Mercurial > repos > abims-sbr > concatphyl
comparison test-data/test_15.out @ 0:6d930f037fea draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
| author | abims-sbr |
|---|---|
| date | Thu, 13 Apr 2017 05:49:32 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:6d930f037fea |
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| 1 ******************** CONCATENATION ******************** | |
| 2 | |
| 3 Process nucleotides concatenation: | |
| 4 Number of taxa aligned = 9 | |
| 5 Number of loci concatenated = 178 | |
| 6 | |
| 7 Total length of the concatenated sequences [All codon positions] = 41262 | |
| 8 Total length of the concatenated sequences [Codon positions 1 & 2] = 27508 | |
| 9 Total length of the concatenated sequences [Codon position 3] = 13754 | |
| 10 | |
| 11 | |
| 12 | |
| 13 ******************** RAxML RUN ******************** | |
| 14 | |
| 15 | |
| 16 | |
| 17 Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" | |
| 18 | |
| 19 | |
| 20 | |
| 21 This is RAxML version 8.2.9 released by Alexandros Stamatakis on July 20 2016. | |
| 22 | |
| 23 With greatly appreciated code contributions by: | |
| 24 Andre Aberer (HITS) | |
| 25 Simon Berger (HITS) | |
| 26 Alexey Kozlov (HITS) | |
| 27 Kassian Kobert (HITS) | |
| 28 David Dao (KIT and HITS) | |
| 29 Sarah Lutteropp (KIT and HITS) | |
| 30 Nick Pattengale (Sandia) | |
| 31 Wayne Pfeiffer (SDSC) | |
| 32 Akifumi S. Tanabe (NRIFS) | |
| 33 Charlie Taylor (UF) | |
| 34 | |
| 35 | |
| 36 Alignment has 564 distinct alignment patterns | |
| 37 | |
| 38 Proportion of gaps and completely undetermined characters in this alignment: 76.95% | |
| 39 | |
| 40 RAxML rapid bootstrapping algorithm | |
| 41 | |
| 42 Using 1 distinct models/data partitions with joint branch length optimization | |
| 43 | |
| 44 | |
| 45 | |
| 46 Executing 100 rapid bootstrap inferences | |
| 47 | |
| 48 All free model parameters will be estimated by RAxML | |
| 49 GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter | |
| 50 | |
| 51 GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units | |
| 52 | |
| 53 Partition: 0 | |
| 54 Alignment Patterns: 564 | |
| 55 Name: No Name Provided | |
| 56 DataType: DNA | |
| 57 Substitution Matrix: GTR | |
| 58 | |
| 59 | |
| 60 | |
| 61 | |
| 62 RAxML was called as follows: | |
| 63 | |
| 64 raxmlHPC -n galaxy_run -s ./03_Concatenation_nuc.phy -m GTRGAMMA -p 1234567890 -N 100 -f d -x 123456789 | |
| 65 | |
| 66 | |
| 67 | |
| 68 Time for BS model parameter optimization 0.210613 | |
| 69 Bootstrap[0]: Time 1.048781 seconds, bootstrap likelihood -75932.545350, best rearrangement setting 15 | |
| 70 Bootstrap[1]: Time 0.370352 seconds, bootstrap likelihood -76007.537590, best rearrangement setting 11 | |
| 71 Bootstrap[2]: Time 0.349113 seconds, bootstrap likelihood -75997.035876, best rearrangement setting 12 | |
| 72 Bootstrap[3]: Time 0.485543 seconds, bootstrap likelihood -76139.230321, best rearrangement setting 12 | |
| 73 Bootstrap[4]: Time 0.448112 seconds, bootstrap likelihood -76104.701291, best rearrangement setting 6 | |
| 74 Bootstrap[5]: Time 0.491783 seconds, bootstrap likelihood -75911.379318, best rearrangement setting 13 | |
| 75 Bootstrap[6]: Time 0.529860 seconds, bootstrap likelihood -76170.094697, best rearrangement setting 15 | |
| 76 Bootstrap[7]: Time 0.497637 seconds, bootstrap likelihood -76207.588083, best rearrangement setting 14 | |
| 77 Bootstrap[8]: Time 0.522369 seconds, bootstrap likelihood -75549.145357, best rearrangement setting 14 | |
