DADA2 set TMPDIR permanently

[mefistofele82]

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:

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…

Error no 28 No space left on device with feature-classifier sklearn

I am having the same issue, running the cmd on a 16 cores 64gb RAM computer, and with plenty of space in each partition. Here my cmd and error: classifier …/…/reference_datasets/16S/silva-132-99-nb-classifier.qza --i-reads deblur/16S_repr_seq_deblur_run#2.qza --o-classification 16S_taxonomy2_run#2.qza Traceback (most recent call last): File “/media/nec3_HDD/miniconda3/envs/qiime2-2018.8/bin/qiime”, line 11, in sys.exit(qiime()) File “/media/nec3_HDD/miniconda3/envs/qiime2-2018.8/lib/pytho…

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

[jwdebelius (Justine Debelius)]

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