mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/tbe_after_tindex_lsi/biosynthesis/RnR-prune_prunedBestTree.biosynthesis.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_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 /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_0/checkpoints/biosynthesis 
[00:00:25] Starting optimizeGeneTreesSlave
LibpllModel LG+R8
[00:00:25] Starting optimizing gene tree
Number of ranks 6
(0.403521, 0.390366, score = 0)
Taxa number: 149
joint: -56858.4  libpll: -56499.2  reconciliation: -359.181  
Initial ll = -56858.4
[00:21:05] SPR Search with radius 1: trying 441 prune nodes
[00:22:01] Found 20 potential better moves
[00:22:01] 	GeneRax will now test and apply all the 20 potential good moves one after each other
	Applying move, ll = -56857.1, 294 299
	Applying move, ll = -56856.4, 357 364
	Applying move, ll = -56852.9, 474 481
	Applying move, ll = -56846.9, 519 586
	Applying move, ll = -56845, 561 568
[00:22:07] SPR Search with radius 1: trying 441 prune nodes
[00:23:21] Found 0 potential better moves
[00:23:21] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -56845  libpll: -56505.9  reconciliation: -339.1  
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
[00:23:22] End of optimizing gene tree after 1377s
[00:23:22] End of optimizeGeneTreesSlave
