[BioSQL-l] Error when loading Gene Ontology to biosql

Song Haili haili at mpiz-koeln.mpg.de
Tue Jul 21 10:11:30 UTC 2009


Dear all, 
I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind by using CPAN a few days before. Until now, I can load taxonomy and sequence data into database successfully. However, I got the following error message when trying to load Gene Ontology data into biosql database. Any help will be appreciated.
Jane

command used:
perl load_ontology.pl --driver Pg --host pg-server --dbname sifter -dbuser sifter --dbpass password −−namespace "Gene Ontology" --format goflat component.ontology process.ontology function.ontology --fmtargs "-defs_file, GO.defs" --noobsolete

error:
------------- EXCEPTION -------------
MSG: Could not open −−namespace: No such file or directory
STACK Bio::Root::IO::_initialize_io /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323
STACK Bio::OntologyIO::dagflat::parse /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:277
STACK Bio::OntologyIO::dagflat::next_ontology /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:330
STACK toplevel load_ontology.pl:604
-------------------------------------






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