[Bioperl-l] error running codeml

Munirul Islam ba6450 at wayne.edu
Mon Jul 23 19:53:22 EDT 2007


Thanks Mauricio. 

I needed to add an environment variable for the paml directiory. 

$ENV{'PAMLDIR'} = 'c:\paml3.15\bin'; 

One question ... I would like to save the temp files.  So, what modification do I need to make such that 
$obj->save_tempfiles returns 1 within codeml.pm? 

Regards 

Munir

---- Original message ----
>Date: Mon, 23 Jul 2007 16:19:24 -0500
>From: Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>  
>Subject: Re: [Bioperl-l] error running codeml  
>To: Munirul Islam <ba6450 at wayne.edu>
>Cc: bioperl-l at lists.open-bio.org
>
>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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>
>-- 
>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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