org.broadinstitute.hellbender.exceptions.GATKException: Cannot run BWA-MEM

GitHub | huangk3 | 7 months ago
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    Unable to load bwa index error when running BwaSpark under version alpha.2-45-ga30af5a

    GitHub | 7 months ago | huangk3
    org.broadinstitute.hellbender.exceptions.GATKException: Cannot run BWA-MEM
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    ADB Connection Error

    Stack Overflow | 4 years ago | Raveesh Lawrance
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    java-forums.org | 8 months ago
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    cloudera.com | 2 years ago
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    Root Cause Analysis

    1. java.io.IOException

      bwa_idx_load failed

      at com.github.lindenb.jbwa.jni.BwaIndex._open()
    2. com.github.lindenb
      BwaIndex.<init>
      1. com.github.lindenb.jbwa.jni.BwaIndex._open(Native Method)
      2. com.github.lindenb.jbwa.jni.BwaIndex.<init>(BwaIndex.java:216)
      2 frames
    3. org.broadinstitute.hellbender
      BwaSparkEngine.lambda$null$1
      1. org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkEngine.lambda$null$1(BwaSparkEngine.java:109)
      1 frame
    4. Spark
      Executor$TaskRunner.run
      1. org.apache.spark.api.java.JavaRDDLike$$anonfun$fn$4$1.apply(JavaRDDLike.scala:159)
      2. org.apache.spark.api.java.JavaRDDLike$$anonfun$fn$4$1.apply(JavaRDDLike.scala:159)
      3. org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$20.apply(RDD.scala:710)
      4. org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$20.apply(RDD.scala:710)
      5. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      6. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
      7. org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
      8. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      9. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
      10. org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
      11. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      12. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
      13. org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
      14. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      15. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
      16. org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
      17. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      18. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
      19. org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
      20. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      21. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
      22. org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
      23. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      24. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
      25. org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
      26. org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:73)
      27. org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
      28. org.apache.spark.scheduler.Task.run(Task.scala:89)
      29. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
      29 frames
    5. Java RT
      Thread.run
      1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
      2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
      3. java.lang.Thread.run(Thread.java:745)
      3 frames