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It could be that there are some permission problems in /opt/calibre. I suggest that you remove the entire /opt/calibre tree (rm -fr /opt/calibre), then reinstall from binary. Your library will be safe unless for some reason you put it inside calibre's install directory.
You might also try a 'which calibre' to see where your system thinks the calibre executable lives. If that file is not in /opt/calibre, then check it to be sure it is a symlink into /opt/calibre.
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