How can I run this step, when I get the overview of the read quality?

[yangyue]

I'm using the tutorial of QIIME2 Moshpit version 2025.4, and I'm sure I've finished the "[Data retrieval]", but I want to know how "demux summary" works, the code as following:

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My warnings as below:

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[timanix (Timur Yergaliyev)]

Hello!

@yangyue

I'm using the tutorial of QIIME2 Moshpit version 2025.4, and I'm sure I've finished the "[Data retrieval]",

Assuming that you are just training and using the same commands as in the tutorial, the outputs should be...

mosh fondue get-all \
    --i-accession-ids ./cache:ids \
    --p-email YOUR.EMAIL@domain.com \
    --p-threads 5 \
    --p-retries 5 \
    --o-paired-reads ./cache:reads_paired \
    --o-metadata ./cache:metadata \
    --o-single-reads ./cache:reads_single \
    --o-failed-runs ./cache:failed_runs \
    --verbose

... either ./cache:reads_paired or ./cache:reads_single

You can try ./cache:reads_paired first and if there is nothing try ./cache:reads_single.

If you modifyed the abovementioned command, make sure that you use the same tag for the following command you run.

Best,

[yangyue]

Thank you!
It is a common point I always neglect. I think it may a common phenonmenon every Qiime2 tutorial user likes to paste and use the code without thinking when they first training their new Qiime2 skills.