Gradle SonarQube Run - "duplicate module key in reactor" - sonarqube

Question

We upgraded our SonarQube server to v5.2. We are using the org.sonarsource.scanner.gradle:sonarqube-gradle-plugin:1.2 Gradle plugin against our Java projects.
Two out of the three Gradle projects we are running it against work just fine. For the third, I get "Duplicate module key in reactor: com.something.goes.here:plugins. We do have various projects underneath several different "plugins" subfolders. For example:
integration:lib:action:plugins:one
integration:lib:action:plugins:two
integration:lib:messageformatter:plugins:three
integration:lib:pal:plugins:four
integration:lib:pal:plugins:five
integration:lib:pal:plugins:six
and so on
What is the best way to narrow down the cause for the exception? Below is the debug log and stack trace.
17:07:14.517 [INFO] [org.sonarqube.gradle.SonarQubeTask] Load global repositories (done) | time=156ms
17:07:14.535 [WARN] [org.sonarqube.gradle.SonarQubeTask] Property 'sonar.jdbc.url' is not supported any more. There is no more DB connection to the SQ database. It will be ignored.
17:07:14.537 [INFO] [org.sonarqube.gradle.SonarQubeTask] User cache: C:\Users\Mark_Scott_Jr\.sonar\cache
17:07:14.716 [INFO] [org.sonarqube.gradle.SonarQubeTask] Load plugins index
17:07:14.716 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] Download: http://1.2.3.4:9000/deploy/plugins/index.txt (HTTP proxy: myproxy:3128)
17:07:14.717 [DEBUG] [sun.net.www.protocol.http.HttpURLConnection] sun.net.www.MessageHeader#7a182c1b7 pairs: {GET http://1.2.3.4:9000/deploy/plugins/index.txt HTTP/1.1: null}{Accept-Encoding: gzip}{Authorization: Basic c29uYXI6c29uYXI=}{User-Agent: SonarQube Gradle/2.10}{Host: 1.2.3.4:9000}{Accept: text/html, image/gif, image/jpeg, *; q=.2, */*; q=.2}{Proxy-Connection: keep-alive}
17:07:14.735 [DEBUG] [sun.net.www.protocol.http.HttpURLConnection] sun.net.www.MessageHeader#3a8035b10 pairs: {null: HTTP/1.1 200 OK}{Server: Apache-Coyote/1.1}{Accept-Ranges: bytes}{ETag: W/"426-1452118396000"}{Last-Modified: Wed, 06 Jan 2016 22:13:16 GMT}{Content-Type: text/plain}{Content-Length: 426}{Date: Fri, 22 Jan 2016 23:07:13 GMT}{Proxy-Connection: keep-alive}{Connection: keep-alive}
17:07:14.786 [INFO] [org.sonarqube.gradle.SonarQubeTask] Load plugins index (done) | time=70ms
17:07:14.787 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] Load plugins
17:07:14.797 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] Load plugins (done) | time=10ms
17:07:14.806 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] API compatibility mode is enabled on plugin Java [java] (built with API lower than 5.2)
17:07:14.809 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] API compatibility mode is enabled on plugin Git [scmgit] (built with API lower than 5.2)
17:07:14.810 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] API compatibility mode is enabled on plugin PDF Report [pdfreport] (built with API lower than 5.2)
17:07:14.811 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] API compatibility mode is enabled on plugin Clover [clover] (built with API lower than 5.2)
17:07:14.813 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] API compatibility mode is enabled on plugin JavaScript [javascript] (built with API lower than 5.2)
17:07:14.926 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] Plugins:
17:07:14.926 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] * Java 3.8 (java)
17:07:14.926 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] * LDAP 1.5.1 (ldap)
17:07:14.927 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] * Git 1.1 (scmgit)
17:07:14.927 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] * PDF Report 1.5-SNAPSHOT (pdfreport)
17:07:14.927 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] * Clover 3.1 (clover)
17:07:14.927 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] * JavaScript 2.9 (javascript)
