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Re: [Gusdev-gusdev] Taxonomy&Ontology problems
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From: <fed...@bi...> - 2005-02-21 17:32:45
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Yes, of course... It's why I don't understand where I have to move it! > 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: >> >> ga GUS::GOPredict::Plugin::LoadGoOntology \ >> > --file_path=/usr/local/src/gus-related/ontology/ \ >> > --process_db_id=3003 \ >> > --process_ext_db_rel=6 \ >> > --function_db_id=3001 \ >> > --function_ext_db_rel=33 \ >> > --component_db_id=3002 \ >> > --component_ext_db_rel=28 \ >> > --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 >> preparation >> for parsing >> Note: did not find file component.ontology in directory >> CBIL::Bio::GeneOntologyParser::Parser=HASH(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=HASH(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=HASH(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 >> preparation >> 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 >> >> I understand it's a problem releted with che *.ontology path, but I >> really >> 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 >> >> >> > Hi Federica, >> > >> > I run thus: >> > >> > GoOntology: >> > >> > ga GUS::GOPredict::Plugin::LoadGoOntology >> > --file_path=/usr/local/db/local/ontology/ --process_db_id=3003 >> > --process_ext_db_rel=6 --function_db_id=3001 --function_ext_db_rel=33 >> > --component_db_id=3002 ââ¬"component_ext_db_rel=28 --create_release >> > >> > See if your files (*.ontology) are in the correct path. >> > >> > *************************************************************************************************** >> > >> > LoadTaxon: >> > >> > ga GUS::Common::Plugin::LoadTaxon >> > -gencode=/usr/local/db/local/taxonomy/gencode.dmp >> > --names=/usr/local/db/local/taxonomy/names.dmp >> > --nodes=/usr/local/db/local/taxonomy/nodes.dmp >> > --merged=/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 >> 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 >> >> this >> >> >>errors: >> >> >>1) for Taxonomy >> >> >>$ ga GUS::Common::Plugin::LoadTaxon \ >> >> >> >> >> >> >> >> >>>--gencode=/usr/local/src/gus_related/taxonomy/gencode.dmp \ >> >> >>>--names=/usr/local/src/gus_related/taxonomy/names.dmp \ >> >> >>>--nodes=/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=/usr/local/src/gus-related/ontology/ \ >> >> >> >> >> >> >> >> >>>--process_db_id=3003 \ >> >> >>>--process_ext_db_rel=165 \ >> >> >>>--function_db_id=3001 \ >> >> >>>--function_ext_db_rel=164 \ >> >> >>>--component_db_id=3002 \ >> >> >>>--component_ext_db_rel=166 \ >> >> >>> >> >> >>> >> >> >> >> >> >>/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=HASH(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=HASH(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=HASH(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=6595&alloc_id=14396&op=click >> >> >>_______________________________________________ >> >> >>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 >> users. >> >> Discover which products truly live up to the hype. Start reading now. >> >> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >> >> _______________________________________________ >> >> Gusdev-gusdev mailing list >> >> Gus...@li... >> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> > >> >> > |
