -197030.575

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.6635 secs using 596.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -196298.521
Optimizing NNI: done in 5.07855 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -196247.980
Optimizing NNI: done in 5.30674 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -196183.246
Optimizing NNI: done in 5.24912 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -196182.385
Optimizing NNI: done in 5.3251 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -196180.744
Optimizing NNI: done in 5.44166 secs using 597.1% CPU
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Optimizing NNI: done in 5.80534 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 10: -196178.199
Iteration 10 / LogL: -196178.199 / Time: 0h:3m:17s
Optimizing NNI: done in 5.15341 secs using 597.3% CPU
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Optimizing NNI: done in 5.49458 secs using 597.4% CPU
Iteration 20 / LogL: -196192.855 / Time: 0h:4m:10s
Finish initializing candidate tree set (20)
Current best tree score: -196178.199 / CPU time: 181.823
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.03895 secs using 597.8% CPU
Optimizing NNI: done in 7.08817 secs using 597.3% CPU
Optimizing NNI: done in 6.37641 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -196148.320
Optimizing NNI: done in 5.75252 secs using 597.8% CPU
Optimizing NNI: done in 6.01147 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -196124.388
Optimizing NNI: done in 5.71747 secs using 596.2% CPU
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Iteration 30 / LogL: -196210.698 / Time: 0h:5m:17s (0h:17m:20s left)
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Iteration 40 / LogL: -196222.200 / Time: 0h:6m:22s (0h:13m:52s left)
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Iteration 50 / LogL: -196211.178 / Time: 0h:7m:24s (0h:11m:19s left)
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Iteration 60 / LogL: -196205.010 / Time: 0h:8m:25s (0h:9m:16s left)
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Iteration 70 / LogL: -196148.708 / Time: 0h:9m:26s (0h:7m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 79: -196123.882
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Iteration 80 / LogL: -196180.405 / Time: 0h:10m:32s (0h:13m:12s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 81: -196119.379
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 89: -196114.841
Optimizing NNI: done in 6.57426 secs using 597.3% CPU
Iteration 90 / LogL: -196163.430 / Time: 0h:11m:41s (0h:13m:0s left)
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Iteration 100 / LogL: -196145.576 / Time: 0h:12m:43s (0h:11m:26s left)
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Iteration 110 / LogL: -196127.692 / Time: 0h:13m:48s (0h:10m:0s left)
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Iteration 120 / LogL: -196139.257 / Time: 0h:14m:52s (0h:8m:37s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 130: -196111.812
Iteration 130 / LogL: -196111.812 / Time: 0h:15m:54s (0h:12m:19s left)
Optimizing NNI: done in 5.99363 secs using 597.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 135: -196106.811
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Iteration 140 / LogL: -196159.181 / Time: 0h:17m:0s (0h:11m:36s left)
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Iteration 150 / LogL: -196128.167 / Time: 0h:18m:3s (0h:10m:17s left)
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Iteration 160 / LogL: -196116.307 / Time: 0h:19m:5s (0h:9m:0s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 169: -196101.297
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Iteration 170 / LogL: -196121.746 / Time: 0h:20m:8s (0h:11m:47s left)
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Iteration 180 / LogL: -196110.458 / Time: 0h:21m:11s (0h:10m:31s left)
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Iteration 190 / LogL: -196179.717 / Time: 0h:22m:11s (0h:9m:16s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 191: -196098.023
Optimizing NNI: done in 6.64219 secs using 597.2% CPU
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Iteration 200 / LogL: -196134.115 / Time: 0h:23m:15s (0h:10m:38s left)
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Iteration 210 / LogL: -196277.624 / Time: 0h:24m:18s (0h:9m:25s left)
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Iteration 230 / LogL: -196127.706 / Time: 0h:26m:22s (0h:7m:1s left)
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Iteration 240 / LogL: -196114.127 / Time: 0h:27m:24s (0h:5m:50s left)
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Iteration 250 / LogL: -196240.718 / Time: 0h:28m:29s (0h:4m:41s left)
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Iteration 260 / LogL: -196131.278 / Time: 0h:29m:29s (0h:3m:31s left)
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Iteration 270 / LogL: -196118.434 / Time: 0h:30m:31s (0h:2m:22s left)
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Iteration 280 / LogL: -196128.546 / Time: 0h:31m:33s (0h:1m:14s left)
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Iteration 290 / LogL: -196112.045 / Time: 0h:32m:37s (0h:0m:6s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 292: -196095.277
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Iteration 300 / LogL: -196155.005 / Time: 0h:33m:44s (0h:10m:22s left)
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Iteration 310 / LogL: -196171.136 / Time: 0h:34m:47s (0h:9m:14s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 315: -196086.741
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Iteration 390 / LogL: -196123.491 / Time: 0h:43m:27s (0h:2m:47s left)
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Iteration 400 / LogL: -196178.229 / Time: 0h:44m:31s (0h:1m:40s left)
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Iteration 410 / LogL: -196098.401 / Time: 0h:45m:38s (0h:0m:33s left)
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Optimizing NNI: done in 6.39693 secs using 598% CPU
TREE SEARCH COMPLETED AFTER 416 ITERATIONS / Time: 0h:46m:17s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -196086.741
Optimal log-likelihood: -196086.738
Site proportion and rates:  (0.015,0.099) (0.054,0.260) (0.121,0.395) (0.252,0.583) (0.128,0.789) (0.219,1.082) (0.116,1.637) (0.095,2.743)
Parameters optimization took 1 rounds (0.564 sec)
BEST SCORE FOUND : -196086.738
Total tree length: 151.117

Total number of iterations: 416
CPU time used for tree search: 16031.645 sec (4h:27m:11s)
Wall-clock time used for tree search: 2708.858 sec (0h:45m:8s)
Total CPU time used: 16444.308 sec (4h:34m:4s)
Total wall-clock time used: 2778.037 sec (0h:46m:18s)

===> START BOOTSTRAP REPLICATE NUMBER 57

Creating bootstrap alignment (seed: 70520)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.255 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196243.034
2. Current log-likelihood: -193237.707
3. Current log-likelihood: -193212.375
4. Current log-likelihood: -193210.671
5. Current log-likelihood: -193207.783
6. Current log-likelihood: -193201.094
7. Current log-likelihood: -193197.131
8. Current log-likelihood: -193196.306
9. Current log-likelihood: -193196.033
Optimal log-likelihood: -193195.929
Site proportion and rates:  (0.010,0.084) (0.045,0.219) (0.105,0.339) (0.227,0.508) (0.170,0.771) (0.154,0.996) (0.171,1.540) (0.119,2.445)
Parameters optimization took 9 rounds (23.277 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 10.7398 secs using 600% CPU
Computing ML distances took 10.740351 sec (of wall-clock time) 64.436156 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00185108 secs using 543.4% CPU
Constructing RapidNJ tree: done in 0.0434291 secs using 687.1% CPU
Computing RapidNJ tree took 0.045355 sec (of wall-clock time) 0.309130 sec (of CPU time)
Log-likelihood of RapidNJ tree: -196062.894
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.965 second
Computing log-likelihood of 98 initial trees ... 22.713 seconds
Current best score: -193195.929

Do NNI search on 20 best initial trees
Optimizing NNI: done in 3.95991 secs using 598.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -192647.739
Optimizing NNI: done in 6.30387 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -192419.100
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -192387.043
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Iteration 10 / LogL: -192428.209 / Time: 0h:2m:39s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 16: -192377.609
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Iteration 20 / LogL: -192409.485 / Time: 0h:3m:45s
Finish initializing candidate tree set (20)
Current best tree score: -192377.609 / CPU time: 189.754
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.27991 secs using 598% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -192329.794
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -192328.106
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Iteration 30 / LogL: -192331.455 / Time: 0h:5m:0s (0h:16m:24s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 37: -192316.835
Optimizing NNI: done in 6.97502 secs using 598.1% CPU
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Iteration 40 / LogL: -192335.112 / Time: 0h:6m:19s (0h:15m:44s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 48: -192285.102
Optimizing NNI: done in 6.5103 secs using 597.9% CPU
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Iteration 50 / LogL: -192323.148 / Time: 0h:7m:32s (0h:15m:3s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 54: -192271.432
Optimizing NNI: done in 6.53796 secs using 597.9% CPU
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Iteration 60 / LogL: -192284.657 / Time: 0h:8m:39s (0h:13m:47s left)
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Iteration 70 / LogL: -192322.636 / Time: 0h:9m:47s (0h:11m:54s left)
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Iteration 80 / LogL: -192505.075 / Time: 0h:10m:55s (0h:10m:13s left)
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Iteration 90 / LogL: -192298.109 / Time: 0h:12m:1s (0h:8m:38s left)
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Iteration 100 / LogL: -192323.286 / Time: 0h:13m:5s (0h:7m:8s left)
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Iteration 110 / LogL: -192329.842 / Time: 0h:14m:9s (0h:5m:42s left)
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Iteration 120 / LogL: -192473.457 / Time: 0h:15m:17s (0h:4m:22s left)
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Iteration 130 / LogL: -192307.060 / Time: 0h:16m:23s (0h:3m:2s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 133: -192263.019
Optimizing NNI: done in 6.08958 secs using 597.7% CPU
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Iteration 140 / LogL: -192343.083 / Time: 0h:17m:34s (0h:11m:45s left)
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Iteration 180 / LogL: -192338.818 / Time: 0h:22m:6s (0h:6m:32s left)
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Iteration 210 / LogL: -192301.572 / Time: 0h:25m:27s (0h:2m:48s left)
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Iteration 220 / LogL: -192275.433 / Time: 0h:26m:35s (0h:1m:34s left)
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Iteration 230 / LogL: -192270.915 / Time: 0h:27m:41s (0h:0m:21s left)
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TREE SEARCH COMPLETED AFTER 234 ITERATIONS / Time: 0h:28m:9s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192263.019
Optimal log-likelihood: -192263.017
Site proportion and rates:  (0.010,0.085) (0.049,0.216) (0.107,0.341) (0.219,0.510) (0.152,0.746) (0.179,0.989) (0.164,1.541) (0.121,2.464)
Parameters optimization took 1 rounds (0.814 sec)
BEST SCORE FOUND : -192263.017
Total tree length: 159.673

Total number of iterations: 234
CPU time used for tree search: 9733.652 sec (2h:42m:13s)
Wall-clock time used for tree search: 1653.710 sec (0h:27m:33s)
Total CPU time used: 9954.422 sec (2h:45m:54s)
Total wall-clock time used: 1690.723 sec (0h:28m:10s)

===> START BOOTSTRAP REPLICATE NUMBER 58

Creating bootstrap alignment (seed: 70521)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.314 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -197443.802
2. Current log-likelihood: -194650.582
3. Current log-likelihood: -194630.567
4. Current log-likelihood: -194630.429
Optimal log-likelihood: -194630.394
Site proportion and rates:  (0.007,0.101) (0.023,0.191) (0.054,0.266) (0.145,0.405) (0.239,0.614) (0.283,0.959) (0.159,1.619) (0.091,2.716)
Parameters optimization took 4 rounds (10.212 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 10.0137 secs using 599.9% CPU
Computing ML distances took 10.014349 sec (of wall-clock time) 60.075542 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00173712 secs using 484.8% CPU
Constructing RapidNJ tree: done in 0.042773 secs using 681.3% CPU
Computing RapidNJ tree took 0.044595 sec (of wall-clock time) 0.300338 sec (of CPU time)
Log-likelihood of RapidNJ tree: -197942.824
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.337 second
Computing log-likelihood of 98 initial trees ... 21.217 seconds
Current best score: -194630.394

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.86148 secs using 596.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -194004.903
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -193927.033
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BETTER TREE FOUND at iteration 3: -193927.033
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -193917.194
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Iteration 10 / LogL: -193950.960 / Time: 0h:2m:49s
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BETTER TREE FOUND at iteration 16: -193917.190
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Iteration 20 / LogL: -193952.667 / Time: 0h:3m:44s
Finish initializing candidate tree set (20)
Current best tree score: -193917.190 / CPU time: 201.861
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -193906.779
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -193875.133
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -193874.552
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Iteration 30 / LogL: -193943.488 / Time: 0h:4m:55s (0h:16m:26s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -193858.839
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Iteration 40 / LogL: -194003.318 / Time: 0h:6m:0s (0h:14m:37s left)
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BETTER TREE FOUND at iteration 47: -193856.781
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Iteration 50 / LogL: -193862.453 / Time: 0h:7m:12s (0h:14m:16s left)
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BETTER TREE FOUND at iteration 56: -193856.357
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Iteration 60 / LogL: -193893.913 / Time: 0h:8m:22s (0h:13m:36s left)
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BETTER TREE FOUND at iteration 62: -193854.268
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 64: -193851.180
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Iteration 70 / LogL: -193901.671 / Time: 0h:9m:30s (0h:12m:57s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 71: -193826.323
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Iteration 80 / LogL: -193863.355 / Time: 0h:10m:36s (0h:12m:12s left)
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Iteration 90 / LogL: -193910.478 / Time: 0h:11m:35s (0h:10m:32s left)
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Iteration 100 / LogL: -194016.859 / Time: 0h:12m:35s (0h:9m:1s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 104: -193825.619
Optimizing NNI: done in 5.44465 secs using 597.5% CPU
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Iteration 110 / LogL: -193867.226 / Time: 0h:13m:36s (0h:11m:43s left)
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Iteration 120 / LogL: -193831.547 / Time: 0h:14m:34s (0h:10m:17s left)
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BETTER TREE FOUND at iteration 122: -193819.740
Optimizing NNI: done in 5.2852 secs using 596.9% CPU
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BETTER TREE FOUND at iteration 124: -193816.002
Optimizing NNI: done in 5.34573 secs using 597.4% CPU
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Iteration 130 / LogL: -193841.119 / Time: 0h:15m:38s (0h:11m:23s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 140: -193807.300
Iteration 140 / LogL: -193807.300 / Time: 0h:16m:40s (0h:11m:59s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 143: -193804.153
Optimizing NNI: done in 5.89769 secs using 597.1% CPU
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Iteration 150 / LogL: -193912.168 / Time: 0h:17m:47s (0h:11m:6s left)
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Iteration 160 / LogL: -193811.754 / Time: 0h:18m:46s (0h:9m:47s left)
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Iteration 170 / LogL: -193807.134 / Time: 0h:19m:47s (0h:8m:32s left)
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Iteration 180 / LogL: -193843.595 / Time: 0h:20m:48s (0h:7m:19s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 181: -193800.375
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Iteration 190 / LogL: -193855.935 / Time: 0h:21m:51s (0h:10m:31s left)
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Iteration 200 / LogL: -193823.949 / Time: 0h:22m:51s (0h:9m:18s left)
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Iteration 210 / LogL: -193820.299 / Time: 0h:23m:54s (0h:8m:7s left)
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Iteration 220 / LogL: -193836.411 / Time: 0h:24m:57s (0h:6m:56s left)
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Iteration 230 / LogL: -193875.723 / Time: 0h:25m:58s (0h:5m:47s left)
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Iteration 240 / LogL: -193844.030 / Time: 0h:26m:58s (0h:4m:37s left)
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Iteration 250 / LogL: -193814.554 / Time: 0h:28m:0s (0h:3m:29s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 256: -193795.596
Optimizing NNI: done in 5.69781 secs using 597.8% CPU
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Iteration 260 / LogL: -193849.975 / Time: 0h:29m:1s (0h:10m:45s left)
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Iteration 270 / LogL: -193833.416 / Time: 0h:30m:0s (0h:9m:35s left)
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Iteration 280 / LogL: -193961.693 / Time: 0h:31m:0s (0h:8m:26s left)
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Iteration 290 / LogL: -193842.524 / Time: 0h:31m:57s (0h:7m:17s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 297: -193794.040
Optimizing NNI: done in 5.32486 secs using 597.8% CPU
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Iteration 300 / LogL: -193845.410 / Time: 0h:32m:58s (0h:10m:41s left)
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Iteration 310 / LogL: -193985.900 / Time: 0h:33m:57s (0h:9m:33s left)
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Iteration 320 / LogL: -193826.397 / Time: 0h:34m:57s (0h:8m:26s left)
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Iteration 330 / LogL: -193804.861 / Time: 0h:35m:54s (0h:7m:18s left)
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Iteration 340 / LogL: -193846.212 / Time: 0h:36m:53s (0h:6m:12s left)
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Iteration 350 / LogL: -194035.427 / Time: 0h:37m:55s (0h:5m:6s left)
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Iteration 360 / LogL: -193806.983 / Time: 0h:38m:56s (0h:4m:0s left)
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Iteration 370 / LogL: -193800.904 / Time: 0h:39m:56s (0h:2m:55s left)
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Iteration 380 / LogL: -193826.725 / Time: 0h:40m:57s (0h:1m:50s left)
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Optimizing NNI: done in 7.14119 secs using 598% CPU
Optimizing NNI: done in 5.84501 secs using 598% CPU
Iteration 390 / LogL: -193813.426 / Time: 0h:42m:0s (0h:0m:45s left)
Optimizing NNI: done in 5.32073 secs using 598.2% CPU
Optimizing NNI: done in 6.05457 secs using 597.9% CPU
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Optimizing NNI: done in 5.87285 secs using 598% CPU
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Optimizing NNI: done in 5.40417 secs using 598.2% CPU
Optimizing NNI: done in 5.73144 secs using 597.3% CPU
TREE SEARCH COMPLETED AFTER 398 ITERATIONS / Time: 0h:42m:48s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -193794.040
Optimal log-likelihood: -193794.036
Site proportion and rates:  (0.008,0.110) (0.047,0.216) (0.137,0.362) (0.220,0.561) (0.155,0.800) (0.191,1.030) (0.157,1.641) (0.086,2.759)
Parameters optimization took 1 rounds (2.074 sec)
BEST SCORE FOUND : -193794.036
Total tree length: 151.485

Total number of iterations: 398
CPU time used for tree search: 15055.214 sec (4h:10m:55s)
Wall-clock time used for tree search: 2545.124 sec (0h:42m:25s)
Total CPU time used: 15204.155 sec (4h:13m:24s)
Total wall-clock time used: 2570.146 sec (0h:42m:50s)

===> START BOOTSTRAP REPLICATE NUMBER 59

Creating bootstrap alignment (seed: 70522)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.319 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -192640.800
2. Current log-likelihood: -190074.854
3. Current log-likelihood: -190048.572
4. Current log-likelihood: -190048.294
Optimal log-likelihood: -190048.254
Site proportion and rates:  (0.011,0.091) (0.019,0.225) (0.061,0.252) (0.160,0.423) (0.299,0.652) (0.199,0.987) (0.159,1.666) (0.092,2.781)
Parameters optimization took 4 rounds (11.111 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 9.84797 secs using 599.9% CPU
Computing ML distances took 9.848651 sec (of wall-clock time) 59.084511 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00181508 secs using 335.9% CPU
Constructing RapidNJ tree: done in 0.037564 secs using 666% CPU
Computing RapidNJ tree took 0.039473 sec (of wall-clock time) 0.256882 sec (of CPU time)
Log-likelihood of RapidNJ tree: -195418.585
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.081 second
Computing log-likelihood of 98 initial trees ... 22.402 seconds
Current best score: -190048.254

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.4818 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -189493.158
Optimizing NNI: done in 6.08174 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -189457.828
Optimizing NNI: done in 5.99055 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -189435.628
Optimizing NNI: done in 6.31759 secs using 597.5% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 8: -189360.721
Optimizing NNI: done in 6.15662 secs using 596.4% CPU
Optimizing NNI: done in 5.52403 secs using 597.2% CPU
Iteration 10 / LogL: -189515.127 / Time: 0h:2m:31s
Optimizing NNI: done in 5.8154 secs using 595.6% CPU
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Optimizing NNI: done in 6.34057 secs using 596.9% CPU
Iteration 20 / LogL: -189518.789 / Time: 0h:3m:32s
Finish initializing candidate tree set (20)
Current best tree score: -189360.721 / CPU time: 188.351
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.14676 secs using 597.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -189330.808
Optimizing NNI: done in 7.87413 secs using 597.2% CPU
Optimizing NNI: done in 6.81814 secs using 598% CPU
Iteration 30 / LogL: -189380.028 / Time: 0h:5m:31s (0h:18m:38s left)
Optimizing NNI: done in 8.57733 secs using 597.4% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -189298.173
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -189295.398
Optimizing NNI: done in 8.15152 secs using 597.6% CPU
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Iteration 40 / LogL: -189309.124 / Time: 0h:6m:51s (0h:16m:52s left)
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Iteration 50 / LogL: -189454.451 / Time: 0h:7m:57s (0h:13m:57s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 53: -189293.809
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 58: -189291.477
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Iteration 60 / LogL: -189337.510 / Time: 0h:9m:16s (0h:15m:24s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 67: -189291.272
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Iteration 70 / LogL: -189300.146 / Time: 0h:10m:28s (0h:14m:43s left)
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Iteration 80 / LogL: -189326.111 / Time: 0h:11m:36s (0h:12m:47s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 83: -189287.203
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Iteration 90 / LogL: -189313.811 / Time: 0h:12m:48s (0h:13m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 94: -189281.899
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Iteration 100 / LogL: -189343.493 / Time: 0h:14m:1s (0h:13m:19s left)
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Iteration 110 / LogL: -189363.646 / Time: 0h:15m:17s (0h:11m:46s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 114: -189275.995
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Iteration 120 / LogL: -189327.041 / Time: 0h:16m:31s (0h:13m:2s left)
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Iteration 130 / LogL: -189277.920 / Time: 0h:17m:41s (0h:11m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 131: -189274.274
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Iteration 140 / LogL: -189304.657 / Time: 0h:18m:54s (0h:12m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 147: -189273.561
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Iteration 150 / LogL: -189300.827 / Time: 0h:20m:9s (0h:13m:7s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 160: -189272.007
Iteration 160 / LogL: -189272.007 / Time: 0h:21m:25s (0h:13m:28s left)
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Iteration 180 / LogL: -189294.038 / Time: 0h:23m:52s (0h:10m:40s left)
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Iteration 190 / LogL: -189327.783 / Time: 0h:25m:1s (0h:9m:15s left)
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Iteration 200 / LogL: -189360.290 / Time: 0h:26m:13s (0h:7m:54s left)
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Iteration 210 / LogL: -189285.507 / Time: 0h:27m:25s (0h:6m:33s left)
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Iteration 220 / LogL: -189284.961 / Time: 0h:28m:39s (0h:5m:14s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 230: -189269.576
Iteration 230 / LogL: -189269.576 / Time: 0h:29m:55s (0h:13m:4s left)
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Iteration 240 / LogL: -189366.151 / Time: 0h:31m:13s (0h:11m:45s left)
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Optimizing NNI: done in 7.38984 secs using 597.6% CPU
Iteration 250 / LogL: -189293.571 / Time: 0h:32m:32s (0h:10m:27s left)
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Optimizing NNI: done in 7.37813 secs using 597.8% CPU
Iteration 260 / LogL: -189292.669 / Time: 0h:33m:43s (0h:9m:6s left)
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Optimizing NNI: done in 7.41628 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 262: -189268.144
Optimizing NNI: done in 6.9681 secs using 597.8% CPU
Optimizing NNI: done in 7.5928 secs using 597.9% CPU
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Iteration 270 / LogL: -189365.774 / Time: 0h:34m:56s (0h:11m:57s left)
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Iteration 280 / LogL: -189322.992 / Time: 0h:36m:9s (0h:10m:37s left)
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Iteration 290 / LogL: -189324.851 / Time: 0h:37m:24s (0h:9m:19s left)
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Iteration 300 / LogL: -189288.698 / Time: 0h:38m:45s (0h:8m:2s left)
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Iteration 310 / LogL: -189344.312 / Time: 0h:40m:1s (0h:6m:44s left)
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Iteration 320 / LogL: -190112.829 / Time: 0h:41m:20s (0h:5m:26s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 324: -189265.174
Optimizing NNI: done in 7.57531 secs using 597.7% CPU
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Iteration 330 / LogL: -189270.360 / Time: 0h:42m:38s (0h:12m:11s left)
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Iteration 340 / LogL: -189329.232 / Time: 0h:43m:55s (0h:10m:52s left)
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Iteration 360 / LogL: -189295.773 / Time: 0h:46m:31s (0h:8m:17s left)
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Iteration 370 / LogL: -189344.794 / Time: 0h:47m:52s (0h:7m:0s left)
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Iteration 380 / LogL: -189317.735 / Time: 0h:49m:9s (0h:5m:42s left)
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Iteration 390 / LogL: -189448.903 / Time: 0h:50m:25s (0h:4m:24s left)
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Iteration 400 / LogL: -189297.750 / Time: 0h:51m:36s (0h:3m:6s left)
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Iteration 410 / LogL: -189309.373 / Time: 0h:52m:41s (0h:1m:48s left)
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Iteration 420 / LogL: -189645.713 / Time: 0h:53m:56s (0h:0m:30s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 424: -189260.163
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Iteration 430 / LogL: -189336.928 / Time: 0h:55m:11s (0h:12m:5s left)
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Iteration 440 / LogL: -189291.990 / Time: 0h:56m:19s (0h:10m:46s left)
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Iteration 460 / LogL: -189388.233 / Time: 0h:58m:33s (0h:8m:9s left)
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Iteration 470 / LogL: -189302.790 / Time: 0h:59m:41s (0h:6m:52s left)
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Iteration 480 / LogL: -189371.681 / Time: 1h:0m:47s (0h:5m:35s left)
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Iteration 490 / LogL: -189292.239 / Time: 1h:1m:54s (0h:4m:18s left)
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Iteration 500 / LogL: -189299.127 / Time: 1h:2m:59s (0h:3m:1s left)
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Iteration 510 / LogL: -189295.274 / Time: 1h:4m:6s (0h:1m:45s left)
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Iteration 520 / LogL: -189325.736 / Time: 1h:5m:13s (0h:0m:30s left)
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Optimizing NNI: done in 6.13232 secs using 597.8% CPU
TREE SEARCH COMPLETED AFTER 525 ITERATIONS / Time: 1h:5m:45s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -189260.163
Optimal log-likelihood: -189260.161
Site proportion and rates:  (0.012,0.094) (0.073,0.249) (0.141,0.401) (0.229,0.604) (0.161,0.784) (0.142,1.070) (0.151,1.693) (0.090,2.804)
Parameters optimization took 1 rounds (0.797 sec)
BEST SCORE FOUND : -189260.161
Total tree length: 147.499

Total number of iterations: 525
CPU time used for tree search: 23283.218 sec (6h:28m:3s)
Wall-clock time used for tree search: 3921.424 sec (1h:5m:21s)
Total CPU time used: 23432.319 sec (6h:30m:32s)
Total wall-clock time used: 3946.481 sec (1h:5m:46s)

===> START BOOTSTRAP REPLICATE NUMBER 60

Creating bootstrap alignment (seed: 70523)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.318 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199956.839
2. Current log-likelihood: -197345.683
3. Current log-likelihood: -197309.434
4. Current log-likelihood: -197308.059
5. Current log-likelihood: -197306.374
6. Current log-likelihood: -197304.025
7. Current log-likelihood: -197302.037
8. Current log-likelihood: -197300.899
9. Current log-likelihood: -197300.266
10. Current log-likelihood: -197299.900
11. Current log-likelihood: -197299.654
12. Current log-likelihood: -197299.465
13. Current log-likelihood: -197299.308
14. Current log-likelihood: -197299.153
15. Current log-likelihood: -197299.008
16. Current log-likelihood: -197298.875
17. Current log-likelihood: -197298.763
Optimal log-likelihood: -197298.669
Site proportion and rates:  (0.009,0.091) (0.063,0.219) (0.144,0.394) (0.244,0.591) (0.158,0.806) (0.135,1.076) (0.145,1.629) (0.102,2.698)
Parameters optimization took 17 rounds (44.344 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 10.9831 secs using 599.9% CPU
Computing ML distances took 10.983788 sec (of wall-clock time) 65.887508 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00147104 secs using 236.6% CPU
Constructing RapidNJ tree: done in 0.040565 secs using 685.8% CPU
Computing RapidNJ tree took 0.042118 sec (of wall-clock time) 0.282205 sec (of CPU time)
Log-likelihood of RapidNJ tree: -202231.248
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.903 second
Computing log-likelihood of 98 initial trees ... 21.937 seconds
Current best score: -197298.669

Do NNI search on 20 best initial trees
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -196724.466
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BETTER TREE FOUND at iteration 9: -196716.627
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Iteration 10 / LogL: -196729.342 / Time: 0h:2m:59s
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BETTER TREE FOUND at iteration 15: -196712.532
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Iteration 20 / LogL: -196817.101 / Time: 0h:4m:5s
Finish initializing candidate tree set (20)
Current best tree score: -196712.532 / CPU time: 187.366
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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BETTER TREE FOUND at iteration 21: -196682.506
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BETTER TREE FOUND at iteration 24: -196667.517
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Iteration 50 / LogL: -196623.903 / Time: 0h:7m:34s (0h:15m:26s left)
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BETTER TREE FOUND at iteration 60: -196615.317
Iteration 60 / LogL: -196615.317 / Time: 0h:8m:38s (0h:14m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 148: -196592.930
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BETTER TREE FOUND at iteration 178: -196592.671
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BETTER TREE FOUND at iteration 209: -196590.813
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Iteration 270 / LogL: -196621.458 / Time: 0h:30m:19s (0h:4m:23s left)
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Iteration 280 / LogL: -197001.306 / Time: 0h:31m:25s (0h:3m:15s left)
Optimizing NNI: done in 6.08095 secs using 597.8% CPU
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Optimizing NNI: done in 6.15786 secs using 595.8% CPU
Optimizing NNI: done in 5.97393 secs using 597.7% CPU
Iteration 290 / LogL: -196638.254 / Time: 0h:32m:23s (0h:2m:7s left)
Optimizing NNI: done in 6.60294 secs using 596.6% CPU
Optimizing NNI: done in 6.68668 secs using 597% CPU
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Optimizing NNI: done in 6.52186 secs using 597.8% CPU
Iteration 300 / LogL: -196610.669 / Time: 0h:33m:27s (0h:1m:0s left)
Optimizing NNI: done in 5.43815 secs using 597.7% CPU
Optimizing NNI: done in 6.06395 secs using 597.4% CPU
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Optimizing NNI: done in 6.01851 secs using 598% CPU
Optimizing NNI: done in 5.76848 secs using 597.6% CPU
Iteration 310 / LogL: -196637.250 / Time: 0h:34m:29s (0h:0m:-7s left)
TREE SEARCH COMPLETED AFTER 310 ITERATIONS / Time: 0h:34m:29s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -196590.813
Optimal log-likelihood: -196590.812
Site proportion and rates:  (0.010,0.096) (0.064,0.226) (0.136,0.391) (0.217,0.576) (0.180,0.776) (0.144,1.062) (0.150,1.632) (0.099,2.716)
Parameters optimization took 1 rounds (0.893 sec)
BEST SCORE FOUND : -196590.812
Total tree length: 156.315

Total number of iterations: 310
CPU time used for tree search: 11869.598 sec (3h:17m:49s)
Wall-clock time used for tree search: 2011.075 sec (0h:33m:31s)
Total CPU time used: 12220.948 sec (3h:23m:40s)
Total wall-clock time used: 2070.028 sec (0h:34m:30s)

===> START BOOTSTRAP REPLICATE NUMBER 61

Creating bootstrap alignment (seed: 70524)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.311 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -189570.243
2. Current log-likelihood: -187182.691
3. Current log-likelihood: -187060.323
4. Current log-likelihood: -187053.306
5. Current log-likelihood: -187052.908
6. Current log-likelihood: -187052.636
7. Current log-likelihood: -187052.406
8. Current log-likelihood: -187052.160
9. Current log-likelihood: -187051.850
10. Current log-likelihood: -187051.467
11. Current log-likelihood: -187051.023
12. Current log-likelihood: -187050.539
13. Current log-likelihood: -187050.042
14. Current log-likelihood: -187049.578
15. Current log-likelihood: -187049.202
16. Current log-likelihood: -187048.919
17. Current log-likelihood: -187048.733
18. Current log-likelihood: -187048.628
Optimal log-likelihood: -187048.552
Site proportion and rates:  (0.023,0.137) (0.089,0.289) (0.121,0.407) (0.211,0.587) (0.127,0.762) (0.182,1.067) (0.160,1.694) (0.087,2.718)
Parameters optimization took 18 rounds (44.681 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 9.80728 secs using 599.9% CPU
Computing ML distances took 9.807971 sec (of wall-clock time) 58.833447 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.001863 secs using 341.4% CPU
Constructing RapidNJ tree: done in 0.041398 secs using 678.4% CPU
Computing RapidNJ tree took 0.043336 sec (of wall-clock time) 0.287672 sec (of CPU time)
Log-likelihood of RapidNJ tree: -191683.657
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.888 second
Computing log-likelihood of 98 initial trees ... 21.439 seconds
Current best score: -187048.552

Do NNI search on 20 best initial trees
Optimizing NNI: done in 3.90001 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -186558.529
Optimizing NNI: done in 4.463 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -186520.406
Optimizing NNI: done in 4.60866 secs using 598.2% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -186480.683
Optimizing NNI: done in 4.80728 secs using 598% CPU
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Iteration 10 / LogL: -186508.273 / Time: 0h:2m:54s
Optimizing NNI: done in 5.89362 secs using 598% CPU
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Iteration 20 / LogL: -186532.950 / Time: 0h:3m:48s
Finish initializing candidate tree set (20)
Current best tree score: -186480.683 / CPU time: 169.181
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.55438 secs using 597.4% CPU
Optimizing NNI: done in 5.8753 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -186460.248
Optimizing NNI: done in 6.62246 secs using 595.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -186444.525
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Iteration 30 / LogL: -186468.063 / Time: 0h:5m:3s (0h:16m:52s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -186415.703
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Iteration 40 / LogL: -186501.706 / Time: 0h:6m:11s (0h:15m:32s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 45: -186411.069
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Iteration 50 / LogL: -186448.779 / Time: 0h:7m:16s (0h:14m:5s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -186407.393
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 60: -186393.546
Iteration 60 / LogL: -186393.546 / Time: 0h:8m:22s (0h:14m:10s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -186386.996
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Iteration 70 / LogL: -186406.708 / Time: 0h:9m:25s (0h:12m:58s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 71: -186384.903
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Iteration 80 / LogL: -186409.859 / Time: 0h:10m:28s (0h:12m:3s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 87: -186382.901
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Iteration 90 / LogL: -186480.285 / Time: 0h:11m:32s (0h:12m:33s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 92: -186376.449
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Iteration 100 / LogL: -186977.608 / Time: 0h:12m:37s (0h:11m:43s left)
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Iteration 110 / LogL: -186470.243 / Time: 0h:13m:20s (0h:10m:1s left)
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Iteration 120 / LogL: -186407.890 / Time: 0h:14m:21s (0h:8m:40s left)
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Iteration 130 / LogL: -186397.400 / Time: 0h:15m:24s (0h:7m:23s left)
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Iteration 140 / LogL: -186416.254 / Time: 0h:16m:27s (0h:6m:9s left)
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Iteration 150 / LogL: -186436.049 / Time: 0h:17m:32s (0h:4m:56s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 152: -186373.446
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Iteration 160 / LogL: -186479.826 / Time: 0h:18m:36s (0h:10m:45s left)
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Iteration 170 / LogL: -186396.332 / Time: 0h:19m:39s (0h:9m:32s left)
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Iteration 180 / LogL: -186486.340 / Time: 0h:20m:43s (0h:8m:19s left)
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Iteration 190 / LogL: -186382.063 / Time: 0h:21m:49s (0h:7m:9s left)
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Iteration 200 / LogL: -186410.129 / Time: 0h:22m:53s (0h:5m:58s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 201: -186362.892
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BETTER TREE FOUND at iteration 209: -186361.692
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Iteration 210 / LogL: -186505.545 / Time: 0h:24m:4s (0h:11m:24s left)
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Iteration 220 / LogL: -186388.962 / Time: 0h:25m:9s (0h:10m:13s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 224: -186357.446
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Iteration 230 / LogL: -186364.672 / Time: 0h:26m:13s (0h:10m:45s left)
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Iteration 240 / LogL: -186370.926 / Time: 0h:27m:15s (0h:9m:34s left)
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Iteration 260 / LogL: -186368.662 / Time: 0h:29m:25s (0h:7m:16s left)
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Iteration 270 / LogL: -186370.793 / Time: 0h:30m:30s (0h:6m:7s left)
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Iteration 280 / LogL: -186446.825 / Time: 0h:31m:37s (0h:4m:59s left)
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Iteration 290 / LogL: -186425.176 / Time: 0h:32m:44s (0h:3m:51s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 291: -186354.379
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 318: -186353.404
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Iteration 400 / LogL: -186452.893 / Time: 0h:44m:52s (0h:2m:1s left)
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Iteration 410 / LogL: -186365.754 / Time: 0h:45m:58s (0h:0m:53s left)
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TREE SEARCH COMPLETED AFTER 419 ITERATIONS / Time: 0h:47m:0s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -186353.404
Optimal log-likelihood: -186353.398
Site proportion and rates:  (0.022,0.139) (0.087,0.282) (0.134,0.411) (0.211,0.593) (0.121,0.781) (0.180,1.073) (0.166,1.724) (0.079,2.767)
Parameters optimization took 1 rounds (1.329 sec)
BEST SCORE FOUND : -186353.398
Total tree length: 143.981

Total number of iterations: 419
CPU time used for tree search: 16353.802 sec (4h:32m:33s)
Wall-clock time used for tree search: 2760.969 sec (0h:46m:0s)
Total CPU time used: 16714.653 sec (4h:38m:34s)
Total wall-clock time used: 2821.505 sec (0h:47m:1s)

===> START BOOTSTRAP REPLICATE NUMBER 62

Creating bootstrap alignment (seed: 70525)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.317 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -197562.660
2. Current log-likelihood: -194754.261
3. Current log-likelihood: -194725.623
4. Current log-likelihood: -194725.248
Optimal log-likelihood: -194725.202
Site proportion and rates:  (0.014,0.086) (0.002,0.258) (0.107,0.284) (0.178,0.449) (0.178,0.630) (0.248,0.938) (0.177,1.552) (0.097,2.774)
Parameters optimization took 4 rounds (12.120 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 11.0345 secs using 599.9% CPU
Computing ML distances took 11.035170 sec (of wall-clock time) 66.195830 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00168109 secs using 422.8% CPU
Constructing RapidNJ tree: done in 0.0396199 secs using 690.4% CPU
Computing RapidNJ tree took 0.041393 sec (of wall-clock time) 0.281213 sec (of CPU time)
Log-likelihood of RapidNJ tree: -199532.806
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.861 second
Computing log-likelihood of 98 initial trees ... 22.710 seconds
Current best score: -194725.202

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.71485 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -194225.484
Optimizing NNI: done in 6.24072 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -194187.024
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -194152.114
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Iteration 10 / LogL: -194249.523 / Time: 0h:2m:34s
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Iteration 20 / LogL: -194177.545 / Time: 0h:3m:39s
Finish initializing candidate tree set (20)
Current best tree score: -194152.114 / CPU time: 193.480
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.1972 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -194140.286
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -194128.343
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Iteration 30 / LogL: -194177.064 / Time: 0h:4m:55s (0h:15m:58s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -194126.807
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -194107.249
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -194090.106
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 39: -194079.246
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Iteration 40 / LogL: -194103.564 / Time: 0h:6m:37s (0h:16m:47s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 43: -194076.280
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Optimizing NNI: done in 6.99342 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 50: -194071.439
Iteration 50 / LogL: -194071.439 / Time: 0h:7m:53s (0h:16m:5s left)
Optimizing NNI: done in 6.28876 secs using 597.3% CPU
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Optimizing NNI: done in 7.1242 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 60: -194065.299
Iteration 60 / LogL: -194065.299 / Time: 0h:9m:2s (0h:15m:18s left)
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Iteration 70 / LogL: -194284.836 / Time: 0h:10m:10s (0h:13m:15s left)
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Iteration 80 / LogL: -194120.994 / Time: 0h:11m:16s (0h:11m:24s left)
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Iteration 90 / LogL: -194083.036 / Time: 0h:12m:20s (0h:9m:41s left)
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Iteration 100 / LogL: -194295.624 / Time: 0h:13m:28s (0h:8m:9s left)
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Iteration 110 / LogL: -194091.803 / Time: 0h:14m:34s (0h:6m:41s left)
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Iteration 120 / LogL: -194066.658 / Time: 0h:15m:39s (0h:5m:15s left)
Optimizing NNI: done in 6.37276 secs using 598% CPU
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Iteration 130 / LogL: -194069.788 / Time: 0h:16m:46s (0h:3m:54s left)
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Iteration 140 / LogL: -194082.118 / Time: 0h:17m:52s (0h:2m:34s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 145: -194063.831
Optimizing NNI: done in 7.06784 secs using 597.4% CPU
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Iteration 150 / LogL: -194074.921 / Time: 0h:19m:1s (0h:12m:7s left)
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Iteration 160 / LogL: -194104.981 / Time: 0h:20m:6s (0h:10m:44s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 164: -194062.409
Optimizing NNI: done in 6.09717 secs using 597.8% CPU
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Iteration 170 / LogL: -194080.103 / Time: 0h:21m:15s (0h:11m:49s left)
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Iteration 180 / LogL: -194083.136 / Time: 0h:22m:22s (0h:10m:29s left)
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Iteration 190 / LogL: -194084.871 / Time: 0h:23m:29s (0h:9m:11s left)
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Iteration 200 / LogL: -194152.244 / Time: 0h:24m:33s (0h:7m:53s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 207: -194061.978
Optimizing NNI: done in 5.4695 secs using 597.7% CPU
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Iteration 210 / LogL: -194094.557 / Time: 0h:25m:40s (0h:11m:54s left)
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Iteration 220 / LogL: -194202.913 / Time: 0h:26m:47s (0h:10m:38s left)
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Iteration 230 / LogL: -194173.635 / Time: 0h:27m:56s (0h:9m:23s left)
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Iteration 240 / LogL: -194072.183 / Time: 0h:28m:59s (0h:8m:7s left)
Optimizing NNI: done in 6.87307 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 241: -194060.912
Optimizing NNI: done in 6.24902 secs using 597.9% CPU
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Iteration 250 / LogL: -194087.274 / Time: 0h:30m:7s (0h:11m:0s left)
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Iteration 260 / LogL: -194091.297 / Time: 0h:31m:17s (0h:9m:46s left)
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Iteration 270 / LogL: -194084.584 / Time: 0h:32m:24s (0h:8m:33s left)
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Iteration 280 / LogL: -194094.164 / Time: 0h:33m:31s (0h:7m:19s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 285: -194060.033
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Iteration 290 / LogL: -194088.546 / Time: 0h:34m:44s (0h:11m:25s left)
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Iteration 300 / LogL: -194083.700 / Time: 0h:35m:54s (0h:10m:12s left)
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Iteration 310 / LogL: -194124.063 / Time: 0h:37m:3s (0h:8m:59s left)
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Iteration 320 / LogL: -194158.081 / Time: 0h:38m:9s (0h:7m:46s left)
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Iteration 330 / LogL: -194081.203 / Time: 0h:39m:12s (0h:6m:33s left)
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Iteration 340 / LogL: -194091.806 / Time: 0h:40m:17s (0h:5m:20s left)
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Iteration 350 / LogL: -194101.451 / Time: 0h:41m:21s (0h:4m:8s left)
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Iteration 360 / LogL: -194215.596 / Time: 0h:42m:24s (0h:2m:57s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 361: -194059.748
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Iteration 370 / LogL: -194095.662 / Time: 0h:43m:26s (0h:10m:42s left)
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Iteration 380 / LogL: -194294.919 / Time: 0h:44m:32s (0h:9m:31s left)
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Iteration 390 / LogL: -194103.392 / Time: 0h:45m:34s (0h:8m:19s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 394: -194057.064
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Iteration 430 / LogL: -194126.921 / Time: 0h:50m:3s (0h:7m:28s left)
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Iteration 440 / LogL: -194085.887 / Time: 0h:51m:7s (0h:6m:17s left)
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Iteration 470 / LogL: -194059.682 / Time: 0h:54m:21s (0h:2m:46s left)
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Iteration 480 / LogL: -194086.193 / Time: 0h:55m:23s (0h:1m:37s left)
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Iteration 490 / LogL: -194198.153 / Time: 0h:56m:28s (0h:0m:27s left)
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TREE SEARCH COMPLETED AFTER 495 ITERATIONS / Time: 0h:57m:1s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -194057.064
Optimal log-likelihood: -194057.052
Site proportion and rates:  (0.014,0.086) (0.083,0.269) (0.105,0.386) (0.170,0.521) (0.140,0.699) (0.220,0.970) (0.172,1.573) (0.096,2.767)
Parameters optimization took 1 rounds (1.825 sec)
BEST SCORE FOUND : -194057.052
Total tree length: 161.174

Total number of iterations: 495
CPU time used for tree search: 20135.227 sec (5h:35m:35s)
Wall-clock time used for tree search: 3395.623 sec (0h:56m:35s)
Total CPU time used: 20300.532 sec (5h:38m:20s)
Total wall-clock time used: 3423.385 sec (0h:57m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 63

Creating bootstrap alignment (seed: 70526)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.283 seconds

NOTE: 227 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -195107.135
2. Current log-likelihood: -192584.220
3. Current log-likelihood: -192500.945
4. Current log-likelihood: -192495.638
5. Current log-likelihood: -192495.035
6. Current log-likelihood: -192494.785
7. Current log-likelihood: -192494.661
Optimal log-likelihood: -192494.600
Site proportion and rates:  (0.008,0.094) (0.058,0.246) (0.101,0.381) (0.197,0.512) (0.202,0.734) (0.216,1.059) (0.119,1.690) (0.099,2.721)
Parameters optimization took 7 rounds (16.627 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 13.9776 secs using 599.9% CPU
Computing ML distances took 13.978323 sec (of wall-clock time) 83.851950 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00166416 secs using 542.4% CPU
Constructing RapidNJ tree: done in 0.035795 secs using 671.1% CPU
Computing RapidNJ tree took 0.037552 sec (of wall-clock time) 0.249810 sec (of CPU time)
Log-likelihood of RapidNJ tree: -196989.287
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.747 second
Computing log-likelihood of 98 initial trees ... 21.880 seconds
Current best score: -192494.600

Do NNI search on 20 best initial trees
Optimizing NNI: done in 3.61416 secs using 598.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -191955.996
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -191932.302
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -191895.975
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -191861.188
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Iteration 10 / LogL: -191914.548 / Time: 0h:2m:45s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 12: -191851.938
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Iteration 20 / LogL: -191979.695 / Time: 0h:3m:51s
Finish initializing candidate tree set (20)
Current best tree score: -191851.938 / CPU time: 197.004
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -191847.310
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Iteration 30 / LogL: -191862.921 / Time: 0h:5m:8s (0h:16m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -191803.384
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -191802.299
Iteration 40 / LogL: -191802.299 / Time: 0h:6m:23s (0h:16m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 41: -191763.539
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Iteration 50 / LogL: -191837.075 / Time: 0h:7m:36s (0h:14m:6s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 52: -191757.844
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Iteration 60 / LogL: -191814.650 / Time: 0h:8m:47s (0h:13m:42s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -191750.708
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Iteration 70 / LogL: -191849.696 / Time: 0h:10m:0s (0h:13m:46s left)
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Iteration 80 / LogL: -191763.272 / Time: 0h:11m:10s (0h:12m:0s left)
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Iteration 90 / LogL: -191766.902 / Time: 0h:12m:22s (0h:10m:25s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 93: -191749.133
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 96: -191746.637
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 99: -191744.332
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Iteration 100 / LogL: -191824.732 / Time: 0h:13m:42s (0h:13m:41s left)
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BETTER TREE FOUND at iteration 120: -191742.698
Iteration 120 / LogL: -191742.698 / Time: 0h:16m:3s (0h:13m:29s left)
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BETTER TREE FOUND at iteration 167: -191704.574
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 267: -191697.706
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Iteration 360 / LogL: -191723.801 / Time: 0h:43m:24s (0h:0m:50s left)
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TREE SEARCH COMPLETED AFTER 368 ITERATIONS / Time: 0h:44m:19s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -191697.706
Optimal log-likelihood: -191697.702
Site proportion and rates:  (0.009,0.093) (0.064,0.251) (0.147,0.402) (0.159,0.544) (0.197,0.741) (0.213,1.075) (0.118,1.715) (0.093,2.783)
Parameters optimization took 1 rounds (1.073 sec)
BEST SCORE FOUND : -191697.702
Total tree length: 149.216

Total number of iterations: 368
CPU time used for tree search: 15542.468 sec (4h:19m:2s)
Wall-clock time used for tree search: 2624.972 sec (0h:43m:44s)
Total CPU time used: 15757.199 sec (4h:22m:37s)
Total wall-clock time used: 2660.973 sec (0h:44m:20s)

===> START BOOTSTRAP REPLICATE NUMBER 64

Creating bootstrap alignment (seed: 70527)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.282 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -200344.598
2. Current log-likelihood: -197806.876
3. Current log-likelihood: -197780.327
4. Current log-likelihood: -197778.614
Optimal log-likelihood: -197778.505
Site proportion and rates:  (0.011,0.102) (0.007,0.244) (0.070,0.252) (0.216,0.420) (0.206,0.662) (0.199,0.967) (0.179,1.546) (0.111,2.533)
Parameters optimization took 4 rounds (11.221 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 11.3544 secs using 599.9% CPU
Computing ML distances took 11.355042 sec (of wall-clock time) 68.118998 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.0016942 secs using 362.6% CPU
Constructing RapidNJ tree: done in 0.0360332 secs using 688.1% CPU
Computing RapidNJ tree took 0.037812 sec (of wall-clock time) 0.254638 sec (of CPU time)
Log-likelihood of RapidNJ tree: -201593.893
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.905 second
Computing log-likelihood of 98 initial trees ... 22.127 seconds
Current best score: -197778.505

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.20008 secs using 598.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -197173.640
Optimizing NNI: done in 7.05664 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -197095.131
Optimizing NNI: done in 9.99571 secs using 597.2% CPU
Optimizing NNI: done in 6.08151 secs using 597.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 8: -197081.667
Optimizing NNI: done in 7.72085 secs using 597.5% CPU
Optimizing NNI: done in 7.83555 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 10: -197078.213
Iteration 10 / LogL: -197078.213 / Time: 0h:3m:13s
Optimizing NNI: done in 6.66457 secs using 597.4% CPU
Optimizing NNI: done in 7.30671 secs using 597.8% CPU
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BETTER TREE FOUND at iteration 12: -197067.488
Optimizing NNI: done in 7.37178 secs using 597.7% CPU
Optimizing NNI: done in 7.18256 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 14: -197001.572
Optimizing NNI: done in 6.66684 secs using 597.2% CPU
Optimizing NNI: done in 8.23984 secs using 597.5% CPU
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Optimizing NNI: done in 7.31653 secs using 597.2% CPU
Optimizing NNI: done in 8.16237 secs using 597.3% CPU
Iteration 20 / LogL: -197120.151 / Time: 0h:4m:48s
Finish initializing candidate tree set (20)
Current best tree score: -197001.572 / CPU time: 261.319
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.39865 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -196984.598
Optimizing NNI: done in 7.31495 secs using 598% CPU
Optimizing NNI: done in 6.4743 secs using 597.5% CPU
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Iteration 30 / LogL: -197161.343 / Time: 0h:6m:6s (0h:19m:7s left)
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Iteration 40 / LogL: -197036.233 / Time: 0h:7m:23s (0h:15m:19s left)
Optimizing NNI: done in 7.85888 secs using 597.7% CPU
Optimizing NNI: done in 8.27582 secs using 596.7% CPU
Optimizing NNI: done in 8.06166 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 43: -196980.762
Optimizing NNI: done in 7.79292 secs using 597.7% CPU
Optimizing NNI: done in 7.64015 secs using 597.9% CPU
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Iteration 50 / LogL: -196998.028 / Time: 0h:8m:42s (0h:16m:31s left)
Optimizing NNI: done in 7.15333 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -196977.249
Optimizing NNI: done in 7.37542 secs using 597.6% CPU
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Iteration 60 / LogL: -197021.013 / Time: 0h:10m:3s (0h:15m:29s left)
Optimizing NNI: done in 7.32886 secs using 597.8% CPU
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Optimizing NNI: done in 7.54454 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -196961.743
Optimizing NNI: done in 7.71537 secs using 597.5% CPU
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Iteration 70 / LogL: -196989.329 / Time: 0h:11m:21s (0h:15m:37s left)
Optimizing NNI: done in 6.90515 secs using 597.9% CPU
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Iteration 80 / LogL: -196982.604 / Time: 0h:12m:37s (0h:13m:34s left)
Optimizing NNI: done in 8.41442 secs using 597.3% CPU
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Optimizing NNI: done in 7.10931 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 86: -196960.288
Optimizing NNI: done in 7.36114 secs using 597.2% CPU
Optimizing NNI: done in 7.76104 secs using 597.7% CPU
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Iteration 90 / LogL: -196971.327 / Time: 0h:13m:56s (0h:15m:2s left)
Optimizing NNI: done in 7.39683 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 91: -196959.220
Optimizing NNI: done in 7.05973 secs using 597.6% CPU
Optimizing NNI: done in 7.02926 secs using 597.8% CPU
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Optimizing NNI: done in 8.25147 secs using 597.9% CPU
Iteration 100 / LogL: -197137.638 / Time: 0h:15m:12s (0h:13m:58s left)
Optimizing NNI: done in 8.01642 secs using 597.6% CPU
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Optimizing NNI: done in 6.958 secs using 597.2% CPU
Optimizing NNI: done in 7.60879 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 106: -196955.749
Optimizing NNI: done in 7.65471 secs using 597.9% CPU
Optimizing NNI: done in 7.79681 secs using 597.9% CPU
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Iteration 110 / LogL: -197002.959 / Time: 0h:16m:33s (0h:14m:34s left)
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Iteration 120 / LogL: -196978.829 / Time: 0h:17m:41s (0h:12m:47s left)
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Iteration 130 / LogL: -197190.725 / Time: 0h:18m:54s (0h:11m:8s left)
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Iteration 140 / LogL: -196957.894 / Time: 0h:20m:7s (0h:9m:33s left)
Optimizing NNI: done in 6.5074 secs using 597.1% CPU
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Iteration 150 / LogL: -197024.103 / Time: 0h:21m:21s (0h:8m:1s left)
Optimizing NNI: done in 7.35449 secs using 597.2% CPU
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Iteration 160 / LogL: -196969.147 / Time: 0h:22m:35s (0h:6m:32s left)
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Iteration 170 / LogL: -197032.755 / Time: 0h:23m:56s (0h:5m:5s left)
Optimizing NNI: done in 5.6369 secs using 597.3% CPU
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Iteration 180 / LogL: -196983.692 / Time: 0h:25m:7s (0h:3m:38s left)
Optimizing NNI: done in 7.01412 secs using 596.9% CPU
Optimizing NNI: done in 6.65388 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 182: -196954.144
Optimizing NNI: done in 5.7602 secs using 597.4% CPU
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Iteration 190 / LogL: -196984.852 / Time: 0h:26m:25s (0h:12m:51s left)
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Iteration 200 / LogL: -197013.758 / Time: 0h:27m:40s (0h:11m:23s left)
Optimizing NNI: done in 6.62052 secs using 598% CPU
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Iteration 210 / LogL: -196962.967 / Time: 0h:28m:53s (0h:9m:56s left)
Optimizing NNI: done in 7.13681 secs using 598% CPU
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Iteration 220 / LogL: -196968.873 / Time: 0h:30m:3s (0h:8m:30s left)
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Iteration 230 / LogL: -197014.742 / Time: 0h:31m:16s (0h:7m:6s left)
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Iteration 240 / LogL: -196974.795 / Time: 0h:32m:30s (0h:5m:42s left)
Optimizing NNI: done in 7.36348 secs using 597.5% CPU
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Iteration 250 / LogL: -197025.777 / Time: 0h:33m:45s (0h:4m:20s left)
Optimizing NNI: done in 6.71819 secs using 597.6% CPU
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Iteration 260 / LogL: -197159.276 / Time: 0h:35m:1s (0h:2m:58s left)
Optimizing NNI: done in 7.68692 secs using 597.5% CPU
Optimizing NNI: done in 7.44296 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 262: -196953.060
Optimizing NNI: done in 7.07067 secs using 598% CPU
Optimizing NNI: done in 6.9622 secs using 598% CPU
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Iteration 270 / LogL: -197007.010 / Time: 0h:36m:19s (0h:12m:25s left)
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Iteration 280 / LogL: -197020.352 / Time: 0h:37m:28s (0h:11m:0s left)
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Iteration 290 / LogL: -196992.560 / Time: 0h:38m:42s (0h:9m:38s left)
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Iteration 300 / LogL: -197006.253 / Time: 0h:39m:51s (0h:8m:15s left)
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Iteration 310 / LogL: -196990.257 / Time: 0h:41m:10s (0h:6m:55s left)
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Iteration 320 / LogL: -197123.583 / Time: 0h:42m:23s (0h:5m:34s left)
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Iteration 330 / LogL: -197010.384 / Time: 0h:43m:36s (0h:4m:14s left)
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Iteration 340 / LogL: -196978.084 / Time: 0h:44m:48s (0h:2m:54s left)
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Iteration 350 / LogL: -196988.103 / Time: 0h:45m:59s (0h:1m:34s left)
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Iteration 360 / LogL: -197176.816 / Time: 0h:47m:13s (0h:0m:15s left)
Optimizing NNI: done in 6.04798 secs using 598.1% CPU
Optimizing NNI: done in 6.38887 secs using 597.7% CPU
Optimizing NNI: done in 8.30195 secs using 597.4% CPU
TREE SEARCH COMPLETED AFTER 363 ITERATIONS / Time: 0h:47m:34s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -196953.060
2. Current log-likelihood: -196953.033
Optimal log-likelihood: -196953.028
Site proportion and rates:  (0.011,0.101) (0.061,0.247) (0.167,0.377) (0.183,0.556) (0.207,0.820) (0.139,1.195) (0.134,1.692) (0.099,2.596)
Parameters optimization took 2 rounds (3.702 sec)
BEST SCORE FOUND : -196953.028
Total tree length: 157.599

Total number of iterations: 363
CPU time used for tree search: 16741.369 sec (4h:39m:1s)
Wall-clock time used for tree search: 2827.382 sec (0h:47m:7s)
Total CPU time used: 16923.600 sec (4h:42m:3s)
Total wall-clock time used: 2857.951 sec (0h:47m:37s)

===> START BOOTSTRAP REPLICATE NUMBER 65

Creating bootstrap alignment (seed: 70528)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.285 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196668.693
2. Current log-likelihood: -193876.418
3. Current log-likelihood: -193848.664
4. Current log-likelihood: -193848.498
Optimal log-likelihood: -193848.425
Site proportion and rates:  (0.015,0.098) (0.038,0.187) (0.069,0.317) (0.177,0.452) (0.226,0.647) (0.208,0.970) (0.164,1.625) (0.102,2.691)
Parameters optimization took 4 rounds (9.975 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 13.378 secs using 599.9% CPU
Computing ML distances took 13.378592 sec (of wall-clock time) 80.258204 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00182796 secs using 376.9% CPU
Constructing RapidNJ tree: done in 0.0431418 secs using 678.6% CPU
Computing RapidNJ tree took 0.045023 sec (of wall-clock time) 0.300044 sec (of CPU time)
Log-likelihood of RapidNJ tree: -197538.347
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.262 second
Computing log-likelihood of 98 initial trees ... 23.419 seconds
Current best score: -193848.425

Do NNI search on 20 best initial trees
Optimizing NNI: done in 3.68855 secs using 598.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -193401.703
Optimizing NNI: done in 6.51809 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -193078.077
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 8: -193067.910
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Iteration 10 / LogL: -193180.396 / Time: 0h:3m:9s
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Iteration 20 / LogL: -193157.382 / Time: 0h:4m:16s
Finish initializing candidate tree set (20)
Current best tree score: -193067.910 / CPU time: 228.799
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -193054.691
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -193052.498
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Iteration 30 / LogL: -193098.755 / Time: 0h:5m:34s (0h:18m:48s left)
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BETTER TREE FOUND at iteration 32: -193030.562
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Iteration 40 / LogL: -193032.316 / Time: 0h:6m:49s (0h:16m:4s left)
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BETTER TREE FOUND at iteration 43: -193029.164
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BETTER TREE FOUND at iteration 47: -193026.679
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 50: -193021.273
Iteration 50 / LogL: -193021.273 / Time: 0h:8m:9s (0h:16m:38s left)
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Iteration 60 / LogL: -193093.773 / Time: 0h:9m:19s (0h:14m:12s left)
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Iteration 70 / LogL: -193028.327 / Time: 0h:10m:30s (0h:12m:10s left)
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Iteration 80 / LogL: -193071.588 / Time: 0h:11m:42s (0h:10m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 84: -193008.177
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 86: -193007.365
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Iteration 90 / LogL: -193022.228 / Time: 0h:12m:58s (0h:13m:59s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 99: -192999.873
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Iteration 100 / LogL: -193193.982 / Time: 0h:14m:9s (0h:14m:9s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 110: -192997.379
Iteration 110 / LogL: -192997.379 / Time: 0h:15m:22s (0h:14m:6s left)
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Iteration 120 / LogL: -193057.455 / Time: 0h:16m:33s (0h:12m:31s left)
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Iteration 130 / LogL: -193037.411 / Time: 0h:17m:42s (0h:10m:58s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 134: -192995.983
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 140: -192990.309
Iteration 140 / LogL: -192990.309 / Time: 0h:19m:0s (0h:13m:40s left)
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Iteration 150 / LogL: -193007.089 / Time: 0h:20m:4s (0h:12m:7s left)
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Iteration 160 / LogL: -193105.617 / Time: 0h:21m:1s (0h:10m:34s left)
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Iteration 180 / LogL: -193125.350 / Time: 0h:23m:17s (0h:7m:48s left)
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Iteration 190 / LogL: -193019.543 / Time: 0h:24m:37s (0h:6m:30s left)
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Iteration 200 / LogL: -193061.369 / Time: 0h:25m:55s (0h:5m:12s left)
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Iteration 210 / LogL: -193003.894 / Time: 0h:27m:16s (0h:3m:54s left)
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Iteration 220 / LogL: -193079.901 / Time: 0h:28m:35s (0h:2m:36s left)
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Iteration 230 / LogL: -193026.023 / Time: 0h:29m:47s (0h:1m:18s left)
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Iteration 240 / LogL: -193111.152 / Time: 0h:30m:59s (0h:0m:0s left)
Optimizing NNI: done in 6.90346 secs using 597.9% CPU
TREE SEARCH COMPLETED AFTER 241 ITERATIONS / Time: 0h:31m:6s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192990.309
Optimal log-likelihood: -192990.309
Site proportion and rates:  (0.015,0.099) (0.044,0.201) (0.150,0.371) (0.221,0.551) (0.150,0.762) (0.159,1.033) (0.162,1.657) (0.097,2.719)
Parameters optimization took 1 rounds (0.555 sec)
BEST SCORE FOUND : -192990.309
Total tree length: 154.369

Total number of iterations: 241
CPU time used for tree search: 10844.090 sec (3h:0m:44s)
Wall-clock time used for tree search: 1838.889 sec (0h:30m:38s)
Total CPU time used: 11010.335 sec (3h:3m:30s)
Total wall-clock time used: 1866.765 sec (0h:31m:6s)

