You've got several issues here. Firstly as @joy points out there could be a problem with the Path used by Java to locate the command so Java may not be finding a command called "ffmpeg". Fixing the Path used for launching your VM should resolve that, or just insert the fully qualified pathname to "ffmpeg".
Secondly: you are trying to run a terminal / shell command. The "|" pipes are normally interpretted correctly by a terminal / shell which breaks the chain into sub-processes linking stdout/stdin. But Java is being asked to run "ffmpeg" passing in some arguments containing "|" which would not be handled as you wish by "ffmpeg".
Check the shell you use:
echo $SHELL
Let's say that printed /bin/bash - you can fix by getting Java to launch the shell and make that interpret the pipe command:
String[] command = new String[] { "/bin/bash", "-c", "ffmpeg -i /home/user/Videos/my-video.mp4 2>&1 | grep Duration | awk '{print $2}' | tr -d ," }; Runtime.getRuntime().exec(cmdarray);