[Primeusers] Problem running primeGSR

[Albert Vilella]

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On Thu, Jun 10, 2010 at 1:49 PM, Albert Vilella <avilella at gmail.com> wrote:
> I am also having problems with "Division by zero" when running primeGSR:
> Here is an example dataset that doesn't work for me:
> http://www.ebi.ac.uk/~avilella/primegsr_test/
>
> eg
>
> node_id=88969.pg
> /nfs/users/nfs_a/avilella/src/primegsr/latest/PrimeGSR_1.0/primeGSR -o
> $node_id.mcmc -i 1000000 -t 100 -Sm JTT -Bp 0.1 0.1 -Bt 1.0  -Ed Gamma
> -Hi test_ultrametric_ape_1.nh $node_id.fasta $node_id.gsmap
>
> On Thu, Jun 10, 2010 at 12:27 PM, Jacky Hess <jacky at ebi.ac.uk> wrote:
>> Hi,
>>
>> I hadn't managed to find a way around it at the time but I am starting
>> to look at it again and would be interested to hear if anyone found a
>> solution to this as well.
>>
>> Best,
>> Jacky
>>
>> On 08/04/2010 12:18, James Cotton wrote:
>>> Hi,
>>>
>>> We've finally got primeGSR running on our data, but we now seem to
>>> have an MCMC that does not move at all, so the posterior for every
>>> parameter consists of a single value, and only a single tree is sampled.
>>>
>>> We get error messages that are the same as those reported by Jacky
>>> Hess on Tue Sep 29 11:38:56 CEST 2009 - lots of 'Tried to set length
>>> of node' messages.
>>>
>>> I'm wondering if Jacky or anyone else on the forum has managed to fix
>>> this kind of problem, and if so, how!
>>>
>>> Thanks
>>> James Cotton
>>> '
>>> _____________________________________________
>>> James Cotton
>>> School of Biological and Chemical Sciences
>>> Queen Mary, University of London
>>> +44 (0)207 882 3645
>>> j.a.cotton at qmul.ac.uk
>>> http://webspace.qmul.ac.uk/jacotton/index.html
>>> http://www.sbcs.qmul.ac.uk/staff/jamescotton.html
>>> _____________________________________________
>>>
>>>
>>>
>>>
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>>> Primeusers at sbc.su.se
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>>>
>>
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>