[Bioperl-l] Error while running load_seqdatabase.pl

George Heller george.heller at yahoo.com
Mon Jan 8 22:27:33 EST 2007


    Hi all. 
   
  I am new to Bioperl and am trying to run the load_seqdatabase.pl script to load sequence data from a file into Postgres database. I am invoking the script through the following command:
   
  perl load_seqdatabase.pl -host localhost -dbname biodb06 -format fasta
-dbuser postgres -driver Pg <name of file>
   
  I have already loaded the taxon data using the load_ncbi_taxonomy.pl script. But while running the load_seqdatabase.pl,
   
  I am getting the following error:
   
  Loading maize_pep.fasta ...
  -------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were ("FGENESHT0000001||AC155633|570|4400|1","FGENESHT0000001||AC155633|570|4400|1","unknown","","0","") FKs (1,<NULL>)
ERROR:  duplicate key violates unique constraint "bioentry_accession_key"
  ---------------------------------------------------
Could not store unknown:
------------- EXCEPTION  -------------
MSG: error while executing statement in Bio::DB::BioSQL::SeqAdaptor::find_by_unique_key: ERROR:  current transaction is aborted, commands ignored until end of transaction block
  STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/lib/perl5/site_perl/5.8.5/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:948
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/lib/perl5/site_perl/5.8.5/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:852
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.5/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:203
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.5/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm:271
STACK (eval) load_seqdatabase.pl:620
STACK toplevel load_seqdatabase.pl:602
  --------------------------------------
   at load_seqdatabase.pl line 633

  
  Can anyone tell me how I can correct this error and get my script running? Thanks!!!
   
  George.

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