[Bioperl-l] model 3 on Codeml.pm

[Jason Stajich]

yes - as I said, a simple script that demonstrates the problem will make this all easier to debug. If you reported the actual error message that might be a good start.  The msg before refers to a different parameter so I'm suspicious.

On Jun 8, 2011, at 2:10 PM, Lorenzo Carretero Paulet wrote:

> Jason,
> I edited the Codeml.pm and posted the version in github. The only change I made was in line 275  'model'    => [0..2,7] was changed to 'model'    => [0..3,7] , so that 3 could be passed as valid value to model. However, I still got the same warning message, and I tested with different alignments and results are different from those obtained running PAML locally. Maybe there are additional changes to be made.
> Lorenzo
> 
> El 08/06/11 07:15, Jason Stajich escribió:
>> it is in github so you can fork a version, make the change, and submit a patch which we can pick up.
>> 
>> I am concerned that this change can't be tested without example code.
>> 
>> Did you just edit the code and make sure your changes worked, the error message seems to refer to a different parameter
>> (ncatG) not model.
>> 
>> Thanks,
>> 
>>> MSG: parameter ncatG specified value  is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value.'
>> 
>> On Jun 7, 2011, at 9:26 PM, Lorenzo Carretero wrote:
>> 
>>> Hi,
>>> I'm trying to run the clade model D (Model D: model = 3, NSsites = 3 ncatG = 2, See reference. Bielawski, J. P., and Z. Yang. 2004. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. Journal of Molecular Evolution 59:121-132. and PAML 4.4 manual page 30) from the Bio::Tools::Run::Phylo::PAML::Codeml module. However, 3 is not among the valid values that can be passed to the module (line 275 'model'    =>  [0..2,7],)  and consequently the following Warning message is returned from lines 689-690:
>>> 'MSG: parameter ncatG specified value  is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value.'
>>> Can line 275: 'model'    =>  [0..2,7], be changed to 'model'    =>  [0..3,7], to accept value 3 or additional changes must be done in other modules to properly run the so-called clade models of PAML.
>>> Thanks,
>>> 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
>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>> 
>>> _______________________________________________
>>> 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
> 
> 
> -- 
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> 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
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l