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_2/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 3 ../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_2/checkpoints/transport 
                                                       LG+F+R9
[03:54:35] Starting optimizing gene tree
Number of ranks 10
(0.365327, 0.259531, score = 0)
Taxa number: 494
joint: -196119  libpll: -195075  reconciliation: -1044.48  
Initial ll = -196119
[04:39:54] SPR Search with radius 3: trying 1476 prune nodes
[05:12:17] Found 21 potential better moves
[05:12:17] 	GeneRax will now test and apply all the 21 potential good moves one after each other
	Applying move, ll = -196119, 942 971
	Applying move, ll = -196117, 951 968
	Applying move, ll = -196117, 1257 259
	Applying move, ll = -196117, 1365 1373
	Applying move, ll = -196116, 1677 399
	Applying move, ll = -196116, 1764 1745
	Applying move, ll = -196116, 1902 477
	Worse likelihood, Move rejected
[05:12:34] SPR Search with radius 3: trying 1476 prune nodes
[05:44:44] Found 4 potential better moves
[05:44:44] 	GeneRax will now test and apply all the 4 potential good moves one after each other
	Applying move, ll = -196116, 912 143
	Applying move, ll = -196115, 914 905
joint: -196115  libpll: -195096  reconciliation: -1019.44  
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
[05:44:50] End of optimizing gene tree after 6614s
[05:44:50] End of optimizeGeneTreesSlave
