fasnicar
commented
2 years ago Dear Rui, many thanks for reporting this. You can downgrade your python in the phylophlan conda env to a version <3.10.
For instance,
conda install python=3.8
Many thanks, Francesco
Guan06
Hi,
I installed phylophlan 3.0 from bioconda, and tried to download the databases via:
_phylophlan -d phylophlan --databasesfolder ./
But got error message as below: Traceback (most recent call last): File "/home/.conda/envs/phylophlan/bin/phylophlan", line 7, in
from phylophlan.phylophlan import phylophlan_main
File "/home/.conda/envs/phylophlan/lib/python3.10/site-packages/phylophlan/phylophlan.py", line 34, in
import dendropy
File "/home/.conda/envs/phylophlan/lib/python3.10/site-packages/dendropy/init.py", line 25, in
from dendropy.dataio.nexusprocessing import get_rooting_argument
File "/home/.conda/envs/phylophlan/lib/python3.10/site-packages/dendropy/dataio/init.py", line 21, in
from dendropy.dataio import newickreader
File "/home/.conda/envs/phylophlan/lib/python3.10/site-packages/dendropy/dataio/newickreader.py", line 30, in
from dendropy.dataio import nexusprocessing
File "/home/.conda/envs/phylophlan/lib/python3.10/site-packages/dendropy/dataio/nexusprocessing.py", line 31, in
from dendropy.utility import container
File "/home/.conda/envs/phylophlan/lib/python3.10/site-packages/dendropy/utility/container.py", line 357, in
class CaseInsensitiveDict(collections.MutableMapping):
AttributeError: module 'collections' has no attribute 'MutableMapping'
I think it is due to the python version, that in python 3.10, the attribute MutableMapping from the module collections have been removed, but don't know how to fix this problem though..
Many thanks and best, Rui