Class org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSourceUnitTest

all > org.broadinstitute.hellbender.engine.spark.datasources > ReadsSparkSourceUnitTest
28

tests
0

failures
2

ignored
3.133s

duration
100%

successful

Tests

Test Duration Result
loadReadsNonExistentReference 0.001s passed
readsSparkSourceTestLenient[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.263s passed
readsSparkSourceTestLenient[1](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.181s passed
readsSparkSourceTestSilent[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.208s passed
readsSparkSourceTestSilent[1](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.159s passed
readsSparkSourceTestStrict[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.048s passed
readsSparkSourceTestStrict[1](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.035s passed
readsSparkSourceTest[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.443s passed
readsSparkSourceTest[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam, null) 0.266s passed
readsSparkSourceTest[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, null) 0.240s passed
readsSparkSourceTest[3](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.186s passed
readsSparkSourceTest[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.cram, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.fasta) 0.235s passed
readsSparkSourceUnknownHostTest 0.026s passed
shardedReadsSparkSourceTest[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.sharded.bam, null) 0.274s passed
testCRAMReferenceFromHDFS - ignored
testCRAMReferenceRequired 0s passed
testCheckCRAMReference 0s passed
testGetHeader[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.031s passed
testGetHeader[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam, null) 0.030s passed
testGetHeader[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, null) 0.030s passed
testGetHeader[3](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.025s passed
testGetHeader[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.cram, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.fasta) 0.026s passed
testHeadersAreStripped 0.143s passed
testIntervals 0.118s passed
testIntervalsWithUnmapped 0.102s passed
testPartitionSizing 0.063s passed
testReadFromFileAndHDFS - ignored
testReject2BitCRAMReference 0s passed

Standard error

16:12:15.241 INFO  MemoryStore - Block broadcast_34 stored as values in memory (estimated size 297.2 KiB, free 1919.6 MiB)
16:12:15.264 INFO  MemoryStore - Block broadcast_34_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1919.5 MiB)
16:12:15.264 INFO  BlockManagerInfo - Added broadcast_34_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.9 MiB)
16:12:15.265 INFO  SparkContext - Created broadcast 34 from newAPIHadoopFile at PathSplitSource.java:96
16:12:15.325 INFO  MemoryStore - Block broadcast_35 stored as values in memory (estimated size 297.2 KiB, free 1919.2 MiB)
16:12:15.336 INFO  MemoryStore - Block broadcast_35_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1919.2 MiB)
16:12:15.336 INFO  BlockManagerInfo - Added broadcast_35_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.9 MiB)
16:12:15.337 INFO  SparkContext - Created broadcast 35 from newAPIHadoopFile at PathSplitSource.java:96
16:12:15.375 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
16:12:15.376 INFO  DAGScheduler - Got job 20 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
16:12:15.376 INFO  DAGScheduler - Final stage: ResultStage 29 (collect at ReadsSparkSourceUnitTest.java:111)
16:12:15.376 INFO  DAGScheduler - Parents of final stage: List()
16:12:15.376 INFO  DAGScheduler - Missing parents: List()
16:12:15.376 INFO  DAGScheduler - Submitting ResultStage 29 (ParallelCollectionRDD[69] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
16:12:15.377 INFO  MemoryStore - Block broadcast_36 stored as values in memory (estimated size 3.0 KiB, free 1919.2 MiB)
16:12:15.378 INFO  MemoryStore - Block broadcast_36_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1919.2 MiB)
16:12:15.378 INFO  BlockManagerInfo - Added broadcast_36_piece0 in memory on localhost:40883 (size: 1780.0 B, free: 1919.9 MiB)
16:12:15.378 INFO  SparkContext - Created broadcast 36 from broadcast at DAGScheduler.scala:1580
16:12:15.379 INFO  DAGScheduler - Submitting 4 missing tasks from ResultStage 29 (ParallelCollectionRDD[69] at parallelize at ReadsSparkSourceUnitTest.java:310) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
16:12:15.379 INFO  TaskSchedulerImpl - Adding task set 29.0 with 4 tasks resource profile 0
16:12:15.380 INFO  TaskSetManager - Starting task 0.0 in stage 29.0 (TID 67) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes) 
16:12:15.381 INFO  TaskSetManager - Starting task 1.0 in stage 29.0 (TID 68) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes) 
16:12:15.382 INFO  TaskSetManager - Starting task 2.0 in stage 29.0 (TID 69) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes) 
16:12:15.384 INFO  TaskSetManager - Starting task 3.0 in stage 29.0 (TID 70) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes) 
16:12:15.385 INFO  Executor - Running task 3.0 in stage 29.0 (TID 70)
16:12:15.385 INFO  Executor - Running task 1.0 in stage 29.0 (TID 68)
16:12:15.385 INFO  Executor - Running task 0.0 in stage 29.0 (TID 67)
16:12:15.386 INFO  Executor - Running task 2.0 in stage 29.0 (TID 69)
16:12:15.395 INFO  Executor - Finished task 3.0 in stage 29.0 (TID 70). 40805 bytes result sent to driver
16:12:15.397 INFO  Executor - Finished task 0.0 in stage 29.0 (TID 67). 40398 bytes result sent to driver
16:12:15.398 INFO  Executor - Finished task 2.0 in stage 29.0 (TID 69). 40423 bytes result sent to driver
16:12:15.399 INFO  Executor - Finished task 1.0 in stage 29.0 (TID 68). 40512 bytes result sent to driver
16:12:15.399 INFO  TaskSetManager - Finished task 3.0 in stage 29.0 (TID 70) in 16 ms on localhost (executor driver) (1/4)
16:12:15.400 INFO  TaskSetManager - Finished task 0.0 in stage 29.0 (TID 67) in 21 ms on localhost (executor driver) (2/4)
16:12:15.401 INFO  TaskSetManager - Finished task 2.0 in stage 29.0 (TID 69) in 19 ms on localhost (executor driver) (3/4)
16:12:15.401 INFO  TaskSetManager - Finished task 1.0 in stage 29.0 (TID 68) in 20 ms on localhost (executor driver) (4/4)
16:12:15.401 INFO  TaskSchedulerImpl - Removed TaskSet 29.0, whose tasks have all completed, from pool 
16:12:15.402 INFO  DAGScheduler - ResultStage 29 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.026 s
16:12:15.402 INFO  DAGScheduler - Job 20 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:15.402 INFO  TaskSchedulerImpl - Killing all running tasks in stage 29: Stage finished
16:12:15.402 INFO  DAGScheduler - Job 20 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.027134 s
16:12:15.419 INFO  FileInputFormat - Total input files to process : 1
16:12:15.475 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
16:12:15.475 INFO  DAGScheduler - Got job 21 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
16:12:15.475 INFO  DAGScheduler - Final stage: ResultStage 30 (collect at ReadsSparkSourceUnitTest.java:112)
16:12:15.475 INFO  DAGScheduler - Parents of final stage: List()
16:12:15.476 INFO  DAGScheduler - Missing parents: List()
16:12:15.476 INFO  DAGScheduler - Submitting ResultStage 30 (MapPartitionsRDD[76] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:15.502 INFO  MemoryStore - Block broadcast_37 stored as values in memory (estimated size 425.0 KiB, free 1918.8 MiB)
16:12:15.504 INFO  MemoryStore - Block broadcast_37_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1918.6 MiB)
16:12:15.505 INFO  BlockManagerInfo - Added broadcast_37_piece0 in memory on localhost:40883 (size: 152.7 KiB, free: 1919.7 MiB)
16:12:15.505 INFO  SparkContext - Created broadcast 37 from broadcast at DAGScheduler.scala:1580
16:12:15.505 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 30 (MapPartitionsRDD[76] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:15.505 INFO  TaskSchedulerImpl - Adding task set 30.0 with 1 tasks resource profile 0
16:12:15.512 INFO  TaskSetManager - Starting task 0.0 in stage 30.0 (TID 71) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
16:12:15.512 INFO  Executor - Running task 0.0 in stage 30.0 (TID 71)
16:12:15.578 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
16:12:15.614 INFO  Executor - Finished task 0.0 in stage 30.0 (TID 71). 159615 bytes result sent to driver
16:12:15.615 INFO  TaskSetManager - Finished task 0.0 in stage 30.0 (TID 71) in 109 ms on localhost (executor driver) (1/1)
16:12:15.615 INFO  TaskSchedulerImpl - Removed TaskSet 30.0, whose tasks have all completed, from pool 
16:12:15.616 INFO  DAGScheduler - ResultStage 30 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.138 s
16:12:15.616 INFO  DAGScheduler - Job 21 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:15.616 INFO  TaskSchedulerImpl - Killing all running tasks in stage 30: Stage finished
16:12:15.616 INFO  DAGScheduler - Job 21 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.141268 s
16:12:15.624 INFO  MemoryStore - Block broadcast_38 stored as values in memory (estimated size 297.3 KiB, free 1918.3 MiB)
16:12:15.633 INFO  MemoryStore - Block broadcast_38_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.3 MiB)
16:12:15.633 INFO  BlockManagerInfo - Added broadcast_38_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1919.7 MiB)
16:12:15.634 INFO  SparkContext - Created broadcast 38 from newAPIHadoopFile at PathSplitSource.java:96
16:12:15.669 INFO  MemoryStore - Block broadcast_39 stored as values in memory (estimated size 297.3 KiB, free 1918.0 MiB)
16:12:15.677 INFO  MemoryStore - Block broadcast_39_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.9 MiB)
16:12:15.677 INFO  BlockManagerInfo - Added broadcast_39_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1919.6 MiB)
16:12:15.677 INFO  SparkContext - Created broadcast 39 from newAPIHadoopFile at PathSplitSource.java:96
16:12:15.704 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
16:12:15.705 INFO  DAGScheduler - Got job 22 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
16:12:15.705 INFO  DAGScheduler - Final stage: ResultStage 31 (collect at ReadsSparkSourceUnitTest.java:111)
16:12:15.705 INFO  DAGScheduler - Parents of final stage: List()
16:12:15.705 INFO  DAGScheduler - Missing parents: List()
16:12:15.705 INFO  DAGScheduler - Submitting ResultStage 31 (ParallelCollectionRDD[82] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
16:12:15.706 INFO  MemoryStore - Block broadcast_40 stored as values in memory (estimated size 3.0 KiB, free 1917.9 MiB)
16:12:15.707 INFO  MemoryStore - Block broadcast_40_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1917.9 MiB)
16:12:15.707 INFO  BlockManagerInfo - Added broadcast_40_piece0 in memory on localhost:40883 (size: 1780.0 B, free: 1919.6 MiB)
16:12:15.707 INFO  SparkContext - Created broadcast 40 from broadcast at DAGScheduler.scala:1580
16:12:15.708 INFO  DAGScheduler - Submitting 4 missing tasks from ResultStage 31 (ParallelCollectionRDD[82] at parallelize at ReadsSparkSourceUnitTest.java:310) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
16:12:15.708 INFO  TaskSchedulerImpl - Adding task set 31.0 with 4 tasks resource profile 0
16:12:15.710 INFO  TaskSetManager - Starting task 0.0 in stage 31.0 (TID 72) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes) 
16:12:15.712 INFO  TaskSetManager - Starting task 1.0 in stage 31.0 (TID 73) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes) 
16:12:15.714 INFO  TaskSetManager - Starting task 2.0 in stage 31.0 (TID 74) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes) 
16:12:15.715 INFO  TaskSetManager - Starting task 3.0 in stage 31.0 (TID 75) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes) 
16:12:15.716 INFO  Executor - Running task 2.0 in stage 31.0 (TID 74)
16:12:15.716 INFO  Executor - Running task 3.0 in stage 31.0 (TID 75)
16:12:15.716 INFO  Executor - Running task 0.0 in stage 31.0 (TID 72)
16:12:15.717 INFO  Executor - Running task 1.0 in stage 31.0 (TID 73)
16:12:15.722 INFO  Executor - Finished task 0.0 in stage 31.0 (TID 72). 163204 bytes result sent to driver
16:12:15.724 INFO  TaskSetManager - Finished task 0.0 in stage 31.0 (TID 72) in 16 ms on localhost (executor driver) (1/4)
16:12:15.726 INFO  Executor - Finished task 2.0 in stage 31.0 (TID 74). 163399 bytes result sent to driver
