mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/ufb_after_tindex_lsi/transport/RnR-prune_prunedBestTree.transport.newick ../Histamine_system/Analysis/ufb_reconciliation_inputFiles/mapping_file_transport.txt ../Histamine_system/Analysis/after_tindex_LSI/transport.fasta ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/species_trees/inferred_species_tree.newick LG+F+R9 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/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 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/results/transport/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/results/transport/stats.txt 0 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/gene_optimization_0/checkpoints/transport 
                                                       LG+F+R9
[00:00:24] Starting optimizing gene tree
Number of ranks 10
(0.424259, 0.465751, score = 0)
Taxa number: 494
joint: -196229  libpll: -194986  reconciliation: -1243.19  
Initial ll = -196229
[01:24:12] SPR Search with radius 1: trying 1476 prune nodes
[01:39:03] Found 126 potential better moves
[01:39:03] GeneRax will try to apply them chunk by chunk...
[01:39:03] 	Applying a chunk of 10 potential good moves simultaneously...
[01:39:05] 	Worse likelihood (-196259)! Rollbacking all moves! -196259
[01:39:07] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -196228, 501 1964
	Applying move, ll = -196227, 517 518
	Applying move, ll = -196223, 543 545
[01:39:18] 	Applying a chunk of 10 potential good moves simultaneously...
[01:39:20] 	Worse likelihood (-196317)! Rollbacking all moves! -196317
[01:39:21] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -196222, 641 620
	Applying move, ll = -196220, 744 771
	Applying move, ll = -196219, 783 790
[01:39:35] 	Applying a chunk of 10 potential good moves simultaneously...
[01:39:37] 	Worse likelihood (-196224)! Rollbacking all moves! -196224
[01:39:38] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -196217, 951 964
	Applying move, ll = -196215, 981 1011
[01:39:45] 	Applying a chunk of 10 potential good moves simultaneously...
[01:39:46] 	Worse likelihood (-196279)! Rollbacking all moves! -196279
[01:39:48] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -196212, 1044 1128
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -196211, 1064 200
	Applying move, ll = -196211, 1074 1076
[01:40:11] 	Applying a chunk of 10 potential good moves simultaneously...
[01:40:13] 	Worse likelihood (-196212)! Rollbacking all moves! -196212
[01:40:15] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -196210, 1098 1122
	Worse likelihood, Move rejected
[01:40:31] 	Applying a chunk of 10 potential good moves simultaneously...
[01:40:33] 	Worse likelihood (-196211)! Rollbacking all moves! -196211
[01:40:34] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -196210, 1167 1206
	Applying move, ll = -196204, 1359 1370
	Applying move, ll = -196201, 1374 1389
[01:40:54] 	Applying a chunk of 10 potential good moves simultaneously...
[01:40:55] 	Worse likelihood (-196229)! Rollbacking all moves! -196229
[01:40:57] 	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 = -196200, 1389 306
	Applying move, ll = -196199, 1458 1465
[01:41:17] 	Applying a chunk of 10 potential good moves simultaneously...
[01:41:19] 	Worse likelihood (-196247)! Rollbacking all moves! -196247
[01:41:20] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -196195, 1572 1680
	Applying move, ll = -196194, 1602 1609
	Applying move, ll = -196193, 1656 397
[01:41:31] 	Applying a chunk of 10 potential good moves simultaneously...
[01:41:36] 	Worse likelihood (-196201)! Rollbacking all moves! -196201
[01:41:37] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -196190, 1707 403
	Applying move, ll = -196186, 1755 1767
[01:41:49] 	Applying a chunk of 10 potential good moves simultaneously...
[01:41:54] 	Worse likelihood (-196190)! Rollbacking all moves! -196190
[01:41:56] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -196179, 1767 1774
	Applying move, ll = -196177, 1779 1810
	Applying move, ll = -196173, 1821 1828
[01:42:07] 	Applying a chunk of 10 potential good moves simultaneously...
[01:42:10] 	After applying the chunk of moves, ll = -196167
[01:42:10] 	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
	Worse likelihood, Move rejected
[01:42:33] 	Applying a chunk of 10 potential good moves simultaneously...
[01:42:35] 	Worse likelihood (-196190)! Rollbacking all moves! -196190
[01:42:37] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -196163, 1899 1953
	Applying move, ll = -196163, 1902 1908
[01:42:51] 	Applying a chunk of 6 potential good moves simultaneously...
[01:42:53] 	After applying the chunk of moves, ll = -196163
[01:42:53] 	GeneRax will now test and apply all the 4 potential good moves one after each other
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
[01:43:06] SPR Search with radius 1: trying 1476 prune nodes
[01:49:27] Found 12 potential better moves
[01:49:27] 	GeneRax will now test and apply all the 12 potential good moves one after each other
	Applying move, ll = -196157, 500 1961
	Applying move, ll = -196154, 957 950
	Applying move, ll = -196151, 1844 1862
[01:49:34] SPR Search with radius 1: trying 1476 prune nodes
[01:57:16] Found 0 potential better moves
[01:57:16] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -196151  libpll: -195065  reconciliation: -1085.94  
Saving tree in ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/results/transport/geneTree.newick
Finished saving  ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/results/transport/geneTree.newick
[01:57:21] End of optimizing gene tree after 7016s
[01:57:21] End of optimizeGeneTreesSlave
