Documentation
Background Jobs

Background Jobs

Running things in the background

If you run things interactively (e.g. calling a program directly, running a script), disconnecting from your terminal session will prematurely terminate the program/script. Why would you disconnect?

  • accidentally close the terminal window
  • computer shuts off unexpectedly
  • internet outtage So, there are best-practices to make sure that programs will continue to run in the event of unexpected disconnections.

with nohup

  • Run commands in the background (i.e. so that you can disconnect and the process will continue running) using nohup. For example, a process normally run with the command:
program argument1 argument2

would be run with:

nohup program argument1 argument2 >& logfile.nohup &

Output normally printed to the screen would be printed to logfile.nohup.

with screen or tmux

An alternative is to use either screen or tmux, which are virtual emulators. These are persistent virtual sessions that can be entered/exited at will and wont terminate programs when you step out of it or get disconnected from it. For simplicity, we’ll just cover screen:

create a screen
screen -S NAME_OF_SCREEN

where NAME_OF_SCREEN is whatever descriptive name you want, like variantcall etc. It will create a fresh terminal session onscreen (all existing terminal text will vanish) using your account’s default login shell (BASH, likely). After that, activate any conda/mamba/etc environments if needed and run programs as you normally would. At any point, you can press CTRL + a then d (+ being “and”, not the actual + key). This will “detatch” the screen session. You can reattach the screen using

reattach a screen
screen -r NAME_OF_SCREEN
Genome Analysis Toolkit (GATK) Variant Calling