LEfSe dataset error report: please give me advice

[pradit22]

Hi everyone, please help me with this matter. Since I’m new here and I tried to upload my data to do LEfSe and follow step in this website: lefse · biobakery/biobakery Wiki · GitHub

Then I used my data and it showed as follows (I also tried upload with the sample data: galaxy-upgrade/galaxy_lefse/hmp_aerobiosis_small.txt at main · biobakery/galaxy-upgrade · GitHub; provided by website as well. However, the error show the same)

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 225, in test_lda_r
AttributeError: ‘NoneType’ object has no attribute ‘rownames’

I have no idea how to fix it.
I would be grateful if anyone could help me solve this problem. Thank you so much.
Here is screenshot of my data that i uploaded

[jennaj]

Hi @pradit22

You’ll need to get support for the Biobakery server at their forum.

Details →

@jennaj

Alternative support forums

When working at certain Galaxy sites, questions are best asked at the places the scientists who run the server host discussions. They can also let you know if there happen to be any current technical problems that may be impacting your analysis.

These are the ones we know about…

Galaxy.bioBakery.org → https://forum.biobakery.org
This server was previously hosted at http://huttenhower.sph.harvard.edu/galaxy/ , and prior Q&A here is tagged galaxy-huttenhower

[pradit22]

@jennaj Thank you for your response.
I then try using another server the general main one.

Would you please provide the example input data format for the LEfSe in this usegalaxy.org instead?

Please see the follow attachments. I want to try upload in this server as well. However the input format i believe it’s not the same as in the biobakery. Please help me with the input format. Thank you so much.

[jennaj]

Hi @pradit22

Try working at UseGalaxy.eu instead for this if you want to learn a bit about how to use the tool directly in Galaxy.

Load up the tool form and in the upper right corner, in the Options menu, is the choice Generate Tour. This will load very small example data into your history that you can use with a tool to see what happens.

Screenshot

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To learn more about common analysis, explore the learning Pathways described here please → Learning Pathways