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_3/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 4 ../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_3/checkpoints/transport 
[05:44:51] Starting optimizeGeneTreesSlave
LibpllModel LG+F+R9
[05:44:51] Starting optimizing gene tree
Number of ranks 10
(0.500039, 0.499996, score = 0)
Taxa number: 494
joint: -196139  libpll: -195095  reconciliation: -1043.46  
Initial ll = -196139
[06:28:23] SPR Search with radius 4: trying 1476 prune nodes
[07:01:05] Found 18 potential better moves
[07:01:05] 	GeneRax will now test and apply all the 18 potential good moves one after each other
	Applying move, ll = -196138, 765 737
	Worse likelihood, Move rejected
	Applying move, ll = -196138, 1187 234
	Applying move, ll = -196137, 1260 1271
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -196137, 1401 314
	Worse likelihood, Move rejected
	Applying move, ll = -196137, 1910 479
[07:01:27] SPR Search with radius 4: trying 1476 prune nodes
[07:33:01] Found 36 potential better moves
[07:33:01] 	GeneRax will now test and apply all the 36 potential good moves one after each other
	Applying move, ll = -196137, 765 94
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
joint: -196137  libpll: -195081  reconciliation: -1056.06  
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
[07:33:38] End of optimizing gene tree after 6527s
[07:33:38] End of optimizeGeneTreesSlave
