[Bioperl-l] Error calling alignment method

[Lorenzo Carretero]

Dave, Jason:

I had already tried running PAML manually with the alignment (I always 
do this to confirm software is properly installed and set up), and ran 
again with an edited version of the alignment removing the stop codons 
(I didn't know stop codons at the ends of the alignmente could affect 
PAML, but inframe stop codons). It worked properly in both cases. I ran 
again my script (see attached testa.pl) using two different methods, one 
constructing the codon alignment using aa_to_dna_aln and another one 
passing the aligned sequences (in both cases after removing the stop 
codons). I had again the message:

------------- EXCEPTION: Bio::Root::NotImplemented -------------
MSG: Unknown format of PAML output did not see seqtype
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::Tools::Phylo::PAML::_parse_summary 
/Library/Perl/5.10.0/Bio/Tools/Phylo/PAML.pm:461
STACK: Bio::Tools::Phylo::PAML::next_result 
/Library/Perl/5.10.0/Bio/Tools/Phylo/PAML.pm:270
STACK: main::GettingBioperlAlignmentAAtoDNAplusPAMLcalculation 
/Users/Lorenzo/Documents/workspace/PlantEvolGen/testa.pl:83
STACK: /Users/Lorenzo/Documents/workspace/PlantEvolGen/testa.pl:23
----------------------------------------------------------------

Thanks,
Lorenzo

On 5/25/11 10:24 PM, Jason Stajich wrote:
>> ------------------------------------------
>>
>> I think the codon alignment is being proberly constructed by the method aa_to_dna_aln, as I can do a Dumper printing of it. So the problem must be in the PAML codeml wrapper not properly recognizing the codon alignment. Could it be related to the alignment format (PAML runs on PHYLIP formatted files)?
> The writing out in phylip format is taking care of by the factory - you are passing in an alignment object so that is not typically the problem.
>
> I would repeat Dave's idea that you just dump the codon alignment file out and you run PAML manually with it.  The parsing error sounds like there are problems when running PAML and you may want to check that you don't have stop codons in your alignment.  It looks like your CDS file has stops as the last codon so if you drop those last 3 bases, how does it work?
>
>> Cheers,
>> Lorenzo
>>
>>
>>
>> -- 
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>> Lorenzo Carretero Paulet
>> Institute for Plant Molecular and Cell Biology - IBMCP (CSIC-UPV)
>> Integrative Systems Biology Group
>> C/ Ingeniero Fausto Elio s/n.
>> 46022 Valencia, Spain
>>
>> Phone:  +34 963879934
>> Fax:    +34 963877859
>> e-mail: locarpau at upvnet.upv.es
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>
>> <test_vs_test.par.nt.1.fas><test_vs_test.par.aa.1.fas><code.pl>_______________________________________________
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>
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-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
Lorenzo Carretero Paulet
Institute for Plant Molecular and Cell Biology - IBMCP (CSIC-UPV)
Integrative Systems Biology Group
C/ Ingeniero Fausto Elio s/n.
46022 Valencia, Spain

Phone:  +34 963879934
Fax:    +34 963877859
e-mail: locarpau at upvnet.upv.es
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*

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