PlugIn error with Picrust

picrust
conda

(Kat) #1

Hi,

I am fairly new to using QIIME 2 but wanted to use the PiCRUST2 plug. I therefore installed (successfully) QIIME 2 (version 2019.1) using conda and then used the code described at :

https://library.qiime2.org/plugins/q2-picrust2/13/

The only modification I made was for the version of QIIME 2.

The installation of PICRUST 2 seemed to have worked as I received a message to say that this was successful.
I then went to add the plugin using the q2-picrust2-0.0.2.zip
The python script seemed to run but then when I went to check using
qiime info
I received the following error message:

File “/Applications/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_picrust2-0.0.2-py3.6.egg/q2_picrust2/_full_pipeline.py”, line 6, in <module>

from q2_types.feature_table import FeatureTable, Frequency

ModuleNotFoundError: No module named 'q2_types’

I checked in the QIIME folder and noticed that several plug ins had been removed from the environment (including q2_types). I therefore uninstalled QIIME 2 and repeated the installation only to find the same error and the same loss of QIIME packages. I would be grateful for advice on how to fix this problem.

I am working in macOS Mojave v10.14.

With thanks,
Kat


(Justine) #2

Hi @Katty8,

I think you have an enviromental conflict. The picrust2 plugin assumes you’re working in a qiime2-2018.11 enviroment.

However, the beautiful thing about conda is that it lets multiple enviroments exist along side eachother. (Trust me, I only have about 5 versions of :qiime2: on my laptop ). I would build a new qiime2-2019.1 enviroment. To do this, I’d run

conda remove --name qiime2-2019.1 --all

And then follow the installation instructions to build a new one.

Then, I’d also install a new conda enviroment for qiime2-2018.11 using the earlier documnetation. (It will ask you on every page is this is what you want. You do.) Finally, install the PICRUSt files in your qiime2-2018.11 enviroment.

To keep them seperate, you just run a different command. So, if you want the qiime2-2019.1, you’ll run

conda activate qiime2-2019.1

And, when you want the enviroment with PICRUSt, you can run

conda activate qiime2-2018.11

Usually, when Im working on a project with multiple environments, I make a note on the top of my script or jupyter notebook so I know that this is supposed to be run in whichever environment. It also makes preserving and citing easier later.

Best,
Justine


(Kat) #3

Thank you so much Justine for your rapid and correct response! This makes complete sense. I had not considered the version compatibility as a potential issue but I see why it would cause a problem. I have reinstalled the 2019 version separately and will now add the 2018.11 version. It is taking a little while to finish but once I have tested this environment with PiCrust I will confirm that you were right.


(Kat) #4

Hi again!
Just an update to say that PiCrust is now running correctly with the test data loaded. Thank you so much for your timely support.