[Gmod-help] gmod_bulk_load_gff3.pl problem

[Scott Cain]

Hi Jason,

Dave and I seem to be working through our email at the same time.  You
need bioperl-live, not the most recent release.  The way the
Bio::Annotation modules work has changed since that release.

Scott


On Thu, Jul 24, 2008 at 4:53 PM, Jason Phillips <japhill at email.unc.edu> wrote:
>
> 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
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory