Please rerun your job and if you have problems, double check the inputs as described in the "Troubleshooting" section of the linked post above. This includes moving to the latest tool version (if not already in use, LefSe was recently updated at Galaxy Main and prior versions may be problematic).
If you cannot determine the problem using the latest tool version, a bug report can be sent in and we can help. If there is a history that has the successful prior runs in it, that can be included in the bug report comments as a shared history link for comparison. Should there be some problem with the tool, characterizing and fixing it is important to us. Please make sure that any histories send in for review have the input and output dataset(s) left undeleted.
Thanks for reporting the issue, Jen, Galaxy team