Missing reference files from the database

[Rafael Ponce]

Hi all,


I installed picrust using:

mamba create -n picrust2 -c bioconda -c conda-forge picrust2=2.6.1

but when I try to run picrust2_pipeline.py I got the following error:

No FASTA file found in specified directory. Expected to find one of:
/home/rafael/anaconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/bacteria/bac_ref/bac_ref.fna.gz
/home/rafael/anaconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/bacteria/bac_ref/bac_ref.fasta.gz
/home/rafael/anaconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/bacteria/bac_ref/bac_ref.fna
/home/rafael/anaconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/bacteria/bac_ref/bac_ref.fasta


In addition to the missing FASTA file, the following expected file(s) could not be found:
/home/rafael/anaconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/bacteria/bac_ref/bac_ref.tre
/home/rafael/anaconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/bacteria/bac_ref/bac_ref.hmm
/home/rafael/anaconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/bacteria/bac_ref/bac_ref.model


Error - missing at least one of the four reference files in this specified directory: /home/rafael/anaconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/bacteria/bac_ref


I searched in the wiki page and this new version is supposed to install the new PICRUST database, right? So I'm not sure why it doesn't work.

I will appreciate if you could give some information how to fix this,

Thanks,

Rafael

[Robyn Wright]

Hi Rafael,

I actually had the same issue and was trying to work out if it was just because I was trying to install in a different environment… so this answers that question. While I work on a proper fix there are a couple of workarounds I can think of:

1. Download the archaea and bacteria folders from default files (archaea and bacteria) and put them into the folder: /home/rafael/anaconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/
2. Install PICRUSt2 from source/Github: instructions here

Robyn

---

From: picrus...@googlegroups.com <picrus...@googlegroups.com> on behalf of Rafael Ponce <biok...@gmail.com>
Sent: Wednesday, April 9, 2025 8:10:41 AM
To: picrust-users <picrus...@googlegroups.com>
Subject: [picrust-users] Missing reference files from the database

 

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[Robyn Wright]

Hi there,

I finally had a chance to properly look into this and it was an issue with the automatic update done by bioconda where it updated most of it, but not where the files were downloaded - it's fixed if you install PICRUSt2 v2.6.2 with bioconda now.

Best wishes,

Robyn