My program in tkinter is working well when I am running it using PyCharm,
when I am creating .exe file using pyinstaller,py
You can compile your code in -w mode or --windowed, but then you have to assign stdin and stderr as well.
So change:
s = subprocess.Popen([EXE,files,'command'],shell=True, stdout=subprocess.PIPE)
to:
s = subprocess.Popen([EXE,files,'command'],shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE)