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comparison test-data/RAxML_parsimonyTree.galaxy.multi @ 1:b0d6eb76ad87 draft

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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
author iuc
date Sat, 25 Jun 2016 19:34:35 -0400
parents 934206441123
children d38fcf1b83c5
comparison
equal deleted inserted replaced
0:934206441123 1:b0d6eb76ad87
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45 45
46 RAxML was called as follows: 46 RAxML was called as follows:
47 47
48 raxmlHPC -s /tmp/tmp_D_Wx1/files/000/dataset_7.dat -n galaxy -m GTRCAT -N 5 -f d -p 1234567890 48 raxmlHPC -s /tmp/tmpS1corm/files/000/dataset_7.dat -n galaxy -m GTRCAT -N 5 -f d -p 1234567890
49 49
50 50
51 Partition: 0 with name: No Name Provided 51 Partition: 0 with name: No Name Provided
52 Base frequencies: 0.325 0.288 0.168 0.218 52 Base frequencies: 0.325 0.288 0.168 0.218
53 53
54 Inference[0]: Time 0.384667 CAT-based likelihood -318.296661, best rearrangement setting 5 54 Inference[0]: Time 0.216205 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 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
56 Inference[1]: Time 0.312805 CAT-based likelihood -320.216685, best rearrangement setting 5 56 Inference[1]: Time 0.156515 CAT-based likelihood -320.216706, 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 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
58 Inference[2]: Time 0.310104 CAT-based likelihood -317.720602, best rearrangement setting 5 58 Inference[2]: Time 0.168518 CAT-based likelihood -317.720618, 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 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
60 Inference[3]: Time 0.361859 CAT-based likelihood -320.856853, best rearrangement setting 5 60 Inference[3]: Time 0.151635 CAT-based likelihood -320.856852, 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 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
62 Inference[4]: Time 0.365067 CAT-based likelihood -320.068835, best rearrangement setting 5 62 Inference[4]: Time 0.148819 CAT-based likelihood -320.068842, 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 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
64 64
65 65
66 Conducting final model optimizations on all 5 trees under GAMMA-based models .... 66 Conducting final model optimizations on all 5 trees under GAMMA-based models ....
67 67
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 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
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 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
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 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
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 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
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 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
73 73
74 74
75 Starting final GAMMA-based thorough Optimization on tree 3 likelihood -377.004344 .... 75 Starting final GAMMA-based thorough Optimization on tree 3 likelihood -377.004321 ....
76 76
77 Final GAMMA-based Score of best tree -377.004344 77 Final GAMMA-based Score of best tree -377.004321
78 78
79 Program execution info written to /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_info.galaxy 79 Program execution info written to /tmp/tmpS1corm/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 80 Best-scoring ML tree written to: /tmp/tmpS1corm/job_working_directory/000/4/RAxML_bestTree.galaxy
81 81
82 Overall execution time: 1.829373 secs or 0.000508 hours or 0.000021 days 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: 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}> 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}>
87 OM: CLI options DEBUG END 87 OM: CLI options DEBUG END