| 78 Bootstrap[9]: Time 0.562428 seconds, bootstrap likelihood -76015.528837, best rearrangement setting 11 | |
| 79 Bootstrap[10]: Time 0.608720 seconds, bootstrap likelihood -76082.832555, best rearrangement setting 11 | |
| 80 Bootstrap[11]: Time 0.584563 seconds, bootstrap likelihood -76301.435377, best rearrangement setting 11 | |
| 81 Bootstrap[12]: Time 0.557597 seconds, bootstrap likelihood -76014.755388, best rearrangement setting 12 | |
| 82 Bootstrap[13]: Time 0.564486 seconds, bootstrap likelihood -75987.806027, best rearrangement setting 9 | |
| 83 Bootstrap[14]: Time 0.310805 seconds, bootstrap likelihood -75952.764120, best rearrangement setting 12 | |
| 84 Bootstrap[15]: Time 0.551613 seconds, bootstrap likelihood -76248.341862, best rearrangement setting 13 | |
| 85 Bootstrap[16]: Time 0.517321 seconds, bootstrap likelihood -76433.446646, best rearrangement setting 7 | |
| 86 Bootstrap[17]: Time 0.499398 seconds, bootstrap likelihood -75691.661860, best rearrangement setting 12 | |
| 87 Bootstrap[18]: Time 0.521698 seconds, bootstrap likelihood -75894.741916, best rearrangement setting 6 | |
| 88 Bootstrap[19]: Time 0.589791 seconds, bootstrap likelihood -76096.718199, best rearrangement setting 7 | |
| 89 Bootstrap[20]: Time 0.696489 seconds, bootstrap likelihood -76159.792619, best rearrangement setting 5 | |
| 90 Bootstrap[21]: Time 0.563807 seconds, bootstrap likelihood -76066.699952, best rearrangement setting 15 | |
| 91 Bootstrap[22]: Time 0.546471 seconds, bootstrap likelihood -76047.310226, best rearrangement setting 5 | |
| 92 Bootstrap[23]: Time 0.565515 seconds, bootstrap likelihood -76209.137153, best rearrangement setting 9 | |
| 93 Bootstrap[24]: Time 0.595023 seconds, bootstrap likelihood -76036.982097, best rearrangement setting 12 | |
| 94 Bootstrap[25]: Time 0.631842 seconds, bootstrap likelihood -76202.050921, best rearrangement setting 6 | |
| 95 Bootstrap[26]: Time 0.552071 seconds, bootstrap likelihood -76282.428248, best rearrangement setting 9 | |
| 96 Bootstrap[27]: Time 0.567584 seconds, bootstrap likelihood -76167.644169, best rearrangement setting 8 | |
| 97 Bootstrap[28]: Time 0.309510 seconds, bootstrap likelihood -76352.659658, best rearrangement setting 14 | |
| 98 Bootstrap[29]: Time 0.509756 seconds, bootstrap likelihood -75634.879367, best rearrangement setting 14 | |
| 99 Bootstrap[30]: Time 0.600830 seconds, bootstrap likelihood -75902.069529, best rearrangement setting 14 | |
| 100 Bootstrap[31]: Time 0.582872 seconds, bootstrap likelihood -75907.870884, best rearrangement setting 8 | |
| 101 Bootstrap[32]: Time 0.516745 seconds, bootstrap likelihood -76141.122211, best rearrangement setting 7 | |
| 102 Bootstrap[33]: Time 0.295958 seconds, bootstrap likelihood -75699.432027, best rearrangement setting 5 | |
| 103 Bootstrap[34]: Time 0.288135 seconds, bootstrap likelihood -76179.780099, best rearrangement setting 10 | |
| 104 Bootstrap[35]: Time 0.603329 seconds, bootstrap likelihood -76033.328115, best rearrangement setting 8 | |
| 105 Bootstrap[36]: Time 0.572087 seconds, bootstrap likelihood -76301.850307, best rearrangement setting 9 | |
| 106 Bootstrap[37]: Time 0.560764 seconds, bootstrap likelihood -75849.124257, best rearrangement setting 13 | |
| 107 Bootstrap[38]: Time 0.539320 seconds, bootstrap likelihood -76022.450184, best rearrangement setting 5 | |
| 108 Bootstrap[39]: Time 0.546802 seconds, bootstrap likelihood -75813.344550, best rearrangement setting 6 | |
