Mercurial > repos > matthias > stacks2_cstacks
comparison test-data/tmp/stacks_outputs/gstacks.log @ 0:e4b371f8a47a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
| author | matthias |
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| date | Thu, 29 Nov 2018 11:41:18 -0500 |
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| -1:000000000000 | 0:e4b371f8a47a |
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| 1 gstacks v2.2, executed 2018-11-28 13:45:54 | |
| 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 | |
| 18 Attempted to assemble and align paired-end reads for 3 loci: | |
| 19 0 loci had no or almost no paired-end reads (0.0%); | |
| 20 0 loci had paired-end reads that couldn't be assembled into a contig (0.0%); | |
| 21 For the remaining 3 loci (100.0%), a paired-end contig was assembled; | |
| 22 Average contig size was 100.3 bp; | |
| 23 0 paired-end contigs overlapped the forward region (0.0%) | |
| 24 Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan; | |
| 25 Out of 126 paired-end reads in these loci (mean 42.0 reads per locus), | |
| 26 126 were successfuly aligned (100.0%); | |
| 27 Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci). | |
| 28 | |
| 29 Genotyped 3 loci: | |
| 30 effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x | |
| 31 mean number of sites per locus: 194.3 | |
| 32 a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing | |
| 33 | |
| 34 gstacks is done. |