[ensembl-dev] problems for running lowcoverage annotation pipeline

Zhang Di aureliano.jz at gmail.com
Fri Oct 28 04:00:18 BST 2011


Thank you, Bronwen!

It is great to known such a script, for I have found the problem is that the
pipeline failed to known the toplevel of my genome is 'scaffold'.

I replied to Kathryn Beal yesterday that I have solved it by replacing
'toplevle' to 'scaffold' in ChunkAndGroupDNA.pm, forgetting to cc the email
to the maillist.

Thank you again, guys!

On Thu, Oct 27, 2011 at 5:30 PM, Bronwen Aken <ba1 at sanger.ac.uk> wrote:

> 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
> Cheers,
> Bronwen
> 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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Zhang Di
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