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

[fernando bueno]

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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