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

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

tests
0

failures
2

ignored
4.012s

duration
100%

successful

Tests

Test Duration Result
loadReadsNonExistentReference 0.001s passed
readsSparkSourceTestLenient[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.311s passed
readsSparkSourceTestLenient[1](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.309s passed
readsSparkSourceTestSilent[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.257s passed
readsSparkSourceTestSilent[1](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.249s passed
readsSparkSourceTestStrict[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.051s passed
readsSparkSourceTestStrict[1](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.050s passed
readsSparkSourceTest[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.575s passed
readsSparkSourceTest[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam, null) 0.365s passed
readsSparkSourceTest[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, null) 0.315s passed
readsSparkSourceTest[3](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.285s passed
readsSparkSourceTest[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.cram, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.fasta) 0.217s passed
readsSparkSourceUnknownHostTest 0.107s 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) 0.286s passed
testCRAMReferenceFromHDFS - ignored
testCRAMReferenceRequired 0s passed
testCheckCRAMReference 0s passed
testGetHeader[0](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam, null) 0.038s passed
testGetHeader[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam, null) 0.032s passed
testGetHeader[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, null) 0.034s passed
testGetHeader[3](/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram, /gatkCloneMountPoint/src/test/resources/human_g1k_v37.chr17_1Mb.fasta) 0.029s passed
testGetHeader[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.cram, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.fasta) 0.029s passed
testHeadersAreStripped 0.149s passed
testIntervals 0.110s passed
testIntervalsWithUnmapped 0.142s passed
testPartitionSizing 0.070s passed
testReadFromFileAndHDFS - ignored
testReject2BitCRAMReference 0s passed

Standard error

20:47:53.884 INFO  BlockManagerInfo - Removed broadcast_7_piece0 on localhost:39529 in memory (size: 326.0 B, free: 1919.9 MiB)
20:47:53.898 INFO  BlockManagerInfo - Removed broadcast_2_piece0 on localhost:39529 in memory (size: 349.0 B, free: 1919.9 MiB)
20:47:53.917 INFO  BlockManagerInfo - Removed broadcast_1_piece0 on localhost:39529 in memory (size: 143.0 B, free: 1919.9 MiB)
20:47:53.928 INFO  BlockManagerInfo - Removed broadcast_18_piece0 on localhost:39529 in memory (size: 2.4 KiB, free: 1919.9 MiB)
20:47:53.940 INFO  BlockManagerInfo - Removed broadcast_4_piece0 on localhost:39529 in memory (size: 4.5 KiB, free: 1919.9 MiB)
20:47:53.951 INFO  BlockManagerInfo - Removed broadcast_9_piece0 on localhost:39529 in memory (size: 4.7 KiB, free: 1919.9 MiB)
20:47:53.972 INFO  BlockManagerInfo - Removed broadcast_12_piece0 on localhost:39529 in memory (size: 2.4 KiB, free: 1919.9 MiB)
20:47:53.983 INFO  BlockManagerInfo - Removed broadcast_27_piece0 on localhost:39529 in memory (size: 5.1 KiB, free: 1919.9 MiB)
20:47:54.006 INFO  BlockManagerInfo - Removed broadcast_3_piece0 on localhost:39529 in memory (size: 4.3 KiB, free: 1919.9 MiB)
20:47:54.016 INFO  BlockManagerInfo - Removed broadcast_19_piece0 on localhost:39529 in memory (size: 2.4 KiB, free: 1919.9 MiB)
20:47:54.023 INFO  BlockManagerInfo - Removed broadcast_11_piece0 on localhost:39529 in memory (size: 2.4 KiB, free: 1919.9 MiB)
20:47:54.036 INFO  MemoryStore - Block broadcast_34 stored as values in memory (estimated size 297.2 KiB, free 1919.6 MiB)
20:47:54.039 INFO  BlockManagerInfo - Removed broadcast_21_piece0 on localhost:39529 in memory (size: 2.4 KiB, free: 1919.9 MiB)
20:47:54.045 INFO  BlockManagerInfo - Removed broadcast_29_piece0 on localhost:39529 in memory (size: 3.8 KiB, free: 1920.0 MiB)
20:47:54.055 INFO  BlockManagerInfo - Removed broadcast_30_piece0 on localhost:39529 in memory (size: 4.7 KiB, free: 1920.0 MiB)
20:47:54.067 INFO  BlockManagerInfo - Removed broadcast_8_piece0 on localhost:39529 in memory (size: 3.8 KiB, free: 1920.0 MiB)
20:47:54.068 INFO  MemoryStore - Block broadcast_34_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1919.5 MiB)
20:47:54.068 INFO  BlockManagerInfo - Added broadcast_34_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.9 MiB)
20:47:54.071 INFO  SparkContext - Created broadcast 34 from newAPIHadoopFile at PathSplitSource.java:96
20:47:54.083 INFO  BlockManagerInfo - Removed broadcast_24_piece0 on localhost:39529 in memory (size: 4.3 KiB, free: 1919.9 MiB)
20:47:54.094 INFO  BlockManagerInfo - Removed broadcast_15_piece0 on localhost:39529 in memory (size: 2.4 KiB, free: 1919.9 MiB)
20:47:54.109 INFO  BlockManagerInfo - Removed broadcast_26_piece0 on localhost:39529 in memory (size: 3.2 KiB, free: 1919.9 MiB)
20:47:54.113 INFO  BlockManagerInfo - Removed broadcast_5_piece0 on localhost:39529 in memory (size: 3.2 KiB, free: 1919.9 MiB)
20:47:54.116 INFO  BlockManagerInfo - Removed broadcast_20_piece0 on localhost:39529 in memory (size: 2.4 KiB, free: 1919.9 MiB)
20:47:54.118 INFO  BlockManagerInfo - Removed broadcast_10_piece0 on localhost:39529 in memory (size: 2.4 KiB, free: 1919.9 MiB)
20:47:54.120 INFO  BlockManagerInfo - Removed broadcast_6_piece0 on localhost:39529 in memory (size: 5.0 KiB, free: 1919.9 MiB)
20:47:54.125 INFO  BlockManagerInfo - Removed broadcast_17_piece0 on localhost:39529 in memory (size: 2.4 KiB, free: 1919.9 MiB)
20:47:54.131 INFO  BlockManagerInfo - Removed broadcast_16_piece0 on localhost:39529 in memory (size: 2.4 KiB, free: 1919.9 MiB)
