mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/results/catabolism/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliation_inputFiles/mapping_file_catabolism.txt ../Histamine_system/Analysis/after_tindex_LSI/catabolism.fasta ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/species_trees/inferred_species_tree.newick WAG+F+I+G4 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_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_catabolism_results/results/catabolism/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/results/catabolism/stats.txt 0 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/gene_optimization_3/checkpoints/catabolism 
[00:05:05] Starting optimizeGeneTreesSlave
LibpllModel WAG+F+I+G4
[00:05:05] Starting optimizing gene tree
Number of ranks 10
(0.386803, 0.341165, score = 0)
Taxa number: 53
joint: -33548.5  libpll: -33429.4  reconciliation: -119.115  
Initial ll = -33548.5
[00:05:12] SPR Search with radius 4: trying 153 prune nodes
[00:07:17] Found 0 potential better moves
[00:07:17] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -33548.5  libpll: -33429.4  reconciliation: -119.115  
Saving tree in ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/results/catabolism/geneTree.newick
Finished saving  ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/results/catabolism/geneTree.newick
[00:07:18] End of optimizing gene tree after 132s
[00:07:18] End of optimizeGeneTreesSlave