===> START BOOTSTRAP REPLICATE NUMBER 66

Creating bootstrap alignment (seed: 70529)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.320 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194160.304
2. Current log-likelihood: -191415.624
3. Current log-likelihood: -191395.826
4. Current log-likelihood: -191395.159
5. Current log-likelihood: -191394.985
Optimal log-likelihood: -191394.944
Site proportion and rates:  (0.012,0.113) (0.005,0.204) (0.047,0.237) (0.144,0.379) (0.270,0.600) (0.261,0.944) (0.164,1.595) (0.097,2.688)
Parameters optimization took 5 rounds (13.418 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.012 secs using 599.9% CPU
Computing ML distances took 19.012576 sec (of wall-clock time) 114.055271 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00150108 secs using 677.8% CPU
Constructing RapidNJ tree: done in 0.0408819 secs using 679.9% CPU
Computing RapidNJ tree took 0.042447 sec (of wall-clock time) 0.288748 sec (of CPU time)
Log-likelihood of RapidNJ tree: -195698.663
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.998 second
Computing log-likelihood of 98 initial trees ... 21.835 seconds
Current best score: -191394.944

Do NNI search on 20 best initial trees
Optimizing NNI: done in 3.78326 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -190814.924
Optimizing NNI: done in 5.34152 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -190713.843
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Iteration 10 / LogL: -190723.330 / Time: 0h:2m:30s
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Iteration 20 / LogL: -190732.988 / Time: 0h:3m:28s
Finish initializing candidate tree set (20)
Current best tree score: -190713.843 / CPU time: 173.243
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.75835 secs using 594.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -190676.711
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -190646.831
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Iteration 30 / LogL: -190772.126 / Time: 0h:4m:35s (0h:15m:39s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 39: -190633.828
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Iteration 40 / LogL: -190711.782 / Time: 0h:5m:40s (0h:14m:24s left)
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Iteration 70 / LogL: -190635.619 / Time: 0h:8m:53s (0h:8m:53s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 75: -190633.266
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 79: -190618.668
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Iteration 100 / LogL: -190691.107 / Time: 0h:12m:2s (0h:9m:36s left)
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Iteration 120 / LogL: -190628.773 / Time: 0h:14m:7s (0h:7m:0s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 177: -190606.987
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Iteration 190 / LogL: -190622.527 / Time: 0h:21m:15s (0h:9m:47s left)
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Iteration 200 / LogL: -190662.334 / Time: 0h:22m:15s (0h:8m:36s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 205: -190605.945
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Iteration 210 / LogL: -190688.827 / Time: 0h:23m:17s (0h:10m:35s left)
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Iteration 220 / LogL: -190663.988 / Time: 0h:24m:15s (0h:9m:24s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 226: -190600.942
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Iteration 280 / LogL: -190677.618 / Time: 0h:30m:21s (0h:5m:0s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 281: -190600.493
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Iteration 330 / LogL: -190679.766 / Time: 0h:35m:33s (0h:5m:30s left)
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Iteration 350 / LogL: -190613.020 / Time: 0h:37m:35s (0h:3m:20s left)
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Iteration 360 / LogL: -190608.572 / Time: 0h:38m:35s (0h:2m:15s left)
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Iteration 370 / LogL: -190627.202 / Time: 0h:39m:36s (0h:1m:10s left)
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Iteration 380 / LogL: -190611.293 / Time: 0h:40m:38s (0h:0m:6s left)
Optimizing NNI: done in 5.64924 secs using 597.6% CPU
Optimizing NNI: done in 6.18749 secs using 597.4% CPU
TREE SEARCH COMPLETED AFTER 382 ITERATIONS / Time: 0h:40m:50s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -190600.493
2. Current log-likelihood: -190600.468
3. Current log-likelihood: -190600.431
4. Current log-likelihood: -190600.381
5. Current log-likelihood: -190600.314
6. Current log-likelihood: -190600.222
7. Current log-likelihood: -190600.104
8. Current log-likelihood: -190599.972
9. Current log-likelihood: -190599.834
10. Current log-likelihood: -190599.699
11. Current log-likelihood: -190599.568
12. Current log-likelihood: -190599.436
13. Current log-likelihood: -190599.300
14. Current log-likelihood: -190599.166
15. Current log-likelihood: -190599.033
16. Current log-likelihood: -190598.906
17. Current log-likelihood: -190598.787
18. Current log-likelihood: -190598.681
19. Current log-likelihood: -190598.586
20. Current log-likelihood: -190598.495
21. Current log-likelihood: -190598.416
22. Current log-likelihood: -190598.336
23. Current log-likelihood: -190598.252
24. Current log-likelihood: -190598.162
25. Current log-likelihood: -190598.071
26. Current log-likelihood: -190597.968
27. Current log-likelihood: -190597.863
28. Current log-likelihood: -190597.745
29. Current log-likelihood: -190597.614
30. Current log-likelihood: -190597.472
31. Current log-likelihood: -190597.317
32. Current log-likelihood: -190597.154
33. Current log-likelihood: -190596.990
34. Current log-likelihood: -190596.829
35. Current log-likelihood: -190596.670
36. Current log-likelihood: -190596.523
37. Current log-likelihood: -190596.392
38. Current log-likelihood: -190596.279
39. Current log-likelihood: -190596.182
40. Current log-likelihood: -190596.099
41. Current log-likelihood: -190596.038
42. Current log-likelihood: -190595.992
43. Current log-likelihood: -190595.961
44. Current log-likelihood: -190595.944
45. Current log-likelihood: -190595.932
Optimal log-likelihood: -190595.932
Site proportion and rates:  (0.015,0.125) (0.056,0.256) (0.136,0.381) (0.236,0.582) (0.099,0.767) (0.197,0.986) (0.163,1.604) (0.097,2.705)
Parameters optimization took 45 rounds (97.199 sec)
BEST SCORE FOUND : -190595.932
Total tree length: 154.948

Total number of iterations: 382
CPU time used for tree search: 14287.176 sec (3h:58m:7s)
Wall-clock time used for tree search: 2415.695 sec (0h:40m:15s)
Total CPU time used: 15076.314 sec (4h:11m:16s)
Total wall-clock time used: 2548.010 sec (0h:42m:28s)

===> START BOOTSTRAP REPLICATE NUMBER 67

Creating bootstrap alignment (seed: 70530)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.346 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -197188.275
2. Current log-likelihood: -194665.058
3. Current log-likelihood: -194643.734
4. Current log-likelihood: -194643.323
5. Current log-likelihood: -194643.098
6. Current log-likelihood: -194642.916
7. Current log-likelihood: -194642.787
Optimal log-likelihood: -194642.736
Site proportion and rates:  (0.009,0.103) (0.042,0.241) (0.024,0.250) (0.163,0.402) (0.235,0.612) (0.257,0.960) (0.166,1.527) (0.104,2.636)
Parameters optimization took 7 rounds (17.655 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 11.1016 secs using 599.6% CPU
Computing ML distances took 11.102233 sec (of wall-clock time) 66.566976 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00131297 secs using 442.4% CPU
Constructing RapidNJ tree: done in 0.04828 secs using 682.1% CPU
Computing RapidNJ tree took 0.049665 sec (of wall-clock time) 0.335543 sec (of CPU time)
Log-likelihood of RapidNJ tree: -198468.837
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.509 second
Computing log-likelihood of 98 initial trees ... 23.805 seconds
Current best score: -194642.736

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.44709 secs using 598.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -194181.415
Optimizing NNI: done in 6.37251 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -194047.151
Optimizing NNI: done in 6.47589 secs using 597.4% CPU
Optimizing NNI: done in 6.19576 secs using 597.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -194031.738
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -194006.693
Optimizing NNI: done in 6.00349 secs using 597.9% CPU
Iteration 10 / LogL: -194185.304 / Time: 0h:2m:43s
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Iteration 20 / LogL: -194035.984 / Time: 0h:3m:46s
Finish initializing candidate tree set (20)
Current best tree score: -194006.693 / CPU time: 194.427
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.95416 secs using 597.9% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -193991.066
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -193969.164
Optimizing NNI: done in 8.76675 secs using 597.8% CPU
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Iteration 30 / LogL: -194081.131 / Time: 0h:5m:5s (0h:17m:12s left)
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Iteration 40 / LogL: -193978.093 / Time: 0h:6m:19s (0h:14m:15s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 46: -193963.317
Optimizing NNI: done in 7.48974 secs using 597.6% CPU
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Iteration 50 / LogL: -193993.426 / Time: 0h:7m:36s (0h:14m:53s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 53: -193958.829
Optimizing NNI: done in 5.88472 secs using 598% CPU
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Iteration 60 / LogL: -193982.604 / Time: 0h:8m:48s (0h:13m:51s left)
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Iteration 70 / LogL: -193970.168 / Time: 0h:9m:56s (0h:11m:56s left)
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BETTER TREE FOUND at iteration 73: -193957.204
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BETTER TREE FOUND at iteration 97: -193955.935
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 171: -193953.276
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Estimate model parameters (epsilon = 0.100)
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BETTER TREE FOUND at iteration 213: -193945.950
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Iteration 290 / LogL: -193956.467 / Time: 0h:36m:52s (0h:2m:56s left)
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Iteration 300 / LogL: -194003.418 / Time: 0h:38m:6s (0h:1m:39s left)
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Iteration 310 / LogL: -194046.576 / Time: 0h:39m:20s (0h:0m:22s left)
Optimizing NNI: done in 5.91118 secs using 598% CPU
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TREE SEARCH COMPLETED AFTER 314 ITERATIONS / Time: 0h:39m:46s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -193945.950
Optimal log-likelihood: -193945.950
Site proportion and rates:  (0.010,0.109) (0.043,0.247) (0.020,0.253) (0.155,0.391) (0.242,0.604) (0.260,0.959) (0.167,1.523) (0.103,2.649)
Parameters optimization took 1 rounds (0.610 sec)
BEST SCORE FOUND : -193945.950
Total tree length: 148.508

Total number of iterations: 314
CPU time used for tree search: 13925.614 sec (3h:52m:5s)
Wall-clock time used for tree search: 2354.901 sec (0h:39m:14s)
Total CPU time used: 14119.876 sec (3h:55m:19s)
Total wall-clock time used: 2387.566 sec (0h:39m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 68

Creating bootstrap alignment (seed: 70531)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.287 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199249.702
2. Current log-likelihood: -196545.060
3. Current log-likelihood: -196516.851
4. Current log-likelihood: -196506.612
5. Current log-likelihood: -196505.055
6. Current log-likelihood: -196504.817
Optimal log-likelihood: -196504.763
Site proportion and rates:  (0.014,0.102) (0.031,0.217) (0.120,0.315) (0.201,0.525) (0.189,0.772) (0.169,1.009) (0.193,1.568) (0.084,2.745)
Parameters optimization took 6 rounds (15.826 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 9.80084 secs using 599.9% CPU
Computing ML distances took 9.801587 sec (of wall-clock time) 58.799411 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00182796 secs using 202% CPU
Constructing RapidNJ tree: done in 0.0410299 secs using 692% CPU
Computing RapidNJ tree took 0.042933 sec (of wall-clock time) 0.288195 sec (of CPU time)
Log-likelihood of RapidNJ tree: -200301.179
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.653 second
Computing log-likelihood of 98 initial trees ... 21.754 seconds
Current best score: -196504.763

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.53967 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -196014.697
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -195965.150
Optimizing NNI: done in 6.75392 secs using 596.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -195905.828
Optimizing NNI: done in 6.76216 secs using 597.4% CPU
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Iteration 10 / LogL: -195929.929 / Time: 0h:2m:38s
Optimizing NNI: done in 6.89976 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 11: -195904.812
Optimizing NNI: done in 6.23084 secs using 597.7% CPU
Optimizing NNI: done in 6.88672 secs using 597.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 16: -195903.060
Optimizing NNI: done in 6.86152 secs using 597.1% CPU
Optimizing NNI: done in 6.60855 secs using 596.9% CPU
Optimizing NNI: done in 6.31684 secs using 597.4% CPU
Optimizing NNI: done in 6.1385 secs using 596.8% CPU
Iteration 20 / LogL: -195956.336 / Time: 0h:3m:56s
Finish initializing candidate tree set (20)
Current best tree score: -195903.060 / CPU time: 208.037
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.48852 secs using 597.6% CPU
Optimizing NNI: done in 7.14197 secs using 595.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -195885.982
Optimizing NNI: done in 8.32008 secs using 598.1% CPU
Optimizing NNI: done in 6.74643 secs using 598% CPU
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BETTER TREE FOUND at iteration 24: -195871.779
Optimizing NNI: done in 6.20179 secs using 597.8% CPU
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Iteration 30 / LogL: -195885.668 / Time: 0h:5m:16s (0h:17m:5s left)
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BETTER TREE FOUND at iteration 37: -195859.555
Optimizing NNI: done in 6.86414 secs using 597.6% CPU
Optimizing NNI: done in 7.2643 secs using 597.7% CPU
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Iteration 40 / LogL: -195868.057 / Time: 0h:6m:26s (0h:16m:1s left)
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Iteration 50 / LogL: -195882.549 / Time: 0h:7m:33s (0h:13m:24s left)
Optimizing NNI: done in 7.28222 secs using 596.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -195851.202
Optimizing NNI: done in 6.56905 secs using 595.4% CPU
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Iteration 60 / LogL: -195941.567 / Time: 0h:8m:49s (0h:13m:35s left)
Optimizing NNI: done in 6.91453 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 61: -195846.211
Optimizing NNI: done in 7.01682 secs using 597.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -195841.309
Optimizing NNI: done in 6.21656 secs using 597.7% CPU
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Iteration 70 / LogL: -195869.305 / Time: 0h:10m:1s (0h:13m:47s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 77: -195838.219
Optimizing NNI: done in 6.26528 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 78: -195835.608
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 80: -195835.552
Iteration 80 / LogL: -195835.552 / Time: 0h:11m:17s (0h:14m:17s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 83: -195831.276
Optimizing NNI: done in 6.4433 secs using 597.3% CPU
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Iteration 90 / LogL: -195847.038 / Time: 0h:12m:28s (0h:13m:1s left)
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Iteration 100 / LogL: -195972.007 / Time: 0h:13m:34s (0h:11m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 103: -195827.973
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Optimizing NNI: done in 6.68981 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 105: -195817.390
Optimizing NNI: done in 6.15619 secs using 597.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 108: -195812.833
Optimizing NNI: done in 6.69949 secs using 597.8% CPU
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Iteration 110 / LogL: -195826.059 / Time: 0h:14m:52s (0h:13m:22s left)
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Iteration 120 / LogL: -195921.794 / Time: 0h:15m:56s (0h:11m:47s left)
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Iteration 130 / LogL: -195880.585 / Time: 0h:17m:2s (0h:10m:18s left)
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Iteration 140 / LogL: -195864.770 / Time: 0h:18m:9s (0h:8m:53s left)
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Iteration 150 / LogL: -195874.196 / Time: 0h:19m:16s (0h:7m:30s left)
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Iteration 160 / LogL: -195829.093 / Time: 0h:20m:21s (0h:6m:8s left)
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Iteration 170 / LogL: -195904.026 / Time: 0h:21m:30s (0h:4m:50s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 175: -195810.621
Optimizing NNI: done in 7.04029 secs using 597.7% CPU
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Iteration 180 / LogL: -195881.734 / Time: 0h:22m:39s (0h:12m:1s left)
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Iteration 190 / LogL: -195857.887 / Time: 0h:23m:45s (0h:10m:41s left)
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Iteration 200 / LogL: -195814.281 / Time: 0h:24m:53s (0h:9m:22s left)
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Iteration 210 / LogL: -195873.611 / Time: 0h:26m:3s (0h:8m:6s left)
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Iteration 220 / LogL: -195810.943 / Time: 0h:27m:12s (0h:6m:49s left)
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Iteration 230 / LogL: -195985.213 / Time: 0h:28m:21s (0h:5m:34s left)
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Iteration 240 / LogL: -195819.618 / Time: 0h:29m:29s (0h:4m:19s left)
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Iteration 250 / LogL: -195946.890 / Time: 0h:30m:37s (0h:3m:4s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 260: -195807.464
Iteration 260 / LogL: -195807.464 / Time: 0h:31m:54s (0h:12m:19s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 265: -195805.965
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Iteration 270 / LogL: -195834.237 / Time: 0h:33m:9s (0h:11m:42s left)
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Iteration 280 / LogL: -195881.854 / Time: 0h:34m:17s (0h:10m:26s left)
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Iteration 290 / LogL: -195829.549 / Time: 0h:35m:29s (0h:9m:12s left)
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Iteration 300 / LogL: -195825.228 / Time: 0h:36m:38s (0h:7m:57s left)
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Iteration 310 / LogL: -195854.604 / Time: 0h:37m:50s (0h:6m:44s left)
Optimizing NNI: done in 6.75242 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 311: -195796.475
Optimizing NNI: done in 6.74874 secs using 597.9% CPU
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Iteration 320 / LogL: -195810.757 / Time: 0h:39m:2s (0h:11m:8s left)
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Iteration 330 / LogL: -195805.395 / Time: 0h:40m:11s (0h:9m:53s left)
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Iteration 340 / LogL: -195870.401 / Time: 0h:41m:17s (0h:8m:38s left)
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Iteration 350 / LogL: -195896.845 / Time: 0h:42m:27s (0h:7m:25s left)
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Iteration 360 / LogL: -195867.091 / Time: 0h:43m:37s (0h:6m:11s left)
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Iteration 370 / LogL: -195954.727 / Time: 0h:44m:42s (0h:4m:58s left)
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Iteration 380 / LogL: -195808.333 / Time: 0h:45m:51s (0h:3m:45s left)
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Iteration 390 / LogL: -195827.600 / Time: 0h:47m:2s (0h:2m:32s left)
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Iteration 400 / LogL: -195815.132 / Time: 0h:48m:9s (0h:1m:19s left)
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Iteration 410 / LogL: -195822.270 / Time: 0h:49m:20s (0h:0m:7s left)
Optimizing NNI: done in 6.44508 secs using 597.4% CPU
Optimizing NNI: done in 6.15934 secs using 598% CPU
TREE SEARCH COMPLETED AFTER 412 ITERATIONS / Time: 0h:49m:33s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -195796.475
Optimal log-likelihood: -195796.471
Site proportion and rates:  (0.014,0.102) (0.059,0.245) (0.099,0.332) (0.213,0.540) (0.201,0.800) (0.149,1.053) (0.184,1.579) (0.083,2.761)
Parameters optimization took 1 rounds (1.321 sec)
BEST SCORE FOUND : -195796.471
Total tree length: 151.907

Total number of iterations: 412
CPU time used for tree search: 17452.272 sec (4h:50m:52s)
Wall-clock time used for tree search: 2945.195 sec (0h:49m:5s)
Total CPU time used: 17628.930 sec (4h:53m:48s)
Total wall-clock time used: 2974.845 sec (0h:49m:34s)

===> START BOOTSTRAP REPLICATE NUMBER 69

Creating bootstrap alignment (seed: 70532)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.377 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -191337.059
2. Current log-likelihood: -189007.084
3. Current log-likelihood: -188972.382
4. Current log-likelihood: -188971.498
Optimal log-likelihood: -188971.441
Site proportion and rates:  (0.011,0.106) (0.023,0.196) (0.079,0.294) (0.092,0.411) (0.279,0.597) (0.225,0.985) (0.220,1.603) (0.070,2.746)
Parameters optimization took 4 rounds (11.546 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 10.5696 secs using 599.9% CPU
Computing ML distances took 10.570335 sec (of wall-clock time) 63.409515 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00152707 secs using 309.9% CPU
Constructing RapidNJ tree: done in 0.0436461 secs using 672.9% CPU
Computing RapidNJ tree took 0.045269 sec (of wall-clock time) 0.299087 sec (of CPU time)
Log-likelihood of RapidNJ tree: -193698.147
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.128 second
Computing log-likelihood of 98 initial trees ... 23.031 seconds
Current best score: -188971.441

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.61671 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -188428.290
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -188256.570
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -188246.302
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Iteration 10 / LogL: -188294.960 / Time: 0h:2m:51s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 12: -188234.220
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Iteration 20 / LogL: -188350.369 / Time: 0h:3m:55s
Finish initializing candidate tree set (20)
Current best tree score: -188234.220 / CPU time: 211.226
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -188231.374
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -188230.483
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -188221.841
Iteration 30 / LogL: -188221.841 / Time: 0h:5m:20s (0h:18m:24s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -188206.088
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Iteration 40 / LogL: -188251.885 / Time: 0h:6m:35s (0h:16m:1s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -188197.888
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Iteration 50 / LogL: -188265.665 / Time: 0h:7m:46s (0h:14m:35s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 55: -188195.348
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Iteration 60 / LogL: -188207.627 / Time: 0h:9m:3s (0h:14m:34s left)
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Iteration 70 / LogL: -188215.496 / Time: 0h:10m:18s (0h:12m:41s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 77: -188188.284
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Iteration 80 / LogL: -188267.297 / Time: 0h:11m:31s (0h:14m:8s left)
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Iteration 90 / LogL: -188207.341 / Time: 0h:12m:44s (0h:12m:26s left)
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Iteration 100 / LogL: -188225.588 / Time: 0h:13m:58s (0h:10m:52s left)
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Iteration 110 / LogL: -188231.531 / Time: 0h:15m:13s (0h:9m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 118: -188180.086
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Iteration 120 / LogL: -188207.272 / Time: 0h:16m:29s (0h:13m:34s left)
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Iteration 130 / LogL: -188201.168 / Time: 0h:17m:43s (0h:12m:5s left)
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Iteration 140 / LogL: -188218.714 / Time: 0h:18m:57s (0h:10m:38s left)
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Iteration 150 / LogL: -188361.278 / Time: 0h:20m:9s (0h:9m:11s left)
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Iteration 160 / LogL: -188235.980 / Time: 0h:21m:25s (0h:7m:48s left)
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Iteration 170 / LogL: -188195.608 / Time: 0h:22m:38s (0h:6m:25s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 173: -188178.620
Optimizing NNI: done in 7.87803 secs using 598.1% CPU
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Iteration 180 / LogL: -188212.328 / Time: 0h:23m:55s (0h:12m:25s left)
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Iteration 190 / LogL: -188189.798 / Time: 0h:25m:10s (0h:11m:3s left)
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Iteration 200 / LogL: -188224.021 / Time: 0h:26m:24s (0h:9m:40s left)
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Iteration 210 / LogL: -188206.222 / Time: 0h:27m:35s (0h:8m:18s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 220: -188171.597
Iteration 220 / LogL: -188171.597 / Time: 0h:28m:50s (0h:13m:10s left)
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Iteration 230 / LogL: -188209.263 / Time: 0h:30m:1s (0h:11m:47s left)
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Iteration 240 / LogL: -188227.488 / Time: 0h:31m:13s (0h:10m:27s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 241: -188155.048
Optimizing NNI: done in 6.9644 secs using 597.8% CPU
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Iteration 270 / LogL: -188173.529 / Time: 0h:34m:47s (0h:9m:10s left)
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Iteration 280 / LogL: -188351.665 / Time: 0h:35m:57s (0h:7m:51s left)
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Iteration 300 / LogL: -188461.125 / Time: 0h:38m:18s (0h:5m:15s left)
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Iteration 310 / LogL: -188179.569 / Time: 0h:39m:28s (0h:3m:57s left)
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Iteration 320 / LogL: -188198.656 / Time: 0h:40m:34s (0h:2m:40s left)
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Iteration 330 / LogL: -188194.964 / Time: 0h:41m:44s (0h:1m:23s left)
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Iteration 340 / LogL: -188166.997 / Time: 0h:42m:53s (0h:0m:7s left)
Optimizing NNI: done in 6.6296 secs using 598.4% CPU
Optimizing NNI: done in 7.17073 secs using 597.4% CPU
TREE SEARCH COMPLETED AFTER 342 ITERATIONS / Time: 0h:43m:7s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -188155.048
Optimal log-likelihood: -188155.044
Site proportion and rates:  (0.017,0.127) (0.038,0.233) (0.119,0.342) (0.259,0.559) (0.134,0.797) (0.163,1.089) (0.200,1.643) (0.069,2.736)
Parameters optimization took 1 rounds (1.220 sec)
BEST SCORE FOUND : -188155.044
Total tree length: 143.141

Total number of iterations: 342
CPU time used for tree search: 15171.517 sec (4h:12m:51s)
Wall-clock time used for tree search: 2563.184 sec (0h:42m:43s)
Total CPU time used: 15324.001 sec (4h:15m:24s)
Total wall-clock time used: 2588.844 sec (0h:43m:8s)

===> START BOOTSTRAP REPLICATE NUMBER 70

Creating bootstrap alignment (seed: 70533)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.282 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -189210.251
2. Current log-likelihood: -186885.642
3. Current log-likelihood: -186816.988
4. Current log-likelihood: -186812.923
5. Current log-likelihood: -186810.181
6. Current log-likelihood: -186806.224
7. Current log-likelihood: -186800.379
8. Current log-likelihood: -186797.875
9. Current log-likelihood: -186797.477
Optimal log-likelihood: -186797.425
Site proportion and rates:  (0.020,0.110) (0.075,0.236) (0.129,0.384) (0.223,0.588) (0.154,0.846) (0.175,1.110) (0.145,1.716) (0.080,2.840)
Parameters optimization took 9 rounds (25.167 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 11.7799 secs using 599.9% CPU
Computing ML distances took 11.780604 sec (of wall-clock time) 70.670743 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00189495 secs using 390.2% CPU
Constructing RapidNJ tree: done in 0.0366759 secs using 689.2% CPU
Computing RapidNJ tree took 0.038696 sec (of wall-clock time) 0.261103 sec (of CPU time)
Log-likelihood of RapidNJ tree: -191781.063
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.670 second
Computing log-likelihood of 98 initial trees ... 22.047 seconds
Current best score: -186797.425

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.85992 secs using 595.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -186262.615
Optimizing NNI: done in 5.5547 secs using 597% CPU
Optimizing NNI: done in 4.86294 secs using 595.6% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -186219.897
Optimizing NNI: done in 6.17598 secs using 597.1% CPU
Optimizing NNI: done in 5.2474 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -186213.584
Optimizing NNI: done in 6.01914 secs using 597.3% CPU
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Iteration 10 / LogL: -186258.540 / Time: 0h:2m:40s
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Iteration 20 / LogL: -186331.797 / Time: 0h:3m:39s
Finish initializing candidate tree set (20)
Current best tree score: -186213.584 / CPU time: 180.314
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.98851 secs using 597.5% CPU
Optimizing NNI: done in 6.48735 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -186189.348
Optimizing NNI: done in 5.8391 secs using 598.1% CPU
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Iteration 30 / LogL: -186191.226 / Time: 0h:4m:47s (0h:15m:10s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 37: -186176.174
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Iteration 40 / LogL: -186295.504 / Time: 0h:5m:53s (0h:14m:37s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 49: -186160.055
Optimizing NNI: done in 6.13583 secs using 597.4% CPU
Iteration 50 / LogL: -186185.741 / Time: 0h:7m:0s (0h:14m:8s left)
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Iteration 60 / LogL: -186252.259 / Time: 0h:8m:2s (0h:12m:8s left)
Optimizing NNI: done in 6.80447 secs using 597.6% CPU
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Iteration 70 / LogL: -186197.315 / Time: 0h:9m:6s (0h:10m:25s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 80: -186157.806
Iteration 80 / LogL: -186157.806 / Time: 0h:10m:10s (0h:12m:52s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 84: -186156.857
Optimizing NNI: done in 7.08142 secs using 597.8% CPU
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Iteration 90 / LogL: -186185.195 / Time: 0h:11m:19s (0h:11m:57s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 92: -186154.657
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Iteration 100 / LogL: -186179.248 / Time: 0h:12m:26s (0h:11m:33s left)
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Iteration 120 / LogL: -186170.954 / Time: 0h:14m:42s (0h:8m:53s left)
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Iteration 130 / LogL: -186188.637 / Time: 0h:15m:46s (0h:7m:34s left)
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Iteration 140 / LogL: -186231.438 / Time: 0h:16m:50s (0h:6m:17s left)
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Iteration 150 / LogL: -186164.811 / Time: 0h:17m:52s (0h:5m:2s left)
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Iteration 160 / LogL: -186200.771 / Time: 0h:18m:56s (0h:3m:48s left)
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Iteration 170 / LogL: -186167.905 / Time: 0h:20m:2s (0h:2m:36s left)
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Iteration 180 / LogL: -186157.865 / Time: 0h:21m:7s (0h:1m:24s left)
Optimizing NNI: done in 6.24676 secs using 597.8% CPU
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Iteration 190 / LogL: -186168.742 / Time: 0h:22m:8s (0h:0m:14s left)
Optimizing NNI: done in 6.1162 secs using 596.9% CPU
Optimizing NNI: done in 5.71849 secs using 597.5% CPU
Optimizing NNI: done in 5.97747 secs using 597.4% CPU
TREE SEARCH COMPLETED AFTER 193 ITERATIONS / Time: 0h:22m:26s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -186154.657
Optimal log-likelihood: -186154.652
Site proportion and rates:  (0.020,0.110) (0.080,0.239) (0.131,0.388) (0.217,0.594) (0.146,0.844) (0.186,1.107) (0.144,1.734) (0.076,2.885)
Parameters optimization took 1 rounds (1.212 sec)
BEST SCORE FOUND : -186154.652
Total tree length: 141.985

Total number of iterations: 193
CPU time used for tree search: 7661.168 sec (2h:7m:41s)
Wall-clock time used for tree search: 1307.179 sec (0h:21m:47s)
Total CPU time used: 7905.131 sec (2h:11m:45s)
Total wall-clock time used: 1348.097 sec (0h:22m:28s)

===> START BOOTSTRAP REPLICATE NUMBER 71

Creating bootstrap alignment (seed: 70534)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.288 seconds

NOTE: 244 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -193043.992
2. Current log-likelihood: -190601.284
3. Current log-likelihood: -190455.707
4. Current log-likelihood: -190446.028
5. Current log-likelihood: -190443.514
6. Current log-likelihood: -190442.215
7. Current log-likelihood: -190441.181
8. Current log-likelihood: -190440.217
9. Current log-likelihood: -190439.361
10. Current log-likelihood: -190438.677
11. Current log-likelihood: -190438.188
12. Current log-likelihood: -190437.899
13. Current log-likelihood: -190437.734
Optimal log-likelihood: -190437.631
Site proportion and rates:  (0.013,0.101) (0.079,0.270) (0.111,0.368) (0.211,0.550) (0.191,0.787) (0.155,1.085) (0.170,1.678) (0.072,3.025)
Parameters optimization took 13 rounds (35.354 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 10.5214 secs using 599.9% CPU
Computing ML distances took 10.522101 sec (of wall-clock time) 63.123689 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00170612 secs using 471.2% CPU
Constructing RapidNJ tree: done in 0.0367782 secs using 681.8% CPU
Computing RapidNJ tree took 0.038575 sec (of wall-clock time) 0.259467 sec (of CPU time)
Log-likelihood of RapidNJ tree: -195971.349
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.018 second
Computing log-likelihood of 98 initial trees ... 25.763 seconds
Current best score: -190437.631

Do NNI search on 20 best initial trees
Optimizing NNI: done in 6.41806 secs using 597.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -189842.548
Optimizing NNI: done in 7.4585 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -189701.920
Optimizing NNI: done in 6.40245 secs using 597.8% CPU
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Iteration 10 / LogL: -189801.004 / Time: 0h:3m:31s
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Iteration 20 / LogL: -189781.270 / Time: 0h:4m:38s
Finish initializing candidate tree set (20)
Current best tree score: -189701.920 / CPU time: 228.485
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.16378 secs using 597.7% CPU
Optimizing NNI: done in 7.17304 secs using 598.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -189655.979
Optimizing NNI: done in 7.63251 secs using 598% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -189652.694
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Iteration 30 / LogL: -189710.446 / Time: 0h:6m:0s (0h:20m:17s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -189642.109
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Iteration 40 / LogL: -189668.950 / Time: 0h:7m:16s (0h:18m:14s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -189631.002
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 50: -189618.164
Iteration 50 / LogL: -189618.164 / Time: 0h:8m:40s (0h:17m:42s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -189609.489
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Iteration 60 / LogL: -189690.636 / Time: 0h:10m:2s (0h:15m:29s left)
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Iteration 70 / LogL: -189667.402 / Time: 0h:11m:24s (0h:13m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 79: -189590.612
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Iteration 80 / LogL: -189646.582 / Time: 0h:12m:50s (0h:16m:5s left)
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Iteration 90 / LogL: -189616.207 / Time: 0h:14m:11s (0h:14m:11s left)
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Iteration 100 / LogL: -189596.534 / Time: 0h:15m:30s (0h:12m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 108: -189574.640
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Iteration 110 / LogL: -189667.181 / Time: 0h:16m:52s (0h:15m:10s left)
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Iteration 120 / LogL: -189625.324 / Time: 0h:18m:8s (0h:13m:24s left)
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BETTER TREE FOUND at iteration 143: -189571.548
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BETTER TREE FOUND at iteration 307: -189551.817
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Iteration 400 / LogL: -189644.383 / Time: 0h:53m:24s (0h:0m:56s left)
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TREE SEARCH COMPLETED AFTER 408 ITERATIONS / Time: 0h:54m:21s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -189551.817
Optimal log-likelihood: -189551.806
Site proportion and rates:  (0.013,0.100) (0.150,0.305) (0.180,0.492) (0.155,0.666) (0.131,0.864) (0.134,1.126) (0.166,1.698) (0.072,3.003)
Parameters optimization took 1 rounds (1.823 sec)
BEST SCORE FOUND : -189551.806
Total tree length: 148.708

Total number of iterations: 408
CPU time used for tree search: 19042.176 sec (5h:17m:22s)
Wall-clock time used for tree search: 3211.413 sec (0h:53m:31s)
Total CPU time used: 19349.450 sec (5h:22m:29s)
Total wall-clock time used: 3262.956 sec (0h:54m:22s)

===> START BOOTSTRAP REPLICATE NUMBER 72

Creating bootstrap alignment (seed: 70535)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.262 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -192600.816
2. Current log-likelihood: -189955.333
3. Current log-likelihood: -189912.581
4. Current log-likelihood: -189909.178
5. Current log-likelihood: -189905.818
6. Current log-likelihood: -189900.558
7. Current log-likelihood: -189896.923
8. Current log-likelihood: -189895.281
9. Current log-likelihood: -189894.795
10. Current log-likelihood: -189894.635
Optimal log-likelihood: -189894.569
Site proportion and rates:  (0.012,0.103) (0.036,0.227) (0.135,0.357) (0.209,0.549) (0.141,0.758) (0.223,1.034) (0.134,1.596) (0.111,2.508)
Parameters optimization took 10 rounds (25.388 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 16.377 secs using 599.8% CPU
Computing ML distances took 16.377706 sec (of wall-clock time) 98.234190 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00147104 secs using 461.5% CPU
Constructing RapidNJ tree: done in 0.0411959 secs using 679.4% CPU
Computing RapidNJ tree took 0.042736 sec (of wall-clock time) 0.287376 sec (of CPU time)
Log-likelihood of RapidNJ tree: -194595.153
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... 30.528 second
Computing log-likelihood of 98 initial trees ... 22.533 seconds
Current best score: -189894.569

Do NNI search on 20 best initial trees
Optimizing NNI: done in 3.45913 secs using 596.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -189273.616
Optimizing NNI: done in 6.61539 secs using 596.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -189186.058
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 10: -189174.961
Iteration 10 / LogL: -189174.961 / Time: 0h:2m:50s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 16: -189161.308
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Iteration 20 / LogL: -189232.654 / Time: 0h:4m:7s
Finish initializing candidate tree set (20)
Current best tree score: -189161.308 / CPU time: 202.560
Number of iterations: 20
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|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -189136.895
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 37: -189106.121
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BETTER TREE FOUND at iteration 55: -189102.624
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BETTER TREE FOUND at iteration 59: -189100.875
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BETTER TREE FOUND at iteration 64: -189099.727
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BETTER TREE FOUND at iteration 83: -189086.761
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BETTER TREE FOUND at iteration 90: -189078.832
Iteration 90 / LogL: -189078.832 / Time: 0h:13m:5s (0h:14m:42s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 97: -189075.670
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 125: -189071.644
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 189: -189062.963
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 213: -189058.416
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 224: -189057.584
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 257: -189056.058
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BETTER TREE FOUND at iteration 269: -189051.192
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BETTER TREE FOUND at iteration 282: -189050.740
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 382: -189045.357
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Iteration 460 / LogL: -189068.277 / Time: 0h:55m:7s (0h:2m:38s left)
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Iteration 470 / LogL: -189150.649 / Time: 0h:56m:13s (0h:1m:26s left)
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Iteration 480 / LogL: -189062.297 / Time: 0h:57m:18s (0h:0m:14s left)
Optimizing NNI: done in 6.63435 secs using 597.1% CPU
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TREE SEARCH COMPLETED AFTER 483 ITERATIONS / Time: 0h:57m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -189045.357
Optimal log-likelihood: -189045.357
Site proportion and rates:  (0.013,0.103) (0.046,0.240) (0.132,0.367) (0.212,0.552) (0.167,0.791) (0.199,1.083) (0.125,1.636) (0.105,2.557)
Parameters optimization took 1 rounds (0.926 sec)
BEST SCORE FOUND : -189045.357
Total tree length: 151.319

Total number of iterations: 483
CPU time used for tree search: 20242.569 sec (5h:37m:22s)
Wall-clock time used for tree search: 3414.326 sec (0h:56m:54s)
Total CPU time used: 20515.262 sec (5h:41m:55s)
Total wall-clock time used: 3460.034 sec (0h:57m:40s)

===> START BOOTSTRAP REPLICATE NUMBER 73

Creating bootstrap alignment (seed: 70536)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.321 seconds

NOTE: 227 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199738.103
2. Current log-likelihood: -196993.330
3. Current log-likelihood: -196972.002
4. Current log-likelihood: -196969.983
5. Current log-likelihood: -196967.603
6. Current log-likelihood: -196964.359
7. Current log-likelihood: -196960.592
8. Current log-likelihood: -196957.971
9. Current log-likelihood: -196956.560
10. Current log-likelihood: -196955.626
11. Current log-likelihood: -196954.768
12. Current log-likelihood: -196953.779
13. Current log-likelihood: -196952.991
14. Current log-likelihood: -196952.382
15. Current log-likelihood: -196951.804
16. Current log-likelihood: -196950.987
17. Current log-likelihood: -196949.499
18. Current log-likelihood: -196947.841
19. Current log-likelihood: -196945.440
20. Current log-likelihood: -196942.414
21. Current log-likelihood: -196939.841
22. Current log-likelihood: -196938.731
23. Current log-likelihood: -196938.570
Optimal log-likelihood: -196938.547
Site proportion and rates:  (0.011,0.091) (0.048,0.229) (0.171,0.370) (0.220,0.574) (0.255,0.907) (0.160,1.484) (0.104,2.186) (0.031,3.275)
Parameters optimization took 23 rounds (52.794 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 10.1585 secs using 599.9% CPU
Computing ML distances took 10.159099 sec (of wall-clock time) 60.942490 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00170708 secs using 700.2% CPU
Constructing RapidNJ tree: done in 0.0367491 secs using 697.8% CPU
Computing RapidNJ tree took 0.038524 sec (of wall-clock time) 0.268717 sec (of CPU time)
Log-likelihood of RapidNJ tree: -200557.474
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.431 second
Computing log-likelihood of 98 initial trees ... 24.513 seconds
Current best score: -196938.547

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.19657 secs using 597% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -196337.468
Optimizing NNI: done in 7.51286 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -196298.851
Optimizing NNI: done in 8.28757 secs using 597.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -196285.235
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -196230.225
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Iteration 10 / LogL: -196258.194 / Time: 0h:3m:32s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 16: -196217.575
Optimizing NNI: done in 7.51715 secs using 597.4% CPU
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Iteration 20 / LogL: -196283.193 / Time: 0h:4m:57s
Finish initializing candidate tree set (20)
Current best tree score: -196217.575 / CPU time: 232.614
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.48271 secs using 598% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -196201.961
Optimizing NNI: done in 6.98232 secs using 597.7% CPU
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Iteration 30 / LogL: -196224.817 / Time: 0h:6m:9s (0h:20m:7s left)
Optimizing NNI: done in 6.77073 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -196195.694
Optimizing NNI: done in 6.36157 secs using 597.9% CPU
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BETTER TREE FOUND at iteration 32: -196191.722
Optimizing NNI: done in 6.61066 secs using 598% CPU
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Iteration 40 / LogL: -196204.597 / Time: 0h:7m:26s (0h:17m:32s left)
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Optimizing NNI: done in 6.1856 secs using 598.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -196184.366
Optimizing NNI: done in 6.62895 secs using 598% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 46: -196175.691
Optimizing NNI: done in 6.83821 secs using 597.6% CPU
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Iteration 50 / LogL: -196193.358 / Time: 0h:8m:45s (0h:17m:9s left)
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Iteration 60 / LogL: -196215.872 / Time: 0h:9m:50s (0h:14m:20s left)
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Iteration 70 / LogL: -196193.279 / Time: 0h:10m:58s (0h:12m:5s left)
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Iteration 80 / LogL: -196193.598 / Time: 0h:12m:11s (0h:10m:10s left)
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Iteration 90 / LogL: -196257.572 / Time: 0h:13m:20s (0h:8m:23s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 92: -196171.277
Optimizing NNI: done in 6.62674 secs using 598.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 93: -196164.608
Optimizing NNI: done in 6.32807 secs using 598% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 100: -196161.204
Iteration 100 / LogL: -196161.204 / Time: 0h:14m:35s (0h:14m:43s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 106: -196160.515
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Iteration 110 / LogL: -196192.071 / Time: 0h:15m:45s (0h:13m:52s left)
Optimizing NNI: done in 6.39131 secs using 598.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 112: -196154.020
Optimizing NNI: done in 7.18056 secs using 598.1% CPU
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Iteration 120 / LogL: -196187.331 / Time: 0h:16m:55s (0h:13m:4s left)
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Iteration 130 / LogL: -196159.465 / Time: 0h:17m:57s (0h:11m:24s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 133: -196143.791
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Iteration 140 / LogL: -196161.772 / Time: 0h:19m:4s (0h:12m:45s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 145: -196139.984
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Iteration 150 / LogL: -196155.644 / Time: 0h:20m:11s (0h:12m:51s left)
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Iteration 160 / LogL: -196187.685 / Time: 0h:21m:13s (0h:11m:20s left)
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Iteration 170 / LogL: -196278.334 / Time: 0h:22m:14s (0h:9m:51s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 179: -196138.616
Optimizing NNI: done in 6.38298 secs using 598.2% CPU
Iteration 180 / LogL: -196233.597 / Time: 0h:23m:15s (0h:12m:51s left)
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Iteration 190 / LogL: -196517.563 / Time: 0h:24m:17s (0h:11m:26s left)
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Iteration 200 / LogL: -196193.177 / Time: 0h:25m:21s (0h:10m:3s left)
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Iteration 210 / LogL: -196148.865 / Time: 0h:26m:24s (0h:8m:42s left)
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Iteration 220 / LogL: -196149.220 / Time: 0h:27m:29s (0h:7m:24s left)
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Iteration 230 / LogL: -196171.360 / Time: 0h:28m:36s (0h:6m:7s left)
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Optimizing NNI: done in 6.27816 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 232: -196137.089
Optimizing NNI: done in 6.49517 secs using 598.1% CPU
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Iteration 240 / LogL: -196562.631 / Time: 0h:29m:46s (0h:11m:27s left)
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Iteration 250 / LogL: -196195.953 / Time: 0h:30m:51s (0h:10m:9s left)
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Iteration 260 / LogL: -196177.386 / Time: 0h:31m:59s (0h:8m:53s left)
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Iteration 270 / LogL: -196173.020 / Time: 0h:33m:7s (0h:7m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 278: -196136.280
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Iteration 280 / LogL: -196171.887 / Time: 0h:34m:18s (0h:12m:2s left)
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Iteration 290 / LogL: -196292.638 / Time: 0h:35m:22s (0h:10m:46s left)
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Iteration 300 / LogL: -196156.371 / Time: 0h:36m:29s (0h:9m:31s left)
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Iteration 310 / LogL: -196170.380 / Time: 0h:37m:37s (0h:8m:16s left)
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Iteration 320 / LogL: -196178.885 / Time: 0h:38m:42s (0h:7m:2s left)
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Optimizing NNI: done in 6.52598 secs using 598% CPU
Iteration 330 / LogL: -196153.701 / Time: 0h:39m:48s (0h:5m:48s left)
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Optimizing NNI: done in 5.87439 secs using 598.4% CPU
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Optimizing NNI: done in 6.55188 secs using 598% CPU
Iteration 340 / LogL: -196562.373 / Time: 0h:40m:52s (0h:4m:34s left)
Optimizing NNI: done in 6.05778 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 341: -196123.616
Optimizing NNI: done in 6.93823 secs using 597.8% CPU
Optimizing NNI: done in 6.12481 secs using 598% CPU
Optimizing NNI: done in 6.50615 secs using 598% CPU
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Iteration 350 / LogL: -196161.225 / Time: 0h:42m:2s (0h:10m:57s left)
Optimizing NNI: done in 6.66258 secs using 598.4% CPU
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Iteration 360 / LogL: -196173.584 / Time: 0h:43m:10s (0h:9m:44s left)
Optimizing NNI: done in 6.39116 secs using 598% CPU
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Iteration 370 / LogL: -196166.566 / Time: 0h:44m:16s (0h:8m:31s left)
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Iteration 380 / LogL: -196163.173 / Time: 0h:45m:19s (0h:7m:17s left)
Optimizing NNI: done in 5.92607 secs using 597.9% CPU
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Iteration 390 / LogL: -196139.230 / Time: 0h:46m:25s (0h:6m:5s left)
Optimizing NNI: done in 6.05677 secs using 598% CPU
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Iteration 400 / LogL: -196249.577 / Time: 0h:47m:30s (0h:4m:52s left)
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Iteration 410 / LogL: -196136.238 / Time: 0h:48m:33s (0h:3m:40s left)
Optimizing NNI: done in 6.67765 secs using 598% CPU
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Iteration 420 / LogL: -196198.046 / Time: 0h:49m:42s (0h:2m:29s left)
Optimizing NNI: done in 6.50573 secs using 598.2% CPU
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Iteration 430 / LogL: -196170.645 / Time: 0h:50m:49s (0h:1m:18s left)
Optimizing NNI: done in 6.8112 secs using 598.1% CPU
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Iteration 440 / LogL: -196162.939 / Time: 0h:51m:57s (0h:0m:7s left)
Optimizing NNI: done in 6.32034 secs using 598.2% CPU
Optimizing NNI: done in 6.70613 secs using 598.5% CPU
TREE SEARCH COMPLETED AFTER 442 ITERATIONS / Time: 0h:52m:10s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -196123.616
Optimal log-likelihood: -196123.612
Site proportion and rates:  (0.013,0.096) (0.098,0.284) (0.143,0.401) (0.213,0.594) (0.237,0.920) (0.163,1.473) (0.098,2.206) (0.035,3.215)
Parameters optimization took 1 rounds (1.491 sec)
BEST SCORE FOUND : -196123.612
Total tree length: 157.492

Total number of iterations: 442
CPU time used for tree search: 18174.254 sec (5h:2m:54s)
Wall-clock time used for tree search: 3065.473 sec (0h:51m:5s)
Total CPU time used: 18571.738 sec (5h:9m:31s)
Total wall-clock time used: 3132.166 sec (0h:52m:12s)

===> START BOOTSTRAP REPLICATE NUMBER 74

Creating bootstrap alignment (seed: 70537)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.285 seconds

NOTE: 244 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194687.204
2. Current log-likelihood: -191995.710
3. Current log-likelihood: -191971.483
4. Current log-likelihood: -191971.152
5. Current log-likelihood: -191971.007
6. Current log-likelihood: -191970.734
7. Current log-likelihood: -191970.287
8. Current log-likelihood: -191969.757
9. Current log-likelihood: -191969.249
10. Current log-likelihood: -191968.793
11. Current log-likelihood: -191968.350
12. Current log-likelihood: -191967.907
13. Current log-likelihood: -191967.486
14. Current log-likelihood: -191967.111
15. Current log-likelihood: -191966.802
16. Current log-likelihood: -191966.549
17. Current log-likelihood: -191966.354
18. Current log-likelihood: -191966.207
Optimal log-likelihood: -191966.108
Site proportion and rates:  (0.010,0.084) (0.064,0.240) (0.126,0.375) (0.178,0.530) (0.137,0.674) (0.223,0.987) (0.134,1.577) (0.128,2.486)
Parameters optimization took 18 rounds (49.594 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 10.1841 secs using 599.9% CPU
Computing ML distances took 10.184940 sec (of wall-clock time) 61.093190 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00171018 secs using 480.4% CPU
Constructing RapidNJ tree: done in 0.036726 secs using 678.4% CPU
Computing RapidNJ tree took 0.038539 sec (of wall-clock time) 0.258174 sec (of CPU time)
Log-likelihood of RapidNJ tree: -195964.286
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.773 second
Computing log-likelihood of 98 initial trees ... 23.523 seconds
Current best score: -191966.108

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.44916 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -191262.894
Optimizing NNI: done in 5.57424 secs using 598.1% CPU
Optimizing NNI: done in 6.06747 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -191228.156
Optimizing NNI: done in 5.77511 secs using 598% CPU
Optimizing NNI: done in 6.81525 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -191137.467
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Iteration 10 / LogL: -191197.778 / Time: 0h:3m:47s
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Iteration 20 / LogL: -191203.234 / Time: 0h:4m:46s
Finish initializing candidate tree set (20)
Current best tree score: -191137.467 / CPU time: 222.482
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.98774 secs using 597.8% CPU
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Iteration 30 / LogL: -191194.224 / Time: 0h:5m:54s (0h:15m:16s left)
Optimizing NNI: done in 7.24688 secs using 598.2% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -191134.552
Optimizing NNI: done in 9.17229 secs using 597.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -191128.896
Optimizing NNI: done in 6.9439 secs using 598.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -191119.083
Iteration 40 / LogL: -191119.083 / Time: 0h:7m:16s (0h:18m:37s left)
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Iteration 50 / LogL: -191246.147 / Time: 0h:8m:26s (0h:15m:29s left)
Optimizing NNI: done in 6.47101 secs using 597.9% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 52: -191107.122
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 59: -191105.999
Optimizing NNI: done in 6.3681 secs using 598.1% CPU
Iteration 60 / LogL: -191159.170 / Time: 0h:9m:39s (0h:16m:12s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 64: -191103.530
Optimizing NNI: done in 6.23336 secs using 597.4% CPU
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Iteration 70 / LogL: -191141.511 / Time: 0h:10m:49s (0h:14m:45s left)
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Iteration 80 / LogL: -191130.366 / Time: 0h:11m:59s (0h:12m:45s left)
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Iteration 90 / LogL: -191123.218 / Time: 0h:13m:6s (0h:10m:53s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 100: -191100.054
Iteration 100 / LogL: -191100.054 / Time: 0h:14m:18s (0h:14m:26s left)
Optimizing NNI: done in 6.8327 secs using 598% CPU
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Iteration 110 / LogL: -191133.313 / Time: 0h:15m:28s (0h:12m:46s left)
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Iteration 120 / LogL: -191198.478 / Time: 0h:16m:35s (0h:11m:8s left)
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Iteration 130 / LogL: -191128.972 / Time: 0h:17m:42s (0h:9m:36s left)
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Iteration 140 / LogL: -191157.644 / Time: 0h:18m:50s (0h:8m:8s left)
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Iteration 150 / LogL: -191242.499 / Time: 0h:19m:57s (0h:6m:41s left)
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Iteration 160 / LogL: -191129.870 / Time: 0h:21m:5s (0h:5m:18s left)
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Iteration 170 / LogL: -191124.142 / Time: 0h:22m:13s (0h:3m:56s left)
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Iteration 180 / LogL: -191101.790 / Time: 0h:23m:19s (0h:2m:36s left)
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Iteration 190 / LogL: -191114.496 / Time: 0h:24m:27s (0h:1m:17s left)
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Iteration 200 / LogL: -191107.175 / Time: 0h:25m:33s (0h:0m:0s left)
Optimizing NNI: done in 6.25034 secs using 597.7% CPU
TREE SEARCH COMPLETED AFTER 201 ITERATIONS / Time: 0h:25m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -191100.054
Optimal log-likelihood: -191100.053
Site proportion and rates:  (0.011,0.085) (0.088,0.270) (0.157,0.413) (0.224,0.600) (0.128,0.863) (0.134,1.051) (0.128,1.572) (0.130,2.483)
Parameters optimization took 1 rounds (1.211 sec)
BEST SCORE FOUND : -191100.053
Total tree length: 152.109

Total number of iterations: 201
CPU time used for tree search: 8669.647 sec (2h:24m:29s)
Wall-clock time used for tree search: 1475.180 sec (0h:24m:35s)
Total CPU time used: 9059.399 sec (2h:30m:59s)
Total wall-clock time used: 1540.553 sec (0h:25m:40s)

===> START BOOTSTRAP REPLICATE NUMBER 75

Creating bootstrap alignment (seed: 70538)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.294 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194853.105
2. Current log-likelihood: -192240.434
3. Current log-likelihood: -192207.825
4. Current log-likelihood: -192198.719
5. Current log-likelihood: -192186.569
6. Current log-likelihood: -192181.098
7. Current log-likelihood: -192180.304
Optimal log-likelihood: -192180.215
Site proportion and rates:  (0.021,0.097) (0.038,0.235) (0.135,0.343) (0.233,0.555) (0.178,0.787) (0.158,1.067) (0.130,1.683) (0.106,2.688)
Parameters optimization took 7 rounds (18.529 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 14.4831 secs using 599.9% CPU
Computing ML distances took 14.483800 sec (of wall-clock time) 86.889382 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00128603 secs using 661.3% CPU
Constructing RapidNJ tree: done in 0.0370021 secs using 679.1% CPU
Computing RapidNJ tree took 0.038380 sec (of wall-clock time) 0.265875 sec (of CPU time)
Log-likelihood of RapidNJ tree: -198005.075
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.884 second
Computing log-likelihood of 98 initial trees ... 23.382 seconds
Current best score: -192180.215

Do NNI search on 20 best initial trees
Optimizing NNI: done in 3.58395 secs using 598.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -191728.528
Optimizing NNI: done in 5.60086 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -191668.433
Optimizing NNI: done in 6.06303 secs using 597.5% CPU
Optimizing NNI: done in 6.41528 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -191618.398
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Iteration 10 / LogL: -191653.714 / Time: 0h:2m:45s
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Iteration 20 / LogL: -191687.836 / Time: 0h:3m:46s
Finish initializing candidate tree set (20)
Current best tree score: -191618.398 / CPU time: 188.246
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.88946 secs using 597.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -191567.111
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -191562.419
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Iteration 30 / LogL: -191566.994 / Time: 0h:5m:1s (0h:16m:4s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -191559.402
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -191556.718
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 37: -191543.648
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -191534.347
Iteration 40 / LogL: -191534.347 / Time: 0h:6m:20s (0h:16m:14s left)
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Iteration 50 / LogL: -191546.324 / Time: 0h:7m:29s (0h:13m:45s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 58: -191527.553
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Iteration 60 / LogL: -191560.309 / Time: 0h:8m:38s (0h:14m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 64: -191520.028
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Iteration 70 / LogL: -191533.016 / Time: 0h:9m:46s (0h:13m:17s left)
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Iteration 80 / LogL: -191549.000 / Time: 0h:10m:50s (0h:11m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 82: -191517.057
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 84: -191514.486
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Iteration 90 / LogL: -191558.224 / Time: 0h:12m:1s (0h:12m:42s left)
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Iteration 100 / LogL: -191532.118 / Time: 0h:13m:7s (0h:11m:7s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 101: -191495.470
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Iteration 120 / LogL: -191584.375 / Time: 0h:15m:22s (0h:10m:27s left)
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Iteration 160 / LogL: -191516.876 / Time: 0h:19m:48s (0h:5m:6s left)
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Iteration 170 / LogL: -191553.544 / Time: 0h:20m:53s (0h:3m:49s left)
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Iteration 180 / LogL: -191535.909 / Time: 0h:21m:56s (0h:2m:34s left)
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Iteration 190 / LogL: -191637.469 / Time: 0h:23m:3s (0h:1m:20s left)
Optimizing NNI: done in 6.98191 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 191: -191492.156
Optimizing NNI: done in 6.69779 secs using 597.7% CPU
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Iteration 200 / LogL: -191496.797 / Time: 0h:24m:14s (0h:11m:4s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 204: -191491.789
Optimizing NNI: done in 7.21096 secs using 597.8% CPU
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Iteration 210 / LogL: -191517.924 / Time: 0h:25m:24s (0h:11m:25s left)
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Iteration 220 / LogL: -191517.948 / Time: 0h:26m:31s (0h:10m:10s left)
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Iteration 230 / LogL: -191524.230 / Time: 0h:27m:39s (0h:8m:56s left)
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Iteration 240 / LogL: -191518.041 / Time: 0h:28m:45s (0h:7m:41s left)
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Iteration 250 / LogL: -191575.055 / Time: 0h:29m:52s (0h:6m:28s left)
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Iteration 260 / LogL: -191577.236 / Time: 0h:31m:0s (0h:5m:15s left)
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Iteration 270 / LogL: -191552.101 / Time: 0h:32m:7s (0h:4m:3s left)
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Iteration 280 / LogL: -191570.267 / Time: 0h:33m:15s (0h:2m:51s left)
Optimizing NNI: done in 6.72097 secs using 597.9% CPU
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Iteration 290 / LogL: -191654.106 / Time: 0h:34m:21s (0h:1m:39s left)
Optimizing NNI: done in 6.95002 secs using 598% CPU
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Iteration 300 / LogL: -191594.084 / Time: 0h:35m:27s (0h:0m:28s left)
Optimizing NNI: done in 8.46869 secs using 597.1% CPU
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Optimizing NNI: done in 6.63805 secs using 597.3% CPU
TREE SEARCH COMPLETED AFTER 305 ITERATIONS / Time: 0h:36m:2s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -191491.789
Optimal log-likelihood: -191491.789
Site proportion and rates:  (0.022,0.097) (0.051,0.252) (0.121,0.347) (0.246,0.559) (0.179,0.803) (0.142,1.084) (0.131,1.684) (0.106,2.688)
Parameters optimization took 1 rounds (0.592 sec)
BEST SCORE FOUND : -191491.789
Total tree length: 150.987

Total number of iterations: 305
CPU time used for tree search: 12548.076 sec (3h:29m:8s)
Wall-clock time used for tree search: 2124.805 sec (0h:35m:24s)
Total CPU time used: 12777.496 sec (3h:32m:57s)
Total wall-clock time used: 2163.259 sec (0h:36m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 76

Creating bootstrap alignment (seed: 70539)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.258 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -201076.026
2. Current log-likelihood: -198322.760
3. Current log-likelihood: -198301.048
4. Current log-likelihood: -198300.316
5. Current log-likelihood: -198299.887
6. Current log-likelihood: -198298.967
7. Current log-likelihood: -198297.158
8. Current log-likelihood: -198292.587
9. Current log-likelihood: -198280.770
10. Current log-likelihood: -198276.460
11. Current log-likelihood: -198275.960
Optimal log-likelihood: -198275.905
Site proportion and rates:  (0.007,0.060) (0.049,0.214) (0.145,0.352) (0.227,0.538) (0.159,0.777) (0.131,1.051) (0.162,1.542) (0.120,2.532)
Parameters optimization took 11 rounds (28.050 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 13.7672 secs using 599.8% CPU
Computing ML distances took 13.767948 sec (of wall-clock time) 82.575598 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.001297 secs using 289.5% CPU
Constructing RapidNJ tree: done in 0.0365059 secs using 675.2% CPU
Computing RapidNJ tree took 0.037894 sec (of wall-clock time) 0.251153 sec (of CPU time)
Log-likelihood of RapidNJ tree: -201797.352
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.413 second
Computing log-likelihood of 98 initial trees ... 22.498 seconds
Current best score: -198275.905

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.56175 secs using 597.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -197575.853
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -197455.955
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 8: -197412.300
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -197404.608
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Iteration 10 / LogL: -197546.954 / Time: 0h:2m:43s
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Iteration 20 / LogL: -197498.548 / Time: 0h:3m:39s
Finish initializing candidate tree set (20)
Current best tree score: -197404.608 / CPU time: 175.415
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -197392.477
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -197370.776
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Iteration 30 / LogL: -197427.437 / Time: 0h:4m:53s (0h:16m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 37: -197337.274
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Iteration 40 / LogL: -197350.508 / Time: 0h:6m:8s (0h:15m:14s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 48: -197301.094
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Iteration 50 / LogL: -197408.126 / Time: 0h:7m:20s (0h:14m:39s left)
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Iteration 60 / LogL: -197309.618 / Time: 0h:8m:31s (0h:12m:42s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 63: -197298.645
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 66: -197296.004
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Iteration 70 / LogL: -197323.978 / Time: 0h:9m:43s (0h:13m:30s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 71: -197290.269
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 75: -197284.039
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Iteration 80 / LogL: -197510.786 / Time: 0h:10m:57s (0h:13m:10s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 82: -197280.593
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Iteration 90 / LogL: -197329.053 / Time: 0h:12m:8s (0h:12m:32s left)
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Iteration 100 / LogL: -197289.516 / Time: 0h:13m:18s (0h:11m:0s left)
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Iteration 110 / LogL: -197314.772 / Time: 0h:14m:30s (0h:9m:34s left)
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Iteration 120 / LogL: -197356.882 / Time: 0h:15m:41s (0h:8m:10s left)
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Iteration 130 / LogL: -197339.525 / Time: 0h:16m:48s (0h:6m:46s left)
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Iteration 140 / LogL: -197418.926 / Time: 0h:17m:59s (0h:5m:26s left)
Optimizing NNI: done in 7.01958 secs using 597.7% CPU
Optimizing NNI: done in 6.97909 secs using 597.7% CPU
Optimizing NNI: done in 6.41147 secs using 597.9% CPU
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Optimizing NNI: done in 6.29594 secs using 597% CPU
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Optimizing NNI: done in 8.28849 secs using 597% CPU
Optimizing NNI: done in 7.53453 secs using 597.4% CPU
Iteration 150 / LogL: -197313.660 / Time: 0h:19m:9s (0h:4m:6s left)
Optimizing NNI: done in 6.46456 secs using 597.5% CPU
Optimizing NNI: done in 6.39735 secs using 597.4% CPU
Optimizing NNI: done in 6.82135 secs using 598% CPU
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Optimizing NNI: done in 7.07557 secs using 598% CPU
Optimizing NNI: done in 7.57875 secs using 597.5% CPU
Iteration 160 / LogL: -197289.543 / Time: 0h:20m:18s (0h:2m:48s left)
Optimizing NNI: done in 6.54861 secs using 597.7% CPU
Optimizing NNI: done in 7.62759 secs using 597.1% CPU
Optimizing NNI: done in 5.79998 secs using 597.5% CPU
Optimizing NNI: done in 8.33034 secs using 597.4% CPU
Optimizing NNI: done in 6.93128 secs using 597.8% CPU
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Optimizing NNI: done in 6.5047 secs using 597.9% CPU
Optimizing NNI: done in 7.93079 secs using 597.4% CPU
Optimizing NNI: done in 7.10574 secs using 597.5% CPU
Optimizing NNI: done in 6.86475 secs using 597.7% CPU
Iteration 170 / LogL: -197293.898 / Time: 0h:21m:29s (0h:1m:31s left)
Optimizing NNI: done in 6.69172 secs using 598.2% CPU
Optimizing NNI: done in 6.57191 secs using 598% CPU
Optimizing NNI: done in 6.93621 secs using 597.2% CPU
Optimizing NNI: done in 7.53455 secs using 598% CPU
Optimizing NNI: done in 8.82659 secs using 597% CPU
Optimizing NNI: done in 7.1864 secs using 597.4% CPU
Optimizing NNI: done in 6.45668 secs using 597.9% CPU
Optimizing NNI: done in 7.14889 secs using 597.6% CPU
Optimizing NNI: done in 6.60797 secs using 597.3% CPU
Optimizing NNI: done in 6.11317 secs using 597.7% CPU
Iteration 180 / LogL: -197339.475 / Time: 0h:22m:39s (0h:0m:15s left)
Optimizing NNI: done in 7.10769 secs using 597.5% CPU
Optimizing NNI: done in 6.63176 secs using 597.8% CPU
Optimizing NNI: done in 6.64994 secs using 597.4% CPU
TREE SEARCH COMPLETED AFTER 183 ITERATIONS / Time: 0h:23m:0s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -197280.593
Optimal log-likelihood: -197280.592
Site proportion and rates:  (0.008,0.074) (0.060,0.228) (0.146,0.362) (0.215,0.544) (0.174,0.785) (0.121,1.075) (0.157,1.568) (0.119,2.548)
Parameters optimization took 1 rounds (0.597 sec)
BEST SCORE FOUND : -197280.592
Total tree length: 157.589

