Hi @sagunmaharjann I still keep getting this error and I am unable to generate the LDA plots.
Kind regards
Kevin
Hello,
I am trying to run LEfSe now and I have the same problem and message that you commented before in this conversation. Id the problem with maintenance unsolved yet?
Error message:
Number of significantly discriminative features: 57 ( 57) before internal wilcoxon
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_ru
Thank you very much in advance!
I am having the same problem too…
Number of significantly discriminative features: 4 ( 38 ) before internal wilcoxon
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
And I am using an old dataset that were previously working 
1 Like
I am also having the same problem with an old dataset that previously worked. Thank you so much for all your help!
Number of significantly discriminative features: 16 ( 16 ) before internal wilcoxon
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_ru
Hello,
I am having also the same problem with a dataset that worked previously.
Number of significantly discriminative features: 12 ( 12 ) before internal wilcoxon
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_ru
Is it a problem with maintenance? When will this be resolved?
Thank you in advance!
Hi,
I am having the same problem, this will be resolved?
Hi everyone, I’m facing the same issue from here on using lefse tool.
Anyone can help me with this?
thanks
Hi all,
I am having the same issue. Was this resolved for anyone recently?
Traceback (most recent call last):
File “/galaxy_venv/bin/lefse_format_input.py”, line 33, in
sys.exit(load_entry_point(‘lefse==1.1.2’, ‘console_scripts’, ‘lefse_format_input.py’)())
File “/galaxy_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse_format_input.py”, line 439, in format_input
File “/galaxy_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse_format_input.py”, line 163, in get_class_slices
IndexError: list index out of range
Thanks
Hello everyone,
I’m trying to run LEfSE analysis on some genes data and for some reason I am unable to continue due to this error during step 3:
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’
Can someone give me a help? I’m pretty stuck. This is the input file:
LefSE.txt (2.5 KB)
Lefse-CDV-level-4.txt (9.6 KB)
I’m unable to get the LDA Effect Size tool to run in Lefse. I get this error message:
Hi,
I am new to running lefse and I was trying out the galaxy interface to run the sample data but it failed on the second step-B) LDA effect size (LEfSe) -see text below
Can you advise if this is a program-wide issue or if I am doing something wrong in following the protocol?
thank you!
Traceback (most recent call last):
File “/galaxy_venv/bin/lefse_run.py”, line 33, in ‹module>
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_Ida_r
AttributeError: ‘NoneTvpe’ obiect has no attribute 'rownames"
Hi, I am having the same issue with LefSe analysis. Has anyone been able to sort the 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 225, in test_lda_r
AttributeError: ‘NoneType’ object has no attribute ‘rownames’
error
An error occurred with this dataset:
Number of significantly discriminative features: 1 ( 16 ) before internal wilcoxon
Traceback (most recent call last):
File “/galaxy_venv/bin/lefse_run.py”, line 33, in
sys.exit(load_entry_point(‘lefse==1.1.2’,
Anyone can help us with these issue?
thanks