[ensembl-dev] Questions about Compara/Hive modules

[Zhang Di]

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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