Problems with format data for LEfSe

Dear all:
After uploading the data, after format data foe LEfSe, an error is reported, as follows:

     Traceback (most recent call last):
     File "/shed_tools/", line 435, in <module>
    feats = numerical_values(feats,params['norm_v'])
    File "/shed_tools/testtoolshed

A screenshot of some of the original data is as follows:

What’s the problem and how to solve it?
Thans for any suggestions!

1 Like

Hi @liuyushu

Potential problems areas are:

  1. The version of LEfse is outdated. Use the latest version available from the Main ToolShed instead of the version from the Test ToolShed.

  2. Outputting tabular (text) data from spreadsheet programs can frequently introduce extra unintended characters and corrupt the format. These may not be obvious to find – for example, a soft return (^M) is invisible in plain text files.

  3. If you are working at this Public Galaxy server, it contains much help for usage along with example inputs. Your format appears to be the data that didn’t pass original filters. Huttenhower Lab

You didn’t state where you are working, but if you are not the administrator, contact the admins of the Galaxy server where you are working and ask if they can update the tool or offer usage advice. Or, choose a different public Galaxy server to work at that hosts the tool (all of the usegalaxy.* servers host it as part of the Mothur tool suite): Galaxy Platform Directory: Servers, Clouds, and Deployable Resources