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comparison test-data/RAxML_parsimonyTree.galaxy.multi @ 5:d38fcf1b83c5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
author iuc
date Mon, 02 Dec 2019 12:51:50 +0000
parents b0d6eb76ad87
children 9dd2607a4ec6
comparison
equal deleted inserted replaced
4:58a0f16c950c 5:d38fcf1b83c5
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
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27
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
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 ....
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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