[ensembl-dev] problems for running lowcoverage annotation pipeline

Zhang Di aureliano.jz at gmail.com
Wed Oct 26 14:15:31 BST 2011

  I'm trying to use the lowcoverage annotation pipeline. At first, after
reading docs in ensembl-doc/pipeline-docs, I found that I have to construct
a compara database containing the whole-genome-alignment results. Then I
checkouted ensembl-compara and ensembl-hive, tried to run the wga pipeline
according to the following steps:
  1. downloaded the reference genome mysql files from ensembl, which works
  2. prepared my interested genome according the guide in
into_ensembl.txt. still seems fine.
  3. prepared conf file and run comparaLoadGenomes.pl and
loadPairAlignerSystem.pl. the tables in compara database seems fine.
  4. run beekeeper.pl. problem ocurs for the second analysis
ChunkAndGroupDNA, there are two jobs to run, one for the reference genome
and the other for my interested genome. The ref genome loaded correctly
while no data refer to my intersted genome loade in dnafrag, dnafrag_chunk
and dna_collection tables. One line in the job_id_3.out (the job id for
ChunkAndGroupDNA for my interested genome) file is: number of seq_regions 0

  The problem seemed that the pipeline failed to see my genome data. Should
I add some special info to the meta table for my interest genome database?

  Thank you.

Zhang Di
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