Installing qiime2-2019.1 environment : Fatal Python error: Py_Initialize: can't initialize sys standard streams

Hi,
I am trying to install qiime2 on Linux with Anaconda3 previously installed.
After this command:
$ conda env create -n qiime2-2019.1 --file qiime2-2019.1-py36-linux-conda.yml

Many packages get through, but eventually, I get this:

##############
Executing transaction: - dbus post-link :: /etc/machine-id not found …
dbus post-link :: … using /proc/sys/kernel/random/boot_id

\ Fatal Python error: Py_Initialize: can’t initialize sys standard streams
Traceback (most recent call last):
File “/home/annawill/anaconda3/lib/python3.7/_bootlocale.py”, line 35, in getpreferredencoding
if sys.flags.utf8_mode:
AttributeError: ‘sys.flags’ object has no attribute ‘utf8_mode’

ERROR conda.core.link:_execute_post_link_actions(658): An error occurred while installing package ‘conda-forge::widgetsnbextension-3.4.2-py36_1000’.
LinkError: post-link script failed for package conda-forge::widgetsnbextension-3.4.2-py36_1000
running your command again with -v will provide additional information
location of failed script: /home/annawill/anaconda3/envs/qiime2-2019.1/bin/.widgetsnbextension-post-link.sh
==> script messages <==
Fatal Python error: Py_Initialize: can’t initialize sys standard streams
Traceback (most recent call last):
File “/home/annawill/anaconda3/lib/python3.7/_bootlocale.py”, line 35, in getpreferredencoding
if sys.flags.utf8_mode:
AttributeError: ‘sys.flags’ object has no attribute ‘utf8_mode’

Attempting to roll back.

failed
ERROR conda.core.link:_execute(568): An error occurred while installing package ‘conda-forge::widgetsnbextension-3.4.2-py36_1000’.
LinkError: post-link script failed for package conda-forge::widgetsnbextension-3.4.2-py36_1000
running your command again with -v will provide additional information
location of failed script: /home/annawill/anaconda3/envs/qiime2-2019.1/bin/.widgetsnbextension-post-link.sh
==> script messages <==
Fatal Python error: Py_Initialize: can’t initialize sys standard streams
Traceback (most recent call last):
File “/home/annawill/anaconda3/lib/python3.7/_bootlocale.py”, line 35, in getpreferredencoding
if sys.flags.utf8_mode:
AttributeError: ‘sys.flags’ object has no attribute ‘utf8_mode’

Attempting to roll back.

Rolling back transaction: done

LinkError: post-link script failed for package conda-forge::widgetsnbextension-3.4.2-py36_1000
running your command again with -v will provide additional information
location of failed script: /home/annawill/anaconda3/envs/qiime2-2019.1/bin/.widgetsnbextension-post-link.sh
==> script messages <==
Fatal Python error: Py_Initialize: can’t initialize sys standard streams
Traceback (most recent call last):
File “/home/annawill/anaconda3/lib/python3.7/_bootlocale.py”, line 35, in getpreferredencoding
if sys.flags.utf8_mode:
AttributeError: ‘sys.flags’ object has no attribute ‘utf8_mode’
#######

Thank you for your help!
Anna

Hmm, that is a new one to me… Have you tried again today? It is possible there was a bad build of something on conda…

Hi Matthew,
Tried again, exactly the same problem…
Any fix is much appreciated, I am running analysis on mac now, but dada2 takes so long…My Linux is more powerful, hoping to get it running!

Thank you!

The error appears to be related to your anaconda installation — maybe make sure everything is up to date there? I don’t really have any other suggestions — as best I can tell this isn’t really something we can fix, since it doesn’t appear to be related to QIIME 2 — sorry, I know that answer isn’t awesome, just want trying to warn you…

Oh, maybe also run env and share that with us - that might help with diagnosing…

Thank you, I removed Anaconda3 and started with Minoconda, looks good for now!
qiime --help does not report any errors

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