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:///

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Solutions on the web5780

  • via Google Groups by Sergei Iakhnin, 6 months ago
    Wrong FS: hdfs:// hh-rover10-1.ebi.ac.uk:8020/user/iakhnin/na12878/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam, expected: file:///
  • Wrong FS: hdfs://bam/NA12878.chrom20.100kb.ILLUMINA.bwa.CEU.exome.20121211.bam, expected: file:///
  • Wrong FS: hdfs://quickstart.cloudera:8020/user/cloudera, expected: file:///
  • Stack trace

    • java.lang.IllegalArgumentException: Wrong FS: hdfs:// hh-rover10-1.ebi.ac.uk:8020/user/iakhnin
    • a12878/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam, expected: file:/// at org.apache.hadoop.fs.FileSystem.checkPath(FileSystem.java:645) at org.apache.hadoop.fs.RawLocalFileSystem.pathToFile(RawLocalFileSystem.java:80) at org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:519) at org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:737) at org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:514) at org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:398) at org.apache.hadoop.fs.FileSystem.isDirectory(FileSystem.java:1413) at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:237) at org.bdgenomics.adam.rdd.ADAMContext$anonfun$loadAlignments$1.apply(ADAMContext.scala:516) at org.bdgenomics.adam.rdd.ADAMContext$anonfun$loadAlignments$1.apply(ADAMContext.scala:513) at org.apache.spark.rdd.Timer.time(Timer.scala:57) at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:511) at org.bdgenomics.adam.cli.Transform.run(Transform.scala:148) at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:53) at org.bdgenomics.adam.cli.Transform.run(Transform.scala:85) at org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:105) at org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at org.apache.spark.deploy.SparkSubmit$.launch(SparkSubmit.scala:358) at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:75) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)

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