Hey @adrian,
It looks like you ran into a limitation of OS X. We've seen this before and what is happening is your computer is automatically deleting data from its temporary directory that is 3 days old.
The solution is to run the command with a different temporary directory set:
# Make a directory to use for temporary storage
mkdir qiime2-tmp/
# Set that directory as our temporary directory for this session
# (this variable only lasts for as long as the terminal exists)
export TMPDIR="$PWD/qiime2-tmp/"
# Run your command again
qiime dada2 denoise-single \
--i-demultiplexed-seqs demux-single-end.qza \
--p-trim-left 0 \
--p-trunc-len 200 \
--o-representative-sequences rep-seqs-dada2.qza \
--o-table table-dada2.qza
Unfortunately you will need to wait another 6 days for the results. But it should complete successfully since you made it to the end the first time.
Once it has completed you can delete qiime2-tmp or keep it as you see fit.
Sorry we don't have a better solution than this at the moment 