java.lang.NullPointerException

broadinstitute.org | 6 months ago
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    Getting more runtime errors with GATK — GATK-Forum

    broadinstitute.org | 6 months ago
    java.lang.NullPointerException
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    broadinstitute.org | 2 months ago
    java.lang.NullPointerException

    Root Cause Analysis

    1. java.lang.NullPointerException

      No message provided

      at java.util.concurrent.locks.AbstractQueuedSynchronizer.hasQueuedPredecessors()
    2. Java RT
      PriorityBlockingQueue.peek
      1. java.util.concurrent.locks.AbstractQueuedSynchronizer.hasQueuedPredecessors(AbstractQueuedSynchronizer.java:1453)
      2. java.util.concurrent.locks.ReentrantLock$FairSync.tryAcquire(ReentrantLock.java:240)
      3. java.util.concurrent.locks.AbstractQueuedSynchronizer.acquire(AbstractQueuedSynchronizer.java:1136)
      4. java.util.concurrent.locks.ReentrantLock$FairSync.lock(ReentrantLock.java:229)
      5. java.util.concurrent.locks.ReentrantLock.lock(ReentrantLock.java:290)
      6. java.util.concurrent.PriorityBlockingQueue.peek(PriorityBlockingQueue.java:286)
      6 frames
    3. org.broadinstitute.sting
      NanoScheduler$MapReduceJob.run
      1. org.broadinstitute.sting.utils.nanoScheduler.Reducer.reduceNextValueInQueue(Reducer.java:89)
      2. org.broadinstitute.sting.utils.nanoScheduler.Reducer.reduceAsMuchAsPossible(Reducer.java:120)
      3. org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$MapReduceJob.run(NanoScheduler.java:510)
      3 frames
    4. Java RT
      Thread.run
      1. java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
      2. java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
      3. java.util.concurrent.FutureTask.run(FutureTask.java:166)
      4. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
      5. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
      6. java.lang.Thread.run(Thread.java:636)
      6 frames