I generated a new data.txt and successfully uploaded and formatted the data set. However, when running LDA Effect Size, I received the following traceback error:
Traceback (most recent call last):
File “/usr/local/bin/lefse_run.py”, line 5, in
from lefse.lefse_run import lefse_run
File “/usr/local/lib/python2.7/dist-packages/lefse/lefse_run.py”, line 4, in
from lefse.lefse import *
ImportError: No module named lefse
To be safe, I re-uploaded a .txt file that I successfully ran in the past and received the same traceback error. The last line, “ImportError: No module named lefse” makes me think that there was an issue with the command line itself rather than my file.
I am trying to use the demo dataset -hmp_aerobiosis_small. However LeFSE continues to fail. here is the error-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. Please help.