java.lang.IllegalArgumentException: unknown SAM format, cannot create RecordReader: file:/Users/louisb/Workspace/gatk/test.sam

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via GitHub by lbergelson
, 1 year ago
unknown SAM format, cannot create RecordReader: file:/Users/louisb/Workspace/gatk/test.sam
via GitHub by lbergelson
, 1 year ago
unknown SAM format, cannot create RecordReader: file:/local/dev/akiezun/bin/gatk/src/test/resources/org/broadinstitute/hellbender/tools/valid.bam
java.lang.IllegalArgumentException: unknown SAM format, cannot create RecordReader: file:/Users/louisb/Workspace/gatk/test.sam
at org.seqdoop.hadoop_bam.AnySAMInputFormat.createRecordReader(AnySAMInputFormat.java:186)
at org.apache.spark.rdd.NewHadoopRDD$$anon$1.(NewHadoopRDD.scala:156)
at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:129)
at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:64)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)

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