ValueError when trying to run humann2

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Marie P

Jan 4, 2020, 9:53:10 AM1/4/20
to HUMAnN Users

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 <module>
  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,


Lauren McIver

Jan 6, 2020, 3:21:06 PM1/6/20
to HUMAnN Users
Hello Marie - It looks like you might possibly have an older version of HUMAnN2 installed with a MetaPhlAn2 version that is not compatible. Would you update to the latest version of HUMAnN2 using either pip or the biobakery conda recipe? I think this should resolve the error you are seeing.


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Marie P

Jan 7, 2020, 3:24:17 PM1/7/20
to HUMAnN Users
Hello Lauren,

thank you very much for your reply! I solved the problem today by removing and re-installing anaconda. Then, I re-installed metaphlan2, humann2 and all databases and now it worked fine!

Thanks again!

All the best,


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