Total number of iterations: 183
CPU time used for tree search: 7828.318 sec (2h:10m:28s)
Wall-clock time used for tree search: 1335.703 sec (0h:22m:15s)
Total CPU time used: 8097.550 sec (2h:14m:57s)
Total wall-clock time used: 1380.845 sec (0h:23m:0s)

===> START BOOTSTRAP REPLICATE NUMBER 77

Creating bootstrap alignment (seed: 70540)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.257 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196870.211
2. Current log-likelihood: -194281.393
3. Current log-likelihood: -194265.804
4. Current log-likelihood: -194261.765
5. Current log-likelihood: -194258.278
6. Current log-likelihood: -194256.618
7. Current log-likelihood: -194255.830
8. Current log-likelihood: -194255.362
9. Current log-likelihood: -194255.072
10. Current log-likelihood: -194254.888
11. Current log-likelihood: -194254.772
Optimal log-likelihood: -194254.706
Site proportion and rates:  (0.004,0.096) (0.083,0.246) (0.098,0.387) (0.165,0.561) (0.194,0.766) (0.197,1.032) (0.125,1.434) (0.135,2.358)
Parameters optimization took 11 rounds (26.338 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 11.5445 secs using 599.9% CPU
Computing ML distances took 11.545148 sec (of wall-clock time) 69.254777 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00168109 secs using 495.1% CPU
Constructing RapidNJ tree: done in 0.03883 secs using 689.6% CPU
Computing RapidNJ tree took 0.040596 sec (of wall-clock time) 0.276694 sec (of CPU time)
Log-likelihood of RapidNJ tree: -197440.759
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.215 second
Computing log-likelihood of 98 initial trees ... 24.151 seconds
Current best score: -194254.706

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.10757 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -193708.063
Optimizing NNI: done in 6.45918 secs using 597.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -193585.279
Optimizing NNI: done in 6.8827 secs using 597.9% CPU
Optimizing NNI: done in 7.88094 secs using 597.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -193521.969
Optimizing NNI: done in 6.11229 secs using 597.4% CPU
Optimizing NNI: done in 7.35783 secs using 598% CPU
Optimizing NNI: done in 6.93027 secs using 597.9% CPU
Optimizing NNI: done in 7.41284 secs using 595.8% CPU
Optimizing NNI: done in 6.18409 secs using 596.3% CPU
Optimizing NNI: done in 6.42187 secs using 598% CPU
Iteration 10 / LogL: -193637.897 / Time: 0h:2m:59s
Optimizing NNI: done in 6.86562 secs using 597.2% CPU
Optimizing NNI: done in 7.58504 secs using 597.6% CPU
Optimizing NNI: done in 6.54338 secs using 597.9% CPU
Optimizing NNI: done in 5.08867 secs using 597.4% CPU
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Optimizing NNI: done in 7.55586 secs using 597.4% CPU
Optimizing NNI: done in 7.27593 secs using 596.9% CPU
Optimizing NNI: done in 7.31183 secs using 597.5% CPU
Optimizing NNI: done in 7.02584 secs using 597.5% CPU
Optimizing NNI: done in 6.80845 secs using 597.5% CPU
Iteration 20 / LogL: -193560.476 / Time: 0h:4m:9s
Finish initializing candidate tree set (20)
Current best tree score: -193521.969 / CPU time: 209.136
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 9.02077 secs using 596.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -193501.734
Optimizing NNI: done in 9.04089 secs using 597.8% CPU
Optimizing NNI: done in 8.11748 secs using 596.1% CPU
Optimizing NNI: done in 8.67478 secs using 597.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -193481.958
Optimizing NNI: done in 7.34673 secs using 597.6% CPU
Optimizing NNI: done in 9.76135 secs using 597.4% CPU
Optimizing NNI: done in 8.18891 secs using 597.4% CPU
Optimizing NNI: done in 7.10075 secs using 598% CPU
Optimizing NNI: done in 9.83937 secs using 597.4% CPU
Optimizing NNI: done in 9.09569 secs using 597.7% CPU
Iteration 30 / LogL: -193598.787 / Time: 0h:5m:44s (0h:18m:35s left)
Optimizing NNI: done in 9.20698 secs using 597.8% CPU
Optimizing NNI: done in 8.33211 secs using 597.7% CPU
Optimizing NNI: done in 9.43074 secs using 597.5% CPU
Optimizing NNI: done in 6.83826 secs using 598% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 34: -193443.375
Optimizing NNI: done in 7.70331 secs using 597.8% CPU
Optimizing NNI: done in 7.57674 secs using 597.4% CPU
Optimizing NNI: done in 5.72058 secs using 598% CPU
Optimizing NNI: done in 8.0749 secs using 598% CPU
Optimizing NNI: done in 7.39751 secs using 597.7% CPU
Optimizing NNI: done in 7.2244 secs using 598.2% CPU
Iteration 40 / LogL: -193523.447 / Time: 0h:7m:32s (0h:18m:9s left)
Optimizing NNI: done in 7.71662 secs using 597.4% CPU
Optimizing NNI: done in 6.92289 secs using 596.1% CPU
Optimizing NNI: done in 7.06241 secs using 597.8% CPU
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Optimizing NNI: done in 7.84519 secs using 597.7% CPU
Optimizing NNI: done in 7.30187 secs using 597.9% CPU
Optimizing NNI: done in 7.31434 secs using 597.2% CPU
Iteration 50 / LogL: -193523.727 / Time: 0h:8m:47s (0h:15m:3s left)
Optimizing NNI: done in 7.01827 secs using 597.8% CPU
Optimizing NNI: done in 7.84243 secs using 597.7% CPU
Optimizing NNI: done in 6.84539 secs using 597.2% CPU
Optimizing NNI: done in 7.64342 secs using 598% CPU
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Optimizing NNI: done in 6.60639 secs using 598% CPU
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Optimizing NNI: done in 6.77422 secs using 597.1% CPU
Optimizing NNI: done in 7.76745 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 59: -193442.666
Optimizing NNI: done in 6.42753 secs using 597.2% CPU
Iteration 60 / LogL: -193456.874 / Time: 0h:10m:2s (0h:16m:49s left)
Optimizing NNI: done in 6.97981 secs using 598.2% CPU
Optimizing NNI: done in 6.50811 secs using 597.9% CPU
Optimizing NNI: done in 6.4947 secs using 597.9% CPU
Optimizing NNI: done in 7.04295 secs using 598.2% CPU
Optimizing NNI: done in 7.63645 secs using 597.2% CPU
Optimizing NNI: done in 7.08837 secs using 598.1% CPU
Optimizing NNI: done in 6.77055 secs using 597.8% CPU
Optimizing NNI: done in 7.07157 secs using 598% CPU
Optimizing NNI: done in 8.09823 secs using 597.5% CPU
Optimizing NNI: done in 6.94869 secs using 597.9% CPU
Iteration 70 / LogL: -193467.000 / Time: 0h:11m:13s (0h:14m:28s left)
Optimizing NNI: done in 6.66522 secs using 597.5% CPU
Optimizing NNI: done in 6.13818 secs using 597.9% CPU
Optimizing NNI: done in 7.49813 secs using 596.4% CPU
Optimizing NNI: done in 7.06579 secs using 597.5% CPU
Optimizing NNI: done in 7.58395 secs using 597.6% CPU
Optimizing NNI: done in 7.3021 secs using 597.9% CPU
Optimizing NNI: done in 7.62163 secs using 598% CPU
Optimizing NNI: done in 7.82571 secs using 597.6% CPU
Optimizing NNI: done in 7.87415 secs using 597.9% CPU
Optimizing NNI: done in 7.58259 secs using 597.6% CPU
Iteration 80 / LogL: -193446.840 / Time: 0h:12m:27s (0h:12m:26s left)
Optimizing NNI: done in 6.91575 secs using 597.6% CPU
Optimizing NNI: done in 8.02547 secs using 597.9% CPU
Optimizing NNI: done in 7.10495 secs using 597.6% CPU
Optimizing NNI: done in 6.64506 secs using 597.8% CPU
Optimizing NNI: done in 7.65841 secs using 597.6% CPU
Optimizing NNI: done in 6.52041 secs using 597.9% CPU
Optimizing NNI: done in 6.11888 secs using 597.6% CPU
Optimizing NNI: done in 7.60481 secs using 597.4% CPU
Optimizing NNI: done in 6.85043 secs using 597.9% CPU
Optimizing NNI: done in 7.62999 secs using 598% CPU
Iteration 90 / LogL: -193470.803 / Time: 0h:13m:38s (0h:10m:34s left)
Optimizing NNI: done in 7.1195 secs using 597.5% CPU
Optimizing NNI: done in 7.31458 secs using 597.7% CPU
Optimizing NNI: done in 7.53109 secs using 598.2% CPU
Optimizing NNI: done in 7.49338 secs using 598.1% CPU
Optimizing NNI: done in 7.28156 secs using 597.8% CPU
Optimizing NNI: done in 7.46726 secs using 597.6% CPU
Optimizing NNI: done in 7.50798 secs using 597.8% CPU
Optimizing NNI: done in 7.59401 secs using 597.9% CPU
Optimizing NNI: done in 7.577 secs using 598.1% CPU
Optimizing NNI: done in 6.48248 secs using 597.3% CPU
Iteration 100 / LogL: -193498.488 / Time: 0h:14m:52s (0h:8m:51s left)
Optimizing NNI: done in 7.44076 secs using 598% CPU
Optimizing NNI: done in 7.49207 secs using 597.7% CPU
Optimizing NNI: done in 7.26856 secs using 597.5% CPU
Optimizing NNI: done in 7.50512 secs using 597.9% CPU
Optimizing NNI: done in 6.72915 secs using 598.1% CPU
Optimizing NNI: done in 8.0732 secs using 597.5% CPU
Optimizing NNI: done in 7.79739 secs using 597.9% CPU
Optimizing NNI: done in 7.24997 secs using 597.9% CPU
Optimizing NNI: done in 7.6549 secs using 597.5% CPU
Optimizing NNI: done in 6.38047 secs using 597.9% CPU
Iteration 110 / LogL: -193499.284 / Time: 0h:16m:6s (0h:7m:14s left)
Optimizing NNI: done in 7.31315 secs using 597.6% CPU
Optimizing NNI: done in 7.31365 secs using 598.1% CPU
Optimizing NNI: done in 7.14897 secs using 597.6% CPU
Optimizing NNI: done in 7.11418 secs using 597.9% CPU
Optimizing NNI: done in 7.8853 secs using 597.9% CPU
Optimizing NNI: done in 7.34267 secs using 597.5% CPU
Optimizing NNI: done in 7.26893 secs using 597.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 117: -193440.833
Optimizing NNI: done in 5.61695 secs using 598.4% CPU
Optimizing NNI: done in 7.6045 secs using 597.9% CPU
Optimizing NNI: done in 7.37576 secs using 597.9% CPU
Iteration 120 / LogL: -193446.222 / Time: 0h:17m:23s (0h:14m:10s left)
Optimizing NNI: done in 7.11367 secs using 597.8% CPU
Optimizing NNI: done in 7.24404 secs using 597.8% CPU
Optimizing NNI: done in 7.60706 secs using 598.2% CPU
Optimizing NNI: done in 6.91827 secs using 597.9% CPU

******************************************************
CHECKPOINT: Resuming analysis from /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.ckp.gz

IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport
Seed:    579302 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Wed Jul  9 10:57:08 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta ... Fasta format detected
Reading fasta file: done in 0.00449204 secs using 98.35% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.00915194 secs using 5595% CPU
Alignment has 495 sequences with 575 columns, 575 distinct patterns
575 parsimony-informative, 0 singleton sites, 0 constant sites
            Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.000277996 secs using 5609% CPU
   1  8nJh6NUzJV   12.00%    passed     10.27%
   2  z0YCu0xtFo   11.30%    passed     15.88%
   3  1JN1q1h7Jh    8.35%    passed      9.02%
   4  E2n5Y5UQiG    8.52%    passed     43.28%
   5  cMoC1WsTO6    8.17%    failed      2.01%
   6  ys0DcEs0US    8.35%    passed     77.31%
   7  1s9qnaxMSp    9.04%    failed      2.14%
   8  FtHEpsU1vB    9.04%    failed      2.61%
   9  oeJuwbyE7Q    9.91%    passed      8.44%
  10  qCgVEYLhzI   17.39%    passed      9.43%
  11  zyhovbZkFP    9.91%    passed      8.44%
  12  jOk4aex96C   19.65%    passed      9.17%
  13  AR0npWZQ83    8.17%    passed     22.96%
  14  F5Si2gBtZe   21.91%    passed     13.69%
  15  FG021XCxMA   18.09%    passed     68.58%
  16  MCX7xygB2V    8.70%    passed     73.82%
  17  iVpOwiZzba    9.04%    passed     21.82%
  18  iPjBM3iYZR   80.35%    failed      2.62%
  19  qbFBJDOQUO    9.39%    passed     92.00%
  20  x5jv5lpB2O    9.22%    passed     43.94%
  21  y5M7y721WQ   11.30%    passed     52.45%
  22  MwDLYKIKBx   16.70%    passed     52.35%
  23  EsTTc2nPxQ    8.00%    passed     56.73%
  24  vnhywKRkFl   13.91%    passed     61.80%
  25  7JZdwvMv24   10.09%    passed     62.94%
  26  dQjyx7OIYV   27.30%    passed     66.63%
  27  irBovt5bLa    8.17%    passed     37.03%
  28  Ewm24Mlvnq    8.17%    failed      0.91%
  29  XDJ4JoLzyH   17.22%    passed     87.03%
  30  4kC0x0kjdn    7.65%    passed     35.61%
  31  RARcF60S6a    8.00%    passed     18.15%
  32  WlelCJO26H   12.17%    passed     15.31%
  33  mhk5OTojgz    7.83%    passed     22.72%
  34  pTM2DvE1xM    7.83%    passed     23.80%
  35  tlXXT5aWqu    8.35%    passed     25.18%
  36  TC8Xnd4iFa    8.35%    passed     68.65%
  37  02HhJs6pa3   11.13%    passed     51.90%
  38  NEeqpPtHg5    9.91%    passed     53.60%
  39  qbTDasygHV    8.00%    failed      4.34%
  40  7Yh1YhvFVC    9.04%    passed     82.42%
  41  VvE6sMyCv8    9.22%    passed     82.98%
  42  WjMMQYeUC2    9.74%    passed     28.42%
  43  W7Mh0FRDU6    9.57%    passed     47.24%
  44  2nrE64urGV    7.83%    failed      0.05%
  45  UzprTJ7K6d    7.83%    failed      0.07%
  46  UlwuxTyGoO    8.17%    passed     35.83%
  47  iaXjDyTif3    9.91%    passed     26.12%
  48  B6M0EvUDsT    8.17%    passed     57.64%
  49  1G5hXRghEG    7.83%    passed     46.06%
  50  gTvhxQmbWZ    7.83%    passed     59.90%
  51  8l37MLA1ms    7.83%    passed     66.42%
  52  vLizyHtRBL    6.96%    passed     45.67%
  53  S5ByYpGeqY    7.30%    passed     14.75%
  54  Fedl6T4xon    7.83%    passed     26.99%
  55  4BymctPkH6    9.22%    passed     90.46%
  56  s5wLZ9vWaO   22.96%    passed     14.42%
  57  awKrv6hUok    8.00%    failed      0.00%
  58  kWFqKgyYB3   18.61%    failed      0.35%
  59  DcYLS8gvW9    8.17%    passed     14.76%
  60  McRlo7Hy0B    8.35%    failed      1.15%
  61  tf71jZDs7S   14.78%    failed      0.00%
  62  vMqsZO8YaG   12.00%    passed     25.19%
  63  5AMYxNwgiK   14.26%    passed     72.77%
  64  wxoZBV0PHy    7.65%    passed     28.65%
  65  KeSH8I0Fea   10.96%    passed     34.97%
  66  KCrIGLQ7Q1    8.87%    passed     28.42%
  67  4LT0U0c0Do    8.17%    passed     45.98%
  68  CGeXrJPsGL    7.30%    passed     26.80%
  69  xxKiyIW1gr    8.35%    passed     42.35%
  70  xs9ieaVe53   24.17%    passed      5.89%
  71  NQWmJIpRFE    8.17%    passed     36.46%
  72  nkfchBpcgh    9.91%    passed     49.94%
  73  jdOhfl36g8    9.91%    passed     49.94%
  74  KVoy4GxdpT    8.70%    passed     30.77%
  75  WUIEff6ikU    9.74%    failed      3.44%
  76  coeQ6zHZ24    8.52%    passed     15.26%
  77  HWG7P94Eio    7.65%    passed     33.53%
  78  9Vw494DXPc    9.74%    passed     30.82%
  79  g6PJxKZvcf    8.17%    passed     67.92%
  80  AvvCKxHYp4    8.87%    passed     94.08%
  81  CemxIJafw8    8.87%    passed     94.94%
  82  dsBdLHptXN    7.30%    passed     26.31%
  83  4MVqW0qAIi    8.17%    passed      7.58%
  84  LcWgRv0iB6    8.17%    passed      6.57%
  85  fd8RtQX78T    8.35%    passed     67.99%
  86  D9LASQ998i    7.13%    passed     64.85%
  87  Uz7TnODNGf    8.17%    passed     61.10%
  88  Sp3Vq6QoAR   12.00%    passed     25.06%
  89  gtPloLimDb   14.61%    passed     16.69%
  90  GFnS6AyinZ   13.74%    passed     62.22%
  91  U9Eib0qR6X    9.39%    passed     80.44%
  92  dZ9ze414KZ    8.52%    passed     34.81%
  93  ydHAIeuwbW    9.04%    passed     24.32%
  94  e67HigPrjf    8.70%    passed     10.03%
  95  U5KrYXobqi    7.83%    passed     28.30%
  96  rqX0m8aZs1    8.52%    passed     74.68%
  97  JTOoSRn6ib    8.52%    passed     63.83%
  98  X4XbPR7Rfa    9.91%    passed     88.47%
  99  etCZH2Htco   11.30%    passed     96.50%
 100  7kS1ZU0pFM    9.74%    passed     63.62%
 101  rUnfYSLNJJ    8.35%    passed     25.59%
 102  YjqMqBCaiv    7.13%    passed     35.60%
 103  YXN7x6IbOx    8.35%    passed     52.18%
 104  bN8jt2Atwp   10.43%    passed     56.67%
 105  hgeyXdJgqq    9.22%    passed     56.85%
 106  1horVoEi3u    7.13%    failed      1.07%
 107  EDGqQf981n   10.09%    passed     86.16%
 108  3nDVNG9sKr   10.61%    passed     15.44%
 109  fFDoKaygf0    8.00%    passed     43.10%
 110  cRRsJgsBlZ    8.70%    passed     85.09%
 111  BI3jho3ECe    9.22%    passed     51.11%
 112  TIeppwLKSz    9.57%    passed     34.47%
 113  a8nt9ktZTC   24.35%    passed     70.98%
 114  GtfO72MtR2   22.26%    passed     65.46%
 115  xKzEmKT1dB   21.39%    passed     47.26%
 116  cTDPKciopP   11.83%    passed     67.98%
 117  xdNOUh7eMp    8.00%    passed     86.96%
 118  k3bzPFly41    8.17%    failed      0.00%
 119  ukUu00fP6L    9.39%    failed      0.29%
 120  up1UWJJzNf    9.22%    failed      3.36%
 121  GZASsy6wnT    8.17%    failed      0.00%
 122  PbkNCoK5ix   10.96%    passed     34.06%
 123  GfLEAInBd6   10.26%    passed     45.24%
 124  7OOuM97Qkr    8.70%    passed     42.00%
 125  d9kVhxwUcH    9.22%    passed     36.90%
 126  pn3nIof2qW    8.70%    passed     82.33%
 127  jYBcxGIen7   19.30%    passed     48.83%
 128  Y2YJcqt3IL   27.30%    passed     72.36%
 129  DQnwdMJsVl    9.39%    passed     17.77%
 130  Gvb4AsKEVi    8.35%    failed      0.00%
 131  d5E6EHDpwi    7.65%    passed     78.94%
 132  yA69Aemq0C    9.57%    passed     51.08%
 133  9f7AMvazZf    8.70%    passed     87.18%
 134  tD3ewCYOQG    9.22%    passed     39.14%
 135  yHwEtbE4JZ    8.87%    passed     51.50%
 136  HZpFQAW00k   12.87%    passed     16.94%
 137  FCPk6mdvI6    8.35%    passed     85.41%
 138  C50stY8CeY    9.22%    passed     15.26%
 139  WQOxpzhoLN    8.17%    passed     95.19%
 140  lU6fN5cAZQ   16.87%    passed     26.00%
 141  w34zJrGIvJ   13.04%    passed     46.23%
 142  R4SazYxajJ   13.22%    passed     24.74%
 143  oyLJTIsT1Z   12.00%    passed     35.61%
 144  95FTGjmRiw   16.87%    passed     10.92%
 145  MVSYHU9DCt   12.17%    passed     83.71%
 146  RhS1O12ekg    8.52%    passed     98.08%
 147  sthKhyT8fy    9.04%    passed     79.34%
 148  O2gQ2myCZn   11.30%    passed     66.29%
 149  B7PVgc3v8q    8.52%    passed     67.20%
 150  FlAHhYz62Q    6.96%    passed     92.12%
 151  PZqL2meUHi    8.35%    passed     89.55%
 152  XJTzBvD6pQ    8.70%    passed     73.32%
 153  FtEYGIUfBM   10.78%    passed     55.74%
 154  NUAWacASLt   10.26%    passed     81.70%
 155  3FdA2TKbHR   10.26%    passed     77.97%
 156  TCgaJethwm    9.74%    passed     51.49%
 157  V8Ort0OUIV    9.39%    passed     75.80%
 158  gKxOBa9lC3   80.35%    failed      4.37%
 159  ZJBcyycwk4   21.91%    passed     83.00%
 160  BXOEqGyzK2    9.04%    passed     82.96%
 161  5yy8DKtZ5c   12.35%    passed     70.92%
 162  cY7oeSnppq    9.74%    passed     78.00%
 163  vUEx5gqasN    9.74%    passed     22.71%
 164  2jCJDig3v9   17.39%    passed     45.79%
 165  lzBWRCtyx0   17.39%    passed     45.79%
 166  DBMxujRgHK   10.43%    passed     76.44%
 167  x3ZrH0XGfQ   13.04%    passed     40.57%
 168  SgWCfVzTG4    9.39%    passed     23.64%
 169  f62ksK5UEj   33.39%    passed     48.62%
 170  hkIztfSCD1   10.09%    passed     60.28%
 171  iRnB4M1GLD   11.30%    passed     35.88%
 172  CU0XuCnsFL   42.61%    failed      1.05%
 173  42tdKq8PSX   12.87%    passed     50.93%
 174  gXeZ52LCvM   12.87%    passed     50.93%
 175  u8cLLIfWEX   12.87%    passed     50.93%
 176  dmOh7r7eKT   12.52%    passed     43.59%
 177  3c6hZoOqvP   12.87%    passed     51.70%
 178  bu2UDzewiZ   16.35%    passed     97.52%
 179  SYc4eSftSt    7.30%    passed     55.76%
 180  zlSzVB3W0P    9.91%    passed     23.47%
 181  3C2pM8OlsA   16.00%    passed     44.07%
 182  Pxcz4xw4KG    8.52%    passed     89.90%
 183  UcghE30qVq   10.26%    passed     98.72%
 184  qIB6gS9bgA   10.26%    passed     99.50%
 185  UDehzYJL1w    9.91%    passed     84.08%
 186  BB4241mZBL    9.74%    passed     18.51%
 187  c6c8r06RzT   14.09%    passed     51.46%
 188  XQT9xr4ybf   14.09%    passed     51.46%
 189  SCnTy3bpY1   12.00%    passed     52.85%
 190  jev8yDUHvc   37.22%    passed     46.96%
 191  bK3G4lRT3G    9.74%    passed     18.84%
 192  Z5XH3L582l    9.39%    passed     64.30%
 193  dhUTnrRr7d    9.04%    passed     17.65%
 194  2ifGWJmasz   13.39%    passed     53.39%
 195  WB36HQui6V   13.22%    passed     13.09%
 196  QNNkPiHWnJ   13.57%    passed     15.99%
 197  WHGNQkrc10   16.70%    passed     15.42%
 198  h5LGHiiOXm   13.04%    passed      8.14%
 199  3zhlkwsAL6   11.65%    passed     68.02%
 200  i2Lb0rchl2   17.74%    passed     40.76%
 201  yMqx9t1LVd   11.83%    passed     95.23%
 202  2W3WY0vBww   18.09%    passed     31.19%
 203  wTTqfzkYo6   12.35%    passed     65.69%
 204  0vKBWD6wpY   19.83%    passed     72.14%
 205  SJgohIdqev   13.04%    passed     56.62%
 206  9DPLpYQWNv    8.35%    passed     79.37%
 207  8uUTsKFjlb    9.74%    passed     57.77%
 208  xVujdvY6Nr   15.65%    passed     86.08%
 209  NImtrhZGKE   18.61%    passed     29.08%
 210  YugOzGk8Ov    8.00%    passed     61.92%
 211  DeWEtikGbq    9.39%    passed     58.48%
 212  x0olbpog9B   10.78%    failed      3.15%
 213  pAhidh8xBZ    9.22%    passed     20.39%
 214  PlPvNaQDzl   78.26%    failed      2.70%
 215  NPvXCeLNmx    9.22%    passed     19.23%
 216  yVup7G0SEF    9.39%    passed      5.94%
 217  vPQhR8sENE    9.22%    passed     25.50%
 218  nU2WbHAcGl    8.00%    passed     38.25%
 219  5LDURAlPH2   18.96%    passed     93.03%
 220  BWFcvfZnO3   19.83%    passed     80.72%
 221  pygYFVFfpx   18.96%    passed     64.25%
 222  SHqN6p0dYV   11.65%    passed     77.47%
 223  qsVXrYaG9q   16.52%    passed     62.49%
 224  3cAaekWMpW   17.57%    passed     67.41%
 225  N40B32hpg1   12.00%    passed     79.79%
 226  JPT5lhIP82   16.17%    passed     61.51%
 227  ZLXDnoVm6b    8.87%    passed     65.21%
 228  X85YtZdfkf    9.04%    passed     76.50%
 229  8UiTG47Ec2    9.04%    passed     76.50%
 230  rIeH6RocN2   11.13%    passed     16.99%
 231  JEeirH12E1   31.48%    passed     21.21%
 232  UzAtwShlJN   15.48%    failed      0.00%
 233  2pVvPoBi2c   15.65%    failed      0.00%
 234  scQ10Wo461   39.13%    passed     23.66%
 235  Nb1rJKftmp   17.91%    failed      0.00%
 236  nhoqJOOPX2   17.04%    passed     88.57%
 237  39gkmZTScW   18.26%    passed     91.96%
 238  BGkr4JUYAf   13.39%    passed     93.93%
 239  DulbVCzsEt   24.35%    passed     66.60%
 240  cSruxLJuyQ   26.96%    passed     10.64%
 241  1XfSwqn4ef   25.04%    passed     39.48%
 242  96xj01KeXJ   68.17%    passed     84.97%
 243  eq1zGc6rtT   29.04%    passed     18.35%
 244  VfUM5i9jsn   41.91%    failed      4.66%
 245  20sicocoSo   23.83%    failed      0.74%
 246  RLpJhYeIPE   25.91%    passed     47.76%
 247  C8YPeCC1NI   28.87%    passed     14.80%
 248  xxnHHiKI8Z   28.52%    passed      5.76%
 249  3Je7M7o4rZ   33.39%    passed     11.10%
 250  47EKfQlPcw   28.35%    passed     38.14%
 251  9C0byE309K   34.43%    passed     22.05%
 252  TsIfWQzrph   28.35%    passed     38.14%
 253  hTPGiqrFV4   42.09%    passed     88.30%
 254  aFMglfB8eH   24.52%    passed     15.36%
 255  JQcRFbokY2   28.35%    passed     32.19%
 256  jFdaAxFg6n   23.13%    passed     47.94%
 257  KRYbednenZ   23.13%    passed     42.60%
 258  FyIDyqrLwr   23.13%    passed     47.94%
 259  8XGfcNsQ09   23.83%    passed     62.09%
 260  QyNf0mVNlz   23.83%    passed     10.54%
 261  f9oKgpE1wE   23.48%    passed     56.82%
 262  REBVZFiPEf   23.30%    passed     27.01%
 263  ItesG8T6sN   23.83%    passed     47.79%
 264  TSGS90hx1G   23.30%    passed     24.55%
 265  ZRAzqCtrNA   24.17%    passed     57.76%
 266  eeM5JHuVuf   24.35%    passed     50.06%
 267  oe9Vawfrxg   24.35%    passed     26.16%
 268  rgglFfiKnC   28.00%    passed     45.26%
 269  bCjdcpAF4v   24.00%    passed     70.09%
 270  OmcerY3zVm   64.35%    passed     66.28%
 271  zcG6I9U7zt   43.13%    passed     73.90%
 272  QKniumy84t   24.00%    passed     71.91%
 273  158IGk2w8A   24.00%    passed     40.59%
 274  kI8iG2U2gQ   23.30%    passed     85.81%
 275  fPZNEk39Af   26.78%    passed     15.99%
 276  hrBvV4AmlN   24.17%    passed     20.25%
 277  myGUzZ8LDH   24.00%    passed     24.24%
 278  sHkv5UU91e   23.65%    passed     10.45%
 279  GNzRUX9ddm   23.65%    passed     13.36%
 280  zsnvwGvGgv   24.00%    passed     30.90%
 281  9OoygEJxNJ   23.13%    passed     19.47%
 282  IjtzwwEpZt   24.70%    passed     32.04%
 283  nSDhHtKOaz   76.87%    passed     72.40%
 284  A0R7Dl6WnL   24.00%    passed     27.63%
 285  CvviaWP5QG   24.17%    passed     57.70%
 286  pPSEGFgq5j   79.13%    passed     12.51%
 287  UdG6KQNIp6   24.52%    passed      9.66%
 288  8EVSPtaAhX   24.35%    passed     42.22%
 289  uiafGbGfwA   27.30%    passed     85.86%
 290  XZFyxFJmTO   24.70%    passed     34.27%
 291  H6HkWi4jLJ   26.26%    passed     57.81%
 292  uALm9y36Bq   28.70%    passed     22.86%
 293  EUEmaNv0jU   23.30%    passed     16.64%
 294  miFIpMQUO8   25.04%    passed      5.34%
 295  qsWsb5TOjf   26.09%    passed     11.23%
 296  WLDkRifOr1   25.74%    passed     31.25%
 297  u7RGaLBmh5   25.74%    passed     85.68%
 298  n4n2Sa9hou   25.39%    passed     53.48%
 299  gZV6bt6UCn   24.17%    passed     46.31%
 300  PortTSlpTI   41.74%    passed     26.87%
 301  2Nn52BMVGD   28.00%    passed     32.50%
 302  sQl8vIYhWL   27.30%    passed     24.87%
 303  nlyynuwvAY   27.13%    passed     84.06%
 304  iM9z6TKAcr   41.39%    passed     18.69%
 305  pVpmbqWKfw   36.70%    failed      1.72%
 306  r4JpMWXYFJ   26.09%    passed     11.04%
 307  CcX8oiPHcg   27.83%    passed     27.83%
 308  G2BVFEVILA   25.04%    passed     61.18%
 309  BNYVmW4TYG   25.91%    passed     54.90%
 310  ExQ8uNPj7h   34.26%    passed     66.82%
 311  whmj06xoF5   28.17%    failed      0.02%
 312  VqFVtnHfVy   25.22%    passed     79.18%
 313  Mqy8imXZ6G   25.91%    failed      0.02%
 314  s0NXcs97L3   25.91%    failed      0.02%
 315  Iqt8ZiOu6k   25.74%    failed      0.00%
 316  XsWTxkH1p7   25.57%    passed     19.64%
 317  zoRaGfFB7U   24.52%    passed     48.77%
 318  qqN1dh1OOy   24.35%    passed     14.36%
 319  T1wQDvF98B   24.35%    passed      7.77%
 320  lkTsXyry76   26.43%    passed     26.11%
 321  hSqg5YYyOm   27.48%    failed      0.44%
 322  puRVWMvppN   28.35%    passed     22.55%
 323  1LbFAdgLuC   25.74%    passed     11.73%
 324  y5MmiioIHk   25.91%    failed      1.83%
 325  BnR8odZPBs   25.91%    passed     15.58%
 326  ajGvkpi5As   25.91%    passed      8.73%
 327  qbTJcwpdwP   26.61%    passed     13.99%
 328  vCxAIjCqNl   24.87%    passed     46.42%
 329  mPlwp1JlUK   27.30%    passed     36.54%
 330  rYWDHuLHvt   29.91%    failed      1.32%
 331  C0RnyRzFMX   71.65%    passed     45.95%
 332  7Aa2sW2uFn   28.00%    failed      3.36%
 333  0djEp2FhF9   28.00%    failed      3.36%
 334  l1pN6WjG1N   80.17%    passed     21.40%
 335  XLgmciWSgo   46.09%    passed     14.00%
 336  D8WaLv1pNN   30.78%    passed     27.06%
 337  12VY0qcAbu   29.39%    passed     74.33%
 338  JNoGNci0kO   28.87%    passed     95.56%
 339  VGEALS8WvR   40.70%    passed     16.49%
 340  D7iWRjKQ8X   25.74%    passed     47.65%
 341  upEmmPcbTB   27.48%    passed     22.48%
 342  UpKcpH8xp2   26.78%    passed      7.74%
 343  hreWbDAWDh   23.65%    passed      8.09%
 344  5oPFYbGk9x   24.52%    passed     66.68%
 345  bKMx8usLZf   35.83%    passed      9.39%
 346  9waTHuOjG2   43.48%    passed     27.73%
 347  y13PUGF6fd   29.39%    passed     50.29%
 348  MCxeCrj6og   25.22%    passed     77.92%
 349  JqQlZRu8jp   25.91%    passed     38.60%
 350  ZrMp8mhVn3   56.35%    passed      9.73%
 351  PVum0t8D9w   48.52%    failed      3.01%
 352  mA0FIy0SqW   24.70%    passed      5.42%
 353  EacivjsFt1   26.61%    passed     43.72%
 354  FKAuFXjrK2   29.57%    failed      2.12%
 355  eOn8Fw1qPv   27.48%    failed      3.53%
 356  D0XDiTOIfD   34.78%    passed      9.81%
 357  910hgdbBRd   28.00%    passed     51.49%
 358  ijUTPEstS6   33.39%    passed     28.87%
 359  bUU4czn7NG   27.83%    passed     60.40%
 360  INEhHLWnmb   37.04%    failed      1.97%
 361  LMA81zzKSe   37.04%    failed      0.01%
 362  TUCOIK4ZQn   33.91%    failed      0.52%
 363  yvso4goGdQ   34.96%    failed      4.00%
 364  YWPX00OZwF   36.00%    failed      3.54%
 365  qKqJ6yzKtT   34.61%    passed     10.13%
 366  49Qin0CHkb   34.61%    passed      9.62%
 367  63Q15egMZA   34.26%    passed      6.18%
 368  nWYlGrbPPc   34.61%    failed      4.67%
 369  JvcE4PBExA   33.74%    passed      7.73%
 370  LUlT7ehgwb   36.00%    passed     26.12%
 371  pVpykOHqYZ   39.48%    failed      0.85%
 372  v2K68153zf   38.26%    failed      0.55%
 373  qYhA4tEOW1   34.78%    failed      0.03%
 374  grGtjFUUTt   34.43%    failed      0.23%
 375  qWhSnx7aMf   44.87%    passed      5.50%
 376  v1oAyLSJtz   50.96%    passed     28.72%
 377  BadtzwpMMs   38.43%    passed      9.62%
 378  6DLNJCEk13   34.61%    passed      8.29%
 379  w2DOMr7ED6   41.39%    failed      3.23%
 380  JK0CadwxtV   33.74%    failed      1.62%
 381  thXzqzsTWd   33.04%    failed      4.58%
 382  cza9cyArKR   33.04%    failed      3.45%
 383  64i2bPRqyf   38.09%    failed      1.24%
 384  Tu05kR9iNy   35.30%    failed      2.13%
 385  ryyuwN9EeF   35.83%    failed      3.08%
 386  9i9iYEz14b   36.87%    passed     43.29%
 387  e5Z7VURlcd   56.00%    failed      0.95%
 388  ndIdlcACpn   34.61%    failed      0.11%
 389  miylOtOHke   36.00%    passed      5.91%
 390  jGxqmOPSFz   33.91%    failed      1.22%
 391  UpRnjomc4O   36.17%    passed     26.63%
 392  ebCUnMXr2f   38.43%    passed     15.56%
 393  21yjS1P784   34.43%    failed      0.27%
 394  XU8ct59Imq   34.26%    failed      0.70%
 395  mWu9nYUMB2   34.26%    passed      5.63%
 396  6N8VC2LDv6   34.26%    passed      5.63%
 397  Tp4oCldie4   38.09%    failed      4.42%
 398  LdahhT5atZ   34.26%    passed      5.63%
 399  ohdNT1wCFZ   34.26%    passed      7.14%
 400  QY3dkiwN48   41.57%    failed      3.72%
 401  Ip06mTdO2e   35.65%    failed      2.00%
 402  P5RXO2szhK   29.57%    passed     33.39%
 403  offjx75l6X   85.22%    passed     26.57%
 404  EdOuOhohBn   33.91%    passed     23.13%
 405  ZjYUAXvbUC   34.26%    passed      8.29%
 406  lpxtOw9xf3   36.52%    passed     12.71%
 407  4bSmqRgfRI   34.09%    passed     12.39%
 408  gminDyGtcG   34.78%    failed      2.44%
 409  lDQWwcBkMU   34.78%    passed     33.99%
 410  CUTMeJuwSv   33.74%    passed     78.03%
 411  OI80q3iM3F   33.74%    passed     81.17%
 412  xnKco929hT   37.57%    passed      8.65%
 413  RPfcmWXHCA   37.57%    passed     20.91%
 414  6mj1jZTKcU   36.17%    failed      4.67%
 415  Gr87dxYVyz   43.83%    failed      4.55%
 416  VGvhdii6IX   73.22%    passed     54.33%
 417  wJTuSg6Gc6   35.65%    passed     75.44%
 418  K3Flz6km5g   35.65%    passed     71.14%
 419  Tu0u89fzoU   35.48%    passed     16.33%
 420  IpceOBVrBQ   35.48%    passed     13.04%
 421  JAjUuwFnV7   36.35%    passed     34.52%
 422  wSnvqYXqTg   32.00%    passed     24.03%
 423  keWKiDv5J1   36.35%    passed     23.38%
 424  r5NSp8dbtM   37.39%    passed     32.60%
 425  wxLKLb6SMC   35.13%    passed     25.74%
 426  qw6gF6ZapY   35.13%    passed     25.74%
 427  ZGvDd4xvwy   37.91%    passed     30.11%
 428  8lXCZuvq8q   34.26%    passed     25.11%
 429  qvg1my8Wlp   48.70%    failed      3.30%
 430  ZdWaANa0Et   32.87%    passed      6.04%
 431  Onz2iyjxH3   42.96%    failed      0.02%
 432  AJImOJUang   66.09%    passed      8.67%
 433  rbo3OKIe4x   36.52%    failed      0.54%
 434  pGufZSTMNB   36.52%    passed     12.14%
 435  FLjy3W79tg   36.52%    passed     17.85%
 436  jYaSjXdhUR   34.78%    passed     22.31%
 437  HGW1EoyaVz   49.22%    passed     75.08%
 438  HQpmvbcKV0   36.35%    passed     71.28%
 439  Us22uQdloc   73.22%    passed     88.61%
 440  Nczi5Cos47   34.96%    passed     68.86%
 441  IV8TgD1mQj   36.52%    passed     65.05%
 442  QKsY8kV1rB   34.43%    passed     49.51%
 443  TrIc96BqkG   34.96%    passed      7.64%
 444  pnjqLcOivm   34.61%    passed      9.34%
 445  SY2alUymun   36.00%    passed     31.87%
 446  GXBps2FgSH   37.57%    failed      4.23%
 447  ZldeYJmzLx   39.48%    failed      0.13%
 448  8biR24Gazc   33.91%    passed     22.85%
 449  NBJ6cvHYoU   34.43%    passed     22.55%
 450  egq7pHRqeL   38.78%    passed     36.06%
 451  y0r2SVxwqI   35.30%    passed     55.80%
 452  evUBWmPjS2   35.30%    passed     23.87%
 453  ikh1qtxydC   36.00%    failed      2.62%
 454  BRdJ9RHZQj   35.65%    passed      8.09%
 455  l25CgIsmfn   35.65%    passed      8.09%
 456  XPdvjShyOo   37.57%    passed      7.82%
 457  M144qciIKM   34.96%    passed     30.15%
 458  BnE96TDyk8   35.48%    passed     26.42%
 459  jeohLZ0eYF   36.87%    failed      0.20%
 460  YvoxlQmxl7   36.87%    failed      0.20%
 461  R0wuUn8J0h   33.57%    passed     30.51%
 462  oeFPRaQBYZ   33.39%    passed     26.87%
 463  xqlhblg6dL   33.91%    passed     25.42%
 464  6Qs9p4Rx4f   34.09%    passed     25.71%
 465  QPlyWfEtzz   34.43%    passed     29.56%
 466  Yo6roMcRLy   35.30%    passed     25.15%
 467  PwuAxgsPD6   42.78%    passed     42.46%
 468  vaFUdeGB10   33.91%    failed      2.49%
 469  8GM1psnK6y   36.87%    failed      0.09%
 470  E6RVlyXu6C   33.74%    passed     45.21%
 471  SuF6hGymBQ   36.00%    failed      2.74%
 472  cgJCegWwAr   70.96%    passed     99.24%
 473  i10ONbBPRV   34.96%    passed     50.77%
 474  FaaaR0oHe4   35.13%    passed     47.29%
 475  RrNP3l8SS7   36.52%    failed      0.47%
 476  BuFyz2PMN4   34.43%    passed     49.11%
 477  Y10Qa1Da4V   38.78%    passed     65.87%
 478  8zkzdNvfM0   34.43%    passed     49.11%
 479  rA4KjQCVx3   32.00%    passed     90.85%
 480  au044S3YHW   35.30%    passed     43.12%
 481  cIR66o13VD   35.65%    passed     81.03%
 482  fkB1xaD3I7   35.83%    passed     66.46%
 483  CwGGcZADEn   35.30%    passed     25.37%
 484  fNHflelF6b   34.61%    passed     14.83%
 485  8zGWBmbKDs   83.65%    passed     77.32%
 486  LC2TsjjWfV   35.65%    passed     44.42%
 487  rsgxiUIZDl   41.74%    passed     41.79%
 488  Srvt2UziZu   34.43%    passed     97.83%
 489  zPT9rylEFV   34.43%    passed     97.83%
 490  rXls0PgjJv   35.48%    passed      5.47%
 491  TcLIjpisFo   51.83%    passed     29.28%
 492  RMfRwwtcqL   32.17%    passed      5.11%
 493  zzJMOnIGaE   34.09%    failed      0.02%
 494  bkj6PiDj99   34.78%    passed     36.79%
 495  QPtDeO8Fse   34.61%    passed     64.43%
WARNING: 19 sequences contain more than 50% gaps/ambiguity
****  TOTAL        23.94%  82 sequences failed composition chi2 test (p-value<5%; df=19)
CHECKPOINT: 76 bootstrap analyses restored

NOTE: Restoring information from model checkpoint file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz

CHECKPOINT: Initial tree restored
Measuring multi-threading efficiency up to 96 CPU cores
Increase to 10 rounds for branch lengths
23 trees examined
Threads: 1 / Time: 96.729 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -471775
Threads: 2 / Time: 64.410 sec / Speedup: 1.502 / Efficiency: 75% / LogL: -471775
Threads: 3 / Time: 43.459 sec / Speedup: 2.226 / Efficiency: 74% / LogL: -471775
Threads: 4 / Time: 43.256 sec / Speedup: 2.236 / Efficiency: 56% / LogL: -471775
Threads: 5 / Time: 39.756 sec / Speedup: 2.433 / Efficiency: 49% / LogL: -471775
Determining AUTO threadcount: done in 287.659 secs using 256.3% CPU
BEST NUMBER OF THREADS: 3

Perform fast likelihood tree search using LG+G model...
CHECKPOINT: Tree restored, LogL: -195489.756
NOTE: ModelFinder requires 455 MB RAM!
ModelFinder will test up to 616 protein models (sample size: 575) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  LG            200322.611   987 402619.222   2352931.222  406916.985
  2  LG+G4         195470.344   988 392916.688   2347180.688  397218.805
  3  LG+R2         196589.598   989 395157.196   2353377.196  399463.668
  4  LG+R3         195780.340   991 393542.681   2359686.681  397857.862
  5  LG+R4         195429.122   993 392844.244   2366928.244  397168.133
  6  LG+R5         195312.276   995 392614.553   2374654.553  396947.151
  7  LG+R6         195240.929   997 392475.859   2382487.859  396817.166
  8  LG+R7         195209.395   999 392416.790   2390416.790  396766.806
  9  LG+R8         195184.144   1001 392370.288   2398374.288  396729.013
 10  LG+R9         195175.348   1003 392356.697   2406380.697  396724.130
 11  LG+R10        195171.997   1005 392353.994   2414413.994  396730.135
 20  LG+F+R8       194402.294   1020 390844.587   2473684.587  395286.045
 21  LG+F+R9       194396.917   1022 390837.834   2481849.834  395288.000
 31  WAG+R8        196252.507   1001 394507.014   2400511.014  398865.738
 32  WAG+R9        196242.300   1003 394490.599   2408514.599  398858.033
 33  WAG+R10       196241.628   1005 394493.256   2416553.256  398869.398
 42  WAG+F+R8      194842.645   1020 391725.291   2474565.291  396166.748
 43  WAG+F+R9      194839.005   1022 391722.011   2482734.011  396172.177
 53  JTT+R8        195608.757   1001 393219.514   2399223.514  397578.238
 54  JTT+R9        195593.125   1003 393192.250   2407216.250  397559.683
 55  JTT+R10       195590.207   1005 393190.414   2415250.414  397566.556
 64  JTT+F+R8      194695.864   1020 391431.729   2474271.729  395873.186
 65  JTT+F+R9      194690.743   1022 391425.486   2482437.486  395875.652
WARNING: Normalizing state frequencies so that sum of them equals to 1
 75  Q.pfam+R8     194892.568   1001 391787.135   2397791.135  396145.860
WARNING: Normalizing state frequencies so that sum of them equals to 1
 76  Q.pfam+R9     194887.665   1003 391781.330   2405805.330  396148.763
WARNING: Normalizing state frequencies so that sum of them equals to 1
 86  Q.pfam+F+R8   194521.401   1020 391082.801   2473922.801  395524.259
WARNING: Normalizing state frequencies so that sum of them equals to 1
 87  Q.pfam+F+R9   194515.431   1022 391074.862   2482086.862  395525.029
WARNING: Normalizing state frequencies so that sum of them equals to 1
 97  Q.bird+R8     197829.393   1001 397660.786   2403664.786  402019.511
WARNING: Normalizing state frequencies so that sum of them equals to 1
 98  Q.bird+R9     197820.275   1003 397646.550   2411670.550  402013.983
WARNING: Normalizing state frequencies so that sum of them equals to 1
 99  Q.bird+R10    197814.318   1005 397638.636   2419698.636  402014.778
WARNING: Normalizing state frequencies so that sum of them equals to 1
108  Q.bird+F+R8   198079.035   1020 398198.069   2481038.069  402639.527
WARNING: Normalizing state frequencies so that sum of them equals to 1
109  Q.bird+F+R9   198072.616   1022 398189.232   2489201.232  402639.398
WARNING: Normalizing state frequencies so that sum of them equals to 1
110  Q.bird+F+R10  198068.569   1024 398185.139   2497385.139  402644.014
WARNING: Normalizing state frequencies so that sum of them equals to 1
119  Q.mammal+R8   196715.407   1001 395432.814   2401436.814  399791.538
WARNING: Normalizing state frequencies so that sum of them equals to 1
120  Q.mammal+R9   196707.402   1003 395420.804   2409444.804  399788.237
WARNING: Normalizing state frequencies so that sum of them equals to 1
121  Q.mammal+R10  196703.479   1005 395416.958   2417476.958  399793.100
WARNING: Normalizing state frequencies so that sum of them equals to 1
130  Q.mammal+F+R8 196877.834   1020 395795.669   2478635.669  400237.126
WARNING: Normalizing state frequencies so that sum of them equals to 1
131  Q.mammal+F+R9 196872.663   1022 395789.327   2486801.327  400239.493
141  Q.insect+R8   195081.318   1001 392164.635   2398168.635  396523.360
142  Q.insect+R9   195076.551   1003 392159.102   2406183.102  396526.535
152  Q.insect+F+R8 194860.269   1020 391760.539   2474600.539  396201.996
153  Q.insect+F+R9 194858.288   1022 391760.576   2482772.576  396210.742
WARNING: Normalizing state frequencies so that sum of them equals to 1
163  Q.plant+R8    194919.373   1001 391840.745   2397844.745  396199.470
WARNING: Normalizing state frequencies so that sum of them equals to 1
164  Q.plant+R9    194913.090   1003 391832.180   2405856.180  396199.613
WARNING: Normalizing state frequencies so that sum of them equals to 1
174  Q.plant+F+R8  194822.604   1020 391685.208   2474525.208  396126.665
WARNING: Normalizing state frequencies so that sum of them equals to 1
175  Q.plant+F+R9  194819.592   1022 391683.184   2482695.184  396133.350
WARNING: Normalizing state frequencies so that sum of them equals to 1
185  Q.yeast+R8    195446.700   1001 392895.400   2398899.400  397254.125
WARNING: Normalizing state frequencies so that sum of them equals to 1
186  Q.yeast+R9    195439.881   1003 392885.762   2406909.762  397253.195
WARNING: Normalizing state frequencies so that sum of them equals to 1
187  Q.yeast+R10   195435.549   1005 392881.097   2414941.097  397257.239
WARNING: Normalizing state frequencies so that sum of them equals to 1
196  Q.yeast+F+R8  194579.068   1020 391198.136   2474038.136  395639.593
WARNING: Normalizing state frequencies so that sum of them equals to 1
197  Q.yeast+F+R9  194573.538   1022 391191.077   2482203.077  395641.243
207  JTTDCMut+R8   195684.064   1001 393370.127   2399374.127  397728.852
208  JTTDCMut+R9   195667.689   1003 393341.377   2407365.377  397708.810
209  JTTDCMut+R10  195664.727   1005 393339.454   2415399.454  397715.596
218  JTTDCMut+F+R8 194737.502   1020 391515.003   2474355.003  395956.461
219  JTTDCMut+F+R9 194732.541   1022 391509.083   2482521.083  395959.249
229  DCMut+R8      198858.399   1001 399718.798   2405722.798  404077.523
230  DCMut+R9      198850.908   1003 399707.816   2413731.816  404075.249
231  DCMut+R10     198848.803   1005 399707.606   2421767.606  404083.748
240  DCMut+F+R8    196826.536   1020 395693.071   2478533.071  400134.529
241  DCMut+F+R9    196816.360   1022 395676.721   2486688.721  400126.887
242  DCMut+F+R10   196813.450   1024 395674.901   2494874.901  400133.776
251  VT+R8         196235.054   1001 394472.109   2400476.109  398830.833
252  VT+R9         196229.175   1003 394464.350   2408488.350  398831.783
262  VT+F+R8       195084.460   1020 392208.920   2475048.920  396650.377
263  VT+F+R9       195080.573   1022 392205.145   2483217.145  396655.311
273  PMB+R8        197315.374   1001 396632.748   2402636.748  400991.472
274  PMB+R9        197308.918   1003 396623.836   2410647.836  400991.269
275  PMB+R10       197306.392   1005 396622.785   2418682.785  400998.926
284  PMB+F+R8      197173.282   1020 396386.563   2479226.563  400828.020
285  PMB+F+R9      197172.042   1022 396388.084   2487400.084  400838.251
295  Blosum62+R8   197539.412   1001 397080.824   2403084.824  401439.549
296  Blosum62+R9   197530.232   1003 397066.464   2411090.464  401433.897
297  Blosum62+R10  197526.017   1005 397062.034   2419122.034  401438.175
306  Blosum62+F+R8 196901.090   1020 395842.180   2478682.180  400283.637
307  Blosum62+F+R9 196899.776   1022 395843.552   2486855.552  400293.718
317  Dayhoff+R8    198852.273   1001 399706.545   2405710.545  404065.270
318  Dayhoff+R9    198844.881   1003 399695.761   2413719.761  404063.195
319  Dayhoff+R10   198842.886   1005 399695.772   2421755.772  404071.914
328  Dayhoff+F+R8  196817.472   1020 395674.945   2478514.945  400116.402
329  Dayhoff+F+R9  196807.436   1022 395658.873   2486670.873  400109.039
330  Dayhoff+F+R10 196804.462   1024 395656.923   2494856.923  400115.798
339  mtREV+R8      202211.703   1001 406425.405   2412429.405  410784.129
340  mtREV+R9      202203.018   1003 406412.035   2420436.035  410779.468
341  mtREV+R10     202198.737   1005 406407.475   2428467.475  410783.617
350  mtREV+F+R8    197257.838   1020 396555.675   2479395.675  400997.133
351  mtREV+F+R9    197248.935   1022 396541.871   2487553.871  400992.037
352  mtREV+F+R10   197245.156   1024 396538.312   2495738.312  400997.187
361  mtART+R8      203583.239   1001 409168.478   2415172.478  413527.203
362  mtART+R9      203529.654   1003 409065.309   2423089.309  413432.742
363  mtART+R10     203525.582   1005 409061.164   2431121.164  413437.306
372  mtART+F+R8    200433.253   1020 402906.506   2485746.506  407347.963
373  mtART+F+R9    200385.741   1022 402815.481   2493827.481  407265.647
374  mtART+F+R10   200379.364   1024 402806.728   2502006.728  407265.603
383  mtZOA+R8      198366.129   1001 398734.257   2404738.257  403092.982
384  mtZOA+R9      198360.117   1003 398726.235   2412750.235  403093.668
394  mtZOA+F+R8    196919.533   1020 395879.066   2478719.066  400320.523
395  mtZOA+F+R9    196898.434   1022 395840.867   2486852.867  400291.033
396  mtZOA+F+R10   196891.474   1024 395830.948   2495030.948  400289.823
405  mtMet+R8      200042.427   1001 402086.853   2408090.853  406445.578
406  mtMet+R9      200019.941   1003 402045.882   2416069.882  406413.316
407  mtMet+R10     200049.839   1005 402109.679   2424169.679  406485.821
416  mtMet+F+R8    196455.394   1020 394950.789   2477790.789  399392.246
417  mtMet+F+R9    196440.614   1022 394925.229   2485937.229  399375.395
418  mtMet+F+R10   196431.320   1024 394910.641   2494110.641  399369.516
427  mtVer+R8      203014.713   1001 408031.426   2414035.426  412390.150
428  mtVer+R9      203008.014   1003 408022.029   2422046.029  412389.462
429  mtVer+R10     202969.843   1005 407949.685   2430009.685  412325.827
438  mtVer+F+R8    198883.127   1020 399806.254   2482646.254  404247.711
439  mtVer+F+R9    198874.584   1022 399793.168   2490805.168  404243.334
440  mtVer+F+R10   198869.999   1024 399787.998   2498987.998  404246.873
449  mtInv+R8      200418.426   1001 402838.852   2408842.852  407197.577
450  mtInv+R9      200410.477   1003 402826.954   2416850.954  407194.387
451  mtInv+R10     200408.596   1005 402827.192   2424887.192  407203.334
460  mtInv+F+R8    195221.172   1020 392482.344   2475322.344  396923.802
461  mtInv+F+R9    195216.016   1022 392476.033   2483488.033  396926.199
471  mtMAM+R8      207137.637   1001 416277.273   2422281.273  420635.998
472  mtMAM+R9      207095.777   1003 416197.555   2430221.555  420564.988
473  mtMAM+R10     207079.072   1005 416168.143   2438228.143  420544.285
482  mtMAM+F+R8    202259.202   1020 406558.403   2489398.403  410999.861
483  mtMAM+F+R9    202225.832   1022 406495.663   2497507.663  410945.830
484  mtMAM+F+R10   202217.624   1024 406483.248   2505683.248  410942.123
WARNING: Normalizing state frequencies so that sum of them equals to 1
493  FLAVI+R8      202777.540   1001 407557.080   2413561.080  411915.804
WARNING: Normalizing state frequencies so that sum of them equals to 1
494  FLAVI+R9      202768.495   1003 407542.991   2421566.991  411910.424
WARNING: Normalizing state frequencies so that sum of them equals to 1
495  FLAVI+R10     202753.049   1005 407516.099   2429576.099  411892.240
WARNING: Normalizing state frequencies so that sum of them equals to 1
504  FLAVI+F+R8    202442.661   1020 406925.322   2489765.322  411366.780
WARNING: Normalizing state frequencies so that sum of them equals to 1
505  FLAVI+F+R9    202434.692   1022 406913.384   2497925.384  411363.551
WARNING: Normalizing state frequencies so that sum of them equals to 1
506  FLAVI+F+R10   202428.582   1024 406905.164   2506105.164  411364.039
515  HIVb+R8       200393.670   1001 402789.341   2408793.341  407148.065
516  HIVb+R9       200381.791   1003 402769.582   2416793.582  407137.016
517  HIVb+R10      200371.459   1005 402752.918   2424812.918  407129.060
526  HIVb+F+R8     198771.236   1020 399582.473   2482422.473  404023.930
527  HIVb+F+R9     198764.928   1022 399573.855   2490585.855  404024.021
537  HIVw+R8       209399.096   1001 420800.192   2426804.192  425158.916
538  HIVw+R9       209380.617   1003 420767.234   2434791.234  425134.668
539  HIVw+R10      209376.097   1005 420762.193   2442822.193  425138.335
548  HIVw+F+R8     204961.158   1020 411962.315   2494802.315  416403.773
549  HIVw+F+R9     204951.516   1022 411947.031   2502959.031  416397.198
550  HIVw+F+R10    204945.555   1024 411939.109   2511139.109  416397.984
559  FLU+R8        200582.056   1001 403166.112   2409170.112  407524.836
560  FLU+R9        200563.618   1003 403133.235   2417157.235  407500.668
561  FLU+R10       200558.394   1005 403126.789   2425186.789  407502.931
570  FLU+F+R8      199008.285   1020 400056.570   2482896.570  404498.027
571  FLU+F+R9      198994.223   1022 400032.445   2491044.445  404482.611
572  FLU+F+R10     198990.836   1024 400029.672   2499229.672  404488.547
581  rtREV+R8      198734.452   1001 399470.904   2405474.904  403829.628
582  rtREV+R9      198720.690   1003 399447.380   2413471.380  403814.813
583  rtREV+R10     198718.347   1005 399446.693   2421506.693  403822.835
592  rtREV+F+R8    196515.045   1020 395070.090   2477910.090  399511.547
593  rtREV+F+R9    196508.638   1022 395061.277   2486073.277  399511.443
594  rtREV+F+R10   196506.672   1024 395061.344   2494261.344  399520.219
603  cpREV+R8      196528.431   1001 395058.861   2401062.861  399417.586
604  cpREV+R9      196515.402   1003 395036.804   2409060.804  399404.237
605  cpREV+R10     196510.888   1005 395031.776   2417091.776  399407.918
614  cpREV+F+R8    195115.409   1020 392270.817   2475110.817  396712.275
615  cpREV+F+R9    195110.263   1022 392264.525   2483276.525  396714.691
Akaike Information Criterion:           LG+F+R9
Corrected Akaike Information Criterion: LG+G4
Bayesian Information Criterion:         LG+F+R8
Best-fit model: LG+F+R8 chosen according to BIC

All model information printed to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz
CPU time for ModelFinder: 742.123 seconds (0h:12m:22s)
Wall-clock time for ModelFinder: 287.992 seconds (0h:4m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 77

Creating bootstrap alignment (seed: 579378)...

