Hi Matthew,
I waited 48 hours and it was still stuck so I aborted and tried running again with --p-n-threads 0. After almost 24 hours it is still stuck on that last step of Denoise remaining samples…the dada2 denoising worked before I concatenated the R1 and R2 files so do you think there is any way to run my samples without this step? I realized that the hyperlink didn’t transfer in my original post but here is the forum post where I got the idea to concatenate the samples (Problem with demux)