# Formatting data for LEfSe

**URL:** <https://forum.biobakery.org/t/formatting-data-for-lefse/6540>\
**Category:** LEfSe\
**Created:** [January 29, 2024, 3:36pm UTC](https://forum.biobakery.org/t/formatting-data-for-lefse/6540 "2024-01-29T15:36:39Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![dtadesse](https://avatars.discourse-cdn.com/v4/letter/d/46a35a/32.png) [@dtadesse](https://forum.biobakery.org/u/dtadesse)\
**Post date:** [January 29, 2024, 3:36pm UTC](https://forum.biobakery.org/t/formatting-data-for-lefse/6540/1 "2024-01-29T15:36:40Z")

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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

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**Author:** ![Kelsey\_Thompson](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kelsey_thompson/32/65_2.png) [@Kelsey\_Thompson](https://forum.biobakery.org/u/Kelsey_Thompson)\
**Post date:** [February 12, 2024, 9:26pm UTC](https://forum.biobakery.org/t/formatting-data-for-lefse/6540/2 "2024-02-12T21:26:53Z")

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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

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<div class="post-metadata">

**Author:** ![dtadesse](https://avatars.discourse-cdn.com/v4/letter/d/46a35a/32.png) [@dtadesse](https://forum.biobakery.org/u/dtadesse)\
**Post date:** [February 20, 2024, 3:02am UTC](https://forum.biobakery.org/t/formatting-data-for-lefse/6540/3 "2024-02-20T03:02:18Z")

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Thanks Kelsey! I will use MaAsLin.