[Bioperl-l] [BioSQL-l] postgres 8.3 - load_seqdatabase.pl / swissprot

[Erik]

Hi,

PostgreSQL 8.3.1
DBD::Pg 2.3.0
perl 5.8.8

(The following error may have to do with the 8.3 problems
that I reported yesterday (bug 2472) - I don't know)

 I ran biosql-schema/scripts/load_ncbi_taxonomy.pl without
problem.

Then I ran scripts/biosql/load_seqdatabase.pl as:

perl scripts/biosql/load_seqdatabase.pl \
  -driver Pg \
  -dbuser xxxxxxx \
  -dbname bioseqdb \
  -namespace swissprot \
  -format swiss \
   /DATA/ms/ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat

It took two hours to load 26504 records (7%) of
uniprot_sprot.dat (is it expected to be so slow?), then
failed with:

Could not store Q2UXW0:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Species) failed to insert or to
be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/Root/Root.pm:357
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
/home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::Persistent::PersistentObject::create
/home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:244
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
/home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
/home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store
/home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: scripts/biosql/load_seqdatabase.pl:630
-----------------------------------------------------------


I don't know if this is directly related to the 8.3
casting problems I reported yesterday (bug 2472), or a
separate Bio::Species issue


regards,

Erik Rijkers