compareTransferredToRefPDBAnnot passes in Eclipse but not from CLI

compareTransferredToRefPDBAnnot passes when run via Eclipse.

Running via the command line as part of the unit test suite (i.e. via ant testng in the jalview directory) fails:
[testng] FAILED: compareTransferredToRefPDBAnnot
   [testng] java.lang.AssertionError:
   [testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
   [testng] at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:24)
   [testng] at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:33)
   [testng] at jalview.structure.Mapping.compareTransferredToRefPDBAnnot(Mapping.java:282)
   [testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   [testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
   [testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   [testng] at java.lang.reflect.Method.invoke(Method.java:498)
   [testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
   [testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
   [testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
   [testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
   [testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
   [testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
   [testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
   [testng] at org.testng.TestRunner.run(TestRunner.java:621)
   [testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
   [testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
   [testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
   [testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
   [testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
   [testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
   [testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
   [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
   [testng] at org.testng.TestNG.run(TestNG.java:1009)
   [testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
   [testng] at org.testng.TestNG.main(TestNG.java:1285)