[Bioperl-l] Clustalw
Offord, Victoria
vofford at rvc.ac.uk
Mon Jun 22 16:10:43 UTC 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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