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

click xu click.xu at gmail.com
Mon Mar 29 23:17:17 EDT 2010


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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