20:47:54.137 INFO  BlockManagerInfo - Removed broadcast_13_piece0 on localhost:39529 in memory (size: 2.4 KiB, free: 1919.9 MiB)
20:47:54.157 INFO  MemoryStore - Block broadcast_35 stored as values in memory (estimated size 297.2 KiB, free 1919.3 MiB)
20:47:54.172 INFO  MemoryStore - Block broadcast_35_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1919.3 MiB)
20:47:54.172 INFO  BlockManagerInfo - Added broadcast_35_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.9 MiB)
20:47:54.173 INFO  SparkContext - Created broadcast 35 from newAPIHadoopFile at PathSplitSource.java:96
20:47:54.237 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:47:54.238 INFO  DAGScheduler - Got job 20 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:47:54.238 INFO  DAGScheduler - Final stage: ResultStage 29 (collect at ReadsSparkSourceUnitTest.java:111)
20:47:54.238 INFO  DAGScheduler - Parents of final stage: List()
20:47:54.238 INFO  DAGScheduler - Missing parents: List()
20:47:54.239 INFO  DAGScheduler - Submitting ResultStage 29 (ParallelCollectionRDD[69] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:47:54.240 INFO  MemoryStore - Block broadcast_36 stored as values in memory (estimated size 3.0 KiB, free 1919.3 MiB)
20:47:54.241 INFO  MemoryStore - Block broadcast_36_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1919.3 MiB)
20:47:54.242 INFO  BlockManagerInfo - Added broadcast_36_piece0 in memory on localhost:39529 (size: 1780.0 B, free: 1919.9 MiB)
20:47:54.242 INFO  SparkContext - Created broadcast 36 from broadcast at DAGScheduler.scala:1580
20:47:54.243 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))
20:47:54.243 INFO  TaskSchedulerImpl - Adding task set 29.0 with 4 tasks resource profile 0
20:47:54.245 INFO  TaskSetManager - Starting task 0.0 in stage 29.0 (TID 67) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes) 
20:47:54.246 INFO  TaskSetManager - Starting task 1.0 in stage 29.0 (TID 68) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes) 
20:47:54.247 INFO  TaskSetManager - Starting task 2.0 in stage 29.0 (TID 69) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes) 
20:47:54.248 INFO  TaskSetManager - Starting task 3.0 in stage 29.0 (TID 70) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes) 
20:47:54.248 INFO  Executor - Running task 0.0 in stage 29.0 (TID 67)
20:47:54.248 INFO  Executor - Running task 2.0 in stage 29.0 (TID 69)
20:47:54.253 INFO  Executor - Running task 3.0 in stage 29.0 (TID 70)
20:47:54.254 INFO  Executor - Running task 1.0 in stage 29.0 (TID 68)
20:47:54.257 INFO  Executor - Finished task 3.0 in stage 29.0 (TID 70). 40805 bytes result sent to driver
20:47:54.260 INFO  Executor - Finished task 0.0 in stage 29.0 (TID 67). 40355 bytes result sent to driver
20:47:54.261 INFO  TaskSetManager - Finished task 0.0 in stage 29.0 (TID 67) in 18 ms on localhost (executor driver) (1/4)
20:47:54.261 INFO  TaskSetManager - Finished task 3.0 in stage 29.0 (TID 70) in 14 ms on localhost (executor driver) (2/4)
20:47:54.262 INFO  Executor - Finished task 1.0 in stage 29.0 (TID 68). 40512 bytes result sent to driver
20:47:54.263 INFO  Executor - Finished task 2.0 in stage 29.0 (TID 69). 40380 bytes result sent to driver
20:47:54.263 INFO  TaskSetManager - Finished task 1.0 in stage 29.0 (TID 68) in 18 ms on localhost (executor driver) (3/4)
20:47:54.264 INFO  TaskSetManager - Finished task 2.0 in stage 29.0 (TID 69) in 18 ms on localhost (executor driver) (4/4)
20:47:54.265 INFO  DAGScheduler - ResultStage 29 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.025 s
20:47:54.265 INFO  DAGScheduler - Job 20 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:54.265 INFO  TaskSchedulerImpl - Removed TaskSet 29.0, whose tasks have all completed, from pool 
20:47:54.265 INFO  TaskSchedulerImpl - Killing all running tasks in stage 29: Stage finished
20:47:54.265 INFO  DAGScheduler - Job 20 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.027548 s
20:47:54.281 INFO  FileInputFormat - Total input files to process : 1
20:47:54.329 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:47:54.329 INFO  DAGScheduler - Got job 21 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:47:54.329 INFO  DAGScheduler - Final stage: ResultStage 30 (collect at ReadsSparkSourceUnitTest.java:112)
20:47:54.329 INFO  DAGScheduler - Parents of final stage: List()
20:47:54.330 INFO  DAGScheduler - Missing parents: List()
20:47:54.330 INFO  DAGScheduler - Submitting ResultStage 30 (MapPartitionsRDD[76] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:54.356 INFO  MemoryStore - Block broadcast_37 stored as values in memory (estimated size 425.0 KiB, free 1918.9 MiB)
20:47:54.359 INFO  MemoryStore - Block broadcast_37_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1918.7 MiB)
20:47:54.359 INFO  BlockManagerInfo - Added broadcast_37_piece0 in memory on localhost:39529 (size: 152.7 KiB, free: 1919.7 MiB)
20:47:54.360 INFO  SparkContext - Created broadcast 37 from broadcast at DAGScheduler.scala:1580
20:47:54.360 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))
20:47:54.360 INFO  TaskSchedulerImpl - Adding task set 30.0 with 1 tasks resource profile 0
20:47:54.367 INFO  TaskSetManager - Starting task 0.0 in stage 30.0 (TID 71) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
20:47:54.368 INFO  Executor - Running task 0.0 in stage 30.0 (TID 71)
20:47:54.440 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
20:47:54.459 INFO  Executor - Finished task 0.0 in stage 30.0 (TID 71). 159615 bytes result sent to driver
20:47:54.461 INFO  TaskSetManager - Finished task 0.0 in stage 30.0 (TID 71) in 100 ms on localhost (executor driver) (1/1)
20:47:54.461 INFO  TaskSchedulerImpl - Removed TaskSet 30.0, whose tasks have all completed, from pool 
20:47:54.462 INFO  DAGScheduler - ResultStage 30 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.130 s
