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 \
How can i integrate picrust2 on qiime 2 ? Could you please communicate to me the appropriate command ?
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.
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.
Did you install it inside of your qiime environment? Which version of qiime are you running?
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:
- Try to install it manually
- If your Q2 version is not 2021.2, try to install it and install picrust inside of qiime2-2021.2 version.
Q2 version 2021.2 is already installed. but picrust was activated accordingly
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.
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