The bioBakery help forum

Error Message for File Format

Hi, I received the following error message for my OTU table while formatting. What does it mean? I thought I made an exact txt file for the LEfSe application.

Thank you!

Traceback (most recent call last):

File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 429, in

class_sl,subclass_sl,class_hierarchy = get_class_slices(zip(*cls.values()))

Fil

Hi -

Sorry for the late response! If you haven’t resolved this, would you mind sharing the input file? You can also reach me at siyuanma@g.harvard.edu if concerned about data safety.

Best,
Siyuan

Hi @sma
I am getting the same error while trying to do LFSe from the galaxy platform.
test1.txt (1.0 KB)

I have attached a test file. Please let me know what is causing that error so that I can edit my input file.

Thanks
Saraswati Awasthi

Hi Saraswati,
I was able to get your data to format/run correctly after deleting an empty line or two at the end of the file. Not sure why that creates problems, but if you delete the empty lines it will run.
I hope that helps, and @Celine maybe something similar is going on with your dataset?
Best,
Meg