Error: Plugin error from diversity “All numbers are identical in kruskal“

Hi @ilhem, thanks for sharing your data with me, that was really helpful!

If you run the following, the problem be more apparent:

qiime metadata tabulate \
  --m-input-file goods_coverage_vector.qza \
  --o-visualization goods_coverage_vector.qzv

Every one of your samples has a Good's Coverage value of 1, so all of the samples are identical, in terms of that measure of alpha diversity. Taking a step back - how was this feature table produced? Since Good's coverage requires the presence of singletons, I think it would be a mistake to try and calculate this measure on a table produced by a method that removes singletons (or doesn't generally produce singletons, like DADA2), but I am curious to hear other opinions on the matter.

Good luck!

2 Likes