Tente criar um subshell com (...)
:
( command_which_takes_time input > output ) &
Exemplo:
~$ ( (sleep 10; date) > /tmp/q ) &
[1] 19521
~$ cat /tmp/q # ENTER
~$ cat /tmp/q # ENTER
(...) #AFTER 10 seconds
~$ cat /tmp/q #ENTER
Wed Jan 11 01:35:55 CET 2012
[1]+ Done ( ( sleep 10; date ) > /tmp/q )