[Bioperl-l] error running load_seqdatabase.pl

[Angshu Kar]

Also how to run the bioperl-db test ? I mean do I have to reinstall it to
run the make test command?



On 12/30/05, Angshu Kar <angshu96 at gmail.com> wrote:
>
> 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/
> > >
> >
> >
>