Mercurial > repos > matthias > stacks2_populations
comparison test-data/gstacks/gstacks.log @ 0:3950b915b7cf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
| author | matthias |
|---|---|
| date | Thu, 29 Nov 2018 11:58:35 -0500 |
| parents | |
| children | 35e673d79262 |
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| -1:000000000000 | 0:3950b915b7cf |
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| 1 gstacks v2.2, executed 2018-11-27 19:48:29 | |
| 2 /home/berntm/miniconda3/envs/__stacks@2.2/bin/gstacks -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1 --var-alpha 0.05 --gt-alpha 0.05 | |
| 3 Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'. | |
| 4 | |
| 5 Configuration for this run: | |
| 6 Input mode: denovo | |
| 7 Population map: '/tmp/tmpSlCHrR/files/000/dataset_3.dat' | |
| 8 Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam' | |
| 9 Output to: 'stacks_outputs/' | |
| 10 Model: marukilow (var_alpha: 0.05, gt_alpha: 0.05) | |
| 11 | |
| 12 Reading BAM headers... | |
| 13 Processing all loci... | |
| 14 20%... | |
| 15 50%... | |
| 16 100% | |
| 17 Input appears to be single-end (no paired-end reads were seen). | |
| 18 | |
| 19 Genotyped 3 loci: | |
| 20 effective per-sample coverage: mean=21.0x, stdev=1.0x, min=20.0x, max=22.0x | |
| 21 mean number of sites per locus: 94.0 | |
| 22 a consistent phasing was found for 2 of out 2 (100.0%) diploid loci needing phasing | |
| 23 | |
| 24 gstacks is done. |