bowtie: extra parameter error

feralBiologist

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Join Date: Jun 2011

Posts: 61
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#1

bowtie: extra parameter error

11-21-2013, 06:05 AM

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.
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