Mercurial > repos > matthias > stacks2_gstacks

comparison test-data/populations/populations.log @ 4:285e1f85c11a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
author matthias
date Wed, 27 Feb 2019 09:56:44 -0500
parents ce90584be117
children aa645d419016
comparison
equal deleted inserted replaced
3:5421b9528827 4:285e1f85c11a
1 populations v2.2, executed 2018-11-27 19:48:37 1 populations v2.3b, executed 2019-02-25 23:06:32
2 /home/berntm/miniconda3/envs/__stacks@2.2/bin/populations -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1 2 populations -t 1 -P stacks_inputs -O stacks_outputs -M /tmp/tmp4FNQre/files/000/dataset_3.dat -p 1 -r 0.0 --min_maf 0.0 --min_mac 0 --merge_prune_lim 1.0
3 Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'. 3 Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.
4 populations parameters selected: 4 populations parameters selected:
5 Percent samples limit per population: 0 5 Percent samples limit per population: 0
6 Locus Population limit: 1 6 Locus Population limit: 1
7 Log liklihood filtering: off; threshold: 0 7 Percent samples overall: 0
8 Minor allele frequency cutoff: 0 8 Minor allele frequency cutoff: 0
9 Maximum observed heterozygosity cutoff: 1 9 Maximum observed heterozygosity cutoff: 1
10 Applying Fst correction: none. 10 Applying Fst correction: none.
11 Pi/Fis kernel smoothing: off 11 Pi/Fis kernel smoothing: off
12 Fstats kernel smoothing: off 12 Fstats kernel smoothing: off
33 More details in 'stacks_outputs/populations.log.distribs'. 33 More details in 'stacks_outputs/populations.log.distribs'.
34 Now processing... 34 Now processing...
35 Batch 1 35 Batch 1
36 36
37 Removed 0 loci that did not pass sample/population constraints from 3 loci. 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. 38 Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained.
39 Mean genotyped sites per locus: 94.00bp (stderr 0.00). 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).
40 44
41 Population summary statistics (more detail in populations.sumstats_summary.tsv): 45 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 46 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
43 Populations is done. 47 Populations is done.