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_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 /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_2/checkpoints/transport 
[03:30:34] Starting optimizeGeneTreesSlave
LibpllModel LG+F+R8
[03:30:34] Starting optimizing gene tree
Number of ranks 29
(0.349794, 0.306047, score = 0)
Taxa number: 494
joint: -196129  libpll: -195085  reconciliation: -1043.85  
Initial ll = -196129
[04:16:52] SPR Search with radius 3: trying 1476 prune nodes
[04:35:11] Found 8 potential better moves
[04:35:11] 	GeneRax will now test and apply all the 8 potential good moves one after each other
	Applying move, ll = -196129, 1503 1725
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
joint: -196129  libpll: -195087  reconciliation: -1042.08  
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
[04:35:26] End of optimizing gene tree after 3891s
[04:35:27] End of optimizeGeneTreesSlave
