LEfSe_run AttributeError

Downstream analysis and statistics LEfSe
1

Hi there,

At the moment I am trying to run the LDA Effect Size step on the Galaxy server after I have successfully uploaded and formatted my data. At the LEfSe_run step, I am getting the same error with various datasets (that worked before):

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’

How can I solve this issue? Thank you for your help!

4 Likes
2

I am also getting this error today when trying to upload files that I have previously uploaded with no problems. I’m not sure if the non-fatal error in the prior data formatting step may be contributing to this issue at the LDA effect size step on the galaxy server.

Error: Cannot count lines in dataset

formatlefse_internal_for

database?

ERROR:galaxy.datatypes.data:Unable to count lines in file /export/galaxy-central/database/files/004/dataset_4015.d

image
image552×1128 79.7 KB

Thanks in advance for your time and help!

1 Like
3

I have exactly the same issue with my dataset which previously worked. I tried to reformat but it’s also the same warning message.

Thanks for your help

4 Likes
4

I have exactly the same issue since the version was modified. I tried data which worked on Friday just before the last modification but now I have the warning message.
Please, I need your help!
Thank you.

3 Likes
5

Hello,

I am also having this exact issue with a dataset that was working fine before the update to the Galaxy server. Please if someone can help us with this issue it would be much appreciated.
Thank you for your help!

2 Likes
6

I am also encountering a similar error while performing LEfSe analyses. More specifically, after uploading and converting my files into the Format data for LEfSe, the error takes place when I try to perform the LDA analysis itself from the Galaxy website. It is as follows:

Fatal error: Exit code 1 ()
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 believe it might be a server problem, considering that it also happens to me when I try to perform the analysis with the tutorial files I found at this webpage (lefse · biobakery/biobakery Wiki · GitHub).
Also, it is worth mentioning that other people in other forums are reporting similar errors (How to fix errors with Lefse - #4 by jennaj - lefse - Galaxy Community Help).

4 Likes
7

Hi, this is server problem as @adelaidepanattoni said.
Please see Kelsey_Thompson’s reply.
Hope they resolve this issue ASAP.