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

28

tests

0

failures

2

ignored

3.991s

duration

100%

successful

Tests

Test Duration Result
loadReadsNonExistentReference 0.001s passed
readsSparkSourceTestLenient[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.314s passed
readsSparkSourceTestLenient[1](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.260s passed
readsSparkSourceTestSilent[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.291s passed
readsSparkSourceTestSilent[1](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.202s passed
readsSparkSourceTestStrict[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.033s 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) 0.595s passed
readsSparkSourceTest[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam, null) 0.357s passed
readsSparkSourceTest[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, null) 0.338s passed
readsSparkSourceTest[3](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.366s passed
readsSparkSourceTest[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.cram, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.fasta) 0.268s passed
readsSparkSourceUnknownHostTest 0.030s 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) 0.253s passed
testCRAMReferenceFromHDFS - ignored
testCRAMReferenceRequired 0s passed
testCheckCRAMReference 0.001s passed
testGetHeader[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.036s passed
testGetHeader[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam, null) 0.038s passed
testGetHeader[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, null) 0.035s passed
testGetHeader[3](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.037s passed
testGetHeader[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.cram, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.fasta) 0.034s passed
testHeadersAreStripped 0.162s passed
testIntervals 0.109s passed
testIntervalsWithUnmapped 0.124s passed
testPartitionSizing 0.071s passed
testReadFromFileAndHDFS - ignored
testReject2BitCRAMReference 0s passed

Standard error

21:17:56.048 INFO  MemoryStore - Block broadcast_34 stored as values in memory (estimated size 297.2 KiB, free 1919.6 MiB)
21:17:56.084 INFO  MemoryStore - Block broadcast_34_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1919.6 MiB)
21:17:56.084 INFO  BlockManagerInfo - Added broadcast_34_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.9 MiB)
21:17:56.085 INFO  SparkContext - Created broadcast 34 from newAPIHadoopFile at PathSplitSource.java:96
21:17:56.159 INFO  MemoryStore - Block broadcast_35 stored as values in memory (estimated size 297.2 KiB, free 1919.3 MiB)
21:17:56.174 INFO  MemoryStore - Block broadcast_35_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1919.2 MiB)
21:17:56.174 INFO  BlockManagerInfo - Added broadcast_35_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.9 MiB)
21:17:56.175 INFO  SparkContext - Created broadcast 35 from newAPIHadoopFile at PathSplitSource.java:96
21:17:56.231 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
21:17:56.232 INFO  DAGScheduler - Got job 20 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
21:17:56.232 INFO  DAGScheduler - Final stage: ResultStage 29 (collect at ReadsSparkSourceUnitTest.java:111)
21:17:56.232 INFO  DAGScheduler - Parents of final stage: List()
21:17:56.232 INFO  DAGScheduler - Missing parents: List()
21:17:56.232 INFO  DAGScheduler - Submitting ResultStage 29 (ParallelCollectionRDD[69] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
21:17:56.233 INFO  MemoryStore - Block broadcast_36 stored as values in memory (estimated size 3.0 KiB, free 1919.2 MiB)
21:17:56.234 INFO  MemoryStore - Block broadcast_36_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1919.2 MiB)
21:17:56.234 INFO  BlockManagerInfo - Added broadcast_36_piece0 in memory on localhost:40577 (size: 1780.0 B, free: 1919.9 MiB)
21:17:56.235 INFO  SparkContext - Created broadcast 36 from broadcast at DAGScheduler.scala:1580
21:17:56.235 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))
21:17:56.235 INFO  TaskSchedulerImpl - Adding task set 29.0 with 4 tasks resource profile 0
21:17:56.237 INFO  TaskSetManager - Starting task 0.0 in stage 29.0 (TID 67) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes) 
21:17:56.238 INFO  TaskSetManager - Starting task 1.0 in stage 29.0 (TID 68) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes) 
21:17:56.239 INFO  TaskSetManager - Starting task 2.0 in stage 29.0 (TID 69) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes) 
21:17:56.240 INFO  TaskSetManager - Starting task 3.0 in stage 29.0 (TID 70) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes) 
21:17:56.241 INFO  Executor - Running task 1.0 in stage 29.0 (TID 68)
21:17:56.241 INFO  Executor - Running task 0.0 in stage 29.0 (TID 67)
21:17:56.241 INFO  Executor - Running task 2.0 in stage 29.0 (TID 69)
21:17:56.243 INFO  Executor - Running task 3.0 in stage 29.0 (TID 70)
21:17:56.247 INFO  Executor - Finished task 3.0 in stage 29.0 (TID 70). 40805 bytes result sent to driver
21:17:56.247 INFO  Executor - Finished task 1.0 in stage 29.0 (TID 68). 40469 bytes result sent to driver
21:17:56.249 INFO  TaskSetManager - Finished task 3.0 in stage 29.0 (TID 70) in 9 ms on localhost (executor driver) (1/4)
21:17:56.249 INFO  Executor - Finished task 2.0 in stage 29.0 (TID 69). 40423 bytes result sent to driver
21:17:56.250 INFO  TaskSetManager - Finished task 2.0 in stage 29.0 (TID 69) in 12 ms on localhost (executor driver) (2/4)
21:17:56.252 INFO  TaskSetManager - Finished task 1.0 in stage 29.0 (TID 68) in 15 ms on localhost (executor driver) (3/4)
21:17:56.253 INFO  Executor - Finished task 0.0 in stage 29.0 (TID 67). 40398 bytes result sent to driver
21:17:56.254 INFO  TaskSetManager - Finished task 0.0 in stage 29.0 (TID 67) in 18 ms on localhost (executor driver) (4/4)
21:17:56.255 INFO  TaskSchedulerImpl - Removed TaskSet 29.0, whose tasks have all completed, from pool 
21:17:56.255 INFO  DAGScheduler - ResultStage 29 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.023 s
21:17:56.255 INFO  DAGScheduler - Job 20 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:56.255 INFO  TaskSchedulerImpl - Killing all running tasks in stage 29: Stage finished
21:17:56.255 INFO  DAGScheduler - Job 20 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.023905 s
21:17:56.274 INFO  FileInputFormat - Total input files to process : 1
21:17:56.358 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
21:17:56.358 INFO  DAGScheduler - Got job 21 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
21:17:56.358 INFO  DAGScheduler - Final stage: ResultStage 30 (collect at ReadsSparkSourceUnitTest.java:112)
21:17:56.358 INFO  DAGScheduler - Parents of final stage: List()
21:17:56.359 INFO  DAGScheduler - Missing parents: List()
21:17:56.359 INFO  DAGScheduler - Submitting ResultStage 30 (MapPartitionsRDD[76] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:56.396 INFO  MemoryStore - Block broadcast_37 stored as values in memory (estimated size 425.0 KiB, free 1918.8 MiB)
21:17:56.399 INFO  MemoryStore - Block broadcast_37_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1918.7 MiB)
21:17:56.399 INFO  BlockManagerInfo - Added broadcast_37_piece0 in memory on localhost:40577 (size: 152.7 KiB, free: 1919.7 MiB)
21:17:56.400 INFO  SparkContext - Created broadcast 37 from broadcast at DAGScheduler.scala:1580
21:17:56.400 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))
21:17:56.400 INFO  TaskSchedulerImpl - Adding task set 30.0 with 1 tasks resource profile 0
21:17:56.407 INFO  TaskSetManager - Starting task 0.0 in stage 30.0 (TID 71) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
21:17:56.408 INFO  Executor - Running task 0.0 in stage 30.0 (TID 71)
21:17:56.516 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
21:17:56.537 INFO  Executor - Finished task 0.0 in stage 30.0 (TID 71). 159615 bytes result sent to driver
21:17:56.539 INFO  TaskSetManager - Finished task 0.0 in stage 30.0 (TID 71) in 138 ms on localhost (executor driver) (1/1)
21:17:56.540 INFO  TaskSchedulerImpl - Removed TaskSet 30.0, whose tasks have all completed, from pool 
21:17:56.540 INFO  DAGScheduler - ResultStage 30 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.179 s
21:17:56.540 INFO  DAGScheduler - Job 21 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:56.540 INFO  TaskSchedulerImpl - Killing all running tasks in stage 30: Stage finished
21:17:56.540 INFO  DAGScheduler - Job 21 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.182473 s
21:17:56.551 INFO  MemoryStore - Block broadcast_38 stored as values in memory (estimated size 297.3 KiB, free 1918.4 MiB)
21:17:56.564 INFO  MemoryStore - Block broadcast_38_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.3 MiB)
21:17:56.565 INFO  BlockManagerInfo - Added broadcast_38_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.7 MiB)
21:17:56.565 INFO  SparkContext - Created broadcast 38 from newAPIHadoopFile at PathSplitSource.java:96
21:17:56.619 INFO  MemoryStore - Block broadcast_39 stored as values in memory (estimated size 297.3 KiB, free 1918.0 MiB)
21:17:56.631 INFO  MemoryStore - Block broadcast_39_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.0 MiB)
21:17:56.631 INFO  BlockManagerInfo - Added broadcast_39_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.6 MiB)
21:17:56.632 INFO  SparkContext - Created broadcast 39 from newAPIHadoopFile at PathSplitSource.java:96
21:17:56.676 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
21:17:56.676 INFO  DAGScheduler - Got job 22 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
21:17:56.677 INFO  DAGScheduler - Final stage: ResultStage 31 (collect at ReadsSparkSourceUnitTest.java:111)
21:17:56.677 INFO  DAGScheduler - Parents of final stage: List()
21:17:56.677 INFO  DAGScheduler - Missing parents: List()
21:17:56.677 INFO  DAGScheduler - Submitting ResultStage 31 (ParallelCollectionRDD[82] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
21:17:56.678 INFO  MemoryStore - Block broadcast_40 stored as values in memory (estimated size 3.0 KiB, free 1918.0 MiB)
21:17:56.679 INFO  MemoryStore - Block broadcast_40_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1918.0 MiB)
21:17:56.679 INFO  BlockManagerInfo - Added broadcast_40_piece0 in memory on localhost:40577 (size: 1780.0 B, free: 1919.6 MiB)
21:17:56.679 INFO  SparkContext - Created broadcast 40 from broadcast at DAGScheduler.scala:1580
21:17:56.679 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))
21:17:56.680 INFO  TaskSchedulerImpl - Adding task set 31.0 with 4 tasks resource profile 0
21:17:56.682 INFO  TaskSetManager - Starting task 0.0 in stage 31.0 (TID 72) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes) 
21:17:56.683 INFO  TaskSetManager - Starting task 1.0 in stage 31.0 (TID 73) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes) 
21:17:56.684 INFO  TaskSetManager - Starting task 2.0 in stage 31.0 (TID 74) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes) 
21:17:56.686 INFO  TaskSetManager - Starting task 3.0 in stage 31.0 (TID 75) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes) 
21:17:56.686 INFO  Executor - Running task 0.0 in stage 31.0 (TID 72)
21:17:56.686 INFO  Executor - Running task 3.0 in stage 31.0 (TID 75)
21:17:56.689 INFO  Executor - Running task 1.0 in stage 31.0 (TID 73)
21:17:56.690 INFO  Executor - Running task 2.0 in stage 31.0 (TID 74)
21:17:56.694 INFO  Executor - Finished task 0.0 in stage 31.0 (TID 72). 163204 bytes result sent to driver
21:17:56.695 INFO  Executor - Finished task 1.0 in stage 31.0 (TID 73). 163411 bytes result sent to driver
21:17:56.696 INFO  Executor - Finished task 2.0 in stage 31.0 (TID 74). 163399 bytes result sent to driver
21:17:56.698 INFO  TaskSetManager - Finished task 0.0 in stage 31.0 (TID 72) in 18 ms on localhost (executor driver) (1/4)
21:17:56.699 INFO  Executor - Finished task 3.0 in stage 31.0 (TID 75). 162737 bytes result sent to driver
