[BioSQL-l] Error using load_seqdatabase.pl

Robert Roth robert.roth at home.se
Wed Oct 8 07:24:25 EDT 2003


Hello,

I'm using Mysql 4.0.15, Bioperl 1.2.3, bioperl-db from the cvs and perl
5.6.1 on WinXP.
After installation I pre-loaded the the biosql database with the NCBI taxon
database using
load_ncbi_taxonomy.pl. Now when I try to load sequence data with
load_seqdatabase.pl I get
the following error,

perl load_seqdatabase.pl --host localhost --dbname biosql --dbus
er root --namespace bioperl --debug --safe --testonly --format
 genbank test.genbank
Loading test.genbank ...
attempting to load adaptor class for Bio::Seq::RichSeq
        attempting to load module Bio::DB::BioSQL::RichSeqAdaptor
attempting to load adaptor class for Bio::Seq
        attempting to load module Bio::DB::BioSQL::SeqAdaptor
instantiating adaptor class Bio::DB::BioSQL::SeqAdaptor
attempting to load adaptor class for Bio::SeqFeature::Generic
        attempting to load module Bio::DB::BioSQL::GenericAdaptor
attempting to load adaptor class for Bio::Root::Root
        attempting to load module Bio::DB::BioSQL::RootAdaptor
Undefined subroutine &Bio::Root::Root::debug called at
E:/Perl/site/lib/Bio/DB/B
ioSQL/BasePersistenceAdaptor.pm line 1502, <GEN0> line 41.

I've tried different formats (swiss and genbank) and different files with
the same
result. The line number given in the error always correspond to the end of
the first
record (and it doesn't matter if the file contains one or more records).
Any ideas?

Many thanks in advance,

Robert




More information about the BioSQL-l mailing list