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

[Herzig, David]

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
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 (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>
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