[Gmod-help] gmod_bulk_load_gff3.pl

[todd.moughamer at syngenta.com]

I run into the following error when trying to load Chado:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile
~/tmp/saccharomyces_cerevisiae.gff.sorted --dbname chadotest
Preparing data for inserting into the chadotest database
(This may take a while ...)
Can't locate object method "database" via package
"Bio::Annotation::SimpleValue" at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 3061, <GEN0>
line 1.
Issuing rollback() for database handle being DESTROY'd without explicit
disconnect().

I found reference to this problem online
(http://www.nabble.com/question-about-gmod_bulk_load_gff3.pl-td15135949.
html) with the recommendation of downloading the 'live' version of
BioPerl. However, upon browsing the latest code in SVN I do not see
inclusion of a "database" method. Is this still the recommended solution
to the problem?

Thanks,

Todd


Todd Moughamer
Bioinformatics Consultancy & Training Group

Syngenta Biotechnology, Inc.
3054 Cornwallis Road, 1243.E
Research Triangle Park, NC 27709-2257
Tel: 919-597-3078
Email: todd.moughamer at syngenta.com
www.syngenta.com


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