[ensembl-dev] Questions about Compara/Hive modules

Javier Herrero jherrero at ebi.ac.uk
Thu Dec 1 18:06:17 GMT 2011

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:
> Hi,
>    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 
> that:
>     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
>     /data/ensembl/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentNetsJobs.pm
>     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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20111201/ed213101/attachment.html>

More information about the Dev mailing list