[Bioperl-l] Error calling alignment method

[Roy Chaudhuri]

Hi Lorenzo,

I tried your code (the one you attached as testa.pl), and the only 
errors that were reported were unininitialized values $Ka at lines 90 
and 150 when you print the output. This is because of typos in your 
script, you have "dA" instead of "dN" (PAML uses the terms "dN" and "dS" 
for Ka and Ks, respectively).

I can only think that the problem you are experiencing is because of 
some change to the PAML output format (although it worked fine for me 
with a just-downloaded PAML4.4 and an older PAML4). From what I recall, 
PAML always did have quite volatile output formats. Older versions of 
PAML are archived, so you could try downgrading:
http://abacus.gene.ucl.ac.uk/software/pamlOld.html

Cheers,
Roy.

On 25/05/2011 23:23, Lorenzo Carretero wrote:
> 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>_______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l