The bioBakery help forum

Error message on galaxy

Dear LEfSe team,
The input data was provided with make.lefse on mothur and then it was grouped by taxonomy (file attached).
I am trying to run LEfSe and getting an error message in the first step which is: format data to LEfSe:
Traceback (most recent call last):
File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 433, in
feats = add_missing_levels(feats)
File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 242, in add_missing_levels
ff[k] = [sum(a) for a in zip(*[[float(fn) for fn in ff[vv]] for vv in v])]
ValueError: could not convert string to float: Desulfomonile

As far as could get from the message above, it is asking to provide missing values, but when I check the input file, there is none values missing.
Still, there might be something wrong with my input data, I just can not see. However, in the lines reported above, there is no error.
Huge thanks in advance.
Kind regards,
Cristiane
attempt2.txt (281.8 KB)

Hi -
Thanks for providing the input! The 520th row of the file, feature Bacteria|Bacteria|Desulfobacterota|Desulfomonilia|Desulfomonilales|Desulfomonilaceae has Desulfomonile as its abundance for the first sample. Replacing it with a number fixed the issue on my end.
Best,
Siyuan

Huge thanks Siyuan! It totally solved the problem.
Best,
Cristiane