[Gmod-help] Problems with gmod_bulk_load_gff3

[Dave Clements, GMOD Help Desk]

Hi Fernando,

Chromosome is a defined term in the sequence ontology.  I believe this
error means that either the "make ontologies" step was not run, or
their was a problem with it.  Was this step run?  Were the
relationship and sequence ontologies loaded?

See
http://gmod.cvs.sourceforge.net/*checkout*/gmod/schema/chado/INSTALL.Chado
for more on the make ontologies step.

Cheers,

Dave C.

On Tue, Jun 30, 2009 at 10:37 AM, fernando bueno<stradlinbueno at gmail.com> wrote:
> Hi!
>
> I'm from Brazil. I'm with a problem to insert data in my CHADO schema.
> When the command :
> gmod_bulk_load_gff3.pl --organism yeast  saccharomyces_cerevisiae.gff
> is executed, this error appears:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: no cvterm for chromosome
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/
> Bio/Root/Root.pm:357
> STACK: Bio::GMOD::DB::Adapter::get_type
> /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm:4224
> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:783
> -----------------------------------------------------------
> Issuing rollback() due to DESTROY without explicit disconnect() of
> DBD::Pg::db handle dbname=chado;port=5432;host=localhost at
> /usr/local/share/perl/5.10.0/Error.pm line 184.
>
>
> could your help me?
>
>
> thanks!!!
>
>



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