ITS extraction error - Missing sequence for record beginning on line 17

I recognize this error from this post. You should be able to run ITSxpress using qiime itsxpress trim-pair instead of qiime q2-itsxpress trim-pair. If that is not the case, maybe there is some problem regarding how you installed ITSxpress. What was your procedure? Maybe solving this solves your original issue: something strange is going on if the proper command doesn't work.

The recommended installing method for ITSxpress, acording to the tutorial, is:

mamba activate qiime2-2024.2
mamba install -c bioconda itsxpress
qiime dev refresh-cache
qiime itsxpress # To check installation

Personally, what I do is directly open the YAML file of the QIIME 2 distribution I'm using, add the latest version¹ and install:

- itsxpress=2.1.3

Rember that, besides itsxpress, we don't need more plugins for running ITSxpress on QIIME 2. ITSxpress is already both standalone and a Q2 plugin.

Best,

Sergio

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¹ 2.1.3 is the latest version as of December 10, 2024