Question: Problems with LEfSe tool
gravatar for anabgs
4 months ago by
anabgs10 wrote:


I have problems with LEfSe tool since a long time.

First of all, the server takes a lot of time to load up my dataset. And then, when I try to use the LEfSe tool, a window appears saying: "uncaught error"

What can I do?



error galaxy lefse • 208 views
ADD COMMENTlink modified 4 months ago by nele.Demeester10 • written 4 months ago by anabgs10
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The tool was recently upgraded at Galaxy Main So, make sure that you are using the most current version. For data uploads, Upload/FTP, in general, has been a bit slower but we are working to improve that near-term.

A Galaxy Training Network (GTN) tutorial includes this tool with example usage in combination with the Mothur tools:

For more usage help, the tool also has a wiki and google group:

There are no known current issues with the LEfSe version hosted at Galaxy Main, but if there are any new ones discovered, that you cannot figure out what might be going wrong based on the help above, we can help (including determining if this is a usage versus tool/server problem. If you have problems at Galaxy Main, or can reproduce the problem there, a bug report can be sent in for review. If the problem occurs at job submission, and no error dataset is produced, a shared history link can be sent in. Be sure to note the datasets involved, the tool settings with inputs filled in (screenshots would be good), so we can reproduce the problem. A link to this Biostars post should be included.

How-to is explained in this prior post (I see your comment there). And this is the direct link to the Support FAQ with the same details:

If you are working at a different public Galaxy server, the administrators of that server can be contacted to find out if this is an input or server-side/tool problem. Contact information is generally on the home page of the server. Some public Galaxy servers also post contact information here:

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson25k

Upvote! 0 gravatar for nele.Demeester 1 hour ago by nele.Demeester • 0


I have the same problem. If I am using the Galaxy Main, I can not use a *.txt file for Lefse? I do not use Mothur, so I would like to use my txt.file as I did in the previous version of the tool.

Thanks in advance, Nele

ADD REPLYlink written 4 months ago by nele.Demeester10


There is an older version of the tool (last updated 2015) in the Galaxy Main ToolShed here:

That is for use in a local, docker, or cloudman Galaxy. Whether it still functions or not I don't know, but if you have problems with it, the tool authors can be contacted through the tool shed (login in/create an account, go to tool, use Repository Actions > Contact author).

Other public servers can also be reviewed - some host this tool but I'm not sure which tool version, you'll need to check:

Try this one first:


ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k

Thanks a lot! It is still working here: Best regards, Nele

ADD REPLYlink written 4 months ago by nele.Demeester10

Oh, it's true. Thanks a lot!!!

It is just what I needed.

Best regards,


ADD REPLYlink written 4 months ago by anabgs10
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