16:12:15.726 INFO  Executor - Finished task 3.0 in stage 31.0 (TID 75). 162737 bytes result sent to driver
16:12:15.728 INFO  TaskSetManager - Finished task 2.0 in stage 31.0 (TID 74) in 16 ms on localhost (executor driver) (2/4)
16:12:15.729 INFO  Executor - Finished task 1.0 in stage 31.0 (TID 73). 163411 bytes result sent to driver
16:12:15.729 INFO  TaskSetManager - Finished task 3.0 in stage 31.0 (TID 75) in 15 ms on localhost (executor driver) (3/4)
16:12:15.730 INFO  TaskSetManager - Finished task 1.0 in stage 31.0 (TID 73) in 20 ms on localhost (executor driver) (4/4)
16:12:15.730 INFO  TaskSchedulerImpl - Removed TaskSet 31.0, whose tasks have all completed, from pool 
16:12:15.731 INFO  DAGScheduler - ResultStage 31 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.026 s
16:12:15.731 INFO  DAGScheduler - Job 22 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:15.731 INFO  TaskSchedulerImpl - Killing all running tasks in stage 31: Stage finished
16:12:15.731 INFO  DAGScheduler - Job 22 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.026421 s
16:12:15.733 INFO  FileInputFormat - Total input files to process : 1
16:12:15.774 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
16:12:15.775 INFO  DAGScheduler - Got job 23 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
16:12:15.775 INFO  DAGScheduler - Final stage: ResultStage 32 (collect at ReadsSparkSourceUnitTest.java:112)
16:12:15.775 INFO  DAGScheduler - Parents of final stage: List()
16:12:15.775 INFO  DAGScheduler - Missing parents: List()
16:12:15.775 INFO  DAGScheduler - Submitting ResultStage 32 (MapPartitionsRDD[89] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:15.795 INFO  MemoryStore - Block broadcast_41 stored as values in memory (estimated size 425.0 KiB, free 1917.5 MiB)
16:12:15.797 INFO  MemoryStore - Block broadcast_41_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.4 MiB)
16:12:15.797 INFO  BlockManagerInfo - Added broadcast_41_piece0 in memory on localhost:40883 (size: 152.7 KiB, free: 1919.5 MiB)
16:12:15.797 INFO  SparkContext - Created broadcast 41 from broadcast at DAGScheduler.scala:1580
16:12:15.798 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 32 (MapPartitionsRDD[89] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:15.798 INFO  TaskSchedulerImpl - Adding task set 32.0 with 1 tasks resource profile 0
16:12:15.799 INFO  TaskSetManager - Starting task 0.0 in stage 32.0 (TID 76) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7875 bytes) 
16:12:15.799 INFO  Executor - Running task 0.0 in stage 32.0 (TID 76)
16:12:15.841 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam:0+221635
16:12:15.877 INFO  Executor - Finished task 0.0 in stage 32.0 (TID 76). 650184 bytes result sent to driver
16:12:15.881 INFO  TaskSetManager - Finished task 0.0 in stage 32.0 (TID 76) in 83 ms on localhost (executor driver) (1/1)
16:12:15.882 INFO  TaskSchedulerImpl - Removed TaskSet 32.0, whose tasks have all completed, from pool 
16:12:15.882 INFO  DAGScheduler - ResultStage 32 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.106 s
16:12:15.882 INFO  DAGScheduler - Job 23 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:15.882 INFO  TaskSchedulerImpl - Killing all running tasks in stage 32: Stage finished
16:12:15.882 INFO  DAGScheduler - Job 23 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.107760 s
16:12:15.891 INFO  MemoryStore - Block broadcast_42 stored as values in memory (estimated size 297.3 KiB, free 1917.1 MiB)
16:12:15.898 INFO  MemoryStore - Block broadcast_42_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.0 MiB)
16:12:15.899 INFO  BlockManagerInfo - Added broadcast_42_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1919.4 MiB)
16:12:15.899 INFO  SparkContext - Created broadcast 42 from newAPIHadoopFile at PathSplitSource.java:96
16:12:15.933 INFO  MemoryStore - Block broadcast_43 stored as values in memory (estimated size 297.3 KiB, free 1916.7 MiB)
16:12:15.940 INFO  MemoryStore - Block broadcast_43_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.7 MiB)
16:12:15.940 INFO  BlockManagerInfo - Added broadcast_43_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1919.4 MiB)
16:12:15.940 INFO  SparkContext - Created broadcast 43 from newAPIHadoopFile at PathSplitSource.java:96
16:12:15.966 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
16:12:15.966 INFO  DAGScheduler - Got job 24 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
16:12:15.966 INFO  DAGScheduler - Final stage: ResultStage 33 (collect at ReadsSparkSourceUnitTest.java:111)
16:12:15.966 INFO  DAGScheduler - Parents of final stage: List()
16:12:15.966 INFO  DAGScheduler - Missing parents: List()
16:12:15.966 INFO  DAGScheduler - Submitting ResultStage 33 (ParallelCollectionRDD[95] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
16:12:15.967 INFO  MemoryStore - Block broadcast_44 stored as values in memory (estimated size 3.0 KiB, free 1916.7 MiB)
16:12:15.968 INFO  MemoryStore - Block broadcast_44_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1916.7 MiB)
16:12:15.968 INFO  BlockManagerInfo - Added broadcast_44_piece0 in memory on localhost:40883 (size: 1780.0 B, free: 1919.4 MiB)
16:12:15.968 INFO  SparkContext - Created broadcast 44 from broadcast at DAGScheduler.scala:1580
16:12:15.969 INFO  DAGScheduler - Submitting 4 missing tasks from ResultStage 33 (ParallelCollectionRDD[95] at parallelize at ReadsSparkSourceUnitTest.java:310) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
16:12:15.969 INFO  TaskSchedulerImpl - Adding task set 33.0 with 4 tasks resource profile 0
16:12:15.970 INFO  TaskSetManager - Starting task 0.0 in stage 33.0 (TID 77) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes) 
16:12:15.971 INFO  TaskSetManager - Starting task 1.0 in stage 33.0 (TID 78) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes) 
16:12:15.972 INFO  TaskSetManager - Starting task 2.0 in stage 33.0 (TID 79) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes) 
16:12:15.973 INFO  TaskSetManager - Starting task 3.0 in stage 33.0 (TID 80) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes) 
16:12:15.973 INFO  Executor - Running task 3.0 in stage 33.0 (TID 80)
16:12:15.973 INFO  Executor - Running task 2.0 in stage 33.0 (TID 79)
16:12:15.973 INFO  Executor - Running task 0.0 in stage 33.0 (TID 77)
16:12:15.973 INFO  Executor - Running task 1.0 in stage 33.0 (TID 78)
16:12:15.979 INFO  Executor - Finished task 2.0 in stage 33.0 (TID 79). 163356 bytes result sent to driver
16:12:15.980 INFO  Executor - Finished task 3.0 in stage 33.0 (TID 80). 162694 bytes result sent to driver
16:12:15.981 INFO  Executor - Finished task 0.0 in stage 33.0 (TID 77). 163161 bytes result sent to driver
16:12:15.981 INFO  Executor - Finished task 1.0 in stage 33.0 (TID 78). 163411 bytes result sent to driver
16:12:15.983 INFO  TaskSetManager - Finished task 3.0 in stage 33.0 (TID 80) in 11 ms on localhost (executor driver) (1/4)
16:12:15.983 INFO  TaskSetManager - Finished task 2.0 in stage 33.0 (TID 79) in 12 ms on localhost (executor driver) (2/4)
16:12:15.983 INFO  TaskSetManager - Finished task 1.0 in stage 33.0 (TID 78) in 13 ms on localhost (executor driver) (3/4)
16:12:15.984 INFO  TaskSetManager - Finished task 0.0 in stage 33.0 (TID 77) in 15 ms on localhost (executor driver) (4/4)
16:12:15.984 INFO  TaskSchedulerImpl - Removed TaskSet 33.0, whose tasks have all completed, from pool 
16:12:15.984 INFO  DAGScheduler - ResultStage 33 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.017 s
16:12:15.984 INFO  DAGScheduler - Job 24 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:15.985 INFO  TaskSchedulerImpl - Killing all running tasks in stage 33: Stage finished
16:12:15.985 INFO  DAGScheduler - Job 24 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.018915 s
16:12:15.987 INFO  FileInputFormat - Total input files to process : 1
16:12:16.027 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
16:12:16.027 INFO  DAGScheduler - Got job 25 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
16:12:16.028 INFO  DAGScheduler - Final stage: ResultStage 34 (collect at ReadsSparkSourceUnitTest.java:112)
16:12:16.028 INFO  DAGScheduler - Parents of final stage: List()
16:12:16.028 INFO  DAGScheduler - Missing parents: List()
16:12:16.028 INFO  DAGScheduler - Submitting ResultStage 34 (MapPartitionsRDD[102] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:16.051 INFO  MemoryStore - Block broadcast_45 stored as values in memory (estimated size 425.0 KiB, free 1916.3 MiB)
16:12:16.053 INFO  MemoryStore - Block broadcast_45_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1916.1 MiB)
16:12:16.053 INFO  BlockManagerInfo - Added broadcast_45_piece0 in memory on localhost:40883 (size: 152.7 KiB, free: 1919.2 MiB)
16:12:16.054 INFO  SparkContext - Created broadcast 45 from broadcast at DAGScheduler.scala:1580
16:12:16.054 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 34 (MapPartitionsRDD[102] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:16.054 INFO  TaskSchedulerImpl - Adding task set 34.0 with 1 tasks resource profile 0
16:12:16.055 INFO  TaskSetManager - Starting task 0.0 in stage 34.0 (TID 81) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7905 bytes) 
16:12:16.055 INFO  Executor - Running task 0.0 in stage 34.0 (TID 81)
16:12:16.097 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam:0+216896
16:12:16.119 INFO  Executor - Finished task 0.0 in stage 34.0 (TID 81). 650184 bytes result sent to driver
16:12:16.122 INFO  TaskSetManager - Finished task 0.0 in stage 34.0 (TID 81) in 67 ms on localhost (executor driver) (1/1)
16:12:16.122 INFO  TaskSchedulerImpl - Removed TaskSet 34.0, whose tasks have all completed, from pool 
16:12:16.122 INFO  DAGScheduler - ResultStage 34 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.094 s
16:12:16.122 INFO  DAGScheduler - Job 25 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:16.122 INFO  TaskSchedulerImpl - Killing all running tasks in stage 34: Stage finished
16:12:16.122 INFO  DAGScheduler - Job 25 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.095512 s
16:12:16.129 INFO  MemoryStore - Block broadcast_46 stored as values in memory (estimated size 528.0 B, free 1916.1 MiB)
16:12:16.130 INFO  MemoryStore - Block broadcast_46_piece0 stored as bytes in memory (estimated size 183.0 B, free 1916.1 MiB)
16:12:16.130 INFO  BlockManagerInfo - Added broadcast_46_piece0 in memory on localhost:40883 (size: 183.0 B, free: 1919.2 MiB)
16:12:16.131 INFO  SparkContext - Created broadcast 46 from broadcast at CramSource.java:114
16:12:16.133 INFO  MemoryStore - Block broadcast_47 stored as values in memory (estimated size 297.2 KiB, free 1915.8 MiB)
16:12:16.140 INFO  MemoryStore - Block broadcast_47_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.8 MiB)
16:12:16.140 INFO  BlockManagerInfo - Added broadcast_47_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.2 MiB)
16:12:16.140 INFO  SparkContext - Created broadcast 47 from newAPIHadoopFile at PathSplitSource.java:96
16:12:16.170 INFO  MemoryStore - Block broadcast_48 stored as values in memory (estimated size 528.0 B, free 1915.8 MiB)
16:12:16.171 INFO  MemoryStore - Block broadcast_48_piece0 stored as bytes in memory (estimated size 183.0 B, free 1915.8 MiB)
16:12:16.171 INFO  BlockManagerInfo - Added broadcast_48_piece0 in memory on localhost:40883 (size: 183.0 B, free: 1919.2 MiB)
16:12:16.172 INFO  SparkContext - Created broadcast 48 from broadcast at CramSource.java:114
16:12:16.174 INFO  MemoryStore - Block broadcast_49 stored as values in memory (estimated size 297.2 KiB, free 1915.5 MiB)
16:12:16.181 INFO  MemoryStore - Block broadcast_49_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.4 MiB)
16:12:16.181 INFO  BlockManagerInfo - Added broadcast_49_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.1 MiB)
16:12:16.182 INFO  SparkContext - Created broadcast 49 from newAPIHadoopFile at PathSplitSource.java:96
16:12:16.200 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
16:12:16.201 INFO  DAGScheduler - Got job 26 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
16:12:16.201 INFO  DAGScheduler - Final stage: ResultStage 35 (collect at ReadsSparkSourceUnitTest.java:111)
16:12:16.201 INFO  DAGScheduler - Parents of final stage: List()
16:12:16.201 INFO  DAGScheduler - Missing parents: List()
16:12:16.201 INFO  DAGScheduler - Submitting ResultStage 35 (ParallelCollectionRDD[107] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
