[ensembl-dev] Questions about Compara/Hive modules

[Zhang Di]

Thank you,  Javier

Sorry for not checking the subsequent output!

The last line
is Bio::EnsEMBL::Compara::Production::DnaFragChunkSet=HASH(0x1e16ed0)

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
DnaFragChunkSet qy_dna_object.

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 $qy_dna_object is always a
> Bio::EnsEMBL::Compara::Production::DnaFragChunk object? I am guessing that
> in subsequent iterations, the variable is set to something different.
>
> Could also please tell us what version of the API you are using?
>
> Thanks
>
> Javier
>
>
> On 01/12/11 08:14, Zhang Di wrote:
>
> Hi,
>
>
>     I'm running the compara pipeline for 2x alignment (first run
> PairAligner then Chain Net).
>    The raw and chain steps works fine.
>    the pipeline failed at the CreateAlignmentNetsJobs step complaining
> that:
>
>  Job with id=8380 died in status 'RUN' for the following reason: Can't
> locate object method "dnafrag" via package
> "Bio::EnsEMBL::Compara::Production::DnaFragChunkSet" at
> /data/ensembl/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentNetsJobs.pm
> line 200.
>
>
>     After some  debug effort (just print "$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
>
>
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>
>
> --
> Javier Herrero, PhD
> Ensembl Compara Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
>
>


-- 
Zhang Di
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