mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/results/transport/geneTree.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_1/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 2 ../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_1/checkpoints/transport 
[01:57:22] Starting optimizeGeneTreesSlave
LibpllModel LG+F+R9
[01:57:22] Starting optimizing gene tree
Number of ranks 10
(0.500007, 0.500007, score = 0)
Taxa number: 494
joint: -196149  libpll: -195058  reconciliation: -1091.18  
Initial ll = -196149
[02:54:20] SPR Search with radius 2: trying 1476 prune nodes
[03:15:39] Found 5 potential better moves
[03:15:39] 	GeneRax will now test and apply all the 5 potential good moves one after each other
	Applying move, ll = -196147, 941 929
	Applying move, ll = -196146, 1245 1223
	Applying move, ll = -196145, 1441 1400
	Applying move, ll = -196144, 1501 343
	Applying move, ll = -196140, 1788 436
[03:15:51] SPR Search with radius 2: trying 1476 prune nodes
[03:35:06] Found 37 potential better moves
[03:35:06] 	GeneRax will now test and apply all the 37 potential good moves one after each other
	Applying move, ll = -196139, 543 23
	Applying move, ll = -196139, 546 24
	Worse likelihood, Move rejected
	Applying move, ll = -196139, 759 98
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -196139, 1371 1343
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -196139, 1692 409
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
[03:35:48] SPR Search with radius 2: trying 1476 prune nodes
[03:54:32] Found 0 potential better moves
[03:54:32] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -196139  libpll: -195077  reconciliation: -1062.3  
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
[03:54:35] End of optimizing gene tree after 7032s
[03:54:35] End of optimizeGeneTreesSlave