16:12:16.202 INFO  MemoryStore - Block broadcast_50 stored as values in memory (estimated size 3.0 KiB, free 1915.4 MiB)
16:12:16.203 INFO  MemoryStore - Block broadcast_50_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1915.4 MiB)
16:12:16.203 INFO  BlockManagerInfo - Added broadcast_50_piece0 in memory on localhost:40883 (size: 1780.0 B, free: 1919.1 MiB)
16:12:16.203 INFO  SparkContext - Created broadcast 50 from broadcast at DAGScheduler.scala:1580
16:12:16.203 INFO  DAGScheduler - Submitting 4 missing tasks from ResultStage 35 (ParallelCollectionRDD[107] at parallelize at ReadsSparkSourceUnitTest.java:310) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
16:12:16.203 INFO  TaskSchedulerImpl - Adding task set 35.0 with 4 tasks resource profile 0
16:12:16.207 INFO  TaskSetManager - Starting task 0.0 in stage 35.0 (TID 82) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes) 
16:12:16.209 INFO  TaskSetManager - Starting task 1.0 in stage 35.0 (TID 83) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes) 
16:12:16.210 INFO  TaskSetManager - Starting task 2.0 in stage 35.0 (TID 84) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes) 
16:12:16.211 INFO  TaskSetManager - Starting task 3.0 in stage 35.0 (TID 85) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes) 
16:12:16.212 INFO  Executor - Running task 0.0 in stage 35.0 (TID 82)
16:12:16.212 INFO  Executor - Running task 2.0 in stage 35.0 (TID 84)
16:12:16.212 INFO  Executor - Running task 3.0 in stage 35.0 (TID 85)
16:12:16.212 INFO  Executor - Running task 1.0 in stage 35.0 (TID 83)
16:12:16.216 INFO  Executor - Finished task 2.0 in stage 35.0 (TID 84). 39070 bytes result sent to driver
16:12:16.216 INFO  Executor - Finished task 3.0 in stage 35.0 (TID 85). 39343 bytes result sent to driver
16:12:16.216 INFO  Executor - Finished task 0.0 in stage 35.0 (TID 82). 38950 bytes result sent to driver
16:12:16.216 INFO  Executor - Finished task 1.0 in stage 35.0 (TID 83). 39130 bytes result sent to driver
16:12:16.217 INFO  TaskSetManager - Finished task 3.0 in stage 35.0 (TID 85) in 7 ms on localhost (executor driver) (1/4)
16:12:16.217 INFO  TaskSetManager - Finished task 0.0 in stage 35.0 (TID 82) in 13 ms on localhost (executor driver) (2/4)
16:12:16.218 INFO  TaskSetManager - Finished task 1.0 in stage 35.0 (TID 83) in 11 ms on localhost (executor driver) (3/4)
16:12:16.218 INFO  TaskSetManager - Finished task 2.0 in stage 35.0 (TID 84) in 9 ms on localhost (executor driver) (4/4)
16:12:16.218 INFO  TaskSchedulerImpl - Removed TaskSet 35.0, whose tasks have all completed, from pool 
16:12:16.218 INFO  DAGScheduler - ResultStage 35 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.016 s
16:12:16.219 INFO  DAGScheduler - Job 26 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:16.219 INFO  TaskSchedulerImpl - Killing all running tasks in stage 35: Stage finished
16:12:16.219 INFO  DAGScheduler - Job 26 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.018445 s
16:12:16.220 INFO  FileInputFormat - Total input files to process : 1
16:12:16.247 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
16:12:16.247 INFO  DAGScheduler - Got job 27 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
16:12:16.247 INFO  DAGScheduler - Final stage: ResultStage 36 (collect at ReadsSparkSourceUnitTest.java:112)
16:12:16.247 INFO  DAGScheduler - Parents of final stage: List()
16:12:16.247 INFO  DAGScheduler - Missing parents: List()
16:12:16.248 INFO  DAGScheduler - Submitting ResultStage 36 (MapPartitionsRDD[113] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:16.260 INFO  MemoryStore - Block broadcast_51 stored as values in memory (estimated size 286.0 KiB, free 1915.2 MiB)
16:12:16.261 INFO  MemoryStore - Block broadcast_51_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1915.1 MiB)
16:12:16.261 INFO  BlockManagerInfo - Added broadcast_51_piece0 in memory on localhost:40883 (size: 103.1 KiB, free: 1919.0 MiB)
16:12:16.262 INFO  SparkContext - Created broadcast 51 from broadcast at DAGScheduler.scala:1580
16:12:16.262 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 36 (MapPartitionsRDD[113] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:16.262 INFO  TaskSchedulerImpl - Adding task set 36.0 with 1 tasks resource profile 0
16:12:16.263 INFO  TaskSetManager - Starting task 0.0 in stage 36.0 (TID 86) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes) 
16:12:16.263 INFO  Executor - Running task 0.0 in stage 36.0 (TID 86)
16:12:16.292 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram:0+50619
16:12:16.306 INFO  Executor - Finished task 0.0 in stage 36.0 (TID 86). 154101 bytes result sent to driver
16:12:16.308 INFO  TaskSetManager - Finished task 0.0 in stage 36.0 (TID 86) in 45 ms on localhost (executor driver) (1/1)
16:12:16.308 INFO  TaskSchedulerImpl - Removed TaskSet 36.0, whose tasks have all completed, from pool 
16:12:16.308 INFO  DAGScheduler - ResultStage 36 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.060 s
16:12:16.308 INFO  DAGScheduler - Job 27 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:16.308 INFO  TaskSchedulerImpl - Killing all running tasks in stage 36: Stage finished
16:12:16.308 INFO  DAGScheduler - Job 27 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.061389 s
16:12:16.313 INFO  MemoryStore - Block broadcast_52 stored as values in memory (estimated size 600.0 B, free 1915.1 MiB)
16:12:16.326 INFO  BlockManagerInfo - Removed broadcast_32_piece0 on localhost:40883 in memory (size: 3.8 KiB, free: 1919.0 MiB)
16:12:16.326 INFO  MemoryStore - Block broadcast_52_piece0 stored as bytes in memory (estimated size 202.0 B, free 1915.1 MiB)
16:12:16.327 INFO  BlockManagerInfo - Added broadcast_52_piece0 in memory on localhost:40883 (size: 202.0 B, free: 1919.0 MiB)
16:12:16.327 INFO  SparkContext - Created broadcast 52 from broadcast at CramSource.java:114
16:12:16.329 INFO  BlockManagerInfo - Removed broadcast_45_piece0 on localhost:40883 in memory (size: 152.7 KiB, free: 1919.2 MiB)
16:12:16.331 INFO  MemoryStore - Block broadcast_53 stored as values in memory (estimated size 297.3 KiB, free 1915.3 MiB)
16:12:16.332 INFO  BlockManagerInfo - Removed broadcast_38_piece0 on localhost:40883 in memory (size: 50.1 KiB, free: 1919.2 MiB)
16:12:16.335 INFO  BlockManagerInfo - Removed broadcast_29_piece0 on localhost:40883 in memory (size: 3.8 KiB, free: 1919.2 MiB)
16:12:16.336 INFO  BlockManagerInfo - Removed broadcast_24_piece0 on localhost:40883 in memory (size: 4.3 KiB, free: 1919.2 MiB)
16:12:16.338 INFO  BlockManagerInfo - Removed broadcast_49_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.3 MiB)
16:12:16.340 INFO  MemoryStore - Block broadcast_53_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.0 MiB)
16:12:16.340 INFO  BlockManagerInfo - Added broadcast_53_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1919.2 MiB)
16:12:16.341 INFO  SparkContext - Created broadcast 53 from newAPIHadoopFile at PathSplitSource.java:96
16:12:16.341 INFO  BlockManagerInfo - Removed broadcast_22_piece0 on localhost:40883 in memory (size: 159.0 B, free: 1919.2 MiB)
16:12:16.343 INFO  BlockManagerInfo - Removed broadcast_28_piece0 on localhost:40883 in memory (size: 320.0 B, free: 1919.2 MiB)
16:12:16.345 INFO  BlockManagerInfo - Removed broadcast_37_piece0 on localhost:40883 in memory (size: 152.7 KiB, free: 1919.4 MiB)
16:12:16.347 INFO  BlockManagerInfo - Removed broadcast_26_piece0 on localhost:40883 in memory (size: 3.2 KiB, free: 1919.4 MiB)
16:12:16.351 INFO  BlockManager - Removing RDD 47
16:12:16.354 INFO  BlockManagerInfo - Removed broadcast_19_piece0 on localhost:40883 in memory (size: 2.4 KiB, free: 1919.4 MiB)
16:12:16.356 INFO  BlockManagerInfo - Removed broadcast_16_piece0 on localhost:40883 in memory (size: 2.4 KiB, free: 1919.4 MiB)
16:12:16.358 INFO  BlockManagerInfo - Removed broadcast_18_piece0 on localhost:40883 in memory (size: 2.4 KiB, free: 1919.4 MiB)
16:12:16.360 INFO  BlockManagerInfo - Removed broadcast_34_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.4 MiB)
16:12:16.361 INFO  BlockManagerInfo - Removed broadcast_20_piece0 on localhost:40883 in memory (size: 2.4 KiB, free: 1919.4 MiB)
16:12:16.364 INFO  BlockManagerInfo - Removed broadcast_35_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.5 MiB)
16:12:16.368 INFO  BlockManagerInfo - Removed broadcast_40_piece0 on localhost:40883 in memory (size: 1780.0 B, free: 1919.5 MiB)
16:12:16.369 INFO  BlockManagerInfo - Removed broadcast_30_piece0 on localhost:40883 in memory (size: 4.7 KiB, free: 1919.5 MiB)
16:12:16.370 INFO  MemoryStore - Block broadcast_54 stored as values in memory (estimated size 600.0 B, free 1917.3 MiB)
16:12:16.371 INFO  BlockManagerInfo - Removed broadcast_25_piece0 on localhost:40883 in memory (size: 4.5 KiB, free: 1919.5 MiB)
16:12:16.371 INFO  MemoryStore - Block broadcast_54_piece0 stored as bytes in memory (estimated size 202.0 B, free 1917.3 MiB)
16:12:16.371 INFO  BlockManagerInfo - Added broadcast_54_piece0 in memory on localhost:40883 (size: 202.0 B, free: 1919.5 MiB)
16:12:16.372 INFO  SparkContext - Created broadcast 54 from broadcast at CramSource.java:114
16:12:16.372 INFO  BlockManagerInfo - Removed broadcast_17_piece0 on localhost:40883 in memory (size: 2.4 KiB, free: 1919.5 MiB)
16:12:16.373 INFO  BlockManagerInfo - Removed broadcast_21_piece0 on localhost:40883 in memory (size: 2.4 KiB, free: 1919.5 MiB)
16:12:16.375 INFO  BlockManagerInfo - Removed broadcast_42_piece0 on localhost:40883 in memory (size: 50.1 KiB, free: 1919.5 MiB)
16:12:16.375 INFO  MemoryStore - Block broadcast_55 stored as values in memory (estimated size 297.3 KiB, free 1917.4 MiB)
16:12:16.376 INFO  BlockManagerInfo - Removed broadcast_43_piece0 on localhost:40883 in memory (size: 50.1 KiB, free: 1919.6 MiB)
16:12:16.379 INFO  BlockManagerInfo - Removed broadcast_33_piece0 on localhost:40883 in memory (size: 4.8 KiB, free: 1919.6 MiB)
16:12:16.380 INFO  BlockManagerInfo - Removed broadcast_39_piece0 on localhost:40883 in memory (size: 50.1 KiB, free: 1919.6 MiB)
16:12:16.381 INFO  BlockManagerInfo - Removed broadcast_47_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.7 MiB)
16:12:16.382 INFO  BlockManagerInfo - Removed broadcast_50_piece0 on localhost:40883 in memory (size: 1780.0 B, free: 1919.7 MiB)
16:12:16.383 INFO  BlockManagerInfo - Removed broadcast_46_piece0 on localhost:40883 in memory (size: 183.0 B, free: 1919.7 MiB)
16:12:16.384 INFO  BlockManagerInfo - Removed broadcast_48_piece0 on localhost:40883 in memory (size: 183.0 B, free: 1919.7 MiB)
16:12:16.384 INFO  BlockManagerInfo - Removed broadcast_51_piece0 on localhost:40883 in memory (size: 103.1 KiB, free: 1919.8 MiB)
16:12:16.385 INFO  MemoryStore - Block broadcast_55_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.7 MiB)
16:12:16.385 INFO  BlockManagerInfo - Added broadcast_55_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1919.7 MiB)
16:12:16.385 INFO  SparkContext - Created broadcast 55 from newAPIHadoopFile at PathSplitSource.java:96
16:12:16.386 INFO  BlockManagerInfo - Removed broadcast_23_piece0 on localhost:40883 in memory (size: 465.0 B, free: 1919.7 MiB)
16:12:16.387 INFO  BlockManagerInfo - Removed broadcast_36_piece0 on localhost:40883 in memory (size: 1780.0 B, free: 1919.7 MiB)
16:12:16.388 INFO  BlockManagerInfo - Removed broadcast_27_piece0 on localhost:40883 in memory (size: 5.1 KiB, free: 1919.8 MiB)
16:12:16.388 INFO  BlockManagerInfo - Removed broadcast_41_piece0 on localhost:40883 in memory (size: 152.7 KiB, free: 1919.9 MiB)
16:12:16.389 INFO  BlockManagerInfo - Removed broadcast_44_piece0 on localhost:40883 in memory (size: 1780.0 B, free: 1919.9 MiB)
16:12:16.390 INFO  BlockManagerInfo - Removed broadcast_31_piece0 on localhost:40883 in memory (size: 320.0 B, free: 1919.9 MiB)
16:12:16.411 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
16:12:16.411 INFO  DAGScheduler - Got job 28 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
16:12:16.411 INFO  DAGScheduler - Final stage: ResultStage 37 (collect at ReadsSparkSourceUnitTest.java:111)
16:12:16.411 INFO  DAGScheduler - Parents of final stage: List()
16:12:16.411 INFO  DAGScheduler - Missing parents: List()
16:12:16.411 INFO  DAGScheduler - Submitting ResultStage 37 (ParallelCollectionRDD[118] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
16:12:16.412 INFO  MemoryStore - Block broadcast_56 stored as values in memory (estimated size 3.0 KiB, free 1919.3 MiB)
