Steps to reproduce:

Run gn args <out_dir> --list

What happens:

ERROR at //build/config/linux/pkg_config.gni:103:17: Script returned non-zero exit code.
    pkgresult = exec_script(pkg_config_script, args, "value")
                ^----------
Current dir: /work/repos/chromium-linux/src/out/Linux/
Command: python -- /work/repos/chromium-linux/src/build/config/linux/pkg-config.py -s /work/repos/chromium-linux/src/build/linux/debian_stretch_amd64-sysroot -a x64 glib-2.0 gmodule-2.0 gobject-2.0 gthread-2.0
Returned 1.
stderr:

Traceback (most recent call last):
  File "/work/repos/chromium-linux/src/build/config/linux/pkg-config.py", line 232, in <module>
    sys.exit(main())
  File "/work/repos/chromium-linux/src/build/config/linux/pkg-config.py", line 139, in main
    prefix = GetPkgConfigPrefixToStrip(options, args)
  File "/work/repos/chromium-linux/src/build/config/linux/pkg-config.py", line 80, in GetPkgConfigPrefixToStrip
    "--variable=prefix"] + args, env=os.environ)
  File "/usr/lib/python2.7/subprocess.py", line 212, in check_output
    process = Popen(stdout=PIPE, *popenargs, **kwargs)
  File "/usr/lib/python2.7/subprocess.py", line 390, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1024, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

See //build/config/linux/BUILD.gn:83:3: whence it was called.
  pkg_config("glib") {
  ^-------------------
See //ui/gfx/BUILD.gn:384:18: which caused the file to be included.
    configs += [ "//build/config/linux:x11" ]
                 ^-------------------------


This is with:

depot_tools revision: 5d6b00fac64a829cca5637bb76abe618291b8b60
chromium revision: 4522efba74e35026b0f62cb1c97d793a92a0d5da

I freshly rebase-updated and gclient sync'd and update_depot_tools.