[ensembl-dev] Import Homo Sapiens GFF3 file from NCBI

Herzig, David david.herzig at roche.com
Wed Jul 4 09:03:24 BST 2018


Hi Ensembl Dev Team

I have set up a mysql db containing homo_sapiens_core_92_38.

After that I tried to import the NCBI file:

ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/ref_GRCh38.p12_top_level.gff3.gz

I use the following perl script to do that:

ensembl-pipeline/scripts/refseq_import/parse_ncbi_gff3.pl

The process will be killed during the loading:

Last output lines:
***
Slice NT_187386.1 found (scaffold:GRCh38:KI270731.1:1:150754:1)
Slice NT_187388.1 found (scaffold:GRCh38:KI270733.1:1:179772:1)
Slice NT_187389.1 found (scaffold:GRCh38:KI270734.1:1:165050:1)
Slice NC_000023.11 found (chromosome:GRCh38:X:1:156040895:1)
Killed
***

Any ideas from your side?

I did the same for other species and this works all fine.

regards,
David

-- 
David Herzig
Senior Scientist
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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