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_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 /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_1/checkpoints/cdhit_phobius_tm_RECEPTORS 
[00:52:53] Starting optimizeGeneTreesSlave
LibpllModel Q.plant+I+R9
[00:52:53] Starting optimizing gene tree
Number of ranks 24
(0.20019, 0.498028, score = 0)
Taxa number: 269
joint: -105971  libpll: -105226  reconciliation: -745.096  
Initial ll = -105971
[01:29:50] SPR Search with radius 2: trying 801 prune nodes
[01:34:01] Found 1 potential better moves
[01:34:01] 	GeneRax will now test and apply all the 1 potential good moves one after each other
	Applying move, ll = -105967, 316 2
[01:34:03] SPR Search with radius 2: trying 801 prune nodes
[01:38:25] Found 0 potential better moves
[01:38:25] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -105967  libpll: -105231  reconciliation: -735.964  
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
[01:38:28] End of optimizing gene tree after 2735s
[01:38:28] End of optimizeGeneTreesSlave
