[Bioperl-l] Error calling alignment method

Wed Jun 1 13:31:37 UTC 2011

I think Dave made some changes after 1.6.1; try upgrading to the latest version on CPAN (1.6.901):

http://search.cpan.org/~cjfields/BioPerl-1.6.901/

chris

On Jun 1, 2011, at 5:52 AM, Lorenzo Carretero Paulet wrote:

> perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' : 1.006001
> Thanks,
> Lorenzo
> El 01/06/11 12:17, Roy Chaudhuri escribió:
>> 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>_______________________________________________ 
>>>>>>> 
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
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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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