mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/results/biosynthesis/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliation_inputFiles/mapping_file_biosynthesis.txt ../Histamine_system/Analysis/after_tindex_LSI/biosynthesis.fasta ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/species_trees/inferred_species_tree.newick LG+R7 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/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 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/results/biosynthesis/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/results/biosynthesis/stats.txt 0 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/gene_optimization_3/checkpoints/biosynthesis 
                                           LibpllModel LG+R7
[00:56:15] Starting optimizing gene tree
Number of ranks 10
(0.393667, 0.318545, score = 0)
Taxa number: 149
joint: -56840  libpll: -56509.1  reconciliation: -330.925  
Initial ll = -56840
[01:04:37] SPR Search with radius 4: trying 441 prune nodes
[01:19:11] Found 0 potential better moves
[01:19:11] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -56840  libpll: -56509.1  reconciliation: -330.925  
Saving tree in ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/results/biosynthesis/geneTree.newick
Finished saving  ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/results/biosynthesis/geneTree.newick
[01:19:12] End of optimizing gene tree after 1376s
[01:19:12] End of optimizeGeneTreesSlave
