SonarQube 5.6 FileNotFound exception during AST Scan

During the AST Scan, I get a FileNotFoundException looking for a symbols-34.pb file:

ERROR: Error during SonarQube Scanner execution
org.sonar.squidbridge.api.AnalysisException: SonarQube is unable to analyze file : '/workingDir/src/main/java/package/JavaFile.java'
    at org.sonar.java.ast.JavaAstScanner.simpleScan(JavaAstScanner.java:93)
    at org.sonar.java.ast.JavaAstScanner.scan(JavaAstScanner.java:67)
    at org.sonar.java.JavaSquid.scanSources(JavaSquid.java:133)
    at org.sonar.java.JavaSquid.scan(JavaSquid.java:126)
    at org.sonar.plugins.java.JavaSquidSensor.execute(JavaSquidSensor.java:93)
    at org.sonar.batch.sensor.SensorWrapper.analyse(SensorWrapper.java:57)
    at org.sonar.batch.phases.SensorsExecutor.executeSensor(SensorsExecutor.java:58)
    at org.sonar.batch.phases.SensorsExecutor.execute(SensorsExecutor.java:50)
    at org.sonar.batch.phases.AbstractPhaseExecutor.execute(AbstractPhaseExecutor.java:83)
    at org.sonar.batch.scan.ModuleScanContainer.doAfterStart(ModuleScanContainer.java:192)
    at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:142)
    at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:127)
    at org.sonar.batch.scan.ProjectScanContainer.scan(ProjectScanContainer.java:241)
    at org.sonar.batch.scan.ProjectScanContainer.scanRecursively(ProjectScanContainer.java:236)
    at org.sonar.batch.scan.ProjectScanContainer.scanRecursively(ProjectScanContainer.java:234)
    at org.sonar.batch.scan.ProjectScanContainer.doAfterStart(ProjectScanContainer.java:226)
    at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:142)
    at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:127)
    at org.sonar.batch.task.ScanTask.execute(ScanTask.java:47)
    at org.sonar.batch.task.TaskContainer.doAfterStart(TaskContainer.java:86)
    at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:142)
    at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:127)
    at org.sonar.batch.bootstrap.GlobalContainer.executeTask(GlobalContainer.java:106)
    at org.sonar.batch.bootstrapper.Batch.executeTask(Batch.java:119)
    at org.sonarsource.scanner.api.internal.batch.BatchIsolatedLauncher.execute(BatchIsolatedLauncher.java:62)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.sonarsource.scanner.api.internal.IsolatedLauncherProxy.invoke(IsolatedLauncherProxy.java:60)
    at com.sun.proxy.$Proxy0.execute(Unknown Source)
    at org.sonarsource.scanner.api.EmbeddedScanner.doExecute(EmbeddedScanner.java:240)
    at org.sonarsource.scanner.api.EmbeddedScanner.runAnalysis(EmbeddedScanner.java:151)
    at org.sonarsource.scanner.cli.Main.runAnalysis(Main.java:110)
    at org.sonarsource.scanner.cli.Main.execute(Main.java:72)
    at org.sonarsource.scanner.cli.Main.main(Main.java:60)
Caused by: org.sonar.core.util.ContextException: Unable to write messages | file=/workingDir/.sonar/batch-report/symbols-34.pb
    at org.sonar.core.util.ContextException.of(ContextException.java:125)
    at org.sonar.core.util.Protobuf.writeStream(Protobuf.java:98)
    at org.sonar.scanner.protocol.output.ScannerReportWriter.writeComponentSymbols(ScannerReportWriter.java:109)
    at org.sonar.batch.sensor.DefaultSensorStorage.store(DefaultSensorStorage.java:202)
    at org.sonar.api.batch.sensor.symbol.internal.DefaultSymbolTable.doSave(DefaultSymbolTable.java:146)
    at org.sonar.api.batch.sensor.internal.DefaultStorable.save(DefaultStorable.java:43)
    at org.sonar.java.ast.visitors.SonarSymbolTableVisitor.visitCompilationUnit(SonarSymbolTableVisitor.java:61)
    at org.sonar.java.model.VisitorsBridge.createSonarSymbolTable(VisitorsBridge.java:176)
    at org.sonar.java.model.VisitorsBridge.visitFile(VisitorsBridge.java:112)
    at org.sonar.java.ast.JavaAstScanner.simpleScan(JavaAstScanner.java:84)
    ... 35 more
Caused by: java.io.FileNotFoundException: /workingDir/.sonar/batch-report/symbols-34.pb (No such file or directory)
    at java.io.FileOutputStream.open0(Native Method)
    at java.io.FileOutputStream.open(FileOutputStream.java:270)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
    at org.sonar.core.util.Protobuf.writeStream(Protobuf.java:95)
    ... 43 more

(Path names changed for anonymity)

The java class is very simple, only containing a couple annotations, could probably compile against Java 6. I am using version 4.0 of the Java plugin in SonarQube 5.6.

Any thought to why this would be occurring?

I was able to resolve this issue. The scans were running on Jenkins using the SonarQube plugin. A second job was being triggered in the same workspace at the same time, which caused the workspace to be cleared by the Jenkins job (which was configured to do so). The symbols.pb file was deleted, and then the FileNotFoundException occurred.