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

Kenric Leung kl1 at sanger.ac.uk
Mon Dec 12 15:38:07 GMT 2011


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?


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