[Gmod-help] no cvterm for ... errors with gmod_bulk_load_gff3.pl

[Michael Yourshaw]

I'm getting exceptions while attempting to load RefSeq into CHADO with
gmod_bulk_load_gff3.pl. I was able to load S. cerevisiae OK, so I assume I
have a mostly good installation. But the human ref seq files are failing
with errors, depending on chromosome, such as

MSG: no cvterm for processed_transcript

or

MSG: no cvterm for Region

 

I found that there is a "region" but not a "Region", so this means pgsql is
case sensitive?

 

I followed the instructions for loading ontologies in the INSTALL.Chado file
and selected all optional ontologies. Then I followed the Load RefSeq into
Chado wiki up to the point where is says to run gmod_load_gff3.pl, could not
be found, so I'm using gmod_bulk_load_gff3.pl.

 

Can you give me some advice?

 

Michael Yourshaw



UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
 <mailto:myourshaw at ucla.edu> myourshaw at ucla.edu
970.691.8299



This message is intended only for the use of the addressee and may contain
information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY
WORK PRODUCT. If you are not the intended recipient, you are hereby notified
that any dissemination of this communication is strictly prohibited. If you
have received this communication in error, please erase all copies of the
message and its attachments and notify us immediately. Thank you.

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20081204/febc01ac/attachment.html>