That will run the program using all available threads, so should run faster due to the --p-n-threads, it will also output more information to the terminal due to --verbose.
Hopefully your mac should start making some noise because all the cores should be going flat out!
EDIT: if no errors are spat out and the cpu is working then its a waiting game!
Just for completeness, that error means that you have duplicated sample IDs and you need to make sure that they are unique. Perhaps this thread will help in this case.
Its certainly a long time but I wold just keep it running.
Removing chimeras is the last step!
Also I just realized I misread how many reads you have, that length of time seems reasonable assuming you’re running it on slightly better than average consumer hardware.
@chacha, would you be able to share a demux summarize visualization of your demultiplexed seqs here? This would give us something to look at while your dada2 process is churning away. Thanks!
Hi @chacha — it is a bit hard using the screenshot for this, so my estimates might be a bit off, but looking at your data, I would personally consider the following :
I wouldn’t cancel your existing denoise command, but maybe consider experimenting with slightly more stringent truncation values, I think you will see a noteworthy decrease in time. Keep us posted!