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Re: [Gusdev-gusdev] Taxonomy&Ontology problems
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From: Poliana M. <pol...@gm...> - 2005-02-21 17:22:39
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In your directory /usr/local/src/gus-related/ontology/ exist the file "component.ontology"?? Poliana On Mon, 21 Feb 2005 18:18:53 +0100 (CET), fed...@bi... <fed...@bi...> wrote: > Thanks Poliana! > For LoadTaxon it's ok!!! > For GoOntology I always have the same error: >=20 > ga GUS::GOPredict::Plugin::LoadGoOntology \ > > --file_path=3D/usr/local/src/gus-related/ontology/ \ > > --process_db_id=3D3003 \ > > --process_ext_db_rel=3D6 \ > > --function_db_id=3D3001 \ > > --function_ext_db_rel=3D33 \ > > --component_db_id=3D3002 \ > > --component_ext_db_rel=3D28 \ > > --create_release > /usr/local/src/gus-related/ontology/Mon Feb 21 18:02:13 2005 loading > all .ontology files in /usr/local/src/gus-related/ontology/ in preparatio= n > for parsing > Note: did not find file component.ontology in directory > CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2380)->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(0x89d2380)->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(0x89d2380)->getPath. > To load this branch of the ontology specified by function.ontology, > please put that file in the directory. > Mon Feb 21 18:02:13 2005 parsing all .ontology files in preparatio= n > for inserting into database > Mon Feb 21 18:02:13 2005 parsing finished; loading ontology into > database > Mon Feb 21 18:02:13 2005 RESULT Created 0 entries in GOTerm, 0 > entries in GORelationship, and 0 entries in GOSynonym. Skipped 0 total > entries >=20 > I understand it's a problem releted with che *.ontology path, but I reall= y > don't know where I have to put my files! I think it suggests the path > ..../CBIL/Bio/GeneOntologyParser: I put there my files but nothing > changed! > Do you understand something more? > Cheers > Federica >=20 >=20 > > 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 =C3=A2=E2=82=AC"component_ext_db_rel=3D28 --c= reate_release > > > > 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 > > > > > > 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 > >> bootstrap > >> instructions!! But nothing good happened! > >> Any other suggestions? > >> Federica > >> > >> > >> > 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 download= ed > >> > 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 > >> this > >> >>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.dmp > >> >>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 preparati= on > >> >> 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 > >> >> > >> >> > >> >> > >> >>------------------------------------------------------- > >> >>SF email is sponsored by - The IT Product Guide > >> >>Read honest & candid reviews on hundreds of IT Products from real > >> users. > >> >>Discover which products truly live up to the hype. Start reading now= . > >> >>http://ads.osdn.com/?ad_id=3D6595&alloc_id=3D14396&op=3Dclick > >> >>_______________________________________________ > >> >>Gusdev-gusdev mailing list > >> >>Gus...@li... > >> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > >> >> > >> >> > >> > > >> > > >> > >> ------------------------------------------------------- > >> SF email is sponsored by - The IT Product Guide > >> Read honest & candid reviews on hundreds of IT Products from real user= s. > >> Discover which products truly live up to the hype. Start reading now. > >> http://ads.osdn.com/?ad_id=3D6595&alloc_id=3D14396&op=3Dclick > >> _______________________________________________ > >> Gusdev-gusdev mailing list > >> Gus...@li... > >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > >> > > >=20 > |
