While changing some source_set targets to static_library I made the change below in chromium\src\native_client\src:

diff --git a/src/trusted/service_runtime/BUILD.gn b/src/trusted/service_runtime/BUILD.gn
index d326b15..707c914 100644
--- a/src/trusted/service_runtime/BUILD.gn
+++ b/src/trusted/service_runtime/BUILD.gn
@@ -46,7 +46,7 @@ source_set("nacl_error_code") {
 }

 if (current_toolchain == nacl_asm_toolchain) {
-  source_set("sel_asm") {
+  static_library("sel_asm") {
     if (current_cpu == "x86") {
       sources = [
         "arch/x86_32/nacl_switch_32.S",

When running "ninja chrome" after this I got the following warnings:

ninja: warning: multiple rules generate fake. builds involving this target will not be correct; continuing anyway [-w dupbuild=warn]
[1 processes, 1/7 @ 863.6/s : 0.001s ] fake
FAILED: fake
fake
CreateProcess failed: The system cannot find the file specified.
ninja: build stopped: subcommand failed.

I was able to identify the problem because I had only made a few BUILD.gn changes but in another situation the diagnosis could have been much harder - the warning message and the failure don't seem to indicate the problem very well.

I'm not sure if my args.gn settings matter but here they are:

is_chrome_branded = true
is_component_build = false
is_debug = false
target_cpu = "x86"