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_3/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 4 /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_3/checkpoints/cdhit_phobius_tm_RECEPTORS 
[03:01:52] Starting optimizeGeneTreesSlave
LibpllModel Q.plant+I+R9
[03:01:52] Starting optimizing gene tree
Number of ranks 24
(0.162846, 0.43837, score = 0)
Taxa number: 269
joint: -105961  libpll: -105246  reconciliation: -715.09  
Initial ll = -105961
[03:50:50] SPR Search with radius 4: trying 801 prune nodes
[04:09:12] Found 0 potential better moves
[04:09:12] 	GeneRax will now test and apply all the 0 potential good moves one after each other
joint: -105961  libpll: -105246  reconciliation: -715.09  
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
[04:09:15] End of optimizing gene tree after 4042s
[04:09:17] End of optimizeGeneTreesSlave
