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As a test, try disabling your AV. You may need to reboot after disabling it to actually get it to take.
Try Calibre again and see if that helps.
If it doesn't, try looking at all the background processes and programs running. Most recent OS's tend to have lots of stuff going on in the background that take up resources. The more programs you have running, the slower things get. Try to turn off as much as possible and see how things work then.
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