[Bioperl-l] error running codeml

Munirul Islam ba6450 at wayne.edu
Mon Jul 23 16:06:14 EDT 2007

Hello everyone:

I am new to bioperl.  I am running perl in Eclipse in Windows.  Here is the 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();


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";

It gives the following error when I try to compile:

------------ 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

Any idea, guys?

Munirul Islam
Phd Student
Computer Science
Wayne State University

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