CHECKPOINT: Initial tree restored

NOTE: 237 MB RAM (0 GB) is required!
CHECKPOINT: Model parameters restored, LogL: -196615.933
Wrote distance file to... 
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
CHECKPOINT: Candidate tree set restored, best LogL: -193440.833
Finish initializing candidate tree set (20)
Current best tree score: -193440.833 / CPU time: 0.000
Number of iterations: 117
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Optimizing NNI: done in 11.6345 secs using 298.2% CPU
Iteration 120 / LogL: -195383.622 / Time: 0h:0m:34s (0h:0m:28s left)
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Iteration 130 / LogL: -195413.635 / Time: 0h:1m:54s (0h:1m:17s left)
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Iteration 140 / LogL: -195562.596 / Time: 0h:3m:11s (0h:1m:46s left)
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Iteration 150 / LogL: -195367.182 / Time: 0h:4m:29s (0h:2m:1s left)
Optimizing NNI: done in 7.44712 secs using 299% CPU
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Iteration 160 / LogL: -195419.766 / Time: 0h:5m:45s (0h:2m:4s left)
Optimizing NNI: done in 7.78256 secs using 299.2% CPU
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Iteration 170 / LogL: -195383.002 / Time: 0h:7m:5s (0h:1m:58s left)
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Iteration 180 / LogL: -195467.332 / Time: 0h:8m:28s (0h:1m:45s left)
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Iteration 190 / LogL: -195542.309 / Time: 0h:9m:45s (0h:1m:23s left)
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Iteration 200 / LogL: -195389.411 / Time: 0h:11m:1s (0h:0m:56s left)
Optimizing NNI: done in 7.58923 secs using 299.3% CPU
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Iteration 210 / LogL: -195445.251 / Time: 0h:12m:19s (0h:0m:24s left)
Optimizing NNI: done in 7.50908 secs using 299.1% CPU
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Optimizing NNI: done in 7.33222 secs using 299.2% CPU
Optimizing NNI: done in 6.96669 secs using 299% CPU
TREE SEARCH COMPLETED AFTER 218 ITERATIONS / Time: 0h:13m:19s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -196615.933
2. Current log-likelihood: -195823.138
3. Current log-likelihood: -195820.697
4. Current log-likelihood: -195820.574
5. Current log-likelihood: -195820.537
Optimal log-likelihood: -195820.529
Site proportion and rates:  (0.026,0.115) (0.096,0.292) (0.197,0.469) (0.186,0.685) (0.211,0.957) (0.141,1.441) (0.111,2.208) (0.032,3.123)
Parameters optimization took 5 rounds (15.359 sec)
BEST SCORE FOUND : -195820.529
Total tree length: 159.367

Total number of iterations: 218
CPU time used for tree search: 2391.102 sec (0h:39m:51s)
Wall-clock time used for tree search: 799.662 sec (0h:13m:19s)
Total CPU time used: 2437.439 sec (0h:40m:37s)
Total wall-clock time used: 815.218 sec (0h:13m:35s)

===> START BOOTSTRAP REPLICATE NUMBER 78

Creating bootstrap alignment (seed: 579379)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.288 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -203752.842
2. Current log-likelihood: -201130.558
3. Current log-likelihood: -201096.094
4. Current log-likelihood: -201094.579
5. Current log-likelihood: -201093.220
6. Current log-likelihood: -201091.691
7. Current log-likelihood: -201090.399
8. Current log-likelihood: -201089.567
9. Current log-likelihood: -201089.051
10. Current log-likelihood: -201088.754
11. Current log-likelihood: -201088.586
Optimal log-likelihood: -201088.493
Site proportion and rates:  (0.008,0.098) (0.059,0.221) (0.129,0.374) (0.198,0.548) (0.163,0.738) (0.211,1.006) (0.135,1.719) (0.097,2.727)
Parameters optimization took 11 rounds (43.890 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 18.7223 secs using 299.9% CPU
Computing ML distances took 18.723119 sec (of wall-clock time) 56.152257 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00258589 secs using 221.4% CPU
Constructing RapidNJ tree: done in 0.015974 secs using 333.4% CPU
Computing RapidNJ tree took 0.018639 sec (of wall-clock time) 0.060394 sec (of CPU time)
Log-likelihood of RapidNJ tree: -204691.963
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... 30.323 second
Computing log-likelihood of 98 initial trees ... 25.946 seconds
Current best score: -201088.493

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.3514 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -200183.532
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -200160.364
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Iteration 10 / LogL: -200171.463 / Time: 0h:3m:19s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 12: -200129.267
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Iteration 20 / LogL: -200268.995 / Time: 0h:4m:47s
Finish initializing candidate tree set (20)
Current best tree score: -200129.267 / CPU time: 219.163
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -200127.975
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -200116.422
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Iteration 30 / LogL: -200149.932 / Time: 0h:6m:18s (0h:21m:5s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -200110.661
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 35: -200108.731
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -200107.099
Iteration 40 / LogL: -200107.099 / Time: 0h:7m:50s (0h:20m:5s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 46: -200096.349
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 50: -200083.106
Iteration 50 / LogL: -200083.106 / Time: 0h:9m:14s (0h:18m:50s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 53: -200080.551
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 59: -200067.872
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Iteration 60 / LogL: -200092.274 / Time: 0h:10m:40s (0h:17m:54s left)
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Iteration 70 / LogL: -200117.617 / Time: 0h:11m:59s (0h:15m:27s left)
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Iteration 80 / LogL: -200135.845 / Time: 0h:13m:13s (0h:13m:12s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 83: -200064.702
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Iteration 90 / LogL: -200121.961 / Time: 0h:14m:37s (0h:15m:16s left)
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Iteration 100 / LogL: -200090.466 / Time: 0h:15m:51s (0h:13m:17s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 101: -200062.156
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 109: -200050.887
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Iteration 110 / LogL: -200066.400 / Time: 0h:17m:17s (0h:15m:42s left)
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Iteration 120 / LogL: -200143.666 / Time: 0h:18m:32s (0h:13m:52s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 122: -200046.154
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Iteration 130 / LogL: -200213.048 / Time: 0h:19m:53s (0h:14m:10s left)
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Iteration 140 / LogL: -200133.512 / Time: 0h:21m:6s (0h:12m:26s left)
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Iteration 150 / LogL: -200092.268 / Time: 0h:22m:21s (0h:10m:48s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 156: -200042.494
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Iteration 160 / LogL: -200088.980 / Time: 0h:23m:38s (0h:14m:16s left)
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Iteration 170 / LogL: -200070.346 / Time: 0h:24m:54s (0h:12m:40s left)
Optimizing NNI: done in 7.36493 secs using 299% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 171: -200034.671
Optimizing NNI: done in 6.91645 secs using 299.2% CPU
Optimizing NNI: done in 7.46052 secs using 298.9% CPU
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Iteration 180 / LogL: -200054.493 / Time: 0h:26m:11s (0h:13m:18s left)
Optimizing NNI: done in 7.0039 secs using 298.9% CPU
Optimizing NNI: done in 8.04152 secs using 299.2% CPU
Optimizing NNI: done in 6.93043 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 183: -200031.934
Optimizing NNI: done in 7.24383 secs using 299.1% CPU
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Iteration 190 / LogL: -200136.574 / Time: 0h:27m:29s (0h:13m:31s left)
Optimizing NNI: done in 7.50652 secs using 299% CPU
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Iteration 200 / LogL: -200127.277 / Time: 0h:28m:47s (0h:12m:0s left)
Optimizing NNI: done in 7.3632 secs using 299% CPU
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Iteration 210 / LogL: -200147.699 / Time: 0h:30m:2s (0h:10m:29s left)
Optimizing NNI: done in 7.70472 secs using 299.2% CPU
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Optimizing NNI: done in 7.91154 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 218: -200029.262
Optimizing NNI: done in 7.42144 secs using 298.8% CPU
Optimizing NNI: done in 7.00464 secs using 299.1% CPU
Iteration 220 / LogL: -200056.308 / Time: 0h:31m:20s (0h:14m:1s left)
Optimizing NNI: done in 7.09417 secs using 299.1% CPU
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Iteration 230 / LogL: -200048.904 / Time: 0h:32m:34s (0h:12m:31s left)
Optimizing NNI: done in 7.39493 secs using 299% CPU
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Iteration 240 / LogL: -200076.265 / Time: 0h:33m:50s (0h:11m:2s left)
Optimizing NNI: done in 7.69179 secs using 299.2% CPU
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Iteration 250 / LogL: -200071.168 / Time: 0h:35m:5s (0h:9m:34s left)
Optimizing NNI: done in 7.38928 secs using 299.1% CPU
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Optimizing NNI: done in 9.26817 secs using 299.2% CPU
Iteration 260 / LogL: -200058.553 / Time: 0h:36m:20s (0h:8m:8s left)
Optimizing NNI: done in 7.58245 secs using 299.2% CPU
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Iteration 270 / LogL: -200130.807 / Time: 0h:37m:38s (0h:6m:43s left)
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Iteration 280 / LogL: -200070.819 / Time: 0h:38m:50s (0h:5m:17s left)
Optimizing NNI: done in 7.37906 secs using 299.1% CPU
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Optimizing NNI: done in 7.17279 secs using 299% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 289: -200028.482
Optimizing NNI: done in 8.7277 secs using 299% CPU
Iteration 290 / LogL: -200062.604 / Time: 0h:40m:10s (0h:13m:45s left)
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Iteration 300 / LogL: -200030.981 / Time: 0h:41m:23s (0h:12m:19s left)
Optimizing NNI: done in 6.80189 secs using 299.1% CPU
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Iteration 310 / LogL: -200049.748 / Time: 0h:42m:37s (0h:10m:53s left)
Optimizing NNI: done in 7.45203 secs using 299.3% CPU
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Iteration 320 / LogL: -200069.786 / Time: 0h:43m:49s (0h:9m:28s left)
Optimizing NNI: done in 6.65713 secs using 299.2% CPU
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Iteration 330 / LogL: -200074.790 / Time: 0h:45m:7s (0h:8m:5s left)
Optimizing NNI: done in 7.20922 secs using 299% CPU
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Iteration 340 / LogL: -200140.431 / Time: 0h:46m:22s (0h:6m:42s left)
Optimizing NNI: done in 7.20233 secs using 299.3% CPU
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Iteration 350 / LogL: -200036.120 / Time: 0h:47m:40s (0h:5m:19s left)
Optimizing NNI: done in 7.72053 secs using 299.1% CPU
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Optimizing NNI: done in 8.14043 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 360: -200026.807
Iteration 360 / LogL: -200026.807 / Time: 0h:48m:59s (0h:13m:38s left)
Optimizing NNI: done in 7.77962 secs using 299.1% CPU
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Iteration 370 / LogL: -200080.383 / Time: 0h:50m:13s (0h:12m:14s left)
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Iteration 380 / LogL: -200054.334 / Time: 0h:51m:27s (0h:10m:51s left)
Optimizing NNI: done in 7.0228 secs using 299.4% CPU
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Iteration 390 / LogL: -200074.116 / Time: 0h:52m:44s (0h:9m:29s left)
Optimizing NNI: done in 7.72355 secs using 299.1% CPU
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Iteration 400 / LogL: -200130.606 / Time: 0h:54m:0s (0h:8m:7s left)
Optimizing NNI: done in 7.55324 secs using 299% CPU
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Iteration 410 / LogL: -200046.937 / Time: 0h:55m:16s (0h:6m:45s left)
Optimizing NNI: done in 7.72452 secs using 299.3% CPU
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Optimizing NNI: done in 7.07897 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 414: -200021.389
Optimizing NNI: done in 7.67904 secs using 299.1% CPU
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Iteration 420 / LogL: -200109.656 / Time: 0h:56m:35s (0h:12m:41s left)
Optimizing NNI: done in 7.10872 secs using 299.2% CPU
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Iteration 430 / LogL: -200047.852 / Time: 0h:57m:50s (0h:11m:19s left)
Optimizing NNI: done in 7.93174 secs using 299% CPU
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Iteration 440 / LogL: -200027.381 / Time: 0h:59m:9s (0h:9m:58s left)
Optimizing NNI: done in 6.34305 secs using 299.2% CPU
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Iteration 450 / LogL: -200111.445 / Time: 1h:0m:22s (0h:8m:36s left)
Optimizing NNI: done in 7.23806 secs using 299.3% CPU
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Iteration 460 / LogL: -200066.495 / Time: 1h:1m:40s (0h:7m:15s left)
Optimizing NNI: done in 7.61516 secs using 299.1% CPU
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Optimizing NNI: done in 7.41725 secs using 299% CPU
Optimizing NNI: done in 7.22657 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 464: -200018.486
Optimizing NNI: done in 6.84774 secs using 299.1% CPU
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Iteration 470 / LogL: -200020.044 / Time: 1h:2m:57s (0h:12m:37s left)
Optimizing NNI: done in 8.04925 secs using 299.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 475: -200016.583
Optimizing NNI: done in 7.15632 secs using 299.1% CPU
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Iteration 480 / LogL: -200025.525 / Time: 1h:4m:17s (0h:12m:45s left)
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Iteration 490 / LogL: -200194.150 / Time: 1h:5m:32s (0h:11m:23s left)
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Iteration 500 / LogL: -200028.865 / Time: 1h:6m:51s (0h:10m:2s left)
Optimizing NNI: done in 7.54207 secs using 299.1% CPU
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Optimizing NNI: done in 7.77799 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 506: -200015.438
Optimizing NNI: done in 7.2813 secs using 299.1% CPU
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Iteration 510 / LogL: -200036.575 / Time: 1h:8m:9s (0h:12m:51s left)
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Iteration 520 / LogL: -200142.948 / Time: 1h:9m:44s (0h:11m:33s left)
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Iteration 530 / LogL: -200018.453 / Time: 1h:10m:57s (0h:10m:11s left)
Optimizing NNI: done in 7.08443 secs using 299% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 533: -200011.489
Optimizing NNI: done in 7.83465 secs using 299.1% CPU
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Iteration 540 / LogL: -200020.728 / Time: 1h:12m:18s (0h:12m:28s left)
Optimizing NNI: done in 6.90696 secs using 299% CPU
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Iteration 550 / LogL: -200026.752 / Time: 1h:13m:35s (0h:11m:7s left)
Optimizing NNI: done in 7.3458 secs using 299.1% CPU
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Iteration 560 / LogL: -200067.290 / Time: 1h:14m:49s (0h:9m:46s left)
Optimizing NNI: done in 7.43799 secs using 298.9% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 566: -200010.730
Optimizing NNI: done in 7.25624 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 567: -200009.194
Optimizing NNI: done in 7.74974 secs using 299.3% CPU
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Iteration 570 / LogL: -200102.991 / Time: 1h:16m:16s (0h:13m:0s left)
Optimizing NNI: done in 7.58908 secs using 299.2% CPU
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Iteration 580 / LogL: -200080.344 / Time: 1h:17m:31s (0h:11m:38s left)
Optimizing NNI: done in 6.26356 secs using 299.3% CPU
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Iteration 590 / LogL: -200052.884 / Time: 1h:18m:45s (0h:10m:17s left)
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Iteration 600 / LogL: -200033.927 / Time: 1h:20m:2s (0h:8m:57s left)
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Iteration 610 / LogL: -200013.211 / Time: 1h:21m:18s (0h:7m:36s left)
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Iteration 620 / LogL: -200040.312 / Time: 1h:22m:33s (0h:6m:16s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 624: -200007.053
Optimizing NNI: done in 7.28609 secs using 299.3% CPU
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Iteration 630 / LogL: -200065.252 / Time: 1h:24m:0s (0h:12m:33s left)
Optimizing NNI: done in 8.47734 secs using 299% CPU
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Iteration 640 / LogL: -200086.999 / Time: 1h:25m:15s (0h:11m:12s left)
Optimizing NNI: done in 7.62019 secs using 298.8% CPU
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Iteration 650 / LogL: -200026.568 / Time: 1h:26m:34s (0h:9m:52s left)
Optimizing NNI: done in 7.22686 secs using 299.2% CPU
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Iteration 660 / LogL: -200083.027 / Time: 1h:27m:48s (0h:8m:31s left)
Optimizing NNI: done in 6.90569 secs using 299% CPU
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Iteration 670 / LogL: -200039.159 / Time: 1h:29m:4s (0h:7m:11s left)
Optimizing NNI: done in 6.80367 secs using 299.1% CPU
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Iteration 680 / LogL: -200083.296 / Time: 1h:30m:18s (0h:5m:51s left)
Optimizing NNI: done in 7.53188 secs using 299.3% CPU
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Iteration 690 / LogL: -200014.051 / Time: 1h:31m:34s (0h:4m:31s left)
Optimizing NNI: done in 7.48864 secs using 299.3% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 696: -200006.509
Optimizing NNI: done in 7.56949 secs using 299.3% CPU
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Iteration 700 / LogL: -200035.425 / Time: 1h:32m:52s (0h:12m:45s left)
Optimizing NNI: done in 6.82101 secs using 299% CPU
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Iteration 710 / LogL: -200067.133 / Time: 1h:34m:4s (0h:11m:24s left)
Optimizing NNI: done in 7.63209 secs using 299.2% CPU
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Iteration 720 / LogL: -200016.961 / Time: 1h:35m:17s (0h:10m:4s left)
Optimizing NNI: done in 7.19979 secs using 299.3% CPU
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Iteration 730 / LogL: -200038.810 / Time: 1h:36m:30s (0h:8m:44s left)
Optimizing NNI: done in 7.3605 secs using 299.2% CPU
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Iteration 740 / LogL: -200058.400 / Time: 1h:37m:46s (0h:7m:24s left)
Optimizing NNI: done in 7.94949 secs using 299.1% CPU
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Optimizing NNI: done in 7.41891 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 744: -200003.116
Optimizing NNI: done in 7.53352 secs using 299.1% CPU
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Iteration 750 / LogL: -200070.780 / Time: 1h:39m:5s (0h:12m:26s left)
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Iteration 760 / LogL: -200103.484 / Time: 1h:40m:22s (0h:11m:6s left)
Optimizing NNI: done in 7.38583 secs using 299% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 763: -199999.380
Optimizing NNI: done in 6.81773 secs using 299.3% CPU
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Iteration 770 / LogL: -200067.557 / Time: 1h:41m:41s (0h:12m:17s left)
Optimizing NNI: done in 6.83675 secs using 299.3% CPU
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Iteration 780 / LogL: -200009.584 / Time: 1h:42m:58s (0h:10m:58s left)
Optimizing NNI: done in 6.77917 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 781: -199996.045
Optimizing NNI: done in 7.91124 secs using 299.2% CPU
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BETTER TREE FOUND at iteration 783: -199994.567
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 869: -199991.998
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Iteration 970 / LogL: -200128.609 / Time: 2h:6m:56s (0h:0m:-8s left)
TREE SEARCH COMPLETED AFTER 970 ITERATIONS / Time: 2h:6m:56s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -199991.998
Optimal log-likelihood: -199991.997
Site proportion and rates:  (0.018,0.136) (0.056,0.244) (0.114,0.369) (0.210,0.540) (0.176,0.753) (0.196,1.021) (0.136,1.720) (0.095,2.761)
Parameters optimization took 1 rounds (1.168 sec)
BEST SCORE FOUND : -199991.997
Total tree length: 154.493

Total number of iterations: 970
CPU time used for tree search: 22515.607 sec (6h:15m:15s)
Wall-clock time used for tree search: 7548.131 sec (2h:5m:48s)
Total CPU time used: 22724.774 sec (6h:18m:44s)
Total wall-clock time used: 7618.109 sec (2h:6m:58s)

===> START BOOTSTRAP REPLICATE NUMBER 79

Creating bootstrap alignment (seed: 579380)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.280 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -197412.185
2. Current log-likelihood: -194877.846
3. Current log-likelihood: -194848.640
4. Current log-likelihood: -194842.582
5. Current log-likelihood: -194836.184
6. Current log-likelihood: -194833.161
7. Current log-likelihood: -194832.584
8. Current log-likelihood: -194832.437
Optimal log-likelihood: -194832.356
Site proportion and rates:  (0.016,0.088) (0.032,0.255) (0.101,0.355) (0.255,0.543) (0.201,0.778) (0.151,1.053) (0.141,1.628) (0.103,2.634)
Parameters optimization took 8 rounds (30.949 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.71 secs using 299.9% CPU
Computing ML distances took 19.710670 sec (of wall-clock time) 59.114702 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00250101 secs using 298.5% CPU
Constructing RapidNJ tree: done in 0.0169139 secs using 379.8% CPU
Computing RapidNJ tree took 0.019491 sec (of wall-clock time) 0.072946 sec (of CPU time)
Log-likelihood of RapidNJ tree: -199162.554
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.097 second
Computing log-likelihood of 98 initial trees ... 25.843 seconds
Current best score: -194832.356

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.56762 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -194260.418
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -194181.646
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -194163.586
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -194160.223
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BETTER TREE FOUND at iteration 8: -194150.471
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Iteration 10 / LogL: -194236.322 / Time: 0h:3m:42s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 17: -194139.012
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Iteration 20 / LogL: -194189.008 / Time: 0h:4m:58s
Finish initializing candidate tree set (20)
Current best tree score: -194139.012 / CPU time: 245.174
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -194113.564
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -194100.182
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BETTER TREE FOUND at iteration 29: -194098.804
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Iteration 30 / LogL: -194109.295 / Time: 0h:6m:42s (0h:22m:51s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -194096.773
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -194071.366
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Iteration 40 / LogL: -194115.381 / Time: 0h:8m:11s (0h:19m:31s left)
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Iteration 50 / LogL: -194105.302 / Time: 0h:9m:26s (0h:15m:59s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 57: -194043.077
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Iteration 60 / LogL: -194152.506 / Time: 0h:10m:48s (0h:17m:46s left)
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Iteration 70 / LogL: -194098.669 / Time: 0h:12m:4s (0h:15m:13s left)
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Iteration 80 / LogL: -194084.869 / Time: 0h:13m:22s (0h:13m:2s left)
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Iteration 90 / LogL: -194084.448 / Time: 0h:14m:37s (0h:11m:0s left)
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Iteration 100 / LogL: -194084.537 / Time: 0h:15m:53s (0h:9m:8s left)
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Iteration 110 / LogL: -194047.717 / Time: 0h:17m:6s (0h:7m:22s left)
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Iteration 120 / LogL: -194072.992 / Time: 0h:18m:22s (0h:5m:42s left)
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Iteration 130 / LogL: -194142.809 / Time: 0h:19m:38s (0h:4m:6s left)
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Iteration 140 / LogL: -194058.879 / Time: 0h:20m:55s (0h:2m:33s left)
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Iteration 150 / LogL: -194102.811 / Time: 0h:22m:11s (0h:1m:2s left)
Optimizing NNI: done in 6.65568 secs using 299% CPU
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Optimizing NNI: done in 7.78403 secs using 299% CPU
TREE SEARCH COMPLETED AFTER 158 ITERATIONS / Time: 0h:23m:7s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -194043.077
Optimal log-likelihood: -194043.077
Site proportion and rates:  (0.017,0.089) (0.095,0.307) (0.078,0.431) (0.227,0.560) (0.206,0.801) (0.150,1.096) (0.125,1.682) (0.101,2.656)
Parameters optimization took 1 rounds (1.073 sec)
BEST SCORE FOUND : -194043.077
Total tree length: 152.580

Total number of iterations: 158
CPU time used for tree search: 3930.418 sec (1h:5m:30s)
Wall-clock time used for tree search: 1334.284 sec (0h:22m:14s)
Total CPU time used: 4093.959 sec (1h:8m:13s)
Total wall-clock time used: 1388.972 sec (0h:23m:8s)

===> START BOOTSTRAP REPLICATE NUMBER 80

Creating bootstrap alignment (seed: 579381)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.253 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196002.650
2. Current log-likelihood: -193478.391
3. Current log-likelihood: -193425.157
4. Current log-likelihood: -193414.417
5. Current log-likelihood: -193404.316
6. Current log-likelihood: -193400.502
7. Current log-likelihood: -193399.923
Optimal log-likelihood: -193399.820
Site proportion and rates:  (0.008,0.086) (0.084,0.228) (0.116,0.372) (0.201,0.541) (0.161,0.755) (0.168,1.047) (0.150,1.630) (0.111,2.577)
Parameters optimization took 7 rounds (26.796 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.7462 secs using 299.9% CPU
Computing ML distances took 19.746883 sec (of wall-clock time) 59.224976 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00247693 secs using 212.2% CPU
Constructing RapidNJ tree: done in 0.0161841 secs using 377.9% CPU
Computing RapidNJ tree took 0.018736 sec (of wall-clock time) 0.067256 sec (of CPU time)
Log-likelihood of RapidNJ tree: -197221.761
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.958 second
Computing log-likelihood of 98 initial trees ... 26.181 seconds
Current best score: -193399.820

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.07489 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -192926.271
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -192833.120
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BETTER TREE FOUND at iteration 4: -192828.444
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BETTER TREE FOUND at iteration 5: -192805.229
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 10: -192801.734
Iteration 10 / LogL: -192801.734 / Time: 0h:3m:44s
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Iteration 20 / LogL: -192839.467 / Time: 0h:4m:54s
Finish initializing candidate tree set (20)
Current best tree score: -192801.734 / CPU time: 239.591
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -192795.425
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BETTER TREE FOUND at iteration 24: -192788.697
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Iteration 30 / LogL: -192790.598 / Time: 0h:6m:35s (0h:22m:14s left)
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BETTER TREE FOUND at iteration 35: -192692.324
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BETTER TREE FOUND at iteration 42: -192686.077
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BETTER TREE FOUND at iteration 47: -192685.938
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 57: -192684.459
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BETTER TREE FOUND at iteration 88: -192677.505
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Iteration 90 / LogL: -192711.976 / Time: 0h:14m:11s (0h:15m:37s left)
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Iteration 100 / LogL: -192778.224 / Time: 0h:15m:25s (0h:13m:42s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 105: -192674.892
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 144: -192672.821
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 153: -192669.621
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 168: -192662.768
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Iteration 190 / LogL: -192751.539 / Time: 0h:26m:27s (0h:10m:55s left)
Optimizing NNI: done in 7.77031 secs using 299% CPU
Optimizing NNI: done in 6.48239 secs using 299.3% CPU
Optimizing NNI: done in 7.32889 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 193: -192656.933
Optimizing NNI: done in 7.28404 secs using 299.1% CPU
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Iteration 200 / LogL: -192716.753 / Time: 0h:27m:44s (0h:12m:57s left)
Optimizing NNI: done in 6.59973 secs using 299% CPU
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Iteration 210 / LogL: -192689.216 / Time: 0h:28m:52s (0h:11m:28s left)
Optimizing NNI: done in 6.82513 secs using 299% CPU
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Iteration 220 / LogL: -192684.187 / Time: 0h:30m:3s (0h:10m:1s left)
Optimizing NNI: done in 7.7261 secs using 299.2% CPU
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Optimizing NNI: done in 7.82289 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 224: -192652.836
Optimizing NNI: done in 7.33248 secs using 299.2% CPU
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Iteration 230 / LogL: -192703.536 / Time: 0h:31m:26s (0h:12m:54s left)
Optimizing NNI: done in 7.27642 secs using 299.2% CPU
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Iteration 240 / LogL: -192710.865 / Time: 0h:32m:34s (0h:11m:26s left)
Optimizing NNI: done in 6.65246 secs using 299.2% CPU
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Optimizing NNI: done in 7.27549 secs using 298.9% CPU
Optimizing NNI: done in 6.98786 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 245: -192648.610
Optimizing NNI: done in 7.11405 secs using 299.2% CPU
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Iteration 250 / LogL: -192663.703 / Time: 0h:33m:48s (0h:12m:53s left)
Optimizing NNI: done in 7.10345 secs using 298.9% CPU
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Iteration 260 / LogL: -192662.968 / Time: 0h:35m:1s (0h:11m:29s left)
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Iteration 270 / LogL: -192698.361 / Time: 0h:36m:12s (0h:10m:5s left)
Optimizing NNI: done in 6.6426 secs using 299.1% CPU
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Iteration 280 / LogL: -192769.991 / Time: 0h:37m:26s (0h:8m:43s left)
Optimizing NNI: done in 7.43719 secs using 299.1% CPU
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Iteration 290 / LogL: -192710.839 / Time: 0h:38m:42s (0h:7m:21s left)
Optimizing NNI: done in 6.43541 secs using 299% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 291: -192646.598
Optimizing NNI: done in 6.77581 secs using 299.2% CPU
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Iteration 300 / LogL: -192665.560 / Time: 0h:39m:52s (0h:12m:8s left)
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Iteration 310 / LogL: -192731.422 / Time: 0h:41m:3s (0h:10m:45s left)
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Iteration 320 / LogL: -192682.575 / Time: 0h:42m:15s (0h:9m:24s left)
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Iteration 330 / LogL: -192666.613 / Time: 0h:43m:25s (0h:8m:3s left)
Optimizing NNI: done in 6.68817 secs using 299.2% CPU
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Iteration 340 / LogL: -192724.343 / Time: 0h:44m:36s (0h:6m:42s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 350: -192645.282
Iteration 350 / LogL: -192645.282 / Time: 0h:45m:51s (0h:13m:8s left)
Optimizing NNI: done in 6.55011 secs using 299.1% CPU
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Iteration 360 / LogL: -192660.956 / Time: 0h:47m:6s (0h:11m:48s left)
Optimizing NNI: done in 7.51071 secs using 299% CPU
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Iteration 370 / LogL: -192663.537 / Time: 0h:48m:16s (0h:10m:28s left)
Optimizing NNI: done in 8.04341 secs using 299% CPU
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Iteration 380 / LogL: -192667.137 / Time: 0h:49m:31s (0h:9m:8s left)
Optimizing NNI: done in 7.57751 secs using 299.1% CPU
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Iteration 390 / LogL: -192836.659 / Time: 0h:50m:46s (0h:7m:49s left)
Optimizing NNI: done in 8.11911 secs using 299.3% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 399: -192643.286
Optimizing NNI: done in 6.99793 secs using 299.2% CPU
Iteration 400 / LogL: -192651.390 / Time: 0h:52m:2s (0h:12m:54s left)
Optimizing NNI: done in 6.58635 secs using 299.1% CPU
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Iteration 410 / LogL: -192683.472 / Time: 0h:53m:13s (0h:11m:34s left)
Optimizing NNI: done in 7.42831 secs using 299.1% CPU
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Iteration 420 / LogL: -192759.197 / Time: 0h:54m:25s (0h:10m:15s left)
Optimizing NNI: done in 6.56881 secs using 298.8% CPU
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Iteration 430 / LogL: -192684.784 / Time: 0h:55m:33s (0h:8m:56s left)
Optimizing NNI: done in 6.84323 secs using 299.3% CPU
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Iteration 440 / LogL: -192707.219 / Time: 0h:56m:43s (0h:7m:37s left)
Optimizing NNI: done in 7.63626 secs using 299.1% CPU
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Iteration 450 / LogL: -192699.953 / Time: 0h:57m:55s (0h:6m:19s left)
Optimizing NNI: done in 6.71042 secs using 299.1% CPU
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Iteration 460 / LogL: -192709.915 / Time: 0h:59m:7s (0h:5m:1s left)
Optimizing NNI: done in 7.88262 secs using 299.3% CPU
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Iteration 470 / LogL: -192662.065 / Time: 1h:0m:20s (0h:3m:43s left)
Optimizing NNI: done in 7.10812 secs using 299.3% CPU
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Iteration 480 / LogL: -192675.267 / Time: 1h:1m:30s (0h:2m:26s left)
Optimizing NNI: done in 6.69915 secs using 299.2% CPU
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Iteration 490 / LogL: -192645.027 / Time: 1h:2m:40s (0h:1m:9s left)
Optimizing NNI: done in 6.68153 secs using 299.4% CPU
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Optimizing NNI: done in 7.44399 secs using 299% CPU
Iteration 500 / LogL: -192695.235 / Time: 1h:3m:52s (0h:0m:-8s left)
TREE SEARCH COMPLETED AFTER 500 ITERATIONS / Time: 1h:3m:52s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192643.286
2. Current log-likelihood: -192643.228
3. Current log-likelihood: -192643.182
Optimal log-likelihood: -192643.182
Site proportion and rates:  (0.018,0.117) (0.101,0.259) (0.108,0.397) (0.190,0.554) (0.154,0.765) (0.167,1.049) (0.156,1.643) (0.105,2.604)
Parameters optimization took 3 rounds (3.043 sec)
BEST SCORE FOUND : -192643.182
Total tree length: 155.899

Total number of iterations: 500
CPU time used for tree search: 11239.137 sec (3h:7m:19s)
Wall-clock time used for tree search: 3777.587 sec (1h:2m:57s)
Total CPU time used: 11412.325 sec (3h:10m:12s)
Total wall-clock time used: 3835.471 sec (1h:3m:55s)

===> START BOOTSTRAP REPLICATE NUMBER 81

Creating bootstrap alignment (seed: 579382)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.317 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -202935.561
2. Current log-likelihood: -200270.008
3. Current log-likelihood: -200242.193
4. Current log-likelihood: -200240.951
5. Current log-likelihood: -200240.849
Optimal log-likelihood: -200240.756
Site proportion and rates:  (0.007,0.058) (0.038,0.206) (0.085,0.301) (0.153,0.463) (0.218,0.650) (0.241,0.984) (0.150,1.601) (0.107,2.578)
Parameters optimization took 5 rounds (19.170 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 21.6742 secs using 299.9% CPU
Computing ML distances took 21.674842 sec (of wall-clock time) 65.011496 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00237989 secs using 340.4% CPU
Constructing RapidNJ tree: done in 0.0168231 secs using 361.2% CPU
Computing RapidNJ tree took 0.019275 sec (of wall-clock time) 0.069804 sec (of CPU time)
Log-likelihood of RapidNJ tree: -204502.965
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.526 second
Computing log-likelihood of 98 initial trees ... 25.672 seconds
Current best score: -200240.756

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.04837 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -199808.535
Optimizing NNI: done in 7.45004 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -199759.668
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -199742.314
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 10: -199697.610
Iteration 10 / LogL: -199697.610 / Time: 0h:3m:37s
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Iteration 20 / LogL: -199745.328 / Time: 0h:5m:0s
Finish initializing candidate tree set (20)
Current best tree score: -199697.610 / CPU time: 256.718
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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BETTER TREE FOUND at iteration 28: -199693.305
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Iteration 30 / LogL: -199724.207 / Time: 0h:6m:37s (0h:22m:22s left)
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BETTER TREE FOUND at iteration 32: -199689.231
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BETTER TREE FOUND at iteration 35: -199676.039
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Iteration 40 / LogL: -199784.211 / Time: 0h:8m:14s (0h:20m:4s left)
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BETTER TREE FOUND at iteration 46: -199674.040
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Iteration 50 / LogL: -199596.748 / Time: 0h:10m:51s (0h:21m:43s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 55: -199585.108
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 59: -199582.245
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Iteration 60 / LogL: -199647.474 / Time: 0h:12m:15s (0h:20m:33s left)
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Iteration 70 / LogL: -199642.027 / Time: 0h:13m:27s (0h:17m:20s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 71: -199579.635
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 75: -199576.286
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 79: -199557.918
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Iteration 80 / LogL: -199644.810 / Time: 0h:14m:52s (0h:18m:38s left)
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Iteration 110 / LogL: -199564.983 / Time: 0h:18m:34s (0h:11m:45s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 125: -199551.485
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Iteration 190 / LogL: -199589.070 / Time: 0h:28m:32s (0h:5m:17s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 198: -199540.959
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Iteration 260 / LogL: -199573.400 / Time: 0h:37m:10s (0h:5m:27s left)
Optimizing NNI: done in 6.95152 secs using 299.1% CPU
Optimizing NNI: done in 6.67755 secs using 299.1% CPU
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Optimizing NNI: done in 7.64863 secs using 299% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 267: -199540.481
Optimizing NNI: done in 7.38895 secs using 299% CPU
Optimizing NNI: done in 7.34817 secs using 299% CPU
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Iteration 270 / LogL: -199547.956 / Time: 0h:38m:26s (0h:13m:51s left)
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Iteration 280 / LogL: -199623.544 / Time: 0h:39m:43s (0h:12m:23s left)
Optimizing NNI: done in 6.92251 secs using 299.3% CPU
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Iteration 290 / LogL: -199560.411 / Time: 0h:40m:59s (0h:10m:55s left)
Optimizing NNI: done in 6.57603 secs using 299% CPU
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Iteration 300 / LogL: -199564.242 / Time: 0h:42m:9s (0h:9m:26s left)
Optimizing NNI: done in 7.48852 secs using 298.8% CPU
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Iteration 310 / LogL: -199560.249 / Time: 0h:43m:23s (0h:8m:0s left)
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Iteration 320 / LogL: -199588.593 / Time: 0h:44m:34s (0h:6m:34s left)
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Iteration 330 / LogL: -199562.425 / Time: 0h:45m:46s (0h:5m:8s left)
Optimizing NNI: done in 7.53981 secs using 299.2% CPU
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Iteration 340 / LogL: -199582.610 / Time: 0h:46m:55s (0h:3m:44s left)
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Iteration 350 / LogL: -199544.305 / Time: 0h:48m:2s (0h:2m:20s left)
Optimizing NNI: done in 5.44946 secs using 299.1% CPU
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Iteration 360 / LogL: -199623.925 / Time: 0h:49m:10s (0h:0m:57s left)
Optimizing NNI: done in 7.21091 secs using 299.2% CPU
Optimizing NNI: done in 6.41289 secs using 299.2% CPU
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Optimizing NNI: done in 6.51968 secs using 298.8% CPU
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Optimizing NNI: done in 6.43196 secs using 299.2% CPU
Optimizing NNI: done in 6.20874 secs using 299% CPU
TREE SEARCH COMPLETED AFTER 368 ITERATIONS / Time: 0h:50m:3s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -199540.481
Optimal log-likelihood: -199540.475
Site proportion and rates:  (0.011,0.083) (0.115,0.270) (0.152,0.457) (0.216,0.627) (0.228,0.951) (0.133,1.442) (0.126,2.207) (0.020,3.881)
Parameters optimization took 1 rounds (2.531 sec)
BEST SCORE FOUND : -199540.475
Total tree length: 160.990

Total number of iterations: 368
CPU time used for tree search: 8790.243 sec (2h:26m:30s)
Wall-clock time used for tree search: 2959.508 sec (0h:49m:19s)
Total CPU time used: 8928.191 sec (2h:28m:48s)
Total wall-clock time used: 3005.676 sec (0h:50m:5s)

===> START BOOTSTRAP REPLICATE NUMBER 82

Creating bootstrap alignment (seed: 579383)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.315 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196229.923
2. Current log-likelihood: -193671.760
3. Current log-likelihood: -193644.133
4. Current log-likelihood: -193643.808
Optimal log-likelihood: -193643.796
Site proportion and rates:  (0.008,0.091) (0.005,0.259) (0.067,0.261) (0.144,0.417) (0.243,0.617) (0.266,0.946) (0.175,1.590) (0.091,2.635)
Parameters optimization took 4 rounds (15.792 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 18.2694 secs using 300% CPU
Computing ML distances took 18.270010 sec (of wall-clock time) 54.800540 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00247097 secs using 210.4% CPU
Constructing RapidNJ tree: done in 0.0162768 secs using 364.8% CPU
Computing RapidNJ tree took 0.018861 sec (of wall-clock time) 0.065936 sec (of CPU time)
Log-likelihood of RapidNJ tree: -198038.963
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.474 second
Computing log-likelihood of 98 initial trees ... 26.251 seconds
Current best score: -193643.796

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.45232 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -192963.769
Optimizing NNI: done in 6.45315 secs using 299.1% CPU
Optimizing NNI: done in 6.73973 secs using 299.2% CPU
Optimizing NNI: done in 6.23023 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -192937.212
Optimizing NNI: done in 6.38327 secs using 299.1% CPU
Optimizing NNI: done in 6.45289 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -192884.020
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Iteration 10 / LogL: -192951.390 / Time: 0h:3m:44s
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Iteration 20 / LogL: -192970.600 / Time: 0h:5m:3s
Finish initializing candidate tree set (20)
Current best tree score: -192884.020 / CPU time: 267.456
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 8.78631 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -192879.718
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -192851.243
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -192844.985
Optimizing NNI: done in 8.99266 secs using 299% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -192812.158
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -192810.014
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Iteration 30 / LogL: -192854.321 / Time: 0h:7m:26s (0h:25m:8s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -192807.629
Optimizing NNI: done in 9.01165 secs using 299.2% CPU
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Iteration 40 / LogL: -192827.853 / Time: 0h:8m:52s (0h:22m:18s left)
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Iteration 50 / LogL: -192835.431 / Time: 0h:10m:18s (0h:18m:29s left)
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Iteration 60 / LogL: -192832.868 / Time: 0h:11m:39s (0h:15m:24s left)
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Iteration 70 / LogL: -192851.906 / Time: 0h:13m:2s (0h:12m:51s left)
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Iteration 80 / LogL: -192895.847 / Time: 0h:14m:30s (0h:10m:39s left)
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Iteration 90 / LogL: -192840.890 / Time: 0h:15m:53s (0h:8m:33s left)
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Iteration 100 / LogL: -192892.485 / Time: 0h:17m:13s (0h:6m:36s left)
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Iteration 110 / LogL: -192821.598 / Time: 0h:18m:33s (0h:4m:46s left)
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Iteration 120 / LogL: -192868.189 / Time: 0h:19m:58s (0h:3m:1s left)
Optimizing NNI: done in 7.87479 secs using 299.1% CPU
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Iteration 130 / LogL: -192900.500 / Time: 0h:21m:21s (0h:1m:19s left)
Optimizing NNI: done in 8.72021 secs using 298.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 131: -192801.732
Optimizing NNI: done in 8.49982 secs using 299.1% CPU
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Iteration 140 / LogL: -192832.358 / Time: 0h:22m:59s (0h:15m:2s left)
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Iteration 150 / LogL: -193018.284 / Time: 0h:24m:37s (0h:13m:23s left)
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Iteration 160 / LogL: -192854.789 / Time: 0h:26m:0s (0h:11m:36s left)
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Iteration 170 / LogL: -192912.000 / Time: 0h:27m:23s (0h:9m:53s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 173: -192797.710
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Iteration 180 / LogL: -193057.700 / Time: 0h:28m:52s (0h:14m:59s left)
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Iteration 190 / LogL: -192808.445 / Time: 0h:30m:19s (0h:13m:18s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 245: -192796.200
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Iteration 250 / LogL: -192877.161 / Time: 0h:38m:58s (0h:14m:51s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 280: -192794.029
Iteration 280 / LogL: -192794.029 / Time: 0h:43m:29s (0h:15m:35s left)
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Iteration 360 / LogL: -192897.012 / Time: 0h:55m:16s (0h:3m:4s left)
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Iteration 370 / LogL: -192822.651 / Time: 0h:56m:42s (0h:1m:32s left)
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Iteration 380 / LogL: -192816.290 / Time: 0h:58m:11s (0h:0m:0s left)
Optimizing NNI: done in 9.01809 secs using 299% CPU
TREE SEARCH COMPLETED AFTER 381 ITERATIONS / Time: 0h:58m:20s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192794.029
2. Current log-likelihood: -192794.017
Optimal log-likelihood: -192794.010
Site proportion and rates:  (0.008,0.093) (0.093,0.285) (0.126,0.423) (0.233,0.615) (0.246,0.915) (0.107,1.342) (0.117,1.823) (0.070,2.783)
Parameters optimization took 2 rounds (2.518 sec)
BEST SCORE FOUND : -192794.010
Total tree length: 145.993

Total number of iterations: 381
CPU time used for tree search: 10297.823 sec (2h:51m:37s)
Wall-clock time used for tree search: 3464.386 sec (0h:57m:44s)
Total CPU time used: 10414.440 sec (2h:53m:34s)
Total wall-clock time used: 3503.412 sec (0h:58m:23s)

===> START BOOTSTRAP REPLICATE NUMBER 83

Creating bootstrap alignment (seed: 579384)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.282 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -193640.352
2. Current log-likelihood: -190923.126
3. Current log-likelihood: -190895.453
4. Current log-likelihood: -190894.113
5. Current log-likelihood: -190893.079
6. Current log-likelihood: -190891.533
7. Current log-likelihood: -190889.304
8. Current log-likelihood: -190886.962
9. Current log-likelihood: -190885.752
10. Current log-likelihood: -190885.235
11. Current log-likelihood: -190884.981
12. Current log-likelihood: -190884.875
Optimal log-likelihood: -190884.819
Site proportion and rates:  (0.004,0.124) (0.076,0.275) (0.152,0.400) (0.212,0.570) (0.138,0.795) (0.165,1.061) (0.142,1.579) (0.112,2.585)
Parameters optimization took 12 rounds (45.186 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.2334 secs using 299.9% CPU
Computing ML distances took 19.234086 sec (of wall-clock time) 57.684226 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00247598 secs using 298.8% CPU
Constructing RapidNJ tree: done in 0.0167229 secs using 376.9% CPU
Computing RapidNJ tree took 0.019265 sec (of wall-clock time) 0.072005 sec (of CPU time)
Log-likelihood of RapidNJ tree: -195190.976
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.867 second
Computing log-likelihood of 98 initial trees ... 25.666 seconds
Current best score: -190884.819

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.39368 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -190314.340
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -190266.478
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -190256.651
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -190246.200
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -190234.752
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Iteration 10 / LogL: -190278.977 / Time: 0h:3m:44s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 18: -190188.419
Optimizing NNI: done in 8.80741 secs using 299% CPU
Optimizing NNI: done in 7.87507 secs using 298.6% CPU
Iteration 20 / LogL: -190281.548 / Time: 0h:5m:8s
Finish initializing candidate tree set (20)
Current best tree score: -190188.419 / CPU time: 240.990
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.63654 secs using 299.2% CPU
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Iteration 30 / LogL: -190220.595 / Time: 0h:6m:22s (0h:19m:21s left)
Optimizing NNI: done in 7.56033 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -190185.191
Optimizing NNI: done in 7.31924 secs using 298.9% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -190181.283
Optimizing NNI: done in 7.14705 secs using 299.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -190176.548
Iteration 40 / LogL: -190176.548 / Time: 0h:7m:52s (0h:20m:11s left)
Optimizing NNI: done in 6.2696 secs using 298.8% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 45: -190169.898
Optimizing NNI: done in 8.42767 secs using 299.2% CPU
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Iteration 50 / LogL: -190249.990 / Time: 0h:9m:11s (0h:17m:49s left)
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BETTER TREE FOUND at iteration 53: -190163.439
Optimizing NNI: done in 7.61437 secs using 299.1% CPU
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BETTER TREE FOUND at iteration 55: -190159.067
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BETTER TREE FOUND at iteration 56: -190157.369
Optimizing NNI: done in 6.56137 secs using 299.1% CPU
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Iteration 60 / LogL: -190216.535 / Time: 0h:10m:47s (0h:17m:32s left)
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BETTER TREE FOUND at iteration 66: -190147.552
Optimizing NNI: done in 7.22212 secs using 299.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 69: -190136.343
Optimizing NNI: done in 6.60944 secs using 299.1% CPU
Iteration 70 / LogL: -190150.436 / Time: 0h:12m:14s (0h:17m:32s left)
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Iteration 80 / LogL: -190163.107 / Time: 0h:13m:28s (0h:15m:10s left)
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Iteration 90 / LogL: -190172.306 / Time: 0h:14m:43s (0h:13m:3s left)
Optimizing NNI: done in 6.95372 secs using 299.4% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 92: -190132.583
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BETTER TREE FOUND at iteration 100: -190132.476
Iteration 100 / LogL: -190132.476 / Time: 0h:16m:1s (0h:16m:11s left)
Optimizing NNI: done in 8.38765 secs using 299% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 106: -190127.385
Optimizing NNI: done in 7.6058 secs using 299.4% CPU
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Iteration 110 / LogL: -190148.557 / Time: 0h:17m:21s (0h:15m:16s left)
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Iteration 120 / LogL: -190154.171 / Time: 0h:18m:35s (0h:13m:26s left)
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Iteration 130 / LogL: -190137.468 / Time: 0h:19m:47s (0h:11m:39s left)
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Iteration 140 / LogL: -190147.193 / Time: 0h:21m:0s (0h:9m:58s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 149: -190126.911
Optimizing NNI: done in 7.60626 secs using 299.2% CPU
Iteration 150 / LogL: -190143.540 / Time: 0h:22m:16s (0h:14m:47s left)
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Iteration 160 / LogL: -190152.644 / Time: 0h:23m:29s (0h:13m:8s left)
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Iteration 170 / LogL: -190137.364 / Time: 0h:24m:41s (0h:11m:32s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 179: -190126.331
Optimizing NNI: done in 6.81758 secs using 299% CPU
Iteration 180 / LogL: -190146.057 / Time: 0h:25m:54s (0h:14m:19s left)
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Iteration 190 / LogL: -190176.827 / Time: 0h:27m:6s (0h:12m:45s left)
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Iteration 200 / LogL: -190233.571 / Time: 0h:28m:17s (0h:11m:13s left)
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Iteration 210 / LogL: -190158.419 / Time: 0h:29m:28s (0h:9m:43s left)
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Iteration 220 / LogL: -190243.933 / Time: 0h:30m:40s (0h:8m:15s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 230: -190125.005
Iteration 230 / LogL: -190125.005 / Time: 0h:31m:55s (0h:13m:56s left)
Optimizing NNI: done in 7.30867 secs using 299% CPU
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Iteration 240 / LogL: -190281.769 / Time: 0h:33m:4s (0h:12m:27s left)
Optimizing NNI: done in 6.54912 secs using 299% CPU
Optimizing NNI: done in 6.88957 secs using 299% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 242: -190117.542
Optimizing NNI: done in 7.61339 secs using 299.2% CPU
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Iteration 250 / LogL: -190174.356 / Time: 0h:34m:20s (0h:12m:41s left)
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Iteration 260 / LogL: -190150.974 / Time: 0h:35m:32s (0h:11m:14s left)
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Iteration 270 / LogL: -190156.703 / Time: 0h:36m:45s (0h:9m:50s left)
Optimizing NNI: done in 7.04147 secs using 299% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 279: -190104.275
Optimizing NNI: done in 7.15401 secs using 299.2% CPU
Iteration 280 / LogL: -190188.889 / Time: 0h:38m:1s (0h:13m:29s left)
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Iteration 290 / LogL: -190225.875 / Time: 0h:39m:12s (0h:12m:4s left)
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Iteration 300 / LogL: -190132.537 / Time: 0h:40m:23s (0h:10m:40s left)
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Iteration 310 / LogL: -190122.275 / Time: 0h:41m:36s (0h:9m:17s left)
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Iteration 320 / LogL: -190107.990 / Time: 0h:42m:47s (0h:7m:54s left)
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Iteration 330 / LogL: -190106.998 / Time: 0h:43m:59s (0h:6m:33s left)
Optimizing NNI: done in 7.32113 secs using 299.3% CPU
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Iteration 340 / LogL: -190122.660 / Time: 0h:45m:12s (0h:5m:11s left)
Optimizing NNI: done in 6.81643 secs using 299.4% CPU
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Optimizing NNI: done in 6.49307 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 350: -190103.578
Iteration 350 / LogL: -190103.578 / Time: 0h:46m:25s (0h:13m:18s left)
Optimizing NNI: done in 7.34593 secs using 299.2% CPU
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Iteration 360 / LogL: -190130.213 / Time: 0h:47m:37s (0h:11m:56s left)
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Iteration 370 / LogL: -190133.711 / Time: 0h:48m:49s (0h:10m:35s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 378: -190102.583
Optimizing NNI: done in 7.03408 secs using 299% CPU
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Iteration 380 / LogL: -190139.379 / Time: 0h:50m:4s (0h:12m:56s left)
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Iteration 390 / LogL: -190162.884 / Time: 0h:51m:15s (0h:11m:35s left)
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Iteration 420 / LogL: -190116.332 / Time: 0h:54m:47s (0h:7m:35s left)
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Iteration 430 / LogL: -190127.029 / Time: 0h:55m:59s (0h:6m:15s left)
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Iteration 440 / LogL: -190119.833 / Time: 0h:57m:7s (0h:4m:56s left)
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Iteration 450 / LogL: -190163.565 / Time: 0h:58m:17s (0h:3m:38s left)
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Iteration 460 / LogL: -190118.830 / Time: 0h:59m:26s (0h:2m:19s left)
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Iteration 470 / LogL: -190144.866 / Time: 1h:0m:38s (0h:1m:2s left)
Optimizing NNI: done in 7.3536 secs using 298.9% CPU
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TREE SEARCH COMPLETED AFTER 479 ITERATIONS / Time: 1h:1m:40s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -190102.583
2. Current log-likelihood: -190102.571
3. Current log-likelihood: -190102.558
Optimal log-likelihood: -190102.549
Site proportion and rates:  (0.006,0.143) (0.057,0.274) (0.166,0.385) (0.217,0.568) (0.122,0.784) (0.185,1.056) (0.145,1.622) (0.102,2.644)
Parameters optimization took 3 rounds (5.310 sec)
BEST SCORE FOUND : -190102.549
Total tree length: 148.579

Total number of iterations: 479
CPU time used for tree search: 10807.665 sec (3h:0m:7s)
Wall-clock time used for tree search: 3633.264 sec (1h:0m:33s)
Total CPU time used: 11025.623 sec (3h:3m:45s)
Total wall-clock time used: 3706.154 sec (1h:1m:46s)

===> START BOOTSTRAP REPLICATE NUMBER 84

Creating bootstrap alignment (seed: 579385)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.286 seconds

NOTE: 227 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194010.505
2. Current log-likelihood: -191196.011
3. Current log-likelihood: -191155.053
4. Current log-likelihood: -191154.327
Optimal log-likelihood: -191154.299
Site proportion and rates:  (0.011,0.102) (0.034,0.200) (0.132,0.332) (0.168,0.505) (0.206,0.698) (0.199,1.029) (0.137,1.542) (0.113,2.694)
Parameters optimization took 4 rounds (13.263 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.0548 secs using 299.9% CPU
Computing ML distances took 19.055439 sec (of wall-clock time) 57.156253 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00231719 secs using 299.3% CPU
Constructing RapidNJ tree: done in 0.016211 secs using 372.3% CPU
Computing RapidNJ tree took 0.018605 sec (of wall-clock time) 0.068697 sec (of CPU time)
Log-likelihood of RapidNJ tree: -196268.798
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.183 second
Computing log-likelihood of 98 initial trees ... 25.309 seconds
Current best score: -191154.299

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.84021 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -190657.016
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -190654.053
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -190622.066
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Iteration 10 / LogL: -190696.002 / Time: 0h:2m:54s
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Iteration 20 / LogL: -190716.860 / Time: 0h:4m:0s
Finish initializing candidate tree set (20)
Current best tree score: -190622.066 / CPU time: 203.472
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.36027 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -190579.489
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -190564.575
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Iteration 30 / LogL: -190595.757 / Time: 0h:5m:42s (0h:19m:16s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 34: -190555.115
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -190536.603
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Iteration 60 / LogL: -190592.963 / Time: 0h:9m:39s (0h:13m:45s left)
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Iteration 70 / LogL: -190552.335 / Time: 0h:10m:52s (0h:11m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 72: -190532.205
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 74: -190529.406
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 82: -190526.145
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Iteration 100 / LogL: -190582.419 / Time: 0h:14m:46s (0h:12m:13s left)
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Iteration 110 / LogL: -190727.665 / Time: 0h:15m:59s (0h:10m:33s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 113: -190525.650
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Iteration 120 / LogL: -190746.708 / Time: 0h:17m:19s (0h:13m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 124: -190520.384
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Iteration 130 / LogL: -190570.485 / Time: 0h:18m:34s (0h:13m:32s left)
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Iteration 140 / LogL: -190542.593 / Time: 0h:19m:44s (0h:11m:55s left)
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Iteration 190 / LogL: -190543.934 / Time: 0h:25m:40s (0h:4m:37s left)
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BETTER TREE FOUND at iteration 208: -190514.497
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 234: -190507.283
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BETTER TREE FOUND at iteration 285: -190498.397
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 335: -190490.448
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Iteration 390 / LogL: -190500.562 / Time: 0h:49m:41s (0h:5m:44s left)
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Iteration 420 / LogL: -190496.680 / Time: 0h:53m:9s (0h:1m:54s left)
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Iteration 430 / LogL: -190599.431 / Time: 0h:54m:23s (0h:0m:38s left)
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TREE SEARCH COMPLETED AFTER 436 ITERATIONS / Time: 0h:55m:6s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -190490.448
Optimal log-likelihood: -190490.443
Site proportion and rates:  (0.012,0.107) (0.037,0.209) (0.145,0.339) (0.176,0.528) (0.192,0.722) (0.203,1.050) (0.119,1.577) (0.115,2.696)
Parameters optimization took 1 rounds (0.767 sec)
BEST SCORE FOUND : -190490.443
Total tree length: 156.909

Total number of iterations: 436
CPU time used for tree search: 9717.248 sec (2h:41m:57s)
Wall-clock time used for tree search: 3269.594 sec (0h:54m:29s)
Total CPU time used: 9829.513 sec (2h:43m:49s)
Total wall-clock time used: 3307.138 sec (0h:55m:7s)

===> START BOOTSTRAP REPLICATE NUMBER 85

Creating bootstrap alignment (seed: 579386)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.405 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -193450.449
2. Current log-likelihood: -190839.295
3. Current log-likelihood: -190795.896
4. Current log-likelihood: -190790.499
5. Current log-likelihood: -190788.473
6. Current log-likelihood: -190787.502
7. Current log-likelihood: -190786.990
8. Current log-likelihood: -190786.738
9. Current log-likelihood: -190786.615
Optimal log-likelihood: -190786.558
Site proportion and rates:  (0.009,0.099) (0.050,0.233) (0.139,0.388) (0.184,0.529) (0.209,0.742) (0.183,1.049) (0.096,1.539) (0.128,2.650)
Parameters optimization took 9 rounds (30.970 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 21.4625 secs using 299.9% CPU
Computing ML distances took 21.463105 sec (of wall-clock time) 64.375608 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.0024848 secs using 185.4% CPU
Constructing RapidNJ tree: done in 0.0162201 secs using 366.8% CPU
Computing RapidNJ tree took 0.018780 sec (of wall-clock time) 0.065853 sec (of CPU time)
Log-likelihood of RapidNJ tree: -196753.537
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.775 second
Computing log-likelihood of 98 initial trees ... 25.298 seconds
Current best score: -190786.558

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.8266 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -190251.184
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BETTER TREE FOUND at iteration 2: -190216.929
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BETTER TREE FOUND at iteration 3: -190168.304
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Iteration 10 / LogL: -190212.531 / Time: 0h:3m:13s
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Iteration 20 / LogL: -190315.034 / Time: 0h:4m:15s
Finish initializing candidate tree set (20)
Current best tree score: -190168.304 / CPU time: 196.227
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.52426 secs using 298.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -190163.866
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BETTER TREE FOUND at iteration 43: -190121.588
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 163: -190116.103
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 263: -190108.573
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BETTER TREE FOUND at iteration 286: -190096.872
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BETTER TREE FOUND at iteration 300: -190087.864
Iteration 300 / LogL: -190087.864 / Time: 0h:39m:57s (0h:13m:21s left)
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BETTER TREE FOUND at iteration 339: -190071.299
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Iteration 420 / LogL: -190100.679 / Time: 0h:54m:43s (0h:2m:28s left)
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Iteration 430 / LogL: -190101.829 / Time: 0h:55m:58s (0h:1m:10s left)
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Iteration 440 / LogL: -190182.540 / Time: 0h:57m:10s (0h:0m:-8s left)
TREE SEARCH COMPLETED AFTER 440 ITERATIONS / Time: 0h:57m:10s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -190071.299
Optimal log-likelihood: -190071.299
Site proportion and rates:  (0.009,0.102) (0.052,0.235) (0.137,0.392) (0.180,0.524) (0.231,0.748) (0.168,1.070) (0.099,1.567) (0.123,2.679)
Parameters optimization took 1 rounds (0.803 sec)
BEST SCORE FOUND : -190071.299
Total tree length: 152.224

Total number of iterations: 440
CPU time used for tree search: 10021.387 sec (2h:47m:1s)
Wall-clock time used for tree search: 3371.613 sec (0h:56m:11s)
Total CPU time used: 10200.079 sec (2h:50m:0s)
Total wall-clock time used: 3431.446 sec (0h:57m:11s)

===> START BOOTSTRAP REPLICATE NUMBER 86

Creating bootstrap alignment (seed: 579387)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.254 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199115.896
2. Current log-likelihood: -196344.932
3. Current log-likelihood: -196242.119
4. Current log-likelihood: -196234.973
5. Current log-likelihood: -196234.192
6. Current log-likelihood: -196234.055
Optimal log-likelihood: -196234.035
Site proportion and rates:  (0.006,0.095) (0.036,0.220) (0.122,0.352) (0.198,0.522) (0.180,0.715) (0.206,1.011) (0.180,1.688) (0.072,2.838)
Parameters optimization took 6 rounds (22.516 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.5774 secs using 300% CPU
Computing ML distances took 19.578057 sec (of wall-clock time) 58.725589 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00250411 secs using 298.9% CPU
Constructing RapidNJ tree: done in 0.0169392 secs using 359.1% CPU
Computing RapidNJ tree took 0.019519 sec (of wall-clock time) 0.071632 sec (of CPU time)
Log-likelihood of RapidNJ tree: -200459.927
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.004 second
Computing log-likelihood of 98 initial trees ... 26.075 seconds
Current best score: -196234.035

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.26885 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -195458.821
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -195369.584
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -195333.728
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Iteration 10 / LogL: -195506.332 / Time: 0h:3m:15s
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Iteration 20 / LogL: -195425.835 / Time: 0h:4m:30s
Finish initializing candidate tree set (20)
Current best tree score: -195333.728 / CPU time: 221.132
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -195327.305
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -195323.970
Iteration 30 / LogL: -195323.970 / Time: 0h:6m:3s (0h:20m:52s left)
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BETTER TREE FOUND at iteration 31: -195281.697
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BETTER TREE FOUND at iteration 39: -195261.388
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Iteration 40 / LogL: -195287.307 / Time: 0h:7m:32s (0h:19m:9s left)
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BETTER TREE FOUND at iteration 46: -195259.757
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -195238.951
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BETTER TREE FOUND at iteration 54: -195233.766
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BETTER TREE FOUND at iteration 71: -195231.882
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BETTER TREE FOUND at iteration 76: -195227.450
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 86: -195212.287
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Iteration 90 / LogL: -195375.652 / Time: 0h:14m:54s (0h:16m:4s left)
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Iteration 100 / LogL: -195248.722 / Time: 0h:16m:15s (0h:14m:7s left)
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Iteration 110 / LogL: -195269.367 / Time: 0h:17m:39s (0h:12m:18s left)
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Iteration 120 / LogL: -195299.269 / Time: 0h:19m:7s (0h:10m:36s left)
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Iteration 130 / LogL: -195273.220 / Time: 0h:20m:32s (0h:8m:54s left)
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Iteration 140 / LogL: -195454.984 / Time: 0h:21m:55s (0h:7m:15s left)
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Optimizing NNI: done in 7.49136 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 145: -195206.504
Optimizing NNI: done in 6.99432 secs using 299.3% CPU
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Iteration 150 / LogL: -195360.011 / Time: 0h:23m:13s (0h:14m:48s left)
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Iteration 160 / LogL: -195309.543 / Time: 0h:24m:31s (0h:13m:6s left)
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Iteration 170 / LogL: -195431.329 / Time: 0h:25m:44s (0h:11m:25s left)
Optimizing NNI: done in 10.7478 secs using 298.7% CPU
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Iteration 180 / LogL: -195262.496 / Time: 0h:27m:18s (0h:9m:54s left)
Optimizing NNI: done in 6.90201 secs using 299.3% CPU
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Iteration 190 / LogL: -195358.788 / Time: 0h:28m:33s (0h:8m:18s left)
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Iteration 200 / LogL: -195263.179 / Time: 0h:29m:51s (0h:6m:44s left)
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Iteration 210 / LogL: -195231.990 / Time: 0h:31m:14s (0h:5m:13s left)
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Iteration 220 / LogL: -195223.539 / Time: 0h:32m:32s (0h:3m:42s left)
Optimizing NNI: done in 10.3118 secs using 299% CPU
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Iteration 230 / LogL: -195266.631 / Time: 0h:33m:54s (0h:2m:13s left)
Optimizing NNI: done in 10.5065 secs using 298.8% CPU
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Iteration 240 / LogL: -195301.508 / Time: 0h:35m:19s (0h:0m:44s left)
Optimizing NNI: done in 6.70831 secs using 299.2% CPU
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TREE SEARCH COMPLETED AFTER 246 ITERATIONS / Time: 0h:36m:5s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -195206.504
Optimal log-likelihood: -195206.502
Site proportion and rates:  (0.006,0.102) (0.036,0.228) (0.127,0.354) (0.206,0.530) (0.186,0.725) (0.191,1.047) (0.176,1.695) (0.071,2.864)
Parameters optimization took 1 rounds (1.284 sec)
BEST SCORE FOUND : -195206.502
Total tree length: 156.733

