mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/ufb_after_tindex_lsi/biosynthesis/RnR-prune_prunedBestTree.biosynthesis.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_0/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 1 ../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_0/checkpoints/biosynthesis 
                                           LibpllModel LG+R7
[00:00:06] Starting optimizing gene tree
Number of ranks 5
(0.41355, 0.365712, score = 0)
Taxa number: 149
joint: -56848.7  libpll: -56502.9  reconciliation: -345.793  
Initial ll = -56848.7
[00:13:20] SPR Search with radius 1: trying 441 prune nodes
[00:16:52] Found 8 potential better moves
[00:16:52] 	GeneRax will now test and apply all the 8 potential good moves one after each other
	Applying move, ll = -56847.8, 360 367
	Applying move, ll = -56840.4, 519 586
[00:16:55] SPR Search with radius 1: trying 441 prune nodes
[00:18:11] Found 0 potential better moves
[00:18:11] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -56840.4  libpll: -56509.5  reconciliation: -330.916  
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
[00:18:12] End of optimizing gene tree after 1086s
[00:18:12] End of optimizeGeneTreesSlave
