Mercurial > repos > matthias > stacks2_refmap
comparison 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
| author | matthias |
|---|---|
| date | Thu, 29 Nov 2018 11:38:05 -0500 |
| parents | |
| children | 466cc910d640 |
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| -1:000000000000 | 0:bd0bf17caa4d |
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| 1 populations v2.2, executed 2018-11-27 19:48:37 | |
| 2 /home/berntm/miniconda3/envs/__stacks@2.2/bin/populations -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1 | |
| 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 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 282 sites; 0 of those sites were filtered, 2 variant sites remained. | |
| 39 Mean genotyped sites per locus: 94.00bp (stderr 0.00). | |
| 40 | |
| 41 Population summary statistics (more detail in populations.sumstats_summary.tsv): | |
| 42 1: 2 samples per locus; pi: 0.66667; all/variant/polymorphic sites: 282/2/2; private alleles: 0 | |
| 43 Populations is done. |