| 109 Bootstrap[40]: Time 0.609194 seconds, bootstrap likelihood -76436.765766, best rearrangement setting 10 | |
| 110 Bootstrap[41]: Time 0.583296 seconds, bootstrap likelihood -75997.559122, best rearrangement setting 8 | |
| 111 Bootstrap[42]: Time 0.560753 seconds, bootstrap likelihood -76239.614653, best rearrangement setting 14 | |
| 112 Bootstrap[43]: Time 0.517432 seconds, bootstrap likelihood -75955.941647, best rearrangement setting 6 | |
| 113 Bootstrap[44]: Time 0.510632 seconds, bootstrap likelihood -75937.030077, best rearrangement setting 15 | |
| 114 Bootstrap[45]: Time 0.555368 seconds, bootstrap likelihood -76124.330062, best rearrangement setting 5 | |
| 115 Bootstrap[46]: Time 0.578972 seconds, bootstrap likelihood -76371.369232, best rearrangement setting 12 | |
| 116 Bootstrap[47]: Time 0.519948 seconds, bootstrap likelihood -75917.775923, best rearrangement setting 14 | |
| 117 Bootstrap[48]: Time 0.537641 seconds, bootstrap likelihood -75993.293598, best rearrangement setting 9 | |
| 118 Bootstrap[49]: Time 0.570051 seconds, bootstrap likelihood -76138.715931, best rearrangement setting 7 | |
| 119 Bootstrap[50]: Time 0.559163 seconds, bootstrap likelihood -76059.959334, best rearrangement setting 7 | |
| 120 Bootstrap[51]: Time 0.499943 seconds, bootstrap likelihood -75692.497159, best rearrangement setting 7 | |
| 121 Bootstrap[52]: Time 0.555316 seconds, bootstrap likelihood -75995.458937, best rearrangement setting 12 | |
| 122 Bootstrap[53]: Time 0.579144 seconds, bootstrap likelihood -75912.810781, best rearrangement setting 12 | |
| 123 Bootstrap[54]: Time 0.538008 seconds, bootstrap likelihood -75961.061510, best rearrangement setting 9 | |
| 124 Bootstrap[55]: Time 0.298026 seconds, bootstrap likelihood -76259.944659, best rearrangement setting 9 | |
| 125 Bootstrap[56]: Time 0.558566 seconds, bootstrap likelihood -76079.378672, best rearrangement setting 6 | |
| 126 Bootstrap[57]: Time 0.590322 seconds, bootstrap likelihood -75749.862721, best rearrangement setting 6 | |
| 127 Bootstrap[58]: Time 0.538738 seconds, bootstrap likelihood -76029.413379, best rearrangement setting 5 | |
| 128 Bootstrap[59]: Time 0.510509 seconds, bootstrap likelihood -75894.234449, best rearrangement setting 5 | |
| 129 Bootstrap[60]: Time 0.513843 seconds, bootstrap likelihood -76154.981497, best rearrangement setting 7 | |
| 130 Bootstrap[61]: Time 0.502247 seconds, bootstrap likelihood -76133.712435, best rearrangement setting 11 | |
| 131 Bootstrap[62]: Time 0.563201 seconds, bootstrap likelihood -76218.876369, best rearrangement setting 5 | |
| 132 Bootstrap[63]: Time 0.522544 seconds, bootstrap likelihood -75774.986219, best rearrangement setting 13 | |
| 133 Bootstrap[64]: Time 0.532345 seconds, bootstrap likelihood -75990.492502, best rearrangement setting 13 | |
| 134 Bootstrap[65]: Time 0.535124 seconds, bootstrap likelihood -76306.072449, best rearrangement setting 12 | |
| 135 Bootstrap[66]: Time 0.554829 seconds, bootstrap likelihood -76332.253655, best rearrangement setting 6 | |
| 136 Bootstrap[67]: Time 0.520356 seconds, bootstrap likelihood -76129.398815, best rearrangement setting 8 | |
| 137 Bootstrap[68]: Time 0.558836 seconds, bootstrap likelihood -76254.564769, best rearrangement setting 15 | |
| 138 Bootstrap[69]: Time 0.550105 seconds, bootstrap likelihood -76046.944289, best rearrangement setting 5 | |
| 139 Bootstrap[70]: Time 0.566401 seconds, bootstrap likelihood -76189.196831, best rearrangement setting 6 | |
