[Bioperl-l] error running codeml

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Mon Jul 23 17:19:24 EDT 2007


Apparently, your script isn't able to locate the codeml executable in 
your Windows environment. Do you have the PAML package installed? 
Instructions on how to install it are located here:

http://abacus.gene.ucl.ac.uk/software/paml.html

Regards,
Mauricio.

Munirul Islam wrote:
> Hello everyone:
> 
> I am new to bioperl.  I am running perl in Eclipse in Windows.  Here is the code:
> 
> [code]
> use Bio::Tools::Run::Phylo::PAML::Codeml;
> use Bio::AlignIO;
> use Bio::TreeIO;
> 
> my $alignio = Bio::AlignIO->new(-format => 'phylip',
> 			         -file   => 'NM_000034.CDSalign.paml');
> 
> my $aln = $alignio->next_aln;
> 
> my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'tree.txt');
> my $tree   = $treeio->next_tree;
> 
> my $codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new();
> 
> $codeml->alignment($aln);
> $codeml->tree($tree);
> 
> my ($rc,$parser) = $codeml->run();
> my $result = $parser->next_result;
> my $MLmatrix = $result->get_MLmatrix();
> print "Ka = ", $MLmatrix->[0]->[1]->{'dN'},"\n";
> print "Ks = ", $MLmatrix->[0]->[1]->{'dS'},"\n";
> print "Ka/Ks = ", $MLmatrix->[0]->[1]->{'omega'},"\n";
> [/code]
> 
> It gives the following error when I try to compile:
> 
> [error]
> ------------ EXCEPTION: Bio::Root::Exception -------------
> MSG: unable to find or run executable for 'codeml'
> STACK: Error::throw
> STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:359
> STACK: C:/Perl/site/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm:572
> -----------------------------------------------------------
> Can't remove directory C:\DOCUME~1\MUNIRU~1\LOCALS~1\Temp\SqSqwJKDLI (Permission denied) at C:/Perl/lib/File/Temp.pm line 898
> [/error]
> 
> Any idea, guys?
> 
> Munirul Islam
> Phd Student
> Computer Science
> Wayne State University
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> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM



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