Do not use /tmp as a scratch space. These directories are not really designed for the size of TMP files that most pipelines generate. You should re-assign temp file generate to
or a space in your lab's data directory
Please remember to delete temporary files when your jobs finish.
There are multiple things that need to be done to reset the TMP directory depending on what programs you are using.
- Set TMPDIR in your bashrc or profile or whatever sets environment variables
- For java programs set -Djava.io.tmpdir=XXX
- For PICARD set TMP_DIR=XXX
Please note that files in /scratch or /fscratch that haven’t been touched in 30 days will be deleted.