Hi SoilRotifer,
These NAs appear in the lefse input file that created with the physeq2lefse.R. I just checked the physeq file created by the qiime2R with the otu_table function, and found that the table was correct, meaning that the physeq file was built correctly. So I think the problem was associate with the phyloseq2lefse.R code.
Besides, only the genus level was tested when you perform the lefse?
Thanks! !
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