[Bioperl-l] error running codeml

Jason Stajich jason at bioperl.org
Tue Jul 24 03:19:18 EDT 2007


when you initialize the Codeml object just pass in my $codeml =
Bio::Tools::Run::Phylo::PAML::Codeml->new(-save_tempfiles => 1);

OR do
$codeml->save_tempfiles(1);

You may want to set you TEMPDIR as well and you print out where the tempdir
is located with
print $codeml->tempdir;
and I think you can get the temp outfile.
my $name = $codeml->outfile_name;
print "name is $name\n";

-jason
On 7/23/07, Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx> wrote:
>
> 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
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki/User:Jason



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