Dada2 Error Return Code 1, Paired-End Seqs

[jairideout (Jai Ram Rideout)]

Hi @MSullivan! It looks like you're running QIIME 2 on a Mac and you ran into a problem where macOS cleaned out the system's temporary directory while DADA2 was running (this is why the error message is trying to open a temporary file that no longer exists). We have an open issue tracking this macOS problem (check it out for more details).

There are a couple of workarounds you can try; the easiest may be to set a new TMPDIR environment variable. See @ebolyen's post for instructions:

Error involving temporary file (?) in de-noise DADA2 step

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/…

Additionally, check out @ebolyen's second post about running DADA2 with multiple threads, which can speed up the denoising process quite a bit:

Error involving temporary file (?) in de-noise DADA2 step

Also, to speed things up, you can use --p-n-threads <some number> which will run some of the steps in parallel. (You can set it to 0 to use every CPU).