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Disko doesn't consider Advanced Format sectors when aligning disks
I understand that disks should be aligned to 1 megabyte boundaries. Disko produces a script that gives "--set-alignment=2048" to sgdisk in all cases. On a 4k disk, this is an 8 megabyte alignment, the proper value is 256 for 1M alignment.
One possible command is "blockdev --getss /dev/disk-name", which returns the logical sector size. Divide 1M by the returned value, you get the needed alignment.