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

GitHub | lbergelson | 9 months ago
tip
Click on the to mark the solution that helps you, Samebug will learn from it.
As a community member, you’ll be rewarded for you help.
  1. 0

    reading a headerless sam file fails

    GitHub | 9 months ago | lbergelson
    java.lang.IllegalArgumentException: unknown SAM format, cannot create RecordReader: file:/Users/louisb/Workspace/gatk/test.sam
  2. 0

    GitHub comment 1417#174655123

    GitHub | 1 year ago | lbergelson
    java.lang.IllegalArgumentException: unknown SAM format, cannot create RecordReader: file:/local/dev/akiezun/bin/gatk/src/test/resources/org/broadinstitute/hellbender/tools/valid.bam

    Root Cause Analysis

    1. java.lang.IllegalArgumentException

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

      at org.seqdoop.hadoop_bam.AnySAMInputFormat.createRecordReader()
    2. org.seqdoop.hadoop_bam
      AnySAMInputFormat.createRecordReader
      1. org.seqdoop.hadoop_bam.AnySAMInputFormat.createRecordReader(AnySAMInputFormat.java:186)
      1 frame
    3. Spark
      RDD.iterator
      1. org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>(NewHadoopRDD.scala:156)
      2. org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:129)
      3. org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:64)
      4. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
      5. org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
      6. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
      7. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
      8. org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
      8 frames