Mercurial > repos > matthias > stacks2_tsv2bam

comparison test-data/gstacks/gstacks.log @ 5:852044374da1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
author matthias
date Thu, 20 Jun 2019 08:13:59 -0400
parents 60c1c4d7d2c1
children
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4:60c1c4d7d2c1 5:852044374da1
1 gstacks v2.3b, executed 2019-02-22 12:51:51 1 gstacks v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11)
2 gstacks -P bam_inputs -M /tmp/tmpZcvUSM/files/000/dataset_3.dat -O stacks_outputs -t 1 --model marukilow --var-alpha 0.01 --gt-alpha 0.05 2 gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
3 Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'. 3 Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.
4 4
5 Configuration for this run: 5 Configuration for this run:
6 Input mode: denovo 6 Input mode: denovo
7 Population map: '/tmp/tmpZcvUSM/files/000/dataset_3.dat' 7 Population map: 'denovo_map/popmap_cstacks.tsv'
8 Input files: 2, e.g. 'bam_inputs/PopA_01.matches.bam' 8 Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
9 Output to: 'stacks_outputs/' 9 Output to: 'stacks_outputs/'
10 Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05) 10 Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)
11 11
12 Reading BAM headers... 12 Reading BAM headers...
13 Processing all loci... 13 Processing all loci...