Hi, I am experiencing the same issue posted previously: https://groups.google.com/g/humann-users/c/w_WrMQlGZWE but can’t come to a resolution.
I followed the steps in the documentation under Legacy databases here: GitHub - biobakery/humann at 2.9
I get stuck at step 2:
[tc6463@gadi-login-06 humann1]$ humann2_humann1_kegg --ikoc humann_legacy-0.99b/data/koc.gz --igenels humann_legacy-0.99b/data/genels.gz --o legacy_kegg_idmapping.tsv
Program started
ete2 is not installed and thus we cannot provide the full taxonomy for the bug, providing only the name
Traceback (most recent call last):
File “/home/562/tc6463/.local/bin/humann2_humann1_kegg”, line 11, in
load_entry_point(‘humann2==2.8.2’, ‘console_scripts’, ‘humann2_humann1_kegg’)()
File “/usr/lib/python3.6/site-packages/pkg_resources/init.py”, line 476, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File “/usr/lib/python3.6/site-packages/pkg_resources/init.py”, line 2700, in load_entry_point
return ep.load()
File “/usr/lib/python3.6/site-packages/pkg_resources/init.py”, line 2318, in load
return self.resolve()
File “/usr/lib/python3.6/site-packages/pkg_resources/init.py”, line 2324, in resolve
module = import(self.module_name, fromlist=[‘name’], level=0)
File “/home/562/tc6463/.local/lib/python3.6/site-packages/humann2/tools/humann2_humann1_kegg.py”, line 200, in
for OrgId, OrgIdName in CommonArea[‘dOrgIdOrgName’].iteritems():
AttributeError: ‘dict’ object has no attribute ‘iteritems’
I have installed ete2 with the following command:
[tc6463@gadi-login-03 humann1]$ pip2 install ete2 --user
Requirement already satisfied: ete2 in /home/562/tc6463/.local/lib/python2.7/site-packages
How should I install ete2?
Thanks!
Tracy