20:47:54.462 INFO  DAGScheduler - Job 21 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:54.462 INFO  TaskSchedulerImpl - Killing all running tasks in stage 30: Stage finished
20:47:54.462 INFO  DAGScheduler - Job 21 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.133109 s
20:47:54.473 INFO  MemoryStore - Block broadcast_38 stored as values in memory (estimated size 297.3 KiB, free 1918.4 MiB)
20:47:54.483 INFO  MemoryStore - Block broadcast_38_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.4 MiB)
20:47:54.484 INFO  BlockManagerInfo - Added broadcast_38_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.7 MiB)
20:47:54.484 INFO  SparkContext - Created broadcast 38 from newAPIHadoopFile at PathSplitSource.java:96
20:47:54.524 INFO  MemoryStore - Block broadcast_39 stored as values in memory (estimated size 297.3 KiB, free 1918.1 MiB)
20:47:54.533 INFO  MemoryStore - Block broadcast_39_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.0 MiB)
20:47:54.533 INFO  BlockManagerInfo - Added broadcast_39_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.6 MiB)
20:47:54.534 INFO  SparkContext - Created broadcast 39 from newAPIHadoopFile at PathSplitSource.java:96
20:47:54.564 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:47:54.564 INFO  DAGScheduler - Got job 22 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:47:54.564 INFO  DAGScheduler - Final stage: ResultStage 31 (collect at ReadsSparkSourceUnitTest.java:111)
20:47:54.564 INFO  DAGScheduler - Parents of final stage: List()
20:47:54.565 INFO  DAGScheduler - Missing parents: List()
20:47:54.565 INFO  DAGScheduler - Submitting ResultStage 31 (ParallelCollectionRDD[82] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:47:54.566 INFO  MemoryStore - Block broadcast_40 stored as values in memory (estimated size 3.0 KiB, free 1918.0 MiB)
20:47:54.568 INFO  MemoryStore - Block broadcast_40_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1918.0 MiB)
20:47:54.568 INFO  BlockManagerInfo - Added broadcast_40_piece0 in memory on localhost:39529 (size: 1780.0 B, free: 1919.6 MiB)
20:47:54.568 INFO  SparkContext - Created broadcast 40 from broadcast at DAGScheduler.scala:1580
20:47:54.569 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))
20:47:54.569 INFO  TaskSchedulerImpl - Adding task set 31.0 with 4 tasks resource profile 0
20:47:54.571 INFO  TaskSetManager - Starting task 0.0 in stage 31.0 (TID 72) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes) 
20:47:54.573 INFO  TaskSetManager - Starting task 1.0 in stage 31.0 (TID 73) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes) 
20:47:54.574 INFO  TaskSetManager - Starting task 2.0 in stage 31.0 (TID 74) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes) 
20:47:54.576 INFO  TaskSetManager - Starting task 3.0 in stage 31.0 (TID 75) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes) 
20:47:54.576 INFO  Executor - Running task 3.0 in stage 31.0 (TID 75)
20:47:54.576 INFO  Executor - Running task 1.0 in stage 31.0 (TID 73)
20:47:54.576 INFO  Executor - Running task 0.0 in stage 31.0 (TID 72)
20:47:54.580 INFO  Executor - Running task 2.0 in stage 31.0 (TID 74)
20:47:54.588 INFO  Executor - Finished task 3.0 in stage 31.0 (TID 75). 162737 bytes result sent to driver
20:47:54.588 INFO  Executor - Finished task 2.0 in stage 31.0 (TID 74). 163442 bytes result sent to driver
20:47:54.590 INFO  Executor - Finished task 0.0 in stage 31.0 (TID 72). 163204 bytes result sent to driver
20:47:54.594 INFO  TaskSetManager - Finished task 2.0 in stage 31.0 (TID 74) in 21 ms on localhost (executor driver) (1/4)
20:47:54.599 INFO  TaskSetManager - Finished task 3.0 in stage 31.0 (TID 75) in 25 ms on localhost (executor driver) (2/4)
20:47:54.601 INFO  Executor - Finished task 1.0 in stage 31.0 (TID 73). 163454 bytes result sent to driver
20:47:54.601 INFO  TaskSetManager - Finished task 0.0 in stage 31.0 (TID 72) in 31 ms on localhost (executor driver) (3/4)
20:47:54.603 INFO  TaskSetManager - Finished task 1.0 in stage 31.0 (TID 73) in 32 ms on localhost (executor driver) (4/4)
20:47:54.603 INFO  TaskSchedulerImpl - Removed TaskSet 31.0, whose tasks have all completed, from pool 
20:47:54.603 INFO  DAGScheduler - ResultStage 31 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.038 s
20:47:54.603 INFO  DAGScheduler - Job 22 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:54.603 INFO  TaskSchedulerImpl - Killing all running tasks in stage 31: Stage finished
20:47:54.604 INFO  DAGScheduler - Job 22 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.039744 s
20:47:54.606 INFO  FileInputFormat - Total input files to process : 1
20:47:54.676 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:47:54.676 INFO  DAGScheduler - Got job 23 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:47:54.676 INFO  DAGScheduler - Final stage: ResultStage 32 (collect at ReadsSparkSourceUnitTest.java:112)
20:47:54.676 INFO  DAGScheduler - Parents of final stage: List()
20:47:54.677 INFO  DAGScheduler - Missing parents: List()
20:47:54.677 INFO  DAGScheduler - Submitting ResultStage 32 (MapPartitionsRDD[89] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:54.710 INFO  MemoryStore - Block broadcast_41 stored as values in memory (estimated size 425.0 KiB, free 1917.6 MiB)
20:47:54.713 INFO  MemoryStore - Block broadcast_41_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.5 MiB)
20:47:54.713 INFO  BlockManagerInfo - Added broadcast_41_piece0 in memory on localhost:39529 (size: 152.7 KiB, free: 1919.5 MiB)
20:47:54.714 INFO  SparkContext - Created broadcast 41 from broadcast at DAGScheduler.scala:1580
20:47:54.714 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))
20:47:54.714 INFO  TaskSchedulerImpl - Adding task set 32.0 with 1 tasks resource profile 0
20:47:54.715 INFO  TaskSetManager - Starting task 0.0 in stage 32.0 (TID 76) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7875 bytes) 
