[Bioperl-l] running a simple example with Bio::Tools::Run::BWA

[Adam Witney]

Hi,

I am trying to run bwa according to the HOWTO listed here:

http://www.bioperl.org/wiki/HOWTO:Short-read_assemblies_with_BWA

To test it i am just trying to reproduce the simple example at the beginning, using this code:

#!/usr/local/bin/perl -w
use warnings;
use strict; 
use Bio::Tools::Run::BWA;

my $bwa = Bio::Tools::Run::BWA->new();
$bwa->out_type('test.sam');

my $assy = $bwa->run( 'myseq.fastq', 'myref.fa' );
print $assy."\n";

My understanding of the example in the HOWTO is that the file "test.sam" (although it looks like it should be producing a .bam file now anyway) should be created, is that correct?

If so my problem is that the file is not created, and from a little digging in  Bio::Tools::Run::BWA I can't see where it would (it does create a tmp file in /tmp/xxxx/, but this is eventually deleted). I think the process is working as i can see bwa and samtools running using "top" and without the out_type line then I do get a Bio::Assembly::ScaffoldI object created in $assy. Its just that the output file is not being copied/moved to the requested out_type.

Have i just misunderstood how this works?

Thanks for any help

Adam