[Bioperl-l] model 3 on Codeml.pm

[Lorenzo Carretero]

Jason,
Thanks for your reply. I also changed the line in 
Bio::Tools::Run::Phylo::PAML::Codeml and 3 is now properly passed as 
value to model, no warning message and the returned lnL values 
corresponded to manual PAML runs  (keeping the rest of parameters 
identical).
Cheers


On 6/9/11 12:27 AM, Jason Stajich wrote:
> well I would just have it run where it doesn't cleanup the tempfiles and look at the produced .ctl file so you can see how it is different from what you expected. All this module is doing is making a .ctl file and a temporary folder so there is likely a setting that isn't get get passed the ctl file properly.
>
> On Jun 8, 2011, at 4:32 PM, Lorenzo Carretero wrote:
>
>> On 6/8/11 11:01 PM, Jason Stajich wrote:
>>> And did you try setting
>>> -no_param_checks =>   1
>>> so that it ignores the testing for valid parameters, this is your fastest route to running the program without it validating parameters...
>>>
>>> On Jun 8, 2011, at 3:21 PM, Lorenzo Carretero Paulet wrote:
>>>
>>>> no_param_checks
>>> _______________________________________________
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>> Yes. The script runs but returns the same message and seemingly unreliable results (different from those obtained through manual runs of PAML). This is really odd...
>> 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
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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
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