Unable to format data for LEfSe

Downstream analysis and statistics LEfSe
1

I have tried reformatting my text file a dozen different ways and cannot figure out what is wrong with it. I keep getting this error:

Traceback (most recent call last):
File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 435, in
feats = numerical_values(feats,params[‘norm_v’])
File "/shed_tools/testtoolshed

anyone know what I am doing wrong? I thought it may have been special characters but I have done find and replace for everything I can think of and looked at every single data entry point and they’re all just regular numbers.

2

Hello,
I’m not sure what might be causing the error, but I’m happy to investigate. Is there a datafile you could send me that reproduces the error?
Thanks,
Meg

3

Thank you so much for the offer!

I think my problem was an extra row of metadata. I have 3 factors and this can only handle 2, so I had to delete one row containing the 3rd factor to be able to use this and then it worked!

4

Good to hear!
Best,
Meg