[Bioperl-l] Error calling alignment method

[Roy Chaudhuri]

Again, works fine for me (after changing the file and directory 
locations, and uncommenting the subroutine calls). Which Bioperl version 
are you using?

On 31/05/2011 20:04, Lorenzo Carretero Paulet wrote:
> Thanks for the reply,
> I attach again the revised versiont of the script I'm working with as
> well as the sequences. I still have the same error. The funny thing is
> that the yn00 subroutine is running properly when the alignment is
> passed directly, but not the codeml one (using either PAML 4.2 or 4.4).
> However, both PAML versions and programs are working fine with my data
> when I ran them manually.
> Any suggestion will be much appreciated.
> CHeers,
> Lorenzo
>
>    and El 31/05/11 19:28, Roy Chaudhuri escribió:
>> 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>_______________________________________________
>>>>>
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