Lefse Problem in module B (run LDA)

Downstream analysis and statistics
1

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.

Peter

2

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.

Regards,
Sagun

3

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