Plugin error from dada2: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more. See above for debug info.

[Nicholas_Bokulich]

Welcome to the forum, @peter_baas!
Looks like you are having the same issue described here. See this post for a potential solution:

Return code 1 running DADA2 with single-end PGM/Ion torrent data

Wow, that is a lot of threads! Looks like you are running out of space, likely in your $TMPDIR. You will want to change that env var to another location with more disk space available (I suggest contacting your sys admin for guidance).

Let us know how that goes