[ensembl-dev] Questions about Compara/Hive modules
aureliano.jz at gmail.com
Fri Dec 2 01:24:02 GMT 2011
Thank you, Javier
Sorry for not checking the subsequent output!
The last line
Seems that it works well
with Bio::EnsEMBL::Compara::Production::DnaFragChunk, without any problem
finding the method 'dnafrag' for it.
I guess that the program died immediately after it met the first
I'm using the version 64 API. checked out 2 mouth ago at a same time.
On Fri, Dec 2, 2011 at 2:05 AM, Javier Herrero <jherrero at ebi.ac.uk> wrote:
> Dear Zhang
> As you mention, if the object is a
> Bio::EnsEMBL::Compara::Production::DnaFragChunk, Perl should be looking for
> the 'dnafrag' method in that module (or one of its parents).
> I have noticed that this call is made in a loop. Could you please check
> that the $qy_dna_object is always a
> Bio::EnsEMBL::Compara::Production::DnaFragChunk object? I am guessing that
> in subsequent iterations, the variable is set to something different.
> Could also please tell us what version of the API you are using?
> On 01/12/11 08:14, Zhang Di wrote:
> I'm running the compara pipeline for 2x alignment (first run
> PairAligner then Chain Net).
> The raw and chain steps works fine.
> the pipeline failed at the CreateAlignmentNetsJobs step complaining
> Job with id=8380 died in status 'RUN' for the following reason: Can't
> locate object method "dnafrag" via package
> "Bio::EnsEMBL::Compara::Production::DnaFragChunkSet" at
> line 200.
> After some debug effort (just print "$qy_dna_object";), I found
> that $qy_dna_object is an instance of
> Bio::EnsEMBL::Compara::Production::DnaFragChunk, and this class has the
> method 'dnafrag'.
> I'm not very familiar with perl object-oriented system. why did it
> try to find method 'dnafrag' via
> package Bio::EnsEMBL::Compara::Production::DnaFragChunkSet while the data
> is an instance of DnaFragChunk?
> Zhang Di
> Dev mailing list Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
> Javier Herrero, PhD
> Ensembl Compara Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
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