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For some reason Calibre won't let me do anything because "drive is full" which I assume has to do with this.
Update: I believe I "fixed" the error with Calibre by using FlatSeal to add environment variable CALIBRE_TEMP_DIR that changes the Temp directory to something else. So far that's the only program I've seen give trouble.
This is completely unrelated to your problem:
The calibre website recommends extremely strongly against using their software packaged by anyone else other than calibre themselves as they are often (see usually) buggy or extremely outdated.
It may be worth it to manually "install" the app from their website somewhere in your ~/.local/ and see if you have less issues using the official package.