That's the not real stacktrace. That stacktrace is saying "when reading the output of the bot_update step, the JSON object it wrote to the file didn't have a 'root' key". Which makes total sense, because bot_update itself failed with a stacktrace, and therefore didn't write to that file. Here's the real stacktrace:

===Running git checkout --force 2515e420da7a6e03d2f250a1cee71b13025d750a===
In directory: /b/build/slave/Android_Cronet_x86_Builder__dbg_/build/src
fatal: reference is not a tree: 2515e420da7a6e03d2f250a1cee71b13025d750a
===Failed in 0.0 mins===
Something failed: git checkout --force 2515e420da7a6e03d2f250a1cee71b13025d750a failed with code 128 in /b/build/slave/Android_Cronet_x86_Builder__dbg_/build/src..
Ran 99.1176700592 seconds past deadline. Aborting.
Traceback (most recent call last):
  File "/b/build/scripts/slave/.recipe_deps/depot_tools/recipes/recipe_modules/bot_update/resources/bot_update.py", line 1169, in <module>
    sys.exit(main())
  File "/b/build/scripts/slave/.recipe_deps/depot_tools/recipes/recipe_modules/bot_update/resources/bot_update.py", line 1153, in main
    checkout(options, git_slns, specs, revisions, step_text, shallow)
  File "/b/build/scripts/slave/.recipe_deps/depot_tools/recipes/recipe_modules/bot_update/resources/bot_update.py", line 1059, in checkout
    gclient_output = ensure_checkout(**checkout_parameters)
  File "/b/build/scripts/slave/.recipe_deps/depot_tools/recipes/recipe_modules/bot_update/resources/bot_update.py", line 759, in ensure_checkout
    cleanup_dir)
  File "/b/build/scripts/slave/.recipe_deps/depot_tools/recipes/recipe_modules/bot_update/resources/bot_update.py", line 560, in git_checkout
    force_revision(sln_dir, revision)
  File "/b/build/scripts/slave/.recipe_deps/depot_tools/recipes/recipe_modules/bot_update/resources/bot_update.py", line 456, in force_revision
    git('checkout', '--force', revision, cwd=folder_name)
  File "/b/build/scripts/slave/.recipe_deps/depot_tools/recipes/recipe_modules/bot_update/resources/bot_update.py", line 211, in git
    return call(*cmd, **kwargs)
  File "/b/build/scripts/slave/.recipe_deps/depot_tools/recipes/recipe_modules/bot_update/resources/bot_update.py", line 192, in call
    code, outval)
__main__.SubprocessFailed: git checkout --force 2515e420da7a6e03d2f250a1cee71b13025d750a failed with code 128 in /b/build/slave/Android_Cronet_x86_Builder__dbg_/build/src.
step returned non-zero exit code: 1

So the real question is why that hash is corrupt ('not a tree').

Looks like a valid hash to me: https://chromium.googlesource.com/chromium/src/+/2515e420da7a6e03d2f250a1cee71b13025d750a

Maybe a corrupt checkout on disk?

I should mention that this appears to be affecting many Cronet bots.  For example here's another:
https://build.chromium.org/p/chromium.android/builders/Android%20Cronet%20ARM64%20Builder%20%28dbg%29?numbuilds=200

The different bots are running on different slaves.

Oh interesting, yep, it's happening in a bunch of places, but with a different hash every time.

Uh oh, I found it. It's googlesource latency. Example:

https://luci-logdog.appspot.com/v/?s=chromium%2Fbb%2Fchromium.android%2FAndroid_Cronet_x86_Builder__dbg_%2F68361%2F%2B%2Frecipes%2Fsteps%2Fbot_update%2F0%2Fstdout

Tries to check out 3df0d0574d1f53e831bd5d9f7ae9c825c0c8cb38

Runs 'git fetch' in the cache, and gets:
From https://chromium.googlesource.com/chromium/src
   0c0ed17d896b..71b25bc67d18  master       -> master

But 71b is the *parent* of 3df (https://chromium.googlesource.com/chromium/src/+/3df0d0574d1f53e831bd5d9f7ae9c825c0c8cb38). So even though 3df has landed in the repo and triggered a job to start, when that job fetches the repo from GoB it doesn't download that commit.

That commit was landed at :49
The job was started at :52
The fetch started at least a minute and a half after that (given step timings prior to bot_update).
So that's a GoB replication latency of ~5 minutes, which is unnaceptably slow.

Filing an internal bug against them.

b/67501786

Adding Trooper label so trooper is aware of this issue. If others report similar symptoms, please dupe into this bug.

 Issue 776498  has been merged into this issue.

New trooper checking in. Looks like the consistency hiccup is still occurring very occasionally:
https://build.chromium.org/p/chromium.android/builders/Android%20Cronet%20x86%20Builder%20%28dbg%29/builds/69451
https://build.chromium.org/p/chromium.android/builders/Android%20Cronet%20x86%20Builder%20%28dbg%29/builds/69430
https://build.chromium.org/p/chromium.android/builders/Android%20Cronet%20x86%20Builder%20%28dbg%29/builds/69417

Not sure what else we can do here. Over to agable to decide if we should just close this as wontfix.

On the day I noticed it, every time I looked at
https://build.chromium.org/p/chromium.gpu.fyi/console
there were 4 or 5 purple bots.
If this could happen on CQ bots wouldn't you have a day of people unable to land changes?
Unless there's reason to believe this is extremely rare and won't get worse it doesn't seem like something to be ignored.

Please post updates on the internal bug; there's nothing we can do from here.

Keeping this bug open isn't helping; all progress here is tracked in GoB team's code-yellow bug: b/35998605