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That error indicates calibre is unable to find the kindle's device node in your sysfs filesystem. The only way that can happen that I know of is if your kernel has something non-standard about it. I suggest you use the connect to folder function in calibre unless you feel like debugging the issue, in which case the relevant code is find_device_nodes() in usbms/device.py and instructions for running calibre from source are under setting upa calibre development environment in the user manual.
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