20:47:54.715 INFO  Executor - Running task 0.0 in stage 32.0 (TID 76)
20:47:54.778 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam:0+221635
20:47:54.821 INFO  Executor - Finished task 0.0 in stage 32.0 (TID 76). 650184 bytes result sent to driver
20:47:54.826 INFO  TaskSetManager - Finished task 0.0 in stage 32.0 (TID 76) in 111 ms on localhost (executor driver) (1/1)
20:47:54.826 INFO  DAGScheduler - ResultStage 32 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.148 s
20:47:54.826 INFO  DAGScheduler - Job 23 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:54.826 INFO  TaskSchedulerImpl - Removed TaskSet 32.0, whose tasks have all completed, from pool 
20:47:54.826 INFO  TaskSchedulerImpl - Killing all running tasks in stage 32: Stage finished
20:47:54.827 INFO  DAGScheduler - Job 23 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.150962 s
20:47:54.837 INFO  MemoryStore - Block broadcast_42 stored as values in memory (estimated size 297.3 KiB, free 1917.2 MiB)
20:47:54.850 INFO  MemoryStore - Block broadcast_42_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.1 MiB)
20:47:54.850 INFO  BlockManagerInfo - Added broadcast_42_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.4 MiB)
20:47:54.851 INFO  SparkContext - Created broadcast 42 from newAPIHadoopFile at PathSplitSource.java:96
20:47:54.903 INFO  MemoryStore - Block broadcast_43 stored as values in memory (estimated size 297.3 KiB, free 1916.8 MiB)
20:47:54.916 INFO  MemoryStore - Block broadcast_43_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.8 MiB)
20:47:54.917 INFO  BlockManagerInfo - Added broadcast_43_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.4 MiB)
20:47:54.917 INFO  SparkContext - Created broadcast 43 from newAPIHadoopFile at PathSplitSource.java:96
20:47:54.954 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:47:54.954 INFO  DAGScheduler - Got job 24 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:47:54.954 INFO  DAGScheduler - Final stage: ResultStage 33 (collect at ReadsSparkSourceUnitTest.java:111)
20:47:54.954 INFO  DAGScheduler - Parents of final stage: List()
20:47:54.954 INFO  DAGScheduler - Missing parents: List()
20:47:54.955 INFO  DAGScheduler - Submitting ResultStage 33 (ParallelCollectionRDD[95] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:47:54.956 INFO  MemoryStore - Block broadcast_44 stored as values in memory (estimated size 3.0 KiB, free 1916.8 MiB)
20:47:54.956 INFO  MemoryStore - Block broadcast_44_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1916.8 MiB)
20:47:54.957 INFO  BlockManagerInfo - Added broadcast_44_piece0 in memory on localhost:39529 (size: 1780.0 B, free: 1919.4 MiB)
20:47:54.957 INFO  SparkContext - Created broadcast 44 from broadcast at DAGScheduler.scala:1580
20:47:54.957 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))
20:47:54.957 INFO  TaskSchedulerImpl - Adding task set 33.0 with 4 tasks resource profile 0
20:47:54.959 INFO  TaskSetManager - Starting task 0.0 in stage 33.0 (TID 77) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes) 
20:47:54.960 INFO  TaskSetManager - Starting task 1.0 in stage 33.0 (TID 78) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes) 
20:47:54.961 INFO  TaskSetManager - Starting task 2.0 in stage 33.0 (TID 79) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes) 
20:47:54.962 INFO  TaskSetManager - Starting task 3.0 in stage 33.0 (TID 80) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes) 
20:47:54.962 INFO  Executor - Running task 1.0 in stage 33.0 (TID 78)
20:47:54.963 INFO  Executor - Running task 0.0 in stage 33.0 (TID 77)
20:47:54.965 INFO  Executor - Running task 3.0 in stage 33.0 (TID 80)
20:47:54.965 INFO  Executor - Running task 2.0 in stage 33.0 (TID 79)
20:47:54.969 INFO  Executor - Finished task 1.0 in stage 33.0 (TID 78). 163454 bytes result sent to driver
20:47:54.969 INFO  Executor - Finished task 0.0 in stage 33.0 (TID 77). 163161 bytes result sent to driver
20:47:54.970 INFO  Executor - Finished task 3.0 in stage 33.0 (TID 80). 162737 bytes result sent to driver
20:47:54.970 INFO  Executor - Finished task 2.0 in stage 33.0 (TID 79). 163399 bytes result sent to driver
20:47:54.971 INFO  TaskSetManager - Finished task 1.0 in stage 33.0 (TID 78) in 12 ms on localhost (executor driver) (1/4)
20:47:54.972 INFO  TaskSetManager - Finished task 2.0 in stage 33.0 (TID 79) in 12 ms on localhost (executor driver) (2/4)
20:47:54.973 INFO  TaskSetManager - Finished task 3.0 in stage 33.0 (TID 80) in 12 ms on localhost (executor driver) (3/4)
20:47:54.975 INFO  TaskSetManager - Finished task 0.0 in stage 33.0 (TID 77) in 17 ms on localhost (executor driver) (4/4)
20:47:54.975 INFO  DAGScheduler - ResultStage 33 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.020 s
20:47:54.975 INFO  DAGScheduler - Job 24 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:54.975 INFO  TaskSchedulerImpl - Removed TaskSet 33.0, whose tasks have all completed, from pool 
20:47:54.975 INFO  TaskSchedulerImpl - Killing all running tasks in stage 33: Stage finished
20:47:54.975 INFO  DAGScheduler - Job 24 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.021320 s
20:47:54.978 INFO  FileInputFormat - Total input files to process : 1
20:47:55.032 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:47:55.033 INFO  DAGScheduler - Got job 25 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:47:55.033 INFO  DAGScheduler - Final stage: ResultStage 34 (collect at ReadsSparkSourceUnitTest.java:112)
20:47:55.033 INFO  DAGScheduler - Parents of final stage: List()
20:47:55.033 INFO  DAGScheduler - Missing parents: List()
20:47:55.034 INFO  DAGScheduler - Submitting ResultStage 34 (MapPartitionsRDD[102] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:55.053 INFO  MemoryStore - Block broadcast_45 stored as values in memory (estimated size 425.0 KiB, free 1916.4 MiB)
20:47:55.056 INFO  MemoryStore - Block broadcast_45_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1916.2 MiB)
