Formatting data for LEfSe

Downstream analysis and statistics LEfSe
1

I am getting error message running LEfSe on the galaxy. The error message is below:-
Traceback (most recent call last):
File “/usr/bin/lefse_format_input.py”, line 10, in
from importlib.metadata import distribution
ModuleNotFoundError: No module named ‘importlib.metadata’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/usr/bin/lefse_format_input.py”, line 13, in
from importlib_metadata import distribution
ModuleNotFoundError: No module named ‘importlib_metadata’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/usr/bin/lefse_format_input.py”, line 15, in
from pkg_resources import load_entry_point
File “/usr/local/lib/python3.6/dist-packages/pkg_resources/init.py”, line 3266, in
@_call_aside
File “/usr/local/lib/python3.6/dist-packages/pkg_resources/init.py”, line 3241, in _call_aside
f(*args, **kwargs)
File “/usr/local/lib/python3.6/dist-packages/pkg_resources/init.py”, line 3279, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File “/usr/local/lib/python3.6/dist-packages/pkg_resources/init.py”, line 573, in _build_master
ws.require(requires)
File “/usr/local/lib/python3.6/dist-packages/pkg_resources/init.py”, line 891, in require
needed = self.resolve(parse_requirements(requirements))
File “/usr/local/lib/python3.6/dist-packages/pkg_resources/init.py”, line 777, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The ‘lefse==1.1.2’ distribution was not found and is required by the application

I was not able to troubleshoot the issue. Do you have any advice how to solve the issue?
Thank you so much for your help on this.

Thanks,
Daniel

1 Like
2

Hi @dtadesse,
Thank you for posting your detailed error. I believe this is a case of a non-specific error. This is an error likely caused by LEfSe not having been written in a python3 ecosystem. LEfSe is not a tool that we regularly maintain, we are working on getting LEfSe compliant with python3, and we will let everyone know once LEfSe on Galaxy is working again.

In the meantime, you can use our other tool MaAsLin, which is under current development in R to complete complimentary tasks.

Best,
Kelsey

3

Thanks Kelsey! I will use MaAsLin.