Every now and then, rebaseline-cl chokes with 'No such file or directory' exceptions.  This happens consistently for a given result set, so it's possible the issue is with the layout test results.

E.g. https://chromium-review.googlesource.com/c/565379:

third_party/WebKit/Tools/Scripts/webkit-patch rebaseline-cl
2017-07-11 13:38:43,639 - Finished try jobs found for all try bots.
2017-07-11 13:38:48,213 - No retry summary available for "linux_trusty_blink_rel".
2017-07-11 13:38:50,745 - Rebaselining compositing/direct-image-compositing.html
2017-07-11 13:38:50,746 - Rebaselining compositing/geometry/horizontal-scroll-composited.html
2017-07-11 13:38:50,746 - Rebaselining compositing/geometry/vertical-scroll-composited.html
...

2017-07-11 13:40:11,696 - Traceback (most recent call last):
  File "/usr/local/google/home/fmalita/src/blink/src/third_party/WebKit/Tools/Scripts/webkit-patch", line 84, in <module>
    main()
  File "/usr/local/google/home/fmalita/src/blink/src/third_party/WebKit/Tools/Scripts/webkit-patch", line 79, in main
    WebKitPatch(os.path.abspath(__file__)).main()
  File "/usr/local/google/home/fmalita/src/blink/src/third_party/WebKit/Tools/Scripts/webkitpy/tool/webkit_patch.py", line 114, in main
    result = command.check_arguments_and_execute(options, args, self)
  File "/usr/local/google/home/fmalita/src/blink/src/third_party/WebKit/Tools/Scripts/webkitpy/tool/commands/command.py", line 110, in check_arguments_and_execute
    return self.execute(options, args, tool) or 0
  File "/usr/local/google/home/fmalita/src/blink/src/third_party/WebKit/Tools/Scripts/webkitpy/tool/commands/optimize_baselines.py", line 48, in execute
    self._optimize_baseline(optimizer, test_name)
  File "/usr/local/google/home/fmalita/src/blink/src/third_party/WebKit/Tools/Scripts/webkitpy/tool/commands/optimize_baselines.py", line 32, in _optimize_baseline
    succeeded = optimizer.optimize(name)
  File "/usr/local/google/home/fmalita/src/blink/src/third_party/WebKit/Tools/Scripts/webkitpy/common/checkout/baseline_optimizer.py", line 64, in optimize
    result = self._optimize_subtree(baseline_name)
  File "/usr/local/google/home/fmalita/src/blink/src/third_party/WebKit/Tools/Scripts/webkitpy/common/checkout/baseline_optimizer.py", line 120, in _optimize_subtree
    self._move_baselines(baseline_name, results_by_directory, new_results_by_directory)
  File "/usr/local/google/home/fmalita/src/blink/src/third_party/WebKit/Tools/Scripts/webkitpy/common/checkout/baseline_optimizer.py", line 128, in _move_baselines
    data_for_result[result] = self._filesystem.read_binary_file(source)
  File "/usr/local/google/home/fmalita/src/blink/src/third_party/WebKit/Tools/Scripts/webkitpy/common/system/filesystem.py", line 210, in read_binary_file
    with file(path, 'rb') as f:
IOError: [Errno 2] No such file or directory: '/usr/local/google/home/fmalita/src/blink/src/third_party/WebKit/LayoutTests/platform/win7/css1/box_properties/padding_left-expected.png'


I'll leave https://chromium-review.googlesource.com/c/565379 in this state, in case you need to investigate/repro.