[Primeusers] Cannot run program

[Bengt Sennblad]

Har du dubbelkollat att web-versionen (som jag antar att hon har?) har  
denna option?

Bengt

3 feb 2010 kl. 12.04 skrev arve:

> I am sorry, the option is "-c 250" (or a number of your choosing,  
> the default is 50).
>
> 	Lars
>
>
>
> Feb 3, 2010 kl. 11:58 AM skrev A.Malhotra:
>
>> arve wrote:
>>> This error has occured before when there are not enough  
>>> discretization points in the species tree to put the gene nodes  
>>> on. Try again with an option "-n 250" and see if that helps.
>>>
>>> 	Best regards,
>>> 	Lars
>>>
>>
>> I have tried this and get the message "unknown option "-n"!
>>
>>>
>>> Jan 28, 2010 kl. 5:02 PM skrev A.Malhotra:
>>>
>>>> OK, I've sorted this out, I think. I then got a lot of errors  
>>>> relating
>>>> to mismatches between the tree file and the gene-species map  
>>>> file, which
>>>> I have also corrected. However, the next error has foxed me again:
>>>> Probability: attempting to divide by zero!
>>>>
>>>> Any ideas what is causing this one?
>>>> Thanks
>>>> Anita
>>>>
>>>> arve wrote:
>>>>> Hi Anita,
>>>>> The error you get should only occur if the file is not found.  
>>>>> Have you double checked the name of the file and its location?
>>>>>
>>>>> Yes, there are several parameters that you need to specify at  
>>>>> this point, for the simple reason that we have not implemented  
>>>>> their inference yet.
>>>>>
>>>>> We do not support partitioning of data at this point.
>>>>>
>>>>> 	Best regards,
>>>>> 	Lars
>>>>>
>>>>> Jan 26, 2010 kl. 3:10 PM skrev A.Malhotra:
>>>>>
>>>>>> I am trying to run an analysis using PrimeGSR but get an error  
>>>>>> message
>>>>>> saying "could not open sequence file". However, this file is in  
>>>>>> fasta
>>>>>> format and I can open it in other programs so there seems to be  
>>>>>> nothing
>>>>>> wrong with it.
>>>>>>
>>>>>> primeGSR -o PLA2.out -i 10000000 -t 2000 -w 100 -Su DNA  
>>>>>> Pi=0.2560 0.2748
>>>>>> 0.2332 0.236 R=1.5842 4.2435 1.0570 1.5330 4.6701 1.0 -Sn 4 -Sa  
>>>>>> 0.7564
>>>>>> -Ed Gamma -Hi vipers.tre nc_nr.fa gs.txt
>>>>>>
>>>>>> I would also appreciate some guidance about setting the model.  
>>>>>> Normally
>>>>>> when running a Bayesian phylgenetic analysis (eg in MrBayes) I  
>>>>>> would not
>>>>>> set all the parameter values at the beginning but let the  
>>>>>> Markov chain
>>>>>> integrate over the uncertainty in these values. However it  
>>>>>> seems that
>>>>>> primeGSR requires you to input them. Is this correct and if so,  
>>>>>> why?
>>>>>> Finally, I wonder is it is possible to analyse partitioned data  
>>>>>> in
>>>>>> primeGSR (eg in MrBayes I can include gaps in the form of a  
>>>>>> simple-coded
>>>>>> matrix as a separate partition)?
>>>>>> Thanks
>>>>>> Anita
>>>>>>
>> *******************************************************************
>> Dr Anita Malhotra         	e-mail: a.malhotra at bangor.ac.uk
>> School of Biological Sciences	Tel(direct line): + 44 1248 383735
>> College of Natural Sciences	Fax: + 44 1248 371644
>> Bangor University		
>> 3rd Floor ECW
>> Deiniol Road, Bangor		
>> Gwynedd LL57 2UW
>> United Kingdom
>> *******************************************************************
>>
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