16:12:16.413 INFO  MemoryStore - Block broadcast_56_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1919.3 MiB)
16:12:16.413 INFO  BlockManagerInfo - Added broadcast_56_piece0 in memory on localhost:40883 (size: 1780.0 B, free: 1919.9 MiB)
16:12:16.413 INFO  SparkContext - Created broadcast 56 from broadcast at DAGScheduler.scala:1580
16:12:16.414 INFO  DAGScheduler - Submitting 4 missing tasks from ResultStage 37 (ParallelCollectionRDD[118] at parallelize at ReadsSparkSourceUnitTest.java:310) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
16:12:16.414 INFO  TaskSchedulerImpl - Adding task set 37.0 with 4 tasks resource profile 0
16:12:16.415 INFO  TaskSetManager - Starting task 0.0 in stage 37.0 (TID 87) (localhost, executor driver, partition 0, PROCESS_LOCAL, 8303 bytes) 
16:12:16.415 INFO  TaskSetManager - Starting task 1.0 in stage 37.0 (TID 88) (localhost, executor driver, partition 1, PROCESS_LOCAL, 8292 bytes) 
16:12:16.415 INFO  TaskSetManager - Starting task 2.0 in stage 37.0 (TID 89) (localhost, executor driver, partition 2, PROCESS_LOCAL, 8292 bytes) 
16:12:16.416 INFO  TaskSetManager - Starting task 3.0 in stage 37.0 (TID 90) (localhost, executor driver, partition 3, PROCESS_LOCAL, 8184 bytes) 
16:12:16.416 INFO  Executor - Running task 0.0 in stage 37.0 (TID 87)
16:12:16.416 INFO  Executor - Running task 3.0 in stage 37.0 (TID 90)
16:12:16.416 INFO  Executor - Running task 1.0 in stage 37.0 (TID 88)
16:12:16.416 INFO  Executor - Running task 2.0 in stage 37.0 (TID 89)
16:12:16.419 INFO  Executor - Finished task 1.0 in stage 37.0 (TID 88). 1567 bytes result sent to driver
16:12:16.420 INFO  Executor - Finished task 2.0 in stage 37.0 (TID 89). 1567 bytes result sent to driver
16:12:16.421 INFO  Executor - Finished task 0.0 in stage 37.0 (TID 87). 1578 bytes result sent to driver
16:12:16.421 INFO  TaskSetManager - Finished task 1.0 in stage 37.0 (TID 88) in 6 ms on localhost (executor driver) (1/4)
16:12:16.422 INFO  Executor - Finished task 3.0 in stage 37.0 (TID 90). 1502 bytes result sent to driver
16:12:16.422 INFO  TaskSetManager - Finished task 2.0 in stage 37.0 (TID 89) in 7 ms on localhost (executor driver) (2/4)
16:12:16.423 INFO  TaskSetManager - Finished task 0.0 in stage 37.0 (TID 87) in 9 ms on localhost (executor driver) (3/4)
16:12:16.423 INFO  TaskSetManager - Finished task 3.0 in stage 37.0 (TID 90) in 8 ms on localhost (executor driver) (4/4)
16:12:16.423 INFO  TaskSchedulerImpl - Removed TaskSet 37.0, whose tasks have all completed, from pool 
16:12:16.424 INFO  DAGScheduler - ResultStage 37 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.012 s
16:12:16.424 INFO  DAGScheduler - Job 28 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:16.424 INFO  TaskSchedulerImpl - Killing all running tasks in stage 37: Stage finished
16:12:16.424 INFO  DAGScheduler - Job 28 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.013130 s
16:12:16.426 INFO  FileInputFormat - Total input files to process : 1
16:12:16.470 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
16:12:16.471 INFO  DAGScheduler - Got job 29 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
16:12:16.471 INFO  DAGScheduler - Final stage: ResultStage 38 (collect at ReadsSparkSourceUnitTest.java:112)
16:12:16.471 INFO  DAGScheduler - Parents of final stage: List()
16:12:16.471 INFO  DAGScheduler - Missing parents: List()
16:12:16.471 INFO  DAGScheduler - Submitting ResultStage 38 (MapPartitionsRDD[124] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:16.492 INFO  MemoryStore - Block broadcast_57 stored as values in memory (estimated size 286.0 KiB, free 1919.0 MiB)
16:12:16.494 INFO  MemoryStore - Block broadcast_57_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1918.9 MiB)
16:12:16.494 INFO  BlockManagerInfo - Added broadcast_57_piece0 in memory on localhost:40883 (size: 103.1 KiB, free: 1919.8 MiB)
16:12:16.494 INFO  SparkContext - Created broadcast 57 from broadcast at DAGScheduler.scala:1580
16:12:16.495 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 38 (MapPartitionsRDD[124] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:16.495 INFO  TaskSchedulerImpl - Adding task set 38.0 with 1 tasks resource profile 0
16:12:16.496 INFO  TaskSetManager - Starting task 0.0 in stage 38.0 (TID 91) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7844 bytes) 
16:12:16.496 INFO  Executor - Running task 0.0 in stage 38.0 (TID 91)
16:12:16.534 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.cram:0+13330
16:12:16.541 INFO  Executor - Finished task 0.0 in stage 38.0 (TID 91). 3736 bytes result sent to driver
16:12:16.542 INFO  TaskSetManager - Finished task 0.0 in stage 38.0 (TID 91) in 47 ms on localhost (executor driver) (1/1)
16:12:16.542 INFO  TaskSchedulerImpl - Removed TaskSet 38.0, whose tasks have all completed, from pool 
16:12:16.542 INFO  DAGScheduler - ResultStage 38 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.070 s
16:12:16.543 INFO  DAGScheduler - Job 29 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:16.543 INFO  TaskSchedulerImpl - Killing all running tasks in stage 38: Stage finished
16:12:16.543 INFO  DAGScheduler - Job 29 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.072146 s
16:12:16.551 INFO  MemoryStore - Block broadcast_58 stored as values in memory (estimated size 297.2 KiB, free 1918.6 MiB)
16:12:16.561 INFO  MemoryStore - Block broadcast_58_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.6 MiB)
16:12:16.562 INFO  BlockManagerInfo - Added broadcast_58_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.8 MiB)
16:12:16.562 INFO  SparkContext - Created broadcast 58 from newAPIHadoopFile at PathSplitSource.java:96
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, The unaligned mate start position is 69400, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, The unaligned mate start position is 69471, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, The unaligned mate start position is 69569, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, The unaligned mate start position is 69592, should be 0
16:12:16.605 INFO  MemoryStore - Block broadcast_59 stored as values in memory (estimated size 297.2 KiB, free 1918.3 MiB)
16:12:16.615 INFO  MemoryStore - Block broadcast_59_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.3 MiB)
16:12:16.615 INFO  BlockManagerInfo - Added broadcast_59_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.7 MiB)
16:12:16.616 INFO  SparkContext - Created broadcast 59 from newAPIHadoopFile at PathSplitSource.java:96
16:12:16.654 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
16:12:16.655 INFO  DAGScheduler - Got job 30 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
16:12:16.655 INFO  DAGScheduler - Final stage: ResultStage 39 (collect at ReadsSparkSourceUnitTest.java:111)
16:12:16.655 INFO  DAGScheduler - Parents of final stage: List()
16:12:16.655 INFO  DAGScheduler - Missing parents: List()
16:12:16.656 INFO  DAGScheduler - Submitting ResultStage 39 (ParallelCollectionRDD[130] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
16:12:16.657 INFO  MemoryStore - Block broadcast_60 stored as values in memory (estimated size 3.0 KiB, free 1918.3 MiB)
16:12:16.658 INFO  MemoryStore - Block broadcast_60_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1918.3 MiB)
16:12:16.658 INFO  BlockManagerInfo - Added broadcast_60_piece0 in memory on localhost:40883 (size: 1780.0 B, free: 1919.7 MiB)
16:12:16.658 INFO  SparkContext - Created broadcast 60 from broadcast at DAGScheduler.scala:1580
16:12:16.659 INFO  DAGScheduler - Submitting 4 missing tasks from ResultStage 39 (ParallelCollectionRDD[130] at parallelize at ReadsSparkSourceUnitTest.java:310) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
16:12:16.659 INFO  TaskSchedulerImpl - Adding task set 39.0 with 4 tasks resource profile 0
16:12:16.660 INFO  TaskSetManager - Starting task 0.0 in stage 39.0 (TID 92) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes) 
16:12:16.661 INFO  TaskSetManager - Starting task 1.0 in stage 39.0 (TID 93) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes) 
16:12:16.661 INFO  TaskSetManager - Starting task 2.0 in stage 39.0 (TID 94) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes) 
16:12:16.662 INFO  TaskSetManager - Starting task 3.0 in stage 39.0 (TID 95) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes) 
16:12:16.662 INFO  Executor - Running task 0.0 in stage 39.0 (TID 92)
16:12:16.665 INFO  Executor - Running task 3.0 in stage 39.0 (TID 95)
16:12:16.665 INFO  Executor - Running task 1.0 in stage 39.0 (TID 93)
16:12:16.665 INFO  Executor - Running task 2.0 in stage 39.0 (TID 94)
16:12:16.667 INFO  Executor - Finished task 2.0 in stage 39.0 (TID 94). 40337 bytes result sent to driver
16:12:16.669 INFO  Executor - Finished task 1.0 in stage 39.0 (TID 93). 40469 bytes result sent to driver
16:12:16.670 INFO  Executor - Finished task 0.0 in stage 39.0 (TID 92). 40355 bytes result sent to driver
16:12:16.670 INFO  TaskSetManager - Finished task 1.0 in stage 39.0 (TID 93) in 10 ms on localhost (executor driver) (1/4)
16:12:16.671 INFO  TaskSetManager - Finished task 0.0 in stage 39.0 (TID 92) in 11 ms on localhost (executor driver) (2/4)
16:12:16.671 INFO  TaskSetManager - Finished task 2.0 in stage 39.0 (TID 94) in 10 ms on localhost (executor driver) (3/4)
16:12:16.671 INFO  Executor - Finished task 3.0 in stage 39.0 (TID 95). 40805 bytes result sent to driver
16:12:16.672 INFO  TaskSetManager - Finished task 3.0 in stage 39.0 (TID 95) in 11 ms on localhost (executor driver) (4/4)
16:12:16.672 INFO  TaskSchedulerImpl - Removed TaskSet 39.0, whose tasks have all completed, from pool 
16:12:16.673 INFO  DAGScheduler - ResultStage 39 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.016 s
16:12:16.673 INFO  DAGScheduler - Job 30 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:16.673 INFO  TaskSchedulerImpl - Killing all running tasks in stage 39: Stage finished
16:12:16.673 INFO  DAGScheduler - Job 30 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.019383 s
16:12:16.675 INFO  FileInputFormat - Total input files to process : 1
16:12:16.734 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
16:12:16.735 INFO  DAGScheduler - Got job 31 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
16:12:16.735 INFO  DAGScheduler - Final stage: ResultStage 40 (collect at ReadsSparkSourceUnitTest.java:112)
16:12:16.735 INFO  DAGScheduler - Parents of final stage: List()
16:12:16.735 INFO  DAGScheduler - Missing parents: List()
16:12:16.735 INFO  DAGScheduler - Submitting ResultStage 40 (MapPartitionsRDD[137] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:16.759 INFO  MemoryStore - Block broadcast_61 stored as values in memory (estimated size 425.0 KiB, free 1917.8 MiB)
16:12:16.761 INFO  MemoryStore - Block broadcast_61_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.7 MiB)
16:12:16.761 INFO  BlockManagerInfo - Added broadcast_61_piece0 in memory on localhost:40883 (size: 152.7 KiB, free: 1919.6 MiB)
16:12:16.761 INFO  SparkContext - Created broadcast 61 from broadcast at DAGScheduler.scala:1580
16:12:16.761 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 40 (MapPartitionsRDD[137] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:16.761 INFO  TaskSchedulerImpl - Adding task set 40.0 with 1 tasks resource profile 0
16:12:16.762 INFO  TaskSetManager - Starting task 0.0 in stage 40.0 (TID 96) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
16:12:16.763 INFO  Executor - Running task 0.0 in stage 40.0 (TID 96)
16:12:16.798 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, The unaligned mate start position is 69400, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, The unaligned mate start position is 69471, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, The unaligned mate start position is 69569, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, The unaligned mate start position is 69592, should be 0
16:12:16.804 INFO  Executor - Finished task 0.0 in stage 40.0 (TID 96). 159572 bytes result sent to driver
16:12:16.805 INFO  TaskSetManager - Finished task 0.0 in stage 40.0 (TID 96) in 43 ms on localhost (executor driver) (1/1)
16:12:16.805 INFO  TaskSchedulerImpl - Removed TaskSet 40.0, whose tasks have all completed, from pool 
16:12:16.806 INFO  DAGScheduler - ResultStage 40 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.070 s
