[Bioperl-l] error running load_seqdatabase.pl

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Thu Dec 29 20:26:48 EST 2005

> 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

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