[Bioperl-l] model 3 on Codeml.pm

[Jason Stajich]

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
> 
> -- 
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> Lorenzo Carretero Paulet
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