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

[Smithies, Russell]

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!
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================