Format Data for Lefse (Error Line8/437)

Downstream analysis and statistics LEfSe
1

Hello! I am currently receiving an error around step A with my analysis. I have already compared my dataset to the sample dataset and found (so far) no differences in format.

L7_species_relativeabundance_modified2.txt (28.8 KB)

When I put the sample dataset through however, it will work. When I put my txt file through Step A/Format data I receive the following message:

Traceback (most recent call last):
File “/usr/bin/lefse_format_input.py”, line 8, in
sys.exit(format_input())
File “/usr/lib/python3.6/site-packages/lefse/lefse_format_input.py”, line 437, in format_input
class_sl,subclass_sl,class_hierarchy = get_class_slices(list(zip(cls[‘class’], cls[‘subclass’], cls[‘subject’])))
KeyError: ‘subject’

Has there been something I’ve missed in my txt file, or is this an issue with the recent update in Lefse? Thank you!

2

Hello @capsola ,
I just tried your input file and everything works as expected. Please make sure that you are passing the Select which row to use as subject and Select which row to use as class for your input file while running galaxy Lefse.

Please feel free to ignore Unable to count lines error in the step1 format input as it will not interfere with the run. We are working on fixing the error message asap.

Regards,
Sagun