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How much free memory do you have? Calibre can consume 125MB+ on my Windows machine; if I've got two conversion processes going at the same time that's 3x that much. Although under OS X those should be copy-on-write forks, so duplicate pages shouldn't be consuming extra memory. But maybe that's not how they work these days. Anyway, point is, if you're low on free memory then using Calibre can cause a lot of disk paging.
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