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Id: 94872
Status: resolved
Priority: 0/
Queue: bioperl-run

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Owner: Nobody in particular
Requestors: marek.piatek [...] kaust.edu.sa
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Subject: bug in Bio::Tools::Run::Bowtie
Date: Sat, 19 Apr 2014 11:25:35 +0300
To: bug-bioperl-run [...] rt.cpan.org
From: Marek Piatek <marek.piatek [...] kaust.edu.sa>
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Fellows, Running the following: --CODE-- my $bowtie_fac = Bio::Tools::Run::Bowtie->new(); $bowtie_fac->set_parameters(-sam_no_sq => 1,); my $index = $bowtie_fac->run( -seq => $in_file, -ind => $index_base, -out => $sam_file, ); --END CODE-- Throws an STACK error about incorrectly constructed bowtie command: Command: /usr/bin/bowtie --sam_nosq -f -S index input.fa output.sam It seems the problem is with passing the '--sam-nosq' argument from 'Bio::Tools::Run::Bowtie', as it should be passed as '--sam-nosq' and NOT as '--sam_nosq' (underscore instead of minus). $ bowtie -h | grep "nosq" --sam-nosq supppress @SQ header lines for SAM output Regards, Marek PS. Additional info: $ perl -MBio::Tools::Run::Bowtie -e 'printf $Bio::Tools::Run::Bowtie::VERSION' 1.006923 $ uname -a Linux localhost 3.13.9-200.fc20.x86_64 #1 SMP Fri Apr 4 12:13:05 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $ bowtie --version bowtie version 1.0.1 -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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Looks like there were two arguments with the s/_/-/ issue, '--sam-nosq' and '--sam-nohead'. I fixed those on github master (f67ec02). On Sat Apr 19 03:25:49 2014, marek.piatek@kaust.edu.sa wrote: Show quoted text
> Fellows, > > Running the following: > > --CODE-- > my $bowtie_fac = Bio::Tools::Run::Bowtie->new(); > $bowtie_fac->set_parameters(-sam_no_sq => 1,); > my $index = $bowtie_fac->run( > -seq => $in_file, > -ind => $index_base, > -out => $sam_file, > ); > --END CODE-- > > Throws an STACK error about incorrectly constructed bowtie command: > Command: /usr/bin/bowtie --sam_nosq -f -S index input.fa output.sam > > It seems the problem is with passing the '--sam-nosq' argument from > 'Bio::Tools::Run::Bowtie', as it should be passed as '--sam-nosq' and > NOT as '--sam_nosq' (underscore instead of minus). > > $ bowtie -h | grep "nosq" > --sam-nosq supppress @SQ header lines for SAM output > > Regards, > Marek > > PS. > Additional info: > $ perl -MBio::Tools::Run::Bowtie -e 'printf > $Bio::Tools::Run::Bowtie::VERSION' > 1.006923 > > $ uname -a > Linux localhost 3.13.9-200.fc20.x86_64 #1 SMP Fri Apr 4 12:13:05 UTC > 2014 x86_64 x86_64 x86_64 GNU/Linux > > $ bowtie --version > bowtie version 1.0.1 >


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