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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 “lefse-plot_res.py” 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)

Commands:

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

  2. run_lefse.py 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. lefse-plot_res.py 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,
Mania

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.
Best,
Meg

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!

Best,
Mania