Lefse Problem in module B (run LDA)

Hello. I am trying to use LEfSe in the new Galaxy 2.0, but when I run the LDA (module B), it give me this issue:

Traceback (most recent call last): File “/galaxy_venv/bin/lefse_run.py”, line 33, in sys.exit(load_entry_point(‘lefse==1.1.2’, ‘console_scripts’, ‘lefse_run.py’)()) File “/galaxy_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse_run.py”, line 90, in lefse_run File “/galaxy_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse.py”, line 222, in test_lda_r AttributeError: ‘NoneType’ object has no attribute ‘rownames’.

I though this was a problem with my new data, but I am having the same issue (even the same message issue) with old data that was working good in the past.

Any sugestion will be apreciated.


Hello @Peter_Janampa,

Could you try again please? We were doing the galaxy maintenance and lefse should work now. Please let us know if any issues.


Hello, I’m also having this same problem. Even when I use the example file. Does anyone have a solution for this?