[BioSQL-l] Problems when trying to persist a sequence in my BioSQL database using BioPerl

[Gabrielle Doan]

Hi all,

I am new to BioPerl and BioSQL so please excuse me if my question is a bit simple. I followed the installation files in the current version of BioPerl very strictly (I used the Bioperl 1.5.2, Developer Release from the bioperl website). After successful installation I tried to persist a genbank file in my BioSQL database, which runs on a database server and is accessible using the mysql command shell. When using bioperl I receive the following error message:

================

$ /usr/bin/bp_load_seqdatabase.pl --host radb --dbname bioseqdb --dbuser myuser --dbpass mypasswd --namespace GenBank /home/doan/db-data/ref_chr1.gbk
Loading /local/doan/db-daten/ref_chr1.gbk ...
Bio::SeqIO: genbank cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::SeqIO::genbank. Weak references are not implemented in the version of perl at /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91
BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91.
Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172.
BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172.
Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm line 425.

STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::Root::Root::_load_module /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:427
STACK: Bio::SeqIO::_load_format_module /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:555
STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:376
STACK: /usr/bin/bp_load_seqdatabase.pl:541
-----------------------------------------------------------

For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run time
Can't call method "next_seq" on an undefined value at /usr/bin/bp_load_seqdatabase.pl line 565.

================

Unfortunately, even Google does not provide any hints when searching for the particular message. It seems that for some reason the path to the Bio::SeqIO::genbank module cannot be found. I am greateful for any hint!

Cheers,
Gabrielle
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