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

(Anna Williford) #1

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

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(Matthew Ryan Dillon) #2

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…

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(Anna Williford) #3

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!

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(Matthew Ryan Dillon) #4

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…

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(Matthew Ryan Dillon) #5

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

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(Anna Williford) #6

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

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