java.lang.IllegalArgumentException: Wrong FS: hdfs://localhost:9000/data/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam, expected: file:///

Google Groups | Sergei Iakhnin | 1 year ago
  1. 0

    exception when transforming from HDFS BAM to HDFS Adam

    Google Groups | 1 year ago | Sergei Iakhnin
    java.lang.IllegalArgumentException: Wrong FS: hdfs://localhost:9000/data/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:///
  3. 0

    Spark Standalone+Markduplicates results in empty BAM or 'Wrong FS' exception

    GitHub | 10 months ago | geetduggal
    java.lang.IllegalArgumentException: Wrong FS: hdfs://bam/NA12878.chrom20.100kb.ILLUMINA.bwa.CEU.exome.20121211.bam, expected: file:///
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  5. 0

    gobblin kafka-hdfs-hive : issue with hive registration

    Stack Overflow | 3 months ago | dashro
    java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Wrong FS: hdfs://localhost:9083, expected: file:///

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    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Wrong FS: hdfs://localhost:9000/data/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:643)
      2. org.apache.hadoop.fs.RawLocalFileSystem.pathToFile(RawLocalFileSystem.java:79)
      3. org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:506)
      4. org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:724)
      5. org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:501)
      6. org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:397)
      7. org.apache.hadoop.fs.FileSystem.isDirectory(FileSystem.java:1411)
      7 frames
    3. org.bdgenomics.adam
      ADAMContext$anonfun$loadAlignments$1.apply
      1. org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:235)
      2. org.bdgenomics.adam.rdd.ADAMContext$anonfun$loadAlignments$1.apply(ADAMContext.scala:491)
      3. org.bdgenomics.adam.rdd.ADAMContext$anonfun$loadAlignments$1.apply(ADAMContext.scala:488)
      3 frames
    4. Spark
      Timer.time
      1. org.apache.spark.rdd.Timer.time(Timer.scala:57)
      1 frame
    5. org.bdgenomics.adam
      ADAMMain.main
      1. org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:486)
      2. org.bdgenomics.adam.cli.Transform.run(Transform.scala:147)
      3. org.bdgenomics.adam.cli.ADAMSparkCommand$class.run(ADAMCommand.scala:57)
      4. org.bdgenomics.adam.cli.Transform.run(Transform.scala:84)
      5. org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:107)
      6. org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
      6 frames
    6. Java RT
      Method.invoke
      1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
      3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      4. java.lang.reflect.Method.invoke(Method.java:606)
      4 frames
    7. Spark
      SparkSubmit.main
      1. org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$runMain(SparkSubmit.scala:569)
      2. org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:166)
      3. org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:189)
      4. org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:110)
      5. org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
      5 frames