[Bioperl-l] met a problem when runBio::Tools::Run::Phylo::PAML::Yn00

[Mark A. Jensen]

Hi Kevin-
maybe you can avoid the proprietary data problem-- can you reproduce the error 
using the
example data that comes with the PAML distribution? That would be great, since 
it looks like
our tests are based on (earlier version's) output from those examples, and we 
could do
a direct comparison to what BioPerl thinks is right- cheers
MAJ
----- Original Message ----- 
From: "kevin fan" <lengjingmao at gmail.com>
To: "Chris Fields" <cjfields at illinois.edu>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Monday, February 09, 2009 9:40 AM
Subject: Re: [Bioperl-l] met a problem when 
runBio::Tools::Run::Phylo::PAML::Yn00


> hi, Chris and Dave,
>
> i will try to get permission from the boss. since the sequences i mentioned
> are from a new species.
>
> kevin.
>
> 2009/2/9 Chris Fields <cjfields at illinois.edu>
>
>> kevin,
>>
>> As Dave mentioned, go ahead and attach any output from PAML 4.2 to the bug
>> report.  I want to make it a priority to get the PAMLM parser working for
>> the 1.6 release series (if not 1.6.1, maybe 1.6.2).
>>
>> chris
>>
>>
>> On Feb 9, 2009, at 7:39 AM, kevin fan wrote:
>>
>>
>>> hi, chris
>>> thank you for the reply. i will use PAML 3.15 instead
>>>
>>> cheers,
>>> kevin
>>> 2009/2/9 Chris Fields <cjfields at illinois.edu>
>>> We do not adequately support PAML v4.0 and up at this time.  Much of this
>>> is due to PAML's constantly shifting output (every release seems to break
>>> our parsers).
>>>
>>> chris
>>>
>>>
>>> On Feb 9, 2009, at 5:57 AM, kevin fan wrote:
>>>
>>> Dear all,
>>> i am using Bio::Tools::Run::Phylo::PAML::Yn00  to calculate Ka/Ks ratio of
>>> pairwise sequences.
>>> bioperl version is 1.6, and PAML version is 4.2
>>>
>>> when i run the Bio::Tools::Run::Phylo::PAML::Yn00 , it warns:
>>>
>>> -------------------- WARNING ---------------------
>>> MSG: There was an error - see error_string for the program output
>>> ---------------------------------------------------
>>>
>>> ------------- EXCEPTION: Bio::Root::NotImplemented -------------
>>> MSG: Unknown format of PAML output did not see seqtype
>>> STACK: Error::throw
>>> STACK: Bio::Root::Root::throw
>>> /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:359
>>> STACK: Bio::Tools::Phylo::PAML::_parse_summary
>>> /usr/local/share/perl/5.10.0/Bio/Tools/Phylo/PAML.pm:441
>>> STACK: Bio::Tools::Phylo::PAML::next_result
>>> /usr/local/share/perl/5.10.0/Bio/Tools/Phylo/PAML.pm:257
>>> STACK: kaks.pl:10
>>> ----------------------------------------------------------------
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>>>
>>>
>>>
>>
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