java.lang.IllegalArgumentException

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  • BwaSpark blows up on some reads
    via GitHub by akiezun
    ,
    • java.lang.IllegalArgumentException: String tag does not have length() == 2: at htsjdk.samtools.SAMTagUtil.makeBinaryTag(SAMTagUtil.java:100) at htsjdk.samtools.SAMRecord.setAttribute(SAMRecord.java:1364) at htsjdk.samtools.SAMLineParser.parseTag(SAMLineParser.java:436) at htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:346) at htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:213) at org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkEngine.lambda$alignWithBWA$464b6154$1(BwaSparkEngine.java:75) at org.apache.spark.api.java.JavaPairRDD$$anonfun$toScalaFunction$1.apply(JavaPairRDD.scala:1015) at scala.collection.Iterator$$anon$11.next(Iterator.scala:328) at scala.collection.Iterator$$anon$11.next(Iterator.scala:328) at scala.collection.Iterator$$anon$11.next(Iterator.scala:328) at scala.collection.Iterator$$anon$11.next(Iterator.scala:328) at org.apache.spark.util.random.SamplingUtils$.reservoirSampleAndCount(SamplingUtils.scala:42) at org.apache.spark.RangePartitioner$$anonfun$9.apply(Partitioner.scala:261) at org.apache.spark.RangePartitioner$$anonfun$9.apply(Partitioner.scala:259) at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1$$anonfun$apply$22.apply(RDD.scala:745) at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1$$anonfun$apply$22.apply(RDD.scala:745) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306) at org.apache.spark.rdd.RDD.iterator(RDD.scala:270) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66) at org.apache.spark.scheduler.Task.run(Task.scala:89) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)
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