Mercurial > repos > matthias > stacks2_cstacks

annotate test-data/gstacks/gstacks.log @ 5:687f84474d33 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
author matthias
date Thu, 20 Jun 2019 08:12:36 -0400
parents 924e7889aa05
children
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687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents: 4
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1 gstacks v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11)
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
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2 gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
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e4b371f8a47a 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/gstacks.log.distribs'.
e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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5 Configuration for this run:
e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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6 Input mode: denovo
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687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents: 4
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7 Population map: 'denovo_map/popmap_cstacks.tsv'
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents: 4
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8 Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
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e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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9 Output to: 'stacks_outputs/'
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924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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10 Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)
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e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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12 Reading BAM headers...
e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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13 Processing all loci...
e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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14 20%...
e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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15 50%...
e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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16 100%
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924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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18 Attempted to assemble and align paired-end reads for 3 loci:
924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
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19 0 loci had no or almost no paired-end reads (0.0%);
924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
parents: 0
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20 0 loci had paired-end reads that couldn't be assembled into a contig (0.0%);
924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
parents: 0
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21 For the remaining 3 loci (100.0%), a paired-end contig was assembled;
924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
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22 Average contig size was 204.3 bp;
924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
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23 0 paired-end contigs overlapped the forward region (0.0%)
924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
parents: 0
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24 Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan;
924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
parents: 0
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25 Out of 252 paired-end reads in these loci (mean 84.0 reads per locus),
924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
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26 252 were successfuly aligned (100.0%);
924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
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27 Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci).
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e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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29 Genotyped 3 loci:
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924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
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30 effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x
924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
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31 mean number of sites per locus: 194.3
924e7889aa05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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32 a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing
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e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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e4b371f8a47a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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34 gstacks is done.