java.lang.IllegalArgumentException: Cannot encode phred score: 243

Google Groups | Sungwook Yoon | 2 years ago
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    adam transform illegal phred score error

    Google Groups | 2 years ago | Sungwook Yoon
    java.lang.IllegalArgumentException: Cannot encode phred score: 243

    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Cannot encode phred score: 243

      at htsjdk.samtools.SAMUtils.phredToFastq()
    2. HTS JDK
      SAMRecord.getBaseQualityString
      1. htsjdk.samtools.SAMUtils.phredToFastq(SAMUtils.java:364)
      2. htsjdk.samtools.SAMUtils.phredToFastq(SAMUtils.java:351)
      3. htsjdk.samtools.SAMUtils.phredToFastq(SAMUtils.java:336)
      4. htsjdk.samtools.SAMRecord.getBaseQualityString(SAMRecord.java:251)
      4 frames
    3. org.bdgenomics.adam
      ADAMContext$$anonfun$loadBam$1.apply
      1. org.bdgenomics.adam.converters.SAMRecordConverter.convert(SAMRecordConverter.scala:68)
      2. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadBam$1.apply(ADAMContext.scala:263)
      3. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadBam$1.apply(ADAMContext.scala:263)
      3 frames
    4. Scala
      Iterator$$anon$11.next
      1. scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
      2. scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
      2 frames
    5. Spark
      Executor$TaskRunner.run
      1. org.apache.spark.rdd.PairRDDFunctions$$anonfun$12.apply(PairRDDFunctions.scala:992)
      2. org.apache.spark.rdd.PairRDDFunctions$$anonfun$12.apply(PairRDDFunctions.scala:969)
      3. org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
      4. org.apache.spark.scheduler.Task.run(Task.scala:56)
      5. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:200)
      5 frames
    6. Java RT
      Thread.run
      1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
      2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
      3. java.lang.Thread.run(Thread.java:745)
      3 frames