Mercurial > repos > iuc > stacks2_kmerfilter
annotate test-data/kmerfilter/kmerfilter.log @ 0:b2e3553e1be2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author | iuc |
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date | Mon, 01 Jul 2019 10:58:28 -0400 |
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b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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1 Using a kmer size of 16 |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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2 Filtering out reads by identifying rare kmers: On. |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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3 A kmer is considered rare when its coverage is at 15% or below the median kmer coverage for the read. |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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4 A read is dropped when it contains 13 or more rare kmers in a row. |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
5 Filtering out reads by identifying abundant kmers: On. |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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6 Kmer is considered abundant when it occurs 20000 or more times. |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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7 A read is dropped when it contains 80% or more abundant kmers. |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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8 Normalizing read depth: Off. |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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9 Found 1 input file(s). |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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10 Found 0 paired input file(s). |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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11 Generating kmer distribution... |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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12 Generating kmers from file 1 of 1 [R1_0001.fastq] |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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13 540 unique k-mers recorded. |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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14 Filtering reads by kmer frequency... |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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15 Processing file 1 of 1 [R1_0001.fastq] |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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16 5 total reads; -0 rare k-mer reads; -0 abundant k-mer reads; 5 retained reads. |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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17 Outputing details to log: 'stacks_outputs/kmer_filter.log' |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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18 |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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19 5 total sequences; |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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20 0 rare k-mer reads; |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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21 0 abundant k-mer reads; |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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22 5 retained reads. |