21:17:56.700 INFO  TaskSetManager - Finished task 1.0 in stage 31.0 (TID 73) in 18 ms on localhost (executor driver) (2/4)
21:17:56.701 INFO  TaskSetManager - Finished task 2.0 in stage 31.0 (TID 74) in 18 ms on localhost (executor driver) (3/4)
21:17:56.702 INFO  TaskSetManager - Finished task 3.0 in stage 31.0 (TID 75) in 17 ms on localhost (executor driver) (4/4)
21:17:56.702 INFO  TaskSchedulerImpl - Removed TaskSet 31.0, whose tasks have all completed, from pool 
21:17:56.702 INFO  DAGScheduler - ResultStage 31 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.025 s
21:17:56.702 INFO  DAGScheduler - Job 22 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:56.702 INFO  TaskSchedulerImpl - Killing all running tasks in stage 31: Stage finished
21:17:56.702 INFO  DAGScheduler - Job 22 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.026068 s
21:17:56.704 INFO  FileInputFormat - Total input files to process : 1
21:17:56.765 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
21:17:56.765 INFO  DAGScheduler - Got job 23 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
21:17:56.765 INFO  DAGScheduler - Final stage: ResultStage 32 (collect at ReadsSparkSourceUnitTest.java:112)
21:17:56.765 INFO  DAGScheduler - Parents of final stage: List()
21:17:56.765 INFO  DAGScheduler - Missing parents: List()
21:17:56.766 INFO  DAGScheduler - Submitting ResultStage 32 (MapPartitionsRDD[89] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:56.785 INFO  MemoryStore - Block broadcast_41 stored as values in memory (estimated size 425.0 KiB, free 1917.6 MiB)
21:17:56.787 INFO  MemoryStore - Block broadcast_41_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.4 MiB)
21:17:56.787 INFO  BlockManagerInfo - Added broadcast_41_piece0 in memory on localhost:40577 (size: 152.7 KiB, free: 1919.5 MiB)
21:17:56.787 INFO  SparkContext - Created broadcast 41 from broadcast at DAGScheduler.scala:1580
21:17:56.788 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))
21:17:56.788 INFO  TaskSchedulerImpl - Adding task set 32.0 with 1 tasks resource profile 0
21:17:56.789 INFO  TaskSetManager - Starting task 0.0 in stage 32.0 (TID 76) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7875 bytes) 
21:17:56.789 INFO  Executor - Running task 0.0 in stage 32.0 (TID 76)
21:17:56.851 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam:0+221635
21:17:56.893 INFO  Executor - Finished task 0.0 in stage 32.0 (TID 76). 650184 bytes result sent to driver
21:17:56.897 INFO  TaskSetManager - Finished task 0.0 in stage 32.0 (TID 76) in 109 ms on localhost (executor driver) (1/1)
21:17:56.897 INFO  TaskSchedulerImpl - Removed TaskSet 32.0, whose tasks have all completed, from pool 
21:17:56.898 INFO  DAGScheduler - ResultStage 32 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.132 s
21:17:56.898 INFO  DAGScheduler - Job 23 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:56.898 INFO  TaskSchedulerImpl - Killing all running tasks in stage 32: Stage finished
21:17:56.898 INFO  DAGScheduler - Job 23 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.133480 s
21:17:56.908 INFO  MemoryStore - Block broadcast_42 stored as values in memory (estimated size 297.3 KiB, free 1917.1 MiB)
21:17:56.920 INFO  MemoryStore - Block broadcast_42_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.1 MiB)
21:17:56.920 INFO  BlockManagerInfo - Added broadcast_42_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.4 MiB)
21:17:56.921 INFO  SparkContext - Created broadcast 42 from newAPIHadoopFile at PathSplitSource.java:96
21:17:56.970 INFO  MemoryStore - Block broadcast_43 stored as values in memory (estimated size 297.3 KiB, free 1916.8 MiB)
21:17:56.982 INFO  MemoryStore - Block broadcast_43_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.7 MiB)
21:17:56.983 INFO  BlockManagerInfo - Added broadcast_43_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.4 MiB)
21:17:56.983 INFO  SparkContext - Created broadcast 43 from newAPIHadoopFile at PathSplitSource.java:96
21:17:57.027 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
21:17:57.027 INFO  DAGScheduler - Got job 24 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
21:17:57.027 INFO  DAGScheduler - Final stage: ResultStage 33 (collect at ReadsSparkSourceUnitTest.java:111)
21:17:57.028 INFO  DAGScheduler - Parents of final stage: List()
21:17:57.028 INFO  DAGScheduler - Missing parents: List()
21:17:57.028 INFO  DAGScheduler - Submitting ResultStage 33 (ParallelCollectionRDD[95] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
21:17:57.029 INFO  MemoryStore - Block broadcast_44 stored as values in memory (estimated size 3.0 KiB, free 1916.7 MiB)
21:17:57.030 INFO  MemoryStore - Block broadcast_44_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1916.7 MiB)
21:17:57.030 INFO  BlockManagerInfo - Added broadcast_44_piece0 in memory on localhost:40577 (size: 1780.0 B, free: 1919.4 MiB)
21:17:57.030 INFO  SparkContext - Created broadcast 44 from broadcast at DAGScheduler.scala:1580
21:17:57.031 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))
21:17:57.031 INFO  TaskSchedulerImpl - Adding task set 33.0 with 4 tasks resource profile 0
21:17:57.032 INFO  TaskSetManager - Starting task 0.0 in stage 33.0 (TID 77) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes) 
21:17:57.033 INFO  TaskSetManager - Starting task 1.0 in stage 33.0 (TID 78) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes) 
21:17:57.035 INFO  TaskSetManager - Starting task 2.0 in stage 33.0 (TID 79) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes) 
21:17:57.036 INFO  TaskSetManager - Starting task 3.0 in stage 33.0 (TID 80) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes) 
21:17:57.036 INFO  Executor - Running task 3.0 in stage 33.0 (TID 80)
21:17:57.038 INFO  Executor - Running task 0.0 in stage 33.0 (TID 77)
21:17:57.039 INFO  Executor - Running task 2.0 in stage 33.0 (TID 79)
21:17:57.040 INFO  Executor - Running task 1.0 in stage 33.0 (TID 78)
21:17:57.042 INFO  Executor - Finished task 3.0 in stage 33.0 (TID 80). 162694 bytes result sent to driver
21:17:57.043 INFO  Executor - Finished task 2.0 in stage 33.0 (TID 79). 163356 bytes result sent to driver
21:17:57.043 INFO  Executor - Finished task 1.0 in stage 33.0 (TID 78). 163368 bytes result sent to driver
21:17:57.044 INFO  Executor - Finished task 0.0 in stage 33.0 (TID 77). 163161 bytes result sent to driver
21:17:57.044 INFO  TaskSetManager - Finished task 3.0 in stage 33.0 (TID 80) in 9 ms on localhost (executor driver) (1/4)
21:17:57.046 INFO  TaskSetManager - Finished task 0.0 in stage 33.0 (TID 77) in 15 ms on localhost (executor driver) (2/4)
21:17:57.047 INFO  TaskSetManager - Finished task 2.0 in stage 33.0 (TID 79) in 14 ms on localhost (executor driver) (3/4)
21:17:57.047 INFO  TaskSetManager - Finished task 1.0 in stage 33.0 (TID 78) in 15 ms on localhost (executor driver) (4/4)
21:17:57.047 INFO  TaskSchedulerImpl - Removed TaskSet 33.0, whose tasks have all completed, from pool 
21:17:57.048 INFO  DAGScheduler - ResultStage 33 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.020 s
21:17:57.048 INFO  DAGScheduler - Job 24 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:57.048 INFO  TaskSchedulerImpl - Killing all running tasks in stage 33: Stage finished
21:17:57.048 INFO  DAGScheduler - Job 24 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.020786 s
21:17:57.050 INFO  FileInputFormat - Total input files to process : 1
21:17:57.114 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
21:17:57.115 INFO  DAGScheduler - Got job 25 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
21:17:57.115 INFO  DAGScheduler - Final stage: ResultStage 34 (collect at ReadsSparkSourceUnitTest.java:112)
21:17:57.115 INFO  DAGScheduler - Parents of final stage: List()
21:17:57.115 INFO  DAGScheduler - Missing parents: List()
21:17:57.115 INFO  DAGScheduler - Submitting ResultStage 34 (MapPartitionsRDD[102] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:57.145 INFO  MemoryStore - Block broadcast_45 stored as values in memory (estimated size 425.0 KiB, free 1916.3 MiB)
21:17:57.148 INFO  MemoryStore - Block broadcast_45_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1916.2 MiB)
21:17:57.148 INFO  BlockManagerInfo - Added broadcast_45_piece0 in memory on localhost:40577 (size: 152.7 KiB, free: 1919.2 MiB)
21:17:57.148 INFO  SparkContext - Created broadcast 45 from broadcast at DAGScheduler.scala:1580
21:17:57.149 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))
21:17:57.149 INFO  TaskSchedulerImpl - Adding task set 34.0 with 1 tasks resource profile 0
21:17:57.149 INFO  TaskSetManager - Starting task 0.0 in stage 34.0 (TID 81) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7905 bytes) 
21:17:57.150 INFO  Executor - Running task 0.0 in stage 34.0 (TID 81)
21:17:57.204 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
21:17:57.230 INFO  Executor - Finished task 0.0 in stage 34.0 (TID 81). 650184 bytes result sent to driver
21:17:57.234 INFO  TaskSetManager - Finished task 0.0 in stage 34.0 (TID 81) in 85 ms on localhost (executor driver) (1/1)
21:17:57.234 INFO  TaskSchedulerImpl - Removed TaskSet 34.0, whose tasks have all completed, from pool 
21:17:57.235 INFO  DAGScheduler - ResultStage 34 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.119 s
21:17:57.235 INFO  DAGScheduler - Job 25 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:57.235 INFO  TaskSchedulerImpl - Killing all running tasks in stage 34: Stage finished
21:17:57.236 INFO  DAGScheduler - Job 25 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.121465 s
21:17:57.245 INFO  MemoryStore - Block broadcast_46 stored as values in memory (estimated size 528.0 B, free 1916.2 MiB)
21:17:57.246 INFO  MemoryStore - Block broadcast_46_piece0 stored as bytes in memory (estimated size 183.0 B, free 1916.2 MiB)
21:17:57.246 INFO  BlockManagerInfo - Added broadcast_46_piece0 in memory on localhost:40577 (size: 183.0 B, free: 1919.2 MiB)
21:17:57.247 INFO  SparkContext - Created broadcast 46 from broadcast at CramSource.java:114
21:17:57.251 INFO  MemoryStore - Block broadcast_47 stored as values in memory (estimated size 297.2 KiB, free 1915.9 MiB)
21:17:57.262 INFO  MemoryStore - Block broadcast_47_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.8 MiB)
21:17:57.262 INFO  BlockManagerInfo - Added broadcast_47_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.2 MiB)
21:17:57.263 INFO  SparkContext - Created broadcast 47 from newAPIHadoopFile at PathSplitSource.java:96
21:17:57.300 INFO  MemoryStore - Block broadcast_48 stored as values in memory (estimated size 528.0 B, free 1915.8 MiB)
21:17:57.301 INFO  MemoryStore - Block broadcast_48_piece0 stored as bytes in memory (estimated size 183.0 B, free 1915.8 MiB)
21:17:57.302 INFO  BlockManagerInfo - Added broadcast_48_piece0 in memory on localhost:40577 (size: 183.0 B, free: 1919.2 MiB)
21:17:57.302 INFO  SparkContext - Created broadcast 48 from broadcast at CramSource.java:114
21:17:57.306 INFO  MemoryStore - Block broadcast_49 stored as values in memory (estimated size 297.2 KiB, free 1915.5 MiB)
21:17:57.317 INFO  MemoryStore - Block broadcast_49_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.5 MiB)
21:17:57.317 INFO  BlockManagerInfo - Added broadcast_49_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.1 MiB)
21:17:57.318 INFO  SparkContext - Created broadcast 49 from newAPIHadoopFile at PathSplitSource.java:96
21:17:57.352 INFO  BlockManagerInfo - Removed broadcast_39_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1919.2 MiB)
21:17:57.354 INFO  BlockManagerInfo - Removed broadcast_40_piece0 on localhost:40577 in memory (size: 1780.0 B, free: 1919.2 MiB)
21:17:57.360 INFO  BlockManagerInfo - Removed broadcast_33_piece0 on localhost:40577 in memory (size: 4.8 KiB, free: 1919.2 MiB)
21:17:57.360 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
21:17:57.362 INFO  DAGScheduler - Got job 26 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
