Race condition when outputting files via CLI ? failing test

Noticed a build failed with the following:
Headless mode output to stdout(./test/jalview/bin/argparser/testfiles/test1.fa ./test/jalview/bin/argparser/testfiles/test2.fa ./test/jalview/bin/argparser/testfiles/test3.fa --all --output -, test/jalview/bin/test1-3.fa, 13000): Test case result
The below summarizes the result of the test "Headless mode output to stdout(./test/jalview/bin/argparser/testfiles/test1.fa ./test/jalview/bin/argparser/testfiles/test2.fa ./test/jalview/bin/argparser/testfiles/test3.fa --all --output -, test/jalview/bin/test1-3.fa, 13000)" in build 2 of Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests. View test case history
DescriptionHeadless mode output to stdout(./test/jalview/bin/argparser/testfiles/test1.fa ./test/jalview/bin/argparser/testfiles/test2.fa ./test/jalview/bin/argparser/testfiles/test3.fa --all --output -, test/jalview/bin/test1-3.fa, 13000)Test classGradle suite > Gradle test > jalview.bin.CommandLineOperationsNGMethodtestHeadlessModeOutputToStdout(./test/jalview/bin/argparser/testfiles/test1.fa ./test/jalview/bin/argparser/testfiles/test2.fa ./test/jalview/bin/argparser/testfiles/test3.fa --all --output -, test/jalview/bin/test1-3.fa, 13000)
Duration3 secsStatusFailed (New Failure)
Error Log
Classname: java.lang.AssertionError
Message: STDOUT from jalview command did not match the comparison file expected [>TEST1/1-4
AAAA
>TEST2/1-4
LLLL
>TEST3/1-5
AAARG
] but found [>TEST1/1-4
AAAA
>TEST2/1-4
LLLL
]
Stacktrace:
java.lang.AssertionError: STDOUT from jalview command did not match the comparison file expected [>TEST1/1-4
AAAA
>TEST2/1-4
LLLL
>TEST3/1-5
AAARG
] but found [>TEST1/1-4
AAAA
>TEST2/1-4
LLLL
]
at org.testng.Assert.fail(Assert.java:94)
at org.testng.Assert.failNotEquals(Assert.java:496)
at org.testng.Assert.assertEquals(Assert.java:125)
at org.testng.Assert.assertEquals(Assert.java:178)
at jalview.bin.CommandLineOperationsNG.testHeadlessModeOutputToStdout(CommandLineOperationsNG.java:410)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)