mpi-scheduler optimizeGeneTrees /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/results/transport/geneTree.newick ../Histamine_system/Analysis/tbe_reconciliation_inputFiles/mapping_file_transport.txt ../Histamine_system/Analysis/after_tindex_LSI/transport.fasta /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/species_trees/inferred_species_tree.newick LG+F+R8 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/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 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/results/transport/geneTree.newick /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/results/transport/stats.txt 0 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/gene_optimization_1/checkpoints/transport 
[02:09:47] Starting optimizeGeneTreesSlave
LibpllModel LG+F+R8
[02:09:47] Starting optimizing gene tree
Number of ranks 29
(0.362221, 0.305727, score = 0)
Taxa number: 494
joint: -196134  libpll: -195061  reconciliation: -1072.68  
Initial ll = -196134
[03:09:40] SPR Search with radius 2: trying 1476 prune nodes
[03:19:02] Found 18 potential better moves
[03:19:02] 	GeneRax will now test and apply all the 18 potential good moves one after each other
	Worse likelihood, Move rejected
	Applying move, ll = -196134, 770 764
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -196133, 1491 337
	Applying move, ll = -196131, 1615 1577
	Applying move, ll = -196131, 1791 439
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
[03:19:36] SPR Search with radius 2: trying 1476 prune nodes
[03:30:21] Found 8 potential better moves
[03:30:21] 	GeneRax will now test and apply all the 8 potential good moves one after each other
	Applying move, ll = -196131, 1350 289
	Applying move, ll = -196131, 1506 1725
joint: -196131  libpll: -195087  reconciliation: -1043.78  
Saving tree in /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/results/transport/geneTree.newick
Finished saving  /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_transport_results/results/transport/geneTree.newick
[03:30:31] End of optimizing gene tree after 4844s
[03:30:31] End of optimizeGeneTreesSlave
