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