[ensembl-dev] Variant effect predictor and local database

[Henrikki Almusa]

Hi,

I was trying to put the variant effect predictor to run in cluster and 
parallelise each chromsome to their own job. I got it running but soon 
encountered a problem with database. I got connection error to database 
on some of the runs. If I run without whole_genome I got some results 
before the execution failed. The log of the error can be seen in attachment.

After a quick peek on the database server, it was noticed that the 
amount of inactive connections went up dramatically. At around 32k 
inactive connections, the errors started and executions failed. One 
execution alone generated thousands of inactive connections, but managed 
to finish before they grew too far.

Why does this generate that huge number of connections? Is there a way 
to not do that as this means that I cannot use this tool in automatic 
fashion (as more than one or two cannot be running at the same time).

Thanks,
-- 
Henrikki Almusa
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