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I haven't actually used this yet so I'll update it (or remove this line) when I can verify that it works.

cleanupCompleteRun doesn't start after last run processes

From Michael:

For each chunk, the individual checkChunk should remove the respective chunk token.  CheckChunk of chunk 1757481 reports it can't find the token (nfs hiccup) but proceeds by design.

After all the merges etc. checkRun checks for remaining tokens and if present chokes on it.  To resolve it I usually just remove the chunk token in question (checking that the chunk was processed properly, of course), and roll back the youngest (if there are more than one) checkRun.  If there isn't any other issue checkRun sets the status to Complete, which triggers cleanupCompleteRun.

It's overkill to roll back from the checkChunk. Maybe even harmful, but I guess the chunk data are still on xrootd.  But this should be verified.