[BioSQL-l] error with load_ontology

Song Haili haili at mpiz-koeln.mpg.de
Wed Aug 26 14:18:09 UTC 2009


Hi All,
I encountered an error message when using load_ontology.pl to load gene ontology into biosql database. The command used is: 

perl load_ontology.pl --driver Pg --host pg-server --dbname dbname --dbuser dbsuer --dbpass dbpass --namespace "Gene Ontology" --format obo /home/data/haili_biosql/GO/gene_ontology.1_2.obo --noobsolete. 

At the beginning,  data can be loaded with warnings, but late an exception occurred and the loading was terminated. Waring and error messages  shown below:

 --------------------- WARNING ---------------------MSG: failed to store term synonym (Bio::DB::BioSQL::TermAdaptor) with values (spHAS RELATED EC:2.4.1.212) (FK 20447 to Bio::Ontology::OBOterm):ERROR:  current transaction is aborted, commands ignored until end of transaction block---------------------------------------------------Could not store term GO:0050501, name 'hyaluronan synthase activity':------------- EXCEPTION -------------MSG: error while executing statement in Bio::DB::BioSQL::DBLinkAdaptor::find_by_unique_key: ERROR:  current transaction is aborted, commands ignored until end of transaction blockSTACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:970STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:873STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:195STACK Bio::DB::BioSQL::TermAdaptor::store_children /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/TermAdaptor.pm:306STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:227STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /perl/lib/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264STACK Bio::DB::Persistent::PersistentObject::store /perl/lib/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284STACK (eval) load_ontology.pl:812STACK main::persist_term load_ontology.pl:794STACK toplevel load_ontology.pl:617-------------------------------------
Can you please help me to solve this problem out? Thank you very much.
Best regards,
song





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