[ensembl-dev] Error on using parse_ncbi_gff3.pl

[Herzig, David]

Hi Ensembl Users

I have setup the ensembl environment for several species. Everything is ok.
After that I imported data from NCBI by using the parse_ncbi_gff3.pl
script. Works fine for almost all species. But for the specie sus scrofa I
have the following issue:

I downloaded the file from NCBI:
/ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/GFF/ref_Sscrofa10.2_top_level.gff3

I used the parse_ncbi_gff3.pl script to import it.

The process starts successfully but after a while I get the following error
message and the process stops:

Can't call method "phase" on an undefined value at
/home/ensembl/release-85/ensembl-pipeline/scripts/refseq_import/
parse_ncbi_gff3.pl line 882, <__ANONIO__> line 1184334.

Any ideas?

regards,
David


-- 

David Herzig
Scientist, 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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