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)
I am trying to use LEfSE , using the demo dataset. However getting error in calculating effect size (step 3).Here is the error. please help.
B) LDA Effect Size (LEfSe)
Dataset Information
Number: 30
Name: B) LDA Effect Size (LEfSe) on data 24
Created: Thu Apr 4 06:59:52 2024 (UTC)
Filesize: 0 bytes
Dbkey: ?
Format: lefse_internal_res
Job Information
Galaxy Tool ID: LEfSe_run
Galaxy Tool Version: 1.0
Tool Version:
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: 1
Job Messages
Fatal error: Exit code 1 ()
History Content API ID: 702897e66004936f
Job API ID: 45c670429e65ac89
History API ID: 22bdbe9d6e0775fe
UUID: 1d91591b-9502-42d7-8a9c-75673abcb8e5
Tool Parameters
Input Parameter Value
Select data
24: A) Format Data for LEfSe on data 22
Alpha value for the factorial Kruskal-Wallis test among classes 0.05
Alpha value for the pairwise Wilcoxon test between subclasses 0.05
Threshold on the logarithmic LDA score for discriminative features 2.0
Do you want the pairwise comparisons among subclasses to be performed only among the subclasses with the same name? No
Set the strategy for multi-class analysis All-against-all (more strict)
Inheritance Chain
B) LDA Effect Size (LEfSe) on data 24
Dataset peek
no peek
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
1 Like
Hi @sagunmaharjann I cannot ignore this issue as it won’t let me use the error dataset in the pipeline. Is there any update on the resolve?
Hi! I met the same error when I used LEfSe.
I run into one error in Step B) Error message:
Number of significantly discriminative features: 36 ( 36 ) 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
I have tried to resolve these problems many different ways, but i did not resolve it. It is greatly appreciated for any help. Thanks a lot!
Hi @Kelsey_Thompson, i have the same problem. I am trying to run the pipeline using new tabular files (I believe to be formatted correctly) and even old ones that successfully worked in the past. I have this error: Any recommandation ? thank you
Fatal error: Exit code 1 ()
Tool generated the following standard error:
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_lda_r
AttributeError: ‘NoneType’ object has no attribute ‘rownames’