picrust2_pipeline.py error

Sayed Mostafa

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Oct 25, 2021, 5:14:56 AM10/25/21

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Hello everyone

I installed PICRUST2 from bioconda, via the following two commands.

conda create -n picrust2 -c bioconda -c conda-forge picrust2=2.4.1 -y

conda activate picrust2

and then the environment was successfully activated.

However, when I tried to run {picrust2_pipeline.py -s dna-sequences.fasta -i feature-table.biom -o picrust2_out_pipeline -p 12 -r /mnt/c/BIO1/miniconda3-1/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref --in_traits COG,EC,KO,PFAM,TIGRFAM} command, I got an error {picrust2_pipeline.py: command not found}.

I wish you help me in this
Thanks in advance

BR

Gavin Douglas

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Oct 25, 2021, 5:58:51 PM10/25/21

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Hi there,

What was printed to the console when you ran the conda create command? It seems like the environment was not created properly so there was likely an error message at some point.

Cheers,

Gavin

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Sayed Mostafa

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Oct 26, 2021, 4:32:22 AM10/26/21

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Thank you so much for your consideration.

I deleted the environment and re-created it again, and then the command worked well. Thanks for your help.