[Bioperl-l] error running load_seqdatabase.pl

[Angshu Kar]

Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl --dbname=USBA
--dbuser=postgres --format=genbank  --driver=Pg --debug  NC_003076.gbk)
 is getting killed after the follwoing step?

Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer for
Bio::DB::BioSQL::BiosequenceAdaptor
preparing SELECT statement: SELECT bioentry_id FROM biosequence WHERE
bioentry_id = ?

Killed

I'm using a linux box. This didn't happen for a different i/p file!

Thanks,
Angshu


On 12/29/05, Angshu Kar <angshu96 at gmail.com> wrote:
>
> I'm sorry that I missed it! Thanks for pointing it out.
> Also thanks Hilmar for the update.
>
> Angshu
>
> On 12/29/05, Torsten Seemann < torsten.seemann at infotech.monash.edu.au >
> wrote:
> >
> > > I'm getting the following error while trying to run :
> > > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser postgres
> > -format
> > > genbank NC_003076.gbk
> > > MSG: failed to open connection: Can't connect to local MySQL server
> > through
> > > socket '/var/lib/mysql/mysql.sock' (2)
> > > But I've a postgreSQL db and not a MySQL one...could anyone please
> > guide me
> > > troubleshoot this?
> >
> > Did you read the documentation for the load_seqdatabase.pl script?
> >
> > It's in the script itself!
> >
> >     =item --driver $driver
> >     the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle [mysql]
> >
> >
> > The default DBI driver is [mysql].
> >
> > I think you want the option "-driver Pg".
> >
> > --
> > Torsten Seemann
> > Victorian Bioinformatics Consortium, Monash University, Australia
> > http://www.vicbioinformatics.com/
> >
>
>