Github user amihalik commented on the issue: https://github.com/apache/incubator-rya/pull/236 @ejwhite922 There's a couple issues with the batch writer and it doesn't have to do with exceptions being caught. (1) the QueueFullChecker thread should not be a daemon thread.... "The Java Virtual Machine exits when the only threads running are all daemon threads" means that the JVM will exit while flushing to mongo. (2) It doesn't seem like the secondary indexer (i.e. geoindexer) is flushed when I close down the sail layer. Can you double check that? Also, it seems like the JVM takes a very long time to exit after I call sailrepository.shutDown(). I think has to do with the BatchWriter as well.
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