Problem using LEfSe on Galaxy - can't format data for LEfSe

Downstream analysis and statistics LEfSe
1

I am new to LEfSe and am trying to do a LEfSe analysis for a microbial dataset I have, and I seem to be having difficulty getting LEfSe to read in my file (can’t seem to attach as a new user) and format it for analysis. I can upload my File into Galaxy, but then I get stuck. Unfortunately, the link to download the example LEfSe input file in the explanation of the steps results in a 404 error.

Once I hit “Execute” on the dialog box to Format Data for LEfSe, I get this error (I’ve tried various options in all places in the drop-down boxes to no avail):
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

I’ve tried to google the error, and all that comes up are unresolved questions in various forums - one answer suggests that the problem arises from special characters being in the metadata file, but my file does not have special characters.

I’d really appreciate some guidance!

Hope you are all safe and well,
Alissa

[Here’s the input file I can’t seem to upload]

sample AHC01 AHC02 AHC03 AHC04 AHC05 AHC06 AHC07 AHC08 AHC09 AHC10 AHC11 AHC12 AHC14 AHC15 AHC16 AHC17 AHC18 AHC19 AHC20 AHC21 AHC22 AHC23 AHC25 AHC26 AHC28 AHC29 AHC30 AHC32 AHC33 AHC34 AHC35 AHC38 AHC39 AHC40 AHC41 AHC43
Sampling_ID C3MB C2MB C3UB C1UB C1MB C2UB C1LB C2LB R2MB R1UB C3UR C1MR C2UR R2LB C3LB R3UB R3MB E2MB E1UB R2UB E3MB E1MB E3UB E3LB R3LB R1MB R2UR R2LR E2UR E3UR R1UR R2MR R3UR R3LR E3MR E2MR
Depth Middle Middle Upper Upper Middle Upper Lower Lower Middle Upper Upper Middle Upper Lower Lower Upper Middle Middle Upper Upper Middle Middle Upper Lower Lower Middle Upper Lower Upper Upper Upper Middle Upper Lower Middle Middle
Sample_Type Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Rhizosphere Rhizosphere Rhizosphere Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Bulk_Soil Rhizosphere Rhizosphere Rhizosphere Rhizosphere Rhizosphere Rhizosphere Rhizosphere Rhizosphere Rhizosphere Rhizosphere
ade5092696cca194ca857a05b9718444 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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2

Hi,

Thanks for providing the input! Standard input for LEfSe shouldn’t have sample ID rows (example input) and I think that might be what’s causing the issue. Taking the first two rows out makes formatting run successfully.

Thanks!
Siyuan

3

Hi Siyuan,

I have the same problem of Alibba,
I got this error report

"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”

I eliminated all the special characters after reviewed your example.
Lefse_VOJ|690x430
Lefse_VOJ_2|690x429

Thanks in advance,
Vanessa

4

Hi -
It’s not clear to me what’s causing the issue. I did notice repeated features (multiple “Bacteria” rows), which I think LEfSe does not expect and could be problematic? If you’d like, you can email an example input to siyuanma@g.harvard.edu.

1 Like
5

Greetings,

i am using the example input file but constantly having this error.
Traceback (most recent call last):
File “/usr/bin/lefse_format_input.py”, line 10, in
from importlib.metadata import distribution
ModuleNotFoundError: No module named ‘importlib.metadata’

6

Hi @Mahrukh_Butt,

I believe the error that you are getting is due to our transition to python3 on Galaxy. LEfSe is a tool not under current development and thus we needed to revisit the code base to get it to work with python3. We will let everyone know when we have updated this in Galaxy.

In the meantime, you can use MaAsLin in R to complete a complementary task.

Best,
Kelsey

7

Greetings,

Thank you so much for replying. Can you tell me an estimate of how long it will take?

Best Regards