| 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> |
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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