Why Does The Order Of -S And -M Parameters In Bowtie Matter?

I'm trying to execute

bowtie –m 1 -S /hts/galaxy/data/references/genomes/mus-musc/ens73/mm73 whole_sample.fastq whole_sample.sam

But I'm getting

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.

bowtie

• 3,500 views • link

updated 12.7 years ago by Istvan Albert

• written 12.7 years ago by Nick

1 answer

I reversed the places of the parameters and it worked:

bowtie -S -m 1 /hts/galaxy/data/references/genomes/mus-musc/ens73/mm73 whole_sample.fastq whole_sample.sam

Strange.

• 275 views • link

written 12.7 years ago by Nick

it is weird stuff, I agree, good to know and thanks for following up

• 0 views • link

written 12.7 years ago by Istvan Albert

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