Issue denoising in PD mouse tutorial

Technical Support
1

I’m doing the PD mouse tutorial using qiime 2 version 2025.10 with miniconda 3 in a WSL running Ubuntu 24.04.1 (I don’t know if any of that is phrased properly). When I run this denoising script as given in the tutorial text:

qiime dada2 denoise-single
--i-demultiplexed-seqs ./demux_seqs.qza
--p-trunc-len 150
--o-table ./dada2_table.qza
--o-representative-sequences ./dada2_rep_set.qza
--o-denoising-stats ./dada2_stats.qza

I get this error:

There was a problem with the command:

(1/1) Missing option ‘– o-base-transition-stats’. (“–output-dir” may also be used)

First off, how do I fix it to keep working through the tutorial? More importantly, what does this mean so I know what to do if I run into a similar error in the future?

I tried this in case the trim was important:

qiime dada2 denoise-single \
--i-demultiplexed-seqs ./demux_seqs.qza \
--p-trim-left 0 \
--p-trunc-len 150\
--o-table ./dada2_table.qza 
--o-representative-sequences ./dada2_rep_set.qza 
--o-denoising-stats ./dada2_stats.qza

and it threw the same error. Thanks for your help!

2

Hello @spark123,

Welcome to the forums! :qiime2:

Looks like you are using a newer version of qiime (2025.10) with an older tutorial:
https://docs.qiime2.org/2024.10/tutorials/pd-mice/

Here's an updated tutorial for 2025.10,

You can see this example includes the extra option --o-base-transition-stats

qiime dada2 denoise-paired \
  --i-demultiplexed-seqs demux.qza \
  --p-trim-left-f 0 \
  --p-trunc-len-f 250 \
  --p-trim-left-r 0 \
  --p-trunc-len-r 250 \
  --o-representative-sequences asv-seqs.qza \
  --o-table asv-table.qza \
  --o-denoising-stats denoising-stats.qza \
  --o-base-transition-stats base-transition-stats.qza

And once you add that option, it won't be missing anymore!

EDIT: There is a brand new visualization plugin for looking at these results.

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