[Bioperl-l] Trouble about Bio::Tools::Run::Alignment::Clustalw

Smithies, Russell Russell.Smithies at agresearch.co.nz
Mon Mar 29 23:25:03 EDT 2010


Do you have enough temp space?
Will clustalw run 'manually' with your parameters from the command line?

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of click xu
> Sent: Tuesday, 30 March 2010 4:17 p.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Trouble about Bio::Tools::Run::Alignment::Clustalw
> 
> Hi,
> I meet a problem when using Clustalw module.
> Here is the error message:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: ClustalW call ( align  -infile=/tmp/AeyAfdxGvH/YpcPbyhYht
> -output=gcg   -matrix=BLOSUM -ktup
> le=2 -outfile=/tmp/AeyAfdxGvH/Z2MbO0ylbF 2>&1) failed to start: 0 |
> cannot find the file or path
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /home/lf/data/BioPerl-
> 1.6.1/Bio/Root/Root.pm:368
> STACK: Bio::Tools::Run::Alignment::Clustalw::_run
> /usr/local/share/perl/5.10.0/Bio/Tools/Run/Alig
> nment/Clustalw.pm:756
> STACK: Bio::Tools::Run::Alignment::Clustalw::align
> /usr/local/share/perl/5.10.0/Bio/Tools/Run/Ali
> gnment/Clustalw.pm:515
> STACK: test.txt:45
> -----------------------------------------------------------
> The test program is described as below:
> -----------------------------------------------------------
> @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
> $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
> # @seq_array is an array of Bio::Seq objects
> $aln = $factory->align(\@seq_array);
> -----------------------------------------------------------
> The work path of clustalw2 has been configured:
> export CLUSTALDIR=/usr/local/bin/clustalw2
> So, what may be reason of the error?
> Thanks!
> 
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