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

GitHub | lbergelson | 4 months ago
  1. 0

    reading a headerless sam file fails

    GitHub | 4 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 | 11 months 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
  3. 0

    problem loading VCF when running adam-submit

    Google Groups | 2 years ago | sjo...@thehyve.nl
    java.lang.IllegalArgumentException: unknown VCF format, cannot create RecordReader: file:/mnt/28genome_SNP.vcf org.seqdoop.hadoop_bam.VCFInputFormat.createRecordReader(VCFInputFormat.java:178) org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>(NewHadoopRDD.scala:115) org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:103) org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:65) org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:262) org.apache.spark.rdd.RDD.iterator(RDD.scala:229) org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:62) org.apache.spark.scheduler.Task.run(Task.scala:54) org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:177) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) java.lang.Thread.run(Thread.java:745) Driver stacktrace:
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  5. 0

    [Markers] Error - unhandled event loop exception

    Eclipse Bugzilla | 7 years ago | t.kernstock
    org.eclipse.swt.SWTException: Failed to execute runnable (java.lang.IllegalArgumentException: unknown format type at )
  6. 0

    Japanese broken (and unit tests inconsistent)

    GitHub | 2 years ago | Cervator
    java.lang.IllegalArgumentException: unknown format type: ??

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    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