Mercurial > repos > matthias > stacks2_denovomap

annotate test-data/sstacks/sstacks.log @ 6:dddd1a6454ce 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 10:59:31 -0400
parents a70c766ce64f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
1 Searching for matches by sequence identity...
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
2 Parsing stacks_inputs/catalog.tags.tsv
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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3 Parsing stacks_inputs/catalog.snps.tsv
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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4 Parsing stacks_inputs/catalog.alleles.tsv
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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5 Populating kmer dictionary for exact matches...done.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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6 Populating kmer dictionary for gapped alignments...done.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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7
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
8 Processing sample 'stacks_inputs/PopA_01' [1 of 2]
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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9 Parsing stacks_inputs/PopA_01.tags.tsv
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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10 Parsing stacks_inputs/PopA_01.snps.tsv
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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11 Parsing stacks_inputs/PopA_01.alleles.tsv
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
12 Searching for sequence matches...
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
13 3 sample loci compared against the catalog containing 3 loci.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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14 3 matching loci, 0 contained no verified haplotypes.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
15 0 loci matched more than one catalog locus and were excluded.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
16 0 loci contained SNPs unaccounted for in the catalog and were excluded.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
17 4 total haplotypes examined from matching loci, 4 verified.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
18 Searching for gapped alignments...
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
19 Out of 3 query loci, 0 gapped alignments attempted.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
20 0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
21 0 loci matched no catalog locus;
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
22 0 loci matched more than one catalog locus and were excluded.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
23 0 loci contained SNPs unaccounted for in the catalog and were excluded.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
24 0 loci had no verified haplotypes.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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25 0 loci had inconsistent alignments to a catalog locus and were excluded.
4
a70c766ce64f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
parents: 0
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26 Outputing to file stacks_inputs/PopA_01.matches.tsv
0
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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27
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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28 Processing sample 'stacks_inputs/PopA_02' [2 of 2]
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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29 Parsing stacks_inputs/PopA_02.tags.tsv
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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30 Parsing stacks_inputs/PopA_02.snps.tsv
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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31 Parsing stacks_inputs/PopA_02.alleles.tsv
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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32 Searching for sequence matches...
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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33 3 sample loci compared against the catalog containing 3 loci.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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34 3 matching loci, 0 contained no verified haplotypes.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
35 0 loci matched more than one catalog locus and were excluded.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
36 0 loci contained SNPs unaccounted for in the catalog and were excluded.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
37 4 total haplotypes examined from matching loci, 4 verified.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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38 Searching for gapped alignments...
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
39 Out of 3 query loci, 0 gapped alignments attempted.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
40 0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
41 0 loci matched no catalog locus;
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
42 0 loci matched more than one catalog locus and were excluded.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
43 0 loci contained SNPs unaccounted for in the catalog and were excluded.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
44 0 loci had no verified haplotypes.
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff changeset
45 0 loci had inconsistent alignments to a catalog locus and were excluded.
4
a70c766ce64f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
parents: 0
diff changeset
46 Outputing to file stacks_inputs/PopA_02.matches.tsv
0
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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47
e5e5617c064a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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48 sstacks is done.