20:47:55.056 INFO  BlockManagerInfo - Added broadcast_45_piece0 in memory on localhost:39529 (size: 152.7 KiB, free: 1919.2 MiB)
20:47:55.057 INFO  SparkContext - Created broadcast 45 from broadcast at DAGScheduler.scala:1580
20:47:55.057 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))
20:47:55.057 INFO  TaskSchedulerImpl - Adding task set 34.0 with 1 tasks resource profile 0
20:47:55.058 INFO  TaskSetManager - Starting task 0.0 in stage 34.0 (TID 81) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7905 bytes) 
20:47:55.059 INFO  Executor - Running task 0.0 in stage 34.0 (TID 81)
20:47:55.111 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
20:47:55.138 INFO  Executor - Finished task 0.0 in stage 34.0 (TID 81). 650184 bytes result sent to driver
20:47:55.141 INFO  TaskSetManager - Finished task 0.0 in stage 34.0 (TID 81) in 83 ms on localhost (executor driver) (1/1)
20:47:55.142 INFO  TaskSchedulerImpl - Removed TaskSet 34.0, whose tasks have all completed, from pool 
20:47:55.142 INFO  DAGScheduler - ResultStage 34 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.108 s
20:47:55.142 INFO  DAGScheduler - Job 25 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:55.142 INFO  TaskSchedulerImpl - Killing all running tasks in stage 34: Stage finished
20:47:55.142 INFO  DAGScheduler - Job 25 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.109595 s
20:47:55.150 INFO  MemoryStore - Block broadcast_46 stored as values in memory (estimated size 528.0 B, free 1916.2 MiB)
20:47:55.153 INFO  MemoryStore - Block broadcast_46_piece0 stored as bytes in memory (estimated size 183.0 B, free 1916.2 MiB)
20:47:55.153 INFO  BlockManagerInfo - Added broadcast_46_piece0 in memory on localhost:39529 (size: 183.0 B, free: 1919.2 MiB)
20:47:55.154 INFO  SparkContext - Created broadcast 46 from broadcast at CramSource.java:114
20:47:55.158 INFO  MemoryStore - Block broadcast_47 stored as values in memory (estimated size 297.2 KiB, free 1915.9 MiB)
20:47:55.169 INFO  MemoryStore - Block broadcast_47_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.9 MiB)
20:47:55.170 INFO  BlockManagerInfo - Added broadcast_47_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.2 MiB)
20:47:55.170 INFO  SparkContext - Created broadcast 47 from newAPIHadoopFile at PathSplitSource.java:96
20:47:55.218 INFO  MemoryStore - Block broadcast_48 stored as values in memory (estimated size 528.0 B, free 1915.9 MiB)
20:47:55.219 INFO  MemoryStore - Block broadcast_48_piece0 stored as bytes in memory (estimated size 183.0 B, free 1915.9 MiB)
20:47:55.219 INFO  BlockManagerInfo - Added broadcast_48_piece0 in memory on localhost:39529 (size: 183.0 B, free: 1919.2 MiB)
20:47:55.220 INFO  SparkContext - Created broadcast 48 from broadcast at CramSource.java:114
20:47:55.223 INFO  MemoryStore - Block broadcast_49 stored as values in memory (estimated size 297.2 KiB, free 1915.6 MiB)
20:47:55.234 INFO  MemoryStore - Block broadcast_49_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.5 MiB)
20:47:55.234 INFO  BlockManagerInfo - Added broadcast_49_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.1 MiB)
20:47:55.235 INFO  SparkContext - Created broadcast 49 from newAPIHadoopFile at PathSplitSource.java:96
20:47:55.265 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:47:55.265 INFO  DAGScheduler - Got job 26 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:47:55.265 INFO  DAGScheduler - Final stage: ResultStage 35 (collect at ReadsSparkSourceUnitTest.java:111)
20:47:55.265 INFO  DAGScheduler - Parents of final stage: List()
20:47:55.265 INFO  DAGScheduler - Missing parents: List()
20:47:55.266 INFO  DAGScheduler - Submitting ResultStage 35 (ParallelCollectionRDD[107] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:47:55.267 INFO  MemoryStore - Block broadcast_50 stored as values in memory (estimated size 3.0 KiB, free 1915.5 MiB)
20:47:55.267 INFO  MemoryStore - Block broadcast_50_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1915.5 MiB)
20:47:55.268 INFO  BlockManagerInfo - Added broadcast_50_piece0 in memory on localhost:39529 (size: 1780.0 B, free: 1919.1 MiB)
20:47:55.268 INFO  SparkContext - Created broadcast 50 from broadcast at DAGScheduler.scala:1580
20:47:55.268 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))
20:47:55.268 INFO  TaskSchedulerImpl - Adding task set 35.0 with 4 tasks resource profile 0
20:47:55.273 INFO  TaskSetManager - Starting task 0.0 in stage 35.0 (TID 82) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes) 
20:47:55.275 INFO  TaskSetManager - Starting task 1.0 in stage 35.0 (TID 83) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes) 
20:47:55.277 INFO  TaskSetManager - Starting task 2.0 in stage 35.0 (TID 84) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes) 
20:47:55.278 INFO  TaskSetManager - Starting task 3.0 in stage 35.0 (TID 85) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes) 
20:47:55.279 INFO  Executor - Running task 0.0 in stage 35.0 (TID 82)
20:47:55.279 INFO  Executor - Running task 1.0 in stage 35.0 (TID 83)
20:47:55.279 INFO  Executor - Running task 2.0 in stage 35.0 (TID 84)
20:47:55.279 INFO  Executor - Running task 3.0 in stage 35.0 (TID 85)
20:47:55.282 INFO  Executor - Finished task 2.0 in stage 35.0 (TID 84). 39070 bytes result sent to driver
20:47:55.282 INFO  Executor - Finished task 3.0 in stage 35.0 (TID 85). 39343 bytes result sent to driver
20:47:55.283 INFO  Executor - Finished task 0.0 in stage 35.0 (TID 82). 38950 bytes result sent to driver
20:47:55.283 INFO  TaskSetManager - Finished task 2.0 in stage 35.0 (TID 84) in 8 ms on localhost (executor driver) (1/4)
20:47:55.283 INFO  TaskSetManager - Finished task 3.0 in stage 35.0 (TID 85) in 6 ms on localhost (executor driver) (2/4)
20:47:55.284 INFO  TaskSetManager - Finished task 0.0 in stage 35.0 (TID 82) in 15 ms on localhost (executor driver) (3/4)
