python subprocess stuck system command - python

I'm not sure if python subprocess stuck the system. I run the GenomeAnalysisTK-3.4-46 as a subprocess through the python os.system(). But the java GenomeAnalysisTK.jar command status turned to "D" which can't be killed. when i run top -u username i get this, but if i click 'c', it stuck the terminal.
Beside, if i run the command ps aux,the command is blocked and the terminal is stuck. Even though the system runs well, it's really annoying monitoring your commands when the terminal stuck all the time.
I tried to figure out how it stuck system command,i prompted strace ps aux,i got this, the process can't be killed, and more and more command blocked when met the process. What i can do is reboot server manually by pressing power off, because restart command didn't work.
My python version is 2.7.6, and ubuntu release is Ubuntu 14.04 LTS.
I want to know how it happened and how to fix it up not by pressing power off.

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