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No differentially abundant features found in tax-otu-table-result.txt. although a number of significantly discriminative features is veryfied

Hi guys!

I’ am trying to perform LEfSe analysis using a collapse.table produced by qiime2-2021.2, formatted by adding metadata (numeric and categorical values included). Although the message “a number of significantly discriminative features” is reported as output, the “” command produces no differentially abundant features in case of both numeric and categorical values.

Can you please enlighten me, why is this happening?
The collapse.tables used are attached
collapse.table_BMI.txt (21.3 KB)
collapse.table_FGF.txt (21.3 KB)
collapse.table_VEGF.txt (21.4 KB)


  1. collapse.table.txt tax-otu-table-form.txt -c 1 -s 0 -u 2 -o 1.0

  2. tax-otu-table-form.txt tax-otu-table-result.txt
    Output: Number of significantly discriminative features: 7 ( 7 ) before internal wilcoxon
    Number of discriminative features with abs LDA score > 2.0 : 0

  3. tax-otu-table-result.txt tax-otu-table-diffabund.pdf
    No differentially abundant features found in tax-otu-table-result.txt

Moreover, I was wondering, if I am working on the right commands, as no .in and .res files are produced.

Thank u in advance,

Hi Mania,
I think this response will help with your question as well: Problme with LEfSe using command line interface - #5 by mishort
The commands you’re using are not the ones from the most updated version of LEfSe; if you update your version it should help.

Thank you very much Meg!
I’ll check it out and if I solve the problem, I will edit my post to inform the community!