Help with QIIME 2 installation

[JP2018]

Hi, There, I am trying to install the most recent version of QIIME2. However get the following error message and seems the installation is not success. Could you help? THank you!
Preparing transaction: done
Verifying transaction: done
Executing transaction: failed
ERROR conda.core.link:_execute(481): An error occurred while installing package ‘bioconda::bioconductor-genomeinfodbdata-1.0.0-r3.4.1_1’.
LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.0.0-r3.4.1_1
running your command again with -v will provide additional information
location of failed script: /Users/jiepingyang/Applications/miniconda2/envs/qiime2-2018.4/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

Attempting to roll back.

Rolling back transaction: done

LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.0.0-r3.4.1_1
running your command again with -v will provide additional information
location of failed script: /Users/jiepingyang/Applications/miniconda2/envs/qiime2-2018.4/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

(qiime2-2018.4) MacBook-Air:~ $ qiime
-bash: qiime: command not found

[colinbrislawn (Colin J Brislawn)]

Good morning,

Thanks for posting the detailed logs of this error. It looks like this error is associated with conda installed in multi-user mode, or conda installed into the admin account.

Did you install miniconda locally, or did you install it with admin / sudo access? If so you could try using sudo to update conda, or simply install miniconda 3 with into your local account.

I hope this helps!
Colin

[JP2018]

Hi, Colin,
The miniconda2 was installed 1) /Users/jp/Applications/miniconda2:
The python in my computer is 2.7.14. Do I need to install python 3 in my computer in order to install miniconda 3.

Thank you for the quick response!
JP

[JP2018]

I also tried to run
“conda env remove -n qiime2-2018.4”
to remove the the QIIME2 installation, but it showed
“EnvironmentLocationNotFound: Not a conda environment: /Users/jp/Applications/miniconda2/envs/qiime2-2018.4”.
And I did not see the folder on Qiime 2 under miniconda folder, and this is what i have,
Jp-MacBook-Air:miniconda2 jp$ ls
LICENSE.txt envs lib share
bin etc pkgs ssl
conda-meta include python.app
Jp-MacBook-Air:miniconda2 jp$

THanks!

[ebolyen (Evan Bolyen)]

Hi @JP2018

@JP2018

The python in my computer is 2.7.14. Do I need to install python 3 in my computer in order to install miniconda 3.

No, that should work as well.

@JP2018

And I did not see the folder on Qiime 2 under miniconda folder, and this is what i have,

It's one more directory down, you'll see it in the envs directory if it exists.

@JP2018

‘bioconda::bioconductor-genomeinfodbdata-1.0.0-r3.4.1_1

Food for thought: this package can be troublesome as it uses the "post-link" step to download its reference database (I only know that because I've had this issue once myself). You might have just gotten unlucky with your network. Do you still the the error if you run:

conda clean -y --all

and then try reinstalling?

[JP2018]

I tried “conda clean -y --all”. it did not work. I then delete the miniconda from my computer, and reinstall miniconda and QIIME2 again. It works now! Thank you!