[Primeusers] Cannot run program

[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
>> *******************************************************************
>>
>>
>> -- 
>> *******************************************************************
>> 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
>> *******************************************************************
>>
>> -- 
>> Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi,
>> gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig
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>> neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar
>> unwaith a dilëwch y neges. Os na fwriadwyd anfon y neges atoch chi,
>> rhaid i chi beidio â defnyddio, cadw neu ddatgelu unrhyw wybodaeth a
>> gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i
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-- 
*******************************************************************
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
*******************************************************************

-- 
Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi,
gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig
gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y
neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar
unwaith a dilëwch y neges. Os na fwriadwyd anfon y neges atoch chi,
rhaid i chi beidio â defnyddio, cadw neu ddatgelu unrhyw wybodaeth a
gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i
hanfonodd yn unig  ac nid yw o anghenraid yn cynrychioli barn
Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu
bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu
100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn
nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract
rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa
Cyllid Prifysgol Bangor.  www.bangor.ac.uk

This email and any attachments may contain confidential material and
is solely for the use of the intended recipient(s).  If you have
received this email in error, please notify the sender immediately
and delete this email.  If you are not the intended recipient(s), you
must not use, retain or disclose any information contained in this
email.  Any views or opinions are solely those of the sender and do
not necessarily represent those of the Bangor University.
Bangor University does not guarantee that this email or
any attachments are free from viruses or 100% secure.  Unless
expressly stated in the body of the text of the email, this email is
not intended to form a binding contract - a list of authorised
signatories is available from the Bangor University Finance
Office.  www.bangor.ac.uk