mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/tbe_after_tindex_lsi/catabolism/RnR-prune_prunedBestTree.catabolism.newick ../Histamine_system/Analysis/tbe_reconciliation_inputFiles/mapping_file_catabolism.txt ../Histamine_system/Analysis/after_tindex_LSI/catabolism.fasta /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_results/species_trees/inferred_species_tree.newick WAG+F+I+G4 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_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_catabolism_results/results/catabolism/geneTree.newick /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_results/results/catabolism/stats.txt 0 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_results/gene_optimization_0/checkpoints/catabolism 
[00:00:14] Starting optimizeGeneTreesSlave
LibpllModel WAG+F+I+G4
[00:00:14] Starting optimizing gene tree
Number of ranks 1
(0.42992, 0.454016, score = 0)
Taxa number: 53
joint: -33550.7  libpll: -33425.6  reconciliation: -125.084  
Initial ll = -33550.7
[00:00:24] SPR Search with radius 1: trying 153 prune nodes
[00:01:22] Found 16 potential better moves
[00:01:22] 	GeneRax will now test and apply all the 16 potential good moves one after each other
	Applying move, ll = -33549.4, 81 193
	Applying move, ll = -33548.8, 114 123
	Applying move, ll = -33548.3, 130 138
	Applying move, ll = -33547.9, 168 170
[00:01:24] SPR Search with radius 1: trying 153 prune nodes
[00:02:23] Found 0 potential better moves
[00:02:23] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -33547.9  libpll: -33427.5  reconciliation: -120.421  
Saving tree in /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_results/results/catabolism/geneTree.newick
Finished saving  /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_results/results/catabolism/geneTree.newick
[00:02:23] End of optimizing gene tree after 129s
[00:02:23] End of optimizeGeneTreesSlave