| 140 Bootstrap[71]: Time 0.508642 seconds, bootstrap likelihood -75960.712756, best rearrangement setting 6 | |
| 141 Bootstrap[72]: Time 0.526512 seconds, bootstrap likelihood -76210.045656, best rearrangement setting 13 | |
| 142 Bootstrap[73]: Time 0.515909 seconds, bootstrap likelihood -76169.812350, best rearrangement setting 9 | |
| 143 Bootstrap[74]: Time 0.579022 seconds, bootstrap likelihood -76025.554093, best rearrangement setting 7 | |
| 144 Bootstrap[75]: Time 0.570090 seconds, bootstrap likelihood -75655.041599, best rearrangement setting 5 | |
| 145 Bootstrap[76]: Time 0.487730 seconds, bootstrap likelihood -75829.406474, best rearrangement setting 13 | |
| 146 Bootstrap[77]: Time 0.254941 seconds, bootstrap likelihood -75860.607115, best rearrangement setting 14 | |
| 147 Bootstrap[78]: Time 0.298414 seconds, bootstrap likelihood -76055.311793, best rearrangement setting 11 | |
| 148 Bootstrap[79]: Time 0.588599 seconds, bootstrap likelihood -75915.374846, best rearrangement setting 6 | |
| 149 Bootstrap[80]: Time 0.667347 seconds, bootstrap likelihood -76261.543583, best rearrangement setting 13 | |
| 150 Bootstrap[81]: Time 0.612976 seconds, bootstrap likelihood -76174.874698, best rearrangement setting 5 | |
| 151 Bootstrap[82]: Time 0.531991 seconds, bootstrap likelihood -75793.101339, best rearrangement setting 5 | |
| 152 Bootstrap[83]: Time 0.585576 seconds, bootstrap likelihood -75938.639400, best rearrangement setting 8 | |
| 153 Bootstrap[84]: Time 0.627221 seconds, bootstrap likelihood -75996.185152, best rearrangement setting 10 | |
| 154 Bootstrap[85]: Time 0.560480 seconds, bootstrap likelihood -76154.783869, best rearrangement setting 10 | |
| 155 Bootstrap[86]: Time 0.596546 seconds, bootstrap likelihood -76215.777177, best rearrangement setting 6 | |
| 156 Bootstrap[87]: Time 0.589085 seconds, bootstrap likelihood -76233.616897, best rearrangement setting 12 | |
| 157 Bootstrap[88]: Time 0.291329 seconds, bootstrap likelihood -75804.735625, best rearrangement setting 6 | |
| 158 Bootstrap[89]: Time 0.553877 seconds, bootstrap likelihood -76026.236128, best rearrangement setting 12 | |
| 159 Bootstrap[90]: Time 0.679948 seconds, bootstrap likelihood -76296.463995, best rearrangement setting 15 | |
| 160 Bootstrap[91]: Time 0.543307 seconds, bootstrap likelihood -76001.064460, best rearrangement setting 15 | |
| 161 Bootstrap[92]: Time 0.624406 seconds, bootstrap likelihood -76140.644926, best rearrangement setting 7 | |
| 162 Bootstrap[93]: Time 0.331340 seconds, bootstrap likelihood -76002.798476, best rearrangement setting 15 | |
| 163 Bootstrap[94]: Time 0.333815 seconds, bootstrap likelihood -75909.186324, best rearrangement setting 14 | |
| 164 Bootstrap[95]: Time 0.317092 seconds, bootstrap likelihood -76442.785521, best rearrangement setting 14 | |
| 165 Bootstrap[96]: Time 0.598750 seconds, bootstrap likelihood -76081.323369, best rearrangement setting 12 | |
| 166 Bootstrap[97]: Time 0.313615 seconds, bootstrap likelihood -75913.019207, best rearrangement setting 5 | |
| 167 Bootstrap[98]: Time 0.620730 seconds, bootstrap likelihood -76178.332365, best rearrangement setting 10 | |
| 168 Bootstrap[99]: Time 0.607763 seconds, bootstrap likelihood -76031.354102, best rearrangement setting 11 | |
| 169 | |
| 170 | |
| 171 Overall Time for 100 Rapid Bootstraps 52.903293 seconds | |
| 172 Average Time per Rapid Bootstrap 0.529033 seconds | |
| 173 All 100 bootstrapped trees written to: /tmp/tmpo3fKpd/job_working_directory/000/3/working/RAxML_bootstrap.galaxy_run |