Total number of iterations: 246
CPU time used for tree search: 6270.109 sec (1h:44m:30s)
Wall-clock time used for tree search: 2116.340 sec (0h:35m:16s)
Total CPU time used: 6421.819 sec (1h:47m:1s)
Total wall-clock time used: 2167.039 sec (0h:36m:7s)

===> START BOOTSTRAP REPLICATE NUMBER 87

Creating bootstrap alignment (seed: 579388)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.315 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -191105.167
2. Current log-likelihood: -188678.495
3. Current log-likelihood: -188618.115
4. Current log-likelihood: -188612.335
5. Current log-likelihood: -188608.046
6. Current log-likelihood: -188605.983
7. Current log-likelihood: -188605.226
8. Current log-likelihood: -188604.957
Optimal log-likelihood: -188604.867
Site proportion and rates:  (0.011,0.086) (0.046,0.250) (0.130,0.369) (0.197,0.575) (0.170,0.766) (0.231,1.057) (0.122,1.658) (0.093,2.692)
Parameters optimization took 8 rounds (29.864 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.8962 secs using 299.9% CPU
Computing ML distances took 19.896815 sec (of wall-clock time) 59.678235 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00255108 secs using 238.6% CPU
Constructing RapidNJ tree: done in 0.0171158 secs using 325.9% CPU
Computing RapidNJ tree took 0.019735 sec (of wall-clock time) 0.061910 sec (of CPU time)
Log-likelihood of RapidNJ tree: -192816.767
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.023 second
Computing log-likelihood of 98 initial trees ... 26.250 seconds
Current best score: -188604.867

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.05366 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -188100.907
Optimizing NNI: done in 6.41627 secs using 299.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -188061.898
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Iteration 10 / LogL: -188131.340 / Time: 0h:3m:9s
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Iteration 20 / LogL: -188154.451 / Time: 0h:4m:15s
Finish initializing candidate tree set (20)
Current best tree score: -188061.898 / CPU time: 202.979
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.1419 secs using 299.2% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -188052.093
Optimizing NNI: done in 5.72676 secs using 299% CPU
Iteration 30 / LogL: -188069.148 / Time: 0h:5m:29s (0h:18m:44s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 31: -188037.730
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 37: -188031.069
Optimizing NNI: done in 7.7069 secs using 299% CPU
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Iteration 40 / LogL: -188120.815 / Time: 0h:6m:55s (0h:17m:13s left)
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Iteration 50 / LogL: -188067.549 / Time: 0h:8m:10s (0h:14m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 54: -188025.762
Optimizing NNI: done in 7.21178 secs using 299.1% CPU
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Iteration 60 / LogL: -188548.470 / Time: 0h:9m:29s (0h:15m:6s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 66: -188018.398
Optimizing NNI: done in 6.87899 secs using 299.1% CPU
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Iteration 70 / LogL: -188110.742 / Time: 0h:10m:45s (0h:14m:57s left)
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Iteration 80 / LogL: -188105.841 / Time: 0h:11m:57s (0h:13m:0s left)
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Iteration 90 / LogL: -188043.682 / Time: 0h:13m:10s (0h:11m:14s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 98: -188015.868
Optimizing NNI: done in 7.67368 secs using 299.2% CPU
Optimizing NNI: done in 8.29124 secs using 299.2% CPU
Iteration 100 / LogL: -188150.362 / Time: 0h:14m:32s (0h:14m:22s left)
Optimizing NNI: done in 6.75998 secs using 299% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 102: -188006.525
Optimizing NNI: done in 6.8396 secs using 299.2% CPU
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Iteration 110 / LogL: -188273.795 / Time: 0h:15m:50s (0h:13m:22s left)
Optimizing NNI: done in 7.32934 secs using 299% CPU
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Iteration 120 / LogL: -188208.246 / Time: 0h:17m:9s (0h:11m:49s left)
Optimizing NNI: done in 7.39221 secs using 299% CPU
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Iteration 130 / LogL: -188057.231 / Time: 0h:18m:26s (0h:10m:17s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 146: -188003.270
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BETTER TREE FOUND at iteration 203: -188003.040
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BETTER TREE FOUND at iteration 205: -188001.313
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BETTER TREE FOUND at iteration 242: -188000.044
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Iteration 330 / LogL: -188037.477 / Time: 0h:43m:38s (0h:1m:35s left)
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Iteration 340 / LogL: -188015.057 / Time: 0h:44m:54s (0h:0m:15s left)
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TREE SEARCH COMPLETED AFTER 343 ITERATIONS / Time: 0h:45m:16s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -188000.044
Optimal log-likelihood: -188000.040
Site proportion and rates:  (0.011,0.086) (0.051,0.253) (0.132,0.375) (0.215,0.591) (0.168,0.801) (0.214,1.079) (0.118,1.680) (0.091,2.701)
Parameters optimization took 1 rounds (1.219 sec)
BEST SCORE FOUND : -188000.040
Total tree length: 141.488

Total number of iterations: 343
CPU time used for tree search: 7906.835 sec (2h:11m:46s)
Wall-clock time used for tree search: 2663.598 sec (0h:44m:23s)
Total CPU time used: 8068.281 sec (2h:14m:28s)
Total wall-clock time used: 2717.603 sec (0h:45m:17s)

===> START BOOTSTRAP REPLICATE NUMBER 88

Creating bootstrap alignment (seed: 579389)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.284 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -192895.571
2. Current log-likelihood: -190452.683
3. Current log-likelihood: -190286.544
4. Current log-likelihood: -190281.030
5. Current log-likelihood: -190280.926
Optimal log-likelihood: -190280.872
Site proportion and rates:  (0.011,0.086) (0.035,0.216) (0.053,0.300) (0.151,0.437) (0.266,0.640) (0.250,1.016) (0.150,1.658) (0.083,2.834)
Parameters optimization took 5 rounds (18.729 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 21.7289 secs using 299.9% CPU
Computing ML distances took 21.729549 sec (of wall-clock time) 65.177264 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00247312 secs using 299% CPU
Constructing RapidNJ tree: done in 0.016572 secs using 353% CPU
Computing RapidNJ tree took 0.019117 sec (of wall-clock time) 0.067706 sec (of CPU time)
Log-likelihood of RapidNJ tree: -194362.156
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.125 second
Computing log-likelihood of 98 initial trees ... 26.081 seconds
Current best score: -190280.872

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.73807 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -189663.268
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -189643.378
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Iteration 10 / LogL: -189704.001 / Time: 0h:3m:5s
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Iteration 20 / LogL: -189678.276 / Time: 0h:4m:9s
Finish initializing candidate tree set (20)
Current best tree score: -189643.378 / CPU time: 203.584
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.05174 secs using 299% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -189609.065
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -189599.397
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -189580.529
Iteration 30 / LogL: -189580.529 / Time: 0h:6m:0s (0h:20m:43s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -189576.013
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Iteration 40 / LogL: -189786.739 / Time: 0h:7m:19s (0h:17m:15s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 41: -189575.162
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Iteration 50 / LogL: -189682.686 / Time: 0h:8m:35s (0h:15m:57s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 58: -189567.955
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Iteration 60 / LogL: -189611.303 / Time: 0h:9m:49s (0h:16m:18s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 62: -189548.513
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Iteration 70 / LogL: -189753.830 / Time: 0h:11m:7s (0h:14m:49s left)
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Iteration 100 / LogL: -189576.529 / Time: 0h:14m:37s (0h:9m:9s left)
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BETTER TREE FOUND at iteration 103: -189540.931
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BETTER TREE FOUND at iteration 108: -189540.492
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BETTER TREE FOUND at iteration 110: -189535.359
Iteration 110 / LogL: -189535.359 / Time: 0h:16m:4s (0h:14m:44s left)
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BETTER TREE FOUND at iteration 130: -189533.337
Iteration 130 / LogL: -189533.337 / Time: 0h:18m:29s (0h:14m:19s left)
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BETTER TREE FOUND at iteration 133: -189521.387
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BETTER TREE FOUND at iteration 158: -189507.517
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Iteration 240 / LogL: -189571.025 / Time: 0h:31m:33s (0h:2m:22s left)
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Iteration 250 / LogL: -189520.390 / Time: 0h:32m:44s (0h:1m:3s left)
Optimizing NNI: done in 6.23312 secs using 299.3% CPU
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TREE SEARCH COMPLETED AFTER 259 ITERATIONS / Time: 0h:33m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -189507.517
Optimal log-likelihood: -189507.515
Site proportion and rates:  (0.012,0.087) (0.062,0.243) (0.137,0.395) (0.233,0.585) (0.125,0.789) (0.202,1.060) (0.145,1.668) (0.085,2.811)
Parameters optimization took 1 rounds (1.233 sec)
BEST SCORE FOUND : -189507.515
Total tree length: 148.734

Total number of iterations: 259
CPU time used for tree search: 5868.418 sec (1h:37m:48s)
Wall-clock time used for tree search: 1981.859 sec (0h:33m:1s)
Total CPU time used: 6009.998 sec (1h:40m:9s)
Total wall-clock time used: 2029.188 sec (0h:33m:49s)

===> START BOOTSTRAP REPLICATE NUMBER 89

Creating bootstrap alignment (seed: 579390)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.253 seconds

NOTE: 242 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199887.398
2. Current log-likelihood: -197070.210
3. Current log-likelihood: -197046.256
4. Current log-likelihood: -197045.481
5. Current log-likelihood: -197045.226
6. Current log-likelihood: -197045.124
Optimal log-likelihood: -197045.064
Site proportion and rates:  (0.003,0.100) (0.049,0.227) (0.077,0.355) (0.059,0.418) (0.267,0.574) (0.290,0.943) (0.155,1.551) (0.100,2.691)
Parameters optimization took 6 rounds (23.038 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.3868 secs using 300% CPU
Computing ML distances took 19.387430 sec (of wall-clock time) 58.152777 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00237799 secs using 178.9% CPU
Constructing RapidNJ tree: done in 0.01613 secs using 361.9% CPU
Computing RapidNJ tree took 0.018574 sec (of wall-clock time) 0.063675 sec (of CPU time)
Log-likelihood of RapidNJ tree: -201996.328
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.458 second
Computing log-likelihood of 98 initial trees ... 26.272 seconds
Current best score: -197045.064

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.49059 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -196444.001
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -196414.730
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Iteration 10 / LogL: -196486.624 / Time: 0h:2m:56s
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Iteration 20 / LogL: -196510.763 / Time: 0h:3m:53s
Finish initializing candidate tree set (20)
Current best tree score: -196414.730 / CPU time: 188.387
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 27: -196394.984
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Iteration 30 / LogL: -196427.197 / Time: 0h:5m:2s (0h:16m:50s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -196384.036
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 38: -196372.186
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Iteration 40 / LogL: -196543.678 / Time: 0h:6m:18s (0h:15m:49s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 48: -196350.099
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Iteration 50 / LogL: -196434.745 / Time: 0h:7m:31s (0h:15m:3s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 52: -196339.198
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 55: -196338.726
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 58: -196335.724
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Iteration 60 / LogL: -196363.048 / Time: 0h:8m:47s (0h:14m:35s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 66: -196318.136
Optimizing NNI: done in 5.61615 secs using 299.3% CPU
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Iteration 70 / LogL: -196398.274 / Time: 0h:9m:55s (0h:13m:48s left)
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Iteration 80 / LogL: -196330.960 / Time: 0h:10m:59s (0h:11m:58s left)
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Iteration 90 / LogL: -196333.651 / Time: 0h:12m:4s (0h:10m:18s left)
Optimizing NNI: done in 7.36185 secs using 299.4% CPU
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Iteration 100 / LogL: -196407.606 / Time: 0h:13m:8s (0h:8m:45s left)
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Iteration 110 / LogL: -196425.212 / Time: 0h:14m:13s (0h:7m:18s left)
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Iteration 120 / LogL: -196346.023 / Time: 0h:15m:22s (0h:5m:56s left)
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Iteration 130 / LogL: -196359.244 / Time: 0h:16m:28s (0h:4m:35s left)
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Iteration 140 / LogL: -196330.052 / Time: 0h:17m:32s (0h:3m:16s left)
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Iteration 150 / LogL: -196352.501 / Time: 0h:18m:35s (0h:1m:59s left)
Optimizing NNI: done in 5.9217 secs using 299.2% CPU
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Iteration 160 / LogL: -196332.829 / Time: 0h:19m:40s (0h:0m:44s left)
Optimizing NNI: done in 7.33112 secs using 299.2% CPU
Optimizing NNI: done in 6.43444 secs using 299.1% CPU
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Optimizing NNI: done in 6.41115 secs using 299.3% CPU
TREE SEARCH COMPLETED AFTER 167 ITERATIONS / Time: 0h:20m:26s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -196318.136
Optimal log-likelihood: -196318.136
Site proportion and rates:  (0.003,0.101) (0.052,0.234) (0.079,0.363) (0.037,0.363) (0.286,0.566) (0.291,0.946) (0.154,1.568) (0.099,2.709)
Parameters optimization took 1 rounds (0.854 sec)
BEST SCORE FOUND : -196318.136
Total tree length: 153.143

Total number of iterations: 167
CPU time used for tree search: 3474.149 sec (0h:57m:54s)
Wall-clock time used for tree search: 1180.886 sec (0h:19m:40s)
Total CPU time used: 3612.362 sec (1h:0m:12s)
Total wall-clock time used: 1227.098 sec (0h:20m:27s)

===> START BOOTSTRAP REPLICATE NUMBER 90

Creating bootstrap alignment (seed: 579391)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.313 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194190.425
2. Current log-likelihood: -191525.813
3. Current log-likelihood: -191472.620
4. Current log-likelihood: -191465.130
5. Current log-likelihood: -191461.374
6. Current log-likelihood: -191458.708
7. Current log-likelihood: -191455.935
8. Current log-likelihood: -191452.474
9. Current log-likelihood: -191449.903
10. Current log-likelihood: -191447.687
11. Current log-likelihood: -191445.062
12. Current log-likelihood: -191442.190
13. Current log-likelihood: -191440.096
14. Current log-likelihood: -191439.119
15. Current log-likelihood: -191438.712
16. Current log-likelihood: -191438.524
Optimal log-likelihood: -191438.444
Site proportion and rates:  (0.017,0.105) (0.130,0.303) (0.220,0.483) (0.180,0.694) (0.197,0.968) (0.100,1.481) (0.101,2.048) (0.056,3.275)
Parameters optimization took 16 rounds (60.973 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.3001 secs using 299.9% CPU
Computing ML distances took 19.300718 sec (of wall-clock time) 57.889567 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00232005 secs using 293.4% CPU
Constructing RapidNJ tree: done in 0.016428 secs using 382.4% CPU
Computing RapidNJ tree took 0.018828 sec (of wall-clock time) 0.071548 sec (of CPU time)
Log-likelihood of RapidNJ tree: -195175.294
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.582 second
Computing log-likelihood of 98 initial trees ... 26.084 seconds
Current best score: -191438.444

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.69359 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -190855.386
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -190745.194
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Iteration 10 / LogL: -190839.710 / Time: 0h:4m:11s
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Iteration 20 / LogL: -190763.462 / Time: 0h:5m:50s
Finish initializing candidate tree set (20)
Current best tree score: -190745.194 / CPU time: 266.170
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 9.20163 secs using 299.2% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -190732.141
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Iteration 30 / LogL: -190803.612 / Time: 0h:7m:21s (0h:24m:20s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -190714.886
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -190706.512
Iteration 40 / LogL: -190706.512 / Time: 0h:8m:57s (0h:22m:57s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 45: -190684.387
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Iteration 50 / LogL: -190720.309 / Time: 0h:10m:33s (0h:20m:28s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 51: -190663.529
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Iteration 60 / LogL: -190669.963 / Time: 0h:12m:1s (0h:18m:32s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 61: -190648.150
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Iteration 70 / LogL: -190657.153 / Time: 0h:13m:32s (0h:17m:51s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 72: -190639.014
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 76: -190637.405
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 78: -190636.969
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Iteration 80 / LogL: -190672.839 / Time: 0h:15m:11s (0h:18m:50s left)
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Iteration 90 / LogL: -190671.150 / Time: 0h:16m:37s (0h:16m:25s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 94: -190636.490
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Iteration 100 / LogL: -190684.039 / Time: 0h:18m:9s (0h:17m:13s left)
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Iteration 110 / LogL: -190640.198 / Time: 0h:19m:35s (0h:15m:5s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 115: -190634.994
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Iteration 120 / LogL: -190643.168 / Time: 0h:21m:9s (0h:16m:53s left)
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Iteration 130 / LogL: -190662.667 / Time: 0h:22m:34s (0h:14m:52s left)
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Iteration 160 / LogL: -190666.369 / Time: 0h:26m:57s (0h:9m:19s left)
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Iteration 170 / LogL: -190672.023 / Time: 0h:28m:19s (0h:7m:32s left)
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Iteration 180 / LogL: -190719.831 / Time: 0h:29m:46s (0h:5m:49s left)
Optimizing NNI: done in 8.48082 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 181: -190631.712
Optimizing NNI: done in 7.62904 secs using 299.1% CPU
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Iteration 190 / LogL: -190641.085 / Time: 0h:31m:16s (0h:15m:3s left)
Optimizing NNI: done in 10.5888 secs using 299% CPU
Optimizing NNI: done in 6.66743 secs using 299.2% CPU
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BETTER TREE FOUND at iteration 192: -190631.336
Optimizing NNI: done in 9.29226 secs using 299.1% CPU
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Iteration 200 / LogL: -190766.577 / Time: 0h:32m:47s (0h:15m:9s left)
Optimizing NNI: done in 7.78631 secs using 298.8% CPU
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Iteration 210 / LogL: -190692.781 / Time: 0h:34m:13s (0h:13m:25s left)
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Iteration 220 / LogL: -190679.004 / Time: 0h:35m:41s (0h:11m:43s left)
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Iteration 230 / LogL: -190702.733 / Time: 0h:37m:9s (0h:10m:3s left)
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Iteration 240 / LogL: -190657.035 / Time: 0h:38m:36s (0h:8m:23s left)
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Iteration 250 / LogL: -190635.669 / Time: 0h:40m:0s (0h:6m:44s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 254: -190628.943
Optimizing NNI: done in 8.6712 secs using 299.3% CPU
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Iteration 260 / LogL: -190647.032 / Time: 0h:41m:32s (0h:15m:4s left)
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Iteration 270 / LogL: -190641.198 / Time: 0h:42m:58s (0h:13m:25s left)
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Iteration 280 / LogL: -190649.407 / Time: 0h:44m:27s (0h:11m:47s left)
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Iteration 290 / LogL: -190686.895 / Time: 0h:45m:54s (0h:10m:9s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 294: -190627.198
Optimizing NNI: done in 8.75948 secs using 299.1% CPU
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Iteration 300 / LogL: -190692.377 / Time: 0h:47m:22s (0h:14m:53s left)
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Iteration 310 / LogL: -190637.190 / Time: 0h:48m:49s (0h:13m:16s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 318: -190624.510
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Iteration 320 / LogL: -191154.438 / Time: 0h:50m:19s (0h:15m:27s left)
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Iteration 330 / LogL: -190650.001 / Time: 0h:51m:46s (0h:13m:50s left)
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Iteration 340 / LogL: -190665.179 / Time: 0h:53m:15s (0h:12m:15s left)
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Iteration 350 / LogL: -190651.979 / Time: 0h:54m:34s (0h:10m:37s left)
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Iteration 360 / LogL: -190641.467 / Time: 0h:56m:2s (0h:9m:3s left)
Optimizing NNI: done in 8.53839 secs using 299.2% CPU
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Iteration 370 / LogL: -190627.332 / Time: 0h:57m:26s (0h:7m:28s left)
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Iteration 380 / LogL: -190818.813 / Time: 0h:58m:55s (0h:5m:54s left)
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Iteration 390 / LogL: -190659.389 / Time: 1h:0m:18s (0h:4m:20s left)
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Iteration 400 / LogL: -190682.970 / Time: 1h:1m:44s (0h:2m:47s left)
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Iteration 410 / LogL: -190633.882 / Time: 1h:3m:10s (0h:1m:14s left)
Optimizing NNI: done in 10.4434 secs using 299% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 412: -190623.409
Optimizing NNI: done in 8.96966 secs using 299.1% CPU
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Iteration 420 / LogL: -190824.241 / Time: 1h:4m:46s (0h:14m:13s left)
Optimizing NNI: done in 6.01082 secs using 299.3% CPU
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Iteration 430 / LogL: -190701.271 / Time: 1h:6m:6s (0h:12m:38s left)
Optimizing NNI: done in 9.65411 secs using 299.1% CPU
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Iteration 440 / LogL: -190625.893 / Time: 1h:7m:36s (0h:11m:5s left)
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Iteration 450 / LogL: -190670.092 / Time: 1h:8m:57s (0h:9m:31s left)
Optimizing NNI: done in 8.47656 secs using 298.8% CPU
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Iteration 460 / LogL: -190752.820 / Time: 1h:10m:17s (0h:7m:57s left)
Optimizing NNI: done in 8.63773 secs using 299% CPU
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Iteration 470 / LogL: -190669.271 / Time: 1h:11m:38s (0h:6m:24s left)
Optimizing NNI: done in 8.38419 secs using 299.1% CPU
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Iteration 480 / LogL: -190637.092 / Time: 1h:13m:0s (0h:4m:52s left)
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Optimizing NNI: done in 8.56065 secs using 299.2% CPU
Iteration 490 / LogL: -190655.911 / Time: 1h:14m:25s (0h:3m:20s left)
Optimizing NNI: done in 7.83016 secs using 299% CPU
Optimizing NNI: done in 8.89117 secs using 299.2% CPU
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Iteration 500 / LogL: -190645.420 / Time: 1h:15m:53s (0h:1m:49s left)
Optimizing NNI: done in 8.33725 secs using 299.2% CPU
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Optimizing NNI: done in 9.09803 secs using 299.1% CPU
Optimizing NNI: done in 9.83429 secs using 298.9% CPU
Iteration 510 / LogL: -190802.653 / Time: 1h:17m:19s (0h:0m:18s left)
Optimizing NNI: done in 9.05626 secs using 299.2% CPU
Optimizing NNI: done in 8.36244 secs using 299.2% CPU
Optimizing NNI: done in 8.44213 secs using 299.3% CPU
TREE SEARCH COMPLETED AFTER 513 ITERATIONS / Time: 1h:17m:45s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -190623.409
Optimal log-likelihood: -190623.397
Site proportion and rates:  (0.023,0.125) (0.133,0.312) (0.226,0.488) (0.195,0.720) (0.180,1.015) (0.099,1.548) (0.087,2.084) (0.057,3.291)
Parameters optimization took 1 rounds (1.584 sec)
BEST SCORE FOUND : -190623.397
Total tree length: 157.562

Total number of iterations: 513
CPU time used for tree search: 13643.953 sec (3h:47m:23s)
Wall-clock time used for tree search: 4581.390 sec (1h:16m:21s)
Total CPU time used: 13900.771 sec (3h:51m:40s)
Total wall-clock time used: 4667.333 sec (1h:17m:47s)

===> START BOOTSTRAP REPLICATE NUMBER 91

Creating bootstrap alignment (seed: 579392)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.285 seconds

NOTE: 242 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -195290.360
2. Current log-likelihood: -192723.018
3. Current log-likelihood: -192698.940
4. Current log-likelihood: -192695.910
5. Current log-likelihood: -192691.696
6. Current log-likelihood: -192688.248
7. Current log-likelihood: -192686.223
8. Current log-likelihood: -192685.165
9. Current log-likelihood: -192684.520
10. Current log-likelihood: -192683.997
11. Current log-likelihood: -192683.538
12. Current log-likelihood: -192683.100
13. Current log-likelihood: -192682.629
14. Current log-likelihood: -192682.035
15. Current log-likelihood: -192680.874
16. Current log-likelihood: -192676.756
17. Current log-likelihood: -192674.580
18. Current log-likelihood: -192674.135
19. Current log-likelihood: -192673.916
20. Current log-likelihood: -192673.738
21. Current log-likelihood: -192673.510
22. Current log-likelihood: -192673.134
23. Current log-likelihood: -192672.620
24. Current log-likelihood: -192672.223
25. Current log-likelihood: -192672.067
Optimal log-likelihood: -192672.024
Site proportion and rates:  (0.011,0.098) (0.056,0.236) (0.153,0.378) (0.252,0.600) (0.250,0.925) (0.128,1.442) (0.101,2.116) (0.048,3.048)
Parameters optimization took 25 rounds (87.612 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 22.1235 secs using 300% CPU
Computing ML distances took 22.124176 sec (of wall-clock time) 66.362254 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00223088 secs using 388.3% CPU
Constructing RapidNJ tree: done in 0.0164599 secs using 361.5% CPU
Computing RapidNJ tree took 0.018753 sec (of wall-clock time) 0.070355 sec (of CPU time)
Log-likelihood of RapidNJ tree: -198509.606
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.112 second
Computing log-likelihood of 98 initial trees ... 26.189 seconds
Current best score: -192672.024

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.11907 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -192136.574
Optimizing NNI: done in 10.5407 secs using 299% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -192110.736
Optimizing NNI: done in 9.50011 secs using 299.1% CPU
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Iteration 10 / LogL: -192142.561 / Time: 0h:4m:56s
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Iteration 20 / LogL: -192150.315 / Time: 0h:6m:33s
Finish initializing candidate tree set (20)
Current best tree score: -192110.736 / CPU time: 273.319
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.60087 secs using 299.3% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -192079.206
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -192078.438
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -192068.941
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Iteration 30 / LogL: -192122.463 / Time: 0h:7m:59s (0h:26m:27s left)
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Iteration 40 / LogL: -192118.698 / Time: 0h:9m:12s (0h:20m:16s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 41: -192059.265
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Iteration 50 / LogL: -192084.406 / Time: 0h:10m:28s (0h:19m:25s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 53: -192051.448
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 59: -192047.179
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Iteration 60 / LogL: -192147.250 / Time: 0h:11m:43s (0h:19m:39s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 68: -192028.604
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Iteration 70 / LogL: -192114.893 / Time: 0h:12m:58s (0h:18m:25s left)
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Iteration 80 / LogL: -192042.241 / Time: 0h:14m:10s (0h:15m:47s left)
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Iteration 90 / LogL: -192054.147 / Time: 0h:15m:23s (0h:13m:28s left)
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Iteration 100 / LogL: -192134.627 / Time: 0h:16m:33s (0h:11m:22s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 109: -192025.632
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Iteration 110 / LogL: -192054.481 / Time: 0h:17m:55s (0h:16m:16s left)
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Iteration 120 / LogL: -192117.590 / Time: 0h:19m:7s (0h:14m:18s left)
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Iteration 130 / LogL: -192391.368 / Time: 0h:20m:20s (0h:12m:27s left)
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Iteration 140 / LogL: -192058.504 / Time: 0h:21m:34s (0h:10m:42s left)
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Iteration 190 / LogL: -192074.040 / Time: 0h:27m:31s (0h:2m:46s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 191: -192020.949
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 199: -192019.263
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Iteration 200 / LogL: -192093.101 / Time: 0h:28m:49s (0h:14m:20s left)
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Iteration 230 / LogL: -192039.791 / Time: 0h:32m:29s (0h:9m:47s left)
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Iteration 240 / LogL: -192076.766 / Time: 0h:34m:6s (0h:8m:25s left)
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Iteration 250 / LogL: -192040.476 / Time: 0h:35m:16s (0h:6m:56s left)
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Iteration 260 / LogL: -192031.006 / Time: 0h:36m:25s (0h:5m:29s left)
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Iteration 270 / LogL: -192048.972 / Time: 0h:37m:34s (0h:4m:3s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 280: -192018.198
Iteration 280 / LogL: -192018.198 / Time: 0h:38m:47s (0h:13m:54s left)
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Iteration 350 / LogL: -192039.233 / Time: 0h:47m:6s (0h:4m:2s left)
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Iteration 360 / LogL: -192037.102 / Time: 0h:48m:17s (0h:2m:41s left)
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Iteration 370 / LogL: -192044.019 / Time: 0h:49m:28s (0h:1m:20s left)
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Iteration 380 / LogL: -192072.641 / Time: 0h:50m:40s (0h:0m:0s left)
Optimizing NNI: done in 7.094 secs using 299.1% CPU
TREE SEARCH COMPLETED AFTER 381 ITERATIONS / Time: 0h:50m:47s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192018.198
Optimal log-likelihood: -192018.196
Site proportion and rates:  (0.012,0.099) (0.057,0.238) (0.154,0.375) (0.265,0.605) (0.244,0.944) (0.142,1.506) (0.105,2.323) (0.020,3.805)
Parameters optimization took 1 rounds (1.320 sec)
BEST SCORE FOUND : -192018.196
Total tree length: 151.996

Total number of iterations: 381
CPU time used for tree search: 8698.747 sec (2h:24m:58s)
Wall-clock time used for tree search: 2927.851 sec (0h:48m:47s)
Total CPU time used: 9060.920 sec (2h:31m:0s)
Total wall-clock time used: 3048.961 sec (0h:50m:48s)

===> START BOOTSTRAP REPLICATE NUMBER 92

Creating bootstrap alignment (seed: 579393)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.254 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -196026.032
2. Current log-likelihood: -193260.861
3. Current log-likelihood: -193232.952
4. Current log-likelihood: -193230.921
5. Current log-likelihood: -193229.761
6. Current log-likelihood: -193229.021
7. Current log-likelihood: -193228.282
8. Current log-likelihood: -193227.443
9. Current log-likelihood: -193226.428
10. Current log-likelihood: -193225.282
11. Current log-likelihood: -193224.128
12. Current log-likelihood: -193223.364
13. Current log-likelihood: -193222.905
14. Current log-likelihood: -193222.666
15. Current log-likelihood: -193222.556
Optimal log-likelihood: -193222.501
Site proportion and rates:  (0.010,0.068) (0.080,0.258) (0.133,0.406) (0.228,0.569) (0.128,0.808) (0.181,1.055) (0.141,1.601) (0.099,2.776)
Parameters optimization took 15 rounds (55.996 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 22.7541 secs using 299.9% CPU
Computing ML distances took 22.754769 sec (of wall-clock time) 68.246958 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00235295 secs using 208.8% CPU
Constructing RapidNJ tree: done in 0.0161219 secs using 404.9% CPU
Computing RapidNJ tree took 0.018543 sec (of wall-clock time) 0.070875 sec (of CPU time)
Log-likelihood of RapidNJ tree: -197155.755
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.075 second
Computing log-likelihood of 98 initial trees ... 26.490 seconds
Current best score: -193222.501

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.59261 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -192545.103
Optimizing NNI: done in 6.84261 secs using 298.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -192448.317
Optimizing NNI: done in 6.35781 secs using 299% CPU
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Iteration 10 / LogL: -192497.168 / Time: 0h:3m:43s
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Iteration 20 / LogL: -192568.588 / Time: 0h:4m:53s
Finish initializing candidate tree set (20)
Current best tree score: -192448.317 / CPU time: 210.584
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.87409 secs using 299.1% CPU
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Iteration 30 / LogL: -192508.206 / Time: 0h:6m:13s (0h:15m:26s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 34: -192436.540
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Iteration 40 / LogL: -192583.230 / Time: 0h:7m:39s (0h:18m:28s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 45: -192428.867
Optimizing NNI: done in 8.32727 secs using 298.9% CPU
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Iteration 50 / LogL: -192464.344 / Time: 0h:9m:5s (0h:17m:37s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 58: -192415.805
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Iteration 60 / LogL: -192452.774 / Time: 0h:10m:29s (0h:17m:25s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -192402.372
Optimizing NNI: done in 9.31342 secs using 299% CPU
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Iteration 70 / LogL: -192417.553 / Time: 0h:11m:56s (0h:16m:26s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 74: -192389.177
Optimizing NNI: done in 8.52652 secs using 299.3% CPU
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Iteration 80 / LogL: -192438.773 / Time: 0h:13m:19s (0h:15m:50s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 82: -192386.774
Optimizing NNI: done in 8.51486 secs using 299.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 87: -192386.239
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Iteration 90 / LogL: -192427.570 / Time: 0h:14m:48s (0h:16m:7s left)
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Iteration 100 / LogL: -192511.794 / Time: 0h:16m:8s (0h:14m:10s left)
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Iteration 110 / LogL: -192447.199 / Time: 0h:17m:28s (0h:12m:20s left)
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BETTER TREE FOUND at iteration 115: -192380.618
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BETTER TREE FOUND at iteration 125: -192377.391
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BETTER TREE FOUND at iteration 128: -192376.716
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BETTER TREE FOUND at iteration 136: -192369.991
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Iteration 190 / LogL: -192380.879 / Time: 0h:28m:27s (0h:6m:55s left)
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Iteration 220 / LogL: -192400.562 / Time: 0h:32m:26s (0h:2m:22s left)
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Iteration 230 / LogL: -192375.936 / Time: 0h:33m:45s (0h:0m:53s left)
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TREE SEARCH COMPLETED AFTER 237 ITERATIONS / Time: 0h:34m:39s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192369.991
2. Current log-likelihood: -192369.979
Optimal log-likelihood: -192369.969
Site proportion and rates:  (0.011,0.070) (0.081,0.261) (0.127,0.396) (0.223,0.555) (0.137,0.797) (0.190,1.070) (0.136,1.628) (0.095,2.829)
Parameters optimization took 2 rounds (3.149 sec)
BEST SCORE FOUND : -192369.969
Total tree length: 156.432

Total number of iterations: 237
CPU time used for tree search: 5911.679 sec (1h:38m:31s)
Wall-clock time used for tree search: 1996.691 sec (0h:33m:16s)
Total CPU time used: 6168.117 sec (1h:42m:48s)
Total wall-clock time used: 2082.421 sec (0h:34m:42s)

===> START BOOTSTRAP REPLICATE NUMBER 93

Creating bootstrap alignment (seed: 579394)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.282 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -195171.514
2. Current log-likelihood: -192810.823
3. Current log-likelihood: -192678.861
4. Current log-likelihood: -192671.546
5. Current log-likelihood: -192671.428
Optimal log-likelihood: -192671.408
Site proportion and rates:  (0.005,0.093) (0.043,0.215) (0.027,0.229) (0.217,0.410) (0.224,0.661) (0.228,1.027) (0.161,1.622) (0.095,2.641)
Parameters optimization took 5 rounds (20.175 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.5906 secs using 300% CPU
Computing ML distances took 19.591222 sec (of wall-clock time) 58.764107 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.002496 secs using 298.3% CPU
Constructing RapidNJ tree: done in 0.016499 secs using 371% CPU
Computing RapidNJ tree took 0.019077 sec (of wall-clock time) 0.069244 sec (of CPU time)
Log-likelihood of RapidNJ tree: -197346.542
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.733 second
Computing log-likelihood of 98 initial trees ... 25.667 seconds
Current best score: -192671.408

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.64767 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -192294.082
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -192212.641
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -192174.735
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Iteration 10 / LogL: -192184.819 / Time: 0h:3m:19s
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BETTER TREE FOUND at iteration 16: -192161.600
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BETTER TREE FOUND at iteration 17: -192136.900
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Iteration 20 / LogL: -192236.946 / Time: 0h:4m:37s
Finish initializing candidate tree set (20)
Current best tree score: -192136.900 / CPU time: 229.217
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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BETTER TREE FOUND at iteration 29: -192118.073
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BETTER TREE FOUND at iteration 30: -192111.439
Iteration 30 / LogL: -192111.439 / Time: 0h:5m:56s (0h:20m:28s left)
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BETTER TREE FOUND at iteration 33: -192097.190
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BETTER TREE FOUND at iteration 35: -192092.048
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Iteration 40 / LogL: -192103.756 / Time: 0h:7m:15s (0h:17m:39s left)
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BETTER TREE FOUND at iteration 49: -192050.504
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BETTER TREE FOUND at iteration 73: -192048.661
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BETTER TREE FOUND at iteration 79: -192046.407
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BETTER TREE FOUND at iteration 100: -192045.954
Iteration 100 / LogL: -192045.954 / Time: 0h:14m:27s (0h:14m:36s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 108: -192045.256
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 112: -192043.382
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Iteration 340 / LogL: -192060.472 / Time: 0h:42m:6s (0h:0m:7s left)
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TREE SEARCH COMPLETED AFTER 342 ITERATIONS / Time: 0h:42m:21s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -192032.673
Optimal log-likelihood: -192032.670
Site proportion and rates:  (0.005,0.094) (0.065,0.219) (0.159,0.373) (0.176,0.555) (0.151,0.761) (0.202,1.084) (0.153,1.672) (0.090,2.666)
Parameters optimization took 1 rounds (1.188 sec)
BEST SCORE FOUND : -192032.670
Total tree length: 145.373

Total number of iterations: 342
CPU time used for tree search: 7399.352 sec (2h:3m:19s)
Wall-clock time used for tree search: 2492.850 sec (0h:41m:32s)
Total CPU time used: 7548.057 sec (2h:5m:48s)
Total wall-clock time used: 2542.580 sec (0h:42m:22s)

===> START BOOTSTRAP REPLICATE NUMBER 94

Creating bootstrap alignment (seed: 579395)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.337 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -200553.614
2. Current log-likelihood: -198040.842
3. Current log-likelihood: -198018.456
4. Current log-likelihood: -198016.588
5. Current log-likelihood: -198015.298
6. Current log-likelihood: -198014.321
7. Current log-likelihood: -198013.256
8. Current log-likelihood: -198011.600
9. Current log-likelihood: -198009.281
10. Current log-likelihood: -198007.654
11. Current log-likelihood: -198006.791
12. Current log-likelihood: -198006.321
13. Current log-likelihood: -198006.096
Optimal log-likelihood: -198005.994
Site proportion and rates:  (0.014,0.122) (0.047,0.276) (0.156,0.395) (0.205,0.563) (0.178,0.810) (0.175,1.068) (0.123,1.649) (0.102,2.685)
Parameters optimization took 13 rounds (50.806 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 21.6176 secs using 299.9% CPU
Computing ML distances took 21.618225 sec (of wall-clock time) 64.841266 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00227594 secs using 386.6% CPU
Constructing RapidNJ tree: done in 0.0167451 secs using 381.6% CPU
Computing RapidNJ tree took 0.019084 sec (of wall-clock time) 0.073237 sec (of CPU time)
Log-likelihood of RapidNJ tree: -202051.814
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.889 second
Computing log-likelihood of 98 initial trees ... 26.048 seconds
Current best score: -198005.994

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.04175 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -197515.496
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -197505.772
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Iteration 10 / LogL: -197545.671 / Time: 0h:3m:57s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 13: -197492.457
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 15: -197482.246
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Iteration 20 / LogL: -197584.324 / Time: 0h:5m:21s
Finish initializing candidate tree set (20)
Current best tree score: -197482.246 / CPU time: 246.173
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -197418.037
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -197402.182
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Iteration 30 / LogL: -197587.090 / Time: 0h:6m:54s (0h:22m:23s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 34: -197398.644
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 40: -197383.475
Iteration 40 / LogL: -197383.475 / Time: 0h:8m:21s (0h:21m:26s left)
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Iteration 50 / LogL: -197423.176 / Time: 0h:9m:35s (0h:17m:36s left)
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BETTER TREE FOUND at iteration 60: -197381.725
Iteration 60 / LogL: -197381.725 / Time: 0h:10m:56s (0h:18m:32s left)
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BETTER TREE FOUND at iteration 63: -197363.189
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BETTER TREE FOUND at iteration 92: -197362.597
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BETTER TREE FOUND at iteration 109: -197357.955
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Iteration 110 / LogL: -197509.546 / Time: 0h:17m:40s (0h:16m:2s left)
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Iteration 130 / LogL: -197362.903 / Time: 0h:20m:7s (0h:12m:19s left)
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BETTER TREE FOUND at iteration 140: -197356.457
Iteration 140 / LogL: -197356.457 / Time: 0h:21m:30s (0h:15m:27s left)
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BETTER TREE FOUND at iteration 141: -197352.872
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Iteration 210 / LogL: -197373.084 / Time: 0h:30m:22s (0h:4m:30s left)
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Iteration 220 / LogL: -197667.242 / Time: 0h:31m:41s (0h:3m:2s left)
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Iteration 230 / LogL: -197403.115 / Time: 0h:32m:55s (0h:1m:34s left)
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Iteration 240 / LogL: -197395.624 / Time: 0h:34m:11s (0h:0m:8s left)
Optimizing NNI: done in 7.13361 secs using 299.4% CPU
Optimizing NNI: done in 7.15027 secs using 299.2% CPU
TREE SEARCH COMPLETED AFTER 242 ITERATIONS / Time: 0h:34m:25s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -197352.872
Optimal log-likelihood: -197352.862
Site proportion and rates:  (0.014,0.122) (0.046,0.280) (0.155,0.394) (0.163,0.545) (0.156,0.718) (0.239,1.020) (0.127,1.662) (0.099,2.704)
Parameters optimization took 1 rounds (1.721 sec)
BEST SCORE FOUND : -197352.862
Total tree length: 150.578

Total number of iterations: 242
CPU time used for tree search: 5893.135 sec (1h:38m:13s)
Wall-clock time used for tree search: 1990.021 sec (0h:33m:10s)
Total CPU time used: 6125.030 sec (1h:42m:5s)
Total wall-clock time used: 2067.590 sec (0h:34m:27s)

===> START BOOTSTRAP REPLICATE NUMBER 95

Creating bootstrap alignment (seed: 579396)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.277 seconds

NOTE: 230 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199893.169
2. Current log-likelihood: -197230.622
3. Current log-likelihood: -197209.456
4. Current log-likelihood: -197207.704
5. Current log-likelihood: -197205.765
6. Current log-likelihood: -197204.174
7. Current log-likelihood: -197203.328
8. Current log-likelihood: -197202.993
9. Current log-likelihood: -197202.865
Optimal log-likelihood: -197202.812
Site proportion and rates:  (0.009,0.076) (0.046,0.231) (0.122,0.379) (0.155,0.515) (0.203,0.689) (0.192,0.963) (0.171,1.577) (0.104,2.596)
Parameters optimization took 9 rounds (33.476 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 18.9212 secs using 299.9% CPU
Computing ML distances took 18.921882 sec (of wall-clock time) 56.752183 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00248599 secs using 258.9% CPU
Constructing RapidNJ tree: done in 0.0162489 secs using 380% CPU
Computing RapidNJ tree took 0.018803 sec (of wall-clock time) 0.069492 sec (of CPU time)
Log-likelihood of RapidNJ tree: -201575.924
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.106 second
Computing log-likelihood of 98 initial trees ... 25.247 seconds
Current best score: -197202.812

Do NNI search on 20 best initial trees
Optimizing NNI: done in 3.74654 secs using 299.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -196621.483
Optimizing NNI: done in 6.42995 secs using 299.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -196479.794
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Iteration 10 / LogL: -196600.224 / Time: 0h:3m:7s
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Iteration 20 / LogL: -196624.979 / Time: 0h:4m:14s
Finish initializing candidate tree set (20)
Current best tree score: -196479.794 / CPU time: 199.626
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 6.24733 secs using 299.3% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -196467.485
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -196463.390
Iteration 30 / LogL: -196463.390 / Time: 0h:5m:35s (0h:19m:15s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 39: -196456.267
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Iteration 40 / LogL: -196472.455 / Time: 0h:6m:51s (0h:17m:22s left)
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BETTER TREE FOUND at iteration 42: -196450.101
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BETTER TREE FOUND at iteration 43: -196442.862
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 47: -196441.393
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Iteration 50 / LogL: -196542.658 / Time: 0h:8m:22s (0h:16m:33s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 55: -196433.488
Optimizing NNI: done in 6.63716 secs using 299.1% CPU
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Iteration 60 / LogL: -196443.047 / Time: 0h:9m:39s (0h:15m:32s left)
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Iteration 70 / LogL: -196439.040 / Time: 0h:10m:49s (0h:13m:19s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 79: -196429.938
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Iteration 80 / LogL: -196451.719 / Time: 0h:12m:5s (0h:15m:9s left)
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BETTER TREE FOUND at iteration 90: -196424.240
Iteration 90 / LogL: -196424.240 / Time: 0h:13m:18s (0h:14m:56s left)
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BETTER TREE FOUND at iteration 100: -196411.303
Iteration 100 / LogL: -196411.303 / Time: 0h:14m:30s (0h:14m:39s left)
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Iteration 140 / LogL: -196421.626 / Time: 0h:19m:46s (0h:8m:31s left)
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BETTER TREE FOUND at iteration 143: -196405.348
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BETTER TREE FOUND at iteration 161: -196400.438
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 181: -196399.894
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Iteration 260 / LogL: -196506.179 / Time: 0h:34m:43s (0h:2m:48s left)
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Iteration 270 / LogL: -196435.050 / Time: 0h:35m:56s (0h:1m:28s left)
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Iteration 280 / LogL: -196405.189 / Time: 0h:37m:7s (0h:0m:7s left)
Optimizing NNI: done in 7.33969 secs using 299.3% CPU
Optimizing NNI: done in 6.10886 secs using 299.1% CPU
TREE SEARCH COMPLETED AFTER 282 ITERATIONS / Time: 0h:37m:21s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -196399.894
Optimal log-likelihood: -196399.882
Site proportion and rates:  (0.009,0.077) (0.040,0.231) (0.124,0.363) (0.162,0.515) (0.204,0.688) (0.191,0.973) (0.171,1.586) (0.099,2.672)
Parameters optimization took 1 rounds (1.897 sec)
BEST SCORE FOUND : -196399.882
Total tree length: 158.286

Total number of iterations: 282
CPU time used for tree search: 6481.335 sec (1h:48m:1s)
Wall-clock time used for tree search: 2186.350 sec (0h:36m:26s)
Total CPU time used: 6651.881 sec (1h:50m:51s)
Total wall-clock time used: 2243.366 sec (0h:37m:23s)

===> START BOOTSTRAP REPLICATE NUMBER 96

Creating bootstrap alignment (seed: 579397)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.317 seconds

NOTE: 237 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199239.101
2. Current log-likelihood: -196617.051
3. Current log-likelihood: -196592.067
4. Current log-likelihood: -196588.176
5. Current log-likelihood: -196586.573
6. Current log-likelihood: -196586.138
7. Current log-likelihood: -196586.024
Optimal log-likelihood: -196585.986
Site proportion and rates:  (0.015,0.098) (0.034,0.238) (0.104,0.348) (0.231,0.535) (0.151,0.738) (0.222,0.992) (0.139,1.633) (0.104,2.613)
Parameters optimization took 7 rounds (26.923 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.8401 secs using 299.9% CPU
Computing ML distances took 19.840718 sec (of wall-clock time) 59.510892 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00247598 secs using 296.3% CPU
Constructing RapidNJ tree: done in 0.0165331 secs using 387.2% CPU
Computing RapidNJ tree took 0.019083 sec (of wall-clock time) 0.072070 sec (of CPU time)
Log-likelihood of RapidNJ tree: -200773.611
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.044 second
Computing log-likelihood of 98 initial trees ... 26.440 seconds
Current best score: -196585.986

Do NNI search on 20 best initial trees
Optimizing NNI: done in 5.66317 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -196016.765
Optimizing NNI: done in 5.14431 secs using 299.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -195872.204
Optimizing NNI: done in 6.26372 secs using 299.1% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -195863.854
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Iteration 10 / LogL: -195937.012 / Time: 0h:3m:15s
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Iteration 20 / LogL: -195901.819 / Time: 0h:4m:19s
Finish initializing candidate tree set (20)
Current best tree score: -195863.854 / CPU time: 205.331
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.46021 secs using 299.2% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -195845.668
Optimizing NNI: done in 7.76519 secs using 299.3% CPU
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Iteration 30 / LogL: -195851.414 / Time: 0h:5m:43s (0h:18m:21s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -195794.093
Optimizing NNI: done in 7.53652 secs using 299.1% CPU
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Iteration 40 / LogL: -195821.019 / Time: 0h:7m:5s (0h:17m:27s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 50: -195766.963
Iteration 50 / LogL: -195766.963 / Time: 0h:8m:25s (0h:17m:10s left)
Optimizing NNI: done in 8.55181 secs using 299.1% CPU
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Iteration 60 / LogL: -195780.011 / Time: 0h:9m:35s (0h:14m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -195764.224
Optimizing NNI: done in 7.03331 secs using 299.1% CPU
Optimizing NNI: done in 7.51344 secs using 298.6% CPU
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Iteration 70 / LogL: -195807.303 / Time: 0h:10m:51s (0h:14m:56s left)
Optimizing NNI: done in 8.10563 secs using 299% CPU
Optimizing NNI: done in 7.54176 secs using 299% CPU
Optimizing NNI: done in 7.22046 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 73: -195764.088
Optimizing NNI: done in 8.29733 secs using 299% CPU
Optimizing NNI: done in 7.912 secs using 299.1% CPU
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Iteration 80 / LogL: -195773.937 / Time: 0h:12m:13s (0h:14m:22s left)
Optimizing NNI: done in 6.57514 secs using 299% CPU
Optimizing NNI: done in 7.6718 secs using 299.2% CPU
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Iteration 90 / LogL: -195810.386 / Time: 0h:13m:25s (0h:12m:30s left)
Optimizing NNI: done in 7.71392 secs using 299.1% CPU
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Iteration 100 / LogL: -195774.738 / Time: 0h:14m:42s (0h:10m:50s left)
Optimizing NNI: done in 6.4347 secs using 299.2% CPU
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Iteration 110 / LogL: -195802.661 / Time: 0h:15m:55s (0h:9m:11s left)
Optimizing NNI: done in 7.95915 secs using 298.3% CPU
Optimizing NNI: done in 6.09227 secs using 299.2% CPU
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Optimizing NNI: done in 7.54395 secs using 299.1% CPU
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Iteration 120 / LogL: -195971.931 / Time: 0h:17m:7s (0h:7m:37s left)
Optimizing NNI: done in 7.26596 secs using 299% CPU
Optimizing NNI: done in 6.63856 secs using 299.2% CPU
Optimizing NNI: done in 7.02972 secs using 299.3% CPU
Optimizing NNI: done in 7.51363 secs using 299.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 124: -195756.606
Optimizing NNI: done in 7.75545 secs using 299.3% CPU
Optimizing NNI: done in 6.40452 secs using 299.3% CPU
Optimizing NNI: done in 7.88476 secs using 299.1% CPU
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Iteration 130 / LogL: -195767.087 / Time: 0h:18m:23s (0h:13m:23s left)
Optimizing NNI: done in 7.55162 secs using 299.2% CPU
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Iteration 140 / LogL: -195814.173 / Time: 0h:19m:33s (0h:11m:49s left)
Optimizing NNI: done in 6.62904 secs using 299.1% CPU
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Optimizing NNI: done in 6.81928 secs using 299.3% CPU
Iteration 150 / LogL: -195862.266 / Time: 0h:20m:44s (0h:10m:18s left)
Optimizing NNI: done in 8.02097 secs using 298.9% CPU
Optimizing NNI: done in 7.61632 secs using 299% CPU
Optimizing NNI: done in 6.80305 secs using 298.9% CPU
Optimizing NNI: done in 6.27058 secs using 299.1% CPU
Optimizing NNI: done in 8.19829 secs using 299.1% CPU
Optimizing NNI: done in 7.73329 secs using 299.3% CPU
Optimizing NNI: done in 6.65696 secs using 299.2% CPU
Optimizing NNI: done in 7.74463 secs using 299.2% CPU
Optimizing NNI: done in 6.6914 secs using 299.3% CPU
Optimizing NNI: done in 7.48928 secs using 299.1% CPU
Iteration 160 / LogL: -195780.404 / Time: 0h:21m:58s (0h:8m:50s left)
Optimizing NNI: done in 7.31619 secs using 299.2% CPU
Optimizing NNI: done in 7.04386 secs using 299.3% CPU
Optimizing NNI: done in 7.85097 secs using 299.2% CPU
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Optimizing NNI: done in 6.26337 secs using 299.1% CPU
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Optimizing NNI: done in 7.51927 secs using 299.3% CPU
Optimizing NNI: done in 7.54658 secs using 299.1% CPU
Optimizing NNI: done in 7.40177 secs using 299.3% CPU
Iteration 170 / LogL: -195779.260 / Time: 0h:23m:13s (0h:7m:25s left)
Optimizing NNI: done in 7.37767 secs using 299.2% CPU
Optimizing NNI: done in 7.00767 secs using 299% CPU
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Optimizing NNI: done in 7.70926 secs using 299.3% CPU
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Optimizing NNI: done in 7.59346 secs using 299.1% CPU
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Optimizing NNI: done in 7.21021 secs using 299.1% CPU
Iteration 180 / LogL: -195829.848 / Time: 0h:24m:27s (0h:6m:0s left)
Optimizing NNI: done in 7.23394 secs using 299.1% CPU
Optimizing NNI: done in 8.75873 secs using 299% CPU
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Optimizing NNI: done in 6.6594 secs using 299.3% CPU
Optimizing NNI: done in 8.05524 secs using 299.2% CPU
Iteration 190 / LogL: -195793.640 / Time: 0h:25m:42s (0h:4m:37s left)
Optimizing NNI: done in 7.04204 secs using 298.9% CPU
Optimizing NNI: done in 7.13777 secs using 298.9% CPU
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Optimizing NNI: done in 6.93228 secs using 299.3% CPU
Optimizing NNI: done in 6.15344 secs using 299.2% CPU
Iteration 200 / LogL: -195911.793 / Time: 0h:26m:56s (0h:3m:14s left)
Optimizing NNI: done in 7.93087 secs using 298.9% CPU
Optimizing NNI: done in 7.9166 secs using 299% CPU
Optimizing NNI: done in 7.03574 secs using 299.1% CPU
Optimizing NNI: done in 7.41343 secs using 299.1% CPU
Optimizing NNI: done in 7.94795 secs using 299% CPU
Optimizing NNI: done in 7.37201 secs using 299.2% CPU
Optimizing NNI: done in 6.13298 secs using 299.3% CPU
Optimizing NNI: done in 6.318 secs using 299% CPU
Optimizing NNI: done in 6.19135 secs using 299.2% CPU
Optimizing NNI: done in 7.89653 secs using 298.9% CPU
Iteration 210 / LogL: -195971.741 / Time: 0h:28m:9s (0h:1m:53s left)
Optimizing NNI: done in 7.49898 secs using 299.2% CPU
Optimizing NNI: done in 7.11959 secs using 299.2% CPU
Optimizing NNI: done in 7.00408 secs using 299.3% CPU
Optimizing NNI: done in 7.66254 secs using 298.9% CPU
Optimizing NNI: done in 7.95043 secs using 299% CPU
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Optimizing NNI: done in 7.69179 secs using 299.2% CPU
Optimizing NNI: done in 7.68443 secs using 299.3% CPU
Optimizing NNI: done in 8.23133 secs using 298.9% CPU
Optimizing NNI: done in 8.71741 secs using 298.9% CPU
Iteration 220 / LogL: -195803.889 / Time: 0h:29m:26s (0h:0m:32s left)
Optimizing NNI: done in 7.1683 secs using 299.3% CPU
Optimizing NNI: done in 6.12048 secs using 299.4% CPU
Optimizing NNI: done in 7.39448 secs using 299% CPU
Optimizing NNI: done in 7.33138 secs using 299.2% CPU
Optimizing NNI: done in 6.77901 secs using 299.1% CPU
TREE SEARCH COMPLETED AFTER 225 ITERATIONS / Time: 0h:30m:1s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -195756.606
Optimal log-likelihood: -195756.601
Site proportion and rates:  (0.017,0.105) (0.059,0.275) (0.088,0.376) (0.237,0.546) (0.163,0.776) (0.195,1.018) (0.133,1.627) (0.108,2.579)
Parameters optimization took 1 rounds (2.108 sec)
BEST SCORE FOUND : -195756.601
Total tree length: 153.136

Total number of iterations: 225
CPU time used for tree search: 5167.194 sec (1h:26m:7s)
Wall-clock time used for tree search: 1747.560 sec (0h:29m:7s)
Total CPU time used: 5335.325 sec (1h:28m:55s)
Total wall-clock time used: 1803.796 sec (0h:30m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 97

Creating bootstrap alignment (seed: 579398)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.255 seconds

NOTE: 232 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -193896.683
2. Current log-likelihood: -191481.622
3. Current log-likelihood: -191454.593
4. Current log-likelihood: -191449.373
5. Current log-likelihood: -191442.149
6. Current log-likelihood: -191427.938
7. Current log-likelihood: -191420.046
8. Current log-likelihood: -191419.417
Optimal log-likelihood: -191419.392
Site proportion and rates:  (0.014,0.108) (0.037,0.234) (0.104,0.371) (0.275,0.550) (0.186,0.824) (0.157,1.113) (0.157,1.710) (0.070,2.911)
Parameters optimization took 8 rounds (28.928 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 20.0126 secs using 300% CPU
Computing ML distances took 20.013299 sec (of wall-clock time) 60.032328 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00224781 secs using 269.3% CPU
Constructing RapidNJ tree: done in 0.016433 secs using 372% CPU
Computing RapidNJ tree took 0.018748 sec (of wall-clock time) 0.068492 sec (of CPU time)
Log-likelihood of RapidNJ tree: -197293.673
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.058 second
Computing log-likelihood of 98 initial trees ... 25.488 seconds
Current best score: -191419.392

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.80346 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -190663.761
Optimizing NNI: done in 7.47843 secs using 299.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -190650.061
                                                   
******************************************************
CHECKPOINT: Resuming analysis from /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.ckp.gz

IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport
Seed:    228807 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Thu Jul 10 10:11:45 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta ... Fasta format detected
Reading fasta file: done in 0.00443387 secs using 91.21% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.00828505 secs using 4321% CPU
Alignment has 495 sequences with 575 columns, 575 distinct patterns
575 parsimony-informative, 0 singleton sites, 0 constant sites
            Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.000378847 secs using 4626% CPU
   1  8nJh6NUzJV   12.00%    passed     10.27%
   2  z0YCu0xtFo   11.30%    passed     15.88%
   3  1JN1q1h7Jh    8.35%    passed      9.02%
   4  E2n5Y5UQiG    8.52%    passed     43.28%
   5  cMoC1WsTO6    8.17%    failed      2.01%
   6  ys0DcEs0US    8.35%    passed     77.31%
   7  1s9qnaxMSp    9.04%    failed      2.14%
   8  FtHEpsU1vB    9.04%    failed      2.61%
   9  oeJuwbyE7Q    9.91%    passed      8.44%
  10  qCgVEYLhzI   17.39%    passed      9.43%
  11  zyhovbZkFP    9.91%    passed      8.44%
  12  jOk4aex96C   19.65%    passed      9.17%
  13  AR0npWZQ83    8.17%    passed     22.96%
  14  F5Si2gBtZe   21.91%    passed     13.69%
  15  FG021XCxMA   18.09%    passed     68.58%
  16  MCX7xygB2V    8.70%    passed     73.82%
  17  iVpOwiZzba    9.04%    passed     21.82%
  18  iPjBM3iYZR   80.35%    failed      2.62%
  19  qbFBJDOQUO    9.39%    passed     92.00%
  20  x5jv5lpB2O    9.22%    passed     43.94%
  21  y5M7y721WQ   11.30%    passed     52.45%
  22  MwDLYKIKBx   16.70%    passed     52.35%
  23  EsTTc2nPxQ    8.00%    passed     56.73%
  24  vnhywKRkFl   13.91%    passed     61.80%
  25  7JZdwvMv24   10.09%    passed     62.94%
  26  dQjyx7OIYV   27.30%    passed     66.63%
  27  irBovt5bLa    8.17%    passed     37.03%
  28  Ewm24Mlvnq    8.17%    failed      0.91%
  29  XDJ4JoLzyH   17.22%    passed     87.03%
  30  4kC0x0kjdn    7.65%    passed     35.61%
  31  RARcF60S6a    8.00%    passed     18.15%
  32  WlelCJO26H   12.17%    passed     15.31%
  33  mhk5OTojgz    7.83%    passed     22.72%
  34  pTM2DvE1xM    7.83%    passed     23.80%
  35  tlXXT5aWqu    8.35%    passed     25.18%
  36  TC8Xnd4iFa    8.35%    passed     68.65%
  37  02HhJs6pa3   11.13%    passed     51.90%
  38  NEeqpPtHg5    9.91%    passed     53.60%
  39  qbTDasygHV    8.00%    failed      4.34%
  40  7Yh1YhvFVC    9.04%    passed     82.42%
  41  VvE6sMyCv8    9.22%    passed     82.98%
  42  WjMMQYeUC2    9.74%    passed     28.42%
  43  W7Mh0FRDU6    9.57%    passed     47.24%
  44  2nrE64urGV    7.83%    failed      0.05%
  45  UzprTJ7K6d    7.83%    failed      0.07%
  46  UlwuxTyGoO    8.17%    passed     35.83%
  47  iaXjDyTif3    9.91%    passed     26.12%
  48  B6M0EvUDsT    8.17%    passed     57.64%
  49  1G5hXRghEG    7.83%    passed     46.06%
  50  gTvhxQmbWZ    7.83%    passed     59.90%
  51  8l37MLA1ms    7.83%    passed     66.42%
  52  vLizyHtRBL    6.96%    passed     45.67%
  53  S5ByYpGeqY    7.30%    passed     14.75%
  54  Fedl6T4xon    7.83%    passed     26.99%
  55  4BymctPkH6    9.22%    passed     90.46%
  56  s5wLZ9vWaO   22.96%    passed     14.42%
  57  awKrv6hUok    8.00%    failed      0.00%
  58  kWFqKgyYB3   18.61%    failed      0.35%
  59  DcYLS8gvW9    8.17%    passed     14.76%
  60  McRlo7Hy0B    8.35%    failed      1.15%
  61  tf71jZDs7S   14.78%    failed      0.00%
  62  vMqsZO8YaG   12.00%    passed     25.19%
  63  5AMYxNwgiK   14.26%    passed     72.77%
  64  wxoZBV0PHy    7.65%    passed     28.65%
  65  KeSH8I0Fea   10.96%    passed     34.97%
  66  KCrIGLQ7Q1    8.87%    passed     28.42%
  67  4LT0U0c0Do    8.17%    passed     45.98%
  68  CGeXrJPsGL    7.30%    passed     26.80%
  69  xxKiyIW1gr    8.35%    passed     42.35%
  70  xs9ieaVe53   24.17%    passed      5.89%
  71  NQWmJIpRFE    8.17%    passed     36.46%
  72  nkfchBpcgh    9.91%    passed     49.94%
  73  jdOhfl36g8    9.91%    passed     49.94%
  74  KVoy4GxdpT    8.70%    passed     30.77%
  75  WUIEff6ikU    9.74%    failed      3.44%
  76  coeQ6zHZ24    8.52%    passed     15.26%
  77  HWG7P94Eio    7.65%    passed     33.53%
  78  9Vw494DXPc    9.74%    passed     30.82%
  79  g6PJxKZvcf    8.17%    passed     67.92%
  80  AvvCKxHYp4    8.87%    passed     94.08%
  81  CemxIJafw8    8.87%    passed     94.94%
  82  dsBdLHptXN    7.30%    passed     26.31%
  83  4MVqW0qAIi    8.17%    passed      7.58%
  84  LcWgRv0iB6    8.17%    passed      6.57%
  85  fd8RtQX78T    8.35%    passed     67.99%
  86  D9LASQ998i    7.13%    passed     64.85%
  87  Uz7TnODNGf    8.17%    passed     61.10%
  88  Sp3Vq6QoAR   12.00%    passed     25.06%
  89  gtPloLimDb   14.61%    passed     16.69%
  90  GFnS6AyinZ   13.74%    passed     62.22%
  91  U9Eib0qR6X    9.39%    passed     80.44%
  92  dZ9ze414KZ    8.52%    passed     34.81%
  93  ydHAIeuwbW    9.04%    passed     24.32%
  94  e67HigPrjf    8.70%    passed     10.03%
  95  U5KrYXobqi    7.83%    passed     28.30%
  96  rqX0m8aZs1    8.52%    passed     74.68%
  97  JTOoSRn6ib    8.52%    passed     63.83%
  98  X4XbPR7Rfa    9.91%    passed     88.47%
  99  etCZH2Htco   11.30%    passed     96.50%
 100  7kS1ZU0pFM    9.74%    passed     63.62%
 101  rUnfYSLNJJ    8.35%    passed     25.59%
 102  YjqMqBCaiv    7.13%    passed     35.60%
 103  YXN7x6IbOx    8.35%    passed     52.18%
 104  bN8jt2Atwp   10.43%    passed     56.67%
 105  hgeyXdJgqq    9.22%    passed     56.85%
 106  1horVoEi3u    7.13%    failed      1.07%
 107  EDGqQf981n   10.09%    passed     86.16%
 108  3nDVNG9sKr   10.61%    passed     15.44%
 109  fFDoKaygf0    8.00%    passed     43.10%
 110  cRRsJgsBlZ    8.70%    passed     85.09%
 111  BI3jho3ECe    9.22%    passed     51.11%
 112  TIeppwLKSz    9.57%    passed     34.47%
 113  a8nt9ktZTC   24.35%    passed     70.98%
 114  GtfO72MtR2   22.26%    passed     65.46%
 115  xKzEmKT1dB   21.39%    passed     47.26%
 116  cTDPKciopP   11.83%    passed     67.98%
 117  xdNOUh7eMp    8.00%    passed     86.96%
 118  k3bzPFly41    8.17%    failed      0.00%
 119  ukUu00fP6L    9.39%    failed      0.29%
 120  up1UWJJzNf    9.22%    failed      3.36%
 121  GZASsy6wnT    8.17%    failed      0.00%
 122  PbkNCoK5ix   10.96%    passed     34.06%
 123  GfLEAInBd6   10.26%    passed     45.24%
 124  7OOuM97Qkr    8.70%    passed     42.00%
 125  d9kVhxwUcH    9.22%    passed     36.90%
 126  pn3nIof2qW    8.70%    passed     82.33%
 127  jYBcxGIen7   19.30%    passed     48.83%
 128  Y2YJcqt3IL   27.30%    passed     72.36%
 129  DQnwdMJsVl    9.39%    passed     17.77%
 130  Gvb4AsKEVi    8.35%    failed      0.00%
 131  d5E6EHDpwi    7.65%    passed     78.94%
 132  yA69Aemq0C    9.57%    passed     51.08%
 133  9f7AMvazZf    8.70%    passed     87.18%
 134  tD3ewCYOQG    9.22%    passed     39.14%
 135  yHwEtbE4JZ    8.87%    passed     51.50%
 136  HZpFQAW00k   12.87%    passed     16.94%
 137  FCPk6mdvI6    8.35%    passed     85.41%
 138  C50stY8CeY    9.22%    passed     15.26%
 139  WQOxpzhoLN    8.17%    passed     95.19%
 140  lU6fN5cAZQ   16.87%    passed     26.00%
 141  w34zJrGIvJ   13.04%    passed     46.23%
 142  R4SazYxajJ   13.22%    passed     24.74%
 143  oyLJTIsT1Z   12.00%    passed     35.61%
 144  95FTGjmRiw   16.87%    passed     10.92%
 145  MVSYHU9DCt   12.17%    passed     83.71%
 146  RhS1O12ekg    8.52%    passed     98.08%
 147  sthKhyT8fy    9.04%    passed     79.34%
 148  O2gQ2myCZn   11.30%    passed     66.29%
 149  B7PVgc3v8q    8.52%    passed     67.20%
 150  FlAHhYz62Q    6.96%    passed     92.12%
 151  PZqL2meUHi    8.35%    passed     89.55%
 152  XJTzBvD6pQ    8.70%    passed     73.32%
 153  FtEYGIUfBM   10.78%    passed     55.74%
 154  NUAWacASLt   10.26%    passed     81.70%
 155  3FdA2TKbHR   10.26%    passed     77.97%
 156  TCgaJethwm    9.74%    passed     51.49%
 157  V8Ort0OUIV    9.39%    passed     75.80%
 158  gKxOBa9lC3   80.35%    failed      4.37%
 159  ZJBcyycwk4   21.91%    passed     83.00%
 160  BXOEqGyzK2    9.04%    passed     82.96%
 161  5yy8DKtZ5c   12.35%    passed     70.92%
 162  cY7oeSnppq    9.74%    passed     78.00%
 163  vUEx5gqasN    9.74%    passed     22.71%
 164  2jCJDig3v9   17.39%    passed     45.79%
 165  lzBWRCtyx0   17.39%    passed     45.79%
 166  DBMxujRgHK   10.43%    passed     76.44%
 167  x3ZrH0XGfQ   13.04%    passed     40.57%
 168  SgWCfVzTG4    9.39%    passed     23.64%
 169  f62ksK5UEj   33.39%    passed     48.62%
 170  hkIztfSCD1   10.09%    passed     60.28%
 171  iRnB4M1GLD   11.30%    passed     35.88%
 172  CU0XuCnsFL   42.61%    failed      1.05%
 173  42tdKq8PSX   12.87%    passed     50.93%
 174  gXeZ52LCvM   12.87%    passed     50.93%
 175  u8cLLIfWEX   12.87%    passed     50.93%
 176  dmOh7r7eKT   12.52%    passed     43.59%
 177  3c6hZoOqvP   12.87%    passed     51.70%
 178  bu2UDzewiZ   16.35%    passed     97.52%
 179  SYc4eSftSt    7.30%    passed     55.76%
 180  zlSzVB3W0P    9.91%    passed     23.47%
 181  3C2pM8OlsA   16.00%    passed     44.07%
 182  Pxcz4xw4KG    8.52%    passed     89.90%
 183  UcghE30qVq   10.26%    passed     98.72%
 184  qIB6gS9bgA   10.26%    passed     99.50%
 185  UDehzYJL1w    9.91%    passed     84.08%
 186  BB4241mZBL    9.74%    passed     18.51%
 187  c6c8r06RzT   14.09%    passed     51.46%
 188  XQT9xr4ybf   14.09%    passed     51.46%
 189  SCnTy3bpY1   12.00%    passed     52.85%
 190  jev8yDUHvc   37.22%    passed     46.96%
 191  bK3G4lRT3G    9.74%    passed     18.84%
 192  Z5XH3L582l    9.39%    passed     64.30%
 193  dhUTnrRr7d    9.04%    passed     17.65%
 194  2ifGWJmasz   13.39%    passed     53.39%
 195  WB36HQui6V   13.22%    passed     13.09%
 196  QNNkPiHWnJ   13.57%    passed     15.99%
 197  WHGNQkrc10   16.70%    passed     15.42%
 198  h5LGHiiOXm   13.04%    passed      8.14%
 199  3zhlkwsAL6   11.65%    passed     68.02%
 200  i2Lb0rchl2   17.74%    passed     40.76%
 201  yMqx9t1LVd   11.83%    passed     95.23%
 202  2W3WY0vBww   18.09%    passed     31.19%
 203  wTTqfzkYo6   12.35%    passed     65.69%
 204  0vKBWD6wpY   19.83%    passed     72.14%
 205  SJgohIdqev   13.04%    passed     56.62%
 206  9DPLpYQWNv    8.35%    passed     79.37%
 207  8uUTsKFjlb    9.74%    passed     57.77%
 208  xVujdvY6Nr   15.65%    passed     86.08%
 209  NImtrhZGKE   18.61%    passed     29.08%
 210  YugOzGk8Ov    8.00%    passed     61.92%
 211  DeWEtikGbq    9.39%    passed     58.48%
 212  x0olbpog9B   10.78%    failed      3.15%
 213  pAhidh8xBZ    9.22%    passed     20.39%
 214  PlPvNaQDzl   78.26%    failed      2.70%
 215  NPvXCeLNmx    9.22%    passed     19.23%
 216  yVup7G0SEF    9.39%    passed      5.94%
 217  vPQhR8sENE    9.22%    passed     25.50%
 218  nU2WbHAcGl    8.00%    passed     38.25%
 219  5LDURAlPH2   18.96%    passed     93.03%
 220  BWFcvfZnO3   19.83%    passed     80.72%
 221  pygYFVFfpx   18.96%    passed     64.25%
 222  SHqN6p0dYV   11.65%    passed     77.47%
 223  qsVXrYaG9q   16.52%    passed     62.49%
 224  3cAaekWMpW   17.57%    passed     67.41%
 225  N40B32hpg1   12.00%    passed     79.79%
 226  JPT5lhIP82   16.17%    passed     61.51%
 227  ZLXDnoVm6b    8.87%    passed     65.21%
 228  X85YtZdfkf    9.04%    passed     76.50%
 229  8UiTG47Ec2    9.04%    passed     76.50%
 230  rIeH6RocN2   11.13%    passed     16.99%
 231  JEeirH12E1   31.48%    passed     21.21%
 232  UzAtwShlJN   15.48%    failed      0.00%
 233  2pVvPoBi2c   15.65%    failed      0.00%
 234  scQ10Wo461   39.13%    passed     23.66%
 235  Nb1rJKftmp   17.91%    failed      0.00%
 236  nhoqJOOPX2   17.04%    passed     88.57%
 237  39gkmZTScW   18.26%    passed     91.96%
 238  BGkr4JUYAf   13.39%    passed     93.93%
 239  DulbVCzsEt   24.35%    passed     66.60%
 240  cSruxLJuyQ   26.96%    passed     10.64%
 241  1XfSwqn4ef   25.04%    passed     39.48%
 242  96xj01KeXJ   68.17%    passed     84.97%
 243  eq1zGc6rtT   29.04%    passed     18.35%
 244  VfUM5i9jsn   41.91%    failed      4.66%
 245  20sicocoSo   23.83%    failed      0.74%
 246  RLpJhYeIPE   25.91%    passed     47.76%
 247  C8YPeCC1NI   28.87%    passed     14.80%
 248  xxnHHiKI8Z   28.52%    passed      5.76%
 249  3Je7M7o4rZ   33.39%    passed     11.10%
 250  47EKfQlPcw   28.35%    passed     38.14%
 251  9C0byE309K   34.43%    passed     22.05%
 252  TsIfWQzrph   28.35%    passed     38.14%
 253  hTPGiqrFV4   42.09%    passed     88.30%
 254  aFMglfB8eH   24.52%    passed     15.36%
 255  JQcRFbokY2   28.35%    passed     32.19%
 256  jFdaAxFg6n   23.13%    passed     47.94%
 257  KRYbednenZ   23.13%    passed     42.60%
 258  FyIDyqrLwr   23.13%    passed     47.94%
 259  8XGfcNsQ09   23.83%    passed     62.09%
 260  QyNf0mVNlz   23.83%    passed     10.54%
 261  f9oKgpE1wE   23.48%    passed     56.82%
 262  REBVZFiPEf   23.30%    passed     27.01%
 263  ItesG8T6sN   23.83%    passed     47.79%
 264  TSGS90hx1G   23.30%    passed     24.55%
 265  ZRAzqCtrNA   24.17%    passed     57.76%
 266  eeM5JHuVuf   24.35%    passed     50.06%
 267  oe9Vawfrxg   24.35%    passed     26.16%
 268  rgglFfiKnC   28.00%    passed     45.26%
 269  bCjdcpAF4v   24.00%    passed     70.09%
 270  OmcerY3zVm   64.35%    passed     66.28%
 271  zcG6I9U7zt   43.13%    passed     73.90%
 272  QKniumy84t   24.00%    passed     71.91%
 273  158IGk2w8A   24.00%    passed     40.59%
 274  kI8iG2U2gQ   23.30%    passed     85.81%
 275  fPZNEk39Af   26.78%    passed     15.99%
 276  hrBvV4AmlN   24.17%    passed     20.25%
 277  myGUzZ8LDH   24.00%    passed     24.24%
 278  sHkv5UU91e   23.65%    passed     10.45%
 279  GNzRUX9ddm   23.65%    passed     13.36%
 280  zsnvwGvGgv   24.00%    passed     30.90%
 281  9OoygEJxNJ   23.13%    passed     19.47%
 282  IjtzwwEpZt   24.70%    passed     32.04%
 283  nSDhHtKOaz   76.87%    passed     72.40%
 284  A0R7Dl6WnL   24.00%    passed     27.63%
 285  CvviaWP5QG   24.17%    passed     57.70%
 286  pPSEGFgq5j   79.13%    passed     12.51%
 287  UdG6KQNIp6   24.52%    passed      9.66%
 288  8EVSPtaAhX   24.35%    passed     42.22%
 289  uiafGbGfwA   27.30%    passed     85.86%
 290  XZFyxFJmTO   24.70%    passed     34.27%
 291  H6HkWi4jLJ   26.26%    passed     57.81%
 292  uALm9y36Bq   28.70%    passed     22.86%
 293  EUEmaNv0jU   23.30%    passed     16.64%
 294  miFIpMQUO8   25.04%    passed      5.34%
 295  qsWsb5TOjf   26.09%    passed     11.23%
 296  WLDkRifOr1   25.74%    passed     31.25%
 297  u7RGaLBmh5   25.74%    passed     85.68%
 298  n4n2Sa9hou   25.39%    passed     53.48%
 299  gZV6bt6UCn   24.17%    passed     46.31%
 300  PortTSlpTI   41.74%    passed     26.87%
 301  2Nn52BMVGD   28.00%    passed     32.50%
 302  sQl8vIYhWL   27.30%    passed     24.87%
 303  nlyynuwvAY   27.13%    passed     84.06%
 304  iM9z6TKAcr   41.39%    passed     18.69%
 305  pVpmbqWKfw   36.70%    failed      1.72%
 306  r4JpMWXYFJ   26.09%    passed     11.04%
 307  CcX8oiPHcg   27.83%    passed     27.83%
 308  G2BVFEVILA   25.04%    passed     61.18%
 309  BNYVmW4TYG   25.91%    passed     54.90%
 310  ExQ8uNPj7h   34.26%    passed     66.82%
 311  whmj06xoF5   28.17%    failed      0.02%
 312  VqFVtnHfVy   25.22%    passed     79.18%
 313  Mqy8imXZ6G   25.91%    failed      0.02%
 314  s0NXcs97L3   25.91%    failed      0.02%
 315  Iqt8ZiOu6k   25.74%    failed      0.00%
 316  XsWTxkH1p7   25.57%    passed     19.64%
 317  zoRaGfFB7U   24.52%    passed     48.77%
 318  qqN1dh1OOy   24.35%    passed     14.36%
 319  T1wQDvF98B   24.35%    passed      7.77%
 320  lkTsXyry76   26.43%    passed     26.11%
 321  hSqg5YYyOm   27.48%    failed      0.44%
 322  puRVWMvppN   28.35%    passed     22.55%
 323  1LbFAdgLuC   25.74%    passed     11.73%
 324  y5MmiioIHk   25.91%    failed      1.83%
 325  BnR8odZPBs   25.91%    passed     15.58%
 326  ajGvkpi5As   25.91%    passed      8.73%
 327  qbTJcwpdwP   26.61%    passed     13.99%
 328  vCxAIjCqNl   24.87%    passed     46.42%
 329  mPlwp1JlUK   27.30%    passed     36.54%
 330  rYWDHuLHvt   29.91%    failed      1.32%
 331  C0RnyRzFMX   71.65%    passed     45.95%
 332  7Aa2sW2uFn   28.00%    failed      3.36%
 333  0djEp2FhF9   28.00%    failed      3.36%
 334  l1pN6WjG1N   80.17%    passed     21.40%
 335  XLgmciWSgo   46.09%    passed     14.00%
 336  D8WaLv1pNN   30.78%    passed     27.06%
 337  12VY0qcAbu   29.39%    passed     74.33%
 338  JNoGNci0kO   28.87%    passed     95.56%
 339  VGEALS8WvR   40.70%    passed     16.49%
 340  D7iWRjKQ8X   25.74%    passed     47.65%
 341  upEmmPcbTB   27.48%    passed     22.48%
 342  UpKcpH8xp2   26.78%    passed      7.74%
 343  hreWbDAWDh   23.65%    passed      8.09%
 344  5oPFYbGk9x   24.52%    passed     66.68%
 345  bKMx8usLZf   35.83%    passed      9.39%
 346  9waTHuOjG2   43.48%    passed     27.73%
 347  y13PUGF6fd   29.39%    passed     50.29%
 348  MCxeCrj6og   25.22%    passed     77.92%
 349  JqQlZRu8jp   25.91%    passed     38.60%
 350  ZrMp8mhVn3   56.35%    passed      9.73%
 351  PVum0t8D9w   48.52%    failed      3.01%
 352  mA0FIy0SqW   24.70%    passed      5.42%
 353  EacivjsFt1   26.61%    passed     43.72%
 354  FKAuFXjrK2   29.57%    failed      2.12%
 355  eOn8Fw1qPv   27.48%    failed      3.53%
 356  D0XDiTOIfD   34.78%    passed      9.81%
 357  910hgdbBRd   28.00%    passed     51.49%
 358  ijUTPEstS6   33.39%    passed     28.87%
 359  bUU4czn7NG   27.83%    passed     60.40%
 360  INEhHLWnmb   37.04%    failed      1.97%
 361  LMA81zzKSe   37.04%    failed      0.01%
 362  TUCOIK4ZQn   33.91%    failed      0.52%
 363  yvso4goGdQ   34.96%    failed      4.00%
 364  YWPX00OZwF   36.00%    failed      3.54%
 365  qKqJ6yzKtT   34.61%    passed     10.13%
 366  49Qin0CHkb   34.61%    passed      9.62%
 367  63Q15egMZA   34.26%    passed      6.18%
 368  nWYlGrbPPc   34.61%    failed      4.67%
 369  JvcE4PBExA   33.74%    passed      7.73%
 370  LUlT7ehgwb   36.00%    passed     26.12%
 371  pVpykOHqYZ   39.48%    failed      0.85%
 372  v2K68153zf   38.26%    failed      0.55%
 373  qYhA4tEOW1   34.78%    failed      0.03%
 374  grGtjFUUTt   34.43%    failed      0.23%
 375  qWhSnx7aMf   44.87%    passed      5.50%
 376  v1oAyLSJtz   50.96%    passed     28.72%
 377  BadtzwpMMs   38.43%    passed      9.62%
 378  6DLNJCEk13   34.61%    passed      8.29%
 379  w2DOMr7ED6   41.39%    failed      3.23%
 380  JK0CadwxtV   33.74%    failed      1.62%
 381  thXzqzsTWd   33.04%    failed      4.58%
 382  cza9cyArKR   33.04%    failed      3.45%
 383  64i2bPRqyf   38.09%    failed      1.24%
 384  Tu05kR9iNy   35.30%    failed      2.13%
 385  ryyuwN9EeF   35.83%    failed      3.08%
 386  9i9iYEz14b   36.87%    passed     43.29%
 387  e5Z7VURlcd   56.00%    failed      0.95%
 388  ndIdlcACpn   34.61%    failed      0.11%
 389  miylOtOHke   36.00%    passed      5.91%
 390  jGxqmOPSFz   33.91%    failed      1.22%
 391  UpRnjomc4O   36.17%    passed     26.63%
 392  ebCUnMXr2f   38.43%    passed     15.56%
 393  21yjS1P784   34.43%    failed      0.27%
 394  XU8ct59Imq   34.26%    failed      0.70%
 395  mWu9nYUMB2   34.26%    passed      5.63%
 396  6N8VC2LDv6   34.26%    passed      5.63%
 397  Tp4oCldie4   38.09%    failed      4.42%
 398  LdahhT5atZ   34.26%    passed      5.63%
 399  ohdNT1wCFZ   34.26%    passed      7.14%
 400  QY3dkiwN48   41.57%    failed      3.72%
 401  Ip06mTdO2e   35.65%    failed      2.00%
 402  P5RXO2szhK   29.57%    passed     33.39%
 403  offjx75l6X   85.22%    passed     26.57%
 404  EdOuOhohBn   33.91%    passed     23.13%
 405  ZjYUAXvbUC   34.26%    passed      8.29%
 406  lpxtOw9xf3   36.52%    passed     12.71%
 407  4bSmqRgfRI   34.09%    passed     12.39%
 408  gminDyGtcG   34.78%    failed      2.44%
 409  lDQWwcBkMU   34.78%    passed     33.99%
 410  CUTMeJuwSv   33.74%    passed     78.03%
 411  OI80q3iM3F   33.74%    passed     81.17%
 412  xnKco929hT   37.57%    passed      8.65%
 413  RPfcmWXHCA   37.57%    passed     20.91%
 414  6mj1jZTKcU   36.17%    failed      4.67%
 415  Gr87dxYVyz   43.83%    failed      4.55%
 416  VGvhdii6IX   73.22%    passed     54.33%
 417  wJTuSg6Gc6   35.65%    passed     75.44%
 418  K3Flz6km5g   35.65%    passed     71.14%
 419  Tu0u89fzoU   35.48%    passed     16.33%
 420  IpceOBVrBQ   35.48%    passed     13.04%
 421  JAjUuwFnV7   36.35%    passed     34.52%
 422  wSnvqYXqTg   32.00%    passed     24.03%
 423  keWKiDv5J1   36.35%    passed     23.38%
 424  r5NSp8dbtM   37.39%    passed     32.60%
 425  wxLKLb6SMC   35.13%    passed     25.74%
 426  qw6gF6ZapY   35.13%    passed     25.74%
 427  ZGvDd4xvwy   37.91%    passed     30.11%
 428  8lXCZuvq8q   34.26%    passed     25.11%
 429  qvg1my8Wlp   48.70%    failed      3.30%
 430  ZdWaANa0Et   32.87%    passed      6.04%
 431  Onz2iyjxH3   42.96%    failed      0.02%
 432  AJImOJUang   66.09%    passed      8.67%
 433  rbo3OKIe4x   36.52%    failed      0.54%
 434  pGufZSTMNB   36.52%    passed     12.14%
 435  FLjy3W79tg   36.52%    passed     17.85%
 436  jYaSjXdhUR   34.78%    passed     22.31%
 437  HGW1EoyaVz   49.22%    passed     75.08%
 438  HQpmvbcKV0   36.35%    passed     71.28%
 439  Us22uQdloc   73.22%    passed     88.61%
 440  Nczi5Cos47   34.96%    passed     68.86%
 441  IV8TgD1mQj   36.52%    passed     65.05%
 442  QKsY8kV1rB   34.43%    passed     49.51%
 443  TrIc96BqkG   34.96%    passed      7.64%
 444  pnjqLcOivm   34.61%    passed      9.34%
 445  SY2alUymun   36.00%    passed     31.87%
 446  GXBps2FgSH   37.57%    failed      4.23%
 447  ZldeYJmzLx   39.48%    failed      0.13%
 448  8biR24Gazc   33.91%    passed     22.85%
 449  NBJ6cvHYoU   34.43%    passed     22.55%
 450  egq7pHRqeL   38.78%    passed     36.06%
 451  y0r2SVxwqI   35.30%    passed     55.80%
 452  evUBWmPjS2   35.30%    passed     23.87%
 453  ikh1qtxydC   36.00%    failed      2.62%
 454  BRdJ9RHZQj   35.65%    passed      8.09%
 455  l25CgIsmfn   35.65%    passed      8.09%
 456  XPdvjShyOo   37.57%    passed      7.82%
 457  M144qciIKM   34.96%    passed     30.15%
 458  BnE96TDyk8   35.48%    passed     26.42%
 459  jeohLZ0eYF   36.87%    failed      0.20%
 460  YvoxlQmxl7   36.87%    failed      0.20%
 461  R0wuUn8J0h   33.57%    passed     30.51%
 462  oeFPRaQBYZ   33.39%    passed     26.87%
 463  xqlhblg6dL   33.91%    passed     25.42%
 464  6Qs9p4Rx4f   34.09%    passed     25.71%
 465  QPlyWfEtzz   34.43%    passed     29.56%
 466  Yo6roMcRLy   35.30%    passed     25.15%
 467  PwuAxgsPD6   42.78%    passed     42.46%
 468  vaFUdeGB10   33.91%    failed      2.49%
 469  8GM1psnK6y   36.87%    failed      0.09%
 470  E6RVlyXu6C   33.74%    passed     45.21%
 471  SuF6hGymBQ   36.00%    failed      2.74%
 472  cgJCegWwAr   70.96%    passed     99.24%
 473  i10ONbBPRV   34.96%    passed     50.77%
 474  FaaaR0oHe4   35.13%    passed     47.29%
 475  RrNP3l8SS7   36.52%    failed      0.47%
 476  BuFyz2PMN4   34.43%    passed     49.11%
 477  Y10Qa1Da4V   38.78%    passed     65.87%
 478  8zkzdNvfM0   34.43%    passed     49.11%
 479  rA4KjQCVx3   32.00%    passed     90.85%
 480  au044S3YHW   35.30%    passed     43.12%
 481  cIR66o13VD   35.65%    passed     81.03%
 482  fkB1xaD3I7   35.83%    passed     66.46%
 483  CwGGcZADEn   35.30%    passed     25.37%
 484  fNHflelF6b   34.61%    passed     14.83%
 485  8zGWBmbKDs   83.65%    passed     77.32%
 486  LC2TsjjWfV   35.65%    passed     44.42%
 487  rsgxiUIZDl   41.74%    passed     41.79%
 488  Srvt2UziZu   34.43%    passed     97.83%
 489  zPT9rylEFV   34.43%    passed     97.83%
 490  rXls0PgjJv   35.48%    passed      5.47%
 491  TcLIjpisFo   51.83%    passed     29.28%
 492  RMfRwwtcqL   32.17%    passed      5.11%
 493  zzJMOnIGaE   34.09%    failed      0.02%
 494  bkj6PiDj99   34.78%    passed     36.79%
 495  QPtDeO8Fse   34.61%    passed     64.43%
WARNING: 19 sequences contain more than 50% gaps/ambiguity
****  TOTAL        23.94%  82 sequences failed composition chi2 test (p-value<5%; df=19)
CHECKPOINT: 96 bootstrap analyses restored

NOTE: Restoring information from model checkpoint file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz

CHECKPOINT: Initial tree restored
Measuring multi-threading efficiency up to 96 CPU cores
Increase to 10 rounds for branch lengths
25 trees examined
Threads: 1 / Time: 99.200 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -470941
Threads: 2 / Time: 59.078 sec / Speedup: 1.679 / Efficiency: 84% / LogL: -470941
Threads: 3 / Time: 50.732 sec / Speedup: 1.955 / Efficiency: 65% / LogL: -470941
Threads: 4 / Time: 46.396 sec / Speedup: 2.138 / Efficiency: 53% / LogL: -470941
Threads: 5 / Time: 39.263 sec / Speedup: 2.527 / Efficiency: 51% / LogL: -470941
Threads: 6 / Time: 39.833 sec / Speedup: 2.490 / Efficiency: 42% / LogL: -470941
Determining AUTO threadcount: done in 334.557 secs using 296.9% CPU
BEST NUMBER OF THREADS: 5

Perform fast likelihood tree search using LG+G model...
CHECKPOINT: Tree restored, LogL: -195489.756
NOTE: ModelFinder requires 455 MB RAM!
ModelFinder will test up to 616 protein models (sample size: 575) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  LG            200322.611   987 402619.222   2352931.222  406916.985
  2  LG+G4         195470.344   988 392916.688   2347180.688  397218.805
  3  LG+R2         196589.598   989 395157.196   2353377.196  399463.668
  4  LG+R3         195780.340   991 393542.681   2359686.681  397857.862
  5  LG+R4         195429.122   993 392844.244   2366928.244  397168.133
  6  LG+R5         195312.276   995 392614.553   2374654.553  396947.151
  7  LG+R6         195240.929   997 392475.859   2382487.859  396817.166
  8  LG+R7         195209.395   999 392416.790   2390416.790  396766.806
  9  LG+R8         195184.144   1001 392370.288   2398374.288  396729.013
 10  LG+R9         195175.348   1003 392356.697   2406380.697  396724.130
 11  LG+R10        195171.997   1005 392353.994   2414413.994  396730.135
 20  LG+F+R8       194402.294   1020 390844.587   2473684.587  395286.045
 21  LG+F+R9       194396.917   1022 390837.834   2481849.834  395288.000
 31  WAG+R8        196252.507   1001 394507.014   2400511.014  398865.738
 32  WAG+R9        196242.300   1003 394490.599   2408514.599  398858.033
 33  WAG+R10       196241.628   1005 394493.256   2416553.256  398869.398
 42  WAG+F+R8      194842.645   1020 391725.291   2474565.291  396166.748
 43  WAG+F+R9      194839.005   1022 391722.011   2482734.011  396172.177
 53  JTT+R8        195608.757   1001 393219.514   2399223.514  397578.238
 54  JTT+R9        195593.125   1003 393192.250   2407216.250  397559.683
 55  JTT+R10       195590.207   1005 393190.414   2415250.414  397566.556
 64  JTT+F+R8      194695.864   1020 391431.729   2474271.729  395873.186
 65  JTT+F+R9      194690.743   1022 391425.486   2482437.486  395875.652
WARNING: Normalizing state frequencies so that sum of them equals to 1
 75  Q.pfam+R8     194892.568   1001 391787.135   2397791.135  396145.860
WARNING: Normalizing state frequencies so that sum of them equals to 1
 76  Q.pfam+R9     194887.665   1003 391781.330   2405805.330  396148.763
WARNING: Normalizing state frequencies so that sum of them equals to 1
 86  Q.pfam+F+R8   194521.401   1020 391082.801   2473922.801  395524.259
WARNING: Normalizing state frequencies so that sum of them equals to 1
 87  Q.pfam+F+R9   194515.431   1022 391074.862   2482086.862  395525.029
WARNING: Normalizing state frequencies so that sum of them equals to 1
 97  Q.bird+R8     197829.393   1001 397660.786   2403664.786  402019.511
WARNING: Normalizing state frequencies so that sum of them equals to 1
 98  Q.bird+R9     197820.275   1003 397646.550   2411670.550  402013.983
WARNING: Normalizing state frequencies so that sum of them equals to 1
 99  Q.bird+R10    197814.318   1005 397638.636   2419698.636  402014.778
WARNING: Normalizing state frequencies so that sum of them equals to 1
108  Q.bird+F+R8   198079.035   1020 398198.069   2481038.069  402639.527
WARNING: Normalizing state frequencies so that sum of them equals to 1
109  Q.bird+F+R9   198072.616   1022 398189.232   2489201.232  402639.398
WARNING: Normalizing state frequencies so that sum of them equals to 1
110  Q.bird+F+R10  198068.569   1024 398185.139   2497385.139  402644.014
WARNING: Normalizing state frequencies so that sum of them equals to 1
119  Q.mammal+R8   196715.407   1001 395432.814   2401436.814  399791.538
WARNING: Normalizing state frequencies so that sum of them equals to 1
120  Q.mammal+R9   196707.402   1003 395420.804   2409444.804  399788.237
WARNING: Normalizing state frequencies so that sum of them equals to 1
121  Q.mammal+R10  196703.479   1005 395416.958   2417476.958  399793.100
WARNING: Normalizing state frequencies so that sum of them equals to 1
130  Q.mammal+F+R8 196877.834   1020 395795.669   2478635.669  400237.126
WARNING: Normalizing state frequencies so that sum of them equals to 1
131  Q.mammal+F+R9 196872.663   1022 395789.327   2486801.327  400239.493
141  Q.insect+R8   195081.318   1001 392164.635   2398168.635  396523.360
142  Q.insect+R9   195076.551   1003 392159.102   2406183.102  396526.535
152  Q.insect+F+R8 194860.269   1020 391760.539   2474600.539  396201.996
153  Q.insect+F+R9 194858.288   1022 391760.576   2482772.576  396210.742
WARNING: Normalizing state frequencies so that sum of them equals to 1
163  Q.plant+R8    194919.373   1001 391840.745   2397844.745  396199.470
WARNING: Normalizing state frequencies so that sum of them equals to 1
164  Q.plant+R9    194913.090   1003 391832.180   2405856.180  396199.613
WARNING: Normalizing state frequencies so that sum of them equals to 1
174  Q.plant+F+R8  194822.604   1020 391685.208   2474525.208  396126.665
WARNING: Normalizing state frequencies so that sum of them equals to 1
175  Q.plant+F+R9  194819.592   1022 391683.184   2482695.184  396133.350
WARNING: Normalizing state frequencies so that sum of them equals to 1
185  Q.yeast+R8    195446.700   1001 392895.400   2398899.400  397254.125
WARNING: Normalizing state frequencies so that sum of them equals to 1
186  Q.yeast+R9    195439.881   1003 392885.762   2406909.762  397253.195
WARNING: Normalizing state frequencies so that sum of them equals to 1
187  Q.yeast+R10   195435.549   1005 392881.097   2414941.097  397257.239
WARNING: Normalizing state frequencies so that sum of them equals to 1
196  Q.yeast+F+R8  194579.068   1020 391198.136   2474038.136  395639.593
WARNING: Normalizing state frequencies so that sum of them equals to 1
197  Q.yeast+F+R9  194573.538   1022 391191.077   2482203.077  395641.243
207  JTTDCMut+R8   195684.064   1001 393370.127   2399374.127  397728.852
208  JTTDCMut+R9   195667.689   1003 393341.377   2407365.377  397708.810
209  JTTDCMut+R10  195664.727   1005 393339.454   2415399.454  397715.596
218  JTTDCMut+F+R8 194737.502   1020 391515.003   2474355.003  395956.461
219  JTTDCMut+F+R9 194732.541   1022 391509.083   2482521.083  395959.249
229  DCMut+R8      198858.399   1001 399718.798   2405722.798  404077.523
230  DCMut+R9      198850.908   1003 399707.816   2413731.816  404075.249
231  DCMut+R10     198848.803   1005 399707.606   2421767.606  404083.748
240  DCMut+F+R8    196826.536   1020 395693.071   2478533.071  400134.529
241  DCMut+F+R9    196816.360   1022 395676.721   2486688.721  400126.887
242  DCMut+F+R10   196813.450   1024 395674.901   2494874.901  400133.776
251  VT+R8         196235.054   1001 394472.109   2400476.109  398830.833
252  VT+R9         196229.175   1003 394464.350   2408488.350  398831.783
262  VT+F+R8       195084.460   1020 392208.920   2475048.920  396650.377
263  VT+F+R9       195080.573   1022 392205.145   2483217.145  396655.311
273  PMB+R8        197315.374   1001 396632.748   2402636.748  400991.472
274  PMB+R9        197308.918   1003 396623.836   2410647.836  400991.269
275  PMB+R10       197306.392   1005 396622.785   2418682.785  400998.926
284  PMB+F+R8      197173.282   1020 396386.563   2479226.563  400828.020
285  PMB+F+R9      197172.042   1022 396388.084   2487400.084  400838.251
295  Blosum62+R8   197539.412   1001 397080.824   2403084.824  401439.549
296  Blosum62+R9   197530.232   1003 397066.464   2411090.464  401433.897
297  Blosum62+R10  197526.017   1005 397062.034   2419122.034  401438.175
306  Blosum62+F+R8 196901.090   1020 395842.180   2478682.180  400283.637
307  Blosum62+F+R9 196899.776   1022 395843.552   2486855.552  400293.718
317  Dayhoff+R8    198852.273   1001 399706.545   2405710.545  404065.270
318  Dayhoff+R9    198844.881   1003 399695.761   2413719.761  404063.195
319  Dayhoff+R10   198842.886   1005 399695.772   2421755.772  404071.914
328  Dayhoff+F+R8  196817.472   1020 395674.945   2478514.945  400116.402
329  Dayhoff+F+R9  196807.436   1022 395658.873   2486670.873  400109.039
330  Dayhoff+F+R10 196804.462   1024 395656.923   2494856.923  400115.798
339  mtREV+R8      202211.703   1001 406425.405   2412429.405  410784.129
340  mtREV+R9      202203.018   1003 406412.035   2420436.035  410779.468
341  mtREV+R10     202198.737   1005 406407.475   2428467.475  410783.617
350  mtREV+F+R8    197257.838   1020 396555.675   2479395.675  400997.133
351  mtREV+F+R9    197248.935   1022 396541.871   2487553.871  400992.037
352  mtREV+F+R10   197245.156   1024 396538.312   2495738.312  400997.187
361  mtART+R8      203583.239   1001 409168.478   2415172.478  413527.203
362  mtART+R9      203529.654   1003 409065.309   2423089.309  413432.742
363  mtART+R10     203525.582   1005 409061.164   2431121.164  413437.306
372  mtART+F+R8    200433.253   1020 402906.506   2485746.506  407347.963
373  mtART+F+R9    200385.741   1022 402815.481   2493827.481  407265.647
374  mtART+F+R10   200379.364   1024 402806.728   2502006.728  407265.603
383  mtZOA+R8      198366.129   1001 398734.257   2404738.257  403092.982
384  mtZOA+R9      198360.117   1003 398726.235   2412750.235  403093.668
394  mtZOA+F+R8    196919.533   1020 395879.066   2478719.066  400320.523
395  mtZOA+F+R9    196898.434   1022 395840.867   2486852.867  400291.033
396  mtZOA+F+R10   196891.474   1024 395830.948   2495030.948  400289.823
405  mtMet+R8      200042.427   1001 402086.853   2408090.853  406445.578
406  mtMet+R9      200019.941   1003 402045.882   2416069.882  406413.316
407  mtMet+R10     200049.839   1005 402109.679   2424169.679  406485.821
416  mtMet+F+R8    196455.394   1020 394950.789   2477790.789  399392.246
417  mtMet+F+R9    196440.614   1022 394925.229   2485937.229  399375.395
418  mtMet+F+R10   196431.320   1024 394910.641   2494110.641  399369.516
427  mtVer+R8      203014.713   1001 408031.426   2414035.426  412390.150
428  mtVer+R9      203008.014   1003 408022.029   2422046.029  412389.462
429  mtVer+R10     202969.843   1005 407949.685   2430009.685  412325.827
438  mtVer+F+R8    198883.127   1020 399806.254   2482646.254  404247.711
439  mtVer+F+R9    198874.584   1022 399793.168   2490805.168  404243.334
440  mtVer+F+R10   198869.999   1024 399787.998   2498987.998  404246.873
449  mtInv+R8      200418.426   1001 402838.852   2408842.852  407197.577
450  mtInv+R9      200410.477   1003 402826.954   2416850.954  407194.387
451  mtInv+R10     200408.596   1005 402827.192   2424887.192  407203.334
460  mtInv+F+R8    195221.172   1020 392482.344   2475322.344  396923.802
461  mtInv+F+R9    195216.016   1022 392476.033   2483488.033  396926.199
471  mtMAM+R8      207137.637   1001 416277.273   2422281.273  420635.998
472  mtMAM+R9      207095.777   1003 416197.555   2430221.555  420564.988
473  mtMAM+R10     207079.072   1005 416168.143   2438228.143  420544.285
482  mtMAM+F+R8    202259.202   1020 406558.403   2489398.403  410999.861
483  mtMAM+F+R9    202225.832   1022 406495.663   2497507.663  410945.830
484  mtMAM+F+R10   202217.624   1024 406483.248   2505683.248  410942.123
WARNING: Normalizing state frequencies so that sum of them equals to 1
493  FLAVI+R8      202777.540   1001 407557.080   2413561.080  411915.804
WARNING: Normalizing state frequencies so that sum of them equals to 1
494  FLAVI+R9      202768.495   1003 407542.991   2421566.991  411910.424
WARNING: Normalizing state frequencies so that sum of them equals to 1
495  FLAVI+R10     202753.049   1005 407516.099   2429576.099  411892.240
WARNING: Normalizing state frequencies so that sum of them equals to 1
504  FLAVI+F+R8    202442.661   1020 406925.322   2489765.322  411366.780
WARNING: Normalizing state frequencies so that sum of them equals to 1
505  FLAVI+F+R9    202434.692   1022 406913.384   2497925.384  411363.551
WARNING: Normalizing state frequencies so that sum of them equals to 1
506  FLAVI+F+R10   202428.582   1024 406905.164   2506105.164  411364.039
515  HIVb+R8       200393.670   1001 402789.341   2408793.341  407148.065
516  HIVb+R9       200381.791   1003 402769.582   2416793.582  407137.016
517  HIVb+R10      200371.459   1005 402752.918   2424812.918  407129.060
526  HIVb+F+R8     198771.236   1020 399582.473   2482422.473  404023.930
527  HIVb+F+R9     198764.928   1022 399573.855   2490585.855  404024.021
537  HIVw+R8       209399.096   1001 420800.192   2426804.192  425158.916
538  HIVw+R9       209380.617   1003 420767.234   2434791.234  425134.668
539  HIVw+R10      209376.097   1005 420762.193   2442822.193  425138.335
548  HIVw+F+R8     204961.158   1020 411962.315   2494802.315  416403.773
549  HIVw+F+R9     204951.516   1022 411947.031   2502959.031  416397.198
550  HIVw+F+R10    204945.555   1024 411939.109   2511139.109  416397.984
559  FLU+R8        200582.056   1001 403166.112   2409170.112  407524.836
560  FLU+R9        200563.618   1003 403133.235   2417157.235  407500.668
561  FLU+R10       200558.394   1005 403126.789   2425186.789  407502.931
570  FLU+F+R8      199008.285   1020 400056.570   2482896.570  404498.027
571  FLU+F+R9      198994.223   1022 400032.445   2491044.445  404482.611
572  FLU+F+R10     198990.836   1024 400029.672   2499229.672  404488.547
581  rtREV+R8      198734.452   1001 399470.904   2405474.904  403829.628
582  rtREV+R9      198720.690   1003 399447.380   2413471.380  403814.813
583  rtREV+R10     198718.347   1005 399446.693   2421506.693  403822.835
592  rtREV+F+R8    196515.045   1020 395070.090   2477910.090  399511.547
593  rtREV+F+R9    196508.638   1022 395061.277   2486073.277  399511.443
594  rtREV+F+R10   196506.672   1024 395061.344   2494261.344  399520.219
603  cpREV+R8      196528.431   1001 395058.861   2401062.861  399417.586
604  cpREV+R9      196515.402   1003 395036.804   2409060.804  399404.237
605  cpREV+R10     196510.888   1005 395031.776   2417091.776  399407.918
614  cpREV+F+R8    195115.409   1020 392270.817   2475110.817  396712.275
615  cpREV+F+R9    195110.263   1022 392264.525   2483276.525  396714.691
Akaike Information Criterion:           LG+F+R9
Corrected Akaike Information Criterion: LG+G4
Bayesian Information Criterion:         LG+F+R8
Best-fit model: LG+F+R8 chosen according to BIC

All model information printed to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz
CPU time for ModelFinder: 997.707 seconds (0h:16m:37s)
Wall-clock time for ModelFinder: 334.861 seconds (0h:5m:34s)

===> START BOOTSTRAP REPLICATE NUMBER 97

Creating bootstrap alignment (seed: 228903)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.289 seconds

NOTE: 239 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -199328.068
2. Current log-likelihood: -196740.287
3. Current log-likelihood: -196725.288
4. Current log-likelihood: -196724.924
5. Current log-likelihood: -196724.792
Optimal log-likelihood: -196724.735
Site proportion and rates:  (0.019,0.102) (0.053,0.247) (0.098,0.364) (0.263,0.544) (0.188,0.816) (0.117,1.054) (0.169,1.666) (0.092,2.685)
Parameters optimization took 5 rounds (13.921 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 19.6844 secs using 499.9% CPU
Computing ML distances took 19.685035 sec (of wall-clock time) 98.411771 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00176907 secs using 498.2% CPU
Constructing RapidNJ tree: done in 0.0470152 secs using 586.7% CPU
Computing RapidNJ tree took 0.048848 sec (of wall-clock time) 0.285238 sec (of CPU time)
Log-likelihood of RapidNJ tree: -200660.337
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.156 second
Computing log-likelihood of 98 initial trees ... 25.288 seconds
Current best score: -196724.735

Do NNI search on 20 best initial trees
Optimizing NNI: done in 4.58508 secs using 498.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -196241.067
Optimizing NNI: done in 6.66932 secs using 498.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -196208.157
Optimizing NNI: done in 8.29397 secs using 498.3% CPU
Optimizing NNI: done in 6.43365 secs using 498.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -196160.023
Optimizing NNI: done in 7.90597 secs using 498.5% CPU
Optimizing NNI: done in 8.35455 secs using 498.2% CPU
Optimizing NNI: done in 5.96522 secs using 498.5% CPU
Optimizing NNI: done in 8.09822 secs using 498.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 8: -196138.866
Optimizing NNI: done in 8.16076 secs using 498.2% CPU
Optimizing NNI: done in 7.52955 secs using 498.2% CPU
Iteration 10 / LogL: -196215.244 / Time: 0h:3m:34s
Optimizing NNI: done in 7.72059 secs using 498.5% CPU
Optimizing NNI: done in 8.22895 secs using 498.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 12: -196122.340
Optimizing NNI: done in 9.55963 secs using 498.5% CPU
Optimizing NNI: done in 8.36634 secs using 498.2% CPU
Optimizing NNI: done in 7.62744 secs using 498.4% CPU
Optimizing NNI: done in 8.43573 secs using 498.4% CPU
Optimizing NNI: done in 8.67932 secs using 498.3% CPU
Optimizing NNI: done in 8.67257 secs using 498.4% CPU
Optimizing NNI: done in 7.88386 secs using 498.6% CPU
Optimizing NNI: done in 7.85599 secs using 498.2% CPU
Iteration 20 / LogL: -196276.381 / Time: 0h:5m:5s
Finish initializing candidate tree set (20)
Current best tree score: -196122.340 / CPU time: 269.336
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 8.33943 secs using 498.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -196111.010
Optimizing NNI: done in 6.47627 secs using 497.4% CPU
Optimizing NNI: done in 6.76975 secs using 497.1% CPU
Optimizing NNI: done in 5.49663 secs using 498% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -196104.339
Optimizing NNI: done in 5.53647 secs using 498.3% CPU
Optimizing NNI: done in 4.95272 secs using 498.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -196097.368
Optimizing NNI: done in 5.81646 secs using 498% CPU
Optimizing NNI: done in 5.36347 secs using 498.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 28: -196092.253
Optimizing NNI: done in 4.94427 secs using 498.4% CPU
Optimizing NNI: done in 5.25175 secs using 498.4% CPU
Iteration 30 / LogL: -196099.748 / Time: 0h:6m:25s (0h:21m:41s left)
Optimizing NNI: done in 5.89363 secs using 498.2% CPU
Optimizing NNI: done in 5.68392 secs using 498.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 32: -196074.483
Optimizing NNI: done in 4.9109 secs using 498.8% CPU
Optimizing NNI: done in 7.49173 secs using 498.2% CPU
Optimizing NNI: done in 5.02867 secs using 499% CPU
Optimizing NNI: done in 4.78802 secs using 498.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 36: -196048.277
Optimizing NNI: done in 5.21797 secs using 498.7% CPU
Optimizing NNI: done in 3.98081 secs using 498.7% CPU
Optimizing NNI: done in 4.89123 secs using 498.7% CPU
Optimizing NNI: done in 5.40445 secs using 498.9% CPU
Iteration 40 / LogL: -196070.877 / Time: 0h:7m:28s (0h:18m:22s left)
Optimizing NNI: done in 6.18517 secs using 498.5% CPU
Optimizing NNI: done in 5.76978 secs using 497.9% CPU
Optimizing NNI: done in 5.51615 secs using 498.4% CPU
Optimizing NNI: done in 5.34286 secs using 498.4% CPU
Optimizing NNI: done in 5.16913 secs using 498.9% CPU
Optimizing NNI: done in 5.50143 secs using 498.4% CPU
Optimizing NNI: done in 5.32841 secs using 498.7% CPU
Optimizing NNI: done in 5.28842 secs using 498% CPU
Optimizing NNI: done in 5.44771 secs using 498.4% CPU
Optimizing NNI: done in 4.65421 secs using 498.8% CPU
Iteration 50 / LogL: -196106.958 / Time: 0h:8m:22s (0h:14m:42s left)
Optimizing NNI: done in 5.35465 secs using 497.9% CPU
Optimizing NNI: done in 5.64195 secs using 498.5% CPU
Optimizing NNI: done in 5.1154 secs using 498.8% CPU
Optimizing NNI: done in 5.19096 secs using 498.5% CPU
Optimizing NNI: done in 5.07923 secs using 498.3% CPU
Optimizing NNI: done in 5.62366 secs using 498% CPU
Optimizing NNI: done in 5.07065 secs using 499.1% CPU
Optimizing NNI: done in 5.05366 secs using 498.8% CPU
Optimizing NNI: done in 4.57862 secs using 498.6% CPU
Optimizing NNI: done in 5.5913 secs using 498% CPU
Iteration 60 / LogL: -196064.663 / Time: 0h:9m:15s (0h:11m:55s left)
Optimizing NNI: done in 5.478 secs using 498.1% CPU
Optimizing NNI: done in 5.89009 secs using 498.4% CPU
Optimizing NNI: done in 5.14286 secs using 498% CPU
Optimizing NNI: done in 5.0499 secs using 498.5% CPU
Optimizing NNI: done in 5.5108 secs using 498.2% CPU
Optimizing NNI: done in 5.78415 secs using 498.4% CPU
Optimizing NNI: done in 4.9664 secs using 498.7% CPU
Optimizing NNI: done in 5.82252 secs using 498.1% CPU
Optimizing NNI: done in 5.46173 secs using 498.1% CPU
Optimizing NNI: done in 4.00167 secs using 498.8% CPU
Iteration 70 / LogL: -196076.162 / Time: 0h:10m:9s (0h:9m:42s left)
Optimizing NNI: done in 5.16716 secs using 498.5% CPU
Optimizing NNI: done in 5.52478 secs using 498.5% CPU
Optimizing NNI: done in 5.54076 secs using 498.5% CPU
Optimizing NNI: done in 5.94211 secs using 498.7% CPU
Optimizing NNI: done in 5.39666 secs using 498.3% CPU
Optimizing NNI: done in 5.38602 secs using 498.6% CPU
Optimizing NNI: done in 5.53186 secs using 497.9% CPU
Optimizing NNI: done in 5.42407 secs using 498.1% CPU
                                                      
******************************************************
CHECKPOINT: Resuming analysis from /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.ckp.gz

IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport
Seed:    827665 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Thu Jul 10 14:44:47 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta ... Fasta format detected
Reading fasta file: done in 0.00332212 secs using 98.46% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.00890613 secs using 5293% CPU
Alignment has 495 sequences with 575 columns, 575 distinct patterns
575 parsimony-informative, 0 singleton sites, 0 constant sites
            Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.000304937 secs using 5430% CPU
   1  8nJh6NUzJV   12.00%    passed     10.27%
   2  z0YCu0xtFo   11.30%    passed     15.88%
   3  1JN1q1h7Jh    8.35%    passed      9.02%
   4  E2n5Y5UQiG    8.52%    passed     43.28%
   5  cMoC1WsTO6    8.17%    failed      2.01%
   6  ys0DcEs0US    8.35%    passed     77.31%
   7  1s9qnaxMSp    9.04%    failed      2.14%
   8  FtHEpsU1vB    9.04%    failed      2.61%
   9  oeJuwbyE7Q    9.91%    passed      8.44%
  10  qCgVEYLhzI   17.39%    passed      9.43%
  11  zyhovbZkFP    9.91%    passed      8.44%
  12  jOk4aex96C   19.65%    passed      9.17%
  13  AR0npWZQ83    8.17%    passed     22.96%
  14  F5Si2gBtZe   21.91%    passed     13.69%
  15  FG021XCxMA   18.09%    passed     68.58%
  16  MCX7xygB2V    8.70%    passed     73.82%
  17  iVpOwiZzba    9.04%    passed     21.82%
  18  iPjBM3iYZR   80.35%    failed      2.62%
  19  qbFBJDOQUO    9.39%    passed     92.00%
  20  x5jv5lpB2O    9.22%    passed     43.94%
  21  y5M7y721WQ   11.30%    passed     52.45%
  22  MwDLYKIKBx   16.70%    passed     52.35%
  23  EsTTc2nPxQ    8.00%    passed     56.73%
  24  vnhywKRkFl   13.91%    passed     61.80%
  25  7JZdwvMv24   10.09%    passed     62.94%
  26  dQjyx7OIYV   27.30%    passed     66.63%
  27  irBovt5bLa    8.17%    passed     37.03%
  28  Ewm24Mlvnq    8.17%    failed      0.91%
  29  XDJ4JoLzyH   17.22%    passed     87.03%
  30  4kC0x0kjdn    7.65%    passed     35.61%
  31  RARcF60S6a    8.00%    passed     18.15%
  32  WlelCJO26H   12.17%    passed     15.31%
  33  mhk5OTojgz    7.83%    passed     22.72%
  34  pTM2DvE1xM    7.83%    passed     23.80%
  35  tlXXT5aWqu    8.35%    passed     25.18%
  36  TC8Xnd4iFa    8.35%    passed     68.65%
  37  02HhJs6pa3   11.13%    passed     51.90%
  38  NEeqpPtHg5    9.91%    passed     53.60%
  39  qbTDasygHV    8.00%    failed      4.34%
  40  7Yh1YhvFVC    9.04%    passed     82.42%
  41  VvE6sMyCv8    9.22%    passed     82.98%
  42  WjMMQYeUC2    9.74%    passed     28.42%
  43  W7Mh0FRDU6    9.57%    passed     47.24%
  44  2nrE64urGV    7.83%    failed      0.05%
  45  UzprTJ7K6d    7.83%    failed      0.07%
  46  UlwuxTyGoO    8.17%    passed     35.83%
  47  iaXjDyTif3    9.91%    passed     26.12%
  48  B6M0EvUDsT    8.17%    passed     57.64%
  49  1G5hXRghEG    7.83%    passed     46.06%
  50  gTvhxQmbWZ    7.83%    passed     59.90%
  51  8l37MLA1ms    7.83%    passed     66.42%
  52  vLizyHtRBL    6.96%    passed     45.67%
  53  S5ByYpGeqY    7.30%    passed     14.75%
  54  Fedl6T4xon    7.83%    passed     26.99%
  55  4BymctPkH6    9.22%    passed     90.46%
  56  s5wLZ9vWaO   22.96%    passed     14.42%
  57  awKrv6hUok    8.00%    failed      0.00%
  58  kWFqKgyYB3   18.61%    failed      0.35%
  59  DcYLS8gvW9    8.17%    passed     14.76%
  60  McRlo7Hy0B    8.35%    failed      1.15%
  61  tf71jZDs7S   14.78%    failed      0.00%
  62  vMqsZO8YaG   12.00%    passed     25.19%
  63  5AMYxNwgiK   14.26%    passed     72.77%
  64  wxoZBV0PHy    7.65%    passed     28.65%
  65  KeSH8I0Fea   10.96%    passed     34.97%
  66  KCrIGLQ7Q1    8.87%    passed     28.42%
  67  4LT0U0c0Do    8.17%    passed     45.98%
  68  CGeXrJPsGL    7.30%    passed     26.80%
  69  xxKiyIW1gr    8.35%    passed     42.35%
  70  xs9ieaVe53   24.17%    passed      5.89%
  71  NQWmJIpRFE    8.17%    passed     36.46%
  72  nkfchBpcgh    9.91%    passed     49.94%
  73  jdOhfl36g8    9.91%    passed     49.94%
  74  KVoy4GxdpT    8.70%    passed     30.77%
  75  WUIEff6ikU    9.74%    failed      3.44%
  76  coeQ6zHZ24    8.52%    passed     15.26%
  77  HWG7P94Eio    7.65%    passed     33.53%
  78  9Vw494DXPc    9.74%    passed     30.82%
  79  g6PJxKZvcf    8.17%    passed     67.92%
  80  AvvCKxHYp4    8.87%    passed     94.08%
  81  CemxIJafw8    8.87%    passed     94.94%
  82  dsBdLHptXN    7.30%    passed     26.31%
  83  4MVqW0qAIi    8.17%    passed      7.58%
  84  LcWgRv0iB6    8.17%    passed      6.57%
  85  fd8RtQX78T    8.35%    passed     67.99%
  86  D9LASQ998i    7.13%    passed     64.85%
  87  Uz7TnODNGf    8.17%    passed     61.10%
  88  Sp3Vq6QoAR   12.00%    passed     25.06%
  89  gtPloLimDb   14.61%    passed     16.69%
  90  GFnS6AyinZ   13.74%    passed     62.22%
  91  U9Eib0qR6X    9.39%    passed     80.44%
  92  dZ9ze414KZ    8.52%    passed     34.81%
  93  ydHAIeuwbW    9.04%    passed     24.32%
  94  e67HigPrjf    8.70%    passed     10.03%
  95  U5KrYXobqi    7.83%    passed     28.30%
  96  rqX0m8aZs1    8.52%    passed     74.68%
  97  JTOoSRn6ib    8.52%    passed     63.83%
  98  X4XbPR7Rfa    9.91%    passed     88.47%
  99  etCZH2Htco   11.30%    passed     96.50%
 100  7kS1ZU0pFM    9.74%    passed     63.62%
 101  rUnfYSLNJJ    8.35%    passed     25.59%
 102  YjqMqBCaiv    7.13%    passed     35.60%
 103  YXN7x6IbOx    8.35%    passed     52.18%
 104  bN8jt2Atwp   10.43%    passed     56.67%
 105  hgeyXdJgqq    9.22%    passed     56.85%
 106  1horVoEi3u    7.13%    failed      1.07%
 107  EDGqQf981n   10.09%    passed     86.16%
 108  3nDVNG9sKr   10.61%    passed     15.44%
 109  fFDoKaygf0    8.00%    passed     43.10%
 110  cRRsJgsBlZ    8.70%    passed     85.09%
 111  BI3jho3ECe    9.22%    passed     51.11%
 112  TIeppwLKSz    9.57%    passed     34.47%
 113  a8nt9ktZTC   24.35%    passed     70.98%
 114  GtfO72MtR2   22.26%    passed     65.46%
 115  xKzEmKT1dB   21.39%    passed     47.26%
 116  cTDPKciopP   11.83%    passed     67.98%
 117  xdNOUh7eMp    8.00%    passed     86.96%
 118  k3bzPFly41    8.17%    failed      0.00%
 119  ukUu00fP6L    9.39%    failed      0.29%
 120  up1UWJJzNf    9.22%    failed      3.36%
 121  GZASsy6wnT    8.17%    failed      0.00%
 122  PbkNCoK5ix   10.96%    passed     34.06%
 123  GfLEAInBd6   10.26%    passed     45.24%
 124  7OOuM97Qkr    8.70%    passed     42.00%
 125  d9kVhxwUcH    9.22%    passed     36.90%
 126  pn3nIof2qW    8.70%    passed     82.33%
 127  jYBcxGIen7   19.30%    passed     48.83%
 128  Y2YJcqt3IL   27.30%    passed     72.36%
 129  DQnwdMJsVl    9.39%    passed     17.77%
 130  Gvb4AsKEVi    8.35%    failed      0.00%
 131  d5E6EHDpwi    7.65%    passed     78.94%
 132  yA69Aemq0C    9.57%    passed     51.08%
 133  9f7AMvazZf    8.70%    passed     87.18%
 134  tD3ewCYOQG    9.22%    passed     39.14%
 135  yHwEtbE4JZ    8.87%    passed     51.50%
 136  HZpFQAW00k   12.87%    passed     16.94%
 137  FCPk6mdvI6    8.35%    passed     85.41%
 138  C50stY8CeY    9.22%    passed     15.26%
 139  WQOxpzhoLN    8.17%    passed     95.19%
 140  lU6fN5cAZQ   16.87%    passed     26.00%
 141  w34zJrGIvJ   13.04%    passed     46.23%
 142  R4SazYxajJ   13.22%    passed     24.74%
 143  oyLJTIsT1Z   12.00%    passed     35.61%
 144  95FTGjmRiw   16.87%    passed     10.92%
 145  MVSYHU9DCt   12.17%    passed     83.71%
 146  RhS1O12ekg    8.52%    passed     98.08%
 147  sthKhyT8fy    9.04%    passed     79.34%
 148  O2gQ2myCZn   11.30%    passed     66.29%
 149  B7PVgc3v8q    8.52%    passed     67.20%
 150  FlAHhYz62Q    6.96%    passed     92.12%
 151  PZqL2meUHi    8.35%    passed     89.55%
 152  XJTzBvD6pQ    8.70%    passed     73.32%
 153  FtEYGIUfBM   10.78%    passed     55.74%
 154  NUAWacASLt   10.26%    passed     81.70%
 155  3FdA2TKbHR   10.26%    passed     77.97%
 156  TCgaJethwm    9.74%    passed     51.49%
 157  V8Ort0OUIV    9.39%    passed     75.80%
 158  gKxOBa9lC3   80.35%    failed      4.37%
 159  ZJBcyycwk4   21.91%    passed     83.00%
 160  BXOEqGyzK2    9.04%    passed     82.96%
 161  5yy8DKtZ5c   12.35%    passed     70.92%
 162  cY7oeSnppq    9.74%    passed     78.00%
 163  vUEx5gqasN    9.74%    passed     22.71%
 164  2jCJDig3v9   17.39%    passed     45.79%
 165  lzBWRCtyx0   17.39%    passed     45.79%
 166  DBMxujRgHK   10.43%    passed     76.44%
 167  x3ZrH0XGfQ   13.04%    passed     40.57%
 168  SgWCfVzTG4    9.39%    passed     23.64%
 169  f62ksK5UEj   33.39%    passed     48.62%
 170  hkIztfSCD1   10.09%    passed     60.28%
 171  iRnB4M1GLD   11.30%    passed     35.88%
 172  CU0XuCnsFL   42.61%    failed      1.05%
 173  42tdKq8PSX   12.87%    passed     50.93%
 174  gXeZ52LCvM   12.87%    passed     50.93%
 175  u8cLLIfWEX   12.87%    passed     50.93%
 176  dmOh7r7eKT   12.52%    passed     43.59%
 177  3c6hZoOqvP   12.87%    passed     51.70%
 178  bu2UDzewiZ   16.35%    passed     97.52%
 179  SYc4eSftSt    7.30%    passed     55.76%
 180  zlSzVB3W0P    9.91%    passed     23.47%
 181  3C2pM8OlsA   16.00%    passed     44.07%
 182  Pxcz4xw4KG    8.52%    passed     89.90%
 183  UcghE30qVq   10.26%    passed     98.72%
 184  qIB6gS9bgA   10.26%    passed     99.50%
 185  UDehzYJL1w    9.91%    passed     84.08%
 186  BB4241mZBL    9.74%    passed     18.51%
 187  c6c8r06RzT   14.09%    passed     51.46%
 188  XQT9xr4ybf   14.09%    passed     51.46%
 189  SCnTy3bpY1   12.00%    passed     52.85%
 190  jev8yDUHvc   37.22%    passed     46.96%
 191  bK3G4lRT3G    9.74%    passed     18.84%
 192  Z5XH3L582l    9.39%    passed     64.30%
 193  dhUTnrRr7d    9.04%    passed     17.65%
 194  2ifGWJmasz   13.39%    passed     53.39%
 195  WB36HQui6V   13.22%    passed     13.09%
 196  QNNkPiHWnJ   13.57%    passed     15.99%
 197  WHGNQkrc10   16.70%    passed     15.42%
 198  h5LGHiiOXm   13.04%    passed      8.14%
 199  3zhlkwsAL6   11.65%    passed     68.02%
 200  i2Lb0rchl2   17.74%    passed     40.76%
 201  yMqx9t1LVd   11.83%    passed     95.23%
 202  2W3WY0vBww   18.09%    passed     31.19%
 203  wTTqfzkYo6   12.35%    passed     65.69%
 204  0vKBWD6wpY   19.83%    passed     72.14%
 205  SJgohIdqev   13.04%    passed     56.62%
 206  9DPLpYQWNv    8.35%    passed     79.37%
 207  8uUTsKFjlb    9.74%    passed     57.77%
 208  xVujdvY6Nr   15.65%    passed     86.08%
 209  NImtrhZGKE   18.61%    passed     29.08%
 210  YugOzGk8Ov    8.00%    passed     61.92%
 211  DeWEtikGbq    9.39%    passed     58.48%
 212  x0olbpog9B   10.78%    failed      3.15%
 213  pAhidh8xBZ    9.22%    passed     20.39%
 214  PlPvNaQDzl   78.26%    failed      2.70%
 215  NPvXCeLNmx    9.22%    passed     19.23%
 216  yVup7G0SEF    9.39%    passed      5.94%
 217  vPQhR8sENE    9.22%    passed     25.50%
 218  nU2WbHAcGl    8.00%    passed     38.25%
 219  5LDURAlPH2   18.96%    passed     93.03%
 220  BWFcvfZnO3   19.83%    passed     80.72%
 221  pygYFVFfpx   18.96%    passed     64.25%
 222  SHqN6p0dYV   11.65%    passed     77.47%
 223  qsVXrYaG9q   16.52%    passed     62.49%
 224  3cAaekWMpW   17.57%    passed     67.41%
 225  N40B32hpg1   12.00%    passed     79.79%
 226  JPT5lhIP82   16.17%    passed     61.51%
 227  ZLXDnoVm6b    8.87%    passed     65.21%
 228  X85YtZdfkf    9.04%    passed     76.50%
 229  8UiTG47Ec2    9.04%    passed     76.50%
 230  rIeH6RocN2   11.13%    passed     16.99%
 231  JEeirH12E1   31.48%    passed     21.21%
 232  UzAtwShlJN   15.48%    failed      0.00%
 233  2pVvPoBi2c   15.65%    failed      0.00%
 234  scQ10Wo461   39.13%    passed     23.66%
 235  Nb1rJKftmp   17.91%    failed      0.00%
 236  nhoqJOOPX2   17.04%    passed     88.57%
 237  39gkmZTScW   18.26%    passed     91.96%
 238  BGkr4JUYAf   13.39%    passed     93.93%
 239  DulbVCzsEt   24.35%    passed     66.60%
 240  cSruxLJuyQ   26.96%    passed     10.64%
 241  1XfSwqn4ef   25.04%    passed     39.48%
 242  96xj01KeXJ   68.17%    passed     84.97%
 243  eq1zGc6rtT   29.04%    passed     18.35%
 244  VfUM5i9jsn   41.91%    failed      4.66%
 245  20sicocoSo   23.83%    failed      0.74%
 246  RLpJhYeIPE   25.91%    passed     47.76%
 247  C8YPeCC1NI   28.87%    passed     14.80%
 248  xxnHHiKI8Z   28.52%    passed      5.76%
 249  3Je7M7o4rZ   33.39%    passed     11.10%
 250  47EKfQlPcw   28.35%    passed     38.14%
 251  9C0byE309K   34.43%    passed     22.05%
 252  TsIfWQzrph   28.35%    passed     38.14%
 253  hTPGiqrFV4   42.09%    passed     88.30%
 254  aFMglfB8eH   24.52%    passed     15.36%
 255  JQcRFbokY2   28.35%    passed     32.19%
 256  jFdaAxFg6n   23.13%    passed     47.94%
 257  KRYbednenZ   23.13%    passed     42.60%
 258  FyIDyqrLwr   23.13%    passed     47.94%
 259  8XGfcNsQ09   23.83%    passed     62.09%
 260  QyNf0mVNlz   23.83%    passed     10.54%
 261  f9oKgpE1wE   23.48%    passed     56.82%
 262  REBVZFiPEf   23.30%    passed     27.01%
 263  ItesG8T6sN   23.83%    passed     47.79%
 264  TSGS90hx1G   23.30%    passed     24.55%
 265  ZRAzqCtrNA   24.17%    passed     57.76%
 266  eeM5JHuVuf   24.35%    passed     50.06%
 267  oe9Vawfrxg   24.35%    passed     26.16%
 268  rgglFfiKnC   28.00%    passed     45.26%
 269  bCjdcpAF4v   24.00%    passed     70.09%
 270  OmcerY3zVm   64.35%    passed     66.28%
 271  zcG6I9U7zt   43.13%    passed     73.90%
 272  QKniumy84t   24.00%    passed     71.91%
 273  158IGk2w8A   24.00%    passed     40.59%
 274  kI8iG2U2gQ   23.30%    passed     85.81%
 275  fPZNEk39Af   26.78%    passed     15.99%
 276  hrBvV4AmlN   24.17%    passed     20.25%
 277  myGUzZ8LDH   24.00%    passed     24.24%
 278  sHkv5UU91e   23.65%    passed     10.45%
 279  GNzRUX9ddm   23.65%    passed     13.36%
 280  zsnvwGvGgv   24.00%    passed     30.90%
 281  9OoygEJxNJ   23.13%    passed     19.47%
 282  IjtzwwEpZt   24.70%    passed     32.04%
 283  nSDhHtKOaz   76.87%    passed     72.40%
 284  A0R7Dl6WnL   24.00%    passed     27.63%
 285  CvviaWP5QG   24.17%    passed     57.70%
 286  pPSEGFgq5j   79.13%    passed     12.51%
 287  UdG6KQNIp6   24.52%    passed      9.66%
 288  8EVSPtaAhX   24.35%    passed     42.22%
 289  uiafGbGfwA   27.30%    passed     85.86%
 290  XZFyxFJmTO   24.70%    passed     34.27%
 291  H6HkWi4jLJ   26.26%    passed     57.81%
 292  uALm9y36Bq   28.70%    passed     22.86%
 293  EUEmaNv0jU   23.30%    passed     16.64%
 294  miFIpMQUO8   25.04%    passed      5.34%
 295  qsWsb5TOjf   26.09%    passed     11.23%
 296  WLDkRifOr1   25.74%    passed     31.25%
 297  u7RGaLBmh5   25.74%    passed     85.68%
 298  n4n2Sa9hou   25.39%    passed     53.48%
 299  gZV6bt6UCn   24.17%    passed     46.31%
 300  PortTSlpTI   41.74%    passed     26.87%
 301  2Nn52BMVGD   28.00%    passed     32.50%
 302  sQl8vIYhWL   27.30%    passed     24.87%
 303  nlyynuwvAY   27.13%    passed     84.06%
 304  iM9z6TKAcr   41.39%    passed     18.69%
 305  pVpmbqWKfw   36.70%    failed      1.72%
 306  r4JpMWXYFJ   26.09%    passed     11.04%
 307  CcX8oiPHcg   27.83%    passed     27.83%
 308  G2BVFEVILA   25.04%    passed     61.18%
 309  BNYVmW4TYG   25.91%    passed     54.90%
 310  ExQ8uNPj7h   34.26%    passed     66.82%
 311  whmj06xoF5   28.17%    failed      0.02%
 312  VqFVtnHfVy   25.22%    passed     79.18%
 313  Mqy8imXZ6G   25.91%    failed      0.02%
 314  s0NXcs97L3   25.91%    failed      0.02%
 315  Iqt8ZiOu6k   25.74%    failed      0.00%
 316  XsWTxkH1p7   25.57%    passed     19.64%
 317  zoRaGfFB7U   24.52%    passed     48.77%
 318  qqN1dh1OOy   24.35%    passed     14.36%
 319  T1wQDvF98B   24.35%    passed      7.77%
 320  lkTsXyry76   26.43%    passed     26.11%
 321  hSqg5YYyOm   27.48%    failed      0.44%
 322  puRVWMvppN   28.35%    passed     22.55%
 323  1LbFAdgLuC   25.74%    passed     11.73%
 324  y5MmiioIHk   25.91%    failed      1.83%
 325  BnR8odZPBs   25.91%    passed     15.58%
 326  ajGvkpi5As   25.91%    passed      8.73%
 327  qbTJcwpdwP   26.61%    passed     13.99%
 328  vCxAIjCqNl   24.87%    passed     46.42%
 329  mPlwp1JlUK   27.30%    passed     36.54%
 330  rYWDHuLHvt   29.91%    failed      1.32%
 331  C0RnyRzFMX   71.65%    passed     45.95%
 332  7Aa2sW2uFn   28.00%    failed      3.36%
 333  0djEp2FhF9   28.00%    failed      3.36%
 334  l1pN6WjG1N   80.17%    passed     21.40%
 335  XLgmciWSgo   46.09%    passed     14.00%
 336  D8WaLv1pNN   30.78%    passed     27.06%
 337  12VY0qcAbu   29.39%    passed     74.33%
 338  JNoGNci0kO   28.87%    passed     95.56%
 339  VGEALS8WvR   40.70%    passed     16.49%
 340  D7iWRjKQ8X   25.74%    passed     47.65%
 341  upEmmPcbTB   27.48%    passed     22.48%
 342  UpKcpH8xp2   26.78%    passed      7.74%
 343  hreWbDAWDh   23.65%    passed      8.09%
 344  5oPFYbGk9x   24.52%    passed     66.68%
 345  bKMx8usLZf   35.83%    passed      9.39%
 346  9waTHuOjG2   43.48%    passed     27.73%
 347  y13PUGF6fd   29.39%    passed     50.29%
 348  MCxeCrj6og   25.22%    passed     77.92%
 349  JqQlZRu8jp   25.91%    passed     38.60%
 350  ZrMp8mhVn3   56.35%    passed      9.73%
 351  PVum0t8D9w   48.52%    failed      3.01%
 352  mA0FIy0SqW   24.70%    passed      5.42%
 353  EacivjsFt1   26.61%    passed     43.72%
 354  FKAuFXjrK2   29.57%    failed      2.12%
 355  eOn8Fw1qPv   27.48%    failed      3.53%
 356  D0XDiTOIfD   34.78%    passed      9.81%
 357  910hgdbBRd   28.00%    passed     51.49%
 358  ijUTPEstS6   33.39%    passed     28.87%
 359  bUU4czn7NG   27.83%    passed     60.40%
 360  INEhHLWnmb   37.04%    failed      1.97%
 361  LMA81zzKSe   37.04%    failed      0.01%
 362  TUCOIK4ZQn   33.91%    failed      0.52%
 363  yvso4goGdQ   34.96%    failed      4.00%
 364  YWPX00OZwF   36.00%    failed      3.54%
 365  qKqJ6yzKtT   34.61%    passed     10.13%
 366  49Qin0CHkb   34.61%    passed      9.62%
 367  63Q15egMZA   34.26%    passed      6.18%
 368  nWYlGrbPPc   34.61%    failed      4.67%
 369  JvcE4PBExA   33.74%    passed      7.73%
 370  LUlT7ehgwb   36.00%    passed     26.12%
 371  pVpykOHqYZ   39.48%    failed      0.85%
 372  v2K68153zf   38.26%    failed      0.55%
 373  qYhA4tEOW1   34.78%    failed      0.03%
 374  grGtjFUUTt   34.43%    failed      0.23%
 375  qWhSnx7aMf   44.87%    passed      5.50%
 376  v1oAyLSJtz   50.96%    passed     28.72%
 377  BadtzwpMMs   38.43%    passed      9.62%
 378  6DLNJCEk13   34.61%    passed      8.29%
 379  w2DOMr7ED6   41.39%    failed      3.23%
 380  JK0CadwxtV   33.74%    failed      1.62%
 381  thXzqzsTWd   33.04%    failed      4.58%
 382  cza9cyArKR   33.04%    failed      3.45%
 383  64i2bPRqyf   38.09%    failed      1.24%
 384  Tu05kR9iNy   35.30%    failed      2.13%
 385  ryyuwN9EeF   35.83%    failed      3.08%
 386  9i9iYEz14b   36.87%    passed     43.29%
 387  e5Z7VURlcd   56.00%    failed      0.95%
 388  ndIdlcACpn   34.61%    failed      0.11%
 389  miylOtOHke   36.00%    passed      5.91%
 390  jGxqmOPSFz   33.91%    failed      1.22%
 391  UpRnjomc4O   36.17%    passed     26.63%
 392  ebCUnMXr2f   38.43%    passed     15.56%
 393  21yjS1P784   34.43%    failed      0.27%
 394  XU8ct59Imq   34.26%    failed      0.70%
 395  mWu9nYUMB2   34.26%    passed      5.63%
 396  6N8VC2LDv6   34.26%    passed      5.63%
 397  Tp4oCldie4   38.09%    failed      4.42%
 398  LdahhT5atZ   34.26%    passed      5.63%
 399  ohdNT1wCFZ   34.26%    passed      7.14%
 400  QY3dkiwN48   41.57%    failed      3.72%
 401  Ip06mTdO2e   35.65%    failed      2.00%
 402  P5RXO2szhK   29.57%    passed     33.39%
 403  offjx75l6X   85.22%    passed     26.57%
 404  EdOuOhohBn   33.91%    passed     23.13%
 405  ZjYUAXvbUC   34.26%    passed      8.29%
 406  lpxtOw9xf3   36.52%    passed     12.71%
 407  4bSmqRgfRI   34.09%    passed     12.39%
 408  gminDyGtcG   34.78%    failed      2.44%
 409  lDQWwcBkMU   34.78%    passed     33.99%
 410  CUTMeJuwSv   33.74%    passed     78.03%
 411  OI80q3iM3F   33.74%    passed     81.17%
 412  xnKco929hT   37.57%    passed      8.65%
 413  RPfcmWXHCA   37.57%    passed     20.91%
 414  6mj1jZTKcU   36.17%    failed      4.67%
 415  Gr87dxYVyz   43.83%    failed      4.55%
 416  VGvhdii6IX   73.22%    passed     54.33%
 417  wJTuSg6Gc6   35.65%    passed     75.44%
 418  K3Flz6km5g   35.65%    passed     71.14%
 419  Tu0u89fzoU   35.48%    passed     16.33%
 420  IpceOBVrBQ   35.48%    passed     13.04%
 421  JAjUuwFnV7   36.35%    passed     34.52%
 422  wSnvqYXqTg   32.00%    passed     24.03%
 423  keWKiDv5J1   36.35%    passed     23.38%
 424  r5NSp8dbtM   37.39%    passed     32.60%
 425  wxLKLb6SMC   35.13%    passed     25.74%
 426  qw6gF6ZapY   35.13%    passed     25.74%
 427  ZGvDd4xvwy   37.91%    passed     30.11%
 428  8lXCZuvq8q   34.26%    passed     25.11%
 429  qvg1my8Wlp   48.70%    failed      3.30%
 430  ZdWaANa0Et   32.87%    passed      6.04%
 431  Onz2iyjxH3   42.96%    failed      0.02%
 432  AJImOJUang   66.09%    passed      8.67%
 433  rbo3OKIe4x   36.52%    failed      0.54%
 434  pGufZSTMNB   36.52%    passed     12.14%
 435  FLjy3W79tg   36.52%    passed     17.85%
 436  jYaSjXdhUR   34.78%    passed     22.31%
 437  HGW1EoyaVz   49.22%    passed     75.08%
 438  HQpmvbcKV0   36.35%    passed     71.28%
 439  Us22uQdloc   73.22%    passed     88.61%
 440  Nczi5Cos47   34.96%    passed     68.86%
 441  IV8TgD1mQj   36.52%    passed     65.05%
 442  QKsY8kV1rB   34.43%    passed     49.51%
 443  TrIc96BqkG   34.96%    passed      7.64%
 444  pnjqLcOivm   34.61%    passed      9.34%
 445  SY2alUymun   36.00%    passed     31.87%
 446  GXBps2FgSH   37.57%    failed      4.23%
 447  ZldeYJmzLx   39.48%    failed      0.13%
 448  8biR24Gazc   33.91%    passed     22.85%
 449  NBJ6cvHYoU   34.43%    passed     22.55%
 450  egq7pHRqeL   38.78%    passed     36.06%
 451  y0r2SVxwqI   35.30%    passed     55.80%
 452  evUBWmPjS2   35.30%    passed     23.87%
 453  ikh1qtxydC   36.00%    failed      2.62%
 454  BRdJ9RHZQj   35.65%    passed      8.09%
 455  l25CgIsmfn   35.65%    passed      8.09%
 456  XPdvjShyOo   37.57%    passed      7.82%
 457  M144qciIKM   34.96%    passed     30.15%
 458  BnE96TDyk8   35.48%    passed     26.42%
 459  jeohLZ0eYF   36.87%    failed      0.20%
 460  YvoxlQmxl7   36.87%    failed      0.20%
 461  R0wuUn8J0h   33.57%    passed     30.51%
 462  oeFPRaQBYZ   33.39%    passed     26.87%
 463  xqlhblg6dL   33.91%    passed     25.42%
 464  6Qs9p4Rx4f   34.09%    passed     25.71%
 465  QPlyWfEtzz   34.43%    passed     29.56%
 466  Yo6roMcRLy   35.30%    passed     25.15%
 467  PwuAxgsPD6   42.78%    passed     42.46%
 468  vaFUdeGB10   33.91%    failed      2.49%
 469  8GM1psnK6y   36.87%    failed      0.09%
 470  E6RVlyXu6C   33.74%    passed     45.21%
 471  SuF6hGymBQ   36.00%    failed      2.74%
 472  cgJCegWwAr   70.96%    passed     99.24%
 473  i10ONbBPRV   34.96%    passed     50.77%
 474  FaaaR0oHe4   35.13%    passed     47.29%
 475  RrNP3l8SS7   36.52%    failed      0.47%
 476  BuFyz2PMN4   34.43%    passed     49.11%
 477  Y10Qa1Da4V   38.78%    passed     65.87%
 478  8zkzdNvfM0   34.43%    passed     49.11%
 479  rA4KjQCVx3   32.00%    passed     90.85%
 480  au044S3YHW   35.30%    passed     43.12%
 481  cIR66o13VD   35.65%    passed     81.03%
 482  fkB1xaD3I7   35.83%    passed     66.46%
 483  CwGGcZADEn   35.30%    passed     25.37%
 484  fNHflelF6b   34.61%    passed     14.83%
 485  8zGWBmbKDs   83.65%    passed     77.32%
 486  LC2TsjjWfV   35.65%    passed     44.42%
 487  rsgxiUIZDl   41.74%    passed     41.79%
 488  Srvt2UziZu   34.43%    passed     97.83%
 489  zPT9rylEFV   34.43%    passed     97.83%
 490  rXls0PgjJv   35.48%    passed      5.47%
 491  TcLIjpisFo   51.83%    passed     29.28%
 492  RMfRwwtcqL   32.17%    passed      5.11%
 493  zzJMOnIGaE   34.09%    failed      0.02%
 494  bkj6PiDj99   34.78%    passed     36.79%
 495  QPtDeO8Fse   34.61%    passed     64.43%
WARNING: 19 sequences contain more than 50% gaps/ambiguity
****  TOTAL        23.94%  82 sequences failed composition chi2 test (p-value<5%; df=19)
CHECKPOINT: 96 bootstrap analyses restored

NOTE: Restoring information from model checkpoint file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz

CHECKPOINT: Initial tree restored
Measuring multi-threading efficiency up to 96 CPU cores
Increase to 10 rounds for branch lengths
24 trees examined
Threads: 1 / Time: 99.304 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -475698
Threads: 2 / Time: 62.179 sec / Speedup: 1.597 / Efficiency: 80% / LogL: -475698
Threads: 3 / Time: 54.638 sec / Speedup: 1.817 / Efficiency: 61% / LogL: -475698
Threads: 4 / Time: 45.621 sec / Speedup: 2.177 / Efficiency: 54% / LogL: -475698
Threads: 5 / Time: 41.503 sec / Speedup: 2.393 / Efficiency: 48% / LogL: -475698
Determining AUTO threadcount: done in 303.29 secs using 258.9% CPU
BEST NUMBER OF THREADS: 4

Perform fast likelihood tree search using LG+G model...
CHECKPOINT: Tree restored, LogL: -195489.756
NOTE: ModelFinder requires 455 MB RAM!
ModelFinder will test up to 616 protein models (sample size: 575) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  LG            200322.611   987 402619.222   2352931.222  406916.985
  2  LG+G4         195470.344   988 392916.688   2347180.688  397218.805
  3  LG+R2         196589.598   989 395157.196   2353377.196  399463.668
  4  LG+R3         195780.340   991 393542.681   2359686.681  397857.862
  5  LG+R4         195429.122   993 392844.244   2366928.244  397168.133
  6  LG+R5         195312.276   995 392614.553   2374654.553  396947.151
  7  LG+R6         195240.929   997 392475.859   2382487.859  396817.166
  8  LG+R7         195209.395   999 392416.790   2390416.790  396766.806
  9  LG+R8         195184.144   1001 392370.288   2398374.288  396729.013
 10  LG+R9         195175.348   1003 392356.697   2406380.697  396724.130
 11  LG+R10        195171.997   1005 392353.994   2414413.994  396730.135
 20  LG+F+R8       194402.294   1020 390844.587   2473684.587  395286.045
 21  LG+F+R9       194396.917   1022 390837.834   2481849.834  395288.000
 31  WAG+R8        196252.507   1001 394507.014   2400511.014  398865.738
 32  WAG+R9        196242.300   1003 394490.599   2408514.599  398858.033
 33  WAG+R10       196241.628   1005 394493.256   2416553.256  398869.398
 42  WAG+F+R8      194842.645   1020 391725.291   2474565.291  396166.748
 43  WAG+F+R9      194839.005   1022 391722.011   2482734.011  396172.177
 53  JTT+R8        195608.757   1001 393219.514   2399223.514  397578.238
 54  JTT+R9        195593.125   1003 393192.250   2407216.250  397559.683
 55  JTT+R10       195590.207   1005 393190.414   2415250.414  397566.556
 64  JTT+F+R8      194695.864   1020 391431.729   2474271.729  395873.186
 65  JTT+F+R9      194690.743   1022 391425.486   2482437.486  395875.652
WARNING: Normalizing state frequencies so that sum of them equals to 1
 75  Q.pfam+R8     194892.568   1001 391787.135   2397791.135  396145.860
WARNING: Normalizing state frequencies so that sum of them equals to 1
 76  Q.pfam+R9     194887.665   1003 391781.330   2405805.330  396148.763
WARNING: Normalizing state frequencies so that sum of them equals to 1
 86  Q.pfam+F+R8   194521.401   1020 391082.801   2473922.801  395524.259
WARNING: Normalizing state frequencies so that sum of them equals to 1
 87  Q.pfam+F+R9   194515.431   1022 391074.862   2482086.862  395525.029
WARNING: Normalizing state frequencies so that sum of them equals to 1
 97  Q.bird+R8     197829.393   1001 397660.786   2403664.786  402019.511
WARNING: Normalizing state frequencies so that sum of them equals to 1
 98  Q.bird+R9     197820.275   1003 397646.550   2411670.550  402013.983
WARNING: Normalizing state frequencies so that sum of them equals to 1
 99  Q.bird+R10    197814.318   1005 397638.636   2419698.636  402014.778
WARNING: Normalizing state frequencies so that sum of them equals to 1
108  Q.bird+F+R8   198079.035   1020 398198.069   2481038.069  402639.527
WARNING: Normalizing state frequencies so that sum of them equals to 1
109  Q.bird+F+R9   198072.616   1022 398189.232   2489201.232  402639.398
WARNING: Normalizing state frequencies so that sum of them equals to 1
110  Q.bird+F+R10  198068.569   1024 398185.139   2497385.139  402644.014
WARNING: Normalizing state frequencies so that sum of them equals to 1
119  Q.mammal+R8   196715.407   1001 395432.814   2401436.814  399791.538
WARNING: Normalizing state frequencies so that sum of them equals to 1
120  Q.mammal+R9   196707.402   1003 395420.804   2409444.804  399788.237
WARNING: Normalizing state frequencies so that sum of them equals to 1
121  Q.mammal+R10  196703.479   1005 395416.958   2417476.958  399793.100
WARNING: Normalizing state frequencies so that sum of them equals to 1
130  Q.mammal+F+R8 196877.834   1020 395795.669   2478635.669  400237.126
WARNING: Normalizing state frequencies so that sum of them equals to 1
131  Q.mammal+F+R9 196872.663   1022 395789.327   2486801.327  400239.493
141  Q.insect+R8   195081.318   1001 392164.635   2398168.635  396523.360
142  Q.insect+R9   195076.551   1003 392159.102   2406183.102  396526.535
152  Q.insect+F+R8 194860.269   1020 391760.539   2474600.539  396201.996
153  Q.insect+F+R9 194858.288   1022 391760.576   2482772.576  396210.742
WARNING: Normalizing state frequencies so that sum of them equals to 1
163  Q.plant+R8    194919.373   1001 391840.745   2397844.745  396199.470
WARNING: Normalizing state frequencies so that sum of them equals to 1
164  Q.plant+R9    194913.090   1003 391832.180   2405856.180  396199.613
WARNING: Normalizing state frequencies so that sum of them equals to 1
174  Q.plant+F+R8  194822.604   1020 391685.208   2474525.208  396126.665
WARNING: Normalizing state frequencies so that sum of them equals to 1
175  Q.plant+F+R9  194819.592   1022 391683.184   2482695.184  396133.350
WARNING: Normalizing state frequencies so that sum of them equals to 1
185  Q.yeast+R8    195446.700   1001 392895.400   2398899.400  397254.125
WARNING: Normalizing state frequencies so that sum of them equals to 1
186  Q.yeast+R9    195439.881   1003 392885.762   2406909.762  397253.195
WARNING: Normalizing state frequencies so that sum of them equals to 1
187  Q.yeast+R10   195435.549   1005 392881.097   2414941.097  397257.239
WARNING: Normalizing state frequencies so that sum of them equals to 1
196  Q.yeast+F+R8  194579.068   1020 391198.136   2474038.136  395639.593
WARNING: Normalizing state frequencies so that sum of them equals to 1
197  Q.yeast+F+R9  194573.538   1022 391191.077   2482203.077  395641.243
207  JTTDCMut+R8   195684.064   1001 393370.127   2399374.127  397728.852
208  JTTDCMut+R9   195667.689   1003 393341.377   2407365.377  397708.810
209  JTTDCMut+R10  195664.727   1005 393339.454   2415399.454  397715.596
218  JTTDCMut+F+R8 194737.502   1020 391515.003   2474355.003  395956.461
219  JTTDCMut+F+R9 194732.541   1022 391509.083   2482521.083  395959.249
229  DCMut+R8      198858.399   1001 399718.798   2405722.798  404077.523
230  DCMut+R9      198850.908   1003 399707.816   2413731.816  404075.249
231  DCMut+R10     198848.803   1005 399707.606   2421767.606  404083.748
240  DCMut+F+R8    196826.536   1020 395693.071   2478533.071  400134.529
241  DCMut+F+R9    196816.360   1022 395676.721   2486688.721  400126.887
242  DCMut+F+R10   196813.450   1024 395674.901   2494874.901  400133.776
251  VT+R8         196235.054   1001 394472.109   2400476.109  398830.833
252  VT+R9         196229.175   1003 394464.350   2408488.350  398831.783
262  VT+F+R8       195084.460   1020 392208.920   2475048.920  396650.377
263  VT+F+R9       195080.573   1022 392205.145   2483217.145  396655.311
273  PMB+R8        197315.374   1001 396632.748   2402636.748  400991.472
274  PMB+R9        197308.918   1003 396623.836   2410647.836  400991.269
275  PMB+R10       197306.392   1005 396622.785   2418682.785  400998.926
284  PMB+F+R8      197173.282   1020 396386.563   2479226.563  400828.020
285  PMB+F+R9      197172.042   1022 396388.084   2487400.084  400838.251
295  Blosum62+R8   197539.412   1001 397080.824   2403084.824  401439.549
296  Blosum62+R9   197530.232   1003 397066.464   2411090.464  401433.897
297  Blosum62+R10  197526.017   1005 397062.034   2419122.034  401438.175
306  Blosum62+F+R8 196901.090   1020 395842.180   2478682.180  400283.637
307  Blosum62+F+R9 196899.776   1022 395843.552   2486855.552  400293.718
317  Dayhoff+R8    198852.273   1001 399706.545   2405710.545  404065.270
318  Dayhoff+R9    198844.881   1003 399695.761   2413719.761  404063.195
319  Dayhoff+R10   198842.886   1005 399695.772   2421755.772  404071.914
328  Dayhoff+F+R8  196817.472   1020 395674.945   2478514.945  400116.402
329  Dayhoff+F+R9  196807.436   1022 395658.873   2486670.873  400109.039
330  Dayhoff+F+R10 196804.462   1024 395656.923   2494856.923  400115.798
339  mtREV+R8      202211.703   1001 406425.405   2412429.405  410784.129
340  mtREV+R9      202203.018   1003 406412.035   2420436.035  410779.468
341  mtREV+R10     202198.737   1005 406407.475   2428467.475  410783.617
350  mtREV+F+R8    197257.838   1020 396555.675   2479395.675  400997.133
351  mtREV+F+R9    197248.935   1022 396541.871   2487553.871  400992.037
352  mtREV+F+R10   197245.156   1024 396538.312   2495738.312  400997.187
361  mtART+R8      203583.239   1001 409168.478   2415172.478  413527.203
362  mtART+R9      203529.654   1003 409065.309   2423089.309  413432.742
363  mtART+R10     203525.582   1005 409061.164   2431121.164  413437.306
372  mtART+F+R8    200433.253   1020 402906.506   2485746.506  407347.963
373  mtART+F+R9    200385.741   1022 402815.481   2493827.481  407265.647
374  mtART+F+R10   200379.364   1024 402806.728   2502006.728  407265.603
383  mtZOA+R8      198366.129   1001 398734.257   2404738.257  403092.982
384  mtZOA+R9      198360.117   1003 398726.235   2412750.235  403093.668
394  mtZOA+F+R8    196919.533   1020 395879.066   2478719.066  400320.523
395  mtZOA+F+R9    196898.434   1022 395840.867   2486852.867  400291.033
396  mtZOA+F+R10   196891.474   1024 395830.948   2495030.948  400289.823
405  mtMet+R8      200042.427   1001 402086.853   2408090.853  406445.578
406  mtMet+R9      200019.941   1003 402045.882   2416069.882  406413.316
407  mtMet+R10     200049.839   1005 402109.679   2424169.679  406485.821
416  mtMet+F+R8    196455.394   1020 394950.789   2477790.789  399392.246
417  mtMet+F+R9    196440.614   1022 394925.229   2485937.229  399375.395
418  mtMet+F+R10   196431.320   1024 394910.641   2494110.641  399369.516
427  mtVer+R8      203014.713   1001 408031.426   2414035.426  412390.150
428  mtVer+R9      203008.014   1003 408022.029   2422046.029  412389.462
429  mtVer+R10     202969.843   1005 407949.685   2430009.685  412325.827
438  mtVer+F+R8    198883.127   1020 399806.254   2482646.254  404247.711
439  mtVer+F+R9    198874.584   1022 399793.168   2490805.168  404243.334
440  mtVer+F+R10   198869.999   1024 399787.998   2498987.998  404246.873
449  mtInv+R8      200418.426   1001 402838.852   2408842.852  407197.577
450  mtInv+R9      200410.477   1003 402826.954   2416850.954  407194.387
451  mtInv+R10     200408.596   1005 402827.192   2424887.192  407203.334
460  mtInv+F+R8    195221.172   1020 392482.344   2475322.344  396923.802
461  mtInv+F+R9    195216.016   1022 392476.033   2483488.033  396926.199
471  mtMAM+R8      207137.637   1001 416277.273   2422281.273  420635.998
472  mtMAM+R9      207095.777   1003 416197.555   2430221.555  420564.988
473  mtMAM+R10     207079.072   1005 416168.143   2438228.143  420544.285
482  mtMAM+F+R8    202259.202   1020 406558.403   2489398.403  410999.861
483  mtMAM+F+R9    202225.832   1022 406495.663   2497507.663  410945.830
484  mtMAM+F+R10   202217.624   1024 406483.248   2505683.248  410942.123
WARNING: Normalizing state frequencies so that sum of them equals to 1
493  FLAVI+R8      202777.540   1001 407557.080   2413561.080  411915.804
WARNING: Normalizing state frequencies so that sum of them equals to 1
494  FLAVI+R9      202768.495   1003 407542.991   2421566.991  411910.424
WARNING: Normalizing state frequencies so that sum of them equals to 1
495  FLAVI+R10     202753.049   1005 407516.099   2429576.099  411892.240
WARNING: Normalizing state frequencies so that sum of them equals to 1
504  FLAVI+F+R8    202442.661   1020 406925.322   2489765.322  411366.780
WARNING: Normalizing state frequencies so that sum of them equals to 1
505  FLAVI+F+R9    202434.692   1022 406913.384   2497925.384  411363.551
WARNING: Normalizing state frequencies so that sum of them equals to 1
506  FLAVI+F+R10   202428.582   1024 406905.164   2506105.164  411364.039
515  HIVb+R8       200393.670   1001 402789.341   2408793.341  407148.065
516  HIVb+R9       200381.791   1003 402769.582   2416793.582  407137.016
517  HIVb+R10      200371.459   1005 402752.918   2424812.918  407129.060
526  HIVb+F+R8     198771.236   1020 399582.473   2482422.473  404023.930
527  HIVb+F+R9     198764.928   1022 399573.855   2490585.855  404024.021
537  HIVw+R8       209399.096   1001 420800.192   2426804.192  425158.916
538  HIVw+R9       209380.617   1003 420767.234   2434791.234  425134.668
539  HIVw+R10      209376.097   1005 420762.193   2442822.193  425138.335
548  HIVw+F+R8     204961.158   1020 411962.315   2494802.315  416403.773
549  HIVw+F+R9     204951.516   1022 411947.031   2502959.031  416397.198
550  HIVw+F+R10    204945.555   1024 411939.109   2511139.109  416397.984
559  FLU+R8        200582.056   1001 403166.112   2409170.112  407524.836
560  FLU+R9        200563.618   1003 403133.235   2417157.235  407500.668
561  FLU+R10       200558.394   1005 403126.789   2425186.789  407502.931
570  FLU+F+R8      199008.285   1020 400056.570   2482896.570  404498.027
571  FLU+F+R9      198994.223   1022 400032.445   2491044.445  404482.611
572  FLU+F+R10     198990.836   1024 400029.672   2499229.672  404488.547
581  rtREV+R8      198734.452   1001 399470.904   2405474.904  403829.628
582  rtREV+R9      198720.690   1003 399447.380   2413471.380  403814.813
583  rtREV+R10     198718.347   1005 399446.693   2421506.693  403822.835
592  rtREV+F+R8    196515.045   1020 395070.090   2477910.090  399511.547
593  rtREV+F+R9    196508.638   1022 395061.277   2486073.277  399511.443
594  rtREV+F+R10   196506.672   1024 395061.344   2494261.344  399520.219
603  cpREV+R8      196528.431   1001 395058.861   2401062.861  399417.586
604  cpREV+R9      196515.402   1003 395036.804   2409060.804  399404.237
605  cpREV+R10     196510.888   1005 395031.776   2417091.776  399407.918
614  cpREV+F+R8    195115.409   1020 392270.817   2475110.817  396712.275
615  cpREV+F+R9    195110.263   1022 392264.525   2483276.525  396714.691
Akaike Information Criterion:           LG+F+R9
Corrected Akaike Information Criterion: LG+G4
Bayesian Information Criterion:         LG+F+R8
Best-fit model: LG+F+R8 chosen according to BIC

All model information printed to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz
CPU time for ModelFinder: 787.371 seconds (0h:13m:7s)
Wall-clock time for ModelFinder: 303.545 seconds (0h:5m:3s)

===> START BOOTSTRAP REPLICATE NUMBER 97

Creating bootstrap alignment (seed: 827761)...

CHECKPOINT: Initial tree restored

NOTE: 232 MB RAM (0 GB) is required!
CHECKPOINT: Model parameters restored, LogL: -188937.768
Wrote distance file to... 
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
CHECKPOINT: Candidate tree set restored, best LogL: -188937.768
Finish initializing candidate tree set (20)
Current best tree score: -188937.768 / CPU time: 0.000
Number of iterations: 73
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 10.5173 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 74: -187593.430
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 75: -187521.887
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Iteration 80 / LogL: -187546.401 / Time: 0h:2m:17s (0h:2m:44s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 81: -187449.843
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Iteration 90 / LogL: -187508.192 / Time: 0h:4m:4s (0h:4m:10s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 100: -187440.067
Iteration 100 / LogL: -187440.067 / Time: 0h:5m:50s (0h:5m:54s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 107: -187438.363
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Iteration 110 / LogL: -187447.984 / Time: 0h:7m:40s (0h:6m:50s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 113: -187434.002
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Iteration 120 / LogL: -187508.203 / Time: 0h:9m:25s (0h:7m:21s left)
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Iteration 150 / LogL: -187450.953 / Time: 0h:14m:0s (0h:5m:55s left)
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Iteration 200 / LogL: -187502.210 / Time: 0h:22m:19s (0h:7m:31s left)
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Iteration 210 / LogL: -187441.754 / Time: 0h:23m:55s (0h:6m:31s left)
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BETTER TREE FOUND at iteration 212: -187426.688
Optimizing NNI: done in 10.7568 secs using 398.8% CPU
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BETTER TREE FOUND at iteration 218: -187426.193
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Iteration 220 / LogL: -187486.739 / Time: 0h:25m:41s (0h:11m:29s left)
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BETTER TREE FOUND at iteration 226: -187419.009
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Iteration 230 / LogL: -187494.547 / Time: 0h:27m:24s (0h:11m:29s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 240: -187412.519
Iteration 240 / LogL: -187412.519 / Time: 0h:29m:5s (0h:12m:10s left)
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Iteration 320 / LogL: -187475.462 / Time: 0h:41m:16s (0h:2m:35s left)
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Iteration 330 / LogL: -187435.164 / Time: 0h:42m:47s (0h:1m:18s left)
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Iteration 340 / LogL: -187489.335 / Time: 0h:44m:13s (0h:0m:0s left)
Optimizing NNI: done in 8.66567 secs using 399% CPU
TREE SEARCH COMPLETED AFTER 341 ITERATIONS / Time: 0h:44m:21s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -187412.519
Optimal log-likelihood: -187412.515
Site proportion and rates:  (0.034,0.154) (0.150,0.348) (0.202,0.527) (0.165,0.726) (0.204,1.003) (0.128,1.527) (0.089,2.310) (0.028,3.898)
Parameters optimization took 1 rounds (1.452 sec)
BEST SCORE FOUND : -187412.515
Total tree length: 150.321

Total number of iterations: 341
CPU time used for tree search: 10612.667 sec (2h:56m:52s)
Wall-clock time used for tree search: 2661.634 sec (0h:44m:21s)
Total CPU time used: 10618.964 sec (2h:56m:58s)
Total wall-clock time used: 2663.251 sec (0h:44m:23s)

===> START BOOTSTRAP REPLICATE NUMBER 98

Creating bootstrap alignment (seed: 827762)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.317 seconds

NOTE: 227 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -186283.427
2. Current log-likelihood: -183597.196
3. Current log-likelihood: -183559.421
4. Current log-likelihood: -183557.083
5. Current log-likelihood: -183551.528
6. Current log-likelihood: -183545.800
7. Current log-likelihood: -183544.535
8. Current log-likelihood: -183544.365
Optimal log-likelihood: -183544.355
Site proportion and rates:  (0.009,0.070) (0.085,0.222) (0.122,0.380) (0.183,0.538) (0.155,0.727) (0.189,1.037) (0.159,1.591) (0.098,2.805)
Parameters optimization took 8 rounds (29.514 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 14.5443 secs using 399.9% CPU
Computing ML distances took 14.545091 sec (of wall-clock time) 58.172249 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00208998 secs using 445.7% CPU
Constructing RapidNJ tree: done in 0.0321519 secs using 491.8% CPU
Computing RapidNJ tree took 0.034319 sec (of wall-clock time) 0.168132 sec (of CPU time)
Log-likelihood of RapidNJ tree: -186742.856
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.868 second
Computing log-likelihood of 98 initial trees ... 27.186 seconds
Current best score: -183544.355

Do NNI search on 20 best initial trees
Optimizing NNI: done in 6.47963 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -182895.693
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -182798.688
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 5: -182790.330
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Iteration 10 / LogL: -182899.258 / Time: 0h:3m:12s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 16: -182761.671
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Iteration 20 / LogL: -182894.913 / Time: 0h:4m:30s
Finish initializing candidate tree set (20)
Current best tree score: -182761.671 / CPU time: 223.578
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 26: -182747.813
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Iteration 30 / LogL: -182832.957 / Time: 0h:5m:50s (0h:19m:19s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 34: -182741.769
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Iteration 40 / LogL: -182774.186 / Time: 0h:7m:9s (0h:17m:14s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 42: -182737.533
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BETTER TREE FOUND at iteration 55: -182729.154
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 60: -182723.932
Iteration 60 / LogL: -182723.932 / Time: 0h:10m:0s (0h:16m:56s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 70: -182714.421
Iteration 70 / LogL: -182714.421 / Time: 0h:11m:28s (0h:16m:37s left)
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BETTER TREE FOUND at iteration 78: -182696.829
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Iteration 80 / LogL: -182797.856 / Time: 0h:12m:51s (0h:15m:56s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 83: -182685.880
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Iteration 90 / LogL: -182722.437 / Time: 0h:14m:12s (0h:14m:50s left)
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Iteration 100 / LogL: -182726.453 / Time: 0h:15m:29s (0h:12m:58s left)
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Iteration 310 / LogL: -182685.216 / Time: 0h:42m:19s (0h:1m:13s left)
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Iteration 320 / LogL: -182674.451 / Time: 0h:43m:36s (0h:0m:-9s left)
TREE SEARCH COMPLETED AFTER 320 ITERATIONS / Time: 0h:43m:36s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -182666.463
Optimal log-likelihood: -182666.457
Site proportion and rates:  (0.010,0.070) (0.083,0.222) (0.130,0.384) (0.177,0.546) (0.161,0.727) (0.183,1.042) (0.160,1.600) (0.096,2.825)
Parameters optimization took 1 rounds (1.629 sec)
BEST SCORE FOUND : -182666.457
Total tree length: 144.582

Total number of iterations: 320
CPU time used for tree search: 10151.988 sec (2h:49m:11s)
Wall-clock time used for tree search: 2569.457 sec (0h:42m:49s)
Total CPU time used: 10345.850 sec (2h:52m:25s)
Total wall-clock time used: 2618.169 sec (0h:43m:38s)

===> START BOOTSTRAP REPLICATE NUMBER 99

Creating bootstrap alignment (seed: 827763)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.311 seconds

NOTE: 234 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -188807.494
2. Current log-likelihood: -186169.548
3. Current log-likelihood: -186130.010
4. Current log-likelihood: -186128.239
5. Current log-likelihood: -186126.876
6. Current log-likelihood: -186124.911
7. Current log-likelihood: -186122.042
8. Current log-likelihood: -186118.597
9. Current log-likelihood: -186115.180
10. Current log-likelihood: -186113.284
11. Current log-likelihood: -186112.657
12. Current log-likelihood: -186112.485
Optimal log-likelihood: -186112.448
Site proportion and rates:  (0.022,0.101) (0.055,0.214) (0.181,0.389) (0.229,0.604) (0.165,0.838) (0.145,1.140) (0.097,1.748) (0.107,2.849)
Parameters optimization took 12 rounds (39.846 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 14.8559 secs using 399.9% CPU
Computing ML distances took 14.856562 sec (of wall-clock time) 59.412064 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00200105 secs using 198.8% CPU
Constructing RapidNJ tree: done in 0.0324092 secs using 479.3% CPU
Computing RapidNJ tree took 0.034475 sec (of wall-clock time) 0.160117 sec (of CPU time)
Log-likelihood of RapidNJ tree: -190345.859
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 29.430 second
Computing log-likelihood of 98 initial trees ... 28.572 seconds
Current best score: -186112.448

Do NNI search on 20 best initial trees
Optimizing NNI: done in 6.03707 secs using 398.5% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -185568.714
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -185458.738
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Iteration 10 / LogL: -185483.607 / Time: 0h:3m:35s
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 14: -185455.171
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Iteration 20 / LogL: -185535.905 / Time: 0h:5m:1s
Finish initializing candidate tree set (20)
Current best tree score: -185455.171 / CPU time: 237.881
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 7.06728 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -185395.446
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 29: -185369.475
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Iteration 30 / LogL: -185388.891 / Time: 0h:6m:37s (0h:22m:36s left)
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Iteration 40 / LogL: -185487.847 / Time: 0h:7m:58s (0h:18m:10s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 45: -185357.146
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Iteration 50 / LogL: -185365.414 / Time: 0h:9m:33s (0h:18m:31s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 60: -185355.984
Iteration 60 / LogL: -185355.984 / Time: 0h:11m:7s (0h:18m:51s left)
Optimizing NNI: done in 9.28299 secs using 398.7% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 66: -185353.425
Optimizing NNI: done in 10.2227 secs using 398.6% CPU
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Iteration 70 / LogL: -185553.960 / Time: 0h:12m:46s (0h:17m:45s left)
Optimizing NNI: done in 8.89174 secs using 398.8% CPU
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BETTER TREE FOUND at iteration 72: -185338.731
Optimizing NNI: done in 8.21065 secs using 398.8% CPU
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Iteration 80 / LogL: -185580.188 / Time: 0h:14m:23s (0h:16m:44s left)
Optimizing NNI: done in 9.22167 secs using 399% CPU
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Iteration 90 / LogL: -185395.145 / Time: 0h:15m:54s (0h:14m:38s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 98: -185335.339
Optimizing NNI: done in 10.8925 secs using 398.6% CPU
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Iteration 100 / LogL: -185354.424 / Time: 0h:17m:34s (0h:17m:23s left)
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Iteration 110 / LogL: -185374.216 / Time: 0h:19m:18s (0h:15m:35s left)
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Iteration 120 / LogL: -185371.215 / Time: 0h:20m:56s (0h:13m:43s left)
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Iteration 130 / LogL: -185594.859 / Time: 0h:22m:34s (0h:11m:54s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 132: -185329.753
Optimizing NNI: done in 9.92813 secs using 398.7% CPU
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Iteration 140 / LogL: -185391.448 / Time: 0h:24m:20s (0h:16m:6s left)
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Iteration 150 / LogL: -185373.664 / Time: 0h:25m:58s (0h:14m:17s left)
Optimizing NNI: done in 8.54817 secs using 399% CPU
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Iteration 160 / LogL: -185391.754 / Time: 0h:27m:36s (0h:12m:30s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 170: -185329.414
Iteration 170 / LogL: -185329.414 / Time: 0h:29m:16s (0h:17m:19s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 173: -185324.846
Optimizing NNI: done in 8.25617 secs using 398.4% CPU
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Iteration 180 / LogL: -185366.389 / Time: 0h:30m:54s (0h:16m:3s left)
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Iteration 190 / LogL: -185338.788 / Time: 0h:32m:27s (0h:14m:15s left)
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Iteration 200 / LogL: -185332.453 / Time: 0h:34m:0s (0h:12m:28s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 203: -185322.754
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Iteration 210 / LogL: -185375.872 / Time: 0h:35m:34s (0h:15m:49s left)
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Iteration 220 / LogL: -185425.198 / Time: 0h:37m:7s (0h:14m:3s left)
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Iteration 230 / LogL: -185330.557 / Time: 0h:38m:46s (0h:12m:21s left)
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Iteration 240 / LogL: -185378.123 / Time: 0h:40m:29s (0h:10m:40s left)
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Iteration 250 / LogL: -185483.602 / Time: 0h:42m:9s (0h:8m:58s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 253: -185321.459
Optimizing NNI: done in 9.06246 secs using 398.4% CPU
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Iteration 260 / LogL: -185406.630 / Time: 0h:43m:52s (0h:15m:45s left)
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Iteration 270 / LogL: -185330.837 / Time: 0h:45m:26s (0h:14m:1s left)
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Iteration 280 / LogL: -185362.101 / Time: 0h:46m:58s (0h:12m:17s left)
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Iteration 290 / LogL: -185386.169 / Time: 0h:48m:30s (0h:10m:34s left)
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Iteration 300 / LogL: -185365.806 / Time: 0h:50m:3s (0h:8m:52s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 307: -185319.686
Optimizing NNI: done in 8.72694 secs using 397.1% CPU
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Iteration 310 / LogL: -185441.634 / Time: 0h:51m:40s (0h:16m:13s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 316: -185312.691
Optimizing NNI: done in 8.24939 secs using 398.5% CPU
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Iteration 320 / LogL: -185337.225 / Time: 0h:53m:9s (0h:15m:59s left)
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Iteration 330 / LogL: -185330.996 / Time: 0h:54m:46s (0h:14m:19s left)
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Iteration 340 / LogL: -185357.737 / Time: 0h:56m:20s (0h:12m:37s left)
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Iteration 350 / LogL: -185336.463 / Time: 0h:57m:51s (0h:10m:56s left)
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Iteration 360 / LogL: -185339.735 / Time: 0h:59m:30s (0h:9m:16s left)
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Iteration 370 / LogL: -185339.569 / Time: 1h:0m:57s (0h:7m:35s left)
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Iteration 380 / LogL: -185369.625 / Time: 1h:2m:26s (0h:5m:55s left)
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Iteration 390 / LogL: -185324.568 / Time: 1h:3m:56s (0h:4m:16s left)
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Iteration 400 / LogL: -185367.714 / Time: 1h:5m:31s (0h:2m:37s left)
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Iteration 410 / LogL: -185368.644 / Time: 1h:7m:2s (0h:0m:59s left)
Optimizing NNI: done in 10.5282 secs using 398.8% CPU
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Optimizing NNI: done in 9.46917 secs using 398.8% CPU
Optimizing NNI: done in 9.27645 secs using 398.9% CPU
TREE SEARCH COMPLETED AFTER 417 ITERATIONS / Time: 1h:8m:12s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -185312.691
2. Current log-likelihood: -185312.648
3. Current log-likelihood: -185312.595
4. Current log-likelihood: -185312.549
5. Current log-likelihood: -185312.510
6. Current log-likelihood: -185312.477
Optimal log-likelihood: -185312.459
Site proportion and rates:  (0.022,0.100) (0.056,0.213) (0.188,0.389) (0.230,0.610) (0.146,0.845) (0.144,1.112) (0.108,1.700) (0.106,2.874)
Parameters optimization took 6 rounds (9.620 sec)
BEST SCORE FOUND : -185312.459
Total tree length: 151.149

Total number of iterations: 417
CPU time used for tree search: 15967.371 sec (4h:26m:7s)
Wall-clock time used for tree search: 4028.673 sec (1h:7m:8s)
Total CPU time used: 16261.238 sec (4h:31m:1s)
Total wall-clock time used: 4102.461 sec (1h:8m:22s)

===> START BOOTSTRAP REPLICATE NUMBER 100

Creating bootstrap alignment (seed: 827764)...

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.346 seconds

NOTE: 244 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194557.748
2. Current log-likelihood: -191948.046
3. Current log-likelihood: -191921.812
4. Current log-likelihood: -191918.192
5. Current log-likelihood: -191913.829
6. Current log-likelihood: -191910.325
7. Current log-likelihood: -191908.063
8. Current log-likelihood: -191906.735
9. Current log-likelihood: -191906.227
10. Current log-likelihood: -191906.075
Optimal log-likelihood: -191906.042
Site proportion and rates:  (0.020,0.083) (0.050,0.209) (0.136,0.372) (0.210,0.567) (0.211,0.810) (0.137,1.098) (0.127,1.658) (0.110,2.615)
Parameters optimization took 10 rounds (36.706 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 17.5686 secs using 399.9% CPU
Computing ML distances took 17.569403 sec (of wall-clock time) 70.262032 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.00213599 secs using 390.6% CPU
Constructing RapidNJ tree: done in 0.033005 secs using 483.6% CPU
Computing RapidNJ tree took 0.035222 sec (of wall-clock time) 0.170789 sec (of CPU time)
Log-likelihood of RapidNJ tree: -196029.813
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 30.364 second
Computing log-likelihood of 98 initial trees ... 29.737 seconds
Current best score: -191906.042

Do NNI search on 20 best initial trees
Optimizing NNI: done in 6.20479 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -191269.420
Optimizing NNI: done in 8.95472 secs using 398.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -191192.191
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -191187.174
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 6: -191154.005
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Iteration 10 / LogL: -191184.692 / Time: 0h:4m:3s
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Iteration 20 / LogL: -191169.013 / Time: 0h:5m:39s
Finish initializing candidate tree set (20)
Current best tree score: -191154.005 / CPU time: 281.528
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 8.95281 secs using 396.5% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -191121.258
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Iteration 30 / LogL: -191131.143 / Time: 0h:7m:19s (0h:23m:29s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 37: -191117.854
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Iteration 40 / LogL: -191142.308 / Time: 0h:8m:55s (0h:22m:10s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 47: -191093.918
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Iteration 50 / LogL: -191112.774 / Time: 0h:10m:34s (0h:20m:56s left)
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Iteration 60 / LogL: -191127.761 / Time: 0h:12m:4s (0h:17m:48s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -191093.657
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Iteration 70 / LogL: -191185.779 / Time: 0h:13m:38s (0h:18m:46s left)
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Iteration 80 / LogL: -191098.956 / Time: 0h:15m:8s (0h:16m:16s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 89: -191089.826
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Iteration 90 / LogL: -191172.333 / Time: 0h:16m:44s (0h:18m:36s left)
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Iteration 100 / LogL: -191126.761 / Time: 0h:18m:9s (0h:16m:19s left)
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Iteration 110 / LogL: -191252.083 / Time: 0h:19m:36s (0h:14m:12s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 117: -191081.670
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Iteration 120 / LogL: -191125.496 / Time: 0h:21m:14s (0h:17m:18s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 129: -191079.614
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Iteration 130 / LogL: -191132.788 / Time: 0h:22m:46s (0h:17m:28s left)
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Iteration 140 / LogL: -191097.845 / Time: 0h:24m:12s (0h:15m:29s left)
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Iteration 150 / LogL: -191126.955 / Time: 0h:25m:40s (0h:13m:36s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 156: -191076.412
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Iteration 160 / LogL: -191108.786 / Time: 0h:27m:12s (0h:16m:25s left)
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Iteration 170 / LogL: -191130.684 / Time: 0h:28m:47s (0h:14m:39s left)
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Iteration 180 / LogL: -191176.185 / Time: 0h:30m:20s (0h:12m:52s left)
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Iteration 190 / LogL: -191092.957 / Time: 0h:31m:50s (0h:11m:7s left)
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Iteration 200 / LogL: -191114.405 / Time: 0h:33m:22s (0h:9m:23s left)
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Optimizing NNI: done in 9.50091 secs using 398.5% CPU
Optimizing NNI: done in 9.09165 secs using 398.2% CPU
Optimizing NNI: done in 8.71591 secs using 398.5% CPU
Optimizing NNI: done in 7.80604 secs using 398.8% CPU
Optimizing NNI: done in 9.93226 secs using 398.4% CPU
Optimizing NNI: done in 8.66132 secs using 398.4% CPU
Optimizing NNI: done in 9.59744 secs using 397.6% CPU
Optimizing NNI: done in 6.67496 secs using 398.8% CPU
Iteration 210 / LogL: -191324.115 / Time: 0h:34m:49s (0h:7m:39s left)
Optimizing NNI: done in 9.48178 secs using 398.4% CPU
Optimizing NNI: done in 8.29585 secs using 398.5% CPU
Optimizing NNI: done in 8.1811 secs using 398% CPU
Optimizing NNI: done in 8.72366 secs using 398.5% CPU
Optimizing NNI: done in 10.4797 secs using 398.4% CPU
Optimizing NNI: done in 8.45933 secs using 398.6% CPU
Optimizing NNI: done in 8.30886 secs using 398.2% CPU
Optimizing NNI: done in 9.23573 secs using 398.2% CPU
Optimizing NNI: done in 8.82407 secs using 398.5% CPU
Optimizing NNI: done in 10.4297 secs using 398.5% CPU
Iteration 220 / LogL: -191188.040 / Time: 0h:36m:20s (0h:5m:58s left)
Optimizing NNI: done in 8.22922 secs using 398.5% CPU
Optimizing NNI: done in 8.6559 secs using 398.5% CPU
Optimizing NNI: done in 8.21339 secs using 398.7% CPU
Optimizing NNI: done in 8.93893 secs using 398.4% CPU
Optimizing NNI: done in 9.20273 secs using 398.8% CPU
Optimizing NNI: done in 8.79472 secs using 398.6% CPU
Optimizing NNI: done in 7.91372 secs using 398.4% CPU
Optimizing NNI: done in 11.3098 secs using 398.4% CPU
Optimizing NNI: done in 10.112 secs using 398.7% CPU
Optimizing NNI: done in 8.8441 secs using 398.4% CPU
Iteration 230 / LogL: -191118.204 / Time: 0h:37m:51s (0h:4m:17s left)
Optimizing NNI: done in 6.0014 secs using 398.8% CPU
Optimizing NNI: done in 12.1398 secs using 398.5% CPU
Optimizing NNI: done in 8.36034 secs using 397.7% CPU
Optimizing NNI: done in 11.034 secs using 398.3% CPU
Optimizing NNI: done in 8.86423 secs using 398.5% CPU
Optimizing NNI: done in 8.36123 secs using 398.5% CPU
Optimizing NNI: done in 8.71494 secs using 398.3% CPU
Optimizing NNI: done in 8.43151 secs using 398.4% CPU
Optimizing NNI: done in 8.26126 secs using 398.7% CPU
Optimizing NNI: done in 9.24355 secs using 398.5% CPU
Iteration 240 / LogL: -191083.679 / Time: 0h:39m:21s (0h:2m:38s left)
Optimizing NNI: done in 6.26397 secs using 398.5% CPU
Optimizing NNI: done in 11.4469 secs using 398.3% CPU
Optimizing NNI: done in 8.54739 secs using 398.5% CPU
Optimizing NNI: done in 9.26204 secs using 398.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 244: -191074.460
Optimizing NNI: done in 8.89018 secs using 398.4% CPU
Optimizing NNI: done in 9.31592 secs using 397.8% CPU
Optimizing NNI: done in 9.13988 secs using 398.6% CPU
Optimizing NNI: done in 8.76377 secs using 398.2% CPU
Optimizing NNI: done in 9.68625 secs using 398.4% CPU
Optimizing NNI: done in 9.1361 secs using 398.4% CPU
Iteration 250 / LogL: -191102.771 / Time: 0h:40m:55s (0h:15m:26s left)
Optimizing NNI: done in 8.14788 secs using 398.7% CPU
Optimizing NNI: done in 8.78512 secs using 398.4% CPU
Optimizing NNI: done in 7.36511 secs using 398.3% CPU
Optimizing NNI: done in 8.71905 secs using 398.5% CPU
Optimizing NNI: done in 8.66689 secs using 398.3% CPU
Optimizing NNI: done in 9.2319 secs using 398.4% CPU
Optimizing NNI: done in 7.78839 secs using 398.5% CPU
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Optimizing NNI: done in 9.03426 secs using 398.5% CPU
Optimizing NNI: done in 8.5967 secs using 397.7% CPU
Iteration 260 / LogL: -191100.766 / Time: 0h:42m:21s (0h:13m:44s left)
Optimizing NNI: done in 7.8839 secs using 398.6% CPU
Optimizing NNI: done in 9.62417 secs using 398.4% CPU
Optimizing NNI: done in 8.99684 secs using 398.4% CPU
Optimizing NNI: done in 8.72651 secs using 398.4% CPU
Optimizing NNI: done in 9.21704 secs using 398.2% CPU
Optimizing NNI: done in 8.80446 secs using 398.7% CPU
Optimizing NNI: done in 9.2593 secs using 398.4% CPU
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Optimizing NNI: done in 8.12456 secs using 398.4% CPU
Optimizing NNI: done in 9.24327 secs using 398.2% CPU
Iteration 270 / LogL: -191130.394 / Time: 0h:43m:49s (0h:12m:3s left)
Optimizing NNI: done in 8.09801 secs using 398.7% CPU
Optimizing NNI: done in 8.55767 secs using 398.4% CPU
Optimizing NNI: done in 8.46549 secs using 398.7% CPU
Optimizing NNI: done in 9.38997 secs using 398.7% CPU
Optimizing NNI: done in 8.5222 secs using 398.2% CPU
Optimizing NNI: done in 7.79869 secs using 398.3% CPU
Optimizing NNI: done in 8.223 secs using 398.5% CPU
Optimizing NNI: done in 8.28363 secs using 398.6% CPU
Optimizing NNI: done in 8.8977 secs using 398.3% CPU
Optimizing NNI: done in 9.1457 secs using 398.5% CPU
Iteration 280 / LogL: -191152.127 / Time: 0h:45m:15s (0h:10m:22s left)
Optimizing NNI: done in 9.01561 secs using 398.6% CPU
Optimizing NNI: done in 8.45489 secs using 398.3% CPU
Optimizing NNI: done in 8.59654 secs using 398.5% CPU
Optimizing NNI: done in 9.90617 secs using 398.8% CPU
Optimizing NNI: done in 8.99182 secs using 398.6% CPU
Optimizing NNI: done in 9.4424 secs using 398.8% CPU
Optimizing NNI: done in 8.676 secs using 398.6% CPU
Optimizing NNI: done in 8.48352 secs using 398.7% CPU
Optimizing NNI: done in 8.93222 secs using 398.8% CPU
Optimizing NNI: done in 9.00012 secs using 398.7% CPU
Iteration 290 / LogL: -191108.887 / Time: 0h:46m:45s (0h:8m:44s left)
Optimizing NNI: done in 7.83114 secs using 398.6% CPU
Optimizing NNI: done in 8.42499 secs using 398.9% CPU
Optimizing NNI: done in 8.86945 secs using 398.7% CPU
Optimizing NNI: done in 9.8286 secs using 396.2% CPU
Optimizing NNI: done in 8.72338 secs using 397.3% CPU
Optimizing NNI: done in 9.59793 secs using 398.3% CPU
Optimizing NNI: done in 9.48573 secs using 398% CPU
Optimizing NNI: done in 8.72359 secs using 398.2% CPU
Optimizing NNI: done in 10.6575 secs using 398.6% CPU
Optimizing NNI: done in 9.64462 secs using 397.9% CPU
Iteration 300 / LogL: -191083.836 / Time: 0h:48m:18s (0h:7m:6s left)
Optimizing NNI: done in 9.63965 secs using 398.6% CPU
Optimizing NNI: done in 8.94227 secs using 398.8% CPU
Optimizing NNI: done in 8.82081 secs using 398.3% CPU
Optimizing NNI: done in 8.844 secs using 398.5% CPU
Optimizing NNI: done in 9.58097 secs using 398.8% CPU
Optimizing NNI: done in 9.74246 secs using 398.9% CPU
Optimizing NNI: done in 8.49292 secs using 398.9% CPU
Optimizing NNI: done in 9.10746 secs using 397.9% CPU
Optimizing NNI: done in 9.78229 secs using 398.8% CPU
Optimizing NNI: done in 8.89587 secs using 398.9% CPU
Iteration 310 / LogL: -191113.901 / Time: 0h:49m:50s (0h:5m:29s left)
Optimizing NNI: done in 7.84693 secs using 398.8% CPU
Optimizing NNI: done in 9.6644 secs using 398.7% CPU
Optimizing NNI: done in 7.27029 secs using 398.2% CPU
Optimizing NNI: done in 9.82023 secs using 398.8% CPU
Optimizing NNI: done in 8.72548 secs using 398.9% CPU
Optimizing NNI: done in 9.80162 secs using 398.6% CPU
Optimizing NNI: done in 8.9207 secs using 398.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 317: -191073.748
Optimizing NNI: done in 8.95522 secs using 398.7% CPU
Optimizing NNI: done in 9.06738 secs using 398.3% CPU
Optimizing NNI: done in 9.07619 secs using 398.6% CPU
Iteration 320 / LogL: -191092.485 / Time: 0h:51m:22s (0h:15m:37s left)
Optimizing NNI: done in 9.13418 secs using 398.7% CPU
Optimizing NNI: done in 8.94965 secs using 398.5% CPU
Optimizing NNI: done in 8.9056 secs using 398.9% CPU
Optimizing NNI: done in 9.66121 secs using 398.8% CPU
Optimizing NNI: done in 10.1259 secs using 398.6% CPU
Optimizing NNI: done in 8.40574 secs using 398.8% CPU
Optimizing NNI: done in 8.5982 secs using 398.9% CPU
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Optimizing NNI: done in 9.12111 secs using 398.9% CPU
Optimizing NNI: done in 6.58133 secs using 398.9% CPU
Iteration 330 / LogL: -191101.704 / Time: 0h:52m:51s (0h:13m:58s left)
Optimizing NNI: done in 8.25923 secs using 398.6% CPU
Optimizing NNI: done in 9.14292 secs using 398% CPU
Optimizing NNI: done in 9.19788 secs using 398.8% CPU
Optimizing NNI: done in 8.39859 secs using 398.9% CPU
Optimizing NNI: done in 8.68342 secs using 398.4% CPU
Optimizing NNI: done in 9.54742 secs using 398.4% CPU
Optimizing NNI: done in 9.66319 secs using 398.5% CPU
Optimizing NNI: done in 8.82815 secs using 398% CPU
Optimizing NNI: done in 10.0307 secs using 398.7% CPU
Optimizing NNI: done in 8.61922 secs using 398.5% CPU
Iteration 340 / LogL: -191079.347 / Time: 0h:54m:22s (0h:12m:21s left)
Optimizing NNI: done in 8.44778 secs using 398.4% CPU
Optimizing NNI: done in 9.1292 secs using 398.6% CPU
Optimizing NNI: done in 9.48042 secs using 398.4% CPU
Optimizing NNI: done in 9.42172 secs using 398.5% CPU
Optimizing NNI: done in 8.25759 secs using 398.5% CPU
Optimizing NNI: done in 9.88017 secs using 398.4% CPU
Optimizing NNI: done in 8.60535 secs using 398.6% CPU
Optimizing NNI: done in 9.62939 secs using 398.7% CPU
Optimizing NNI: done in 8.22051 secs using 398% CPU
Optimizing NNI: done in 9.66577 secs using 398.6% CPU
Iteration 350 / LogL: -191095.156 / Time: 0h:55m:54s (0h:10m:43s left)
Optimizing NNI: done in 8.16925 secs using 398.4% CPU
Optimizing NNI: done in 8.85508 secs using 398.4% CPU
Optimizing NNI: done in 7.11087 secs using 398.8% CPU
Optimizing NNI: done in 9.38275 secs using 398.5% CPU
Optimizing NNI: done in 8.82583 secs using 397.8% CPU
Optimizing NNI: done in 8.89345 secs using 398.5% CPU
Optimizing NNI: done in 8.9624 secs using 398.7% CPU
Optimizing NNI: done in 8.52841 secs using 398.7% CPU
Optimizing NNI: done in 9.56016 secs using 398.4% CPU
Optimizing NNI: done in 9.23667 secs using 398.4% CPU
Iteration 360 / LogL: -191096.461 / Time: 0h:57m:22s (0h:9m:6s left)
Optimizing NNI: done in 8.96791 secs using 398.4% CPU
Optimizing NNI: done in 8.5878 secs using 398.3% CPU
Optimizing NNI: done in 9.2002 secs using 398.5% CPU
Optimizing NNI: done in 9.54648 secs using 398.2% CPU
Optimizing NNI: done in 8.08342 secs using 398.7% CPU
Optimizing NNI: done in 8.4944 secs using 397.7% CPU
Optimizing NNI: done in 7.93826 secs using 398.4% CPU
Optimizing NNI: done in 8.95623 secs using 398.6% CPU
Optimizing NNI: done in 8.4941 secs using 398.4% CPU
Optimizing NNI: done in 8.80967 secs using 398.4% CPU
Iteration 370 / LogL: -191082.447 / Time: 0h:58m:50s (0h:7m:29s left)
Optimizing NNI: done in 8.72098 secs using 398.5% CPU
Optimizing NNI: done in 8.30956 secs using 397.7% CPU
Optimizing NNI: done in 9.4596 secs using 398.7% CPU
Optimizing NNI: done in 8.46135 secs using 398.5% CPU
Optimizing NNI: done in 8.84252 secs using 398.2% CPU
Optimizing NNI: done in 7.79995 secs using 398.5% CPU
Optimizing NNI: done in 7.90372 secs using 398.6% CPU
Optimizing NNI: done in 8.80291 secs using 398.4% CPU
Optimizing NNI: done in 9.26329 secs using 398.5% CPU
Optimizing NNI: done in 11.7964 secs using 398.2% CPU
Iteration 380 / LogL: -191089.296 / Time: 1h:0m:20s (0h:5m:53s left)
Optimizing NNI: done in 7.47595 secs using 398.5% CPU
Optimizing NNI: done in 8.92794 secs using 398.6% CPU
Optimizing NNI: done in 8.19794 secs using 398.6% CPU
Optimizing NNI: done in 9.29779 secs using 398.6% CPU
Optimizing NNI: done in 8.42515 secs using 398.5% CPU
Optimizing NNI: done in 8.2373 secs using 398.6% CPU
Optimizing NNI: done in 9.02559 secs using 398.2% CPU
Optimizing NNI: done in 8.64193 secs using 398.5% CPU
Optimizing NNI: done in 8.90117 secs using 398.3% CPU
Optimizing NNI: done in 8.08142 secs using 398.7% CPU
Iteration 390 / LogL: -191178.091 / Time: 1h:1m:46s (0h:4m:17s left)
Optimizing NNI: done in 8.69274 secs using 398.5% CPU
Optimizing NNI: done in 8.64282 secs using 398.4% CPU
Optimizing NNI: done in 9.1051 secs using 398.2% CPU
Optimizing NNI: done in 8.1474 secs using 398.1% CPU
Optimizing NNI: done in 9.03123 secs using 398.8% CPU
Optimizing NNI: done in 8.69947 secs using 398.5% CPU
Optimizing NNI: done in 8.17534 secs using 398.6% CPU

