Re: [Gusdev-gusdev] Taxonomy&Ontology problems

[Deborah P. <pi...@pc...>]

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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