DADA2 set TMPDIR permanently

Dear,

I got a quite commom problem running dada2,

[No space left on device]

the TMPDIR is full or to small for running a big computational problem as is the denoising on a wide dataset.

So, as suggested in different discussions:


I made a new directory and with:
$ export TMPDIR=’/newdirectory’

I moved the tmp dir to the new one.

My questions are:

  1. Should I define every time that I use qiime the new tmpdir? Is there any way to set it permanently?
  2. When I have done all my jobs, can I empty the tmpdir, deleting all the files?

Thanks

HI @mefistofele82,

First, check out your .bashrc and .bash_profile files. (~/.bashrc). A quick Google turned up a couple of posts for set up from Stack Overflow and Make Tech Easier, but I just grabbed the top result here, so I’d suggest doing more research on your own.

Im not sure if there is an automated clean-up script that does it for you, maybe you could set up a Cron job that would empty it at some pre-set interval. You just want to make sure that the computer isn’t emptying while you’re still running something!

Best,
Justine

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