Hi @Francis29029!
q2-diversity does not currently allow the use of relative-frequency data in calculating alpha/beta diversity. Check out my response to shighlander above for instructions on downloading, installing, and getting command-specific help for q2-diversity-lib.
Please note: although I believe all of the tools available in the in-development plugin mentioned above are sound, it has not been officially released yet. Please post to the forum and @mention me if you run into any unexpected issues.
Thanks,
Chris