20:47:55.284 INFO  Executor - Finished task 1.0 in stage 35.0 (TID 83). 39130 bytes result sent to driver
20:47:55.285 INFO  TaskSetManager - Finished task 1.0 in stage 35.0 (TID 83) in 12 ms on localhost (executor driver) (4/4)
20:47:55.285 INFO  TaskSchedulerImpl - Removed TaskSet 35.0, whose tasks have all completed, from pool 
20:47:55.286 INFO  DAGScheduler - ResultStage 35 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.020 s
20:47:55.286 INFO  DAGScheduler - Job 26 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:55.286 INFO  TaskSchedulerImpl - Killing all running tasks in stage 35: Stage finished
20:47:55.286 INFO  DAGScheduler - Job 26 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.021181 s
20:47:55.288 INFO  FileInputFormat - Total input files to process : 1
20:47:55.329 INFO  BlockManagerInfo - Removed broadcast_36_piece0 on localhost:39529 in memory (size: 1780.0 B, free: 1919.1 MiB)
20:47:55.332 INFO  BlockManagerInfo - Removed broadcast_45_piece0 on localhost:39529 in memory (size: 152.7 KiB, free: 1919.3 MiB)
20:47:55.336 INFO  BlockManagerInfo - Removed broadcast_41_piece0 on localhost:39529 in memory (size: 152.7 KiB, free: 1919.4 MiB)
20:47:55.339 INFO  BlockManagerInfo - Removed broadcast_38_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1919.5 MiB)
20:47:55.342 INFO  BlockManagerInfo - Removed broadcast_28_piece0 on localhost:39529 in memory (size: 320.0 B, free: 1919.5 MiB)
20:47:55.344 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:47:55.345 INFO  DAGScheduler - Got job 27 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:47:55.345 INFO  DAGScheduler - Final stage: ResultStage 36 (collect at ReadsSparkSourceUnitTest.java:112)
20:47:55.345 INFO  DAGScheduler - Parents of final stage: List()
20:47:55.345 INFO  BlockManagerInfo - Removed broadcast_34_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.5 MiB)
20:47:55.345 INFO  DAGScheduler - Missing parents: List()
20:47:55.346 INFO  DAGScheduler - Submitting ResultStage 36 (MapPartitionsRDD[113] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:55.348 INFO  BlockManagerInfo - Removed broadcast_32_piece0 on localhost:39529 in memory (size: 3.8 KiB, free: 1919.5 MiB)
20:47:55.351 INFO  BlockManager - Removing RDD 47
20:47:55.353 INFO  BlockManagerInfo - Removed broadcast_50_piece0 on localhost:39529 in memory (size: 1780.0 B, free: 1919.5 MiB)
20:47:55.355 INFO  BlockManagerInfo - Removed broadcast_22_piece0 on localhost:39529 in memory (size: 159.0 B, free: 1919.5 MiB)
20:47:55.356 INFO  BlockManagerInfo - Removed broadcast_37_piece0 on localhost:39529 in memory (size: 152.7 KiB, free: 1919.7 MiB)
20:47:55.359 INFO  BlockManagerInfo - Removed broadcast_42_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1919.7 MiB)
20:47:55.361 INFO  BlockManagerInfo - Removed broadcast_31_piece0 on localhost:39529 in memory (size: 320.0 B, free: 1919.7 MiB)
20:47:55.363 INFO  BlockManagerInfo - Removed broadcast_23_piece0 on localhost:39529 in memory (size: 465.0 B, free: 1919.7 MiB)
20:47:55.365 INFO  BlockManagerInfo - Removed broadcast_47_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.8 MiB)
20:47:55.369 INFO  BlockManagerInfo - Removed broadcast_33_piece0 on localhost:39529 in memory (size: 4.8 KiB, free: 1919.8 MiB)
20:47:55.371 INFO  BlockManagerInfo - Removed broadcast_43_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1919.8 MiB)
20:47:55.371 INFO  MemoryStore - Block broadcast_51 stored as values in memory (estimated size 286.0 KiB, free 1918.7 MiB)
20:47:55.372 INFO  MemoryStore - Block broadcast_51_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1918.6 MiB)
20:47:55.373 INFO  BlockManagerInfo - Removed broadcast_39_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1919.9 MiB)
20:47:55.373 INFO  BlockManagerInfo - Added broadcast_51_piece0 in memory on localhost:39529 (size: 103.1 KiB, free: 1919.8 MiB)
20:47:55.374 INFO  SparkContext - Created broadcast 51 from broadcast at DAGScheduler.scala:1580
20:47:55.374 INFO  BlockManagerInfo - Removed broadcast_35_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.8 MiB)
20:47:55.374 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))
20:47:55.374 INFO  TaskSchedulerImpl - Adding task set 36.0 with 1 tasks resource profile 0
20:47:55.375 INFO  BlockManagerInfo - Removed broadcast_44_piece0 on localhost:39529 in memory (size: 1780.0 B, free: 1919.8 MiB)
20:47:55.375 INFO  TaskSetManager - Starting task 0.0 in stage 36.0 (TID 86) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes) 
20:47:55.376 INFO  Executor - Running task 0.0 in stage 36.0 (TID 86)
20:47:55.376 INFO  BlockManagerInfo - Removed broadcast_40_piece0 on localhost:39529 in memory (size: 1780.0 B, free: 1919.9 MiB)
20:47:55.377 INFO  BlockManagerInfo - Removed broadcast_46_piece0 on localhost:39529 in memory (size: 183.0 B, free: 1919.9 MiB)
20:47:55.404 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram:0+50619
20:47:55.425 INFO  Executor - Finished task 0.0 in stage 36.0 (TID 86). 154101 bytes result sent to driver
20:47:55.426 INFO  TaskSetManager - Finished task 0.0 in stage 36.0 (TID 86) in 51 ms on localhost (executor driver) (1/1)
20:47:55.426 INFO  TaskSchedulerImpl - Removed TaskSet 36.0, whose tasks have all completed, from pool 
20:47:55.427 INFO  DAGScheduler - ResultStage 36 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.080 s
20:47:55.427 INFO  DAGScheduler - Job 27 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:55.427 INFO  TaskSchedulerImpl - Killing all running tasks in stage 36: Stage finished
20:47:55.427 INFO  DAGScheduler - Job 27 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.082963 s
20:47:55.433 INFO  MemoryStore - Block broadcast_52 stored as values in memory (estimated size 600.0 B, free 1919.3 MiB)
20:47:55.434 INFO  MemoryStore - Block broadcast_52_piece0 stored as bytes in memory (estimated size 202.0 B, free 1919.3 MiB)
