Comment 14 for bug 1642386

What we see from your debug output is that gpgv is not returning any sensible information:

Summary:
  Good:
  Bad:
  Worthless:
  SoonWorthless:
  NoPubKey:

You could try running apt-key verify manually on a few InRelease files (like apt-key verify /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_xenial_InRelease) and see if that gives us any clue - or at least look at the files (especially in partial/), maybe they are garbage.