annotate test-data/kmerfilter/kmerfilter.log @ 0:1b6d07160736 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460

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.