Re: [Gusdev-gusdev] Taxonomy&Ontology problems

[<fed...@bi...>]

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
>>
>>
>>
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>
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