Need help with humann tool

Microbial community profiling HUMAnN
1

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 (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

2

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

3

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

4

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

Thanks,
Lauren