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

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via Stack Overflow by satish chandra
, 5 months ago
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(FileSystem.java:643)
at org.apache.hadoop.fs.RawLocalFileSystem.pathToFile(RawLocalFileSystem.java:79)
at org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:506)
at org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:724)
at org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:501)
at org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:397)
at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:235)
at org.bdgenomics.adam.rdd.ADAMContext$anonfun$loadAlignments$1.apply(ADAMContext.scala:491)
at org.bdgenomics.adam.rdd.ADAMContext$anonfun$loadAlignments$1.apply(ADAMContext.scala:488)
at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:486)
at org.bdgenomics.adam.cli.Transform.run(Transform.scala:147)
at org.bdgenomics.adam.cli.ADAMSparkCommand$class.run(ADAMCommand.scala:57)
at org.bdgenomics.adam.cli.Transform.run(Transform.scala:84)
at org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:107)
at org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$runMain(SparkSubmit.scala:569)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:166)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:189)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:110)

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