Re: [Gusdev-gusdev] Taxonomy&Ontology problems

[Poliana M. <pol...@gm...>]

Hi Federica,

I run thus:

GoOntology:

ga GUS::GOPredict::Plugin::LoadGoOntology
--file_path=3D/usr/local/db/local/ontology/ --process_db_id=3D3003
--process_ext_db_rel=3D6 --function_db_id=3D3001 --function_ext_db_rel=3D33
--component_db_id=3D3002 =E2=80=93component_ext_db_rel=3D28  --create_relea=
se

See if your files (*.ontology) are in the correct path.

***************************************************************************=
************************

LoadTaxon:

ga GUS::Common::Plugin::LoadTaxon
-gencode=3D/usr/local/db/local/taxonomy/gencode.dmp
  --names=3D/usr/local/db/local/taxonomy/names.dmp
  --nodes=3D/usr/local/db/local/taxonomy/nodes.dmp
    --merged=3D/usr/local/db/local/taxonomy/merged.dmp   =20


Change for its your path....

Poliana


On Mon, 21 Feb 2005 16:37:22 +0100 (CET), fed...@bi...
<fed...@bi...> wrote:
> Thanks, but I've downloaded from there, and I also have right privileges.=
..!
> I tried also to include merged.dmp even if it's not named in the bootstra=
p
> instructions!! But nothing good happened!
> Any other suggestions?
> Federica
>=20
>=20
> > For LoadTaxon, you need to supply the names with path for all for file,
> > gencode.dmp,name.dmp,nodes.dump,merged.dmp. These files are downloaded
> > from NCBI (ftp://ftp.ncbi.nih.gov/pub/taxonomy) as a tarball,
> > taxdump.tar.Z or taxdump.tar.gz and uncompressed.
> >
> >
> > Debbie
> >
> >
> >
> >
> >
> >
> > fed...@bi... wrote:
> >
> >>Hi everybody!
> >>I'm here again! I'm inserting data following the bootstrap but I had th=
is
> >>errors:
> >>1) for Taxonomy
> >>$ ga GUS::Common::Plugin::LoadTaxon \
> >>
> >>
> >>>--gencode=3D/usr/local/src/gus_related/taxonomy/gencode.dmp \
> >>>--names=3D/usr/local/src/gus_related/taxonomy/names.dmp \
> >>>--nodes=3D/usr/local/src/gus_related/taxonomy/nodes.dmp
> >>>
> >>>
> >>ERROR: The names of the names.dmp, nodes.dmp, gencode.dmp and merged.dm=
p
> >>files must
> >>be provided on the command line.
> >>2) for GO Ontology
> >>$ ga GUS::GOPredict::Plugin::LoadGoOntology
> >>--file_path=3D/usr/local/src/gus-related/ontology/ \
> >>
> >>
> >>>--process_db_id=3D3003 \
> >>>--process_ext_db_rel=3D165 \
> >>>--function_db_id=3D3001 \
> >>>--function_ext_db_rel=3D164 \
> >>>--component_db_id=3D3002 \
> >>>--component_ext_db_rel=3D166 \
> >>>
> >>>
> >>
> >>/usr/local/src/gus-related/ontology/Mon Feb 21 15:45:51 2005    loading
> >> all
> >>.ontology files in /usr/local/src/gus-related/ontology/ in preparation
> >> for
> >>parsing
> >>Note: did not find file component.ontology in directory
> >>CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2180)->getPath.
> >> To load this branch of the ontology specified by component.ontology,
> >> please put that file in the directory.
> >>Note: did not find file process.ontology in directory
> >>CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2180)->getPath.
> >> To load this branch of the ontology specified by process.ontology,
> >> please put that file in the directory.
> >>Note: did not find file function.ontology in directory
> >>CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2180)->getPath.
> >> To load this branch of the ontology specified by function.ontology,
> >> please put that file in the directory.
> >>Mon Feb 21 15:45:51 2005        parsing all .ontology files in
> >> preparation
> >>for
> >>inserting into database
> >>Mon Feb 21 15:45:51 2005        parsing finished; loading ontology into
> >>database
> >>Mon Feb 21 15:45:51 2005        RESULT  Created 0 entries in GOTerm, 0
> >>entries in
> >>GORelationship, and 0 entries in GOSynonym.  Skipped 0 total entries
> >>
> >>Any help?
> >>Cheers,
> >>Federica
> >>
> >>
> >>
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> >>
> >
> >
>=20
> -------------------------------------------------------
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