20:47:55.434 INFO  BlockManagerInfo - Added broadcast_52_piece0 in memory on localhost:39529 (size: 202.0 B, free: 1919.9 MiB)
20:47:55.434 INFO  SparkContext - Created broadcast 52 from broadcast at CramSource.java:114
20:47:55.437 INFO  MemoryStore - Block broadcast_53 stored as values in memory (estimated size 297.3 KiB, free 1919.0 MiB)
20:47:55.444 INFO  MemoryStore - Block broadcast_53_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.9 MiB)
20:47:55.444 INFO  BlockManagerInfo - Added broadcast_53_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.8 MiB)
20:47:55.444 INFO  SparkContext - Created broadcast 53 from newAPIHadoopFile at PathSplitSource.java:96
20:47:55.467 INFO  MemoryStore - Block broadcast_54 stored as values in memory (estimated size 600.0 B, free 1918.9 MiB)
20:47:55.468 INFO  MemoryStore - Block broadcast_54_piece0 stored as bytes in memory (estimated size 202.0 B, free 1918.9 MiB)
20:47:55.468 INFO  BlockManagerInfo - Added broadcast_54_piece0 in memory on localhost:39529 (size: 202.0 B, free: 1919.8 MiB)
20:47:55.468 INFO  SparkContext - Created broadcast 54 from broadcast at CramSource.java:114
20:47:55.471 INFO  MemoryStore - Block broadcast_55 stored as values in memory (estimated size 297.3 KiB, free 1918.6 MiB)
20:47:55.477 INFO  MemoryStore - Block broadcast_55_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.6 MiB)
20:47:55.477 INFO  BlockManagerInfo - Added broadcast_55_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.8 MiB)
20:47:55.478 INFO  SparkContext - Created broadcast 55 from newAPIHadoopFile at PathSplitSource.java:96
20:47:55.497 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:47:55.497 INFO  DAGScheduler - Got job 28 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:47:55.497 INFO  DAGScheduler - Final stage: ResultStage 37 (collect at ReadsSparkSourceUnitTest.java:111)
20:47:55.497 INFO  DAGScheduler - Parents of final stage: List()
20:47:55.497 INFO  DAGScheduler - Missing parents: List()
20:47:55.498 INFO  DAGScheduler - Submitting ResultStage 37 (ParallelCollectionRDD[118] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:47:55.498 INFO  MemoryStore - Block broadcast_56 stored as values in memory (estimated size 3.0 KiB, free 1918.6 MiB)
20:47:55.499 INFO  MemoryStore - Block broadcast_56_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1918.6 MiB)
20:47:55.499 INFO  BlockManagerInfo - Added broadcast_56_piece0 in memory on localhost:39529 (size: 1780.0 B, free: 1919.8 MiB)
20:47:55.500 INFO  SparkContext - Created broadcast 56 from broadcast at DAGScheduler.scala:1580
20:47:55.500 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))
20:47:55.500 INFO  TaskSchedulerImpl - Adding task set 37.0 with 4 tasks resource profile 0
20:47:55.501 INFO  TaskSetManager - Starting task 0.0 in stage 37.0 (TID 87) (localhost, executor driver, partition 0, PROCESS_LOCAL, 8303 bytes) 
20:47:55.501 INFO  TaskSetManager - Starting task 1.0 in stage 37.0 (TID 88) (localhost, executor driver, partition 1, PROCESS_LOCAL, 8292 bytes) 
20:47:55.501 INFO  TaskSetManager - Starting task 2.0 in stage 37.0 (TID 89) (localhost, executor driver, partition 2, PROCESS_LOCAL, 8292 bytes) 
20:47:55.501 INFO  TaskSetManager - Starting task 3.0 in stage 37.0 (TID 90) (localhost, executor driver, partition 3, PROCESS_LOCAL, 8184 bytes) 
20:47:55.502 INFO  Executor - Running task 1.0 in stage 37.0 (TID 88)
20:47:55.503 INFO  Executor - Running task 3.0 in stage 37.0 (TID 90)
20:47:55.504 INFO  Executor - Finished task 1.0 in stage 37.0 (TID 88). 1567 bytes result sent to driver
20:47:55.504 INFO  Executor - Running task 0.0 in stage 37.0 (TID 87)
20:47:55.504 INFO  Executor - Running task 2.0 in stage 37.0 (TID 89)
20:47:55.505 INFO  TaskSetManager - Finished task 1.0 in stage 37.0 (TID 88) in 4 ms on localhost (executor driver) (1/4)
20:47:55.506 INFO  Executor - Finished task 0.0 in stage 37.0 (TID 87). 1578 bytes result sent to driver
20:47:55.507 INFO  Executor - Finished task 2.0 in stage 37.0 (TID 89). 1567 bytes result sent to driver
20:47:55.507 INFO  Executor - Finished task 3.0 in stage 37.0 (TID 90). 1459 bytes result sent to driver
20:47:55.508 INFO  TaskSetManager - Finished task 0.0 in stage 37.0 (TID 87) in 7 ms on localhost (executor driver) (2/4)
20:47:55.510 INFO  TaskSetManager - Finished task 2.0 in stage 37.0 (TID 89) in 9 ms on localhost (executor driver) (3/4)
20:47:55.510 INFO  TaskSetManager - Finished task 3.0 in stage 37.0 (TID 90) in 9 ms on localhost (executor driver) (4/4)
20:47:55.510 INFO  TaskSchedulerImpl - Removed TaskSet 37.0, whose tasks have all completed, from pool 
20:47:55.511 INFO  DAGScheduler - ResultStage 37 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.013 s
20:47:55.511 INFO  DAGScheduler - Job 28 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:55.511 INFO  TaskSchedulerImpl - Killing all running tasks in stage 37: Stage finished
20:47:55.511 INFO  DAGScheduler - Job 28 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.014121 s
20:47:55.513 INFO  FileInputFormat - Total input files to process : 1
20:47:55.559 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:47:55.560 INFO  DAGScheduler - Got job 29 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:47:55.560 INFO  DAGScheduler - Final stage: ResultStage 38 (collect at ReadsSparkSourceUnitTest.java:112)
20:47:55.560 INFO  DAGScheduler - Parents of final stage: List()
20:47:55.560 INFO  DAGScheduler - Missing parents: List()
20:47:55.560 INFO  DAGScheduler - Submitting ResultStage 38 (MapPartitionsRDD[124] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:55.585 INFO  MemoryStore - Block broadcast_57 stored as values in memory (estimated size 286.0 KiB, free 1918.3 MiB)
20:47:55.587 INFO  MemoryStore - Block broadcast_57_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1918.2 MiB)
