I have found the problem. It turns out, clock is passed to the target only after scope.default_setup()
To launch the target, we need to pull down the nRST and then release it.
So, I added lines to reset target
scope.io.nrst = 'low'
time.sleep(0.05)
scope.io.nrst = 'high_z'
with these strings everything works fine.
Thanks for your assistance!