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

Question

[Nick]

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.

Answer 1

[Nick]

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.

[Istvan Albert]

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