The bioBakery help forum

Issues with LEfSe Galaxy platform

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/”, line 151, in
else: plot_histo_hor(params[‘output_file’],params,data,len(data[‘cls’]) == 2)
File “/shed_tools/”, 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/”, line 54, in
if bcl: data[‘rows’].sort(key=lambda ab: fabs(float(ab[3]))
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!


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.

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?


Hi Sagun,

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