view test-data/tmp/stacks_outputs/populations.log @ 0:2fb24beef45a draft

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

populations v2.2, executed 2018-11-28 13:45:58
/home/berntm/miniconda3/envs/__stacks@2.2/bin/populations -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1 --fstats --fasta_loci --fasta_samples --vcf --genepop --structure --radpainter --plink --phylip --phylip_var --phylip_var_all --fasta_samples_raw
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

FASTA consensus sequences for each locus in the metapopulation  will be written to 'stacks_outputs/populations.loci.fa'
FASTA consensus sequences for each sample will be written to 'stacks_outputs/populations.samples.fa'
SNPs and calls will be written in VCF format to 'stacks_outputs/populations.snps.vcf'
Haplotypes will be written in VCF format to 'stacks_outputs/populations.haps.vcf'
Polymorphic sites in GenePop format will be written to 'stacks_outputs/populations.snps.genepop'
Polymorphic loci in GenePop format will be written to 'stacks_outputs/populations.haps.genepop'
Polymorphic sites in Structure format will be written to 'stacks_outputs/populations.structure'
Polymorphic loci in RADpainter/fineRADstructure format will be written to 'stacks_outputs/populations.haps.radpainter'
Polymorphic sites in PLINK format will be written to 'stacks_outputs/populations.plink.ped'
Fixed difference sites in Phylip format will be written to 'stacks_outputs/populations.fixed.phylip'
   Individual sites written will be logged to 'stacks_outputs/populations.fixed.phylip.log'
Polymorphic sites in Phylip format will be written to 'stacks_outputs/populations.var.phylip'
   Individual sites written will be logged to 'stacks_outputs/populations.var.phylip.log'
Raw FASTA consensus sequences for each sample will be written to 'stacks_outputs/populations.samples-raw.fa'
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
  * compute F-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

Population pair divergence statistics (more in populations.fst_summary.tsv and populations.phistats_summary.tsv):

Populations is done.