17:07:14.940 [INFO] [org.sonarqube.gradle.SonarQubeTask] Default locale: "en_US", source code encoding: "windows-1252" (analysis is platform dependent)
17:07:14.941 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] Work directory: C:\code\my_folder\target\sonar
17:07:14.941 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] Execution getVersion
17:07:14.941 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] Execution execute
17:07:15.021 [INFO] [org.sonarqube.gradle.SonarQubeTask] Process project properties
17:07:20.403 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] Process project properties (done) | time=5382ms
17:07:20.578 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] cache: C:\Users\Mark_Scott_Jr\.sonar\ws_cache\http%3A%2F%2F1.2.3.4%3A9000\5.2\projects\com.something.goes.here%3Abase
17:07:20.580 [INFO] [org.sonarqube.gradle.SonarQubeTask] Load project repositories
17:07:20.580 [DEBUG] [org.sonarqube.gradle.SonarQubeTask] Download: http://1.2.3.4:9000/batch/project.protobuf?key=com.something.goes.here%3Abase (HTTP proxy: myproxy:3128)
17:07:20.581 [DEBUG] [sun.net.www.protocol.http.HttpURLConnection] sun.net.www.MessageHeader#4e764a1b7 pairs: {GET http://1.2.3.4:9000/batch/project.protobuf?key=com.something.goes.here%3Abase HTTP/1.1: null}{Accept-Encoding: gzip}{Authorization: Basic c29uYXI6c29uYXI=}{User-Agent: SonarQube Gradle/2.10}{Host: 1.2.3.4:9000}{Accept: text/html, image/gif, image/jpeg, *; q=.2, */*; q=.2}{Proxy-Connection: keep-alive}
17:07:20.634 [DEBUG] [sun.net.www.protocol.http.HttpURLConnection] sun.net.www.MessageHeader#5d28828b14 pairs: {null: HTTP/1.1 200 OK}{Server: Apache-Coyote/1.1}{Set-Cookie: JSESSIONID=9DE0576E32F2316DD16B4F49AFDF9714; Path=/; HttpOnly}{X-Runtime: 41}{ETag: "a4b13283d33b7ea57ec5dbf546506f9c"}{Cache-Control: private, max-age=0, must-revalidate}{X-Frame-Options: SAMEORIGIN}{X-XSS-Protection: 1; mode=block}{X-Content-Type-Options: nosniff}{Content-Type: application/x-protobuf;charset=utf-8}{Content-Length: 113674}{Date: Fri, 22 Jan 2016 23:07:20 GMT}{Proxy-Connection: keep-alive}{Connection: keep-alive}
17:07:20.729 [INFO] [org.sonarqube.gradle.SonarQubeTask] Load project repositories (done) | time=149ms
17:07:20.740 [INFO] [org.sonarqube.gradle.SonarQubeTask] Apply project exclusions
17:07:20.748 [DEBUG] [org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter] Finished executing task ':sonarqube'
17:07:20.748 [LIFECYCLE] [class org.gradle.TaskExecutionLogger] :sonarqube FAILED
17:07:20.748 [INFO] [org.gradle.execution.taskgraph.AbstractTaskPlanExecutor] :sonarqube (Thread[Daemon worker,5,main]) completed. Took 1 mins 8.201 secs.
17:07:20.749 [DEBUG] [org.gradle.execution.taskgraph.AbstractTaskPlanExecutor] Task worker [Thread[Daemon worker,5,main]] finished, busy: 1 mins 8.201 secs, idle: 0.002 secs
17:07:20.780 [LIFECYCLE] [org.gradle.BuildResultLogger]
17:07:20.781 [LIFECYCLE] [org.gradle.BuildResultLogger] BUILD FAILED
17:07:20.781 [LIFECYCLE] [org.gradle.BuildResultLogger]
17:07:20.781 [LIFECYCLE] [org.gradle.BuildResultLogger] Total time: 1 mins 45.612 secs
Stack Trace:
17:11:56.561 [ERROR] [org.gradle.BuildExceptionReporter]
17:11:56.562 [ERROR] [org.gradle.BuildExceptionReporter] FAILURE: Build failed with an exception.
17:11:56.562 [ERROR] [org.gradle.BuildExceptionReporter]
17:11:56.562 [ERROR] [org.gradle.BuildExceptionReporter] * What went wrong:
17:11:56.562 [ERROR] [org.gradle.BuildExceptionReporter] Execution failed for task ':sonarqube'.
17:11:56.563 [ERROR] [org.gradle.BuildExceptionReporter] > Duplicate module key in reactor: com.dell.enterprise.common:plugins
17:11:56.563 [ERROR] [org.gradle.BuildExceptionReporter]
17:11:56.563 [ERROR] [org.gradle.BuildExceptionReporter] * Exception is:
17:11:56.564 [ERROR] [org.gradle.BuildExceptionReporter] org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':sonarqube'.
