Format data for Lefse step error

Downstream analysis and statistics LEfSe
1

Hi there,

I am currently trying to analyse my microbiome data using Lefse. Uploading data went fine, but I keep getting the following error message for the output file of the ‘format data for Lefse’ step:

Traceback (most recent call last): File “/usr/bin/lefse_format_input.py”, line 8, in sys.exit(format_input()) File “/usr/lib/python3.6/site-packages/lefse/lefse_format_input.py”, line 437, in format_input class_sl,subclass_sl,class_h

Could someone please help me with this?

Kind regards,
Vasilisa

2

This was my input file:
Vasilisa lefse male 5 wks.txt (45.6 KB)

3

I’m having the same issue. Did you figure out a solution?

4

Hi ddurgan,

I think after the server maintenance, Lefse now requires you to have a Subclass and Subject in order to work. As our analysis didn’t require either of these, my supervisor and I fixed this issue by adding two empty columns in our input file after the Group column: Subclass and Subject.

Please find my input file that worked attached:
Vasilisa lefse male 5 wks.txt (45.7 KB)

Hope this helps!

Kind regards,
Vasilisa

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