21:17:57.362 INFO  DAGScheduler - Final stage: ResultStage 35 (collect at ReadsSparkSourceUnitTest.java:111)
21:17:57.362 INFO  DAGScheduler - Parents of final stage: List()
21:17:57.362 INFO  DAGScheduler - Missing parents: List()
21:17:57.362 INFO  DAGScheduler - Submitting ResultStage 35 (ParallelCollectionRDD[107] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
21:17:57.363 INFO  MemoryStore - Block broadcast_50 stored as values in memory (estimated size 3.0 KiB, free 1915.8 MiB)
21:17:57.364 INFO  MemoryStore - Block broadcast_50_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1915.8 MiB)
21:17:57.364 INFO  BlockManagerInfo - Removed broadcast_24_piece0 on localhost:40577 in memory (size: 4.3 KiB, free: 1919.2 MiB)
21:17:57.364 INFO  BlockManagerInfo - Added broadcast_50_piece0 in memory on localhost:40577 (size: 1780.0 B, free: 1919.2 MiB)
21:17:57.366 INFO  SparkContext - Created broadcast 50 from broadcast at DAGScheduler.scala:1580
21:17:57.367 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))
21:17:57.367 INFO  TaskSchedulerImpl - Adding task set 35.0 with 4 tasks resource profile 0
21:17:57.374 INFO  BlockManagerInfo - Removed broadcast_38_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1919.2 MiB)
21:17:57.376 INFO  TaskSetManager - Starting task 0.0 in stage 35.0 (TID 82) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes) 
21:17:57.382 INFO  TaskSetManager - Starting task 1.0 in stage 35.0 (TID 83) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes) 
21:17:57.387 INFO  BlockManagerInfo - Removed broadcast_27_piece0 on localhost:40577 in memory (size: 5.1 KiB, free: 1919.2 MiB)
21:17:57.387 INFO  TaskSetManager - Starting task 2.0 in stage 35.0 (TID 84) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes) 
21:17:57.388 INFO  TaskSetManager - Starting task 3.0 in stage 35.0 (TID 85) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes) 
21:17:57.390 INFO  Executor - Running task 0.0 in stage 35.0 (TID 82)
21:17:57.390 INFO  Executor - Running task 2.0 in stage 35.0 (TID 84)
21:17:57.391 INFO  Executor - Running task 3.0 in stage 35.0 (TID 85)
21:17:57.392 INFO  Executor - Running task 1.0 in stage 35.0 (TID 83)
21:17:57.394 INFO  Executor - Finished task 1.0 in stage 35.0 (TID 83). 39087 bytes result sent to driver
21:17:57.395 INFO  Executor - Finished task 2.0 in stage 35.0 (TID 84). 39070 bytes result sent to driver
21:17:57.396 INFO  Executor - Finished task 3.0 in stage 35.0 (TID 85). 39343 bytes result sent to driver
21:17:57.397 INFO  Executor - Finished task 0.0 in stage 35.0 (TID 82). 38993 bytes result sent to driver
21:17:57.399 INFO  BlockManagerInfo - Removed broadcast_29_piece0 on localhost:40577 in memory (size: 3.8 KiB, free: 1919.2 MiB)
21:17:57.400 INFO  TaskSetManager - Finished task 2.0 in stage 35.0 (TID 84) in 18 ms on localhost (executor driver) (1/4)
21:17:57.400 INFO  TaskSetManager - Finished task 3.0 in stage 35.0 (TID 85) in 13 ms on localhost (executor driver) (2/4)
21:17:57.400 INFO  TaskSetManager - Finished task 0.0 in stage 35.0 (TID 82) in 33 ms on localhost (executor driver) (3/4)
21:17:57.402 INFO  TaskSetManager - Finished task 1.0 in stage 35.0 (TID 83) in 26 ms on localhost (executor driver) (4/4)
21:17:57.402 INFO  TaskSchedulerImpl - Removed TaskSet 35.0, whose tasks have all completed, from pool 
21:17:57.402 INFO  DAGScheduler - ResultStage 35 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.039 s
21:17:57.402 INFO  DAGScheduler - Job 26 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:57.402 INFO  TaskSchedulerImpl - Killing all running tasks in stage 35: Stage finished
21:17:57.402 INFO  DAGScheduler - Job 26 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.041894 s
21:17:57.404 INFO  FileInputFormat - Total input files to process : 1
21:17:57.405 INFO  BlockManagerInfo - Removed broadcast_45_piece0 on localhost:40577 in memory (size: 152.7 KiB, free: 1919.4 MiB)
21:17:57.411 INFO  BlockManagerInfo - Removed broadcast_25_piece0 on localhost:40577 in memory (size: 4.5 KiB, free: 1919.4 MiB)
21:17:57.416 INFO  BlockManagerInfo - Removed broadcast_42_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1919.4 MiB)
21:17:57.423 INFO  BlockManagerInfo - Removed broadcast_23_piece0 on localhost:40577 in memory (size: 465.0 B, free: 1919.4 MiB)
21:17:57.428 INFO  BlockManagerInfo - Removed broadcast_46_piece0 on localhost:40577 in memory (size: 183.0 B, free: 1919.4 MiB)
21:17:57.431 INFO  BlockManagerInfo - Removed broadcast_34_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.5 MiB)
21:17:57.435 INFO  BlockManager - Removing RDD 47
21:17:57.439 INFO  BlockManagerInfo - Removed broadcast_47_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.5 MiB)
21:17:57.441 INFO  BlockManagerInfo - Removed broadcast_32_piece0 on localhost:40577 in memory (size: 3.8 KiB, free: 1919.5 MiB)
21:17:57.443 INFO  BlockManagerInfo - Removed broadcast_28_piece0 on localhost:40577 in memory (size: 320.0 B, free: 1919.5 MiB)
21:17:57.446 INFO  BlockManagerInfo - Removed broadcast_30_piece0 on localhost:40577 in memory (size: 4.7 KiB, free: 1919.5 MiB)
21:17:57.448 INFO  BlockManagerInfo - Removed broadcast_22_piece0 on localhost:40577 in memory (size: 159.0 B, free: 1919.5 MiB)
21:17:57.451 INFO  BlockManagerInfo - Removed broadcast_31_piece0 on localhost:40577 in memory (size: 320.0 B, free: 1919.5 MiB)
21:17:57.454 INFO  BlockManagerInfo - Removed broadcast_44_piece0 on localhost:40577 in memory (size: 1780.0 B, free: 1919.5 MiB)
21:17:57.456 INFO  BlockManagerInfo - Removed broadcast_43_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1919.6 MiB)
21:17:57.458 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
21:17:57.458 INFO  BlockManagerInfo - Removed broadcast_41_piece0 on localhost:40577 in memory (size: 152.7 KiB, free: 1919.7 MiB)
21:17:57.458 INFO  DAGScheduler - Got job 27 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
21:17:57.458 INFO  DAGScheduler - Final stage: ResultStage 36 (collect at ReadsSparkSourceUnitTest.java:112)
21:17:57.458 INFO  DAGScheduler - Parents of final stage: List()
21:17:57.459 INFO  DAGScheduler - Missing parents: List()
21:17:57.459 INFO  DAGScheduler - Submitting ResultStage 36 (MapPartitionsRDD[113] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:57.459 INFO  BlockManagerInfo - Removed broadcast_26_piece0 on localhost:40577 in memory (size: 3.2 KiB, free: 1919.7 MiB)
21:17:57.461 INFO  BlockManagerInfo - Removed broadcast_35_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.8 MiB)
21:17:57.462 INFO  BlockManagerInfo - Removed broadcast_36_piece0 on localhost:40577 in memory (size: 1780.0 B, free: 1919.8 MiB)
21:17:57.462 INFO  BlockManagerInfo - Removed broadcast_37_piece0 on localhost:40577 in memory (size: 152.7 KiB, free: 1919.9 MiB)
21:17:57.488 INFO  MemoryStore - Block broadcast_51 stored as values in memory (estimated size 286.0 KiB, free 1919.4 MiB)
21:17:57.493 INFO  MemoryStore - Block broadcast_51_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1919.3 MiB)
21:17:57.493 INFO  BlockManagerInfo - Added broadcast_51_piece0 in memory on localhost:40577 (size: 103.1 KiB, free: 1919.8 MiB)
21:17:57.495 INFO  SparkContext - Created broadcast 51 from broadcast at DAGScheduler.scala:1580
21:17:57.506 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))
21:17:57.506 INFO  TaskSchedulerImpl - Adding task set 36.0 with 1 tasks resource profile 0
21:17:57.507 INFO  TaskSetManager - Starting task 0.0 in stage 36.0 (TID 86) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes) 
21:17:57.508 INFO  Executor - Running task 0.0 in stage 36.0 (TID 86)
21:17:57.556 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram:0+50619
21:17:57.596 INFO  Executor - Finished task 0.0 in stage 36.0 (TID 86). 154101 bytes result sent to driver
21:17:57.598 INFO  TaskSetManager - Finished task 0.0 in stage 36.0 (TID 86) in 91 ms on localhost (executor driver) (1/1)
21:17:57.599 INFO  TaskSchedulerImpl - Removed TaskSet 36.0, whose tasks have all completed, from pool 
21:17:57.602 INFO  DAGScheduler - ResultStage 36 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.143 s
21:17:57.602 INFO  DAGScheduler - Job 27 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:57.602 INFO  TaskSchedulerImpl - Killing all running tasks in stage 36: Stage finished
21:17:57.602 INFO  DAGScheduler - Job 27 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.144436 s
21:17:57.626 INFO  MemoryStore - Block broadcast_52 stored as values in memory (estimated size 600.0 B, free 1919.3 MiB)
21:17:57.627 INFO  MemoryStore - Block broadcast_52_piece0 stored as bytes in memory (estimated size 202.0 B, free 1919.3 MiB)
21:17:57.629 INFO  BlockManagerInfo - Added broadcast_52_piece0 in memory on localhost:40577 (size: 202.0 B, free: 1919.8 MiB)
21:17:57.629 INFO  SparkContext - Created broadcast 52 from broadcast at CramSource.java:114
21:17:57.634 INFO  MemoryStore - Block broadcast_53 stored as values in memory (estimated size 297.3 KiB, free 1919.0 MiB)
21:17:57.645 INFO  MemoryStore - Block broadcast_53_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.9 MiB)
21:17:57.646 INFO  BlockManagerInfo - Added broadcast_53_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.8 MiB)
21:17:57.647 INFO  SparkContext - Created broadcast 53 from newAPIHadoopFile at PathSplitSource.java:96
21:17:57.684 INFO  MemoryStore - Block broadcast_54 stored as values in memory (estimated size 600.0 B, free 1918.9 MiB)
21:17:57.685 INFO  MemoryStore - Block broadcast_54_piece0 stored as bytes in memory (estimated size 202.0 B, free 1918.9 MiB)
21:17:57.685 INFO  BlockManagerInfo - Added broadcast_54_piece0 in memory on localhost:40577 (size: 202.0 B, free: 1919.8 MiB)
21:17:57.686 INFO  SparkContext - Created broadcast 54 from broadcast at CramSource.java:114
21:17:57.690 INFO  MemoryStore - Block broadcast_55 stored as values in memory (estimated size 297.3 KiB, free 1918.6 MiB)
21:17:57.701 INFO  MemoryStore - Block broadcast_55_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.6 MiB)
21:17:57.701 INFO  BlockManagerInfo - Added broadcast_55_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.8 MiB)
21:17:57.702 INFO  SparkContext - Created broadcast 55 from newAPIHadoopFile at PathSplitSource.java:96
21:17:57.735 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
21:17:57.735 INFO  DAGScheduler - Got job 28 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
21:17:57.735 INFO  DAGScheduler - Final stage: ResultStage 37 (collect at ReadsSparkSourceUnitTest.java:111)
21:17:57.735 INFO  DAGScheduler - Parents of final stage: List()
21:17:57.735 INFO  DAGScheduler - Missing parents: List()
21:17:57.736 INFO  DAGScheduler - Submitting ResultStage 37 (ParallelCollectionRDD[118] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
21:17:57.736 INFO  MemoryStore - Block broadcast_56 stored as values in memory (estimated size 3.0 KiB, free 1918.6 MiB)
21:17:57.739 INFO  MemoryStore - Block broadcast_56_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1918.6 MiB)
21:17:57.739 INFO  BlockManagerInfo - Added broadcast_56_piece0 in memory on localhost:40577 (size: 1780.0 B, free: 1919.7 MiB)
21:17:57.739 INFO  SparkContext - Created broadcast 56 from broadcast at DAGScheduler.scala:1580
21:17:57.740 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))
21:17:57.740 INFO  TaskSchedulerImpl - Adding task set 37.0 with 4 tasks resource profile 0
21:17:57.742 INFO  TaskSetManager - Starting task 0.0 in stage 37.0 (TID 87) (localhost, executor driver, partition 0, PROCESS_LOCAL, 8303 bytes) 
21:17:57.742 INFO  TaskSetManager - Starting task 1.0 in stage 37.0 (TID 88) (localhost, executor driver, partition 1, PROCESS_LOCAL, 8292 bytes) 
21:17:57.742 INFO  TaskSetManager - Starting task 2.0 in stage 37.0 (TID 89) (localhost, executor driver, partition 2, PROCESS_LOCAL, 8292 bytes) 
21:17:57.743 INFO  TaskSetManager - Starting task 3.0 in stage 37.0 (TID 90) (localhost, executor driver, partition 3, PROCESS_LOCAL, 8184 bytes) 
