[Primeusers] Problem running primeGSR

Thu Jul 15 16:32:56 CEST 2010

Hi again,

I've been told by systems that the version we have from the library
isn't the correct one for primeGSRf.
Any news on a potentially statically-linked version?

Cheers

On Tue, Jun 15, 2010 at 3:36 PM, Albert Vilella <avilella at gmail.com> wrote:
> Thanks lars,
>
> I've just tried the binary, but it complains about the lapack library:
>
> /nfs/users/nfs_a/avilella/src/primegsr/latest/primeGSRf: error while
> loading shared libraries: libmkl_lapack.so: cannot open shared object
> file: No such file or directory
>
> If you are not confident about releasing the source code yet, I can
> give you access to the Sanger farm to compile it there for us. I know
> the 1.0 release compiles just fine, I did it last week.
>
> Cheers,
>
> Albert.
>
> On Tue, Jun 15, 2010 at 3:17 PM, Lars Arvestad <arve at csc.kth.se> wrote:
>> OK, the PrIME-GSR download page,
>> http://prime.sbc.su.se/primeGSR/download.html
>> now has a section with a link to a preview version of a faster version
>> tentatively called PrimeGSRf.
>> I have had to play around with the values on some new options regarding
>> discretization to get a larger testcase working:
>>   -Dt <float>
>>       Approximate discretization timestep. Set to 0 to divide every edge in
>> equally
>>       many parts (see -Di). Defaults to 0.05. See -Dtt for edge above root.
>>   -Di <unsigned int>
>>       Minimum number of parts to slice each edge in. If -Dt is set to 0,
>> this becomes
>>       the exact number of parts. Minimum 2. Defaults to 3. See -Dtt for edge
>> above root.
>>   -Dtt <unsigned int>
>>       Override number of discretization points for edge above root in host
>> tree.
>>       By default, irrespective of time span, this is set to the number
>>       of points for a (hypothetical) root-to-leaf edge.
>> Let us know if you have problems!
>> Lars
>> --
>> Computational Biology at School of Computer Science and Communication
>> and Stockholm Bioinformatics Center
>> http://www.csc.kth.se/~arve
>>
>>
>>
>>
>> Jun 14, 2010 kl. 4:00 PM skrev Albert Vilella:
>>
>> That would be grat, thanks Lars and Joel. We've got many cases where
>> the branch length is very short. Each Ensembl production produces
>> ~20.000 trees, out of which about ~10.000 have a good number of
>> sequences with a variety of branch lengths.
>>
>> Any method that would solve this problem for this dataset would be
>> great to be tried. Apart from the example I pointed below, if you want
>> a bunch of other examples you can use our data dumps:
>>
>> ftp://ftp.ensembl.org/pub/current_emf/ensembl-compara/homologies/Compara.gene_trees.58.cds.fasta.gz
>>
>> But I'll also try it myself once I get hold of the code.
>>
>> On Mon, Jun 14, 2010 at 1:17 PM, Lars Arvestad <arve at csc.kth.se> wrote:
>>
>> This is a problem which occurs due to the discretization of the species tree
>> that our method needs. Two issues seems to appear. Either there is a branch
>> in the species tree which is very short and we don't get enough (or any!)
>> discretization points on the edge, making it impossible to put a putative
>> duplication there, or the input sequences are so many that the
>> discretization you have asked for is not enough on some parts of the species
>> tree.
>>
>> The solution is to ask for more discretization points, but that incurs a bad
>> slowdown. Our student Joel Sjöstrand has worked on improving the handling of
>> discretization and algorithmic improvements to avoid massive slowdowns, but
>> we are not done testing them. In the tests I have run, one still has to try
>> out some different parameter settings on "tough" data.
>>
>> We can offer a binary for those of you whom are interested in trying this
>> faster version of Prime-GSR on linux?
>>
>>        Best regards,
>>
>>        Lars
>>
>> --
>>
>> Computational Biology at School of Computer Science and Communication
>>
>> and Stockholm Bioinformatics Center
>>
>> http://www.csc.kth.se/~arve
>>
>>
>>
>>
>>
>> Jun 10, 2010 kl. 2:49 PM skrev 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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