After multiple failures to format my data files (some of which were previously successfully formatted), I tried hmp_small_aerobiosis.txt. LefSe failed to format this file too. Below is error message
Dataset generation errors
Dataset 6: A) Format Data for LEfSe on data 5
Tool execution generated the following error message:
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.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: skin
Hello,
I was just able to successfully upload and format the hmp_aerobiosis_small file (attached), would you mind trying it one more time? If it’s still causing problems I’ll put you in touch with the person who maintains our Galaxy server.
Thanks,
Meg hmp_aerobiosis_small.txt (660.1 KB)
I tried Galaxy-Lefse using file that you attached to your email. I tried Firefox, Chrome, Edge. Lefse failed to format data. Here is the error from Edge
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.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: skin
Hello Gurjit,
Typically these issues result from files formatted not in a way lefse expects it.
If you send me your email, I can email you a file that you can use as sample and works.
Best regards,
George Weingart PhD
Huttenhower Lab george.weingart@gmail.com