Turns out this happened because I was running hpodder by hand, but it also runs hourly from a cron job. The db was locked because that one was still running.
It seems that if hpodder is run twice concurrently, it fails as described in this bug report, throwing the exception and essentially hanging. In fact, _both_ instances eventually do this. Hmm, this means that if my hourly cron job takes longer than an hour to run, hpodders will pile up one on top of the other each failing to do anything.. -- see shy jo
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