[Gmod-help] Re: [Gmod-schema] Problems with gmod_bulk_load_gff3

[fernando bueno]

hello Dave!


the steps related in chado install were executed.
this erro appears when I execute the commans listed in this How to

http://gmod.org/wiki/Load_GFF_Into_Chado


forgive my poor english!


thank you!


Fernando


2009/6/30 Dave Clements, GMOD Help Desk <gmodhelp at googlemail.com>

> 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 Mon, Jun 29, 2009 at 10:33 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!!!
> >
> >
> > Fernando
> >
> >
> >
> ------------------------------------------------------------------------------
> >
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> >
> >
>
>
>
> --
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
> Learn more about GMOD at:
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>   (BioMart, Chado, Galaxy, InterMine)
>
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