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_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 /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_4/checkpoints/transport 
[05:45:11] Starting optimizeGeneTreesSlave
LibpllModel LG+F+R8
[05:45:11] Starting optimizing gene tree
Number of ranks 29
(0.350376, 0.303787, score = 0)
Taxa number: 494
joint: -196128  libpll: -195086  reconciliation: -1042.01  
Initial ll = -196128
[06:33:35] SPR Search with radius 5: trying 1476 prune nodes
[06:57:26] Found 0 potential better moves
[06:57:26] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -196128  libpll: -195086  reconciliation: -1042.01  
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
[06:57:30] End of optimizing gene tree after 4338s
[06:57:30] End of optimizeGeneTreesSlave
