[ensembl-dev] Database timeouts for Ensembl API script

[Simon Andrews]

A script we've been using for years has started to become flaky very recently, with repeated losses of connections to the back end database.

Eg:

DBD::mysql::st execute failed: Lost connection to MySQL server during query at /home/andrewss/EnsemblAPI/ensembl/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm line 109, <STDIN> line 1.
DBD::mysql::st execute failed: MySQL server has gone away at /home/andrewss/EnsemblAPI/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line 481, <IN> line 1243757.

The script runs for a pretty long time (a few hours) and just iterates through every chromosome / gene / transcript / CDS in a target genome.  We've not seen these types of timeout before.

The failures are not consistent - I've had the same chromosome fail a couple of times, and then work on a subsequent attempt.  Is there anything we can do from the client side to keep these connections alive (or reconnect?), or are there any known issues at the moment which might be affecting the stability of the database?

If it helps, the script I'm running can be seen at:
https://github.com/s-andrews/SeqMonk/blob/master/Scripts/export_annotated_embl_from_assembly.pl

Cheers

Simon.

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