[ensembl-dev] Error on loading NCBI data into release 87

[Thibaut Hourlier]

Hi David,
The problem is in the database. It appears that the last analysis in the analysis table, ‘goa_import’ is using the last analysis_id possible, 65535.

You will need to first change the analysis_id of this analysis, I have chosen 9000 but you can put a different value:
UPDATE analysis SET analysis_id = 9000 WHERE analysis_id = 65535; ALTER TABLE analysis AUTO_INCREMENT = 1; UPDATE analysis_description SET analysis_id = 9000 WHERE analysis_id = 65535; UPDATE object_xref SET analysis_id = 9000 WHERE analysis_id = 65535;

If you rerun the import script it should work fine.

Thanks,
Thibaut

> On 10 Feb 2017, at 13:21, Herzig, David <david.herzig at roche.com <mailto:david.herzig at roche.com>> wrote:
> 
> Hi Ensembl Team
> 
> I had an issue with loading the NCBI data (mus musculus) into release 87.
> 
> I have used the same process as for version 85 (where is works fine).
> 
> 
> With version 85 I got the success output:
> ------------------------------------------
> 46189 genes parsed
> 118972 transcripts parsed
> 1205181 exons parsed
> 23538 non coding genes parsed
> 0 Curated Genomic genes parsed
> 35 rRNA genes parsed
> 425 tRNA genes parsed
> ------------------------------------------
> 46189 genes stored
> 
> 
> 
> 
> With the version 87 I got the following error:
> -------------------- EXCEPTION --------------------
> MSG: Could not retrieve just stored analysis from database.
> Possibly incorrect db permissions or missing analysis table
> 
> STACK Bio::EnsEMBL::DBSQL::AnalysisAdaptor::store /home/ensembl/release-87/ensembl/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm:425
> STACK Bio::EnsEMBL::DBSQL::GeneAdaptor::store /home/ensembl/release-87/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm:1264
> STACK toplevel /home/ensembl/release-87/ensembl-pipeline/scripts/refseq_import/parse_ncbi_gff3.pl:986 <http://parse_ncbi_gff3.pl:986/>
> Date (localtime)    = Fri Feb 10 13:18:53 2017
> Ensembl API version = 87
> ---------------------------------------------------
> 
> I used the same GFF3 file: ref_GRCm38.p4_top_level.gff3.gz
> For loading I used the script: ensembl-pipeline/scripts/refseq_import/parse_ncbi_gff3.pl <http://parse_ncbi_gff3.pl/> (correct one for version 85 and 87 (if there is a difference))
> 
> For other species (e.g. r norvegicus) it is working fine.
> 
> Any ideas from your side?
> 
> regards,
> David
> 
> -- 
> David Herzig
> Scientific Application Developer
> SIAD Solution Delivery & Architecture, pRED Informatics
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> 
> F. Hoffmann-La Roche Ltd
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
> Phone +41 61 687 31 70
> Learn more about pRED Informatics at http://go.roche.com/pREDi <http://go.roche.com/pREDi>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org>
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev <http://lists.ensembl.org/mailman/listinfo/dev>
> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20170313/2804009e/attachment.html>