annotate test-data/populations/populations.log @ 0:ad7a60726fc3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460

populations v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11)
populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
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
  Percent samples overall: 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 613 sites; 0 of those sites were filtered, 6 variant sites remained.
Number of loci with PE contig: 3.00 (100.0%);
  Mean length of loci: 194.33bp (stderr 0.33);
Number of loci with SE/PE overlap: 0.00 (0.0%);
  Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00);
Mean genotyped sites per locus: 194.33bp (stderr 0.33).

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.