mpi-scheduler optimizeGeneTrees /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_biosynthesis_results/results/biosynthesis/geneTree.newick ../Histamine_system/Analysis/tbe_reconciliation_inputFiles/mapping_file_biosynthesis.txt ../Histamine_system/Analysis/after_tindex_LSI/biosynthesis.fasta /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_biosynthesis_results/species_trees/inferred_species_tree.newick LG+R8 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_biosynthesis_results/gene_optimization_3/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 4 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_biosynthesis_results/results/biosynthesis/geneTree.newick /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_biosynthesis_results/results/biosynthesis/stats.txt 0 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_biosynthesis_results/gene_optimization_3/checkpoints/biosynthesis 
[01:06:28] Starting optimizeGeneTreesSlave
LibpllModel LG+R8
[01:06:28] Starting optimizing gene tree
Number of ranks 24
(0.385099, 0.33994, score = 0)
Taxa number: 149
joint: -56844.3  libpll: -56505.2  reconciliation: -339.125  
Initial ll = -56844.3
[01:25:32] SPR Search with radius 4: trying 441 prune nodes
[01:28:54] Found 0 potential better moves
[01:28:54] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -56844.3  libpll: -56505.2  reconciliation: -339.125  
Saving tree in /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_biosynthesis_results/results/biosynthesis/geneTree.newick
Finished saving  /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_biosynthesis_results/results/biosynthesis/geneTree.newick
[01:28:55] End of optimizing gene tree after 1347s
[01:28:55] End of optimizeGeneTreesSlave
