The bioBakery help forum

LefSe error message on galaxy

Downstream analysis and statistics LEfSe
#1

Hello everyone,

I and trying to run LefSe analysis on galaxy but keep getting the error message as below:

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 <module>
    feats = numerical_values(feats,params['norm_v'])
  File "/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py", line 174, in numerical_values
    feats[k] = [float(val) for val in v]
ValueError: could not convert string to float: no

I’ve looked at other posts and change the format but still get the same error.
Please find the sample data attached. Any suggestions will be appreciated. Thanks!

test.txt (1.8 KB)

#2

Hi!

I apologize for the delayed response! I looked at your attached data and I believe this issue is the e- in the numbers. If convert everything to just the numbers, I think this could fix the issue. If you try that and it doesn’t work please let me know!

Best,
Kelsey

#3

were you able to get this to work? I’m getting the same error and can’t figure out what I’m doing wrong with my dataset.

I see below someone commented it was the scientific notation, but I can get a sample file to run with scientific notation so I’m not sure that that is the problem (and I’m not using scientific notation in my current data set)

#4

Hi @henganl2 and @AbbiHern,

I only suggested the scientific notation because when I open the file it automatically converted it and I received no errors when taking that test file running it through Galaxy. The caveat to that is I can replicate the error If I do not assign the first three rows as the subject, class, and subclass. For either of you, are you assigning any row with a character in it to those categories in the format stage? If you are, I am unable to replicate this error and would need a minimally reproducible example. The only time we see this error typically is if there is a row of characters or a random cell of characters in the feature table. Apologies I cannot be of more assistance.

Best,
Kelsey

#5

I understand - I appreciate you being helpful!

I think my problem with my current dataset was that there was a metadata column than wasn’t being used (I have 3 factors). When I delete that, I can get it to run.

Thanks for the input!