mpi-scheduler optimizeGeneTrees ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliation_inputFiles/mapping_file_cdhit_phobius_tm_RECEPTORS.txt ../Histamine_system/Analysis/after_tindex_LSI/cdhit_phobius_tm_RECEPTORS.fasta ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/species_trees/inferred_species_tree.newick LG+F+R9 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/gene_optimization_4/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 5 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/stats.txt 0 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/gene_optimization_4/checkpoints/cdhit_phobius_tm_RECEPTORS 
                                                       LG+F+R9
[03:28:02] Starting optimizing gene tree
Number of ranks 10
(0.16403, 0.440219, score = 0)
Taxa number: 269
joint: -106261  libpll: -105523  reconciliation: -738.062  
Initial ll = -106261
[03:52:01] SPR Search with radius 5: trying 801 prune nodes
[04:04:38] Found 4 potential better moves
[04:04:38] 	GeneRax will now test and apply all the 4 potential good moves one after each other
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
joint: -106261  libpll: -105523  reconciliation: -738.062  
Saving tree in ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick
Finished saving  ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick
[04:04:42] End of optimizing gene tree after 2200s
[04:04:42] End of optimizeGeneTreesSlave
