[ensembl-dev] Questions about Compara/Hive modules

Zhang Di aureliano.jz at gmail.com
Thu Dec 1 08:14:46 GMT 2011


   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
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