MinPath12hmp.py:804 error humann3

[franzosa]

The initial issue posted here was discussed here:

No species identified and empty pathway files created

Hello, I received this message humann v3.7 MetaPhlAn version 3.0.9 (17 May 2021) Bowtie2 version 2.2.3 home/kbrokordt/miniconda3/lib/python3.12/site-packages/humann/quantify/MinPath12hmp.py:804: SyntaxWarning: invalid escape sequence ‘\d’ m = re.match(‘[1]+(?P\d+)’, aline) /home/kbrokordt/miniconda3/lib/python3.12/site-packages/humann/quantify/MinPath12hmp.py:804: SyntaxWarning: invalid escape sequence ‘\d’ m = re.match(‘[2]+(?P\d+)’, aline) Output files will be written to: /home/kbroko…

It’s due to a change in Python’s regex engine in v3.12. If you install HUMAnN in an environment based on an earlier Python version it should resolve this error.