[Primeusers] Cannot run program

[arve]

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


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
>>> *******************************************************************
>>> 
>>> 
>>> -- 
>>> *******************************************************************
>>> 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
>>> 
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>> 
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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
> 
> _______________________________________________
> Primeusers mailing list
> Primeusers at sbc.su.se
> https://mail.sbc.su.se/mailman/listinfo/primeusers