java.lang.IllegalArgumentException

Cannot encode phred score: 243

Samebug tips0

There are no available Samebug tips for this exception. If you know how to solve this issue, help other users by writing a short tip.

Don't give up yet. Paste your full stack trace to get a solution.

Solutions on the web4069

  • via Google Groups by Sungwook Yoon, 6 months ago
    Cannot encode phred score: 243
  • via GitHub by wichne
    , 2 months ago
    Cannot score V, O
  • Cannot score R, ?
  • Stack trace

    • java.lang.IllegalArgumentException: Cannot encode phred score: 243 at htsjdk.samtools.SAMUtils.phredToFastq(SAMUtils.java:364) at htsjdk.samtools.SAMUtils.phredToFastq(SAMUtils.java:351) at htsjdk.samtools.SAMUtils.phredToFastq(SAMUtils.java:336) at htsjdk.samtools.SAMRecord.getBaseQualityString(SAMRecord.java:251) at org.bdgenomics.adam.converters.SAMRecordConverter.convert(SAMRecordConverter.scala:68) at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadBam$1.apply(ADAMContext.scala:263) at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadBam$1.apply(ADAMContext.scala:263) at scala.collection.Iterator$$anon$11.next(Iterator.scala:328) at scala.collection.Iterator$$anon$11.next(Iterator.scala:328) at org.apache.spark.rdd.PairRDDFunctions$$anonfun$12.apply(PairRDDFunctions.scala:992) at org.apache.spark.rdd.PairRDDFunctions$$anonfun$12.apply(PairRDDFunctions.scala:969) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61) at org.apache.spark.scheduler.Task.run(Task.scala:56) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:200) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745)

    Write tip

    You have a different solution? A short tip here would help you and many other users who saw this issue last week.

    Users with the same issue

    You’re the first here who have seen this exception.