[ensembl-dev] problems for running lowcoverage annotation pipeline

Kathryn Beal kbeal at ebi.ac.uk
Wed Oct 26 14:44:42 BST 2011

Could you send me the conf file you used? Can you check in the genome_db table that the locator field points
to the location of the core database?


> Hi
>   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
> fine.
>   2. prepared my interested genome according the guide in
> ensembl-doc/loading_sequence_
> 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.
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Dr Kathryn Beal
EMBL-European Bioinformatics Institute       Tel. +44 (0)1223 494458
Wellcome Trust Genome Campus, Hinxton        Fax. +44 (0)1223 494468
Cambridge CB10 1SD, UK

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