[ensembl-dev] connection lost when trying to get GeneAdaptor

Monika Komorowska monika at ebi.ac.uk
Mon Dec 12 15:48:15 GMT 2011

Hi Kenric

You can use set_disconnect_when_inactive Registry method, which will establish a new connection for each query.

On 12 Dec 2011, at 15:38, Kenric Leung wrote:

> Hi,
> I'm getting these errors when running my script using ensembl 58:
> DBD::mysql::st execute failed: MySQL server has gone away at /software/pubseq/PerlModules/Ensembl/www_58_1/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm line 694, <DATA> line 9.
> DBD::mysql::st execute failed: Lost connection to MySQL server during query at /software/pubseq/PerlModules/Ensembl/www_58_1/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm line 694, <DATA> line 7
> I see there is a new method ->set_reconnect_when_lost() in ensembl 64 but we currenlty can't use the newer version at the moment.  Is there any way to keep the connection alive for v58 whilst the script is running?
> Thanks,
> Kenric
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

Monika Komorowska
EnsEMBL Software Developer

European Bioinformatics Institute (EMBL-EBI)
tel: +44(0) 1233 494 409

More information about the Dev mailing list