[Bioperl-l] Error calling alignment method

Wed Jun 1 10:52:51 UTC 2011

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>_______________________________________________ 
>>>>>>
>>>>>>
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>>>>>
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>>>>
>>>>
>>>>
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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
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*