annotate test-data/gstacks/gstacks.log @ 3:cfb504394ae1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"

gstacks v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11)
gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.

Configuration for this run:
  Input mode: denovo
  Population map: 'denovo_map/popmap_cstacks.tsv'
  Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
  Output to: 'stacks_outputs/'
  Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)

Reading BAM headers...
Processing all loci...
20%...
50%...
100%

Attempted to assemble and align paired-end reads for 3 loci:
  0 loci had no or almost no paired-end reads (0.0%);
  0 loci had paired-end reads that couldn't be assembled into a contig (0.0%);
  For the remaining 3 loci (100.0%), a paired-end contig was assembled;
    Average contig size was 204.3 bp;
  0 paired-end contigs overlapped the forward region (0.0%)
    Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan;
  Out of 252 paired-end reads in these loci (mean 84.0 reads per locus),
    252 were successfuly aligned (100.0%);
  Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci).

Genotyped 3 loci:
  effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x
  mean number of sites per locus: 194.3
  a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing

gstacks is done.