[Bioperl-l] error running codeml

[Mauricio Herrera Cuadra]

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