This requires ubuntu packages shntools and cuetools.
cuebreakpoints MYFILE.cue | sed s/$/0/ | shnsplit -o flac MYFILE.wav
Found on: http://www.linuxquestions.org/questions/linux-software-2/shnsplit-error-m-ss-ff-format-can-only-be-used-with-cd-quality-files-solution-913764/