I am installing the Q2 on my desktop and I am running in a issue.
The "conda" and "source" commands work fine before I create the qiime-2017.1 environment.
Once I do that, both commands give me the reload error as shown bellow.
The qiime seems to be installed, as I can get all the info when I type "qiime".
I must say it seems to be a problem on my machine, since I have installed and ran Q2 on my notebook. However, I need a more powerful computer to run all my samples.
Any input would be appreciated.
Thanks for your time!
R!
Hmm! Thanks for writing, @rgloreto --- something certainly looks a little strange related to your base conda install.
What happens when you run
$ conda update conda
If that doesn't do anything, you might want to try reinstalling conda, since it looks like something might have gone wrong at that step. Keep us posted!
Any command, including the suggested one, gives me the same error. Again, it only happens after I create the qiime2 environment. Indeed, if only delete the qiime env, the conda commands works again. I have tried re-installing miniconda3 and it works ok until I install qiime2.
However, I managed to get around it by installing miniconda2 instead. I know it is not a solution for the error, but it allows me to continue my work.
Hi @rgloreto! It sounds like you have a workaround (using Miniconda2) but we can continue to debug this if you'd like. We've had success using Miniconda3 and qiime2 -- it's actually the method we use more often than Miniconda2. I suspect it has to do with conflicting versions of Python on your system (could be related to your $PATH environment variable and how Miniconda is being installed). Let me know if you would like to continue to debugging this; I am happy to assist. Thanks!
Great! Here are a series of commands that I'd like you to run in a few different contexts (see below for instructions on when to run them). Some of these commands are expected to fail; please run all of them anyways and send me the complete output.
Debug commands:
echo $PATH
echo $PYTHONPATH
echo $PYTHONHOME
ls -la $HOME/.local/lib
which python
python --version
alias python
which qiime
which conda
conda info -a
conda list
Contexts:
Uninstall Miniconda2 and Miniconda3 completely so that conda does not exist on your system (see these instructions). Open a new terminal, run the debug commands above, and send the output.
Reinstall Miniconda3 following these instructions. Open a new terminal, run conda clean -y --all, and then conda update conda. After that, run the debug commands above and send the output.
Install QIIME 2 2017.11 following these instructions. Before activating the new qiime2 environment, run the debug commands above and send the output.
Activate the qiime2-2017.11 conda environment, run the debug commands above, and send the output.
I know this is a lot of info to request -- hopefully this will give me what I need to figure out what's going on with your installation. Thanks!
@jairideout sorry for the delay.
I will get you all the info as soon I finish the analysis I am running now. I need to get this data to the collaborator. Once it is done - 1 or 2 days from now - I will uninstall the miniconda3 and follow the steps you describe as well as give you the output for those commands you listed. Many thanks for the help! I will get back to you soon.
@jairideout My apologies for the delay.
I visiting my collaborator at the moment but I will get back to you next week.
Again, my apologies for delaying this. I do want to debug this.
