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 :
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 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 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.
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.
on my laptop ). I would build a new qiime2-2019.1 enviroment. To do this, I'd run