ValueError starting humann2


I used the humann2 tool previously for my clinical-based data analyses. However, when I wanted to use it again a few months later, it did not work anymore. Consequently, I re-installed humann2 and the required databases but I still get the following error message, when I try to run humann2:

Decompressing gzipped file …

Running …

Traceback (most recent call last):
File “/miniconda3/bin/humann2”, line 11, in
File “/miniconda3/lib/python2.7/site-packages/humann2/”, line 906, in main
custom_database = prescreen.create_custom_database(config.nucleotide_database, bug_file)
File “/miniconda3/lib/python2.7/site-packages/humann2/search/”, line 93, in create_custom_database
ValueError: invalid literal for float(): 2|1239|91061|186826|1300|1301|2803

Do you have a bit of advice on what I can do about it?

Thank you very, very much in advance!

Kind regards,


Hello Marie, Sorry for the slow response. It looks like your HUMAnN v2 version is a bit out of sync with your MetaPhlAn v2 version. If you update your HUMAnN v2 version (to v2.8.1) it should resolve the error you are seeing.

Thank you,