21:17:57.743 INFO  Executor - Running task 0.0 in stage 37.0 (TID 87)
21:17:57.743 INFO  Executor - Running task 3.0 in stage 37.0 (TID 90)
21:17:57.747 INFO  Executor - Finished task 3.0 in stage 37.0 (TID 90). 1459 bytes result sent to driver
21:17:57.748 INFO  Executor - Running task 1.0 in stage 37.0 (TID 88)
21:17:57.748 INFO  Executor - Running task 2.0 in stage 37.0 (TID 89)
21:17:57.748 INFO  TaskSetManager - Finished task 3.0 in stage 37.0 (TID 90) in 6 ms on localhost (executor driver) (1/4)
21:17:57.750 INFO  Executor - Finished task 2.0 in stage 37.0 (TID 89). 1567 bytes result sent to driver
21:17:57.751 INFO  Executor - Finished task 1.0 in stage 37.0 (TID 88). 1567 bytes result sent to driver
21:17:57.752 INFO  Executor - Finished task 0.0 in stage 37.0 (TID 87). 1578 bytes result sent to driver
21:17:57.752 INFO  TaskSetManager - Finished task 2.0 in stage 37.0 (TID 89) in 10 ms on localhost (executor driver) (2/4)
21:17:57.753 INFO  TaskSetManager - Finished task 1.0 in stage 37.0 (TID 88) in 11 ms on localhost (executor driver) (3/4)
21:17:57.753 INFO  TaskSetManager - Finished task 0.0 in stage 37.0 (TID 87) in 11 ms on localhost (executor driver) (4/4)
21:17:57.753 INFO  TaskSchedulerImpl - Removed TaskSet 37.0, whose tasks have all completed, from pool 
21:17:57.753 INFO  DAGScheduler - ResultStage 37 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.017 s
21:17:57.753 INFO  DAGScheduler - Job 28 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:57.753 INFO  TaskSchedulerImpl - Killing all running tasks in stage 37: Stage finished
21:17:57.758 INFO  DAGScheduler - Job 28 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.023352 s
21:17:57.760 INFO  FileInputFormat - Total input files to process : 1
21:17:57.809 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
21:17:57.809 INFO  DAGScheduler - Got job 29 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
21:17:57.809 INFO  DAGScheduler - Final stage: ResultStage 38 (collect at ReadsSparkSourceUnitTest.java:112)
21:17:57.809 INFO  DAGScheduler - Parents of final stage: List()
21:17:57.809 INFO  DAGScheduler - Missing parents: List()
21:17:57.810 INFO  DAGScheduler - Submitting ResultStage 38 (MapPartitionsRDD[124] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:57.824 INFO  MemoryStore - Block broadcast_57 stored as values in memory (estimated size 286.0 KiB, free 1918.3 MiB)
21:17:57.825 INFO  MemoryStore - Block broadcast_57_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1918.2 MiB)
21:17:57.825 INFO  BlockManagerInfo - Added broadcast_57_piece0 in memory on localhost:40577 (size: 103.1 KiB, free: 1919.6 MiB)
21:17:57.826 INFO  SparkContext - Created broadcast 57 from broadcast at DAGScheduler.scala:1580
21:17:57.826 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))
21:17:57.826 INFO  TaskSchedulerImpl - Adding task set 38.0 with 1 tasks resource profile 0
21:17:57.827 INFO  TaskSetManager - Starting task 0.0 in stage 38.0 (TID 91) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7844 bytes) 
21:17:57.827 INFO  Executor - Running task 0.0 in stage 38.0 (TID 91)
21:17:57.860 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.cram:0+13330
21:17:57.866 INFO  Executor - Finished task 0.0 in stage 38.0 (TID 91). 3736 bytes result sent to driver
21:17:57.867 INFO  TaskSetManager - Finished task 0.0 in stage 38.0 (TID 91) in 41 ms on localhost (executor driver) (1/1)
21:17:57.867 INFO  TaskSchedulerImpl - Removed TaskSet 38.0, whose tasks have all completed, from pool 
21:17:57.868 INFO  DAGScheduler - ResultStage 38 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.057 s
21:17:57.868 INFO  DAGScheduler - Job 29 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:57.868 INFO  TaskSchedulerImpl - Killing all running tasks in stage 38: Stage finished
21:17:57.869 INFO  DAGScheduler - Job 29 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.060040 s
21:17:57.878 INFO  MemoryStore - Block broadcast_58 stored as values in memory (estimated size 297.2 KiB, free 1917.9 MiB)
21:17:57.893 INFO  MemoryStore - Block broadcast_58_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.9 MiB)
21:17:57.894 INFO  BlockManagerInfo - Added broadcast_58_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.6 MiB)
21:17:57.895 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
21:17:57.942 INFO  MemoryStore - Block broadcast_59 stored as values in memory (estimated size 297.2 KiB, free 1917.6 MiB)
21:17:57.953 INFO  MemoryStore - Block broadcast_59_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.5 MiB)
21:17:57.954 INFO  BlockManagerInfo - Added broadcast_59_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.6 MiB)
21:17:57.955 INFO  SparkContext - Created broadcast 59 from newAPIHadoopFile at PathSplitSource.java:96
21:17:57.996 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
21:17:57.997 INFO  DAGScheduler - Got job 30 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
21:17:57.997 INFO  DAGScheduler - Final stage: ResultStage 39 (collect at ReadsSparkSourceUnitTest.java:111)
21:17:57.997 INFO  DAGScheduler - Parents of final stage: List()
21:17:57.997 INFO  DAGScheduler - Missing parents: List()
21:17:57.998 INFO  DAGScheduler - Submitting ResultStage 39 (ParallelCollectionRDD[130] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
21:17:58.000 INFO  MemoryStore - Block broadcast_60 stored as values in memory (estimated size 3.0 KiB, free 1917.5 MiB)
21:17:58.000 INFO  MemoryStore - Block broadcast_60_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1917.5 MiB)
21:17:58.003 INFO  BlockManagerInfo - Added broadcast_60_piece0 in memory on localhost:40577 (size: 1780.0 B, free: 1919.5 MiB)
21:17:58.004 INFO  SparkContext - Created broadcast 60 from broadcast at DAGScheduler.scala:1580
21:17:58.004 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))
21:17:58.004 INFO  TaskSchedulerImpl - Adding task set 39.0 with 4 tasks resource profile 0
21:17:58.005 INFO  TaskSetManager - Starting task 0.0 in stage 39.0 (TID 92) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes) 
21:17:58.005 INFO  TaskSetManager - Starting task 1.0 in stage 39.0 (TID 93) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes) 
21:17:58.006 INFO  TaskSetManager - Starting task 2.0 in stage 39.0 (TID 94) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes) 
21:17:58.006 INFO  TaskSetManager - Starting task 3.0 in stage 39.0 (TID 95) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes) 
21:17:58.006 INFO  Executor - Running task 3.0 in stage 39.0 (TID 95)
21:17:58.006 INFO  Executor - Running task 1.0 in stage 39.0 (TID 93)
21:17:58.008 INFO  Executor - Running task 0.0 in stage 39.0 (TID 92)
21:17:58.008 INFO  Executor - Running task 2.0 in stage 39.0 (TID 94)
21:17:58.011 INFO  Executor - Finished task 3.0 in stage 39.0 (TID 95). 40805 bytes result sent to driver
21:17:58.012 INFO  Executor - Finished task 2.0 in stage 39.0 (TID 94). 40380 bytes result sent to driver
21:17:58.014 INFO  Executor - Finished task 0.0 in stage 39.0 (TID 92). 40355 bytes result sent to driver
21:17:58.016 INFO  Executor - Finished task 1.0 in stage 39.0 (TID 93). 40469 bytes result sent to driver
21:17:58.022 INFO  TaskSetManager - Finished task 3.0 in stage 39.0 (TID 95) in 16 ms on localhost (executor driver) (1/4)
21:17:58.022 INFO  TaskSetManager - Finished task 2.0 in stage 39.0 (TID 94) in 17 ms on localhost (executor driver) (2/4)
21:17:58.022 INFO  TaskSetManager - Finished task 0.0 in stage 39.0 (TID 92) in 18 ms on localhost (executor driver) (3/4)
21:17:58.023 INFO  TaskSetManager - Finished task 1.0 in stage 39.0 (TID 93) in 18 ms on localhost (executor driver) (4/4)
21:17:58.023 INFO  TaskSchedulerImpl - Removed TaskSet 39.0, whose tasks have all completed, from pool 
21:17:58.024 INFO  DAGScheduler - ResultStage 39 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.025 s
21:17:58.024 INFO  DAGScheduler - Job 30 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:58.024 INFO  TaskSchedulerImpl - Killing all running tasks in stage 39: Stage finished
21:17:58.024 INFO  DAGScheduler - Job 30 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.027463 s
21:17:58.026 INFO  FileInputFormat - Total input files to process : 1
21:17:58.097 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
21:17:58.099 INFO  DAGScheduler - Got job 31 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
21:17:58.099 INFO  DAGScheduler - Final stage: ResultStage 40 (collect at ReadsSparkSourceUnitTest.java:112)
21:17:58.099 INFO  DAGScheduler - Parents of final stage: List()
21:17:58.099 INFO  DAGScheduler - Missing parents: List()
21:17:58.099 INFO  DAGScheduler - Submitting ResultStage 40 (MapPartitionsRDD[137] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:58.119 INFO  MemoryStore - Block broadcast_61 stored as values in memory (estimated size 425.0 KiB, free 1917.1 MiB)
21:17:58.122 INFO  MemoryStore - Block broadcast_61_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.0 MiB)
21:17:58.122 INFO  BlockManagerInfo - Added broadcast_61_piece0 in memory on localhost:40577 (size: 152.7 KiB, free: 1919.4 MiB)
21:17:58.122 INFO  SparkContext - Created broadcast 61 from broadcast at DAGScheduler.scala:1580
21:17:58.123 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))
21:17:58.123 INFO  TaskSchedulerImpl - Adding task set 40.0 with 1 tasks resource profile 0
21:17:58.123 INFO  TaskSetManager - Starting task 0.0 in stage 40.0 (TID 96) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
21:17:58.124 INFO  Executor - Running task 0.0 in stage 40.0 (TID 96)
21:17:58.172 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
21:17:58.181 INFO  Executor - Finished task 0.0 in stage 40.0 (TID 96). 159572 bytes result sent to driver
21:17:58.183 INFO  TaskSetManager - Finished task 0.0 in stage 40.0 (TID 96) in 60 ms on localhost (executor driver) (1/1)
21:17:58.183 INFO  TaskSchedulerImpl - Removed TaskSet 40.0, whose tasks have all completed, from pool 
21:17:58.183 INFO  DAGScheduler - ResultStage 40 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.083 s
21:17:58.183 INFO  DAGScheduler - Job 31 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:58.183 INFO  TaskSchedulerImpl - Killing all running tasks in stage 40: Stage finished
21:17:58.184 INFO  DAGScheduler - Job 31 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.086523 s
21:17:58.189 INFO  MemoryStore - Block broadcast_62 stored as values in memory (estimated size 528.0 B, free 1917.0 MiB)
21:17:58.191 INFO  MemoryStore - Block broadcast_62_piece0 stored as bytes in memory (estimated size 183.0 B, free 1917.0 MiB)
21:17:58.191 INFO  BlockManagerInfo - Added broadcast_62_piece0 in memory on localhost:40577 (size: 183.0 B, free: 1919.4 MiB)
21:17:58.191 INFO  SparkContext - Created broadcast 62 from broadcast at CramSource.java:114
21:17:58.195 INFO  MemoryStore - Block broadcast_63 stored as values in memory (estimated size 297.2 KiB, free 1916.7 MiB)
21:17:58.207 INFO  MemoryStore - Block broadcast_63_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.6 MiB)
21:17:58.207 INFO  BlockManagerInfo - Added broadcast_63_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.4 MiB)
21:17:58.208 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
21:17:58.248 INFO  MemoryStore - Block broadcast_64 stored as values in memory (estimated size 528.0 B, free 1916.6 MiB)
21:17:58.250 INFO  MemoryStore - Block broadcast_64_piece0 stored as bytes in memory (estimated size 183.0 B, free 1916.6 MiB)
21:17:58.250 INFO  BlockManagerInfo - Added broadcast_64_piece0 in memory on localhost:40577 (size: 183.0 B, free: 1919.4 MiB)
21:17:58.251 INFO  SparkContext - Created broadcast 64 from broadcast at CramSource.java:114
21:17:58.254 INFO  MemoryStore - Block broadcast_65 stored as values in memory (estimated size 297.2 KiB, free 1916.3 MiB)
21:17:58.269 INFO  MemoryStore - Block broadcast_65_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.3 MiB)
21:17:58.269 INFO  BlockManagerInfo - Added broadcast_65_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.3 MiB)
