I used Elasticsearch-1.1.0 to index tweets. The indexing process is okay. Then I upgraded the version. Now I use Elasticsearch-1.3.2, and I get this message randomly:
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For what it's worth, I found that this seems to be related to a broken index state.
It's very difficult to reliably recreate this issue, but I've seen it several times; operations run as normal except certain ones which periodically seem to hang ES (specifically refreshing an index it seems).
Deleting an index (curl -XDELETE http://localhost:9200/foo) and reindexing from scratch fixed this for me.
I recommend periodically clearing and reindexing if you see this behaviour.