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Reads2coverage NPEs on unmapped reads #1227

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fnothaft opened this issue Oct 27, 2016 · 0 comments
Closed

Reads2coverage NPEs on unmapped reads #1227

fnothaft opened this issue Oct 27, 2016 · 0 comments
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@fnothaft fnothaft commented Oct 27, 2016

Stack trace:

16/10/27 07:28:39 WARN scheduler.TaskSetManager: Lost task 369.0 in stage 0.0 (TID 352, amp-bdg-09.amplab.net): java.lang.NullPointerException
    at scala.Predef$.Long2long(Predef.scala:393)
    at org.bdgenomics.adam.rdd.read.AlignmentRecordRDD$$anonfun$2.apply(AlignmentRecordRDD.scala:102)
    at org.bdgenomics.adam.rdd.read.AlignmentRecordRDD$$anonfun$2.apply(AlignmentRecordRDD.scala:101)
    at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
    at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:192)
    at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:64)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:73)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
    at org.apache.spark.scheduler.Task.run(Task.scala:89)
    at org.apache.spark.executor.Executor$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)

Specifically, we should filter unmapped reads before the flatMap at https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala#L101.

@fnothaft fnothaft added the bug label Oct 27, 2016
@fnothaft fnothaft self-assigned this Oct 27, 2016
fnothaft added a commit to fnothaft/adam that referenced this issue Oct 27, 2016
Resolves bigdatagenomics#1227. Filters out unmapped reads before counting coverage.
@heuermh heuermh closed this in #1230 Nov 2, 2016
heuermh added a commit that referenced this issue Nov 2, 2016
Resolves #1227. Filters out unmapped reads before counting coverage.
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