[ensembl-dev] problems for running lowcoverage annotation pipeline

Bronwen Aken ba1 at sanger.ac.uk
Thu Oct 27 10:30:19 BST 2011

Hi there,

Did the set_toplevel.pl script run successfully when you were loading your assembly? This script will add seq_region_attributes to your toplevel sequence regions:

cd ensembl-pipeline/scripts
perl ./set_toplevel.pl -dbhost host -dbuser user -dbname my_db -dbpass ****  -dbport port


On 26 Oct 2011, at 14:15, Zhang Di wrote:

> 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.
> -- 
> Zhang Di
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