21:17:58.270 INFO  SparkContext - Created broadcast 65 from newAPIHadoopFile at PathSplitSource.java:96
21:17:58.298 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
21:17:58.299 INFO  DAGScheduler - Got job 32 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
21:17:58.299 INFO  DAGScheduler - Final stage: ResultStage 41 (collect at ReadsSparkSourceUnitTest.java:111)
21:17:58.299 INFO  DAGScheduler - Parents of final stage: List()
21:17:58.299 INFO  DAGScheduler - Missing parents: List()
21:17:58.299 INFO  DAGScheduler - Submitting ResultStage 41 (ParallelCollectionRDD[142] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
21:17:58.300 INFO  MemoryStore - Block broadcast_66 stored as values in memory (estimated size 3.0 KiB, free 1916.3 MiB)
21:17:58.301 INFO  MemoryStore - Block broadcast_66_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1916.3 MiB)
21:17:58.302 INFO  BlockManagerInfo - Added broadcast_66_piece0 in memory on localhost:40577 (size: 1780.0 B, free: 1919.3 MiB)
21:17:58.302 INFO  SparkContext - Created broadcast 66 from broadcast at DAGScheduler.scala:1580
21:17:58.302 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))
21:17:58.302 INFO  TaskSchedulerImpl - Adding task set 41.0 with 4 tasks resource profile 0
21:17:58.304 INFO  TaskSetManager - Starting task 0.0 in stage 41.0 (TID 97) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes) 
21:17:58.305 INFO  TaskSetManager - Starting task 1.0 in stage 41.0 (TID 98) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes) 
21:17:58.306 INFO  TaskSetManager - Starting task 2.0 in stage 41.0 (TID 99) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes) 
21:17:58.307 INFO  TaskSetManager - Starting task 3.0 in stage 41.0 (TID 100) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes) 
21:17:58.307 INFO  Executor - Running task 3.0 in stage 41.0 (TID 100)
21:17:58.307 INFO  Executor - Running task 0.0 in stage 41.0 (TID 97)
21:17:58.308 INFO  Executor - Running task 2.0 in stage 41.0 (TID 99)
21:17:58.310 INFO  Executor - Finished task 2.0 in stage 41.0 (TID 99). 39027 bytes result sent to driver
21:17:58.310 INFO  Executor - Running task 1.0 in stage 41.0 (TID 98)
21:17:58.311 INFO  Executor - Finished task 0.0 in stage 41.0 (TID 97). 38950 bytes result sent to driver
21:17:58.312 INFO  Executor - Finished task 1.0 in stage 41.0 (TID 98). 39087 bytes result sent to driver
21:17:58.312 INFO  Executor - Finished task 3.0 in stage 41.0 (TID 100). 39343 bytes result sent to driver
21:17:58.313 INFO  TaskSetManager - Finished task 0.0 in stage 41.0 (TID 97) in 10 ms on localhost (executor driver) (1/4)
21:17:58.313 INFO  TaskSetManager - Finished task 2.0 in stage 41.0 (TID 99) in 8 ms on localhost (executor driver) (2/4)
21:17:58.314 INFO  TaskSetManager - Finished task 1.0 in stage 41.0 (TID 98) in 10 ms on localhost (executor driver) (3/4)
21:17:58.314 INFO  TaskSetManager - Finished task 3.0 in stage 41.0 (TID 100) in 8 ms on localhost (executor driver) (4/4)
21:17:58.314 INFO  TaskSchedulerImpl - Removed TaskSet 41.0, whose tasks have all completed, from pool 
21:17:58.315 INFO  DAGScheduler - ResultStage 41 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.015 s
21:17:58.315 INFO  DAGScheduler - Job 32 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:58.315 INFO  TaskSchedulerImpl - Killing all running tasks in stage 41: Stage finished
21:17:58.316 INFO  DAGScheduler - Job 32 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.017949 s
21:17:58.318 INFO  FileInputFormat - Total input files to process : 1
21:17:58.364 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
21:17:58.365 INFO  DAGScheduler - Got job 33 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
21:17:58.365 INFO  DAGScheduler - Final stage: ResultStage 42 (collect at ReadsSparkSourceUnitTest.java:112)
21:17:58.365 INFO  DAGScheduler - Parents of final stage: List()
21:17:58.365 INFO  DAGScheduler - Missing parents: List()
21:17:58.365 INFO  DAGScheduler - Submitting ResultStage 42 (MapPartitionsRDD[148] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:58.387 INFO  MemoryStore - Block broadcast_67 stored as values in memory (estimated size 286.0 KiB, free 1916.0 MiB)
21:17:58.389 INFO  MemoryStore - Block broadcast_67_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1915.9 MiB)
21:17:58.389 INFO  BlockManagerInfo - Added broadcast_67_piece0 in memory on localhost:40577 (size: 103.1 KiB, free: 1919.2 MiB)
21:17:58.389 INFO  SparkContext - Created broadcast 67 from broadcast at DAGScheduler.scala:1580
21:17:58.390 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))
21:17:58.390 INFO  TaskSchedulerImpl - Adding task set 42.0 with 1 tasks resource profile 0
21:17:58.390 INFO  TaskSetManager - Starting task 0.0 in stage 42.0 (TID 101) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes) 
21:17:58.391 INFO  Executor - Running task 0.0 in stage 42.0 (TID 101)
21:17:58.426 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
21:17:58.442 INFO  Executor - Finished task 0.0 in stage 42.0 (TID 101). 154101 bytes result sent to driver
21:17:58.443 INFO  TaskSetManager - Finished task 0.0 in stage 42.0 (TID 101) in 53 ms on localhost (executor driver) (1/1)
21:17:58.444 INFO  TaskSchedulerImpl - Removed TaskSet 42.0, whose tasks have all completed, from pool 
21:17:58.444 INFO  DAGScheduler - ResultStage 42 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.077 s
21:17:58.444 INFO  DAGScheduler - Job 33 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:58.444 INFO  TaskSchedulerImpl - Killing all running tasks in stage 42: Stage finished
21:17:58.444 INFO  DAGScheduler - Job 33 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.080170 s
21:17:58.451 INFO  MemoryStore - Block broadcast_68 stored as values in memory (estimated size 297.2 KiB, free 1915.6 MiB)
21:17:58.462 INFO  MemoryStore - Block broadcast_68_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.6 MiB)
21:17:58.462 INFO  BlockManagerInfo - Added broadcast_68_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.2 MiB)
21:17:58.462 INFO  SparkContext - Created broadcast 68 from newAPIHadoopFile at PathSplitSource.java:96
21:17:58.504 INFO  MemoryStore - Block broadcast_69 stored as values in memory (estimated size 297.2 KiB, free 1915.3 MiB)
21:17:58.515 INFO  MemoryStore - Block broadcast_69_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.2 MiB)
21:17:58.515 INFO  BlockManagerInfo - Added broadcast_69_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.1 MiB)
21:17:58.515 INFO  SparkContext - Created broadcast 69 from newAPIHadoopFile at PathSplitSource.java:96
21:17:58.555 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
21:17:58.556 INFO  DAGScheduler - Got job 34 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
21:17:58.556 INFO  DAGScheduler - Final stage: ResultStage 43 (collect at ReadsSparkSourceUnitTest.java:111)
21:17:58.556 INFO  DAGScheduler - Parents of final stage: List()
21:17:58.556 INFO  DAGScheduler - Missing parents: List()
21:17:58.556 INFO  DAGScheduler - Submitting ResultStage 43 (ParallelCollectionRDD[154] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
21:17:58.557 INFO  MemoryStore - Block broadcast_70 stored as values in memory (estimated size 3.0 KiB, free 1915.2 MiB)
21:17:58.558 INFO  MemoryStore - Block broadcast_70_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1915.2 MiB)
21:17:58.559 INFO  BlockManagerInfo - Added broadcast_70_piece0 in memory on localhost:40577 (size: 1780.0 B, free: 1919.1 MiB)
21:17:58.559 INFO  SparkContext - Created broadcast 70 from broadcast at DAGScheduler.scala:1580
21:17:58.559 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))
21:17:58.559 INFO  TaskSchedulerImpl - Adding task set 43.0 with 4 tasks resource profile 0
21:17:58.562 INFO  TaskSetManager - Starting task 0.0 in stage 43.0 (TID 102) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes) 
21:17:58.563 INFO  TaskSetManager - Starting task 1.0 in stage 43.0 (TID 103) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes) 
21:17:58.563 INFO  TaskSetManager - Starting task 2.0 in stage 43.0 (TID 104) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes) 
21:17:58.563 INFO  TaskSetManager - Starting task 3.0 in stage 43.0 (TID 105) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes) 
21:17:58.566 INFO  Executor - Running task 0.0 in stage 43.0 (TID 102)
21:17:58.566 INFO  Executor - Running task 3.0 in stage 43.0 (TID 105)
21:17:58.566 INFO  Executor - Running task 2.0 in stage 43.0 (TID 104)
21:17:58.566 INFO  Executor - Running task 1.0 in stage 43.0 (TID 103)
21:17:58.569 INFO  Executor - Finished task 3.0 in stage 43.0 (TID 105). 40805 bytes result sent to driver
21:17:58.570 INFO  TaskSetManager - Finished task 3.0 in stage 43.0 (TID 105) in 7 ms on localhost (executor driver) (1/4)
21:17:58.571 INFO  Executor - Finished task 2.0 in stage 43.0 (TID 104). 40380 bytes result sent to driver
21:17:58.571 INFO  TaskSetManager - Finished task 2.0 in stage 43.0 (TID 104) in 8 ms on localhost (executor driver) (2/4)
21:17:58.572 INFO  Executor - Finished task 0.0 in stage 43.0 (TID 102). 40355 bytes result sent to driver
21:17:58.572 INFO  TaskSetManager - Finished task 0.0 in stage 43.0 (TID 102) in 10 ms on localhost (executor driver) (3/4)
21:17:58.572 INFO  Executor - Finished task 1.0 in stage 43.0 (TID 103). 40469 bytes result sent to driver
21:17:58.573 INFO  TaskSetManager - Finished task 1.0 in stage 43.0 (TID 103) in 10 ms on localhost (executor driver) (4/4)
21:17:58.573 INFO  TaskSchedulerImpl - Removed TaskSet 43.0, whose tasks have all completed, from pool 
21:17:58.574 INFO  DAGScheduler - ResultStage 43 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.017 s
21:17:58.574 INFO  DAGScheduler - Job 34 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:58.574 INFO  TaskSchedulerImpl - Killing all running tasks in stage 43: Stage finished
21:17:58.574 INFO  DAGScheduler - Job 34 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.019218 s
21:17:58.576 INFO  FileInputFormat - Total input files to process : 1
21:17:58.637 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
21:17:58.638 INFO  DAGScheduler - Got job 35 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
21:17:58.638 INFO  DAGScheduler - Final stage: ResultStage 44 (collect at ReadsSparkSourceUnitTest.java:112)
21:17:58.638 INFO  DAGScheduler - Parents of final stage: List()
21:17:58.638 INFO  DAGScheduler - Missing parents: List()
21:17:58.638 INFO  DAGScheduler - Submitting ResultStage 44 (MapPartitionsRDD[161] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:58.669 INFO  MemoryStore - Block broadcast_71 stored as values in memory (estimated size 425.0 KiB, free 1914.8 MiB)
21:17:58.671 INFO  MemoryStore - Block broadcast_71_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1914.7 MiB)
21:17:58.671 INFO  BlockManagerInfo - Added broadcast_71_piece0 in memory on localhost:40577 (size: 152.7 KiB, free: 1919.0 MiB)
21:17:58.671 INFO  SparkContext - Created broadcast 71 from broadcast at DAGScheduler.scala:1580
21:17:58.672 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))
21:17:58.672 INFO  TaskSchedulerImpl - Adding task set 44.0 with 1 tasks resource profile 0
21:17:58.673 INFO  TaskSetManager - Starting task 0.0 in stage 44.0 (TID 106) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
21:17:58.673 INFO  Executor - Running task 0.0 in stage 44.0 (TID 106)
21:17:58.724 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
21:17:58.732 INFO  Executor - Finished task 0.0 in stage 44.0 (TID 106). 159572 bytes result sent to driver
21:17:58.733 INFO  TaskSetManager - Finished task 0.0 in stage 44.0 (TID 106) in 61 ms on localhost (executor driver) (1/1)
21:17:58.733 INFO  TaskSchedulerImpl - Removed TaskSet 44.0, whose tasks have all completed, from pool 
21:17:58.733 INFO  DAGScheduler - ResultStage 44 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.094 s
