mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/tbe_after_tindex_lsi/cdhit_phobius_tm_RECEPTORS/RnR-prune_prunedBestTree.cdhit_phobius_tm_RECEPTORS.newick ../Histamine_system/Analysis/tbe_reconciliation_inputFiles/mapping_file_cdhit_phobius_tm_RECEPTORS.txt ../Histamine_system/Analysis/after_tindex_LSI/cdhit_phobius_tm_RECEPTORS.fasta /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/species_trees/inferred_species_tree.newick Q.plant+I+R9 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_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_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/stats.txt 0 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/gene_optimization_0/checkpoints/cdhit_phobius_tm_RECEPTORS 
[00:00:33] Starting optimizeGeneTreesSlave
LibpllModel Q.plant+I+R9
[00:00:33] Starting optimizing gene tree
Number of ranks 12
(0.27677, 0.648378, score = 0)
Taxa number: 269
joint: -106078  libpll: -105162  reconciliation: -915.228  
Initial ll = -106078
[00:43:06] SPR Search with radius 1: trying 801 prune nodes
[00:45:01] Found 106 potential better moves
[00:45:01] GeneRax will try to apply them chunk by chunk...
[00:45:01] 	Applying a chunk of 10 potential good moves simultaneously...
[00:45:01] 	Worse likelihood (-106102)! Rollbacking all moves! -106102
[00:45:02] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -106075, 273 3
	Applying move, ll = -106070, 372 378
	Applying move, ll = -106066, 384 391
[00:45:09] 	Applying a chunk of 10 potential good moves simultaneously...
[00:45:10] 	Worse likelihood (-106068)! Rollbacking all moves! -106068
[00:45:10] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -106061, 402 398
	Applying move, ll = -106057, 406 423
	Applying move, ll = -106052, 411 418
[00:45:17] 	Applying a chunk of 10 potential good moves simultaneously...
[00:45:18] 	Worse likelihood (-106095)! Rollbacking all moves! -106095
[00:45:18] 	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 = -106052, 482 473
	Applying move, ll = -106050, 645 647
[00:45:28] 	Applying a chunk of 10 potential good moves simultaneously...
[00:45:29] 	Worse likelihood (-106070)! Rollbacking all moves! -106070
[00:45:30] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -106042, 669 676
	Worse likelihood, Move rejected
	Applying move, ll = -106042, 681 688
[00:45:37] 	Applying a chunk of 10 potential good moves simultaneously...
[00:45:38] 	Worse likelihood (-106052)! Rollbacking all moves! -106052
[00:45:38] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -106039, 690 697
	Applying move, ll = -106036, 735 747
[00:45:43] 	Applying a chunk of 10 potential good moves simultaneously...
[00:45:43] 	Worse likelihood (-106040)! Rollbacking all moves! -106040
[00:45:44] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -106035, 764 167
	Applying move, ll = -106035, 804 816
	Applying move, ll = -106029, 822 828
[00:45:53] 	Applying a chunk of 10 potential good moves simultaneously...
[00:45:54] 	After applying the chunk of moves, ll = -106028
[00:45:54] 	GeneRax will now test and apply all the 7 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -106026, 827 821
[00:45:59] 	Applying a chunk of 10 potential good moves simultaneously...
[00:45:59] 	Worse likelihood (-106042)! Rollbacking all moves! -106042
[00:46:00] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -106024, 879 895
	Applying move, ll = -106020, 885 892
	Applying move, ll = -106020, 912 914
[00:46:09] 	Applying a chunk of 10 potential good moves simultaneously...
[00:46:10] 	Worse likelihood (-106058)! Rollbacking all moves! -106058
[00:46:11] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -106019, 924 223
	Applying move, ll = -106016, 951 1017
[00:46:17] 	Applying a chunk of 10 potential good moves simultaneously...
[00:46:18] 	Worse likelihood (-106026)! Rollbacking all moves! -106026
[00:46:19] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -106015, 960 962
	Applying move, ll = -106011, 981 993
[00:46:26] 	Applying a chunk of 6 potential good moves simultaneously...
[00:46:27] 	Worse likelihood (-106027)! Rollbacking all moves! -106027
[00:46:27] 	GeneRax will now test and apply all the 6 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -106011, 1056 1063
[00:46:33] SPR Search with radius 1: trying 801 prune nodes
[00:48:29] Found 36 potential better moves
[00:48:29] 	GeneRax will now test and apply all the 36 potential good moves one after each other
	Applying move, ll = -106010, 381 386
	Applying move, ll = -106005, 668 665
	Applying move, ll = -106004, 681 143
	Applying move, ll = -106000, 810 803
	Applying move, ll = -105997, 821 194
	Applying move, ll = -105989, 828 193
	Applying move, ll = -105988, 921 923
	Applying move, ll = -105988, 950 1013
	Applying move, ll = -105987, 1041 1058
[00:48:47] SPR Search with radius 1: trying 801 prune nodes
[00:50:44] Found 4 potential better moves
[00:50:44] 	GeneRax will now test and apply all the 4 potential good moves one after each other
	Applying move, ll = -105987, 825 827
[00:50:47] SPR Search with radius 1: trying 801 prune nodes
[00:52:44] Found 4 potential better moves
[00:52:44] 	GeneRax will now test and apply all the 4 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -105987, 384 386
joint: -105987  libpll: -105232  reconciliation: -754.311  
Saving tree in /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick
Finished saving  /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick
[00:52:51] End of optimizing gene tree after 3138s
[00:52:51] End of optimizeGeneTreesSlave
