Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" 



This is RAxML version 8.2.4 released by Alexandros Stamatakis on October 02 2015.

With greatly appreciated code contributions by:
Andre Aberer      (HITS)
Simon Berger      (HITS)
Alexey Kozlov     (HITS)
Kassian Kobert    (HITS)
David Dao         (KIT and HITS)
Nick Pattengale   (Sandia)
Wayne Pfeiffer    (SDSC)
Akifumi S. Tanabe (NRIFS)

Alignment has 34 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.00%

RAxML rapid hill-climbing mode

Using 1 distinct models/data partitions with joint branch length optimization


Executing 5 inferences on the original alignment using 5 distinct randomized MP trees

All free model parameters will be estimated by RAxML
ML estimate of 25 per site rate categories

Likelihood of final tree will be evaluated and optimized under GAMMA

GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units

Partition: 0
Alignment Patterns: 34
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR




RAxML was called as follows:

raxmlHPC -s /tmp/tmp_D_Wx1/files/000/dataset_7.dat -n galaxy -m GTRCAT -N 5 -f d -p 1234567890 


Partition: 0 with name: No Name Provided
Base frequencies: 0.325 0.288 0.168 0.218 

Inference[0]: Time 0.384667 CAT-based likelihood -318.296661, best rearrangement setting 5
alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 156.921091 909.963678 698.791844 49.826026 1853.987180 1.000000 
Inference[1]: Time 0.312805 CAT-based likelihood -320.216685, best rearrangement setting 5
alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 984.966228 1693.994555 1327.595110 133.225736 5344.810756 1.000000 
Inference[2]: Time 0.310104 CAT-based likelihood -317.720602, best rearrangement setting 5
alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 467.622832 1755.681465 1079.971295 84.603657 3889.976834 1.000000 
Inference[3]: Time 0.361859 CAT-based likelihood -320.856853, best rearrangement setting 5
alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 951.251278 1754.861720 1010.715785 104.248328 4976.318155 1.000000 
Inference[4]: Time 0.365067 CAT-based likelihood -320.068835, best rearrangement setting 5
alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 1216.935051 2115.369469 1728.113008 157.211587 6783.037433 1.000000 


Conducting final model optimizations on all 5 trees under GAMMA-based models ....

Inference[0] final GAMMA-based Likelihood: -378.273623 tree written to file /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_result.galaxy.RUN.0
Inference[1] final GAMMA-based Likelihood: -378.202275 tree written to file /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_result.galaxy.RUN.1
Inference[2] final GAMMA-based Likelihood: -377.272786 tree written to file /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_result.galaxy.RUN.2
Inference[3] final GAMMA-based Likelihood: -377.004344 tree written to file /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_result.galaxy.RUN.3
Inference[4] final GAMMA-based Likelihood: -378.202275 tree written to file /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_result.galaxy.RUN.4


Starting final GAMMA-based thorough Optimization on tree 3 likelihood -377.004344 .... 

Final GAMMA-based Score of best tree -377.004344

Program execution info written to /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_info.galaxy
Best-scoring ML tree written to: /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_bestTree.galaxy

Overall execution time: 1.829373 secs or 0.000508 hours or 0.000021 days


OM: CLI options DEBUG START:
<Values at 0x7fd1fab4d518: {'bootseed': None, 'groupingfile': None, 'posterior_bootstopping_analysis': None, 'print_branch_lengths': None, 'starting_tree': None, 'model_opt_precision': None, 'weightfile': None, 'use_median_approximation': None, 'majority_rule_consensus': None, 'excludefile': None, 'save_memory_gappy_alignments': None, 'binary': 'raxmlHPC', 'numofcats': None, 'multistate_sub_model': None, 'multiple_model': None, 'search_complete_random_tree': None, 'source': '/tmp/tmp_D_Wx1/files/000/dataset_7.dat', 'outgroup_name': None, 'estimate_individual_branch_lengths': None, 'ml_search_convergence': None, 'file_multiple_trees': None, 'rapid_bootstrap_random_seed': None, 'random_seed': 1234567890, 'disable_undetermined_seq_check': None, 'save_memory_cat_model': None, 'enable_evol_heuristics': None, 'aa_empirical_freq': None, 'threads': 1, 'external_protein_model': None, 'search_algorithm': 'd', 'constraint_file': None, 'secondary_structure_model': None, 'number_of_runs': 5, 'name': None, 'initial_rearrangement_setting': None, 'secondary_structure_file': None, 'model_type': 'nucleotide', 'aa_search_matrix': None, 'disable_rate_heterogeneity': None, 'base_model': 'GTRCAT', 'parsimony_starting_tree_only': None, 'number_of_runs_bootstop': None, 'sliding_window_size': None, 'bin_model_parameter_file': None}>
OM: CLI options DEBUG END