mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/ufb_after_tindex_lsi/catabolism/RnR-prune_prunedBestTree.catabolism.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_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_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_0/checkpoints/catabolism 
[00:00:01] Starting optimizeGeneTreesSlave
LibpllModel WAG+F+I+G4
[00:00:01] Starting optimizing gene tree
Number of ranks 2
(0.50001, 0.5, score = 0)
Taxa number: 53
joint: -33554  libpll: -33425.7  reconciliation: -128.292  
Initial ll = -33554
[00:00:13] SPR Search with radius 1: trying 153 prune nodes
[00:00:49] Found 20 potential better moves
[00:00:49] 	GeneRax will now test and apply all the 20 potential good moves one after each other
	Applying move, ll = -33552.1, 84 196
	Applying move, ll = -33551.6, 117 126
	Applying move, ll = -33551.4, 144 185
	Applying move, ll = -33550.4, 147 153
	Applying move, ll = -33550.1, 171 173
[00:00:52] SPR Search with radius 1: trying 153 prune nodes
[00:01:22] Found 8 potential better moves
[00:01:22] 	GeneRax will now test and apply all the 8 potential good moves one after each other
	Applying move, ll = -33549.6, 132 125
	Applying move, ll = -33548.4, 141 143
[00:01:23] SPR Search with radius 1: trying 153 prune nodes
[00:01:56] Found 0 potential better moves
[00:01:56] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -33548.4  libpll: -33428.8  reconciliation: -119.594  
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
[00:01:57] End of optimizing gene tree after 116s
[00:01:57] End of optimizeGeneTreesSlave
