Pielou_e sometime crash with division by zero error

[Patg13]

Normally happening during the metric step without rarefaction, temporary workaround is to remove the | exit_on_error on the alpha-significance check, that will skip the QZV generation. It's however not a good long term solution, It must be addressed.

Because metrics are more useful with rarefied data, this issue is low priority

For now, a bypass mecanism was added to the metric generation command so if it fails, it does not stop the script, the other metrics will still be generated. It is not a fix, so the issue is not closed, but it's not that problematic anymore

[Patg13]

Problem is caused by the pielou formula itself in python (qiime2 source code scikit-bio/skbio/diversity/alpha
/_base.py):

counts = _validate_counts_vector(counts)
return ((np.exp(shannon(counts, base=np.e)) - 1) /
(observed_otus(counts) - 1))

If the count of an observed feature is 1, the denominator will 1-1, so 0, causing the division by zero error.

[Patg13]

One potential solution would be to force add 1 feature to every features < 2