# Format input file for Lefse
**URL:** https://forum.biobakery.org/t/format-input-file-for-lefse/5518
**Category:** LEfSe
**Created:** [June 22, 2023, 6:36pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518 "2023-06-22T18:36:02Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@Josias](https://forum.biobakery.org/u/Josias)
#### Post date: [June 22, 2023, 6:36pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/1 "2023-06-22T18:36:02Z")
Hi,
Even using the website suggested input file, I was unable to pass from the format step: Error:
error
An error occurred with this dataset:
Traceback (most recent call last):
File “/usr/bin/lefse\_format\_input.py”, line 8, in
sys.exit(format\_input())
File “/usr/lib/python3.6/site-packages/lefse/lefse\_format\_input.py”, line 441, in format\_input
feats = add\_missing\_levels(f
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### Author:  [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)
#### Post date: [June 23, 2023, 4:00pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/2 "2023-06-23T16:00:47Z")
Hello @Josias ,
Please make sure that you are passing the subclass and subjectId parameters as well in the lefse galaxy run.
Regards,
Sagun
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### Author:  [@Josias](https://forum.biobakery.org/u/Josias)
#### Post date: [June 24, 2023, 12:17pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/3 "2023-06-24T12:17:19Z")
Dear Sagun,
Thanks for your quick response. Yet, it seems no to be the case. I have running galaxy tools for over one year, facing no major issue. I am having problems with the workflow just now.
Josias
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### Author:  [@Josias](https://forum.biobakery.org/u/Josias)
#### Post date: [June 26, 2023, 12:56pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/4 "2023-06-26T12:56:51Z")
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### Author:  [@Lauren](https://forum.biobakery.org/u/Lauren)
#### Post date: [June 26, 2023, 6:44pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/5 "2023-06-26T18:44:12Z")
I am also having the same issue. I have run Lefse many times in the last 2 years, and like @Josias I am only now running into this error.
I cannot identify any formatting issue on my end.
Please let me know if I can supply any information to help you identify the problem.
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### Author:  [@archaea](https://forum.biobakery.org/u/archaea)
#### Post date: [June 27, 2023, 4:07pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/6 "2023-06-27T16:07:18Z")
Hi,
I have the same problem. I cannot get past the LEfSe formatting step. I used previous files that used to work perfectly on here. I even tried to use the example file that is given on the galaxy module, and it does not work either.
Thanks.
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### Author:  [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)
#### Post date: [June 27, 2023, 5:56pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/7 "2023-06-27T17:56:14Z")
Hello @archaea , @Lauren and @Josias ,
Can you please attach your lefse input file? I can check the formatting from my side. Please note that the galaxy LEfSe version was updated from [v1.1](https://github.com/SegataLab/lefse/releases/tag/1.1) to [v1.1.2](https://github.com/SegataLab/lefse/releases/tag/1.1.2).
Regards,
Sagun
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### Author:  [@archaea](https://forum.biobakery.org/u/archaea)
#### Post date: [June 27, 2023, 6:18pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/8 "2023-06-27T18:18:12Z")
Here is a file that used to work and does not at the moment.
Thanks for your help!
[crbac\_genus\_sex.txt](https://forum.biobakery.org/uploads/short-url/2gWxtus9ZHKwlfgbX3FhOTQ7fN2.txt) (287.3 KB)
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### Author:  [@Josias](https://forum.biobakery.org/u/Josias)
#### Post date: [June 27, 2023, 6:18pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/9 "2023-06-27T18:18:46Z")
[test.txt](https://forum.biobakery.org/uploads/short-url/opscc9Ptav94faiSMG6p2umtgd1.txt) (531.3 KB)
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### Author:  [@Lauren](https://forum.biobakery.org/u/Lauren)
#### Post date: [June 27, 2023, 9:03pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/10 "2023-06-27T21:03:23Z")
My data is working again today for some reason, not sure why if others are still having issues, but it appears fixed on my end for now.
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### Author:  [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)
#### Post date: [June 28, 2023, 5:02am UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/11 "2023-06-28T05:02:19Z")
Hello @Josias ,
Please replace all the “,” with “.” in the input file.
`Error: ValueError: could not convert string to float: '4,34E-01'`
eg. 4,34E-01 =\> 4.34E-01
Regards,
Sagun
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### Author:  [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)
#### Post date: [June 28, 2023, 5:07am UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/12 "2023-06-28T05:07:13Z")
Hello @archaea ,
Can you make sure that you are selecting the all 3 options parameters for input columns i.e.
- Select which row to use as class
- Select which row to use as subclass
- Select which row to use as subject
When you provide the column names for each one of the above options in galaxy LEfSe, your input file works fine.
Regards,
Sagun
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### Author:  [@archaea](https://forum.biobakery.org/u/archaea)
#### Post date: [June 28, 2023, 9:36am UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/13 "2023-06-28T09:36:24Z")
It still isn’t working for me. I have no subclass and subject rows. When I leave it as ‘no subclass’ and ‘no subject’, I get the error message. Should I add empty rows to my input files ?
Thanks.
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### Author:  [@Josias](https://forum.biobakery.org/u/Josias)
#### Post date: [June 28, 2023, 10:46am UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/14 "2023-06-28T10:46:02Z")
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### Author:  [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)
#### Post date: [June 28, 2023, 3:00pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/15 "2023-06-28T15:00:24Z")
Hi @Josias ,
Here is your initial input file(after changes) which works. Please try it out and let me know if any issues.
[test.txt](https://forum.biobakery.org/uploads/short-url/amROmteO3ifTQvSS5H7newPquop.txt) (531.3 KB)
Regards,
Sagun
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### Author:  [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)
#### Post date: [June 28, 2023, 3:02pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/16 "2023-06-28T15:02:17Z")
Hi @archaea,
Yes, both subclass and subject rows are required parameters. Try adding empty rows please.
Regards,
Sagun
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### Author:  [@Josias](https://forum.biobakery.org/u/Josias)
#### Post date: [June 28, 2023, 3:32pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/17 "2023-06-28T15:32:26Z")
Great Sagun!
It really worked on my end, as well. Now I need to work on my own file. So, could you please inform was was wrong with the “test.txt”?
regards
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### Author:  [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)
#### Post date: [June 28, 2023, 4:51pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/18 "2023-06-28T16:51:59Z")
Hello @Josias ,
I replaced all the “,” (commas) with “.” (dot) for you input file that worked out for me.
Regards,
Sagun
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### Author:  [@archaea](https://forum.biobakery.org/u/archaea)
#### Post date: [June 28, 2023, 6:58pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/19 "2023-06-28T18:58:05Z")
Yes it works now. FYI, empty rows don’t work, they have to be filled.
Thanks!
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### Author:  [@hina](https://forum.biobakery.org/u/hina)
#### Post date: [June 30, 2023, 12:45am UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518/20 "2023-06-30T00:45:09Z")
Hlo guys, i am running the same problem. It’s not working for me also. Can someone tell me what’s the problem in my file also?
[fecal galaxy3.txt](https://forum.biobakery.org/uploads/short-url/8LSk3GeYCZGC2NGczzMNFi5RbaB.txt) (41.7 KB)
I have run this file one time and it worked but now its not working. couldn’t pass formating in galaxy.
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