Mercurial > repos > matthias > stacks2_denovomap

annotate test-data/tmp/stacks_outputs/populations.log @ 0:e5e5617c064a 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 11:50:28 -0500
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e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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1 populations v2.2, executed 2018-11-28 13:45:58
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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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
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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3 Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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4 populations parameters selected:
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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5 Percent samples limit per population: 0
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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6 Locus Population limit: 1
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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7 Log liklihood filtering: off; threshold: 0
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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8 Minor allele frequency cutoff: 0
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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9 Maximum observed heterozygosity cutoff: 1
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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10 Applying Fst correction: none.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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11 Pi/Fis kernel smoothing: off
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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12 Fstats kernel smoothing: off
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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13 Bootstrap resampling: off
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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14
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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15 Parsing population map...
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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16 The population map contained 2 samples, 1 population(s), 1 group(s).
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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17 Working on 2 samples.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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18 Working on 1 population(s):
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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19 1: PopA_01, PopA_02
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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20 Working on 1 group(s) of populations:
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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21 defaultgrp: 1
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22
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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23 FASTA consensus sequences for each locus in the metapopulation will be written to 'stacks_outputs/populations.loci.fa'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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24 FASTA consensus sequences for each sample will be written to 'stacks_outputs/populations.samples.fa'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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25 SNPs and calls will be written in VCF format to 'stacks_outputs/populations.snps.vcf'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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26 Haplotypes will be written in VCF format to 'stacks_outputs/populations.haps.vcf'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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27 Polymorphic sites in GenePop format will be written to 'stacks_outputs/populations.snps.genepop'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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28 Polymorphic loci in GenePop format will be written to 'stacks_outputs/populations.haps.genepop'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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29 Polymorphic sites in Structure format will be written to 'stacks_outputs/populations.structure'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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30 Polymorphic loci in RADpainter/fineRADstructure format will be written to 'stacks_outputs/populations.haps.radpainter'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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31 Polymorphic sites in PLINK format will be written to 'stacks_outputs/populations.plink.ped'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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32 Fixed difference sites in Phylip format will be written to 'stacks_outputs/populations.fixed.phylip'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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33 Individual sites written will be logged to 'stacks_outputs/populations.fixed.phylip.log'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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34 Polymorphic sites in Phylip format will be written to 'stacks_outputs/populations.var.phylip'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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35 Individual sites written will be logged to 'stacks_outputs/populations.var.phylip.log'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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36 Raw FASTA consensus sequences for each sample will be written to 'stacks_outputs/populations.samples-raw.fa'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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37 Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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38 Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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39 Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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40 Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv'
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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41
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42 Processing data in batches:
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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43 * load a batch of catalog loci and apply filters
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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44 * compute SNP- and haplotype-wise per-population statistics
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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45 * compute F-statistics
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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46 * write the above statistics in the output files
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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47 * export the genotypes/haplotypes in specified format(s)
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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48 More details in 'stacks_outputs/populations.log.distribs'.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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49 Now processing...
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50 Batch 1
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51
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52 Removed 0 loci that did not pass sample/population constraints from 3 loci.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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53 Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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54 Number of loci with PE contig: 3.00 (100.0%);
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55 Mean length of loci: 194.33bp (stderr 0.33);
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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56 Number of loci with SE/PE overlap: 0.00 (0.0%);
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57 Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00);
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58 Mean genotyped sites per locus: 194.33bp (stderr 0.33).
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59
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60 Population summary statistics (more detail in populations.sumstats_summary.tsv):
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61 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
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62
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63 Population pair divergence statistics (more in populations.fst_summary.tsv and populations.phistats_summary.tsv):
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64
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65 Populations is done.