21:17:58.734 INFO  DAGScheduler - Job 35 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:58.734 INFO  TaskSchedulerImpl - Killing all running tasks in stage 44: Stage finished
21:17:58.734 INFO  DAGScheduler - Job 35 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.097307 s
21:17:58.741 INFO  MemoryStore - Block broadcast_72 stored as values in memory (estimated size 528.0 B, free 1914.7 MiB)
21:17:58.741 INFO  MemoryStore - Block broadcast_72_piece0 stored as bytes in memory (estimated size 183.0 B, free 1914.7 MiB)
21:17:58.742 INFO  BlockManagerInfo - Added broadcast_72_piece0 in memory on localhost:40577 (size: 183.0 B, free: 1919.0 MiB)
21:17:58.743 INFO  SparkContext - Created broadcast 72 from broadcast at CramSource.java:114
21:17:58.747 INFO  MemoryStore - Block broadcast_73 stored as values in memory (estimated size 297.2 KiB, free 1914.4 MiB)
21:17:58.754 INFO  MemoryStore - Block broadcast_73_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1914.3 MiB)
21:17:58.754 INFO  BlockManagerInfo - Added broadcast_73_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1918.9 MiB)
21:17:58.755 INFO  SparkContext - Created broadcast 73 from newAPIHadoopFile at PathSplitSource.java:96
21:17:58.779 INFO  MemoryStore - Block broadcast_74 stored as values in memory (estimated size 528.0 B, free 1914.3 MiB)
21:17:58.780 INFO  MemoryStore - Block broadcast_74_piece0 stored as bytes in memory (estimated size 183.0 B, free 1914.3 MiB)
21:17:58.780 INFO  BlockManagerInfo - Added broadcast_74_piece0 in memory on localhost:40577 (size: 183.0 B, free: 1918.9 MiB)
21:17:58.781 INFO  SparkContext - Created broadcast 74 from broadcast at CramSource.java:114
21:17:58.784 INFO  MemoryStore - Block broadcast_75 stored as values in memory (estimated size 297.2 KiB, free 1914.0 MiB)
21:17:58.790 INFO  MemoryStore - Block broadcast_75_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1914.0 MiB)
21:17:58.790 INFO  BlockManagerInfo - Added broadcast_75_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1918.9 MiB)
21:17:58.791 INFO  SparkContext - Created broadcast 75 from newAPIHadoopFile at PathSplitSource.java:96
21:17:58.819 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
21:17:58.819 INFO  DAGScheduler - Got job 36 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
21:17:58.819 INFO  DAGScheduler - Final stage: ResultStage 45 (collect at ReadsSparkSourceUnitTest.java:111)
21:17:58.819 INFO  DAGScheduler - Parents of final stage: List()
21:17:58.820 INFO  DAGScheduler - Missing parents: List()
21:17:58.820 INFO  DAGScheduler - Submitting ResultStage 45 (ParallelCollectionRDD[166] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
21:17:58.821 INFO  MemoryStore - Block broadcast_76 stored as values in memory (estimated size 3.0 KiB, free 1914.3 MiB)
21:17:58.821 INFO  MemoryStore - Block broadcast_76_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1914.3 MiB)
21:17:58.821 INFO  BlockManagerInfo - Removed broadcast_49_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1918.9 MiB)
21:17:58.822 INFO  BlockManagerInfo - Added broadcast_76_piece0 in memory on localhost:40577 (size: 1780.0 B, free: 1918.9 MiB)
21:17:58.822 INFO  SparkContext - Created broadcast 76 from broadcast at DAGScheduler.scala:1580
21:17:58.822 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))
21:17:58.822 INFO  TaskSchedulerImpl - Adding task set 45.0 with 4 tasks resource profile 0
21:17:58.823 INFO  TaskSetManager - Starting task 0.0 in stage 45.0 (TID 107) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes) 
21:17:58.824 INFO  TaskSetManager - Starting task 1.0 in stage 45.0 (TID 108) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes) 
21:17:58.824 INFO  TaskSetManager - Starting task 2.0 in stage 45.0 (TID 109) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes) 
21:17:58.825 INFO  TaskSetManager - Starting task 3.0 in stage 45.0 (TID 110) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes) 
21:17:58.825 INFO  Executor - Running task 0.0 in stage 45.0 (TID 107)
21:17:58.827 INFO  Executor - Finished task 0.0 in stage 45.0 (TID 107). 38950 bytes result sent to driver
21:17:58.828 INFO  Executor - Running task 2.0 in stage 45.0 (TID 109)
21:17:58.828 INFO  Executor - Running task 3.0 in stage 45.0 (TID 110)
21:17:58.828 INFO  BlockManagerInfo - Removed broadcast_69_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1918.9 MiB)
21:17:58.828 INFO  Executor - Running task 1.0 in stage 45.0 (TID 108)
21:17:58.828 INFO  TaskSetManager - Finished task 0.0 in stage 45.0 (TID 107) in 5 ms on localhost (executor driver) (1/4)
21:17:58.830 INFO  Executor - Finished task 3.0 in stage 45.0 (TID 110). 39343 bytes result sent to driver
21:17:58.831 INFO  BlockManagerInfo - Removed broadcast_56_piece0 on localhost:40577 in memory (size: 1780.0 B, free: 1919.0 MiB)
21:17:58.832 INFO  TaskSetManager - Finished task 3.0 in stage 45.0 (TID 110) in 8 ms on localhost (executor driver) (2/4)
21:17:58.833 INFO  Executor - Finished task 2.0 in stage 45.0 (TID 109). 39070 bytes result sent to driver
21:17:58.834 INFO  BlockManagerInfo - Removed broadcast_61_piece0 on localhost:40577 in memory (size: 152.7 KiB, free: 1919.1 MiB)
21:17:58.835 INFO  TaskSetManager - Finished task 2.0 in stage 45.0 (TID 109) in 11 ms on localhost (executor driver) (3/4)
21:17:58.835 INFO  BlockManagerInfo - Removed broadcast_68_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.1 MiB)
21:17:58.836 INFO  BlockManagerInfo - Removed broadcast_55_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1919.2 MiB)
21:17:58.836 INFO  Executor - Finished task 1.0 in stage 45.0 (TID 108). 39173 bytes result sent to driver
21:17:58.837 INFO  TaskSetManager - Finished task 1.0 in stage 45.0 (TID 108) in 14 ms on localhost (executor driver) (4/4)
21:17:58.837 INFO  TaskSchedulerImpl - Removed TaskSet 45.0, whose tasks have all completed, from pool 
21:17:58.838 INFO  DAGScheduler - ResultStage 45 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.018 s
21:17:58.838 INFO  DAGScheduler - Job 36 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:58.838 INFO  TaskSchedulerImpl - Killing all running tasks in stage 45: Stage finished
21:17:58.838 INFO  DAGScheduler - Job 36 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.018886 s
21:17:58.839 INFO  FileInputFormat - Total input files to process : 1
21:17:58.840 INFO  BlockManagerInfo - Removed broadcast_53_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1919.2 MiB)
21:17:58.841 INFO  BlockManagerInfo - Removed broadcast_62_piece0 on localhost:40577 in memory (size: 183.0 B, free: 1919.2 MiB)
21:17:58.843 INFO  BlockManagerInfo - Removed broadcast_64_piece0 on localhost:40577 in memory (size: 183.0 B, free: 1919.2 MiB)
21:17:58.845 INFO  BlockManagerInfo - Removed broadcast_52_piece0 on localhost:40577 in memory (size: 202.0 B, free: 1919.2 MiB)
21:17:58.846 INFO  BlockManagerInfo - Removed broadcast_66_piece0 on localhost:40577 in memory (size: 1780.0 B, free: 1919.2 MiB)
21:17:58.848 INFO  BlockManagerInfo - Removed broadcast_50_piece0 on localhost:40577 in memory (size: 1780.0 B, free: 1919.2 MiB)
21:17:58.849 INFO  BlockManagerInfo - Removed broadcast_60_piece0 on localhost:40577 in memory (size: 1780.0 B, free: 1919.3 MiB)
21:17:58.850 INFO  BlockManagerInfo - Removed broadcast_48_piece0 on localhost:40577 in memory (size: 183.0 B, free: 1919.3 MiB)
21:17:58.851 INFO  BlockManagerInfo - Removed broadcast_63_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.3 MiB)
21:17:58.852 INFO  BlockManagerInfo - Removed broadcast_65_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.3 MiB)
21:17:58.855 INFO  BlockManagerInfo - Removed broadcast_70_piece0 on localhost:40577 in memory (size: 1780.0 B, free: 1919.4 MiB)
21:17:58.855 INFO  BlockManagerInfo - Removed broadcast_59_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.4 MiB)
21:17:58.856 INFO  BlockManagerInfo - Removed broadcast_67_piece0 on localhost:40577 in memory (size: 103.1 KiB, free: 1919.5 MiB)
21:17:58.859 INFO  BlockManagerInfo - Removed broadcast_71_piece0 on localhost:40577 in memory (size: 152.7 KiB, free: 1919.6 MiB)
21:17:58.860 INFO  BlockManagerInfo - Removed broadcast_72_piece0 on localhost:40577 in memory (size: 183.0 B, free: 1919.7 MiB)
21:17:58.862 INFO  BlockManagerInfo - Removed broadcast_58_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.7 MiB)
21:17:58.864 INFO  BlockManagerInfo - Removed broadcast_57_piece0 on localhost:40577 in memory (size: 103.1 KiB, free: 1919.8 MiB)
21:17:58.864 INFO  BlockManagerInfo - Removed broadcast_73_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.8 MiB)
21:17:58.865 INFO  BlockManagerInfo - Removed broadcast_51_piece0 on localhost:40577 in memory (size: 103.1 KiB, free: 1919.9 MiB)
21:17:58.866 INFO  BlockManagerInfo - Removed broadcast_54_piece0 on localhost:40577 in memory (size: 202.0 B, free: 1919.9 MiB)
21:17:58.878 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
21:17:58.879 INFO  DAGScheduler - Got job 37 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
21:17:58.879 INFO  DAGScheduler - Final stage: ResultStage 46 (collect at ReadsSparkSourceUnitTest.java:112)
21:17:58.879 INFO  DAGScheduler - Parents of final stage: List()
21:17:58.879 INFO  DAGScheduler - Missing parents: List()
21:17:58.880 INFO  DAGScheduler - Submitting ResultStage 46 (MapPartitionsRDD[172] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:58.892 INFO  MemoryStore - Block broadcast_77 stored as values in memory (estimated size 286.0 KiB, free 1919.4 MiB)
21:17:58.894 INFO  MemoryStore - Block broadcast_77_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1919.3 MiB)
21:17:58.894 INFO  BlockManagerInfo - Added broadcast_77_piece0 in memory on localhost:40577 (size: 103.1 KiB, free: 1919.8 MiB)
21:17:58.894 INFO  SparkContext - Created broadcast 77 from broadcast at DAGScheduler.scala:1580
21:17:58.895 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))
21:17:58.895 INFO  TaskSchedulerImpl - Adding task set 46.0 with 1 tasks resource profile 0
21:17:58.896 INFO  TaskSetManager - Starting task 0.0 in stage 46.0 (TID 111) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes) 
21:17:58.896 INFO  Executor - Running task 0.0 in stage 46.0 (TID 111)
21:17:58.923 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram:0+50619
21:17:58.936 INFO  Executor - Finished task 0.0 in stage 46.0 (TID 111). 154058 bytes result sent to driver
21:17:58.937 INFO  TaskSetManager - Finished task 0.0 in stage 46.0 (TID 111) in 42 ms on localhost (executor driver) (1/1)
21:17:58.937 INFO  TaskSchedulerImpl - Removed TaskSet 46.0, whose tasks have all completed, from pool 
21:17:58.937 INFO  DAGScheduler - ResultStage 46 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.056 s
21:17:58.937 INFO  DAGScheduler - Job 37 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:58.937 INFO  TaskSchedulerImpl - Killing all running tasks in stage 46: Stage finished
21:17:58.937 INFO  DAGScheduler - Job 37 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.059194 s
21:17:58.942 INFO  MemoryStore - Block broadcast_78 stored as values in memory (estimated size 297.2 KiB, free 1919.0 MiB)
21:17:58.949 INFO  MemoryStore - Block broadcast_78_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.9 MiB)
21:17:58.950 INFO  BlockManagerInfo - Added broadcast_78_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.8 MiB)
21:17:58.950 INFO  SparkContext - Created broadcast 78 from newAPIHadoopFile at PathSplitSource.java:96
21:17:58.975 INFO  MemoryStore - Block broadcast_79 stored as values in memory (estimated size 528.0 B, free 1918.9 MiB)
21:17:58.975 INFO  MemoryStore - Block broadcast_79_piece0 stored as bytes in memory (estimated size 183.0 B, free 1918.9 MiB)
21:17:58.976 INFO  BlockManagerInfo - Added broadcast_79_piece0 in memory on localhost:40577 (size: 183.0 B, free: 1919.8 MiB)
21:17:58.976 INFO  SparkContext - Created broadcast 79 from broadcast at CramSource.java:114
21:17:58.978 INFO  MemoryStore - Block broadcast_80 stored as values in memory (estimated size 297.2 KiB, free 1918.6 MiB)
