# Issues with LEfSe Galaxy platform

**URL:** <https://forum.biobakery.org/t/issues-with-lefse-galaxy-platform/2356>\
**Category:** LEfSe\
**Created:** [July 12, 2021, 9:48pm UTC](https://forum.biobakery.org/t/issues-with-lefse-galaxy-platform/2356 "2021-07-12T21:48:10Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![fquerdasi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fquerdasi/32/927_2.png) [@fquerdasi](https://forum.biobakery.org/u/fquerdasi)\
**Post date:** [July 12, 2021, 9:48pm UTC](https://forum.biobakery.org/t/issues-with-lefse-galaxy-platform/2356/1 "2021-07-12T21:48:10Z")

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Hi! I am new to LEfSe and the Galaxy platform so I apologize in advance if these have already been addressed elsewhere (I am posting because I have not been able to find answers).

I am using the Galaxy webpage to conduct LEfSe analyses, and am wondering if it is possible to download the results of the analysis in a format that can be read by other applications (e.g., a .txt or .csv file). When I try to download the results of step B) LDA effect size, the file has the extension “.lefse\_internal\_res” and I cannot open it.

Secondly, when I attempt to perofrm step C) Visualize LEfSe results, I obtain the following error:

“Traceback (most recent call last):  
File “/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/./plot\_res.py”, line 151, in   
else: plot\_histo\_hor(params[‘output\_file’],params,data,len(data[‘cls’]) == 2)  
File “/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/./plot\_res.py”, line 54, in plot\_histo\_hor  
if bcl: data[‘rows’].sort(key=lambda ab: fabs(float(ab[3]))\*(cls.index(ab[2])_2-1))  
File “/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/./plot\_res.py”, line 54, in   
if bcl: data[‘rows’].sort(key=lambda ab: fabs(float(ab[3]))_(cls.index(ab[2])\*2-1))  
ValueError: could not convert string to float: not”

The option to report the error via the webpage is not working, so I wanted to post it here instead.

Thank you in advance for any help you can provide!

Best,  
Fran

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**Author:** ![fquerdasi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fquerdasi/32/927_2.png) [@fquerdasi](https://forum.biobakery.org/u/fquerdasi)\
**Post date:** [July 12, 2021, 11:19pm UTC](https://forum.biobakery.org/t/issues-with-lefse-galaxy-platform/2356/2 "2021-07-12T23:19:40Z")

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Never mind on one of the questions – I fixed the error by changing my grouping variables to numeric (1 vs 0) from strings. However, when I attempt to plot the results they do not render on my screen (refreshing the page does not work), and when I download them as .png I get an error when trying to open them. If I select .pdf as the download format, the resulting download is in .png format rather than .pdf. In sum, I am having trouble viewing and downloading the results of the analysis I conducted via the online module.

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**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [July 17, 2021, 12:00am UTC](https://forum.biobakery.org/t/issues-with-lefse-galaxy-platform/2356/3 "2021-07-17T00:00:07Z")

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Hi @fquerdasi ,

Thank you for reaching out to bioBakery. Would it be possible to attach your input file please? I can take a look over it if that sounds good?

Regards,  
Sagun

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**Author:** ![fquerdasi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fquerdasi/32/927_2.png) [@fquerdasi](https://forum.biobakery.org/u/fquerdasi)\
**Post date:** [July 19, 2021, 7:38pm UTC](https://forum.biobakery.org/t/issues-with-lefse-galaxy-platform/2356/4 "2021-07-19T19:38:05Z")

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Hi Sagun,

Thank you for the offer! However, no need, as I ended up figuring out the issues.

Best,  
Fran