16:12:16.806 INFO  DAGScheduler - Job 31 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:16.806 INFO  TaskSchedulerImpl - Killing all running tasks in stage 40: Stage finished
16:12:16.806 INFO  DAGScheduler - Job 31 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.071565 s
16:12:16.810 INFO  MemoryStore - Block broadcast_62 stored as values in memory (estimated size 528.0 B, free 1917.7 MiB)
16:12:16.810 INFO  MemoryStore - Block broadcast_62_piece0 stored as bytes in memory (estimated size 183.0 B, free 1917.7 MiB)
16:12:16.810 INFO  BlockManagerInfo - Added broadcast_62_piece0 in memory on localhost:40883 (size: 183.0 B, free: 1919.6 MiB)
16:12:16.811 INFO  SparkContext - Created broadcast 62 from broadcast at CramSource.java:114
16:12:16.813 INFO  MemoryStore - Block broadcast_63 stored as values in memory (estimated size 297.2 KiB, free 1917.4 MiB)
16:12:16.820 INFO  MemoryStore - Block broadcast_63_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.3 MiB)
16:12:16.820 INFO  BlockManagerInfo - Added broadcast_63_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.5 MiB)
16:12:16.820 INFO  SparkContext - Created broadcast 63 from newAPIHadoopFile at PathSplitSource.java:96
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, The unaligned mate start position is 69400, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, The unaligned mate start position is 69471, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, The unaligned mate start position is 69569, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, The unaligned mate start position is 69592, should be 0
16:12:16.850 INFO  MemoryStore - Block broadcast_64 stored as values in memory (estimated size 528.0 B, free 1917.3 MiB)
16:12:16.851 INFO  MemoryStore - Block broadcast_64_piece0 stored as bytes in memory (estimated size 183.0 B, free 1917.3 MiB)
16:12:16.851 INFO  BlockManagerInfo - Added broadcast_64_piece0 in memory on localhost:40883 (size: 183.0 B, free: 1919.5 MiB)
16:12:16.851 INFO  SparkContext - Created broadcast 64 from broadcast at CramSource.java:114
16:12:16.853 INFO  MemoryStore - Block broadcast_65 stored as values in memory (estimated size 297.2 KiB, free 1917.1 MiB)
16:12:16.860 INFO  MemoryStore - Block broadcast_65_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.0 MiB)
16:12:16.860 INFO  BlockManagerInfo - Added broadcast_65_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.5 MiB)
16:12:16.860 INFO  SparkContext - Created broadcast 65 from newAPIHadoopFile at PathSplitSource.java:96
16:12:16.878 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
16:12:16.878 INFO  DAGScheduler - Got job 32 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
16:12:16.878 INFO  DAGScheduler - Final stage: ResultStage 41 (collect at ReadsSparkSourceUnitTest.java:111)
16:12:16.878 INFO  DAGScheduler - Parents of final stage: List()
16:12:16.878 INFO  DAGScheduler - Missing parents: List()
16:12:16.879 INFO  DAGScheduler - Submitting ResultStage 41 (ParallelCollectionRDD[142] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
16:12:16.879 INFO  MemoryStore - Block broadcast_66 stored as values in memory (estimated size 3.0 KiB, free 1917.0 MiB)
16:12:16.880 INFO  MemoryStore - Block broadcast_66_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1917.0 MiB)
16:12:16.880 INFO  BlockManagerInfo - Added broadcast_66_piece0 in memory on localhost:40883 (size: 1780.0 B, free: 1919.5 MiB)
16:12:16.880 INFO  SparkContext - Created broadcast 66 from broadcast at DAGScheduler.scala:1580
16:12:16.881 INFO  DAGScheduler - Submitting 4 missing tasks from ResultStage 41 (ParallelCollectionRDD[142] at parallelize at ReadsSparkSourceUnitTest.java:310) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
16:12:16.881 INFO  TaskSchedulerImpl - Adding task set 41.0 with 4 tasks resource profile 0
16:12:16.882 INFO  TaskSetManager - Starting task 0.0 in stage 41.0 (TID 97) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes) 
16:12:16.883 INFO  TaskSetManager - Starting task 1.0 in stage 41.0 (TID 98) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes) 
16:12:16.884 INFO  TaskSetManager - Starting task 2.0 in stage 41.0 (TID 99) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes) 
16:12:16.885 INFO  TaskSetManager - Starting task 3.0 in stage 41.0 (TID 100) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes) 
16:12:16.885 INFO  Executor - Running task 2.0 in stage 41.0 (TID 99)
16:12:16.885 INFO  Executor - Running task 1.0 in stage 41.0 (TID 98)
16:12:16.885 INFO  Executor - Running task 0.0 in stage 41.0 (TID 97)
16:12:16.885 INFO  Executor - Running task 3.0 in stage 41.0 (TID 100)
16:12:16.888 INFO  Executor - Finished task 0.0 in stage 41.0 (TID 97). 38950 bytes result sent to driver
16:12:16.888 INFO  Executor - Finished task 2.0 in stage 41.0 (TID 99). 39070 bytes result sent to driver
16:12:16.889 INFO  TaskSetManager - Finished task 2.0 in stage 41.0 (TID 99) in 6 ms on localhost (executor driver) (1/4)
16:12:16.889 INFO  Executor - Finished task 1.0 in stage 41.0 (TID 98). 39130 bytes result sent to driver
16:12:16.889 INFO  TaskSetManager - Finished task 0.0 in stage 41.0 (TID 97) in 8 ms on localhost (executor driver) (2/4)
16:12:16.890 INFO  Executor - Finished task 3.0 in stage 41.0 (TID 100). 39343 bytes result sent to driver
16:12:16.890 INFO  TaskSetManager - Finished task 1.0 in stage 41.0 (TID 98) in 8 ms on localhost (executor driver) (3/4)
16:12:16.891 INFO  TaskSetManager - Finished task 3.0 in stage 41.0 (TID 100) in 7 ms on localhost (executor driver) (4/4)
16:12:16.891 INFO  TaskSchedulerImpl - Removed TaskSet 41.0, whose tasks have all completed, from pool 
16:12:16.891 INFO  DAGScheduler - ResultStage 41 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.012 s
16:12:16.891 INFO  DAGScheduler - Job 32 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:16.891 INFO  TaskSchedulerImpl - Killing all running tasks in stage 41: Stage finished
16:12:16.891 INFO  DAGScheduler - Job 32 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.013089 s
16:12:16.892 INFO  FileInputFormat - Total input files to process : 1
16:12:16.929 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
16:12:16.929 INFO  DAGScheduler - Got job 33 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
16:12:16.929 INFO  DAGScheduler - Final stage: ResultStage 42 (collect at ReadsSparkSourceUnitTest.java:112)
16:12:16.929 INFO  DAGScheduler - Parents of final stage: List()
16:12:16.929 INFO  DAGScheduler - Missing parents: List()
16:12:16.930 INFO  DAGScheduler - Submitting ResultStage 42 (MapPartitionsRDD[148] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:16.942 INFO  MemoryStore - Block broadcast_67 stored as values in memory (estimated size 286.0 KiB, free 1916.7 MiB)
16:12:16.943 INFO  MemoryStore - Block broadcast_67_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1916.6 MiB)
16:12:16.943 INFO  BlockManagerInfo - Added broadcast_67_piece0 in memory on localhost:40883 (size: 103.1 KiB, free: 1919.4 MiB)
16:12:16.943 INFO  SparkContext - Created broadcast 67 from broadcast at DAGScheduler.scala:1580
16:12:16.944 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 42 (MapPartitionsRDD[148] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:16.944 INFO  TaskSchedulerImpl - Adding task set 42.0 with 1 tasks resource profile 0
16:12:16.945 INFO  TaskSetManager - Starting task 0.0 in stage 42.0 (TID 101) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes) 
16:12:16.945 INFO  Executor - Running task 0.0 in stage 42.0 (TID 101)
16:12:16.973 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram:0+50619
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, The unaligned mate start position is 69400, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, The unaligned mate start position is 69471, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, The unaligned mate start position is 69569, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, The unaligned mate start position is 69592, should be 0
16:12:16.986 INFO  Executor - Finished task 0.0 in stage 42.0 (TID 101). 154101 bytes result sent to driver
16:12:16.987 INFO  TaskSetManager - Finished task 0.0 in stage 42.0 (TID 101) in 43 ms on localhost (executor driver) (1/1)
16:12:16.987 INFO  TaskSchedulerImpl - Removed TaskSet 42.0, whose tasks have all completed, from pool 
16:12:16.987 INFO  DAGScheduler - ResultStage 42 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.057 s
16:12:16.987 INFO  DAGScheduler - Job 33 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:16.987 INFO  TaskSchedulerImpl - Killing all running tasks in stage 42: Stage finished
16:12:16.987 INFO  DAGScheduler - Job 33 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.058540 s
16:12:16.994 INFO  MemoryStore - Block broadcast_68 stored as values in memory (estimated size 297.2 KiB, free 1916.3 MiB)
16:12:17.005 INFO  MemoryStore - Block broadcast_68_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.3 MiB)
16:12:17.005 INFO  BlockManagerInfo - Added broadcast_68_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.3 MiB)
16:12:17.005 INFO  SparkContext - Created broadcast 68 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.036 INFO  MemoryStore - Block broadcast_69 stored as values in memory (estimated size 297.2 KiB, free 1916.0 MiB)
16:12:17.043 INFO  MemoryStore - Block broadcast_69_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.9 MiB)
16:12:17.043 INFO  BlockManagerInfo - Added broadcast_69_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.3 MiB)
16:12:17.043 INFO  SparkContext - Created broadcast 69 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.067 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
16:12:17.067 INFO  DAGScheduler - Got job 34 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
16:12:17.067 INFO  DAGScheduler - Final stage: ResultStage 43 (collect at ReadsSparkSourceUnitTest.java:111)
16:12:17.067 INFO  DAGScheduler - Parents of final stage: List()
16:12:17.067 INFO  DAGScheduler - Missing parents: List()
16:12:17.067 INFO  DAGScheduler - Submitting ResultStage 43 (ParallelCollectionRDD[154] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
16:12:17.068 INFO  MemoryStore - Block broadcast_70 stored as values in memory (estimated size 3.0 KiB, free 1915.9 MiB)
16:12:17.070 INFO  MemoryStore - Block broadcast_70_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1915.9 MiB)
16:12:17.070 INFO  BlockManagerInfo - Added broadcast_70_piece0 in memory on localhost:40883 (size: 1780.0 B, free: 1919.3 MiB)
16:12:17.070 INFO  SparkContext - Created broadcast 70 from broadcast at DAGScheduler.scala:1580
16:12:17.070 INFO  DAGScheduler - Submitting 4 missing tasks from ResultStage 43 (ParallelCollectionRDD[154] at parallelize at ReadsSparkSourceUnitTest.java:310) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
16:12:17.071 INFO  TaskSchedulerImpl - Adding task set 43.0 with 4 tasks resource profile 0
16:12:17.072 INFO  TaskSetManager - Starting task 0.0 in stage 43.0 (TID 102) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes) 
16:12:17.072 INFO  TaskSetManager - Starting task 1.0 in stage 43.0 (TID 103) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes) 
16:12:17.072 INFO  TaskSetManager - Starting task 2.0 in stage 43.0 (TID 104) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes) 
16:12:17.073 INFO  TaskSetManager - Starting task 3.0 in stage 43.0 (TID 105) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes) 
16:12:17.073 INFO  Executor - Running task 0.0 in stage 43.0 (TID 102)
16:12:17.075 INFO  Executor - Running task 1.0 in stage 43.0 (TID 103)
16:12:17.075 INFO  Executor - Finished task 0.0 in stage 43.0 (TID 102). 40355 bytes result sent to driver
16:12:17.076 INFO  TaskSetManager - Finished task 0.0 in stage 43.0 (TID 102) in 5 ms on localhost (executor driver) (1/4)
16:12:17.076 INFO  Executor - Running task 2.0 in stage 43.0 (TID 104)
16:12:17.077 INFO  Executor - Running task 3.0 in stage 43.0 (TID 105)
16:12:17.078 INFO  Executor - Finished task 2.0 in stage 43.0 (TID 104). 40337 bytes result sent to driver
16:12:17.078 INFO  TaskSetManager - Finished task 2.0 in stage 43.0 (TID 104) in 6 ms on localhost (executor driver) (2/4)
16:12:17.079 INFO  Executor - Finished task 1.0 in stage 43.0 (TID 103). 40469 bytes result sent to driver
16:12:17.080 INFO  TaskSetManager - Finished task 1.0 in stage 43.0 (TID 103) in 8 ms on localhost (executor driver) (3/4)
