That's very slow - even the old 2-million-issue JIRA I looked after only took half a day on what would be considered "low end" hardware nowadays.
You'll need to monitor your system to find out what it is actually doing during the process - the things to start with would be CPU and memory usage, network use (if the database is remote), and possibly most important - disk i/o.
I'm assuming your main data disk is a local physical drive, and that you're not running the server on Windows with an active virus scanner too - those are the two things that would immediately cripple it.
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