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Rename your calibre config directory, uninstall and re-install. Make sure you aren't running from an obsolete source checkout of the calibre code. The number of ways you can screw up something as complex as calibre are infinite and not even countably so. And then of course you may well be trying to convert a non reflowable epub, or an epub with scanned images oftext instead of actual text. Who knows. This whole thing would be a lot easier if you follow the instructions in the sticky on how to ask conversion questions.
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