mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/tbe_after_tindex_lsi/transport/RnR-prune_prunedBestTree.transport.newick ../Histamine_system/Analysis/tbe_reconciliation_inputFiles/mapping_file_transport.txt ../Histamine_system/Analysis/after_tindex_LSI/transport.fasta /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/species_trees/inferred_species_tree.newick LG+F+R8 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/gene_optimization_0/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 1 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/results/transport/geneTree.newick /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/results/transport/stats.txt 0 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/gene_optimization_0/checkpoints/transport 
[00:15:55] Starting optimizeGeneTreesSlave
LibpllModel LG+F+R8
[00:15:55] Starting optimizing gene tree
Number of ranks 14
(0.442342, 0.507475, score = 0)
Taxa number: 494
joint: -196257  libpll: -194992  reconciliation: -1265.19  
Initial ll = -196257
[01:20:27] SPR Search with radius 1: trying 1476 prune nodes
[01:30:43] Found 117 potential better moves
[01:30:43] GeneRax will try to apply them chunk by chunk...
[01:30:43] 	Applying a chunk of 10 potential good moves simultaneously...
[01:30:44] 	Worse likelihood (-196259)! Rollbacking all moves! -196259
[01:30:46] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -196257, 510 520
	Applying move, ll = -196250, 636 642
	Worse likelihood, Move rejected
[01:31:06] 	Applying a chunk of 10 potential good moves simultaneously...
[01:31:08] 	After applying the chunk of moves, ll = -196250
[01:31:08] 	GeneRax will now test and apply all the 4 potential good moves one after each other
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
[01:31:29] 	Applying a chunk of 10 potential good moves simultaneously...
[01:31:31] 	Worse likelihood (-196307)! Rollbacking all moves! -196307
[01:31:32] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -196249, 783 790
	Applying move, ll = -196246, 951 964
	Applying move, ll = -196245, 981 1011
[01:31:48] 	Applying a chunk of 10 potential good moves simultaneously...
[01:31:53] 	Worse likelihood (-196298)! Rollbacking all moves! -196298
[01:31:56] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -196240, 1044 1128
	Worse likelihood, Move rejected
	Applying move, ll = -196240, 1074 1076
[01:32:19] 	Applying a chunk of 10 potential good moves simultaneously...
[01:32:29] 	After applying the chunk of moves, ll = -196236
[01:32:29] 	GeneRax will now test and apply all the 4 potential good moves one after each other
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
[01:32:49] 	Applying a chunk of 10 potential good moves simultaneously...
[01:32:53] 	Worse likelihood (-196250)! Rollbacking all moves! -196250
[01:32:55] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -196229, 1359 1370
	Applying move, ll = -196227, 1374 1389
[01:33:07] 	Applying a chunk of 10 potential good moves simultaneously...
[01:33:09] 	Worse likelihood (-196237)! Rollbacking all moves! -196237
[01:33:10] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -196225, 1459 1418
	Applying move, ll = -196222, 1548 1567
[01:33:32] 	Applying a chunk of 10 potential good moves simultaneously...
[01:33:37] 	Worse likelihood (-196243)! Rollbacking all moves! -196243
[01:33:39] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -196222, 1572 1680
	Applying move, ll = -196221, 1602 1609
	Applying move, ll = -196218, 1707 403
[01:33:53] 	Applying a chunk of 10 potential good moves simultaneously...
[01:33:57] 	After applying the chunk of moves, ll = -196217
[01:33:57] 	GeneRax will now test and apply all the 6 potential good moves one after each other
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
[01:34:16] 	Applying a chunk of 10 potential good moves simultaneously...
[01:34:18] 	Worse likelihood (-196259)! Rollbacking all moves! -196259
[01:34:20] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -196215, 1779 1810
	Applying move, ll = -196213, 1830 454
	Applying move, ll = -196205, 1845 1866
[01:34:34] 	Applying a chunk of 10 potential good moves simultaneously...
[01:34:41] 	Worse likelihood (-196207)! Rollbacking all moves! -196207
[01:34:43] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -196202, 1899 1953
	Applying move, ll = -196201, 1962 524
[01:35:00] 	Applying a chunk of 7 potential good moves simultaneously...
[01:35:02] 	After applying the chunk of moves, ll = -196201
[01:35:02] 	GeneRax will now test and apply all the 6 potential good moves one after each other
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
[01:35:14] SPR Search with radius 1: trying 1476 prune nodes
[01:42:00] Found 47 potential better moves
[01:42:00] 	GeneRax will now test and apply all the 47 potential good moves one after each other
	Applying move, ll = -196195, 519 1964
	Applying move, ll = -196189, 633 53
	Applying move, ll = -196189, 738 747
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -196189, 941 932
	Applying move, ll = -196186, 957 950
	Applying move, ll = -196186, 1097 1118
	Worse likelihood, Move rejected
	Applying move, ll = -196184, 1151 1199
	Applying move, ll = -196184, 1389 306
	Applying move, ll = -196175, 1757 1774
	Applying move, ll = -196173, 1844 1862
[01:43:08] SPR Search with radius 1: trying 1476 prune nodes
[01:49:38] Found 31 potential better moves
[01:49:38] 	GeneRax will now test and apply all the 31 potential good moves one after each other
	Applying move, ll = -196168, 518 1961
	Applying move, ll = -196167, 738 89
	Applying move, ll = -196167, 745 91
	Applying move, ll = -196163, 933 936
	Worse likelihood, Move rejected
	Applying move, ll = -196163, 1074 202
	Applying move, ll = -196163, 1092 1121
	Worse likelihood, Move rejected
[01:50:15] SPR Search with radius 1: trying 1476 prune nodes
[01:56:25] Found 12 potential better moves
[01:56:25] 	GeneRax will now test and apply all the 12 potential good moves one after each other
	Applying move, ll = -196162, 738 747
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -196162, 1079 202
[01:56:49] SPR Search with radius 1: trying 1476 prune nodes
[02:03:22] Found 8 potential better moves
[02:03:22] 	GeneRax will now test and apply all the 8 potential good moves one after each other
	Applying move, ll = -196161, 738 89
	Applying move, ll = -196160, 745 731
[02:03:32] SPR Search with radius 1: trying 1476 prune nodes
[02:09:36] Found 0 potential better moves
[02:09:36] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -196160  libpll: -195073  reconciliation: -1087.11  
Saving tree in /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/results/transport/geneTree.newick
Finished saving  /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/results/transport/geneTree.newick
[02:09:42] End of optimizing gene tree after 6826s
[02:09:42] End of optimizeGeneTreesSlave
