[ensembl-dev] problems for running lowcoverage annotation pipeline

[Zhang Di]

Thank you Kathryn!

Bronwen suggest me to run the script 'set_toplevel.pl' for my core database,
better solved my problem than my own solution.



On Thu, Oct 27, 2011 at 5:40 PM, Kathryn Beal <kbeal at ebi.ac.uk> wrote:

> Hi,
> Thats great - I was in the process of writing a little test script for you
> to see if you were getting the
> toplevel slices. However, I suspect the problem may be a core one and have
> asked a colleague with more
> knowledge of the core database schema to take a look.
>
> Cheers
> Kathryn
>
> > Hi,
> >   I get this to work! edited 'toplevel' to 'scaffold' in
> ChunkAndGroupDNA.pm
> > line 310: chromosomes = $SliceAdaptor->fetch_all('toplevel' ...
> >
> >  It seems that the pipeline failed to find the toplevel of my genome is
> > 'scaffold'. I checked coord_system and meta tables, found nowhere to set
> it.
> >
> >
> >
> > On Thu, Oct 27, 2011 at 11:16 AM, Zhang Di <aureliano.jz at gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >>  Attached is my conf file. I think it is ok, because the analysis table
> and
> >> jo table is ok.
> >>
> >>  The genome_db table is ok.
> >>
> >>  Thank you for your help.
> >>
> >>
> >> On Wed, Oct 26, 2011 at 9:44 PM, Kathryn Beal <kbeal at ebi.ac.uk> wrote:
> >>
> >>> Hi,
> >>> 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?
> >>>
> >>> Cheers
> >>> Kathryn
> >>>
> >>>> 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.
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Dev mailing list    Dev at ensembl.org
> >>>> List admin (including subscribe/unsubscribe):
> >>> http://lists.ensembl.org/mailman/listinfo/dev
> >>>> Ensembl Blog: http://www.ensembl.info/
> >>>
> >>>
> >>> --
> >>> Dr Kathryn Beal
> >>> EnsEMBL
> >>> EMBL-European Bioinformatics Institute       Tel. +44 (0)1223 494458
> >>> Wellcome Trust Genome Campus, Hinxton        Fax. +44 (0)1223 494468
> >>> Cambridge CB10 1SD, UK
> >>>
> >>
> >>
> >>
> >> --
> >> Zhang Di
> >>
> >
> >
> >
>
>
> --
> Dr Kathryn Beal
> EnsEMBL
> EMBL-European Bioinformatics Institute       Tel. +44 (0)1223 494458
> Wellcome Trust Genome Campus, Hinxton        Fax. +44 (0)1223 494468
> Cambridge CB10 1SD, UK
>



-- 
Zhang Di
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