[Primeusers] Cannot run program

A.Malhotra bss111 at bangor.ac.uk
Wed Feb 3 11:58:33 CET 2010


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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