Mercurial > repos > iuc > stacks2_cstacks
diff test-data/kmerfilter/kmerfilter.log @ 0:da351b9031de 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 11:03:59 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kmerfilter/kmerfilter.log Mon Jul 01 11:03:59 2019 -0400 @@ -0,0 +1,22 @@ +Using a kmer size of 16 +Filtering out reads by identifying rare kmers: On. + A kmer is considered rare when its coverage is at 15% or below the median kmer coverage for the read. + A read is dropped when it contains 13 or more rare kmers in a row. +Filtering out reads by identifying abundant kmers: On. + Kmer is considered abundant when it occurs 20000 or more times. + A read is dropped when it contains 80% or more abundant kmers. +Normalizing read depth: Off. +Found 1 input file(s). +Found 0 paired input file(s). +Generating kmer distribution... +Generating kmers from file 1 of 1 [R1_0001.fastq] +540 unique k-mers recorded. +Filtering reads by kmer frequency... +Processing file 1 of 1 [R1_0001.fastq] + 5 total reads; -0 rare k-mer reads; -0 abundant k-mer reads; 5 retained reads. +Outputing details to log: 'stacks_outputs/kmer_filter.log' + +5 total sequences; + 0 rare k-mer reads; + 0 abundant k-mer reads; +5 retained reads.