view test-data/populations/populations.log @ 0:bd0bf17caa4d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty

populations v2.2, executed 2018-11-27 19:48:37
/home/berntm/miniconda3/envs/__stacks@2.2/bin/populations -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1
Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.
populations parameters selected:
  Percent samples limit per population: 0
  Locus Population limit: 1
  Log liklihood filtering: off; threshold: 0
  Minor allele frequency cutoff: 0
  Maximum observed heterozygosity cutoff: 1
  Applying Fst correction: none.
  Pi/Fis kernel smoothing: off
  Fstats kernel smoothing: off
  Bootstrap resampling: off

Parsing population map...
The population map contained 2 samples, 1 population(s), 1 group(s).
Working on 2 samples.
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
  * compute SNP- and haplotype-wise per-population statistics
  * write the above statistics in the output files
  * export the genotypes/haplotypes in specified format(s)
More details in 'stacks_outputs/populations.log.distribs'.
Now processing...
Batch 1 

Removed 0 loci that did not pass sample/population constraints from 3 loci.
Kept 3 loci, composed of 282 sites; 0 of those sites were filtered, 2 variant sites remained.
Mean genotyped sites per locus: 94.00bp (stderr 0.00).

Population summary statistics (more detail in populations.sumstats_summary.tsv):
  1: 2 samples per locus; pi: 0.66667; all/variant/polymorphic sites: 282/2/2; private alleles: 0
Populations is done.