Mercurial > repos > matthias > stacks2_ustacks

comparison test-data/tmp/stacks_outputs/populations.log @ 0:e7aacfd67288 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
author matthias
date Thu, 29 Nov 2018 11:36:12 -0500
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-1:000000000000 0:e7aacfd67288
1 populations v2.2, executed 2018-11-28 13:45:58
2 /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
3 Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.
4 populations parameters selected:
5 Percent samples limit per population: 0
6 Locus Population limit: 1
7 Log liklihood filtering: off; threshold: 0
8 Minor allele frequency cutoff: 0
9 Maximum observed heterozygosity cutoff: 1
10 Applying Fst correction: none.
11 Pi/Fis kernel smoothing: off
12 Fstats kernel smoothing: off
13 Bootstrap resampling: off
14
15 Parsing population map...
16 The population map contained 2 samples, 1 population(s), 1 group(s).
17 Working on 2 samples.
18 Working on 1 population(s):
19 1: PopA_01, PopA_02
20 Working on 1 group(s) of populations:
21 defaultgrp: 1
22
23 FASTA consensus sequences for each locus in the metapopulation will be written to 'stacks_outputs/populations.loci.fa'
24 FASTA consensus sequences for each sample will be written to 'stacks_outputs/populations.samples.fa'
25 SNPs and calls will be written in VCF format to 'stacks_outputs/populations.snps.vcf'
26 Haplotypes will be written in VCF format to 'stacks_outputs/populations.haps.vcf'
27 Polymorphic sites in GenePop format will be written to 'stacks_outputs/populations.snps.genepop'
28 Polymorphic loci in GenePop format will be written to 'stacks_outputs/populations.haps.genepop'
29 Polymorphic sites in Structure format will be written to 'stacks_outputs/populations.structure'
30 Polymorphic loci in RADpainter/fineRADstructure format will be written to 'stacks_outputs/populations.haps.radpainter'
31 Polymorphic sites in PLINK format will be written to 'stacks_outputs/populations.plink.ped'
32 Fixed difference sites in Phylip format will be written to 'stacks_outputs/populations.fixed.phylip'
33 Individual sites written will be logged to 'stacks_outputs/populations.fixed.phylip.log'
34 Polymorphic sites in Phylip format will be written to 'stacks_outputs/populations.var.phylip'
35 Individual sites written will be logged to 'stacks_outputs/populations.var.phylip.log'
36 Raw FASTA consensus sequences for each sample will be written to 'stacks_outputs/populations.samples-raw.fa'
37 Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv'
38 Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'
39 Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'
40 Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv'
41
42 Processing data in batches:
43 * load a batch of catalog loci and apply filters
44 * compute SNP- and haplotype-wise per-population statistics
45 * compute F-statistics
46 * write the above statistics in the output files
47 * export the genotypes/haplotypes in specified format(s)
48 More details in 'stacks_outputs/populations.log.distribs'.
49 Now processing...
50 Batch 1
51
52 Removed 0 loci that did not pass sample/population constraints from 3 loci.
53 Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained.
54 Number of loci with PE contig: 3.00 (100.0%);
55 Mean length of loci: 194.33bp (stderr 0.33);
56 Number of loci with SE/PE overlap: 0.00 (0.0%);
57 Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00);
58 Mean genotyped sites per locus: 194.33bp (stderr 0.33).
59
60 Population summary statistics (more detail in populations.sumstats_summary.tsv):
61 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
62
63 Population pair divergence statistics (more in populations.fst_summary.tsv and populations.phistats_summary.tsv):
64
65 Populations is done.