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_1/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 2 ../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_1/checkpoints/cdhit_phobius_tm_RECEPTORS 
[01:02:46] Starting optimizeGeneTreesSlave
LibpllModel LG+F+R9
[01:02:46] Starting optimizing gene tree
Number of ranks 10
(0.197676, 0.504758, score = 0)
Taxa number: 269
joint: -106285  libpll: -105509  reconciliation: -775.981  
Initial ll = -106285
[01:45:01] SPR Search with radius 2: trying 801 prune nodes
[01:52:13] Found 16 potential better moves
[01:52:13] 	GeneRax will now test and apply all the 16 potential good moves one after each other
	Applying move, ll = -106276, 322 23
	Worse likelihood, Move rejected
	Applying move, ll = -106275, 427 62
	Applying move, ll = -106273, 526 398
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
	Applying move, ll = -106272, 870 209
	Applying move, ll = -106268, 1045 246
[01:52:34] SPR Search with radius 2: trying 801 prune nodes
[02:02:43] Found 12 potential better moves
[02:02:43] 	GeneRax will now test and apply all the 12 potential good moves one after each other
	Applying move, ll = -106266, 435 426
	Applying move, ll = -106264, 528 567
	Worse likelihood, Move rejected
	Worse likelihood, Move rejected
[02:02:49] SPR Search with radius 2: trying 801 prune nodes
[02:11:55] Found 4 potential better moves
[02:11:55] 	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: -106264  libpll: -105525  reconciliation: -738.942  
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
[02:12:00] End of optimizing gene tree after 4154s
[02:12:04] End of optimizeGeneTreesSlave
