Mercurial > repos > iuc > raxml
comparison test-data/RAxML_parsimonyTree.galaxy.multi @ 2:a4b71be30c3c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
author | iuc |
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date | Mon, 02 Dec 2019 07:52:10 -0500 |
parents | 6805e85573b8 |
children | 29ff6a849eac |
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1:ba29b5e2a4be | 2:a4b71be30c3c |
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1 | 1 ((Whale:0.00000100000050002909,(((Human:0.53594305845070155936,Seal:0.02530146292078635367):0.22193621954611089664,Frog:0.10286092072478680848):0.21862941933399418493,(Chicken:0.20757792196205043789,(Mouse:0.08330390883767016530,Rat:0.08037715347256141341):0.07528731153882931015):0.12712658591923928220):0.03338415401578518488):0.14391313040760642106,(Carp:0.35121248438619490084,Loach:0.00000100000050002909):0.21735437670664689569,Cow:0.06259549717909577982):0.0; |
2 | |
3 Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" | |
4 | |
5 | |
6 | |
7 This is RAxML version 8.2.4 released by Alexandros Stamatakis on October 02 2015. | |
8 | |
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) | |
18 | |
19 Alignment has 34 distinct alignment patterns | |
20 | |
21 Proportion of gaps and completely undetermined characters in this alignment: 0.00% | |
22 | |
23 RAxML rapid hill-climbing mode | |
24 | |
25 Using 1 distinct models/data partitions with joint branch length optimization | |
26 | |
27 | |
28 Executing 5 inferences on the original alignment using 5 distinct randomized MP trees | |
29 | |
30 All free model parameters will be estimated by RAxML | |
31 ML estimate of 25 per site rate categories | |
32 | |
33 Likelihood of final tree will be evaluated and optimized under GAMMA | |
34 | |
35 GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units | |
36 | |
37 Partition: 0 | |
38 Alignment Patterns: 34 | |
39 Name: No Name Provided | |
40 DataType: DNA | |
41 Substitution Matrix: GTR | |
42 | |
43 | |
44 | |
45 | |
46 RAxML was called as follows: | |
47 | |
48 raxmlHPC -s /tmp/tmpS1corm/files/000/dataset_7.dat -n galaxy -m GTRCAT -N 5 -f d -p 1234567890 | |
49 | |
50 | |
51 Partition: 0 with name: No Name Provided | |
52 Base frequencies: 0.325 0.288 0.168 0.218 | |
53 | |
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: 156.924095 909.973305 698.798586 49.826281 1854.008494 1.000000 | |
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: 984.611489 1694.475132 1327.909793 133.166551 5344.045057 1.000000 | |
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: 467.628294 1755.581565 1080.117186 84.613232 3889.913949 1.000000 | |
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: 951.225250 1754.836760 1010.717630 104.250644 4976.305821 1.000000 | |
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: 1216.938988 2115.384600 1728.203983 157.161613 6782.996281 1.000000 | |
64 | |
65 | |
66 Conducting final model optimizations on all 5 trees under GAMMA-based models .... | |
67 | |
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: -378.202304 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.1 | |
70 Inference[2] final GAMMA-based Likelihood: -377.272824 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.2 | |
71 Inference[3] final GAMMA-based Likelihood: -377.004321 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.3 | |
72 Inference[4] final GAMMA-based Likelihood: -378.202304 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.4 | |
73 | |
74 | |
75 Starting final GAMMA-based thorough Optimization on tree 3 likelihood -377.004321 .... | |
76 | |
77 Final GAMMA-based Score of best tree -377.004321 | |
78 | |
79 Program execution info written to /tmp/tmpS1corm/job_working_directory/000/4/RAxML_info.galaxy | |
80 Best-scoring ML tree written to: /tmp/tmpS1corm/job_working_directory/000/4/RAxML_bestTree.galaxy | |
81 | |
82 Overall execution time: 0.917038 secs or 0.000255 hours or 0.000011 days | |
83 | |
84 | |
85 OM: CLI options DEBUG START: | |
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 |