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

[fernando bueno]

all right Dave!

thank you!

2009/7/2 Dave Clements, GMOD Help Desk <gmodhelp at googlemail.com>

> Hi Fernando,
>
> You also need to load the Chado feature properties ontology, which my
> memory tell me can also be loaded with make ontologies.
>
> On Wed, Jul 1, 2009 at 11:06 AM, fernando bueno<stradlinbueno at gmail.com>
> wrote:
> > an using the sequence ontology appears this error
> >
> >
> > Preparing data for inserting into the chado database
> > (This may take a while ...)
> >
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: I couldn't find the 'Note' cvterm in the database;
> > Did you load the feature property controlled vocabulary?
> > 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::handle_note
> > /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm:3512
> > STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:908
> > -----------------------------------------------------------
> > 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.
> >
> >
> > 2009/7/1 fernando bueno <stradlinbueno at gmail.com>
> >>
> >> 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
> >>> >
> >>> >
> >>> >
> >>> >
> ------------------------------------------------------------------------------
> >>> >
> >>> > _______________________________________________
> >>> > Gmod-schema mailing list
> >>> > Gmod-schema at lists.sourceforge.net
> >>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >>> >
> >>> >
> >>>
> >>>
> >>>
> >>> --
> >>> Was this helpful?  Let us know at
> http://gmod.org/wiki/Help_Desk_Feedback
> >>>
> >>> Learn more about GMOD at:
> >>>  ISMB/ECCB: http://www.iscb.org/ismbeccb2009/
> >>>   (BioMart, Chado, Galaxy, InterMine)
> >>
> >
> >
>
>
>
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