comparison test-data/gstacks/gstacks.log @ 0:d35cb34f2b85 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 10:59:14 -0400
parents
children 1d839ead7ad3
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-1:000000000000 0:d35cb34f2b85
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.