Mercurial > repos > iuc > stacks2_cstacks

comparison test-data/populations/populations.log @ 0:da351b9031de draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 11:03:59 -0400
parents
children fcce77c09289
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-1:000000000000 0:da351b9031de
1 populations v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11)
2 populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
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 Percent samples overall: 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 Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv'
24 Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'
25 Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'
26 Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv'
27
28 Processing data in batches:
29 * load a batch of catalog loci and apply filters
30 * compute SNP- and haplotype-wise per-population statistics
31 * write the above statistics in the output files
32 * export the genotypes/haplotypes in specified format(s)
33 More details in 'stacks_outputs/populations.log.distribs'.
34 Now processing...
35 Batch 1
36
37 Removed 0 loci that did not pass sample/population constraints from 3 loci.
38 Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained.
39 Number of loci with PE contig: 3.00 (100.0%);
40 Mean length of loci: 194.33bp (stderr 0.33);
41 Number of loci with SE/PE overlap: 0.00 (0.0%);
42 Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00);
43 Mean genotyped sites per locus: 194.33bp (stderr 0.33).
44
45 Population summary statistics (more detail in populations.sumstats_summary.tsv):
46 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
47 Populations is done.