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_4/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 5 ../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_4/checkpoints/transport 
                                                       LG+F+R9
[07:33:39] Starting optimizing gene tree
Number of ranks 10
(0.390427, 0.255607, score = 0)
Taxa number: 494
joint: -196119  libpll: -195080  reconciliation: -1038.43  
Initial ll = -196119
[08:22:03] SPR Search with radius 5: trying 1476 prune nodes
[09:18:35] Found 10 potential better moves
[09:18:35] 	GeneRax will now test and apply all the 10 potential good moves one after each other
	Applying move, ll = -196118, 802 113
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -196117, 1682 1676
	Applying move, ll = -196117, 1770 1751
[09:18:49] SPR Search with radius 5: trying 1476 prune nodes
[10:16:16] Found 7 potential better moves
[10:16:16] 	GeneRax will now test and apply all the 7 potential good moves one after each other
	Applying move, ll = -196117, 800 810
	Applying move, ll = -196116, 806 110
joint: -196116  libpll: -195095  reconciliation: -1021.23  
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
[10:16:22] End of optimizing gene tree after 9763s
[10:16:22] End of optimizeGeneTreesSlave
