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
The second step of running the lefes reported an error. How should I fix it
In the context of Lefse executed in Galaxy, that would probably fit what is going on generally.
And rownames indicates a problem with a label or header in an input file.
So, start by checking the format of your inputs – and any data entered on the tool form used as a label – for technical errors. Most tools parse singleword values better than those with spaces. Some can also interpret underscores. Most other characters are not accepted, and can lead to errors.
Please give that a try, and if you are stuck, provide more details:
Where are you working? Public Galaxy server URL or describe if other
Exact tool name including the version
Screenshots or shared history links to give others an idea about what the inputs + tool form settings are that produce the error.
I have also been trying to perform a LEfSe analysis ever since yesterday and I get the exact same error. Problem is, I also get it when I upload the test data that are given in the tutorial page. Do we know if there is something wrong with the website in general? I also have been trying to solve it but I don’t know what to do and I cannot find a lot of help online. Another post also reported the same mistake yesterday.