21:17:58.984 INFO  MemoryStore - Block broadcast_80_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.6 MiB)
21:17:58.984 INFO  BlockManagerInfo - Added broadcast_80_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.8 MiB)
21:17:58.985 INFO  SparkContext - Created broadcast 80 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.037 WARN  FileSystem - Failed to initialize filesystem hdfs://bogus/path.bam: java.lang.IllegalArgumentException: java.net.UnknownHostException: bogus
21:17:59.042 INFO  MemoryStore - Block broadcast_81 stored as values in memory (estimated size 297.3 KiB, free 1918.3 MiB)
21:17:59.050 INFO  MemoryStore - Block broadcast_81_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.3 MiB)
21:17:59.050 INFO  BlockManagerInfo - Added broadcast_81_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.7 MiB)
21:17:59.050 INFO  SparkContext - Created broadcast 81 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.085 INFO  MemoryStore - Block broadcast_82 stored as values in memory (estimated size 297.3 KiB, free 1918.0 MiB)
21:17:59.092 INFO  MemoryStore - Block broadcast_82_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.9 MiB)
21:17:59.092 INFO  BlockManagerInfo - Added broadcast_82_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.7 MiB)
21:17:59.092 INFO  SparkContext - Created broadcast 82 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.117 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:154
21:17:59.118 INFO  DAGScheduler - Got job 38 (collect at ReadsSparkSourceUnitTest.java:154) with 4 output partitions
21:17:59.118 INFO  DAGScheduler - Final stage: ResultStage 47 (collect at ReadsSparkSourceUnitTest.java:154)
21:17:59.118 INFO  DAGScheduler - Parents of final stage: List()
21:17:59.118 INFO  DAGScheduler - Missing parents: List()
21:17:59.118 INFO  DAGScheduler - Submitting ResultStage 47 (ParallelCollectionRDD[187] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
21:17:59.119 INFO  MemoryStore - Block broadcast_83 stored as values in memory (estimated size 3.0 KiB, free 1917.9 MiB)
21:17:59.120 INFO  MemoryStore - Block broadcast_83_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1917.9 MiB)
21:17:59.120 INFO  BlockManagerInfo - Added broadcast_83_piece0 in memory on localhost:40577 (size: 1780.0 B, free: 1919.7 MiB)
21:17:59.121 INFO  SparkContext - Created broadcast 83 from broadcast at DAGScheduler.scala:1580
21:17:59.121 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))
21:17:59.121 INFO  TaskSchedulerImpl - Adding task set 47.0 with 4 tasks resource profile 0
21:17:59.122 INFO  TaskSetManager - Starting task 0.0 in stage 47.0 (TID 112) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes) 
21:17:59.122 INFO  TaskSetManager - Starting task 1.0 in stage 47.0 (TID 113) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes) 
21:17:59.123 INFO  TaskSetManager - Starting task 2.0 in stage 47.0 (TID 114) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes) 
21:17:59.123 INFO  TaskSetManager - Starting task 3.0 in stage 47.0 (TID 115) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes) 
21:17:59.124 INFO  Executor - Running task 3.0 in stage 47.0 (TID 115)
21:17:59.125 INFO  Executor - Running task 1.0 in stage 47.0 (TID 113)
21:17:59.126 INFO  Executor - Finished task 3.0 in stage 47.0 (TID 115). 162694 bytes result sent to driver
21:17:59.127 INFO  Executor - Running task 0.0 in stage 47.0 (TID 112)
21:17:59.127 INFO  Executor - Running task 2.0 in stage 47.0 (TID 114)
21:17:59.128 INFO  Executor - Finished task 1.0 in stage 47.0 (TID 113). 163325 bytes result sent to driver
21:17:59.128 INFO  Executor - Finished task 0.0 in stage 47.0 (TID 112). 163118 bytes result sent to driver
21:17:59.129 INFO  TaskSetManager - Finished task 1.0 in stage 47.0 (TID 113) in 6 ms on localhost (executor driver) (1/4)
21:17:59.130 INFO  Executor - Finished task 2.0 in stage 47.0 (TID 114). 163356 bytes result sent to driver
21:17:59.130 INFO  TaskSetManager - Finished task 3.0 in stage 47.0 (TID 115) in 7 ms on localhost (executor driver) (2/4)
21:17:59.132 INFO  TaskSetManager - Finished task 2.0 in stage 47.0 (TID 114) in 10 ms on localhost (executor driver) (3/4)
21:17:59.132 INFO  TaskSetManager - Finished task 0.0 in stage 47.0 (TID 112) in 10 ms on localhost (executor driver) (4/4)
21:17:59.132 INFO  TaskSchedulerImpl - Removed TaskSet 47.0, whose tasks have all completed, from pool 
21:17:59.132 INFO  DAGScheduler - ResultStage 47 (collect at ReadsSparkSourceUnitTest.java:154) finished in 0.014 s
21:17:59.132 INFO  DAGScheduler - Job 38 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:59.132 INFO  TaskSchedulerImpl - Killing all running tasks in stage 47: Stage finished
21:17:59.132 INFO  DAGScheduler - Job 38 finished: collect at ReadsSparkSourceUnitTest.java:154, took 0.015054 s
21:17:59.143 INFO  FileInputFormat - Total input files to process : 2
21:17:59.179 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:155
21:17:59.179 INFO  DAGScheduler - Got job 39 (collect at ReadsSparkSourceUnitTest.java:155) with 2 output partitions
21:17:59.179 INFO  DAGScheduler - Final stage: ResultStage 48 (collect at ReadsSparkSourceUnitTest.java:155)
21:17:59.179 INFO  DAGScheduler - Parents of final stage: List()
21:17:59.179 INFO  DAGScheduler - Missing parents: List()
21:17:59.180 INFO  DAGScheduler - Submitting ResultStage 48 (MapPartitionsRDD[194] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:59.201 INFO  MemoryStore - Block broadcast_84 stored as values in memory (estimated size 425.0 KiB, free 1917.5 MiB)
21:17:59.203 INFO  MemoryStore - Block broadcast_84_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.3 MiB)
21:17:59.203 INFO  BlockManagerInfo - Added broadcast_84_piece0 in memory on localhost:40577 (size: 152.7 KiB, free: 1919.5 MiB)
21:17:59.203 INFO  SparkContext - Created broadcast 84 from broadcast at DAGScheduler.scala:1580
21:17:59.204 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))
21:17:59.204 INFO  TaskSchedulerImpl - Adding task set 48.0 with 2 tasks resource profile 0
21:17:59.205 INFO  TaskSetManager - Starting task 0.0 in stage 48.0 (TID 116) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7921 bytes) 
21:17:59.205 INFO  TaskSetManager - Starting task 1.0 in stage 48.0 (TID 117) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7921 bytes) 
21:17:59.205 INFO  Executor - Running task 0.0 in stage 48.0 (TID 116)
21:17:59.206 INFO  Executor - Running task 1.0 in stage 48.0 (TID 117)
21:17:59.256 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
21:17:59.258 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
21:17:59.279 INFO  Executor - Finished task 1.0 in stage 48.0 (TID 117). 325590 bytes result sent to driver
21:17:59.280 INFO  TaskSetManager - Finished task 1.0 in stage 48.0 (TID 117) in 75 ms on localhost (executor driver) (1/2)
21:17:59.288 INFO  Executor - Finished task 0.0 in stage 48.0 (TID 116). 325590 bytes result sent to driver
21:17:59.290 INFO  TaskSetManager - Finished task 0.0 in stage 48.0 (TID 116) in 86 ms on localhost (executor driver) (2/2)
21:17:59.290 INFO  TaskSchedulerImpl - Removed TaskSet 48.0, whose tasks have all completed, from pool 
21:17:59.290 INFO  DAGScheduler - ResultStage 48 (collect at ReadsSparkSourceUnitTest.java:155) finished in 0.110 s
21:17:59.290 INFO  DAGScheduler - Job 39 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:59.290 INFO  TaskSchedulerImpl - Killing all running tasks in stage 48: Stage finished
21:17:59.291 INFO  DAGScheduler - Job 39 finished: collect at ReadsSparkSourceUnitTest.java:155, took 0.111837 s
21:17:59.297 INFO  MemoryStore - Block broadcast_85 stored as values in memory (estimated size 297.2 KiB, free 1917.1 MiB)
21:17:59.308 INFO  MemoryStore - Block broadcast_85_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.0 MiB)
21:17:59.308 INFO  BlockManagerInfo - Added broadcast_85_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.5 MiB)
21:17:59.309 INFO  SparkContext - Created broadcast 85 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.334 INFO  MemoryStore - Block broadcast_86 stored as values in memory (estimated size 297.3 KiB, free 1916.7 MiB)
21:17:59.345 INFO  MemoryStore - Block broadcast_86_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.7 MiB)
21:17:59.345 INFO  BlockManagerInfo - Added broadcast_86_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.4 MiB)
21:17:59.345 INFO  SparkContext - Created broadcast 86 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.372 INFO  MemoryStore - Block broadcast_87 stored as values in memory (estimated size 297.3 KiB, free 1916.4 MiB)
21:17:59.382 INFO  MemoryStore - Block broadcast_87_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.3 MiB)
21:17:59.383 INFO  BlockManagerInfo - Added broadcast_87_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.4 MiB)
21:17:59.383 INFO  SparkContext - Created broadcast 87 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.405 INFO  MemoryStore - Block broadcast_88 stored as values in memory (estimated size 528.0 B, free 1916.3 MiB)
21:17:59.406 INFO  MemoryStore - Block broadcast_88_piece0 stored as bytes in memory (estimated size 183.0 B, free 1916.3 MiB)
21:17:59.406 INFO  BlockManagerInfo - Added broadcast_88_piece0 in memory on localhost:40577 (size: 183.0 B, free: 1919.4 MiB)
21:17:59.406 INFO  SparkContext - Created broadcast 88 from broadcast at CramSource.java:114
21:17:59.408 INFO  MemoryStore - Block broadcast_89 stored as values in memory (estimated size 297.2 KiB, free 1916.0 MiB)
21:17:59.419 INFO  MemoryStore - Block broadcast_89_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.0 MiB)
21:17:59.419 INFO  BlockManagerInfo - Added broadcast_89_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.3 MiB)
21:17:59.419 INFO  SparkContext - Created broadcast 89 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.441 INFO  MemoryStore - Block broadcast_90 stored as values in memory (estimated size 600.0 B, free 1916.0 MiB)
21:17:59.442 INFO  MemoryStore - Block broadcast_90_piece0 stored as bytes in memory (estimated size 202.0 B, free 1916.0 MiB)
21:17:59.443 INFO  BlockManagerInfo - Added broadcast_90_piece0 in memory on localhost:40577 (size: 202.0 B, free: 1919.3 MiB)
21:17:59.443 INFO  SparkContext - Created broadcast 90 from broadcast at CramSource.java:114
21:17:59.444 INFO  MemoryStore - Block broadcast_91 stored as values in memory (estimated size 297.3 KiB, free 1915.7 MiB)
21:17:59.455 INFO  MemoryStore - Block broadcast_91_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1915.7 MiB)
21:17:59.456 INFO  BlockManagerInfo - Added broadcast_91_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.3 MiB)
21:17:59.456 INFO  SparkContext - Created broadcast 91 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.477 INFO  MemoryStore - Block broadcast_92 stored as values in memory (estimated size 297.3 KiB, free 1915.4 MiB)
21:17:59.483 INFO  MemoryStore - Block broadcast_92_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1915.3 MiB)
21:17:59.484 INFO  BlockManagerInfo - Added broadcast_92_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.2 MiB)
21:17:59.484 INFO  SparkContext - Created broadcast 92 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.505 INFO  FileInputFormat - Total input files to process : 1
21:17:59.541 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:163
21:17:59.542 INFO  DAGScheduler - Got job 40 (collect at ReadsSparkSourceUnitTest.java:163) with 1 output partitions
21:17:59.542 INFO  DAGScheduler - Final stage: ResultStage 49 (collect at ReadsSparkSourceUnitTest.java:163)
21:17:59.542 INFO  DAGScheduler - Parents of final stage: List()
21:17:59.542 INFO  DAGScheduler - Missing parents: List()
21:17:59.542 INFO  DAGScheduler - Submitting ResultStage 49 (MapPartitionsRDD[224] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:59.560 INFO  MemoryStore - Block broadcast_93 stored as values in memory (estimated size 425.0 KiB, free 1914.9 MiB)
