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annotate test-data/RAxML_parsimonyTree.galaxy.multi @ 2:6f7ff8a3bd79 draft

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planemo upload for repository https://github.com/stamatak/standard-RAxML commit bcfc8451fa622a6bf3aa31fa1e308c394feefb38
author iuc
date Mon, 14 Nov 2016 13:11:14 -0500
parents b0d6eb76ad87
children d38fcf1b83c5
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934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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3 Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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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:
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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10 Andre Aberer (HITS)
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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11 Simon Berger (HITS)
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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12 Alexey Kozlov (HITS)
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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13 Kassian Kobert (HITS)
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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14 David Dao (KIT and HITS)
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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15 Nick Pattengale (Sandia)
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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16 Wayne Pfeiffer (SDSC)
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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17 Akifumi S. Tanabe (NRIFS)
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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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
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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30 All free model parameters will be estimated by RAxML
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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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
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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38 Alignment Patterns: 34
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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39 Name: No Name Provided
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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40 DataType: DNA
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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41 Substitution Matrix: GTR
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46 RAxML was called as follows:
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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48 raxmlHPC -s /tmp/tmpS1corm/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
934206441123 planemo upload for repository https://github.com/stamatak/standard-RAxML commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
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52 Base frequencies: 0.325 0.288 0.168 0.218
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54 Inference[0]: Time 0.216205 CAT-based likelihood -318.296661, best rearrangement setting 5
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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55 alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 156.924095 909.973305 698.798586 49.826281 1854.008494 1.000000
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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56 Inference[1]: Time 0.156515 CAT-based likelihood -320.216706, best rearrangement setting 5
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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57 alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 984.611489 1694.475132 1327.909793 133.166551 5344.045057 1.000000
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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58 Inference[2]: Time 0.168518 CAT-based likelihood -317.720618, best rearrangement setting 5
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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59 alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 467.628294 1755.581565 1080.117186 84.613232 3889.913949 1.000000
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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60 Inference[3]: Time 0.151635 CAT-based likelihood -320.856852, best rearrangement setting 5
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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61 alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 951.225250 1754.836760 1010.717630 104.250644 4976.305821 1.000000
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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62 Inference[4]: Time 0.148819 CAT-based likelihood -320.068842, best rearrangement setting 5
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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63 alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 1216.938988 2115.384600 1728.203983 157.161613 6782.996281 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: -378.273666 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.0
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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69 Inference[1] final GAMMA-based Likelihood: -378.202304 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.1
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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70 Inference[2] final GAMMA-based Likelihood: -377.272824 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.2
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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71 Inference[3] final GAMMA-based Likelihood: -377.004321 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.3
b0d6eb76ad87 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
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72 Inference[4] final GAMMA-based Likelihood: -378.202304 tree written to file /tmp/tmpS1corm/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 -377.004321 ....
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77 Final GAMMA-based Score of best tree -377.004321
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79 Program execution info written to /tmp/tmpS1corm/job_working_directory/000/4/RAxML_info.galaxy
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80 Best-scoring ML tree written to: /tmp/tmpS1corm/job_working_directory/000/4/RAxML_bestTree.galaxy
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82 Overall execution time: 0.917038 secs or 0.000255 hours or 0.000011 days
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85 OM: CLI options DEBUG START:
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86 <Values at 0x7f8e104919e0: {'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/tmpS1corm/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}>
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87 OM: CLI options DEBUG END