but the issue was closed; it is a real bug, though.
I’m having the same error and couldn’t find any solution yet…
Update: I fixed it by modifying the script following this:
“In Python 3,
dict.iteritems was renamed to
dict.items . You should do this renaming in your code as well. In Python 2,
dict.items works too, though this will give back a list of items, whereas
dict.iteritems in Python 2 (and
dict.items in Python 3) gives back a generator, enabling low-memory looping over the items.”
I had a second issue, after running the humann_genefamilies_genus_level script my output was not simplified at the genus level. In my case, I’m using a customized database based on GTDB for the tax screening which is giving me a higher number of mapped reads. However, my output looks like this (it uses a “;” to separate genus from species)
while humann’s output by default looks like this (it uses a “.” to separate genus from species)
I replaced that “;” for a “.” using sed and it worked perfectly.
Hope this helps.