17:11:56.564 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:69)
17:11:56.565 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:46)
17:11:56.565 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.tasks.execution.PostExecutionAnalysisTaskExecuter.execute(PostExecutionAnalysisTaskExecuter.java:35)
17:11:56.565 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:64)
17:11:56.565 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
17:11:56.565 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:52)
17:11:56.566 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
17:11:56.566 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:53)
17:11:56.566 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
17:11:56.566 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:203)
17:11:56.566 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:185)
17:11:56.567 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.processTask(AbstractTaskPlanExecutor.java:66)
17:11:56.567 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.run(AbstractTaskPlanExecutor.java:50)
17:11:56.567 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:25)
17:11:56.567 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:110)
17:11:56.567 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37)
17:11:56.567 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
17:11:56.568 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23)
17:11:56.568 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43)
17:11:56.568 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:32)
17:11:56.568 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
17:11:56.568 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30)
17:11:56.569 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.initialization.DefaultGradleLauncher$4.run(DefaultGradleLauncher.java:154)
17:11:56.569 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.internal.Factories$1.create(Factories.java:22)
17:11:56.569 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:90)
17:11:56.569 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:52)
17:11:56.569 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:151)
17:11:56.570 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.initialization.DefaultGradleLauncher.access$200(DefaultGradleLauncher.java:32)
17:11:56.570 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:99)
17:11:56.570 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:93)
17:11:56.570 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:90)
17:11:56.570 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:62)
17:11:56.570 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:93)
17:11:56.571 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:82)
17:11:56.571 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.exec.InProcessBuildActionExecuter$DefaultBuildController.run(InProcessBuildActionExecuter.java:94)
17:11:56.571 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
17:11:56.571 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
17:11:56.571 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:43)
17:11:56.572 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:28)
17:11:56.572 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.exec.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:78)
17:11:56.572 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.exec.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:48)
17:11:56.572 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:52)
17:11:56.572 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
17:11:56.573 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
17:11:56.573 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37)
17:11:56.573 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
17:11:56.573 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26)
17:11:56.573 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
17:11:56.574 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34)
17:11:56.574 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
17:11:56.574 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74)
17:11:56.574 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72)
17:11:56.574 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.util.Swapper.swap(Swapper.java:38)
17:11:56.575 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72)
17:11:56.575 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
17:11:56.575 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.health.DaemonHealthTracker.execute(DaemonHealthTracker.java:47)
17:11:56.575 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
17:11:56.575 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:66)
17:11:56.575 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
17:11:56.576 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
17:11:56.576 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:72)
17:11:56.576 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
17:11:56.576 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
17:11:56.576 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.health.HintGCAfterBuild.execute(HintGCAfterBuild.java:41)
17:11:56.577 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
17:11:56.577 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50)
17:11:56.577 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:246)
17:11:56.577 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54)
17:11:56.577 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40)
17:11:56.577 [ERROR] [org.gradle.BuildExceptionReporter] Caused by: java.lang.IllegalStateException: Duplicate module key in reactor: com.something.goes.here:plugins
17:11:56.577 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.batch.scan.ImmutableProjectReactor.collectProjects(ImmutableProjectReactor.java:55)
17:11:56.578 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.batch.scan.ImmutableProjectReactor.collectProjects(ImmutableProjectReactor.java:59)
17:11:56.578 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.batch.scan.ImmutableProjectReactor.collectProjects(ImmutableProjectReactor.java:59)
17:11:56.578 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.batch.scan.ImmutableProjectReactor.collectProjects(ImmutableProjectReactor.java:59)
