The bioBakery help forum

Lefse bug fix request

Hi,

I’m trying to run the first step of LEfSe microbiome analysis from Huttenhower lab on the left menu, running:

LEfSe: A) Format data for LEfSe

I’m getting the following error for the last two days:

“Tool request failed
Uncaught exception in the exposed API method:”

It worked just fine last week. Can you please let me know how to correct this issue?

Many thanks in advance

Hi Nevenka !
Can you try to run the sample lefse file that we provide and let me know if it works ?
I am posting the file gere, just in case …
Also, how big is the file that you are trying to process?
And: Can you compare the internal structure of your file to the sample file we provide ?
Let me know,
Best regards,
George Weingart PhD
Huttenhower Lab
73.txt (82.9 KB)

Hi Nevenka,
I saw two problems:

  1. The third row does not have all the columns
  2. The row names have some problem - for example - row 61 has double quotes.
    I replaced the rownames with generic a1…a101 and ran it successfully.

Hope this helps.
Enclosed a text file that works as well as screen print of a successful run.
Best regards,
George
test2.txt (146.2 KB)

1 Like

Thank you!! I will check all the names again, and fix it they appeared fine in Excel.