Hard to say anything concrete. If you look at top so you see the picard process consuming any CPU?

Dear blur, Hi

maybe you can use "ps aux" or :

ps aux | grep program-name

Process state codes:

D uninterruptible sleep (usually IO)

R running or runnable (on run queue)

S interruptible sleep (waiting for an event to complete)

T stopped, either by a job control signal or because it is being traced

W paging (not valid since the 2.6.xx kernel)

X dead (should never be seen)

Z defunct ("zombie") process, terminated but not reaped by its parent

< high-priority (not nice to other users)

N low-priority (nice to other users)

L has pages locked into memory (for real-time and custom IO)

s is a session leader

l is multi-threaded (using CLONE_THREAD, like NPTL pthreads do)

(plus sign +) is in the foreground process group

what's your version of picard ? what's the input ? for WGS this tool can take hours or days.