Mercurial > repos > iuc > stacks2_tsv2bam
comparison test-data/gstacks/gstacks.log @ 0:1b270fc77c81 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
| author | iuc |
|---|---|
| date | Mon, 01 Jul 2019 10:59:53 -0400 |
| parents | |
| children | bf0e43ab0416 |
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| -1:000000000000 | 0:1b270fc77c81 |
|---|---|
| 1 gstacks v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11) | |
| 2 gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv | |
| 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: 'denovo_map/popmap_cstacks.tsv' | |
| 8 Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam' | |
| 9 Output to: 'stacks_outputs/' | |
| 10 Model: marukilow (var_alpha: 0.01, 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 204.3 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 252 paired-end reads in these loci (mean 84.0 reads per locus), | |
| 26 252 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. |