[Primeusers] Cannot run program

Wed Feb 3 12:43:35 CET 2010

Ja.

Feb 3, 2010 kl. 12:22 PM skrev 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
>>> *******************************************************************
>>> 
>>> -- 
>>> 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
>> 
>> _______________________________________________
>> Primeusers mailing list
>> Primeusers at sbc.su.se
>> https://mail.sbc.su.se/mailman/listinfo/primeusers
> 
> _______________________________________________
> Primeusers mailing list
> Primeusers at sbc.su.se
> https://mail.sbc.su.se/mailman/listinfo/primeusers