When I run LEfSe in version 1.44.0, the mothur logfile indicates that significant features have been identified but no values are reported in the class, LDA or p-values columns in the LEfSe summary file. When, I re-ran LEfSE with the same files in earlier version of mothur (1.36.1) significant features are identified and the summary file includes the class, LDA and p-values, so I think this is likely a bug in LEfSe in 1.44.0.
Thank you for reporting this bug. I opened an issue for it, https://github.com/mothur/mothur/issues/709, which you can follow for updates on the fix.
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I am not able to reproduce this with our test data. Could you send your shared and design file to mothur.bugs@gmail.com so I can take a closer look?