[Primeusers] Problem running primeGSR

[Albert Vilella]

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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>
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