comparison test-data/gstacks/gstacks.log @ 4:60c1c4d7d2c1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty

3:56eb0bc12179

gstacks v2.2, executed 2018-11-27 19:48:29
/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
Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.

Configuration for this run:
  Input mode: denovo
  Population map: '/tmp/tmpSlCHrR/files/000/dataset_3.dat'
  Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
  Output to: 'stacks_outputs/'
  Model: marukilow (var_alpha: 0.05, gt_alpha: 0.05)

Reading BAM headers...
Processing all loci...
20%...
50%...
100%
Input appears to be single-end (no paired-end reads were seen).

Genotyped 3 loci:
  effective per-sample coverage: mean=21.0x, stdev=1.0x, min=20.0x, max=22.0x
  mean number of sites per locus: 94.0
  a consistent phasing was found for 2 of out 2 (100.0%) diploid loci needing phasing

gstacks is done.

4:60c1c4d7d2c1

gstacks v2.3b, executed 2019-02-22 12:51:51
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
Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.

Configuration for this run:
  Input mode: denovo
  Population map: '/tmp/tmpZcvUSM/files/000/dataset_3.dat'
  Input files: 2, e.g. 'bam_inputs/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.