[Gmod-help] gmod_bulk_load_gff3.pl problem

[Jason Phillips]

I'm having a problem with loading some sample gff3 data using the gmod 1.0 
scripts.

I have the latest version of bioperl and the latest version of postgresql 
installed.

Here's what I do:

1.  I run the command:
gmod_bulk_load_gff3.pl --unique_target --organism='monkey flower' -a 
--skip --dbname chado  -g test.gff

on a simple sample gff3 file that looks like this:

scaffold_4361   Swiss_Prot      gene    1968    2646    .       +       .       ID=jasoQ9LNG5
scaffold_4361   Swiss_Prot      exon    1968    2420    .       +       .       Parent=jasoQ9LNG5
scaffold_4361   Swiss_Prot      exon    2497    2646    .       +       .       Parent=jasoQ9LNG5
scaffold_4364   Swiss_Prot      gene    1337    1594    .       +       .       ID=jasoQ9LM55
scaffold_4364   Swiss_Prot      exon    1337    1594    .       +       .       Parent=jasoQ9LM55
scaffold_4515   Swiss_Prot      gene    1009    3024    .       +       .       ID=jasoO49340
scaffold_4515   Swiss_Prot      exon    1009    1134    .       +       .       Parent=jasoO49340
scaffold_4515   Swiss_Prot      exon    2581    3024    .       +       .       Parent=jasoO49340

2.  I get an output that looks like this:
Preparing data for inserting into the chado database
(This may take a while ...)
Can't bind a reference (Bio::Annotation::SimpleValue=HASH(0x18c3470)) at 
/usr/lib/perl5/site_perl/5.8.0/Bio/GMOD/DB/Adapter.pm line 972, <GEN0> 
line 1.
Database handle destroyed without explicit disconnect.


3. Then I beat my head against the wall.  Nothing gets inserted into the 
database.


Can you clue me in as to why this message error message appears and 
what it means?

Thank you

Jason Phillips