Mercurial > repos > iuc > stacks2_ustacks

annotate test-data/gstacks/gstacks.log @ 1:21d2aa544835 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author iuc
date Mon, 30 Sep 2019 14:16:43 -0400
parents 7e5a174bc201
children d033e1ccb386
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7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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1 gstacks v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11)
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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2 gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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3 Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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5 Configuration for this run:
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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6 Input mode: denovo
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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7 Population map: 'denovo_map/popmap_cstacks.tsv'
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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8 Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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9 Output to: 'stacks_outputs/'
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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10 Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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11
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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12 Reading BAM headers...
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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13 Processing all loci...
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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14 20%...
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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15 50%...
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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16 100%
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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18 Attempted to assemble and align paired-end reads for 3 loci:
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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19 0 loci had no or almost no paired-end reads (0.0%);
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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20 0 loci had paired-end reads that couldn't be assembled into a contig (0.0%);
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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21 For the remaining 3 loci (100.0%), a paired-end contig was assembled;
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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22 Average contig size was 204.3 bp;
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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23 0 paired-end contigs overlapped the forward region (0.0%)
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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24 Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan;
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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25 Out of 252 paired-end reads in these loci (mean 84.0 reads per locus),
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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26 252 were successfuly aligned (100.0%);
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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27 Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci).
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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29 Genotyped 3 loci:
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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30 effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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31 mean number of sites per locus: 194.3
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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32 a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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34 gstacks is done.