[Bioperl-l] tables missing in mysql biosql instance

[David Guzman]

Hi:

I executed DROP on the swissprot - biosql db created yesterday. And
today I have just repeated the process including the --safe flag, with
the following command:

[david at mandrake scripts]$ perl load_seqdatabase.pl --host localhost
--dbname swbiosql --dbuser root --dbpass XXXXXX --driver mysql
--namespace bioperl --safe --format swiss
/opt/protdb/swissprot/sprot40.dat

I checked the size of the folder containing the db (331M), is better
than yesterday (24M), but it should be larger (399M) according to the
HOWTO (my GBank with MySQL).In the screen I obtained similar error
messages, like:

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::SpeciesAdaptor (driver) failed, values
were ("IAP-IL3","a-particle:Mouse intracisternal:Intracisternal
A-particles:Retroviridae:Retroid viruses:Viruses","11754","Mouse
intracisternal a-particle","-") FKs ()
Duplicate entry 'Mouse intracisternal a-particle--' for key 3
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Could not store P12894: 

and ...

DBD::mysql::st execute failed: Duplicate entry '101583-178464' for key 1
at
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
line 402, <GEN0> line 6360694.

--lookup flag would help??? (for "Duplicate entry" complain?).

Then I am checking everything step by step, and I discovered that there
are 2 tables missing: remote_seqfeature_name and ontology_relationship,
how can I correct this problem with biosql-schema?.
Any suggestions??

Thanks for your help. I need to handle this in a proper way to promote
it in my bioinformatics lectures and practical activities.

                                   David