Hey @apzlo,
It looks like dada2 wasn't able to find one of your forward reads (16_S11_L001_R1_001.fastq.gz). Another user is also having a similar issue (but with a missing reverse read file).
Right now we aren't quite sure what is going on, so we're interested in understanding what is inside of the artifact demux-paired-end.qza. Would you be able to do the following:
qiime tools export (path to demux-paired-end.qza) --output-path debug-demux/
and give use the results of:
ls debug-demux/
and we can get started from there, thanks!