I think it is not strange since when specifying no subclass (-s 1), input_format.py produces subclasses that is identical to classes, then perform wilcoxon test which is by default set to be performed (–wilc 1). Could you please answer the latest question in this thread, that when specifying --wilc to 0, why are there no p-value reported whenever K-W is significant? Reproducible example is in Question about LEfSe input_format.py when specifing no subclass
I think we need developers who were involved in publication of LEfSe
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