When I run that manually (after first doing "ninja -C out\Default base" to get the prerequisites built) from the out\Default directory it succeeds. If you run it manually it will, presumably, fail. But now you can start investigating to find out why. You could see if message_compiler.py exists, modify message_compiler.py to add more diagnostics, and check for the existence of all of the referenced files. Here are my checks:
C:\src\chromium4\src\out\debug> c:/src/depot_tools/python276_bin/python.exe ../../build/win/message_compiler.py environment.x64 -h gen/base/trace_event/etw_manifest -r gen/base/trace_event/etw_manifest -u -um ../../base/trace_event/etw_manifest/chrome_events_win.man
C:\src\chromium4\src\out\debug>dir ..\..\build\win\message_compiler.py
Volume in drive C has no label.
Volume Serial Number is 18D4-8BE5
Directory of C:\src\chromium4\src\build\win
02/01/2017 12:36 PM 2,609 message_compiler.py
1 File(s) 2,609 bytes
0 Dir(s) 237,694,472,192 bytes free
C:\src\chromium4\src\out\debug>dir gen\base\trace_event\etw_manifest
Volume in drive C has no label.
Volume Serial Number is 18D4-8BE5
Directory of C:\src\chromium4\src\out\debug\gen\base\trace_event\etw_manifest
05/15/2017 01:42 PM <DIR> .
05/15/2017 01:42 PM <DIR> ..
05/15/2017 01:43 PM 12,901 chrome_events_win.h
05/15/2017 01:43 PM 84 chrome_events_win.rc
05/15/2017 01:43 PM 1,386 chrome_events_winTEMP.BIN
05/15/2017 01:43 PM 180 MSG00001.bin
4 File(s) 14,551 bytes
2 Dir(s) 237,694,373,888 bytes free
C:\src\chromium4\src\out\debug>dir ..\..\base\trace_event\etw_manifest\chrome_events_win.man
Volume in drive C has no label.
Volume Serial Number is 18D4-8BE5
Directory of C:\src\chromium4\src\base\trace_event\etw_manifest
02/16/2016 06:05 PM 2,494 chrome_events_win.man
1 File(s) 2,494 bytes
0 Dir(s) 237,694,373,888 bytes free