java.lang.IllegalArgumentException: Wrong FS: hdfs:// hh-rover10-1.ebi.ac.uk:8020/user/iakhnin/na12878/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam, expected: file:///

Google Groups | Sergei Iakhnin | 2 years ago
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  1. 0

    exception when transforming from HDFS BAM to HDFS Adam

    Google Groups | 2 years ago | Sergei Iakhnin
    java.lang.IllegalArgumentException: Wrong FS: hdfs:// hh-rover10-1.ebi.ac.uk:8020/user/iakhnin/na12878/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam, expected: file:///
  2. 0

    Spark can't find Hadoop

    GitHub | 2 years ago | beaunorgeot
    java.lang.IllegalArgumentException: Wrong FS: hdfs://spark-master:8020/C835.HCC1143_BL._.bam, expected: file:///

    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Wrong FS: hdfs:// hh-rover10-1.ebi.ac.uk:8020/user/iakhnin/na12878/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam, expected: file:///

      at org.apache.hadoop.fs.FileSystem.checkPath()
    2. Hadoop
      FileSystem.isDirectory
      1. org.apache.hadoop.fs.FileSystem.checkPath(FileSystem.java:645)
      2. org.apache.hadoop.fs.RawLocalFileSystem.pathToFile(RawLocalFileSystem.java:80)
      3. org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:519)
      4. org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:737)
      5. org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:514)
      6. org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:398)
      7. org.apache.hadoop.fs.FileSystem.isDirectory(FileSystem.java:1413)
      7 frames
    3. org.bdgenomics.adam
      ADAMContext$$anonfun$loadAlignments$1.apply
      1. org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:237)
      2. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:516)
      3. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:513)
      3 frames
    4. Spark
      Timer.time
      1. org.apache.spark.rdd.Timer.time(Timer.scala:57)
      1 frame
    5. org.bdgenomics.adam
      Transform.run
      1. org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:511)
      2. org.bdgenomics.adam.cli.Transform.run(Transform.scala:148)
      2 frames
    6. org.bdgenomics.utils
      BDGSparkCommand$class.run
      1. org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:53)
      1 frame
    7. org.bdgenomics.adam
      ADAMMain.main
      1. org.bdgenomics.adam.cli.Transform.run(Transform.scala:85)
      2. org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:105)
      3. org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
      3 frames
    8. 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:497)
      4 frames
    9. Spark
      SparkSubmit.main
      1. org.apache.spark.deploy.SparkSubmit$.launch(SparkSubmit.scala:358)
      2. org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:75)
      3. org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
      3 frames