[Primeusers] Cannot run program

[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
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