HG19_BED_ANNOTATION dataset select and materialize issue

[acanakoglu]

I tried to run the query below and I got the error as I mentioned in the end of the issue.

DATA_SET_VAR = SELECT() HG19_BED_ANNOTATION;
MATERIALIZE DATA_SET_VAR INTO RESULT_DS;

This error has happened for the specific annotation types which are:

• exons
• gene

The error from log in the interface is as below:

2017-09-07 13:20:47,526 ERROR [Executor] Exception in task 0.0 in stage 8.0 (TID 7)
java.lang.IllegalArgumentException: Comparison method violates its general contract!
at org.apache.spark.util.collection.TimSort$SortState.mergeLo(TimSort.java:794)
at org.apache.spark.util.collection.TimSort$SortState.mergeAt(TimSort.java:525)
at org.apache.spark.util.collection.TimSort$SortState.mergeCollapse(TimSort.java:453)
at org.apache.spark.util.collection.TimSort$SortState.access$200(TimSort.java:325)
at org.apache.spark.util.collection.TimSort.sort(TimSort.java:153)
at org.apache.spark.util.collection.Sorter.sort(Sorter.scala:37)
at org.apache.spark.util.collection.PartitionedPairBuffer.partitionedDestructiveSortedIterator(PartitionedPairBuffer.scala:78)
at org.apache.spark.util.collection.ExternalSorter.partitionedIterator(ExternalSorter.scala:659)
at org.apache.spark.util.collection.ExternalSorter.iterator(ExternalSorter.scala:673)
at org.apache.spark.shuffle.BlockStoreShuffleReader.read(BlockStoreShuffleReader.scala:106)
at org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:105)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
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)