comparison test-data/denovo_map/denovo_map.log @ 2:fcce77c09289 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"

1:f4aab9196d1e

denovo_map.pl version 2.4 started at 2019-06-18 10:34:45
/home/berntm/miniconda3/envs/mulled-v1-2b57e7596f85ebb3b321e6c9681e8fd9250523a80d97945c46ac7743359454e7/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired

ustacks
==========

Sample 1 of 2 'PopA_01'

PopA_01: 22.00x
PopA_02: 20.00x

cstacks
==========
cstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv

cstacks parameters selected:
  Loci matched based on sequence identity.
  Number of mismatches allowed between stacks: 1
  Gapped alignments: enabled

Working on 1 population(s):
    1: PopA_01, PopA_02
Working on 1 group(s) of populations:
    defaultgrp: 1

Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv'
Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'
Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'
Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv'

Processing data in batches:
  * load a batch of catalog loci and apply filters

Population summary statistics (more detail in populations.sumstats_summary.tsv):
  1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
Populations is done.
denovo_map.pl is done.

denovo_map.pl completed at 2019-06-18 10:34:45

2:fcce77c09289

denovo_map.pl version 2.52 started at 2020-03-16 15:39:40
/home/berntm/miniconda3/envs/__stacks@2.52/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired

ustacks
==========

Sample 1 of 2 'PopA_01'

PopA_01: 22.00x
PopA_02: 20.00x

cstacks
==========
cstacks -M denovo_map/popmap_cstacks.tsv -P stacks_outputs

cstacks parameters selected:
  Loci matched based on sequence identity.
  Number of mismatches allowed between stacks: 1
  Gapped alignments: enabled

Working on 1 population(s):
    1: PopA_01, PopA_02
Working on 1 group(s) of populations:
    defaultgrp: 1

Raw haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'
Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'
Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv'

Processing data in batches:
  * load a batch of catalog loci and apply filters

Population summary statistics (more detail in populations.sumstats_summary.tsv):
  1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
Populations is done.
denovo_map.pl is done.

denovo_map.pl completed at 2020-03-16 15:39:40