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  • feralBiologist
    Member
    • Jun 2011
    • 61
    #1

    bowtie: extra parameter error

    I'm trying to execute

    Code:
    bowtie –m 1 -S /hts/galaxy/data/references/genomes/mus-musc/ens73/mm73 whole_sample.fastq whole_sample.sam
    but I'm getting

    Code:
    Extra parameter(s) specified: "whole_sample.fastq", "whole_sample.sam"
    This is quite annoying and I am sure there is some stupid syntax error on my part. Can you help spot it? This is bowtie version 1.0.

    --EDIT: I reversed the place of the parameters:

    Code:
    bowtie -S -m 1  /hts/galaxy/data/references/genomes/mus-musc/ens73/mm73 whole_sample.fastq whole_sample.sam
    and now it works. This is bizarre. Apparently, the sequence of the parameters makes a difference but it is not something I find obvious from the bowtie manual.
    Last edited by feralBiologist; 11-21-2013, 06:09 AM.
    Tags: bowtie
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