[Bioperl-l] Clustalw

Offord, Victoria vofford at rvc.ac.uk
Mon Jun 22 12:10:43 EDT 2009


Hi,

 

Can anyone help and tell me where I am going wrong please J 

I am getting this error from the following script:

 

 

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: ClustalW call (clustalw align  -infile=/tmp/8PVli9JWEa/L_pxrEtzD1
-output=gcg   -matrix=BLOSUM -ktuple=2
-outfile=/tmp/8PVli9JWEa/XtAremlqau 2>&1) failed to start: 0 | No such
file or directory

STACK: Error::throw

STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357

STACK: Bio::Tools::Run::Alignment::Clustalw::_run
/usr/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/Clustalw.pm:756

STACK: Bio::Tools::Run::Alignment::Clustalw::align
/usr/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/Clustalw.pm:515

STACK: tester.pl:25

-----------------------------------------------------------

 

 

 

 

#--------------------------------------------SCRIPT---------------------
--------------------------#

#!/usr/bin/perl -w

use Bio::Tools::Run::Alignment::Clustalw;

$ENV{CLUSTALDIR} = '/var/local/clustalw-2.0.9';

use Bio::Seq;

 

 my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');

 my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);

 

my $a = "NPFECDCSMEWMQRVNNLTARQHPKILDLPNVECIMPHARGTPIRPIISLKPKDFLCK";

my $b =
"NPFECDCSMEWLQRINNLTTRQHPHVVDLGNIECLMPHSRSAPLRPLASLSASDFVCKYESHCPP";

my $seq1 = Bio::Seq->new ( -seq  => $a,

                           -id   => 'real',

                           -desc => 'this is a real Seq');

 my $seq2 = Bio::Seq->new ( -seq  => $b,

                           -id   => 'test',

                           -desc => 'this is a test Seq');


                           

my @seq_array = ($seq1,$seq2);

 

my $seq_array_ref = \@seq_array;

my $aln = $factory->align($seq_array_ref);

 

 

 




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