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#318 -u/--qupto arg must be at least 1

v0.9.0
open
nobody
None
5
2014-07-31
2014-07-30
Astrid
No

Hi
I get this error message with bowtie2 and the following:
bowtie2 -x myref -U myseqs.fastq -S Alignment_bowtie_out.sam --local --met-file metrics_female -un unalignedseqs -p 5 -D 10 -R 2 -N 1 -L 22 -i S,1,1.75 --rdg 4,2 --rfg 4,2 --mp 5,1
However, if I run the same input data only specifying only --local I dont get an error
I would appreciate any help here

Discussion

  • Val
    Val
    2014-07-31

    Hi Astrid,

    I could not reproduce the problem you are having. Can you double check the bowtie version you are using? Can you provide an example fastq file which triggers the problem?

    thanks,
    Val