Mercurial > repos > matthias > stacks2_shortreads

annotate test-data/populations/populations.log @ 6:fc02f1545768 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3
author matthias
date Tue, 25 Jun 2019 10:58:06 -0400
parents 56d3555cf5f7
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56d3555cf5f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
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1 populations v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11)
56d3555cf5f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
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2 populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
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061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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3 Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.
061c9e133d1e 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:
061c9e133d1e 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
061c9e133d1e 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
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c23695f62bdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
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7 Percent samples overall: 0
0
061c9e133d1e 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
061c9e133d1e 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
061c9e133d1e 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.
061c9e133d1e 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
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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12 Fstats kernel smoothing: off
061c9e133d1e 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
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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061c9e133d1e 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...
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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16 The population map contained 2 samples, 1 population(s), 1 group(s).
061c9e133d1e 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.
061c9e133d1e 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):
061c9e133d1e 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
061c9e133d1e 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:
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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21 defaultgrp: 1
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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23 Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv'
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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24 Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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25 Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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26 Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv'
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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28 Processing data in batches:
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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29 * load a batch of catalog loci and apply filters
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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30 * compute SNP- and haplotype-wise per-population statistics
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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31 * write the above statistics in the output files
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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32 * export the genotypes/haplotypes in specified format(s)
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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33 More details in 'stacks_outputs/populations.log.distribs'.
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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34 Now processing...
061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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35 Batch 1
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061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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37 Removed 0 loci that did not pass sample/population constraints from 3 loci.
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c23695f62bdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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38 Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained.
c23695f62bdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
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39 Number of loci with PE contig: 3.00 (100.0%);
c23695f62bdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
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40 Mean length of loci: 194.33bp (stderr 0.33);
c23695f62bdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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41 Number of loci with SE/PE overlap: 0.00 (0.0%);
c23695f62bdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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42 Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00);
c23695f62bdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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43 Mean genotyped sites per locus: 194.33bp (stderr 0.33).
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061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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45 Population summary statistics (more detail in populations.sumstats_summary.tsv):
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c23695f62bdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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46 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
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061c9e133d1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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47 Populations is done.