# Need help with humann tool

**URL:** https://forum.biobakery.org/t/need-help-with-humann-tool/4812
**Category:** HUMAnN
**Created:** [February 17, 2023, 3:45pm UTC](https://forum.biobakery.org/t/need-help-with-humann-tool/4812 "2023-02-17T15:45:45Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![Rishav\_Sahil](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/rishav_sahil/32/1963_2.png) [@Rishav\_Sahil](https://forum.biobakery.org/u/Rishav_Sahil)
#### Post date: [February 17, 2023, 3:45pm UTC](https://forum.biobakery.org/t/need-help-with-humann-tool/4812/1 "2023-02-17T15:45:45Z")

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Hello all,

Greetings of the day.  
I am trying to analyze shotgun metagenome data through humann but I am getting an error.  
This is the code that I used:  
humann --input u4.tsv --output result #Here, u4.tsv is the abundance table, It looks like this.

[merged\_abundance\_table\_species.csv](https://forum.biobakery.org/uploads/short-url/pLBmFZ3iTMpTFRgLKxAPJThlQK2.csv) (990 Bytes)

and the error that i am getting is this:  
Process the sam mapping results …  
Traceback (most recent call last):  
File “/home/rishav/anaconda3/envs/seurat4/bin/humann”, line 33, in   
sys.exit(load\_entry\_point(‘humann==3.6’, ‘console\_scripts’, ‘humann’)())  
File “/home/rishav/anaconda3/envs/seurat4/lib/python3.7/site-packages/humann/humann.py”, line 1079, in main  
args.input, alignments, unaligned\_reads\_store, keep\_sam=True)  
File “/home/rishav/anaconda3/envs/seurat4/lib/python3.7/site-packages/humann/search/nucleotide.py”, line 263, in unaligned\_reads  
if int(info[config.sam\_flag\_index]) & config.sam\_unmapped\_flag != 0:  
ValueError: invalid literal for int() with base 10: ‘C27a\_N’

Kindly help regarding this concern.  
I tried to convert my table to numeric also but then also this error is showing

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### Author: ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)
#### Post date: [February 24, 2023, 9:49pm UTC](https://forum.biobakery.org/t/need-help-with-humann-tool/4812/2 "2023-02-24T21:49:13Z")

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Hello, Does your abundance file contain data for multiple samples? If so, if you split it into a single file per sample this should resolve the error you are seeing if the file is of the expected format with a single row for each feature. HUMAnN expects a single file per run with each file representing a single sample.

Thank you,  
Lauren

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### Author: ![Rishav\_Sahil](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/rishav_sahil/32/1963_2.png) [@Rishav\_Sahil](https://forum.biobakery.org/u/Rishav_Sahil)
#### Post date: [February 25, 2023, 2:20pm UTC](https://forum.biobakery.org/t/need-help-with-humann-tool/4812/3 "2023-02-25T14:20:10Z")

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Ok, I try to do as per your suggestion,  
Thanking you  
Rishav Sahil

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### Author: ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)
#### Post date: [February 28, 2023, 6:10pm UTC](https://forum.biobakery.org/t/need-help-with-humann-tool/4812/4 "2023-02-28T18:10:43Z")

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Great! Please post again if you continue to run into issues.

Thanks,  
Lauren