******************************************************
CHECKPOINT: Resuming analysis from /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.ckp.gz

IQ-TREE multicore version 2.2.2.7 COVID-edition for Linux 64-bit built May 31 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    Arjun (AVX512, FMA3, 251 GB RAM)
Command: iqtree2 -s /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta -b 100 --tbe -T AUTO --prefix /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport
Seed:    429942 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Fri Jul 11 10:11:30 2025
Kernel:  AVX+FMA - auto-detect threads (96 CPU cores detected)

Reading alignment file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/trimaI_alignment/transport.fasta ... Fasta format detected
Reading fasta file: done in 0.00441408 secs using 95.67% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.00801802 secs using 6772% CPU
Alignment has 495 sequences with 575 columns, 575 distinct patterns
575 parsimony-informative, 0 singleton sites, 0 constant sites
            Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.00020504 secs using 6655% CPU
   1  8nJh6NUzJV   12.00%    passed     10.27%
   2  z0YCu0xtFo   11.30%    passed     15.88%
   3  1JN1q1h7Jh    8.35%    passed      9.02%
   4  E2n5Y5UQiG    8.52%    passed     43.28%
   5  cMoC1WsTO6    8.17%    failed      2.01%
   6  ys0DcEs0US    8.35%    passed     77.31%
   7  1s9qnaxMSp    9.04%    failed      2.14%
   8  FtHEpsU1vB    9.04%    failed      2.61%
   9  oeJuwbyE7Q    9.91%    passed      8.44%
  10  qCgVEYLhzI   17.39%    passed      9.43%
  11  zyhovbZkFP    9.91%    passed      8.44%
  12  jOk4aex96C   19.65%    passed      9.17%
  13  AR0npWZQ83    8.17%    passed     22.96%
  14  F5Si2gBtZe   21.91%    passed     13.69%
  15  FG021XCxMA   18.09%    passed     68.58%
  16  MCX7xygB2V    8.70%    passed     73.82%
  17  iVpOwiZzba    9.04%    passed     21.82%
  18  iPjBM3iYZR   80.35%    failed      2.62%
  19  qbFBJDOQUO    9.39%    passed     92.00%
  20  x5jv5lpB2O    9.22%    passed     43.94%
  21  y5M7y721WQ   11.30%    passed     52.45%
  22  MwDLYKIKBx   16.70%    passed     52.35%
  23  EsTTc2nPxQ    8.00%    passed     56.73%
  24  vnhywKRkFl   13.91%    passed     61.80%
  25  7JZdwvMv24   10.09%    passed     62.94%
  26  dQjyx7OIYV   27.30%    passed     66.63%
  27  irBovt5bLa    8.17%    passed     37.03%
  28  Ewm24Mlvnq    8.17%    failed      0.91%
  29  XDJ4JoLzyH   17.22%    passed     87.03%
  30  4kC0x0kjdn    7.65%    passed     35.61%
  31  RARcF60S6a    8.00%    passed     18.15%
  32  WlelCJO26H   12.17%    passed     15.31%
  33  mhk5OTojgz    7.83%    passed     22.72%
  34  pTM2DvE1xM    7.83%    passed     23.80%
  35  tlXXT5aWqu    8.35%    passed     25.18%
  36  TC8Xnd4iFa    8.35%    passed     68.65%
  37  02HhJs6pa3   11.13%    passed     51.90%
  38  NEeqpPtHg5    9.91%    passed     53.60%
  39  qbTDasygHV    8.00%    failed      4.34%
  40  7Yh1YhvFVC    9.04%    passed     82.42%
  41  VvE6sMyCv8    9.22%    passed     82.98%
  42  WjMMQYeUC2    9.74%    passed     28.42%
  43  W7Mh0FRDU6    9.57%    passed     47.24%
  44  2nrE64urGV    7.83%    failed      0.05%
  45  UzprTJ7K6d    7.83%    failed      0.07%
  46  UlwuxTyGoO    8.17%    passed     35.83%
  47  iaXjDyTif3    9.91%    passed     26.12%
  48  B6M0EvUDsT    8.17%    passed     57.64%
  49  1G5hXRghEG    7.83%    passed     46.06%
  50  gTvhxQmbWZ    7.83%    passed     59.90%
  51  8l37MLA1ms    7.83%    passed     66.42%
  52  vLizyHtRBL    6.96%    passed     45.67%
  53  S5ByYpGeqY    7.30%    passed     14.75%
  54  Fedl6T4xon    7.83%    passed     26.99%
  55  4BymctPkH6    9.22%    passed     90.46%
  56  s5wLZ9vWaO   22.96%    passed     14.42%
  57  awKrv6hUok    8.00%    failed      0.00%
  58  kWFqKgyYB3   18.61%    failed      0.35%
  59  DcYLS8gvW9    8.17%    passed     14.76%
  60  McRlo7Hy0B    8.35%    failed      1.15%
  61  tf71jZDs7S   14.78%    failed      0.00%
  62  vMqsZO8YaG   12.00%    passed     25.19%
  63  5AMYxNwgiK   14.26%    passed     72.77%
  64  wxoZBV0PHy    7.65%    passed     28.65%
  65  KeSH8I0Fea   10.96%    passed     34.97%
  66  KCrIGLQ7Q1    8.87%    passed     28.42%
  67  4LT0U0c0Do    8.17%    passed     45.98%
  68  CGeXrJPsGL    7.30%    passed     26.80%
  69  xxKiyIW1gr    8.35%    passed     42.35%
  70  xs9ieaVe53   24.17%    passed      5.89%
  71  NQWmJIpRFE    8.17%    passed     36.46%
  72  nkfchBpcgh    9.91%    passed     49.94%
  73  jdOhfl36g8    9.91%    passed     49.94%
  74  KVoy4GxdpT    8.70%    passed     30.77%
  75  WUIEff6ikU    9.74%    failed      3.44%
  76  coeQ6zHZ24    8.52%    passed     15.26%
  77  HWG7P94Eio    7.65%    passed     33.53%
  78  9Vw494DXPc    9.74%    passed     30.82%
  79  g6PJxKZvcf    8.17%    passed     67.92%
  80  AvvCKxHYp4    8.87%    passed     94.08%
  81  CemxIJafw8    8.87%    passed     94.94%
  82  dsBdLHptXN    7.30%    passed     26.31%
  83  4MVqW0qAIi    8.17%    passed      7.58%
  84  LcWgRv0iB6    8.17%    passed      6.57%
  85  fd8RtQX78T    8.35%    passed     67.99%
  86  D9LASQ998i    7.13%    passed     64.85%
  87  Uz7TnODNGf    8.17%    passed     61.10%
  88  Sp3Vq6QoAR   12.00%    passed     25.06%
  89  gtPloLimDb   14.61%    passed     16.69%
  90  GFnS6AyinZ   13.74%    passed     62.22%
  91  U9Eib0qR6X    9.39%    passed     80.44%
  92  dZ9ze414KZ    8.52%    passed     34.81%
  93  ydHAIeuwbW    9.04%    passed     24.32%
  94  e67HigPrjf    8.70%    passed     10.03%
  95  U5KrYXobqi    7.83%    passed     28.30%
  96  rqX0m8aZs1    8.52%    passed     74.68%
  97  JTOoSRn6ib    8.52%    passed     63.83%
  98  X4XbPR7Rfa    9.91%    passed     88.47%
  99  etCZH2Htco   11.30%    passed     96.50%
 100  7kS1ZU0pFM    9.74%    passed     63.62%
 101  rUnfYSLNJJ    8.35%    passed     25.59%
 102  YjqMqBCaiv    7.13%    passed     35.60%
 103  YXN7x6IbOx    8.35%    passed     52.18%
 104  bN8jt2Atwp   10.43%    passed     56.67%
 105  hgeyXdJgqq    9.22%    passed     56.85%
 106  1horVoEi3u    7.13%    failed      1.07%
 107  EDGqQf981n   10.09%    passed     86.16%
 108  3nDVNG9sKr   10.61%    passed     15.44%
 109  fFDoKaygf0    8.00%    passed     43.10%
 110  cRRsJgsBlZ    8.70%    passed     85.09%
 111  BI3jho3ECe    9.22%    passed     51.11%
 112  TIeppwLKSz    9.57%    passed     34.47%
 113  a8nt9ktZTC   24.35%    passed     70.98%
 114  GtfO72MtR2   22.26%    passed     65.46%
 115  xKzEmKT1dB   21.39%    passed     47.26%
 116  cTDPKciopP   11.83%    passed     67.98%
 117  xdNOUh7eMp    8.00%    passed     86.96%
 118  k3bzPFly41    8.17%    failed      0.00%
 119  ukUu00fP6L    9.39%    failed      0.29%
 120  up1UWJJzNf    9.22%    failed      3.36%
 121  GZASsy6wnT    8.17%    failed      0.00%
 122  PbkNCoK5ix   10.96%    passed     34.06%
 123  GfLEAInBd6   10.26%    passed     45.24%
 124  7OOuM97Qkr    8.70%    passed     42.00%
 125  d9kVhxwUcH    9.22%    passed     36.90%
 126  pn3nIof2qW    8.70%    passed     82.33%
 127  jYBcxGIen7   19.30%    passed     48.83%
 128  Y2YJcqt3IL   27.30%    passed     72.36%
 129  DQnwdMJsVl    9.39%    passed     17.77%
 130  Gvb4AsKEVi    8.35%    failed      0.00%
 131  d5E6EHDpwi    7.65%    passed     78.94%
 132  yA69Aemq0C    9.57%    passed     51.08%
 133  9f7AMvazZf    8.70%    passed     87.18%
 134  tD3ewCYOQG    9.22%    passed     39.14%
 135  yHwEtbE4JZ    8.87%    passed     51.50%
 136  HZpFQAW00k   12.87%    passed     16.94%
 137  FCPk6mdvI6    8.35%    passed     85.41%
 138  C50stY8CeY    9.22%    passed     15.26%
 139  WQOxpzhoLN    8.17%    passed     95.19%
 140  lU6fN5cAZQ   16.87%    passed     26.00%
 141  w34zJrGIvJ   13.04%    passed     46.23%
 142  R4SazYxajJ   13.22%    passed     24.74%
 143  oyLJTIsT1Z   12.00%    passed     35.61%
 144  95FTGjmRiw   16.87%    passed     10.92%
 145  MVSYHU9DCt   12.17%    passed     83.71%
 146  RhS1O12ekg    8.52%    passed     98.08%
 147  sthKhyT8fy    9.04%    passed     79.34%
 148  O2gQ2myCZn   11.30%    passed     66.29%
 149  B7PVgc3v8q    8.52%    passed     67.20%
 150  FlAHhYz62Q    6.96%    passed     92.12%
 151  PZqL2meUHi    8.35%    passed     89.55%
 152  XJTzBvD6pQ    8.70%    passed     73.32%
 153  FtEYGIUfBM   10.78%    passed     55.74%
 154  NUAWacASLt   10.26%    passed     81.70%
 155  3FdA2TKbHR   10.26%    passed     77.97%
 156  TCgaJethwm    9.74%    passed     51.49%
 157  V8Ort0OUIV    9.39%    passed     75.80%
 158  gKxOBa9lC3   80.35%    failed      4.37%
 159  ZJBcyycwk4   21.91%    passed     83.00%
 160  BXOEqGyzK2    9.04%    passed     82.96%
 161  5yy8DKtZ5c   12.35%    passed     70.92%
 162  cY7oeSnppq    9.74%    passed     78.00%
 163  vUEx5gqasN    9.74%    passed     22.71%
 164  2jCJDig3v9   17.39%    passed     45.79%
 165  lzBWRCtyx0   17.39%    passed     45.79%
 166  DBMxujRgHK   10.43%    passed     76.44%
 167  x3ZrH0XGfQ   13.04%    passed     40.57%
 168  SgWCfVzTG4    9.39%    passed     23.64%
 169  f62ksK5UEj   33.39%    passed     48.62%
 170  hkIztfSCD1   10.09%    passed     60.28%
 171  iRnB4M1GLD   11.30%    passed     35.88%
 172  CU0XuCnsFL   42.61%    failed      1.05%
 173  42tdKq8PSX   12.87%    passed     50.93%
 174  gXeZ52LCvM   12.87%    passed     50.93%
 175  u8cLLIfWEX   12.87%    passed     50.93%
 176  dmOh7r7eKT   12.52%    passed     43.59%
 177  3c6hZoOqvP   12.87%    passed     51.70%
 178  bu2UDzewiZ   16.35%    passed     97.52%
 179  SYc4eSftSt    7.30%    passed     55.76%
 180  zlSzVB3W0P    9.91%    passed     23.47%
 181  3C2pM8OlsA   16.00%    passed     44.07%
 182  Pxcz4xw4KG    8.52%    passed     89.90%
 183  UcghE30qVq   10.26%    passed     98.72%
 184  qIB6gS9bgA   10.26%    passed     99.50%
 185  UDehzYJL1w    9.91%    passed     84.08%
 186  BB4241mZBL    9.74%    passed     18.51%
 187  c6c8r06RzT   14.09%    passed     51.46%
 188  XQT9xr4ybf   14.09%    passed     51.46%
 189  SCnTy3bpY1   12.00%    passed     52.85%
 190  jev8yDUHvc   37.22%    passed     46.96%
 191  bK3G4lRT3G    9.74%    passed     18.84%
 192  Z5XH3L582l    9.39%    passed     64.30%
 193  dhUTnrRr7d    9.04%    passed     17.65%
 194  2ifGWJmasz   13.39%    passed     53.39%
 195  WB36HQui6V   13.22%    passed     13.09%
 196  QNNkPiHWnJ   13.57%    passed     15.99%
 197  WHGNQkrc10   16.70%    passed     15.42%
 198  h5LGHiiOXm   13.04%    passed      8.14%
 199  3zhlkwsAL6   11.65%    passed     68.02%
 200  i2Lb0rchl2   17.74%    passed     40.76%
 201  yMqx9t1LVd   11.83%    passed     95.23%
 202  2W3WY0vBww   18.09%    passed     31.19%
 203  wTTqfzkYo6   12.35%    passed     65.69%
 204  0vKBWD6wpY   19.83%    passed     72.14%
 205  SJgohIdqev   13.04%    passed     56.62%
 206  9DPLpYQWNv    8.35%    passed     79.37%
 207  8uUTsKFjlb    9.74%    passed     57.77%
 208  xVujdvY6Nr   15.65%    passed     86.08%
 209  NImtrhZGKE   18.61%    passed     29.08%
 210  YugOzGk8Ov    8.00%    passed     61.92%
 211  DeWEtikGbq    9.39%    passed     58.48%
 212  x0olbpog9B   10.78%    failed      3.15%
 213  pAhidh8xBZ    9.22%    passed     20.39%
 214  PlPvNaQDzl   78.26%    failed      2.70%
 215  NPvXCeLNmx    9.22%    passed     19.23%
 216  yVup7G0SEF    9.39%    passed      5.94%
 217  vPQhR8sENE    9.22%    passed     25.50%
 218  nU2WbHAcGl    8.00%    passed     38.25%
 219  5LDURAlPH2   18.96%    passed     93.03%
 220  BWFcvfZnO3   19.83%    passed     80.72%
 221  pygYFVFfpx   18.96%    passed     64.25%
 222  SHqN6p0dYV   11.65%    passed     77.47%
 223  qsVXrYaG9q   16.52%    passed     62.49%
 224  3cAaekWMpW   17.57%    passed     67.41%
 225  N40B32hpg1   12.00%    passed     79.79%
 226  JPT5lhIP82   16.17%    passed     61.51%
 227  ZLXDnoVm6b    8.87%    passed     65.21%
 228  X85YtZdfkf    9.04%    passed     76.50%
 229  8UiTG47Ec2    9.04%    passed     76.50%
 230  rIeH6RocN2   11.13%    passed     16.99%
 231  JEeirH12E1   31.48%    passed     21.21%
 232  UzAtwShlJN   15.48%    failed      0.00%
 233  2pVvPoBi2c   15.65%    failed      0.00%
 234  scQ10Wo461   39.13%    passed     23.66%
 235  Nb1rJKftmp   17.91%    failed      0.00%
 236  nhoqJOOPX2   17.04%    passed     88.57%
 237  39gkmZTScW   18.26%    passed     91.96%
 238  BGkr4JUYAf   13.39%    passed     93.93%
 239  DulbVCzsEt   24.35%    passed     66.60%
 240  cSruxLJuyQ   26.96%    passed     10.64%
 241  1XfSwqn4ef   25.04%    passed     39.48%
 242  96xj01KeXJ   68.17%    passed     84.97%
 243  eq1zGc6rtT   29.04%    passed     18.35%
 244  VfUM5i9jsn   41.91%    failed      4.66%
 245  20sicocoSo   23.83%    failed      0.74%
 246  RLpJhYeIPE   25.91%    passed     47.76%
 247  C8YPeCC1NI   28.87%    passed     14.80%
 248  xxnHHiKI8Z   28.52%    passed      5.76%
 249  3Je7M7o4rZ   33.39%    passed     11.10%
 250  47EKfQlPcw   28.35%    passed     38.14%
 251  9C0byE309K   34.43%    passed     22.05%
 252  TsIfWQzrph   28.35%    passed     38.14%
 253  hTPGiqrFV4   42.09%    passed     88.30%
 254  aFMglfB8eH   24.52%    passed     15.36%
 255  JQcRFbokY2   28.35%    passed     32.19%
 256  jFdaAxFg6n   23.13%    passed     47.94%
 257  KRYbednenZ   23.13%    passed     42.60%
 258  FyIDyqrLwr   23.13%    passed     47.94%
 259  8XGfcNsQ09   23.83%    passed     62.09%
 260  QyNf0mVNlz   23.83%    passed     10.54%
 261  f9oKgpE1wE   23.48%    passed     56.82%
 262  REBVZFiPEf   23.30%    passed     27.01%
 263  ItesG8T6sN   23.83%    passed     47.79%
 264  TSGS90hx1G   23.30%    passed     24.55%
 265  ZRAzqCtrNA   24.17%    passed     57.76%
 266  eeM5JHuVuf   24.35%    passed     50.06%
 267  oe9Vawfrxg   24.35%    passed     26.16%
 268  rgglFfiKnC   28.00%    passed     45.26%
 269  bCjdcpAF4v   24.00%    passed     70.09%
 270  OmcerY3zVm   64.35%    passed     66.28%
 271  zcG6I9U7zt   43.13%    passed     73.90%
 272  QKniumy84t   24.00%    passed     71.91%
 273  158IGk2w8A   24.00%    passed     40.59%
 274  kI8iG2U2gQ   23.30%    passed     85.81%
 275  fPZNEk39Af   26.78%    passed     15.99%
 276  hrBvV4AmlN   24.17%    passed     20.25%
 277  myGUzZ8LDH   24.00%    passed     24.24%
 278  sHkv5UU91e   23.65%    passed     10.45%
 279  GNzRUX9ddm   23.65%    passed     13.36%
 280  zsnvwGvGgv   24.00%    passed     30.90%
 281  9OoygEJxNJ   23.13%    passed     19.47%
 282  IjtzwwEpZt   24.70%    passed     32.04%
 283  nSDhHtKOaz   76.87%    passed     72.40%
 284  A0R7Dl6WnL   24.00%    passed     27.63%
 285  CvviaWP5QG   24.17%    passed     57.70%
 286  pPSEGFgq5j   79.13%    passed     12.51%
 287  UdG6KQNIp6   24.52%    passed      9.66%
 288  8EVSPtaAhX   24.35%    passed     42.22%
 289  uiafGbGfwA   27.30%    passed     85.86%
 290  XZFyxFJmTO   24.70%    passed     34.27%
 291  H6HkWi4jLJ   26.26%    passed     57.81%
 292  uALm9y36Bq   28.70%    passed     22.86%
 293  EUEmaNv0jU   23.30%    passed     16.64%
 294  miFIpMQUO8   25.04%    passed      5.34%
 295  qsWsb5TOjf   26.09%    passed     11.23%
 296  WLDkRifOr1   25.74%    passed     31.25%
 297  u7RGaLBmh5   25.74%    passed     85.68%
 298  n4n2Sa9hou   25.39%    passed     53.48%
 299  gZV6bt6UCn   24.17%    passed     46.31%
 300  PortTSlpTI   41.74%    passed     26.87%
 301  2Nn52BMVGD   28.00%    passed     32.50%
 302  sQl8vIYhWL   27.30%    passed     24.87%
 303  nlyynuwvAY   27.13%    passed     84.06%
 304  iM9z6TKAcr   41.39%    passed     18.69%
 305  pVpmbqWKfw   36.70%    failed      1.72%
 306  r4JpMWXYFJ   26.09%    passed     11.04%
 307  CcX8oiPHcg   27.83%    passed     27.83%
 308  G2BVFEVILA   25.04%    passed     61.18%
 309  BNYVmW4TYG   25.91%    passed     54.90%
 310  ExQ8uNPj7h   34.26%    passed     66.82%
 311  whmj06xoF5   28.17%    failed      0.02%
 312  VqFVtnHfVy   25.22%    passed     79.18%
 313  Mqy8imXZ6G   25.91%    failed      0.02%
 314  s0NXcs97L3   25.91%    failed      0.02%
 315  Iqt8ZiOu6k   25.74%    failed      0.00%
 316  XsWTxkH1p7   25.57%    passed     19.64%
 317  zoRaGfFB7U   24.52%    passed     48.77%
 318  qqN1dh1OOy   24.35%    passed     14.36%
 319  T1wQDvF98B   24.35%    passed      7.77%
 320  lkTsXyry76   26.43%    passed     26.11%
 321  hSqg5YYyOm   27.48%    failed      0.44%
 322  puRVWMvppN   28.35%    passed     22.55%
 323  1LbFAdgLuC   25.74%    passed     11.73%
 324  y5MmiioIHk   25.91%    failed      1.83%
 325  BnR8odZPBs   25.91%    passed     15.58%
 326  ajGvkpi5As   25.91%    passed      8.73%
 327  qbTJcwpdwP   26.61%    passed     13.99%
 328  vCxAIjCqNl   24.87%    passed     46.42%
 329  mPlwp1JlUK   27.30%    passed     36.54%
 330  rYWDHuLHvt   29.91%    failed      1.32%
 331  C0RnyRzFMX   71.65%    passed     45.95%
 332  7Aa2sW2uFn   28.00%    failed      3.36%
 333  0djEp2FhF9   28.00%    failed      3.36%
 334  l1pN6WjG1N   80.17%    passed     21.40%
 335  XLgmciWSgo   46.09%    passed     14.00%
 336  D8WaLv1pNN   30.78%    passed     27.06%
 337  12VY0qcAbu   29.39%    passed     74.33%
 338  JNoGNci0kO   28.87%    passed     95.56%
 339  VGEALS8WvR   40.70%    passed     16.49%
 340  D7iWRjKQ8X   25.74%    passed     47.65%
 341  upEmmPcbTB   27.48%    passed     22.48%
 342  UpKcpH8xp2   26.78%    passed      7.74%
 343  hreWbDAWDh   23.65%    passed      8.09%
 344  5oPFYbGk9x   24.52%    passed     66.68%
 345  bKMx8usLZf   35.83%    passed      9.39%
 346  9waTHuOjG2   43.48%    passed     27.73%
 347  y13PUGF6fd   29.39%    passed     50.29%
 348  MCxeCrj6og   25.22%    passed     77.92%
 349  JqQlZRu8jp   25.91%    passed     38.60%
 350  ZrMp8mhVn3   56.35%    passed      9.73%
 351  PVum0t8D9w   48.52%    failed      3.01%
 352  mA0FIy0SqW   24.70%    passed      5.42%
 353  EacivjsFt1   26.61%    passed     43.72%
 354  FKAuFXjrK2   29.57%    failed      2.12%
 355  eOn8Fw1qPv   27.48%    failed      3.53%
 356  D0XDiTOIfD   34.78%    passed      9.81%
 357  910hgdbBRd   28.00%    passed     51.49%
 358  ijUTPEstS6   33.39%    passed     28.87%
 359  bUU4czn7NG   27.83%    passed     60.40%
 360  INEhHLWnmb   37.04%    failed      1.97%
 361  LMA81zzKSe   37.04%    failed      0.01%
 362  TUCOIK4ZQn   33.91%    failed      0.52%
 363  yvso4goGdQ   34.96%    failed      4.00%
 364  YWPX00OZwF   36.00%    failed      3.54%
 365  qKqJ6yzKtT   34.61%    passed     10.13%
 366  49Qin0CHkb   34.61%    passed      9.62%
 367  63Q15egMZA   34.26%    passed      6.18%
 368  nWYlGrbPPc   34.61%    failed      4.67%
 369  JvcE4PBExA   33.74%    passed      7.73%
 370  LUlT7ehgwb   36.00%    passed     26.12%
 371  pVpykOHqYZ   39.48%    failed      0.85%
 372  v2K68153zf   38.26%    failed      0.55%
 373  qYhA4tEOW1   34.78%    failed      0.03%
 374  grGtjFUUTt   34.43%    failed      0.23%
 375  qWhSnx7aMf   44.87%    passed      5.50%
 376  v1oAyLSJtz   50.96%    passed     28.72%
 377  BadtzwpMMs   38.43%    passed      9.62%
 378  6DLNJCEk13   34.61%    passed      8.29%
 379  w2DOMr7ED6   41.39%    failed      3.23%
 380  JK0CadwxtV   33.74%    failed      1.62%
 381  thXzqzsTWd   33.04%    failed      4.58%
 382  cza9cyArKR   33.04%    failed      3.45%
 383  64i2bPRqyf   38.09%    failed      1.24%
 384  Tu05kR9iNy   35.30%    failed      2.13%
 385  ryyuwN9EeF   35.83%    failed      3.08%
 386  9i9iYEz14b   36.87%    passed     43.29%
 387  e5Z7VURlcd   56.00%    failed      0.95%
 388  ndIdlcACpn   34.61%    failed      0.11%
 389  miylOtOHke   36.00%    passed      5.91%
 390  jGxqmOPSFz   33.91%    failed      1.22%
 391  UpRnjomc4O   36.17%    passed     26.63%
 392  ebCUnMXr2f   38.43%    passed     15.56%
 393  21yjS1P784   34.43%    failed      0.27%
 394  XU8ct59Imq   34.26%    failed      0.70%
 395  mWu9nYUMB2   34.26%    passed      5.63%
 396  6N8VC2LDv6   34.26%    passed      5.63%
 397  Tp4oCldie4   38.09%    failed      4.42%
 398  LdahhT5atZ   34.26%    passed      5.63%
 399  ohdNT1wCFZ   34.26%    passed      7.14%
 400  QY3dkiwN48   41.57%    failed      3.72%
 401  Ip06mTdO2e   35.65%    failed      2.00%
 402  P5RXO2szhK   29.57%    passed     33.39%
 403  offjx75l6X   85.22%    passed     26.57%
 404  EdOuOhohBn   33.91%    passed     23.13%
 405  ZjYUAXvbUC   34.26%    passed      8.29%
 406  lpxtOw9xf3   36.52%    passed     12.71%
 407  4bSmqRgfRI   34.09%    passed     12.39%
 408  gminDyGtcG   34.78%    failed      2.44%
 409  lDQWwcBkMU   34.78%    passed     33.99%
 410  CUTMeJuwSv   33.74%    passed     78.03%
 411  OI80q3iM3F   33.74%    passed     81.17%
 412  xnKco929hT   37.57%    passed      8.65%
 413  RPfcmWXHCA   37.57%    passed     20.91%
 414  6mj1jZTKcU   36.17%    failed      4.67%
 415  Gr87dxYVyz   43.83%    failed      4.55%
 416  VGvhdii6IX   73.22%    passed     54.33%
 417  wJTuSg6Gc6   35.65%    passed     75.44%
 418  K3Flz6km5g   35.65%    passed     71.14%
 419  Tu0u89fzoU   35.48%    passed     16.33%
 420  IpceOBVrBQ   35.48%    passed     13.04%
 421  JAjUuwFnV7   36.35%    passed     34.52%
 422  wSnvqYXqTg   32.00%    passed     24.03%
 423  keWKiDv5J1   36.35%    passed     23.38%
 424  r5NSp8dbtM   37.39%    passed     32.60%
 425  wxLKLb6SMC   35.13%    passed     25.74%
 426  qw6gF6ZapY   35.13%    passed     25.74%
 427  ZGvDd4xvwy   37.91%    passed     30.11%
 428  8lXCZuvq8q   34.26%    passed     25.11%
 429  qvg1my8Wlp   48.70%    failed      3.30%
 430  ZdWaANa0Et   32.87%    passed      6.04%
 431  Onz2iyjxH3   42.96%    failed      0.02%
 432  AJImOJUang   66.09%    passed      8.67%
 433  rbo3OKIe4x   36.52%    failed      0.54%
 434  pGufZSTMNB   36.52%    passed     12.14%
 435  FLjy3W79tg   36.52%    passed     17.85%
 436  jYaSjXdhUR   34.78%    passed     22.31%
 437  HGW1EoyaVz   49.22%    passed     75.08%
 438  HQpmvbcKV0   36.35%    passed     71.28%
 439  Us22uQdloc   73.22%    passed     88.61%
 440  Nczi5Cos47   34.96%    passed     68.86%
 441  IV8TgD1mQj   36.52%    passed     65.05%
 442  QKsY8kV1rB   34.43%    passed     49.51%
 443  TrIc96BqkG   34.96%    passed      7.64%
 444  pnjqLcOivm   34.61%    passed      9.34%
 445  SY2alUymun   36.00%    passed     31.87%
 446  GXBps2FgSH   37.57%    failed      4.23%
 447  ZldeYJmzLx   39.48%    failed      0.13%
 448  8biR24Gazc   33.91%    passed     22.85%
 449  NBJ6cvHYoU   34.43%    passed     22.55%
 450  egq7pHRqeL   38.78%    passed     36.06%
 451  y0r2SVxwqI   35.30%    passed     55.80%
 452  evUBWmPjS2   35.30%    passed     23.87%
 453  ikh1qtxydC   36.00%    failed      2.62%
 454  BRdJ9RHZQj   35.65%    passed      8.09%
 455  l25CgIsmfn   35.65%    passed      8.09%
 456  XPdvjShyOo   37.57%    passed      7.82%
 457  M144qciIKM   34.96%    passed     30.15%
 458  BnE96TDyk8   35.48%    passed     26.42%
 459  jeohLZ0eYF   36.87%    failed      0.20%
 460  YvoxlQmxl7   36.87%    failed      0.20%
 461  R0wuUn8J0h   33.57%    passed     30.51%
 462  oeFPRaQBYZ   33.39%    passed     26.87%
 463  xqlhblg6dL   33.91%    passed     25.42%
 464  6Qs9p4Rx4f   34.09%    passed     25.71%
 465  QPlyWfEtzz   34.43%    passed     29.56%
 466  Yo6roMcRLy   35.30%    passed     25.15%
 467  PwuAxgsPD6   42.78%    passed     42.46%
 468  vaFUdeGB10   33.91%    failed      2.49%
 469  8GM1psnK6y   36.87%    failed      0.09%
 470  E6RVlyXu6C   33.74%    passed     45.21%
 471  SuF6hGymBQ   36.00%    failed      2.74%
 472  cgJCegWwAr   70.96%    passed     99.24%
 473  i10ONbBPRV   34.96%    passed     50.77%
 474  FaaaR0oHe4   35.13%    passed     47.29%
 475  RrNP3l8SS7   36.52%    failed      0.47%
 476  BuFyz2PMN4   34.43%    passed     49.11%
 477  Y10Qa1Da4V   38.78%    passed     65.87%
 478  8zkzdNvfM0   34.43%    passed     49.11%
 479  rA4KjQCVx3   32.00%    passed     90.85%
 480  au044S3YHW   35.30%    passed     43.12%
 481  cIR66o13VD   35.65%    passed     81.03%
 482  fkB1xaD3I7   35.83%    passed     66.46%
 483  CwGGcZADEn   35.30%    passed     25.37%
 484  fNHflelF6b   34.61%    passed     14.83%
 485  8zGWBmbKDs   83.65%    passed     77.32%
 486  LC2TsjjWfV   35.65%    passed     44.42%
 487  rsgxiUIZDl   41.74%    passed     41.79%
 488  Srvt2UziZu   34.43%    passed     97.83%
 489  zPT9rylEFV   34.43%    passed     97.83%
 490  rXls0PgjJv   35.48%    passed      5.47%
 491  TcLIjpisFo   51.83%    passed     29.28%
 492  RMfRwwtcqL   32.17%    passed      5.11%
 493  zzJMOnIGaE   34.09%    failed      0.02%
 494  bkj6PiDj99   34.78%    passed     36.79%
 495  QPtDeO8Fse   34.61%    passed     64.43%
WARNING: 19 sequences contain more than 50% gaps/ambiguity
****  TOTAL        23.94%  82 sequences failed composition chi2 test (p-value<5%; df=19)
CHECKPOINT: 99 bootstrap analyses restored

NOTE: Restoring information from model checkpoint file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz

CHECKPOINT: Initial tree restored
Measuring multi-threading efficiency up to 96 CPU cores
Increase to 10 rounds for branch lengths
24 trees examined
Threads: 1 / Time: 98.784 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -473144
Threads: 2 / Time: 68.680 sec / Speedup: 1.438 / Efficiency: 72% / LogL: -473144
Threads: 3 / Time: 51.592 sec / Speedup: 1.915 / Efficiency: 64% / LogL: -473144
Threads: 4 / Time: 46.474 sec / Speedup: 2.126 / Efficiency: 53% / LogL: -473144
Threads: 5 / Time: 41.913 sec / Speedup: 2.357 / Efficiency: 47% / LogL: -473144
Determining AUTO threadcount: done in 307.49 secs using 259% CPU
BEST NUMBER OF THREADS: 4

Perform fast likelihood tree search using LG+G model...
CHECKPOINT: Tree restored, LogL: -195489.756
NOTE: ModelFinder requires 455 MB RAM!
ModelFinder will test up to 616 protein models (sample size: 575) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  LG            200322.611   987 402619.222   2352931.222  406916.985
  2  LG+G4         195470.344   988 392916.688   2347180.688  397218.805
  3  LG+R2         196589.598   989 395157.196   2353377.196  399463.668
  4  LG+R3         195780.340   991 393542.681   2359686.681  397857.862
  5  LG+R4         195429.122   993 392844.244   2366928.244  397168.133
  6  LG+R5         195312.276   995 392614.553   2374654.553  396947.151
  7  LG+R6         195240.929   997 392475.859   2382487.859  396817.166
  8  LG+R7         195209.395   999 392416.790   2390416.790  396766.806
  9  LG+R8         195184.144   1001 392370.288   2398374.288  396729.013
 10  LG+R9         195175.348   1003 392356.697   2406380.697  396724.130
 11  LG+R10        195171.997   1005 392353.994   2414413.994  396730.135
 20  LG+F+R8       194402.294   1020 390844.587   2473684.587  395286.045
 21  LG+F+R9       194396.917   1022 390837.834   2481849.834  395288.000
 31  WAG+R8        196252.507   1001 394507.014   2400511.014  398865.738
 32  WAG+R9        196242.300   1003 394490.599   2408514.599  398858.033
 33  WAG+R10       196241.628   1005 394493.256   2416553.256  398869.398
 42  WAG+F+R8      194842.645   1020 391725.291   2474565.291  396166.748
 43  WAG+F+R9      194839.005   1022 391722.011   2482734.011  396172.177
 53  JTT+R8        195608.757   1001 393219.514   2399223.514  397578.238
 54  JTT+R9        195593.125   1003 393192.250   2407216.250  397559.683
 55  JTT+R10       195590.207   1005 393190.414   2415250.414  397566.556
 64  JTT+F+R8      194695.864   1020 391431.729   2474271.729  395873.186
 65  JTT+F+R9      194690.743   1022 391425.486   2482437.486  395875.652
WARNING: Normalizing state frequencies so that sum of them equals to 1
 75  Q.pfam+R8     194892.568   1001 391787.135   2397791.135  396145.860
WARNING: Normalizing state frequencies so that sum of them equals to 1
 76  Q.pfam+R9     194887.665   1003 391781.330   2405805.330  396148.763
WARNING: Normalizing state frequencies so that sum of them equals to 1
 86  Q.pfam+F+R8   194521.401   1020 391082.801   2473922.801  395524.259
WARNING: Normalizing state frequencies so that sum of them equals to 1
 87  Q.pfam+F+R9   194515.431   1022 391074.862   2482086.862  395525.029
WARNING: Normalizing state frequencies so that sum of them equals to 1
 97  Q.bird+R8     197829.393   1001 397660.786   2403664.786  402019.511
WARNING: Normalizing state frequencies so that sum of them equals to 1
 98  Q.bird+R9     197820.275   1003 397646.550   2411670.550  402013.983
WARNING: Normalizing state frequencies so that sum of them equals to 1
 99  Q.bird+R10    197814.318   1005 397638.636   2419698.636  402014.778
WARNING: Normalizing state frequencies so that sum of them equals to 1
108  Q.bird+F+R8   198079.035   1020 398198.069   2481038.069  402639.527
WARNING: Normalizing state frequencies so that sum of them equals to 1
109  Q.bird+F+R9   198072.616   1022 398189.232   2489201.232  402639.398
WARNING: Normalizing state frequencies so that sum of them equals to 1
110  Q.bird+F+R10  198068.569   1024 398185.139   2497385.139  402644.014
WARNING: Normalizing state frequencies so that sum of them equals to 1
119  Q.mammal+R8   196715.407   1001 395432.814   2401436.814  399791.538
WARNING: Normalizing state frequencies so that sum of them equals to 1
120  Q.mammal+R9   196707.402   1003 395420.804   2409444.804  399788.237
WARNING: Normalizing state frequencies so that sum of them equals to 1
121  Q.mammal+R10  196703.479   1005 395416.958   2417476.958  399793.100
WARNING: Normalizing state frequencies so that sum of them equals to 1
130  Q.mammal+F+R8 196877.834   1020 395795.669   2478635.669  400237.126
WARNING: Normalizing state frequencies so that sum of them equals to 1
131  Q.mammal+F+R9 196872.663   1022 395789.327   2486801.327  400239.493
141  Q.insect+R8   195081.318   1001 392164.635   2398168.635  396523.360
142  Q.insect+R9   195076.551   1003 392159.102   2406183.102  396526.535
152  Q.insect+F+R8 194860.269   1020 391760.539   2474600.539  396201.996
153  Q.insect+F+R9 194858.288   1022 391760.576   2482772.576  396210.742
WARNING: Normalizing state frequencies so that sum of them equals to 1
163  Q.plant+R8    194919.373   1001 391840.745   2397844.745  396199.470
WARNING: Normalizing state frequencies so that sum of them equals to 1
164  Q.plant+R9    194913.090   1003 391832.180   2405856.180  396199.613
WARNING: Normalizing state frequencies so that sum of them equals to 1
174  Q.plant+F+R8  194822.604   1020 391685.208   2474525.208  396126.665
WARNING: Normalizing state frequencies so that sum of them equals to 1
175  Q.plant+F+R9  194819.592   1022 391683.184   2482695.184  396133.350
WARNING: Normalizing state frequencies so that sum of them equals to 1
185  Q.yeast+R8    195446.700   1001 392895.400   2398899.400  397254.125
WARNING: Normalizing state frequencies so that sum of them equals to 1
186  Q.yeast+R9    195439.881   1003 392885.762   2406909.762  397253.195
WARNING: Normalizing state frequencies so that sum of them equals to 1
187  Q.yeast+R10   195435.549   1005 392881.097   2414941.097  397257.239
WARNING: Normalizing state frequencies so that sum of them equals to 1
196  Q.yeast+F+R8  194579.068   1020 391198.136   2474038.136  395639.593
WARNING: Normalizing state frequencies so that sum of them equals to 1
197  Q.yeast+F+R9  194573.538   1022 391191.077   2482203.077  395641.243
207  JTTDCMut+R8   195684.064   1001 393370.127   2399374.127  397728.852
208  JTTDCMut+R9   195667.689   1003 393341.377   2407365.377  397708.810
209  JTTDCMut+R10  195664.727   1005 393339.454   2415399.454  397715.596
218  JTTDCMut+F+R8 194737.502   1020 391515.003   2474355.003  395956.461
219  JTTDCMut+F+R9 194732.541   1022 391509.083   2482521.083  395959.249
229  DCMut+R8      198858.399   1001 399718.798   2405722.798  404077.523
230  DCMut+R9      198850.908   1003 399707.816   2413731.816  404075.249
231  DCMut+R10     198848.803   1005 399707.606   2421767.606  404083.748
240  DCMut+F+R8    196826.536   1020 395693.071   2478533.071  400134.529
241  DCMut+F+R9    196816.360   1022 395676.721   2486688.721  400126.887
242  DCMut+F+R10   196813.450   1024 395674.901   2494874.901  400133.776
251  VT+R8         196235.054   1001 394472.109   2400476.109  398830.833
252  VT+R9         196229.175   1003 394464.350   2408488.350  398831.783
262  VT+F+R8       195084.460   1020 392208.920   2475048.920  396650.377
263  VT+F+R9       195080.573   1022 392205.145   2483217.145  396655.311
273  PMB+R8        197315.374   1001 396632.748   2402636.748  400991.472
274  PMB+R9        197308.918   1003 396623.836   2410647.836  400991.269
275  PMB+R10       197306.392   1005 396622.785   2418682.785  400998.926
284  PMB+F+R8      197173.282   1020 396386.563   2479226.563  400828.020
285  PMB+F+R9      197172.042   1022 396388.084   2487400.084  400838.251
295  Blosum62+R8   197539.412   1001 397080.824   2403084.824  401439.549
296  Blosum62+R9   197530.232   1003 397066.464   2411090.464  401433.897
297  Blosum62+R10  197526.017   1005 397062.034   2419122.034  401438.175
306  Blosum62+F+R8 196901.090   1020 395842.180   2478682.180  400283.637
307  Blosum62+F+R9 196899.776   1022 395843.552   2486855.552  400293.718
317  Dayhoff+R8    198852.273   1001 399706.545   2405710.545  404065.270
318  Dayhoff+R9    198844.881   1003 399695.761   2413719.761  404063.195
319  Dayhoff+R10   198842.886   1005 399695.772   2421755.772  404071.914
328  Dayhoff+F+R8  196817.472   1020 395674.945   2478514.945  400116.402
329  Dayhoff+F+R9  196807.436   1022 395658.873   2486670.873  400109.039
330  Dayhoff+F+R10 196804.462   1024 395656.923   2494856.923  400115.798
339  mtREV+R8      202211.703   1001 406425.405   2412429.405  410784.129
340  mtREV+R9      202203.018   1003 406412.035   2420436.035  410779.468
341  mtREV+R10     202198.737   1005 406407.475   2428467.475  410783.617
350  mtREV+F+R8    197257.838   1020 396555.675   2479395.675  400997.133
351  mtREV+F+R9    197248.935   1022 396541.871   2487553.871  400992.037
352  mtREV+F+R10   197245.156   1024 396538.312   2495738.312  400997.187
361  mtART+R8      203583.239   1001 409168.478   2415172.478  413527.203
362  mtART+R9      203529.654   1003 409065.309   2423089.309  413432.742
363  mtART+R10     203525.582   1005 409061.164   2431121.164  413437.306
372  mtART+F+R8    200433.253   1020 402906.506   2485746.506  407347.963
373  mtART+F+R9    200385.741   1022 402815.481   2493827.481  407265.647
374  mtART+F+R10   200379.364   1024 402806.728   2502006.728  407265.603
383  mtZOA+R8      198366.129   1001 398734.257   2404738.257  403092.982
384  mtZOA+R9      198360.117   1003 398726.235   2412750.235  403093.668
394  mtZOA+F+R8    196919.533   1020 395879.066   2478719.066  400320.523
395  mtZOA+F+R9    196898.434   1022 395840.867   2486852.867  400291.033
396  mtZOA+F+R10   196891.474   1024 395830.948   2495030.948  400289.823
405  mtMet+R8      200042.427   1001 402086.853   2408090.853  406445.578
406  mtMet+R9      200019.941   1003 402045.882   2416069.882  406413.316
407  mtMet+R10     200049.839   1005 402109.679   2424169.679  406485.821
416  mtMet+F+R8    196455.394   1020 394950.789   2477790.789  399392.246
417  mtMet+F+R9    196440.614   1022 394925.229   2485937.229  399375.395
418  mtMet+F+R10   196431.320   1024 394910.641   2494110.641  399369.516
427  mtVer+R8      203014.713   1001 408031.426   2414035.426  412390.150
428  mtVer+R9      203008.014   1003 408022.029   2422046.029  412389.462
429  mtVer+R10     202969.843   1005 407949.685   2430009.685  412325.827
438  mtVer+F+R8    198883.127   1020 399806.254   2482646.254  404247.711
439  mtVer+F+R9    198874.584   1022 399793.168   2490805.168  404243.334
440  mtVer+F+R10   198869.999   1024 399787.998   2498987.998  404246.873
449  mtInv+R8      200418.426   1001 402838.852   2408842.852  407197.577
450  mtInv+R9      200410.477   1003 402826.954   2416850.954  407194.387
451  mtInv+R10     200408.596   1005 402827.192   2424887.192  407203.334
460  mtInv+F+R8    195221.172   1020 392482.344   2475322.344  396923.802
461  mtInv+F+R9    195216.016   1022 392476.033   2483488.033  396926.199
471  mtMAM+R8      207137.637   1001 416277.273   2422281.273  420635.998
472  mtMAM+R9      207095.777   1003 416197.555   2430221.555  420564.988
473  mtMAM+R10     207079.072   1005 416168.143   2438228.143  420544.285
482  mtMAM+F+R8    202259.202   1020 406558.403   2489398.403  410999.861
483  mtMAM+F+R9    202225.832   1022 406495.663   2497507.663  410945.830
484  mtMAM+F+R10   202217.624   1024 406483.248   2505683.248  410942.123
WARNING: Normalizing state frequencies so that sum of them equals to 1
493  FLAVI+R8      202777.540   1001 407557.080   2413561.080  411915.804
WARNING: Normalizing state frequencies so that sum of them equals to 1
494  FLAVI+R9      202768.495   1003 407542.991   2421566.991  411910.424
WARNING: Normalizing state frequencies so that sum of them equals to 1
495  FLAVI+R10     202753.049   1005 407516.099   2429576.099  411892.240
WARNING: Normalizing state frequencies so that sum of them equals to 1
504  FLAVI+F+R8    202442.661   1020 406925.322   2489765.322  411366.780
WARNING: Normalizing state frequencies so that sum of them equals to 1
505  FLAVI+F+R9    202434.692   1022 406913.384   2497925.384  411363.551
WARNING: Normalizing state frequencies so that sum of them equals to 1
506  FLAVI+F+R10   202428.582   1024 406905.164   2506105.164  411364.039
515  HIVb+R8       200393.670   1001 402789.341   2408793.341  407148.065
516  HIVb+R9       200381.791   1003 402769.582   2416793.582  407137.016
517  HIVb+R10      200371.459   1005 402752.918   2424812.918  407129.060
526  HIVb+F+R8     198771.236   1020 399582.473   2482422.473  404023.930
527  HIVb+F+R9     198764.928   1022 399573.855   2490585.855  404024.021
537  HIVw+R8       209399.096   1001 420800.192   2426804.192  425158.916
538  HIVw+R9       209380.617   1003 420767.234   2434791.234  425134.668
539  HIVw+R10      209376.097   1005 420762.193   2442822.193  425138.335
548  HIVw+F+R8     204961.158   1020 411962.315   2494802.315  416403.773
549  HIVw+F+R9     204951.516   1022 411947.031   2502959.031  416397.198
550  HIVw+F+R10    204945.555   1024 411939.109   2511139.109  416397.984
559  FLU+R8        200582.056   1001 403166.112   2409170.112  407524.836
560  FLU+R9        200563.618   1003 403133.235   2417157.235  407500.668
561  FLU+R10       200558.394   1005 403126.789   2425186.789  407502.931
570  FLU+F+R8      199008.285   1020 400056.570   2482896.570  404498.027
571  FLU+F+R9      198994.223   1022 400032.445   2491044.445  404482.611
572  FLU+F+R10     198990.836   1024 400029.672   2499229.672  404488.547
581  rtREV+R8      198734.452   1001 399470.904   2405474.904  403829.628
582  rtREV+R9      198720.690   1003 399447.380   2413471.380  403814.813
583  rtREV+R10     198718.347   1005 399446.693   2421506.693  403822.835
592  rtREV+F+R8    196515.045   1020 395070.090   2477910.090  399511.547
593  rtREV+F+R9    196508.638   1022 395061.277   2486073.277  399511.443
594  rtREV+F+R10   196506.672   1024 395061.344   2494261.344  399520.219
603  cpREV+R8      196528.431   1001 395058.861   2401062.861  399417.586
604  cpREV+R9      196515.402   1003 395036.804   2409060.804  399404.237
605  cpREV+R10     196510.888   1005 395031.776   2417091.776  399407.918
614  cpREV+F+R8    195115.409   1020 392270.817   2475110.817  396712.275
615  cpREV+F+R9    195110.263   1022 392264.525   2483276.525  396714.691
Akaike Information Criterion:           LG+F+R9
Corrected Akaike Information Criterion: LG+G4
Bayesian Information Criterion:         LG+F+R8
Best-fit model: LG+F+R8 chosen according to BIC

All model information printed to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.model.gz
CPU time for ModelFinder: 798.596 seconds (0h:13m:18s)
Wall-clock time for ModelFinder: 307.742 seconds (0h:5m:7s)

===> START BOOTSTRAP REPLICATE NUMBER 100

Creating bootstrap alignment (seed: 430041)...

CHECKPOINT: Initial tree restored

NOTE: 230 MB RAM (0 GB) is required!
CHECKPOINT: Model parameters restored, LogL: -197573.757
Wrote distance file to... 
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
CHECKPOINT: Candidate tree set restored, best LogL: -191073.748
Finish initializing candidate tree set (20)
Current best tree score: -191073.748 / CPU time: 0.000
Number of iterations: 392
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Optimizing NNI: done in 10.4839 secs using 398.9% CPU
Optimizing NNI: done in 10.7239 secs using 398.7% CPU
Optimizing NNI: done in 10.0273 secs using 398.7% CPU
Optimizing NNI: done in 11.2746 secs using 398.7% CPU
Optimizing NNI: done in 9.52475 secs using 396.4% CPU
Optimizing NNI: done in 10.6542 secs using 398.7% CPU
Optimizing NNI: done in 10.9928 secs using 397.8% CPU
Optimizing NNI: done in 11.1106 secs using 398.7% CPU
Iteration 400 / LogL: -195773.103 / Time: 0h:1m:25s (0h:0m:3s left)
Optimizing NNI: done in 11.5185 secs using 398.7% CPU
Optimizing NNI: done in 11.4065 secs using 398.6% CPU
Optimizing NNI: done in 11.6723 secs using 398.7% CPU
Optimizing NNI: done in 10.2737 secs using 398.7% CPU
Optimizing NNI: done in 11.7901 secs using 398.5% CPU
Optimizing NNI: done in 11.6493 secs using 398.5% CPU
Optimizing NNI: done in 11.9386 secs using 398.6% CPU
Optimizing NNI: done in 11.0923 secs using 398.5% CPU
Optimizing NNI: done in 11.1433 secs using 398.4% CPU
Optimizing NNI: done in 13.4359 secs using 398.6% CPU
Iteration 410 / LogL: -195848.859 / Time: 0h:3m:22s (0h:0m:3s left)
Optimizing NNI: done in 10.8739 secs using 398.6% CPU
Optimizing NNI: done in 10.7746 secs using 398.6% CPU
Optimizing NNI: done in 11.5731 secs using 398.6% CPU
Optimizing NNI: done in 11.4111 secs using 398.7% CPU
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Optimizing NNI: done in 11.8336 secs using 398.8% CPU
TREE SEARCH COMPLETED AFTER 418 ITERATIONS / Time: 0h:4m:51s

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|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -197573.757
2. Current log-likelihood: -196338.410
3. Current log-likelihood: -196333.820
4. Current log-likelihood: -196333.705
5. Current log-likelihood: -196333.691
Optimal log-likelihood: -196333.688
Site proportion and rates:  (0.006,0.106) (0.081,0.221) (0.101,0.348) (0.227,0.540) (0.151,0.797) (0.165,1.018) (0.175,1.636) (0.094,2.649)
Parameters optimization took 5 rounds (14.040 sec)
BEST SCORE FOUND : -196333.688
Total tree length: 157.180

Total number of iterations: 418
CPU time used for tree search: 1160.128 sec (0h:19m:20s)
Wall-clock time used for tree search: 291.137 sec (0h:4m:51s)
Total CPU time used: 1216.399 sec (0h:20m:16s)
Total wall-clock time used: 305.344 sec (0h:5m:5s)

===> COMPUTE CONSENSUS TREE FROM 100 BOOTSTRAP TREES

Reading tree(s) file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.boottrees ...
100 tree(s) loaded (0 rooted and 100 unrooted)
0 split(s) discarded because frequency <= -1.000
3162 splits found
Consensus tree written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.contree

===> START ANALYSIS ON THE ORIGINAL ALIGNMENT


NOTE: 364 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -194565.181
2. Current log-likelihood: -194424.766
3. Current log-likelihood: -194423.065
4. Current log-likelihood: -194422.932
Optimal log-likelihood: -194422.894
Site proportion and rates:  (0.013,0.097) (0.051,0.237) (0.130,0.368) (0.215,0.554) (0.156,0.773) (0.186,1.037) (0.150,1.624) (0.100,2.640)
Parameters optimization took 4 rounds (21.419 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 16.0534 secs using 399.9% CPU
Computing ML distances took 16.054249 sec (of wall-clock time) 64.204781 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.0020988 secs using 445.5% CPU
Constructing RapidNJ tree: done in 0.0299962 secs using 495.5% CPU
Computing RapidNJ tree took 0.032249 sec (of wall-clock time) 0.159039 sec (of CPU time)
Log-likelihood of RapidNJ tree: -198105.497
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|             INITIALIZING CANDIDATE TREE SET                      |
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Generating 98 parsimony trees... 29.690 second
Computing log-likelihood of 98 initial trees ... 41.301 seconds
Current best score: -194422.894

Do NNI search on 20 best initial trees
Optimizing NNI: done in 3.09026 secs using 398.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -194416.932
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -194396.235
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -194388.361
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Iteration 20 / LogL: -194430.587 / Time: 0h:5m:45s
Finish initializing candidate tree set (20)
Current best tree score: -194388.361 / CPU time: 303.889
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -194381.151
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 213: -194356.334
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Estimate model parameters (epsilon = 0.100)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 264: -194352.040
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 268: -194350.140
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Iteration 360 / LogL: -194361.773 / Time: 1h:5m:53s (0h:1m:28s left)
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TREE SEARCH COMPLETED AFTER 369 ITERATIONS / Time: 1h:7m:28s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -194350.140
Optimal log-likelihood: -194350.140
Site proportion and rates:  (0.013,0.098) (0.057,0.244) (0.128,0.372) (0.213,0.555) (0.155,0.773) (0.183,1.038) (0.149,1.613) (0.102,2.637)
Parameters optimization took 1 rounds (1.098 sec)
BEST SCORE FOUND : -194350.140
Total tree length: 153.006

Total number of iterations: 369
CPU time used for tree search: 15873.460 sec (4h:24m:33s)
Wall-clock time used for tree search: 4006.602 sec (1h:6m:46s)
Total CPU time used: 16043.652 sec (4h:27m:23s)
Total wall-clock time used: 4049.287 sec (1h:7m:29s)
Reading input trees file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.contree
Log-likelihood of consensus tree: -194376.927

===> ASSIGN BOOTSTRAP SUPPORTS TO THE TREE FROM ORIGINAL ALIGNMENT

Reading tree /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.treefile ...
unrooted tree detected
Reading tree(s) file /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.boottrees ...
100 tree(s) loaded (0 rooted and 100 unrooted)
Rescaling split weights by 1.000
3162 splits found
Creating bootstrap support values...
Tree with assigned support written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.treefile

Analysis results written to: 
  IQ-TREE report:                /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.iqtree
  Maximum-likelihood tree:       /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.treefile
  Likelihood distances:          /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.mldist
  Screen log file:               /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.log

Performing transfer bootstrap expectation...
TBE tree written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.tbe.tree
TBE statistic written to /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.tbe.stat

Total CPU time for bootstrap: 18077.250 seconds.
Total wall-clock time for bootstrap: 4668.823 seconds.

Non-parametric bootstrap results written to:
  Bootstrap trees:          /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.boottrees
  Consensus tree:           /home/mahesh/phd_students/ankit/Histamine_system/Analysis/TBE/transport.contree

Date and Time: Fri Jul 11 11:29:19 2025