17:11:56.578 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.batch.scan.ImmutableProjectReactor.collectProjects(ImmutableProjectReactor.java:59)
17:11:56.578 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.batch.scan.ImmutableProjectReactor.<init>(ImmutableProjectReactor.java:43)
17:11:56.578 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.batch.scan.ImmutableProjectReactorProvider.provide(ImmutableProjectReactorProvider.java:40)
17:11:56.579 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.MethodInjector.invokeMethod(MethodInjector.java:129)
17:11:56.579 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.MethodInjector.access$000(MethodInjector.java:39)
17:11:56.579 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.MethodInjector$2.run(MethodInjector.java:113)
17:11:56.579 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270)
17:11:56.579 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.MethodInjector.decorateComponentInstance(MethodInjector.java:120)
17:11:56.579 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.CompositeInjector.decorateComponentInstance(CompositeInjector.java:58)
17:11:56.580 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.Reinjector.reinject(Reinjector.java:142)
17:11:56.580 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.ProviderAdapter.getComponentInstance(ProviderAdapter.java:96)
17:11:56.580 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:699)
17:11:56.580 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:647)
17:11:56.580 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:632)
17:11:56.580 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.parameters.BasicComponentParameter$1.resolveInstance(BasicComponentParameter.java:118)
17:11:56.581 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.parameters.ComponentParameter$1.resolveInstance(ComponentParameter.java:136)
17:11:56.581 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.SingleMemberInjector.getParameter(SingleMemberInjector.java:78)
17:11:56.581 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.ConstructorInjector$CtorAndAdapters.getParameterArguments(ConstructorInjector.java:309)
17:11:56.581 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.ConstructorInjector$1.run(ConstructorInjector.java:335)
17:11:56.581 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270)
17:11:56.581 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.ConstructorInjector.getComponentInstance(ConstructorInjector.java:364)
17:11:56.582 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.injectors.AbstractInjectionFactory$LifecycleAdapter.getComponentInstance(AbstractInjectionFactory.java:56)
17:11:56.582 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64)
17:11:56.582 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.behaviors.Stored.getComponentInstance(Stored.java:91)
17:11:56.582 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.DefaultPicoContainer.instantiateComponentAsIsStartable(DefaultPicoContainer.java:1034)
17:11:56.582 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.DefaultPicoContainer.addAdapterIfStartable(DefaultPicoContainer.java:1026)
17:11:56.582 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.DefaultPicoContainer.startAdapters(DefaultPicoContainer.java:1003)
17:11:56.583 [ERROR] [org.gradle.BuildExceptionReporter] at org.picocontainer.DefaultPicoContainer.start(DefaultPicoContainer.java:767)
17:11:56.583 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:99)
17:11:56.583 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:85)
17:11:56.583 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.batch.bootstrap.GlobalContainer.executeAnalysis(GlobalContainer.java:153)
17:11:56.583 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.batch.bootstrapper.Batch.executeTask(Batch.java:110)
17:11:56.583 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.runner.batch.BatchIsolatedLauncher.execute(BatchIsolatedLauncher.java:67)
17:11:56.584 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.runner.impl.IsolatedLauncherProxy.invoke(IsolatedLauncherProxy.java:61)
17:11:56.584 [ERROR] [org.gradle.BuildExceptionReporter] at com.sun.proxy.$Proxy70.execute(Unknown Source)
17:11:56.584 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.runner.api.EmbeddedRunner.doExecute(EmbeddedRunner.java:274)
17:11:56.584 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.runner.api.EmbeddedRunner.runAnalysis(EmbeddedRunner.java:165)
17:11:56.584 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonar.runner.api.EmbeddedRunner.runAnalysis(EmbeddedRunner.java:152)
17:11:56.584 [ERROR] [org.gradle.BuildExceptionReporter] at org.sonarqube.gradle.SonarQubeTask.run(SonarQubeTask.java:84)
17:11:56.585 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:75)
17:11:56.585 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.project.taskfactory.AnnotationProcessingTaskFactory$StandardTaskAction.doExecute(AnnotationProcessingTaskFactory.java:227)
17:11:56.585 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.project.taskfactory.AnnotationProcessingTaskFactory$StandardTaskAction.execute(AnnotationProcessingTaskFactory.java:220)
17:11:56.585 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.project.taskfactory.AnnotationProcessingTaskFactory$StandardTaskAction.execute(AnnotationProcessingTaskFactory.java:209)
17:11:56.585 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:585)
17:11:56.586 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:568)
17:11:56.586 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:80)
17:11:56.586 [ERROR] [org.gradle.BuildExceptionReporter] at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:61)
17:11:56.586 [ERROR] [org.gradle.BuildExceptionReporter] ... 68 more
17:11:56.587 [ERROR] [org.gradle.BuildExceptionReporter]

Answer 1

You can run the same command with -DsonarRunner.dumpToFile=out.txt this should dump all SonarQube properties to the given file. Then look at this file (especially sonar.modules properties) in order to rebuild the multi-module tree and see what is causing the issue. If you can produce a small reproducer please post on SonarQube user group and we'll see how we can fix the issue.