HOW TO integrate PICRUST ON QIIME2 plugin ?

Hello,

I run the following command but i get an error message (QIIME2 HAS NO PLUGIN/Command named 'picrust2').

qiime picrust2 full-pipeline \
   --i-table mammal_biom.qza \
   --i-seq mammal_seqs.qza \
   --output-dir q2-picrust2_output \
   --p-placement-tool sepp \
   --p-threads 1 \
   --p-hsp-method pic \
   --p-max-nsti 2 \
   --verbose
How can i integrate picrust2 on qiime 2 ? Could you please communicate to me the appropriate command ?

Thanks

Hello @M_F ,
Did you already install q2-picrust2 plugin? This plugin is not installed with Qiime2, you need to activate Qiime2 environment and install plugin in order to use it.
BTW, here is a nice tutorial in case you missed it.

1 Like

Hi @timanix,

Thanks a lot

Hello @timanix ,

The plugin q2-picrust2 was installed accordingly QIIME 2 Library but how can i activate it ? It seems it's not yet recognized.

I can't run the pipeline with picrust.

Best

Did you install it inside of your qiime environment? Which version of qiime are you running?

Hi @timanix ,

i run qiime2.2021

There are several Q2 versions from 2021 already. Are you using qiime2-2021.2?
Just installed it on my machine:


So, I would suggest to:

  1. Try to install it manually
  2. If your Q2 version is not 2021.2, try to install it and install picrust inside of qiime2-2021.2 version.

Hi @timanix,

Q2 version 2021.2 is already installed. but picrust was activated accordingly
picrust2_pipeline.py .

I have two questions :

  1. how can i generate biom file using qiime2 because i will use the following command ?:

picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 1
2) how can i filter negative controls using qiime2 from fna file to get filtered fna file ?

Thanks

Looks like you want to run picrust2 standalone commands with q2-picrust2.
So, if you started your analysis in Qiime2 and now you have Qimme2 produced files, such as feature-table.qza, rep-seqs.qza, you can directly use them to run q2-picrust2 as described in the tutorial I already linked in my first comment.
If you have a biom files and sequences as a fasta, you should install and use picrust2 standalone version.