Hi @Mandy,
Thanks for providing your output files and commands, they are certainly helpful!
From looking at your dada2 result summary table it looks as though almost all of your reads are failing to merge, this is because your reads do not overlap based on your truncating parameters. This topic has been extensively covered in the forum, please have another through, keeping an eye out on keywords like dada2, overlap, merging etc.
One example is here or here, keep in mind min overlap for merging is now 12 nts (not 20). Have a read through those and see if you can figure out optimum truncating parameters and let us know if you are still having issues.
Good luck!
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