java.io.FileNotFoundException: File file:/tmp/a7.adam/_rgdict.avro does not exist

GitHub | ooliynyk | 6 months ago
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    File _rgdict.avro does not exist

    GitHub | 6 months ago | ooliynyk
    java.io.FileNotFoundException: File file:/tmp/a7.adam/_rgdict.avro does not exist
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Root Cause Analysis

  1. java.io.FileNotFoundException

    File file:/tmp/a7.adam/_rgdict.avro does not exist

    at org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus()
  2. Hadoop
    FileSystem.open
    1. org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:534)
    2. org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:747)
    3. org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:524)
    4. org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:409)
    5. org.apache.hadoop.fs.ChecksumFileSystem$ChecksumFSInputChecker.<init>(ChecksumFileSystem.java:140)
    6. org.apache.hadoop.fs.ChecksumFileSystem.open(ChecksumFileSystem.java:341)
    7. org.apache.hadoop.fs.FileSystem.open(FileSystem.java:766)
    7 frames
  3. org.bdgenomics.adam
    ADAMContext$$anonfun$loadAlignments$1.apply
    1. org.bdgenomics.adam.rdd.ADAMContext.loadAvro(ADAMContext.scala:442)
    2. org.bdgenomics.adam.rdd.ADAMContext.loadAvroReadGroupMetadata(ADAMContext.scala:160)
    3. org.bdgenomics.adam.rdd.ADAMContext.loadParquetAlignments(ADAMContext.scala:520)
    4. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:1023)
    5. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:1002)
    5 frames
  4. Scala
    Option.fold
    1. scala.Option.fold(Option.scala:157)
    1 frame
  5. Spark
    Timer.time
    1. org.apache.spark.rdd.Timer.time(Timer.scala:48)
    1 frame
  6. org.bdgenomics.adam
    CountReadKmers.run
    1. org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:1000)
    2. org.bdgenomics.adam.cli.CountReadKmers.run(CountReadKmers.scala:63)
    2 frames
  7. org.bdgenomics.utils
    BDGSparkCommand$class.run
    1. org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:55)
    1 frame
  8. org.bdgenomics.adam
    ADAMMain.main
    1. org.bdgenomics.adam.cli.CountReadKmers.run(CountReadKmers.scala:54)
    2. org.bdgenomics.adam.cli.ADAMMain.apply(ADAMMain.scala:132)
    3. org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:72)
    4. org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
    4 frames
  9. Java RT
    Method.invoke
    1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    4. java.lang.reflect.Method.invoke(Method.java:498)
    4 frames
  10. Spark
    SparkSubmit.main
    1. org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:674)
    2. org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
    3. org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
    4. org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
    5. org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
    5 frames