# LefSe Galaxy module not working

**URL:** <https://forum.biobakery.org/t/lefse-galaxy-module-not-working/4733>\
**Category:** LEfSe\
**Created:** [January 31, 2023, 5:15pm UTC](https://forum.biobakery.org/t/lefse-galaxy-module-not-working/4733 "2023-01-31T17:15:52Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![gsidhu](https://avatars.discourse-cdn.com/v4/letter/g/97f17d/32.png) [@gsidhu](https://forum.biobakery.org/u/gsidhu)\
**Post date:** [January 31, 2023, 5:15pm UTC](https://forum.biobakery.org/t/lefse-galaxy-module-not-working/4733/1 "2023-01-31T17:15:52Z")

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After multiple failures to format my data files (some of which were previously successfully formatted), I tried hmp\_small\_aerobiosis.txt. LefSe failed to format this file too. Below is error message

Dataset generation errors

Dataset 6: A) Format Data for LEfSe on data 5  
Tool execution generated the following error message:

Traceback (most recent call last):  
File “/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format\_input.py”, line 435, in   
feats = numerical\_values(feats,params[‘norm\_v’])  
File “/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format\_input.py”, line 174, in numerical\_values  
feats[k] = [float(val) for val in v]  
ValueError: could not convert string to float: skin

I would appreciate if you could lokk into this.

Thanks

Gurjit

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**Author:** ![mishort](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mishort/32/556_2.png) [@mishort](https://forum.biobakery.org/u/mishort)\
**Post date:** [January 31, 2023, 7:04pm UTC](https://forum.biobakery.org/t/lefse-galaxy-module-not-working/4733/2 "2023-01-31T19:04:32Z")

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Hello,  
I was just able to successfully upload and format the hmp\_aerobiosis\_small file (attached), would you mind trying it one more time? If it’s still causing problems I’ll put you in touch with the person who maintains our Galaxy server.  
Thanks,  
Meg  
[hmp\_aerobiosis\_small.txt](https://forum.biobakery.org/uploads/short-url/8bGid9UaAs0YjKFrYfSAPslFjeP.txt) (660.1 KB)

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<div class="post-metadata">

**Author:** ![gsidhu](https://avatars.discourse-cdn.com/v4/letter/g/97f17d/32.png) [@gsidhu](https://forum.biobakery.org/u/gsidhu)\
**Post date:** [January 31, 2023, 7:32pm UTC](https://forum.biobakery.org/t/lefse-galaxy-module-not-working/4733/3 "2023-01-31T19:32:28Z")

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Hi Meg

Thanks for the response.

I tried Galaxy-Lefse using file that you attached to your email. I tried Firefox, Chrome, Edge. Lefse failed to format data. Here is the error from Edge

Traceback (most recent call last):  
File “/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format\_input.py”, line 435, in   
feats = numerical\_values(feats,params[‘norm\_v’])  
File “/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format\_input.py”, line 174, in numerical\_values  
feats[k] = [float(val) for val in v]  
ValueError: could not convert string to float: skin

Regards

Gurjit

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<div class="post-metadata">

**Author:** ![george-weingart](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/george-weingart/32/256_2.png) [@george-weingart](https://forum.biobakery.org/u/george-weingart)\
**Post date:** [February 2, 2023, 5:57pm UTC](https://forum.biobakery.org/t/lefse-galaxy-module-not-working/4733/4 "2023-02-02T17:57:20Z")

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Hello Gurjit,  
Typically these issues result from files formatted not in a way lefse expects it.  
If you send me your email, I can email you a file that you can use as sample and works.  
Best regards,  
George Weingart PhD  
Huttenhower Lab  
[george.weingart@gmail.com](mailto:george.weingart@gmail.com)