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From: <fed...@bi...> - 2005-02-21 15:01:52
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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 |
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From: Deborah P. <pi...@pc...> - 2005-02-21 15:18:37
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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 > > |
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From: <fed...@bi...> - 2005-02-21 15:37:33
|
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 >> >> > > |
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From: Poliana M. <pol...@gm...> - 2005-02-21 15:49:58
|
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
> >>
> >>
> >>
> >>-------------------------------------------------------
> >>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
> >>
> >>
> >
> >
>=20
> -------------------------------------------------------
> 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
>
|
|
From: Poliana M. <pol...@gm...> - 2005-02-21 17:22:39
|
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 > |
|
From: <fed...@bi...> - 2005-02-21 17:32:45
|
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 >> >> >> > >> >> > |
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