java.lang.IllegalArgumentException

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  • adam transform illegal phred score error
    via by Sungwook Yoon,
    • 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)
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