diff --git a/lib/cc/engine/analyzers/command_line_runner.rb b/lib/cc/engine/analyzers/command_line_runner.rb
index 66e09aae..59d0a698 100644
--- a/lib/cc/engine/analyzers/command_line_runner.rb
+++ b/lib/cc/engine/analyzers/command_line_runner.rb
@@ -15,6 +15,9 @@ def initialize(command, timeout = DEFAULT_TIMEOUT)
         def run(input)
           Timeout.timeout(timeout) do
             out, err, status = Open3.capture3(command, stdin_data: input)
+
+            status ||= handle_open3_race_condition(out)
+
             if status.success?
               yield out
             else
@@ -26,6 +29,25 @@ def run(input)
         private
 
         attr_reader :command, :timeout
+
+        # Work around a race condition in JRuby's Open3.capture3 that can lead
+        # to a nil status returned. We'll consider the process successful if it
+        # produced output that can be parsed as JSON.
+        #
+        # https://github.com/jruby/jruby/blob/master/lib/ruby/stdlib/open3.rb#L200-L201
+        #
+        def handle_open3_race_condition(out)
+          JSON.parse(out)
+          NullStatus.new(true, 0)
+        rescue JSON::ParserError
+          NullStatus.new(false, 1)
+        end
+
+        NullStatus = Struct.new(:success, :exitstatus) do
+          def success?
+            success
+          end
+        end
       end
     end
   end
diff --git a/spec/cc/engine/analyzers/command_line_runner_spec.rb b/spec/cc/engine/analyzers/command_line_runner_spec.rb
new file mode 100644
index 00000000..5de8e5b1
--- /dev/null
+++ b/spec/cc/engine/analyzers/command_line_runner_spec.rb
@@ -0,0 +1,52 @@
+require "spec_helper"
+require "cc/engine/duplication"
+
+module CC::Engine::Analyzers
+  RSpec.describe CommandLineRunner do
+    describe "#run" do
+      it "runs the command on the input and yields the output" do
+        runner = CommandLineRunner.new("cat; echo hi")
+
+        output = runner.run("oh ") { |o| o }
+
+        expect(output).to eq "oh hi\n"
+      end
+
+
+      it "raises on errors" do
+        runner = CommandLineRunner.new("echo error output >&2; false")
+
+        expect { runner.run("") }.to raise_error(
+          ParserError, /code 1:\nerror output/
+        )
+      end
+
+      it "times out commands" do
+        runner = CommandLineRunner.new("sleep 3", 0.01)
+
+        expect { runner.run("") }.to raise_error(Timeout::Error)
+      end
+
+      context "when Open3 returns a nil status" do
+        it "accepts it if the output parses as JSON" do
+          runner = CommandLineRunner.new("")
+
+          allow(Open3).to receive(:capture3).and_return(["{\"type\":\"issue\"}", "", nil])
+
+          output = runner.run("") { |o| o }
+          expect(output).to eq "{\"type\":\"issue\"}"
+        end
+
+        it "raises if the output was not valid JSON" do
+          runner = CommandLineRunner.new("")
+
+          allow(Open3).to receive(:capture3).and_return(["", "error output", nil])
+
+          expect { runner.run("") }.to raise_error(
+            ParserError, /code 1:\nerror output/
+          )
+        end
+      end
+    end
+  end
+end