mpi-scheduler optimizeGeneTrees /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick ../Histamine_system/Analysis/tbe_reconciliation_inputFiles/mapping_file_cdhit_phobius_tm_RECEPTORS.txt ../Histamine_system/Analysis/after_tindex_LSI/cdhit_phobius_tm_RECEPTORS.fasta /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/species_trees/inferred_species_tree.newick Q.plant+I+R9 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/gene_optimization_2/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 3 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/stats.txt 0 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/gene_optimization_2/checkpoints/cdhit_phobius_tm_RECEPTORS 
[01:38:29] Starting optimizeGeneTreesSlave
LibpllModel Q.plant+I+R9
[01:38:29] Starting optimizing gene tree
Number of ranks 24
(0.161371, 0.442157, score = 0)
Taxa number: 269
joint: -105966  libpll: -105231  reconciliation: -735.604  
Initial ll = -105966
[02:26:55] SPR Search with radius 3: trying 801 prune nodes
[02:41:01] Found 5 potential better moves
[02:41:01] 	GeneRax will now test and apply all the 5 potential good moves one after each other
	Applying move, ll = -105965, 502 106
	Worse likelihood, Move rejected
	Applying move, ll = -105965, 803 794
[02:41:09] SPR Search with radius 3: trying 801 prune nodes
[02:51:28] Found 11 potential better moves
[02:51:28] 	GeneRax will now test and apply all the 11 potential good moves one after each other
	Applying move, ll = -105964, 561 630
	Applying move, ll = -105963, 564 626
	Worse likelihood, Move rejected
	Applying move, ll = -105963, 1046 1040
[02:51:40] SPR Search with radius 3: trying 801 prune nodes
[03:01:43] Found 0 potential better moves
[03:01:43] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -105963  libpll: -105248  reconciliation: -715.143  
Saving tree in /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick
Finished saving  /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_cdhit_phobius_tm_RECEPTORS_results/results/cdhit_phobius_tm_RECEPTORS/geneTree.newick
[03:01:47] End of optimizing gene tree after 4998s
[03:01:48] End of optimizeGeneTreesSlave
