Anaconda PYTHONPATH Issue

User Support
1

HI all,
I am not very familiar with conda and python and I got stuck during Qiime2 installation. I follow all the steps from the "instalation Qiime2". It looks like instalation went well, however after 'source activate qiime2' I run 'qiime' and got this error:
Your PYTHONPATH points to a site-packages dir for Python 2.x but you are running Python 3.x!
PYTHONPATH is currently: "/usr/local/lib/python2.7/site-packages:"
You should unset PYTHONPATH to fix this.

Could you help me how to fix that, please?
Thanks
Daniel

2

Hi @latild, sorry to hear that you are running into trouble. Looks like something might be strange with your conda installation. It would be helpful to get a little more info about your installation/environment. Can you run the following terminal commands and send us the output?

$ conda info

and

$ echo $PYTHONPATH

Feel free to just reply directly to this message. Thanks!

3

Thanks for your reply. I really appreciate your help.

Here are the output for conda info:
Current conda install:

GIs-Mac-Pro:~ gibugs$ conda info
Current conda install:

           platform : osx-64
      conda version : 4.2.13
   conda is private : False
  conda-env version : 4.2.13
conda-build version : not installed
     python version : 2.7.12.final.0
   requests version : 2.12.1
   root environment : /Users/gibugs/miniconda  (writable)
default environment : /Users/gibugs/miniconda
   envs directories : /Users/gibugs/miniconda/envs
      package cache : /Users/gibugs/miniconda/pkgs
       channel URLs : https://repo.continuum.io/pkgs/free/osx-64
                      https://repo.continuum.io/pkgs/free/noarch
                      https://repo.continuum.io/pkgs/pro/osx-64
                      https://repo.continuum.io/pkgs/pro/noarch
        config file : None
       offline mode : False

echo $PYTHONPATH
/usr/local/lib/python2.7/site-packages:

I have also installed MacQiime.

Best,
Daniel

4

Hi @latild, looks like your $PYTHONPATH is the culprit! Please see this page for more details:

http://conda.pydata.org/docs/troubleshooting.html#resolution-for-python-packages-make-sure-you-have-not-set-the-pythonpath-or-pythonhome-variable

For your current terminal session you can run unset PYTHONPATH and that should take care of things.

5

Thank you! I still have many things to learn.

1 Like
6

PYTHONPATH is used by the python interpreter to determine which modules to load.

PATH is used by the shell to determine which executables to run.

More on...Python Path

1 Like