Dada2 [Errno 2] No such file or directory: '/tmp/tmpdftfsbgd'

[thermokarst]

Hi there @Brightbeard!

@Brightbeard

[Errno 2] No such file or directory: ‘/tmp/tmpdftfsbgd’

This looks like your host OS might've cleaned up your temp dir before the job had finished processing.

First off, it looks like you aren't trimming or truncating your reads at all --- this can have a huge impact on DADA2 runtime --- it is a function of the quality of the reads, so by trimming low quality positions, you help reduce the burden applied to the algorithm. If you would like us to weight on on some suggestions for those values, please run demux summarize and post the results here.

@Brightbeard

Due to the long running time, I’ve been backgrounding the process

This can also potentially cause problems with the OS and the tempdir cleanup - it might be worth exploring some other options, like screen or tmux.

You can change the tempdir to a new location that the OS doesn't clean up automatically, see this post for more details:

No space left on device classifier TMPDIR

Hi @arsalane1978! First off, do you have a directory on your machine at /data? You can check by running: $ ls /data If you see something like ls: /data: No such file or directory, then you will first need to make the directory: $ mkdir /data Then, you can export that environment variable: $ export TMPDIR='/data' You can check that the variable is set by running: $ echo $TMPDIR It should display /data. If not, you will need to export it again. Give that a shot and please let us know how…

Let us know how it goes!