[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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