[Bioperl-l] Problem with PAML/Codeml wrapper

Alexander Donath alex at bioinf.uni-leipzig.de
Mon Mar 8 10:45:14 EST 2010


Hi,

I do have a problem with the PAML/Codeml wrapper. I want to calculate all 
pairwise K_a,K_s values from a given alignment, using the example 
procedure of http://www.bioperl.org/wiki/HOWTO:PAML

<snip>
     my $dna_aln = aa_to_dna_aln($aln, \%seqs);
     my $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new(
 	-params => { 'runmode' => -2,
 		     'seqtype' => 1,}
 	);

     $kaks_factory->alignment($dna_aln);
     my ($rc,$parser) = $kaks_factory->run();
     my $result = $parser->next_result();
</snip>


But I receive an error:

-------------------- WARNING ---------------------
MSG: There was an error - see error_string for the program output
---------------------------------------------------

------------- EXCEPTION: Bio::Root::NotImplemented -------------
MSG: Unknown format of PAML output did not see seqtype
STACK: Error::throw
STACK: Bio::Root::Root::throw 
/usr/lib/perl5/vendor_perl/5.10.0/Bio/Root/Root.pm:359
STACK: Bio::Tools::Phylo::PAML::_parse_summary 
/usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Phylo/PAML.pm:441
STACK: Bio::Tools::Phylo::PAML::next_result 
/usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Phylo/PAML.pm:257


I use PAML4.4. Could this be the reason?

Best,
Alex


---
By the time you've read this, you've already read it!


More information about the Bioperl-l mailing list