16:12:17.081 INFO  Executor - Finished task 3.0 in stage 43.0 (TID 105). 40848 bytes result sent to driver
16:12:17.082 INFO  TaskSetManager - Finished task 3.0 in stage 43.0 (TID 105) in 10 ms on localhost (executor driver) (4/4)
16:12:17.082 INFO  TaskSchedulerImpl - Removed TaskSet 43.0, whose tasks have all completed, from pool 
16:12:17.083 INFO  DAGScheduler - ResultStage 43 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.015 s
16:12:17.083 INFO  DAGScheduler - Job 34 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:17.083 INFO  TaskSchedulerImpl - Killing all running tasks in stage 43: Stage finished
16:12:17.083 INFO  DAGScheduler - Job 34 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.016664 s
16:12:17.085 INFO  FileInputFormat - Total input files to process : 1
16:12:17.123 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
16:12:17.124 INFO  DAGScheduler - Got job 35 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
16:12:17.124 INFO  DAGScheduler - Final stage: ResultStage 44 (collect at ReadsSparkSourceUnitTest.java:112)
16:12:17.124 INFO  DAGScheduler - Parents of final stage: List()
16:12:17.124 INFO  DAGScheduler - Missing parents: List()
16:12:17.124 INFO  DAGScheduler - Submitting ResultStage 44 (MapPartitionsRDD[161] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:17.142 INFO  MemoryStore - Block broadcast_71 stored as values in memory (estimated size 425.0 KiB, free 1915.5 MiB)
16:12:17.144 INFO  MemoryStore - Block broadcast_71_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1915.4 MiB)
16:12:17.144 INFO  BlockManagerInfo - Added broadcast_71_piece0 in memory on localhost:40883 (size: 152.7 KiB, free: 1919.1 MiB)
16:12:17.144 INFO  SparkContext - Created broadcast 71 from broadcast at DAGScheduler.scala:1580
16:12:17.145 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 44 (MapPartitionsRDD[161] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:17.145 INFO  TaskSchedulerImpl - Adding task set 44.0 with 1 tasks resource profile 0
16:12:17.146 INFO  TaskSetManager - Starting task 0.0 in stage 44.0 (TID 106) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
16:12:17.146 INFO  Executor - Running task 0.0 in stage 44.0 (TID 106)
16:12:17.189 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
16:12:17.194 INFO  Executor - Finished task 0.0 in stage 44.0 (TID 106). 159572 bytes result sent to driver
16:12:17.195 INFO  TaskSetManager - Finished task 0.0 in stage 44.0 (TID 106) in 50 ms on localhost (executor driver) (1/1)
16:12:17.195 INFO  TaskSchedulerImpl - Removed TaskSet 44.0, whose tasks have all completed, from pool 
16:12:17.196 INFO  DAGScheduler - ResultStage 44 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.072 s
16:12:17.196 INFO  DAGScheduler - Job 35 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:17.196 INFO  TaskSchedulerImpl - Killing all running tasks in stage 44: Stage finished
16:12:17.196 INFO  DAGScheduler - Job 35 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.073085 s
16:12:17.200 INFO  MemoryStore - Block broadcast_72 stored as values in memory (estimated size 528.0 B, free 1915.4 MiB)
16:12:17.201 INFO  MemoryStore - Block broadcast_72_piece0 stored as bytes in memory (estimated size 183.0 B, free 1915.4 MiB)
16:12:17.201 INFO  BlockManagerInfo - Added broadcast_72_piece0 in memory on localhost:40883 (size: 183.0 B, free: 1919.1 MiB)
16:12:17.201 INFO  SparkContext - Created broadcast 72 from broadcast at CramSource.java:114
16:12:17.203 INFO  MemoryStore - Block broadcast_73 stored as values in memory (estimated size 297.2 KiB, free 1915.1 MiB)
16:12:17.210 INFO  MemoryStore - Block broadcast_73_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.0 MiB)
16:12:17.210 INFO  BlockManagerInfo - Added broadcast_73_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.1 MiB)
16:12:17.210 INFO  SparkContext - Created broadcast 73 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.233 INFO  MemoryStore - Block broadcast_74 stored as values in memory (estimated size 528.0 B, free 1915.0 MiB)
16:12:17.234 INFO  MemoryStore - Block broadcast_74_piece0 stored as bytes in memory (estimated size 183.0 B, free 1915.0 MiB)
16:12:17.234 INFO  BlockManagerInfo - Added broadcast_74_piece0 in memory on localhost:40883 (size: 183.0 B, free: 1919.1 MiB)
16:12:17.234 INFO  SparkContext - Created broadcast 74 from broadcast at CramSource.java:114
16:12:17.237 INFO  MemoryStore - Block broadcast_75 stored as values in memory (estimated size 297.2 KiB, free 1914.7 MiB)
16:12:17.243 INFO  MemoryStore - Block broadcast_75_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1914.7 MiB)
16:12:17.243 INFO  BlockManagerInfo - Added broadcast_75_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.0 MiB)
16:12:17.243 INFO  SparkContext - Created broadcast 75 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.261 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
16:12:17.261 INFO  DAGScheduler - Got job 36 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
16:12:17.261 INFO  DAGScheduler - Final stage: ResultStage 45 (collect at ReadsSparkSourceUnitTest.java:111)
16:12:17.261 INFO  DAGScheduler - Parents of final stage: List()
16:12:17.261 INFO  DAGScheduler - Missing parents: List()
16:12:17.261 INFO  DAGScheduler - Submitting ResultStage 45 (ParallelCollectionRDD[166] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
16:12:17.262 INFO  MemoryStore - Block broadcast_76 stored as values in memory (estimated size 3.0 KiB, free 1914.7 MiB)
16:12:17.263 INFO  MemoryStore - Block broadcast_76_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1914.7 MiB)
16:12:17.263 INFO  BlockManagerInfo - Added broadcast_76_piece0 in memory on localhost:40883 (size: 1780.0 B, free: 1919.0 MiB)
16:12:17.263 INFO  SparkContext - Created broadcast 76 from broadcast at DAGScheduler.scala:1580
16:12:17.263 INFO  DAGScheduler - Submitting 4 missing tasks from ResultStage 45 (ParallelCollectionRDD[166] at parallelize at ReadsSparkSourceUnitTest.java:310) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
16:12:17.264 INFO  TaskSchedulerImpl - Adding task set 45.0 with 4 tasks resource profile 0
16:12:17.265 INFO  TaskSetManager - Starting task 0.0 in stage 45.0 (TID 107) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes) 
16:12:17.265 INFO  TaskSetManager - Starting task 1.0 in stage 45.0 (TID 108) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes) 
16:12:17.266 INFO  TaskSetManager - Starting task 2.0 in stage 45.0 (TID 109) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes) 
16:12:17.267 INFO  TaskSetManager - Starting task 3.0 in stage 45.0 (TID 110) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes) 
16:12:17.267 INFO  Executor - Running task 0.0 in stage 45.0 (TID 107)
16:12:17.267 INFO  Executor - Running task 1.0 in stage 45.0 (TID 108)
16:12:17.268 INFO  Executor - Running task 2.0 in stage 45.0 (TID 109)
16:12:17.268 INFO  Executor - Running task 3.0 in stage 45.0 (TID 110)
16:12:17.270 INFO  Executor - Finished task 0.0 in stage 45.0 (TID 107). 38950 bytes result sent to driver
16:12:17.270 INFO  Executor - Finished task 2.0 in stage 45.0 (TID 109). 39027 bytes result sent to driver
16:12:17.270 INFO  Executor - Finished task 3.0 in stage 45.0 (TID 110). 39300 bytes result sent to driver
16:12:17.270 INFO  Executor - Finished task 1.0 in stage 45.0 (TID 108). 39130 bytes result sent to driver
16:12:17.271 INFO  TaskSetManager - Finished task 0.0 in stage 45.0 (TID 107) in 7 ms on localhost (executor driver) (1/4)
16:12:17.271 INFO  TaskSetManager - Finished task 2.0 in stage 45.0 (TID 109) in 6 ms on localhost (executor driver) (2/4)
16:12:17.272 INFO  TaskSetManager - Finished task 3.0 in stage 45.0 (TID 110) in 6 ms on localhost (executor driver) (3/4)
16:12:17.272 INFO  TaskSetManager - Finished task 1.0 in stage 45.0 (TID 108) in 7 ms on localhost (executor driver) (4/4)
16:12:17.272 INFO  TaskSchedulerImpl - Removed TaskSet 45.0, whose tasks have all completed, from pool 
16:12:17.272 INFO  DAGScheduler - ResultStage 45 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.010 s
16:12:17.272 INFO  DAGScheduler - Job 36 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:17.272 INFO  TaskSchedulerImpl - Killing all running tasks in stage 45: Stage finished
16:12:17.273 INFO  DAGScheduler - Job 36 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.011794 s
16:12:17.274 INFO  FileInputFormat - Total input files to process : 1
16:12:17.300 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
16:12:17.300 INFO  DAGScheduler - Got job 37 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
16:12:17.300 INFO  DAGScheduler - Final stage: ResultStage 46 (collect at ReadsSparkSourceUnitTest.java:112)
16:12:17.300 INFO  DAGScheduler - Parents of final stage: List()
16:12:17.300 INFO  DAGScheduler - Missing parents: List()
16:12:17.301 INFO  DAGScheduler - Submitting ResultStage 46 (MapPartitionsRDD[172] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:17.313 INFO  MemoryStore - Block broadcast_77 stored as values in memory (estimated size 286.0 KiB, free 1914.4 MiB)
16:12:17.314 INFO  MemoryStore - Block broadcast_77_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1914.3 MiB)
16:12:17.314 INFO  BlockManagerInfo - Added broadcast_77_piece0 in memory on localhost:40883 (size: 103.1 KiB, free: 1918.9 MiB)
16:12:17.315 INFO  SparkContext - Created broadcast 77 from broadcast at DAGScheduler.scala:1580
16:12:17.315 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 46 (MapPartitionsRDD[172] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:17.315 INFO  TaskSchedulerImpl - Adding task set 46.0 with 1 tasks resource profile 0
16:12:17.316 INFO  TaskSetManager - Starting task 0.0 in stage 46.0 (TID 111) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes) 
16:12:17.316 INFO  Executor - Running task 0.0 in stage 46.0 (TID 111)
16:12:17.342 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram:0+50619
16:12:17.354 INFO  Executor - Finished task 0.0 in stage 46.0 (TID 111). 154101 bytes result sent to driver
16:12:17.355 INFO  TaskSetManager - Finished task 0.0 in stage 46.0 (TID 111) in 39 ms on localhost (executor driver) (1/1)
16:12:17.355 INFO  TaskSchedulerImpl - Removed TaskSet 46.0, whose tasks have all completed, from pool 
16:12:17.355 INFO  DAGScheduler - ResultStage 46 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.054 s
16:12:17.356 INFO  DAGScheduler - Job 37 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:17.356 INFO  TaskSchedulerImpl - Killing all running tasks in stage 46: Stage finished
16:12:17.356 INFO  DAGScheduler - Job 37 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.055893 s
16:12:17.361 INFO  MemoryStore - Block broadcast_78 stored as values in memory (estimated size 297.2 KiB, free 1914.0 MiB)
16:12:17.372 INFO  MemoryStore - Block broadcast_78_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1914.0 MiB)
16:12:17.372 INFO  BlockManagerInfo - Added broadcast_78_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1918.9 MiB)
16:12:17.372 INFO  SparkContext - Created broadcast 78 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.409 INFO  MemoryStore - Block broadcast_79 stored as values in memory (estimated size 528.0 B, free 1914.0 MiB)
16:12:17.409 INFO  MemoryStore - Block broadcast_79_piece0 stored as bytes in memory (estimated size 183.0 B, free 1914.0 MiB)
16:12:17.410 INFO  BlockManagerInfo - Added broadcast_79_piece0 in memory on localhost:40883 (size: 183.0 B, free: 1918.9 MiB)
16:12:17.410 INFO  SparkContext - Created broadcast 79 from broadcast at CramSource.java:114
16:12:17.412 INFO  MemoryStore - Block broadcast_80 stored as values in memory (estimated size 297.2 KiB, free 1913.7 MiB)
16:12:17.419 INFO  MemoryStore - Block broadcast_80_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1913.6 MiB)
16:12:17.419 INFO  BlockManagerInfo - Added broadcast_80_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1918.8 MiB)
16:12:17.419 INFO  SparkContext - Created broadcast 80 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.466 WARN  FileSystem - Failed to initialize filesystem hdfs://bogus/path.bam: java.lang.IllegalArgumentException: java.net.UnknownHostException: bogus
16:12:17.471 INFO  MemoryStore - Block broadcast_81 stored as values in memory (estimated size 297.3 KiB, free 1913.3 MiB)
16:12:17.478 INFO  MemoryStore - Block broadcast_81_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1913.3 MiB)