21:17:59.562 INFO  MemoryStore - Block broadcast_93_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1914.7 MiB)
21:17:59.562 INFO  BlockManagerInfo - Added broadcast_93_piece0 in memory on localhost:40577 (size: 152.7 KiB, free: 1919.1 MiB)
21:17:59.562 INFO  SparkContext - Created broadcast 93 from broadcast at DAGScheduler.scala:1580
21:17:59.562 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))
21:17:59.562 INFO  TaskSchedulerImpl - Adding task set 49.0 with 1 tasks resource profile 0
21:17:59.563 INFO  TaskSetManager - Starting task 0.0 in stage 49.0 (TID 118) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7875 bytes) 
21:17:59.564 INFO  Executor - Running task 0.0 in stage 49.0 (TID 118)
21:17:59.613 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam:0+221635
21:17:59.631 INFO  Executor - Finished task 0.0 in stage 49.0 (TID 118). 650184 bytes result sent to driver
21:17:59.634 INFO  TaskSetManager - Finished task 0.0 in stage 49.0 (TID 118) in 70 ms on localhost (executor driver) (1/1)
21:17:59.634 INFO  TaskSchedulerImpl - Removed TaskSet 49.0, whose tasks have all completed, from pool 
21:17:59.634 INFO  DAGScheduler - ResultStage 49 (collect at ReadsSparkSourceUnitTest.java:163) finished in 0.091 s
21:17:59.634 INFO  DAGScheduler - Job 40 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:59.634 INFO  TaskSchedulerImpl - Killing all running tasks in stage 49: Stage finished
21:17:59.634 INFO  DAGScheduler - Job 40 finished: collect at ReadsSparkSourceUnitTest.java:163, took 0.092778 s
21:17:59.638 INFO  MemoryStore - Block broadcast_94 stored as values in memory (estimated size 208.0 B, free 1914.7 MiB)
21:17:59.640 INFO  MemoryStore - Block broadcast_94_piece0 stored as bytes in memory (estimated size 239.0 B, free 1914.7 MiB)
21:17:59.640 INFO  BlockManagerInfo - Added broadcast_94_piece0 in memory on localhost:40577 (size: 239.0 B, free: 1919.1 MiB)
21:17:59.641 INFO  SparkContext - Created broadcast 94 from broadcast at AbstractBinarySamSource.java:82
21:17:59.642 INFO  MemoryStore - Block broadcast_95 stored as values in memory (estimated size 297.2 KiB, free 1914.5 MiB)
21:17:59.653 INFO  MemoryStore - Block broadcast_95_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1914.4 MiB)
21:17:59.653 INFO  BlockManagerInfo - Added broadcast_95_piece0 in memory on localhost:40577 (size: 50.0 KiB, free: 1919.0 MiB)
21:17:59.654 INFO  SparkContext - Created broadcast 95 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.678 INFO  FileInputFormat - Total input files to process : 1
21:17:59.682 INFO  SparkContext - Starting job: count at ReadsSparkSourceUnitTest.java:265
21:17:59.682 INFO  DAGScheduler - Got job 41 (count at ReadsSparkSourceUnitTest.java:265) with 1 output partitions
21:17:59.682 INFO  DAGScheduler - Final stage: ResultStage 50 (count at ReadsSparkSourceUnitTest.java:265)
21:17:59.682 INFO  DAGScheduler - Parents of final stage: List()
21:17:59.682 INFO  DAGScheduler - Missing parents: List()
21:17:59.683 INFO  DAGScheduler - Submitting ResultStage 50 (MapPartitionsRDD[231] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:59.700 INFO  MemoryStore - Block broadcast_96 stored as values in memory (estimated size 424.9 KiB, free 1914.0 MiB)
21:17:59.702 INFO  MemoryStore - Block broadcast_96_piece0 stored as bytes in memory (estimated size 152.8 KiB, free 1913.8 MiB)
21:17:59.702 INFO  BlockManagerInfo - Added broadcast_96_piece0 in memory on localhost:40577 (size: 152.8 KiB, free: 1918.9 MiB)
21:17:59.702 INFO  SparkContext - Created broadcast 96 from broadcast at DAGScheduler.scala:1580
21:17:59.703 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))
21:17:59.703 INFO  TaskSchedulerImpl - Adding task set 50.0 with 1 tasks resource profile 0
21:17:59.703 INFO  TaskSetManager - Starting task 0.0 in stage 50.0 (TID 119) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
21:17:59.704 INFO  Executor - Running task 0.0 in stage 50.0 (TID 119)
21:17:59.737 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
21:17:59.743 INFO  Executor - Finished task 0.0 in stage 50.0 (TID 119). 989 bytes result sent to driver
21:17:59.744 INFO  TaskSetManager - Finished task 0.0 in stage 50.0 (TID 119) in 41 ms on localhost (executor driver) (1/1)
21:17:59.744 INFO  TaskSchedulerImpl - Removed TaskSet 50.0, whose tasks have all completed, from pool 
21:17:59.744 INFO  DAGScheduler - ResultStage 50 (count at ReadsSparkSourceUnitTest.java:265) finished in 0.061 s
21:17:59.744 INFO  DAGScheduler - Job 41 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:59.744 INFO  TaskSchedulerImpl - Killing all running tasks in stage 50: Stage finished
21:17:59.744 INFO  DAGScheduler - Job 41 finished: count at ReadsSparkSourceUnitTest.java:265, took 0.062521 s
21:17:59.747 INFO  MemoryStore - Block broadcast_97 stored as values in memory (estimated size 160.0 B, free 1913.8 MiB)
21:17:59.748 INFO  MemoryStore - Block broadcast_97_piece0 stored as bytes in memory (estimated size 229.0 B, free 1913.8 MiB)
21:17:59.748 INFO  BlockManagerInfo - Added broadcast_97_piece0 in memory on localhost:40577 (size: 229.0 B, free: 1918.9 MiB)
21:17:59.748 INFO  SparkContext - Created broadcast 97 from broadcast at AbstractBinarySamSource.java:82
21:17:59.749 INFO  MemoryStore - Block broadcast_98 stored as values in memory (estimated size 297.3 KiB, free 1913.6 MiB)
21:17:59.756 INFO  MemoryStore - Block broadcast_98_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1913.5 MiB)
21:17:59.756 INFO  BlockManagerInfo - Added broadcast_98_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1918.8 MiB)
21:17:59.756 INFO  SparkContext - Created broadcast 98 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.778 INFO  FileInputFormat - Total input files to process : 1
21:17:59.781 INFO  SparkContext - Starting job: count at ReadsSparkSourceUnitTest.java:286
21:17:59.781 INFO  DAGScheduler - Got job 42 (count at ReadsSparkSourceUnitTest.java:286) with 1 output partitions
21:17:59.781 INFO  DAGScheduler - Final stage: ResultStage 51 (count at ReadsSparkSourceUnitTest.java:286)
21:17:59.781 INFO  DAGScheduler - Parents of final stage: List()
21:17:59.781 INFO  DAGScheduler - Missing parents: List()
21:17:59.782 INFO  DAGScheduler - Submitting ResultStage 51 (MapPartitionsRDD[238] at filter at ReadsSparkSource.java:96), which has no missing parents
21:17:59.800 INFO  MemoryStore - Block broadcast_99 stored as values in memory (estimated size 424.9 KiB, free 1913.1 MiB)
21:17:59.801 INFO  MemoryStore - Block broadcast_99_piece0 stored as bytes in memory (estimated size 152.8 KiB, free 1912.9 MiB)
21:17:59.801 INFO  BlockManagerInfo - Added broadcast_99_piece0 in memory on localhost:40577 (size: 152.8 KiB, free: 1918.7 MiB)
21:17:59.802 INFO  SparkContext - Created broadcast 99 from broadcast at DAGScheduler.scala:1580
21:17:59.802 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))
21:17:59.802 INFO  TaskSchedulerImpl - Adding task set 51.0 with 1 tasks resource profile 0
21:17:59.803 INFO  TaskSetManager - Starting task 0.0 in stage 51.0 (TID 120) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7891 bytes) 
21:17:59.803 INFO  Executor - Running task 0.0 in stage 51.0 (TID 120)
21:17:59.817 INFO  BlockManagerInfo - Removed broadcast_91_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1918.7 MiB)
21:17:59.818 INFO  BlockManagerInfo - Removed broadcast_81_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1918.8 MiB)
21:17:59.819 INFO  BlockManagerInfo - Removed broadcast_96_piece0 on localhost:40577 in memory (size: 152.8 KiB, free: 1918.9 MiB)
21:17:59.820 INFO  BlockManagerInfo - Removed broadcast_94_piece0 on localhost:40577 in memory (size: 239.0 B, free: 1918.9 MiB)
21:17:59.821 INFO  BlockManagerInfo - Removed broadcast_88_piece0 on localhost:40577 in memory (size: 183.0 B, free: 1918.9 MiB)
21:17:59.822 INFO  BlockManagerInfo - Removed broadcast_93_piece0 on localhost:40577 in memory (size: 152.7 KiB, free: 1919.1 MiB)
21:17:59.823 INFO  BlockManagerInfo - Removed broadcast_92_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1919.1 MiB)
21:17:59.823 INFO  BlockManagerInfo - Removed broadcast_76_piece0 on localhost:40577 in memory (size: 1780.0 B, free: 1919.1 MiB)
21:17:59.824 INFO  BlockManagerInfo - Removed broadcast_74_piece0 on localhost:40577 in memory (size: 183.0 B, free: 1919.1 MiB)
21:17:59.825 INFO  BlockManagerInfo - Removed broadcast_95_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.2 MiB)
21:17:59.826 INFO  BlockManagerInfo - Removed broadcast_80_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.2 MiB)
21:17:59.830 INFO  BlockManagerInfo - Removed broadcast_75_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.3 MiB)
21:17:59.832 INFO  BlockManagerInfo - Removed broadcast_89_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.3 MiB)
21:17:59.834 INFO  BlockManagerInfo - Removed broadcast_86_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1919.4 MiB)
21:17:59.835 INFO  BlockManagerInfo - Removed broadcast_82_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1919.4 MiB)
21:17:59.836 INFO  BlockManagerInfo - Removed broadcast_83_piece0 on localhost:40577 in memory (size: 1780.0 B, free: 1919.4 MiB)
21:17:59.837 INFO  BlockManagerInfo - Removed broadcast_79_piece0 on localhost:40577 in memory (size: 183.0 B, free: 1919.4 MiB)
21:17:59.838 INFO  BlockManagerInfo - Removed broadcast_90_piece0 on localhost:40577 in memory (size: 202.0 B, free: 1919.4 MiB)
21:17:59.838 INFO  BlockManagerInfo - Removed broadcast_87_piece0 on localhost:40577 in memory (size: 50.1 KiB, free: 1919.5 MiB)
21:17:59.839 INFO  BlockManagerInfo - Removed broadcast_78_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.5 MiB)
21:17:59.842 INFO  BlockManagerInfo - Removed broadcast_84_piece0 on localhost:40577 in memory (size: 152.7 KiB, free: 1919.7 MiB)
21:17:59.842 INFO  BlockManagerInfo - Removed broadcast_85_piece0 on localhost:40577 in memory (size: 50.0 KiB, free: 1919.7 MiB)
21:17:59.843 INFO  BlockManagerInfo - Removed broadcast_77_piece0 on localhost:40577 in memory (size: 103.1 KiB, free: 1919.8 MiB)
21:17:59.860 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam:0+2184
21:17:59.868 INFO  Executor - Finished task 0.0 in stage 51.0 (TID 120). 1032 bytes result sent to driver
21:17:59.869 INFO  TaskSetManager - Finished task 0.0 in stage 51.0 (TID 120) in 67 ms on localhost (executor driver) (1/1)
21:17:59.869 INFO  TaskSchedulerImpl - Removed TaskSet 51.0, whose tasks have all completed, from pool 
21:17:59.869 INFO  DAGScheduler - ResultStage 51 (count at ReadsSparkSourceUnitTest.java:286) finished in 0.087 s
21:17:59.869 INFO  DAGScheduler - Job 42 is finished. Cancelling potential speculative or zombie tasks for this job
21:17:59.869 INFO  TaskSchedulerImpl - Killing all running tasks in stage 51: Stage finished
21:17:59.870 INFO  DAGScheduler - Job 42 finished: count at ReadsSparkSourceUnitTest.java:286, took 0.088850 s
21:17:59.875 INFO  MemoryStore - Block broadcast_100 stored as values in memory (estimated size 297.3 KiB, free 1918.8 MiB)
21:17:59.888 INFO  MemoryStore - Block broadcast_100_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.8 MiB)
21:17:59.888 INFO  BlockManagerInfo - Added broadcast_100_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.8 MiB)
21:17:59.889 INFO  SparkContext - Created broadcast 100 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.913 INFO  MemoryStore - Block broadcast_101 stored as values in memory (estimated size 297.4 KiB, free 1918.5 MiB)
21:17:59.921 INFO  MemoryStore - Block broadcast_101_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.4 MiB)
21:17:59.921 INFO  BlockManagerInfo - Added broadcast_101_piece0 in memory on localhost:40577 (size: 50.1 KiB, free: 1919.7 MiB)
21:17:59.921 INFO  SparkContext - Created broadcast 101 from newAPIHadoopFile at PathSplitSource.java:96
21:17:59.942 INFO  FileInputFormat - Total input files to process : 1
21:17:59.942 INFO  FileInputFormat - Total input files to process : 1