compare_alpha_diversity.py avoid Warning: Invalid value encountered in percentile

[Susan]

Hi,

just wanted to say, for anyone having this problem, in commands like:

compare_alpha_diversity.py -i rarefaction2/alpha_div_collated/simpson.txt -m mapping.txt -c treatment,site -o compare_simpson -t nonparametric

I have found that you must find the lowest number of iterations in simpson.txt (or whatever measure it is) that does not have an n/a, and use that value with -d, e.g.

compare_alpha_diversity.py -i rarefaction2/alpha_div_collated/simpson.txt -m mapping.txt -c treatment,site -o compare_simpson -t nonparametric -d 22835

I couldn't find an answer to this elsewhere so thought maybe this might help someone.