16:12:17.478 INFO  BlockManagerInfo - Added broadcast_81_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1918.8 MiB)
16:12:17.478 INFO  SparkContext - Created broadcast 81 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.512 INFO  MemoryStore - Block broadcast_82 stored as values in memory (estimated size 297.3 KiB, free 1913.0 MiB)
16:12:17.518 INFO  MemoryStore - Block broadcast_82_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1913.0 MiB)
16:12:17.519 INFO  BlockManagerInfo - Added broadcast_82_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1918.7 MiB)
16:12:17.519 INFO  SparkContext - Created broadcast 82 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.545 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:154
16:12:17.545 INFO  DAGScheduler - Got job 38 (collect at ReadsSparkSourceUnitTest.java:154) with 4 output partitions
16:12:17.545 INFO  DAGScheduler - Final stage: ResultStage 47 (collect at ReadsSparkSourceUnitTest.java:154)
16:12:17.545 INFO  DAGScheduler - Parents of final stage: List()
16:12:17.545 INFO  DAGScheduler - Missing parents: List()
16:12:17.545 INFO  DAGScheduler - Submitting ResultStage 47 (ParallelCollectionRDD[187] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
16:12:17.546 INFO  MemoryStore - Block broadcast_83 stored as values in memory (estimated size 3.0 KiB, free 1913.0 MiB)
16:12:17.547 INFO  MemoryStore - Block broadcast_83_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1913.0 MiB)
16:12:17.547 INFO  BlockManagerInfo - Added broadcast_83_piece0 in memory on localhost:40883 (size: 1780.0 B, free: 1918.7 MiB)
16:12:17.547 INFO  SparkContext - Created broadcast 83 from broadcast at DAGScheduler.scala:1580
16:12:17.547 INFO  DAGScheduler - Submitting 4 missing tasks from ResultStage 47 (ParallelCollectionRDD[187] at parallelize at ReadsSparkSourceUnitTest.java:310) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
16:12:17.547 INFO  TaskSchedulerImpl - Adding task set 47.0 with 4 tasks resource profile 0
16:12:17.548 INFO  TaskSetManager - Starting task 0.0 in stage 47.0 (TID 112) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes) 
16:12:17.549 INFO  TaskSetManager - Starting task 1.0 in stage 47.0 (TID 113) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes) 
16:12:17.549 INFO  TaskSetManager - Starting task 2.0 in stage 47.0 (TID 114) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes) 
16:12:17.550 INFO  TaskSetManager - Starting task 3.0 in stage 47.0 (TID 115) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes) 
16:12:17.550 INFO  Executor - Running task 3.0 in stage 47.0 (TID 115)
16:12:17.550 INFO  Executor - Running task 0.0 in stage 47.0 (TID 112)
16:12:17.551 INFO  Executor - Running task 2.0 in stage 47.0 (TID 114)
16:12:17.552 INFO  Executor - Running task 1.0 in stage 47.0 (TID 113)
16:12:17.554 INFO  Executor - Finished task 0.0 in stage 47.0 (TID 112). 163161 bytes result sent to driver
16:12:17.554 INFO  Executor - Finished task 3.0 in stage 47.0 (TID 115). 162694 bytes result sent to driver
16:12:17.555 INFO  Executor - Finished task 2.0 in stage 47.0 (TID 114). 163356 bytes result sent to driver
16:12:17.556 INFO  TaskSetManager - Finished task 3.0 in stage 47.0 (TID 115) in 7 ms on localhost (executor driver) (1/4)
16:12:17.557 INFO  Executor - Finished task 1.0 in stage 47.0 (TID 113). 163368 bytes result sent to driver
16:12:17.557 INFO  TaskSetManager - Finished task 2.0 in stage 47.0 (TID 114) in 8 ms on localhost (executor driver) (2/4)
16:12:17.557 INFO  TaskSetManager - Finished task 0.0 in stage 47.0 (TID 112) in 9 ms on localhost (executor driver) (3/4)
16:12:17.558 INFO  TaskSetManager - Finished task 1.0 in stage 47.0 (TID 113) in 10 ms on localhost (executor driver) (4/4)
16:12:17.558 INFO  TaskSchedulerImpl - Removed TaskSet 47.0, whose tasks have all completed, from pool 
16:12:17.558 INFO  DAGScheduler - ResultStage 47 (collect at ReadsSparkSourceUnitTest.java:154) finished in 0.012 s
16:12:17.558 INFO  DAGScheduler - Job 38 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:17.558 INFO  TaskSchedulerImpl - Killing all running tasks in stage 47: Stage finished
16:12:17.558 INFO  DAGScheduler - Job 38 finished: collect at ReadsSparkSourceUnitTest.java:154, took 0.013458 s
16:12:17.567 INFO  FileInputFormat - Total input files to process : 2
16:12:17.599 INFO  BlockManagerInfo - Removed broadcast_83_piece0 on localhost:40883 in memory (size: 1780.0 B, free: 1918.7 MiB)
16:12:17.600 INFO  BlockManagerInfo - Removed broadcast_53_piece0 on localhost:40883 in memory (size: 50.1 KiB, free: 1918.8 MiB)
16:12:17.601 INFO  BlockManagerInfo - Removed broadcast_79_piece0 on localhost:40883 in memory (size: 183.0 B, free: 1918.8 MiB)
16:12:17.602 INFO  BlockManagerInfo - Removed broadcast_55_piece0 on localhost:40883 in memory (size: 50.1 KiB, free: 1918.8 MiB)
16:12:17.603 INFO  BlockManagerInfo - Removed broadcast_73_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1918.9 MiB)
16:12:17.604 INFO  BlockManagerInfo - Removed broadcast_75_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1918.9 MiB)
16:12:17.605 INFO  BlockManagerInfo - Removed broadcast_72_piece0 on localhost:40883 in memory (size: 183.0 B, free: 1918.9 MiB)
16:12:17.607 INFO  BlockManagerInfo - Removed broadcast_64_piece0 on localhost:40883 in memory (size: 183.0 B, free: 1918.9 MiB)
16:12:17.608 INFO  BlockManagerInfo - Removed broadcast_70_piece0 on localhost:40883 in memory (size: 1780.0 B, free: 1918.9 MiB)
16:12:17.610 INFO  BlockManagerInfo - Removed broadcast_60_piece0 on localhost:40883 in memory (size: 1780.0 B, free: 1918.9 MiB)
16:12:17.612 INFO  BlockManagerInfo - Removed broadcast_80_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.0 MiB)
16:12:17.613 INFO  BlockManagerInfo - Removed broadcast_63_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.0 MiB)
16:12:17.614 INFO  BlockManagerInfo - Removed broadcast_59_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.1 MiB)
16:12:17.615 INFO  BlockManagerInfo - Removed broadcast_66_piece0 on localhost:40883 in memory (size: 1780.0 B, free: 1919.1 MiB)
16:12:17.616 INFO  BlockManagerInfo - Removed broadcast_68_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.1 MiB)
16:12:17.617 INFO  BlockManagerInfo - Removed broadcast_77_piece0 on localhost:40883 in memory (size: 103.1 KiB, free: 1919.2 MiB)
16:12:17.618 INFO  BlockManagerInfo - Removed broadcast_57_piece0 on localhost:40883 in memory (size: 103.1 KiB, free: 1919.3 MiB)
16:12:17.619 INFO  BlockManagerInfo - Removed broadcast_61_piece0 on localhost:40883 in memory (size: 152.7 KiB, free: 1919.5 MiB)
16:12:17.620 INFO  BlockManagerInfo - Removed broadcast_54_piece0 on localhost:40883 in memory (size: 202.0 B, free: 1919.5 MiB)
16:12:17.621 INFO  BlockManagerInfo - Removed broadcast_71_piece0 on localhost:40883 in memory (size: 152.7 KiB, free: 1919.6 MiB)
16:12:17.621 INFO  BlockManagerInfo - Removed broadcast_81_piece0 on localhost:40883 in memory (size: 50.1 KiB, free: 1919.7 MiB)
16:12:17.623 INFO  BlockManagerInfo - Removed broadcast_58_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.7 MiB)
16:12:17.624 INFO  BlockManagerInfo - Removed broadcast_67_piece0 on localhost:40883 in memory (size: 103.1 KiB, free: 1919.8 MiB)
16:12:17.625 INFO  BlockManagerInfo - Removed broadcast_69_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.8 MiB)
16:12:17.626 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:155
16:12:17.626 INFO  BlockManagerInfo - Removed broadcast_52_piece0 on localhost:40883 in memory (size: 202.0 B, free: 1919.8 MiB)
16:12:17.627 INFO  DAGScheduler - Got job 39 (collect at ReadsSparkSourceUnitTest.java:155) with 2 output partitions
16:12:17.627 INFO  DAGScheduler - Final stage: ResultStage 48 (collect at ReadsSparkSourceUnitTest.java:155)
16:12:17.627 INFO  DAGScheduler - Parents of final stage: List()
16:12:17.627 INFO  DAGScheduler - Missing parents: List()
16:12:17.627 INFO  DAGScheduler - Submitting ResultStage 48 (MapPartitionsRDD[194] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:17.629 INFO  BlockManagerInfo - Removed broadcast_76_piece0 on localhost:40883 in memory (size: 1780.0 B, free: 1919.9 MiB)
16:12:17.630 INFO  BlockManagerInfo - Removed broadcast_65_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.9 MiB)
16:12:17.630 INFO  BlockManagerInfo - Removed broadcast_62_piece0 on localhost:40883 in memory (size: 183.0 B, free: 1919.9 MiB)
16:12:17.632 INFO  BlockManagerInfo - Removed broadcast_78_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.9 MiB)
16:12:17.633 INFO  BlockManagerInfo - Removed broadcast_74_piece0 on localhost:40883 in memory (size: 183.0 B, free: 1919.9 MiB)
16:12:17.634 INFO  BlockManagerInfo - Removed broadcast_56_piece0 on localhost:40883 in memory (size: 1780.0 B, free: 1920.0 MiB)
16:12:17.658 INFO  MemoryStore - Block broadcast_84 stored as values in memory (estimated size 425.0 KiB, free 1919.2 MiB)
16:12:17.660 INFO  MemoryStore - Block broadcast_84_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1919.1 MiB)
16:12:17.660 INFO  BlockManagerInfo - Added broadcast_84_piece0 in memory on localhost:40883 (size: 152.7 KiB, free: 1919.8 MiB)
16:12:17.661 INFO  SparkContext - Created broadcast 84 from broadcast at DAGScheduler.scala:1580
16:12:17.661 INFO  DAGScheduler - Submitting 2 missing tasks from ResultStage 48 (MapPartitionsRDD[194] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0, 1))
16:12:17.661 INFO  TaskSchedulerImpl - Adding task set 48.0 with 2 tasks resource profile 0
16:12:17.662 INFO  TaskSetManager - Starting task 0.0 in stage 48.0 (TID 116) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7921 bytes) 
16:12:17.662 INFO  TaskSetManager - Starting task 1.0 in stage 48.0 (TID 117) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7921 bytes) 
16:12:17.663 INFO  Executor - Running task 1.0 in stage 48.0 (TID 117)
16:12:17.664 INFO  Executor - Running task 0.0 in stage 48.0 (TID 116)
16:12:17.715 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.sharded.bam/part-r-00000.bam:0+131967
16:12:17.722 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.sharded.bam/part-r-00001.bam:0+131967
16:12:17.732 INFO  Executor - Finished task 0.0 in stage 48.0 (TID 116). 325590 bytes result sent to driver
16:12:17.734 INFO  TaskSetManager - Finished task 0.0 in stage 48.0 (TID 116) in 72 ms on localhost (executor driver) (1/2)
16:12:17.738 INFO  Executor - Finished task 1.0 in stage 48.0 (TID 117). 325633 bytes result sent to driver
16:12:17.740 INFO  TaskSetManager - Finished task 1.0 in stage 48.0 (TID 117) in 78 ms on localhost (executor driver) (2/2)
16:12:17.740 INFO  TaskSchedulerImpl - Removed TaskSet 48.0, whose tasks have all completed, from pool 
16:12:17.740 INFO  DAGScheduler - ResultStage 48 (collect at ReadsSparkSourceUnitTest.java:155) finished in 0.112 s
16:12:17.741 INFO  DAGScheduler - Job 39 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:17.741 INFO  TaskSchedulerImpl - Killing all running tasks in stage 48: Stage finished
16:12:17.741 INFO  DAGScheduler - Job 39 finished: collect at ReadsSparkSourceUnitTest.java:155, took 0.114369 s
16:12:17.746 INFO  MemoryStore - Block broadcast_85 stored as values in memory (estimated size 297.2 KiB, free 1918.8 MiB)
16:12:17.753 INFO  MemoryStore - Block broadcast_85_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.8 MiB)
16:12:17.753 INFO  BlockManagerInfo - Added broadcast_85_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.8 MiB)
16:12:17.753 INFO  SparkContext - Created broadcast 85 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.779 INFO  MemoryStore - Block broadcast_86 stored as values in memory (estimated size 297.3 KiB, free 1918.5 MiB)
16:12:17.785 INFO  MemoryStore - Block broadcast_86_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.4 MiB)
16:12:17.786 INFO  BlockManagerInfo - Added broadcast_86_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1919.7 MiB)
16:12:17.786 INFO  SparkContext - Created broadcast 86 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.809 INFO  MemoryStore - Block broadcast_87 stored as values in memory (estimated size 297.3 KiB, free 1918.1 MiB)
16:12:17.815 INFO  MemoryStore - Block broadcast_87_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.1 MiB)
16:12:17.816 INFO  BlockManagerInfo - Added broadcast_87_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1919.7 MiB)
