[BioSQL-l] load_seqdatabase.pl warnings and errors

[Peter]

On Tue, May 19, 2009 at 9:17 AM, michael watson (IAH-C)
<michael.watson at bbsrc.ac.uk> wrote:
>
> Hi
>
> I'm using:
>
> biosql-1.0.1
> bioperl-db-1.5.2_100
> bioperl-1.5.2_102
>
> When I run load_seqdatabase.pl on about 3000 GenBank sequences,
> I get:
>
> Loading fmd_180509.gbk ...
> ...
> ---------------------------------------------------
>
> Could not store NC_011452:
>
> ------------- EXCEPTION  -------------
>
> MSG: create: object (Bio::Annotation::Reference) failed to insert or to
> be found by unique key
>
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
> B/BioSQL/BasePersistenceAdaptor.pm:206
>
> ...
>
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
> B/Persistent/PersistentObject.pm:271
>
> STACK (eval) load_seqdatabase.pl:622
>
> STACK toplevel load_seqdatabase.pl:604
>
> --------------------------------------
>
>  at load_seqdatabase.pl line 635
>
> Any clues?

You got a lot of warning about feature keys (which I am guessing are
from different GenBank entries), but the failure seems to be from
something to do with the annotation in NC_011452.

Try downloading just NC_011452 in GenBank format, and testing that:
http://www.ncbi.nlm.nih.gov/nuccore/NC_011452

I would expect that to fail in the same way, and you would at least
have isolated the issue to a smaller test case. If it works, then
maybe the copy of NC_011452 in your file is corrupted somehow - check
for differences.

Peter