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comparison test-data/RAxML_parsimonyTree.galaxy.multi @ 0:934206441123 draft

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planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
author iuc
date Mon, 30 Nov 2015 22:03:09 -0500
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children b0d6eb76ad87
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-1:000000000000 0:934206441123
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3 Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
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7 This is RAxML version 8.2.4 released by Alexandros Stamatakis on October 02 2015.
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9 With greatly appreciated code contributions by:
10 Andre Aberer (HITS)
11 Simon Berger (HITS)
12 Alexey Kozlov (HITS)
13 Kassian Kobert (HITS)
14 David Dao (KIT and HITS)
15 Nick Pattengale (Sandia)
16 Wayne Pfeiffer (SDSC)
17 Akifumi S. Tanabe (NRIFS)
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19 Alignment has 34 distinct alignment patterns
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21 Proportion of gaps and completely undetermined characters in this alignment: 0.00%
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23 RAxML rapid hill-climbing mode
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25 Using 1 distinct models/data partitions with joint branch length optimization
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28 Executing 5 inferences on the original alignment using 5 distinct randomized MP trees
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30 All free model parameters will be estimated by RAxML
31 ML estimate of 25 per site rate categories
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33 Likelihood of final tree will be evaluated and optimized under GAMMA
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35 GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
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37 Partition: 0
38 Alignment Patterns: 34
39 Name: No Name Provided
40 DataType: DNA
41 Substitution Matrix: GTR
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46 RAxML was called as follows:
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48 raxmlHPC -s /tmp/tmp_D_Wx1/files/000/dataset_7.dat -n galaxy -m GTRCAT -N 5 -f d -p 1234567890
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51 Partition: 0 with name: No Name Provided
52 Base frequencies: 0.325 0.288 0.168 0.218
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54 Inference[0]: Time 0.384667 CAT-based likelihood -318.296661, best rearrangement setting 5
55 alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 156.921091 909.963678 698.791844 49.826026 1853.987180 1.000000
56 Inference[1]: Time 0.312805 CAT-based likelihood -320.216685, best rearrangement setting 5
57 alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 984.966228 1693.994555 1327.595110 133.225736 5344.810756 1.000000
58 Inference[2]: Time 0.310104 CAT-based likelihood -317.720602, best rearrangement setting 5
59 alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 467.622832 1755.681465 1079.971295 84.603657 3889.976834 1.000000
60 Inference[3]: Time 0.361859 CAT-based likelihood -320.856853, best rearrangement setting 5
61 alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 951.251278 1754.861720 1010.715785 104.248328 4976.318155 1.000000
62 Inference[4]: Time 0.365067 CAT-based likelihood -320.068835, best rearrangement setting 5
63 alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 1216.935051 2115.369469 1728.113008 157.211587 6783.037433 1.000000
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66 Conducting final model optimizations on all 5 trees under GAMMA-based models ....
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68 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
69 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
70 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
71 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
72 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
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75 Starting final GAMMA-based thorough Optimization on tree 3 likelihood -377.004344 ....
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77 Final GAMMA-based Score of best tree -377.004344
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79 Program execution info written to /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_info.galaxy
80 Best-scoring ML tree written to: /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_bestTree.galaxy
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82 Overall execution time: 1.829373 secs or 0.000508 hours or 0.000021 days
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85 OM: CLI options DEBUG START:
86 <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}>
87 OM: CLI options DEBUG END