16:12:17.816 INFO  SparkContext - Created broadcast 87 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.838 INFO  MemoryStore - Block broadcast_88 stored as values in memory (estimated size 528.0 B, free 1918.1 MiB)
16:12:17.838 INFO  MemoryStore - Block broadcast_88_piece0 stored as bytes in memory (estimated size 183.0 B, free 1918.1 MiB)
16:12:17.838 INFO  BlockManagerInfo - Added broadcast_88_piece0 in memory on localhost:40883 (size: 183.0 B, free: 1919.7 MiB)
16:12:17.839 INFO  SparkContext - Created broadcast 88 from broadcast at CramSource.java:114
16:12:17.840 INFO  MemoryStore - Block broadcast_89 stored as values in memory (estimated size 297.2 KiB, free 1917.8 MiB)
16:12:17.847 INFO  MemoryStore - Block broadcast_89_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.7 MiB)
16:12:17.847 INFO  BlockManagerInfo - Added broadcast_89_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.6 MiB)
16:12:17.847 INFO  SparkContext - Created broadcast 89 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.863 INFO  MemoryStore - Block broadcast_90 stored as values in memory (estimated size 600.0 B, free 1917.7 MiB)
16:12:17.863 INFO  MemoryStore - Block broadcast_90_piece0 stored as bytes in memory (estimated size 202.0 B, free 1917.7 MiB)
16:12:17.864 INFO  BlockManagerInfo - Added broadcast_90_piece0 in memory on localhost:40883 (size: 202.0 B, free: 1919.6 MiB)
16:12:17.864 INFO  SparkContext - Created broadcast 90 from broadcast at CramSource.java:114
16:12:17.865 INFO  MemoryStore - Block broadcast_91 stored as values in memory (estimated size 297.3 KiB, free 1917.4 MiB)
16:12:17.872 INFO  MemoryStore - Block broadcast_91_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.4 MiB)
16:12:17.872 INFO  BlockManagerInfo - Added broadcast_91_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1919.6 MiB)
16:12:17.872 INFO  SparkContext - Created broadcast 91 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.892 INFO  MemoryStore - Block broadcast_92 stored as values in memory (estimated size 297.3 KiB, free 1917.1 MiB)
16:12:17.899 INFO  MemoryStore - Block broadcast_92_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.1 MiB)
16:12:17.899 INFO  BlockManagerInfo - Added broadcast_92_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1919.5 MiB)
16:12:17.899 INFO  SparkContext - Created broadcast 92 from newAPIHadoopFile at PathSplitSource.java:96
16:12:17.922 INFO  FileInputFormat - Total input files to process : 1
16:12:17.958 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:163
16:12:17.958 INFO  DAGScheduler - Got job 40 (collect at ReadsSparkSourceUnitTest.java:163) with 1 output partitions
16:12:17.959 INFO  DAGScheduler - Final stage: ResultStage 49 (collect at ReadsSparkSourceUnitTest.java:163)
16:12:17.959 INFO  DAGScheduler - Parents of final stage: List()
16:12:17.959 INFO  DAGScheduler - Missing parents: List()
16:12:17.959 INFO  DAGScheduler - Submitting ResultStage 49 (MapPartitionsRDD[224] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:17.977 INFO  MemoryStore - Block broadcast_93 stored as values in memory (estimated size 425.0 KiB, free 1916.6 MiB)
16:12:17.978 INFO  MemoryStore - Block broadcast_93_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1916.5 MiB)
16:12:17.979 INFO  BlockManagerInfo - Added broadcast_93_piece0 in memory on localhost:40883 (size: 152.7 KiB, free: 1919.4 MiB)
16:12:17.979 INFO  SparkContext - Created broadcast 93 from broadcast at DAGScheduler.scala:1580
16:12:17.979 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 49 (MapPartitionsRDD[224] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:17.979 INFO  TaskSchedulerImpl - Adding task set 49.0 with 1 tasks resource profile 0
16:12:17.980 INFO  TaskSetManager - Starting task 0.0 in stage 49.0 (TID 118) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7875 bytes) 
16:12:17.980 INFO  Executor - Running task 0.0 in stage 49.0 (TID 118)
16:12:18.013 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam:0+221635
16:12:18.026 INFO  Executor - Finished task 0.0 in stage 49.0 (TID 118). 650184 bytes result sent to driver
16:12:18.028 INFO  TaskSetManager - Finished task 0.0 in stage 49.0 (TID 118) in 48 ms on localhost (executor driver) (1/1)
16:12:18.028 INFO  TaskSchedulerImpl - Removed TaskSet 49.0, whose tasks have all completed, from pool 
16:12:18.028 INFO  DAGScheduler - ResultStage 49 (collect at ReadsSparkSourceUnitTest.java:163) finished in 0.069 s
16:12:18.029 INFO  DAGScheduler - Job 40 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:18.029 INFO  TaskSchedulerImpl - Killing all running tasks in stage 49: Stage finished
16:12:18.029 INFO  DAGScheduler - Job 40 finished: collect at ReadsSparkSourceUnitTest.java:163, took 0.070723 s
16:12:18.033 INFO  MemoryStore - Block broadcast_94 stored as values in memory (estimated size 208.0 B, free 1916.5 MiB)
16:12:18.035 INFO  MemoryStore - Block broadcast_94_piece0 stored as bytes in memory (estimated size 239.0 B, free 1916.5 MiB)
16:12:18.035 INFO  BlockManagerInfo - Added broadcast_94_piece0 in memory on localhost:40883 (size: 239.0 B, free: 1919.4 MiB)
16:12:18.036 INFO  SparkContext - Created broadcast 94 from broadcast at AbstractBinarySamSource.java:82
16:12:18.038 INFO  MemoryStore - Block broadcast_95 stored as values in memory (estimated size 297.2 KiB, free 1916.2 MiB)
16:12:18.050 INFO  MemoryStore - Block broadcast_95_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.2 MiB)
16:12:18.050 INFO  BlockManagerInfo - Added broadcast_95_piece0 in memory on localhost:40883 (size: 50.0 KiB, free: 1919.3 MiB)
16:12:18.050 INFO  SparkContext - Created broadcast 95 from newAPIHadoopFile at PathSplitSource.java:96
16:12:18.078 INFO  FileInputFormat - Total input files to process : 1
16:12:18.082 INFO  SparkContext - Starting job: count at ReadsSparkSourceUnitTest.java:265
16:12:18.082 INFO  DAGScheduler - Got job 41 (count at ReadsSparkSourceUnitTest.java:265) with 1 output partitions
16:12:18.082 INFO  DAGScheduler - Final stage: ResultStage 50 (count at ReadsSparkSourceUnitTest.java:265)
16:12:18.082 INFO  DAGScheduler - Parents of final stage: List()
16:12:18.082 INFO  DAGScheduler - Missing parents: List()
16:12:18.082 INFO  DAGScheduler - Submitting ResultStage 50 (MapPartitionsRDD[231] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:18.106 INFO  MemoryStore - Block broadcast_96 stored as values in memory (estimated size 424.9 KiB, free 1915.7 MiB)
16:12:18.107 INFO  MemoryStore - Block broadcast_96_piece0 stored as bytes in memory (estimated size 152.8 KiB, free 1915.6 MiB)
16:12:18.107 INFO  BlockManagerInfo - Added broadcast_96_piece0 in memory on localhost:40883 (size: 152.8 KiB, free: 1919.2 MiB)
16:12:18.108 INFO  SparkContext - Created broadcast 96 from broadcast at DAGScheduler.scala:1580
16:12:18.108 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 50 (MapPartitionsRDD[231] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:18.108 INFO  TaskSchedulerImpl - Adding task set 50.0 with 1 tasks resource profile 0
16:12:18.109 INFO  TaskSetManager - Starting task 0.0 in stage 50.0 (TID 119) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
16:12:18.109 INFO  Executor - Running task 0.0 in stage 50.0 (TID 119)
16:12:18.141 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
16:12:18.147 INFO  Executor - Finished task 0.0 in stage 50.0 (TID 119). 989 bytes result sent to driver
16:12:18.147 INFO  TaskSetManager - Finished task 0.0 in stage 50.0 (TID 119) in 39 ms on localhost (executor driver) (1/1)
16:12:18.147 INFO  TaskSchedulerImpl - Removed TaskSet 50.0, whose tasks have all completed, from pool 
16:12:18.147 INFO  DAGScheduler - ResultStage 50 (count at ReadsSparkSourceUnitTest.java:265) finished in 0.064 s
16:12:18.147 INFO  DAGScheduler - Job 41 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:18.148 INFO  TaskSchedulerImpl - Killing all running tasks in stage 50: Stage finished
16:12:18.148 INFO  DAGScheduler - Job 41 finished: count at ReadsSparkSourceUnitTest.java:265, took 0.066186 s
16:12:18.151 INFO  MemoryStore - Block broadcast_97 stored as values in memory (estimated size 160.0 B, free 1915.6 MiB)
16:12:18.151 INFO  MemoryStore - Block broadcast_97_piece0 stored as bytes in memory (estimated size 229.0 B, free 1915.6 MiB)
16:12:18.152 INFO  BlockManagerInfo - Added broadcast_97_piece0 in memory on localhost:40883 (size: 229.0 B, free: 1919.2 MiB)
16:12:18.152 INFO  SparkContext - Created broadcast 97 from broadcast at AbstractBinarySamSource.java:82
16:12:18.153 INFO  MemoryStore - Block broadcast_98 stored as values in memory (estimated size 297.3 KiB, free 1915.3 MiB)
16:12:18.160 INFO  MemoryStore - Block broadcast_98_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1915.3 MiB)
16:12:18.160 INFO  BlockManagerInfo - Added broadcast_98_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1919.1 MiB)
16:12:18.160 INFO  SparkContext - Created broadcast 98 from newAPIHadoopFile at PathSplitSource.java:96
16:12:18.186 INFO  FileInputFormat - Total input files to process : 1
16:12:18.190 INFO  SparkContext - Starting job: count at ReadsSparkSourceUnitTest.java:286
16:12:18.190 INFO  DAGScheduler - Got job 42 (count at ReadsSparkSourceUnitTest.java:286) with 1 output partitions
16:12:18.190 INFO  DAGScheduler - Final stage: ResultStage 51 (count at ReadsSparkSourceUnitTest.java:286)
16:12:18.190 INFO  DAGScheduler - Parents of final stage: List()
16:12:18.190 INFO  DAGScheduler - Missing parents: List()
16:12:18.191 INFO  DAGScheduler - Submitting ResultStage 51 (MapPartitionsRDD[238] at filter at ReadsSparkSource.java:96), which has no missing parents
16:12:18.208 INFO  MemoryStore - Block broadcast_99 stored as values in memory (estimated size 424.9 KiB, free 1914.8 MiB)
16:12:18.210 INFO  MemoryStore - Block broadcast_99_piece0 stored as bytes in memory (estimated size 152.8 KiB, free 1914.7 MiB)
16:12:18.210 INFO  BlockManagerInfo - Added broadcast_99_piece0 in memory on localhost:40883 (size: 152.8 KiB, free: 1919.0 MiB)
16:12:18.210 INFO  SparkContext - Created broadcast 99 from broadcast at DAGScheduler.scala:1580
16:12:18.210 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 51 (MapPartitionsRDD[238] at filter at ReadsSparkSource.java:96) (first 15 tasks are for partitions Vector(0))
16:12:18.210 INFO  TaskSchedulerImpl - Adding task set 51.0 with 1 tasks resource profile 0
16:12:18.211 INFO  TaskSetManager - Starting task 0.0 in stage 51.0 (TID 120) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7891 bytes) 
16:12:18.211 INFO  Executor - Running task 0.0 in stage 51.0 (TID 120)
16:12:18.243 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam:0+2184
16:12:18.249 INFO  Executor - Finished task 0.0 in stage 51.0 (TID 120). 989 bytes result sent to driver
16:12:18.250 INFO  TaskSetManager - Finished task 0.0 in stage 51.0 (TID 120) in 39 ms on localhost (executor driver) (1/1)
16:12:18.250 INFO  TaskSchedulerImpl - Removed TaskSet 51.0, whose tasks have all completed, from pool 
16:12:18.250 INFO  DAGScheduler - ResultStage 51 (count at ReadsSparkSourceUnitTest.java:286) finished in 0.059 s
16:12:18.250 INFO  DAGScheduler - Job 42 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:18.250 INFO  TaskSchedulerImpl - Killing all running tasks in stage 51: Stage finished
16:12:18.250 INFO  DAGScheduler - Job 42 finished: count at ReadsSparkSourceUnitTest.java:286, took 0.060437 s
16:12:18.254 INFO  MemoryStore - Block broadcast_100 stored as values in memory (estimated size 297.3 KiB, free 1914.4 MiB)
16:12:18.261 INFO  MemoryStore - Block broadcast_100_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1914.3 MiB)
16:12:18.261 INFO  BlockManagerInfo - Added broadcast_100_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1918.9 MiB)
16:12:18.261 INFO  SparkContext - Created broadcast 100 from newAPIHadoopFile at PathSplitSource.java:96
16:12:18.286 INFO  MemoryStore - Block broadcast_101 stored as values in memory (estimated size 297.4 KiB, free 1914.1 MiB)
16:12:18.292 INFO  MemoryStore - Block broadcast_101_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1914.0 MiB)
16:12:18.292 INFO  BlockManagerInfo - Added broadcast_101_piece0 in memory on localhost:40883 (size: 50.1 KiB, free: 1918.9 MiB)
16:12:18.293 INFO  SparkContext - Created broadcast 101 from newAPIHadoopFile at PathSplitSource.java:96
16:12:18.313 INFO  FileInputFormat - Total input files to process : 1
16:12:18.314 INFO  FileInputFormat - Total input files to process : 1