mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/ufb_after_tindex_lsi/cdhit_phobius_tm_RECEPTORS/RnR-prune_prunedBestTree.cdhit_phobius_tm_RECEPTORS.newick ../Histamine_system/Analysis/ufb_reconciliation_inputFiles/mapping_file_cdhit_phobius_tm_RECEPTORS.txt ../Histamine_system/Analysis/after_tindex_LSI/cdhit_phobius_tm_RECEPTORS.fasta ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/species_trees/inferred_species_tree.newick LG+F+R9 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/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 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/stats.txt 0 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/gene_optimization_0/checkpoints/cdhit_phobius_tm_RECEPTORS 
[00:00:10] Starting optimizeGeneTreesSlave
LibpllModel LG+F+R9
[00:00:10] Starting optimizing gene tree
Number of ranks 10
(0.278888, 0.646301, score = 0)
Taxa number: 269
joint: -106382  libpll: -105453  reconciliation: -929.026  
Initial ll = -106382
[00:51:30] SPR Search with radius 1: trying 801 prune nodes
[00:52:45] Found 102 potential better moves
[00:52:45] GeneRax will try to apply them chunk by chunk...
[00:52:45] 	Applying a chunk of 10 potential good moves simultaneously...
[00:52:45] 	After applying the chunk of moves, ll = -106379
[00:52:45] 	GeneRax will now test and apply all the 3 potential good moves one after each other
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -106375, 403 409
[00:52:50] 	Applying a chunk of 10 potential good moves simultaneously...
[00:52:55] 	Worse likelihood (-106386)! Rollbacking all moves! -106386
[00:52:56] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -106370, 408 398
	Applying move, ll = -106370, 429 455
	Applying move, ll = -106369, 444 453
[00:53:02] 	Applying a chunk of 10 potential good moves simultaneously...
[00:53:08] 	Worse likelihood (-106402)! Rollbacking all moves! -106402
[00:53:09] 	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 = -106367, 477 492
[00:53:19] 	Applying a chunk of 10 potential good moves simultaneously...
[00:53:20] 	Worse likelihood (-106387)! Rollbacking all moves! -106387
[00:53:21] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -106365, 645 647
	Applying move, ll = -106364, 663 139
	Applying move, ll = -106360, 669 676
[00:53:29] 	Applying a chunk of 10 potential good moves simultaneously...
[00:53:30] 	Worse likelihood (-106383)! Rollbacking all moves! -106383
[00:53:31] 	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 = -106359, 681 688
[00:53:40] 	Applying a chunk of 10 potential good moves simultaneously...
[00:53:41] 	Worse likelihood (-106366)! Rollbacking all moves! -106366
[00:53:42] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -106355, 690 697
	Applying move, ll = -106352, 735 747
	Applying move, ll = -106350, 807 814
[00:53:50] 	Applying a chunk of 10 potential good moves simultaneously...
[00:53:51] 	After applying the chunk of moves, ll = -106342
[00:53:51] 	GeneRax will now test and apply all the 5 potential good moves one after each other
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
[00:54:04] 	Applying a chunk of 10 potential good moves simultaneously...
[00:54:05] 	Worse likelihood (-106343)! Rollbacking all moves! -106343
[00:54:06] 	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 = -106340, 835 193
	Applying move, ll = -106337, 870 872
[00:54:17] 	Applying a chunk of 10 potential good moves simultaneously...
[00:54:18] 	Worse likelihood (-106375)! Rollbacking all moves! -106375
[00:54:19] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -106335, 882 209
	Applying move, ll = -106333, 903 941
	Applying move, ll = -106331, 915 931
[00:54:27] 	Applying a chunk of 10 potential good moves simultaneously...
[00:54:28] 	Worse likelihood (-106347)! Rollbacking all moves! -106347
[00:54:29] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -106326, 960 962
	Applying move, ll = -106326, 1056 1063
[00:54:34] 	Applying a chunk of 2 potential good moves simultaneously...
[00:54:35] 	After applying the chunk of moves, ll = -106326
[00:54:35] 	GeneRax will now test and apply all the 0 potential good moves one after each other
[00:54:36] SPR Search with radius 1: trying 801 prune nodes
[00:57:03] Found 28 potential better moves
[00:57:03] 	GeneRax will now test and apply all the 28 potential good moves one after each other
	Applying move, ll = -106321, 375 390
	Applying move, ll = -106320, 401 51
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -106317, 668 665
	Applying move, ll = -106312, 821 192
	Applying move, ll = -106308, 879 881
	Applying move, ll = -106307, 1041 1058
[00:57:24] SPR Search with radius 1: trying 801 prune nodes
[00:59:48] Found 15 potential better moves
[00:59:48] 	GeneRax will now test and apply all the 15 potential good moves one after each other
	Applying move, ll = -106307, 401 407
	Applying move, ll = -106302, 405 398
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -106302, 750 775
[01:00:02] SPR Search with radius 1: trying 801 prune nodes
[01:02:36] Found 4 potential better moves
[01:02:36] 	GeneRax will now test and apply all the 4 potential good moves one after each other
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
joint: -106302  libpll: -105519  reconciliation: -783.127  
Saving tree in ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick
Finished saving  ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick
[01:02:45] End of optimizing gene tree after 3754s
[01:02:45] End of optimizeGeneTreesSlave
