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.
Q2 version 2021.2 is already installed. but picrust was activated accordingly
picrust2_pipeline.py .
I have two questions :
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 ?
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.