20:47:55.587 INFO  BlockManagerInfo - Added broadcast_57_piece0 in memory on localhost:39529 (size: 103.1 KiB, free: 1919.6 MiB)
20:47:55.588 INFO  SparkContext - Created broadcast 57 from broadcast at DAGScheduler.scala:1580
20:47:55.588 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))
20:47:55.588 INFO  TaskSchedulerImpl - Adding task set 38.0 with 1 tasks resource profile 0
20:47:55.589 INFO  TaskSetManager - Starting task 0.0 in stage 38.0 (TID 91) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7844 bytes) 
20:47:55.590 INFO  Executor - Running task 0.0 in stage 38.0 (TID 91)
20:47:55.632 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.cram:0+13330
20:47:55.642 INFO  Executor - Finished task 0.0 in stage 38.0 (TID 91). 3736 bytes result sent to driver
20:47:55.643 INFO  TaskSetManager - Finished task 0.0 in stage 38.0 (TID 91) in 54 ms on localhost (executor driver) (1/1)
20:47:55.643 INFO  TaskSchedulerImpl - Removed TaskSet 38.0, whose tasks have all completed, from pool 
20:47:55.644 INFO  DAGScheduler - ResultStage 38 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.083 s
20:47:55.644 INFO  DAGScheduler - Job 29 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:55.644 INFO  TaskSchedulerImpl - Killing all running tasks in stage 38: Stage finished
20:47:55.644 INFO  DAGScheduler - Job 29 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.085377 s
20:47:55.656 INFO  MemoryStore - Block broadcast_58 stored as values in memory (estimated size 297.2 KiB, free 1917.9 MiB)
20:47:55.665 INFO  MemoryStore - Block broadcast_58_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.9 MiB)
20:47:55.665 INFO  BlockManagerInfo - Added broadcast_58_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.6 MiB)
20:47:55.666 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
20:47:55.712 INFO  MemoryStore - Block broadcast_59 stored as values in memory (estimated size 297.2 KiB, free 1917.6 MiB)
20:47:55.723 INFO  MemoryStore - Block broadcast_59_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.5 MiB)
20:47:55.723 INFO  BlockManagerInfo - Added broadcast_59_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.6 MiB)
20:47:55.724 INFO  SparkContext - Created broadcast 59 from newAPIHadoopFile at PathSplitSource.java:96
20:47:55.766 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:47:55.767 INFO  DAGScheduler - Got job 30 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:47:55.767 INFO  DAGScheduler - Final stage: ResultStage 39 (collect at ReadsSparkSourceUnitTest.java:111)
20:47:55.767 INFO  DAGScheduler - Parents of final stage: List()
20:47:55.767 INFO  DAGScheduler - Missing parents: List()
20:47:55.767 INFO  DAGScheduler - Submitting ResultStage 39 (ParallelCollectionRDD[130] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:47:55.768 INFO  MemoryStore - Block broadcast_60 stored as values in memory (estimated size 3.0 KiB, free 1917.5 MiB)
20:47:55.769 INFO  MemoryStore - Block broadcast_60_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1917.5 MiB)
20:47:55.769 INFO  BlockManagerInfo - Added broadcast_60_piece0 in memory on localhost:39529 (size: 1780.0 B, free: 1919.6 MiB)
20:47:55.770 INFO  SparkContext - Created broadcast 60 from broadcast at DAGScheduler.scala:1580
20:47:55.770 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))
20:47:55.770 INFO  TaskSchedulerImpl - Adding task set 39.0 with 4 tasks resource profile 0
20:47:55.771 INFO  TaskSetManager - Starting task 0.0 in stage 39.0 (TID 92) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes) 
20:47:55.772 INFO  TaskSetManager - Starting task 1.0 in stage 39.0 (TID 93) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes) 
20:47:55.772 INFO  TaskSetManager - Starting task 2.0 in stage 39.0 (TID 94) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes) 
20:47:55.773 INFO  TaskSetManager - Starting task 3.0 in stage 39.0 (TID 95) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes) 
20:47:55.773 INFO  Executor - Running task 0.0 in stage 39.0 (TID 92)
20:47:55.775 INFO  Executor - Running task 3.0 in stage 39.0 (TID 95)
20:47:55.776 INFO  Executor - Running task 1.0 in stage 39.0 (TID 93)
20:47:55.776 INFO  Executor - Running task 2.0 in stage 39.0 (TID 94)
20:47:55.777 INFO  Executor - Finished task 0.0 in stage 39.0 (TID 92). 40355 bytes result sent to driver
20:47:55.779 INFO  Executor - Finished task 2.0 in stage 39.0 (TID 94). 40380 bytes result sent to driver
20:47:55.780 INFO  TaskSetManager - Finished task 0.0 in stage 39.0 (TID 92) in 9 ms on localhost (executor driver) (1/4)
20:47:55.780 INFO  TaskSetManager - Finished task 2.0 in stage 39.0 (TID 94) in 8 ms on localhost (executor driver) (2/4)
20:47:55.782 INFO  Executor - Finished task 3.0 in stage 39.0 (TID 95). 40805 bytes result sent to driver
20:47:55.783 INFO  Executor - Finished task 1.0 in stage 39.0 (TID 93). 40469 bytes result sent to driver
20:47:55.784 INFO  TaskSetManager - Finished task 3.0 in stage 39.0 (TID 95) in 10 ms on localhost (executor driver) (3/4)
20:47:55.784 INFO  TaskSetManager - Finished task 1.0 in stage 39.0 (TID 93) in 12 ms on localhost (executor driver) (4/4)
20:47:55.784 INFO  TaskSchedulerImpl - Removed TaskSet 39.0, whose tasks have all completed, from pool 
20:47:55.785 INFO  DAGScheduler - ResultStage 39 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.018 s
20:47:55.786 INFO  DAGScheduler - Job 30 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:55.786 INFO  TaskSchedulerImpl - Killing all running tasks in stage 39: Stage finished
20:47:55.786 INFO  DAGScheduler - Job 30 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.020231 s
20:47:55.788 INFO  FileInputFormat - Total input files to process : 1
20:47:55.852 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:47:55.853 INFO  DAGScheduler - Got job 31 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:47:55.853 INFO  DAGScheduler - Final stage: ResultStage 40 (collect at ReadsSparkSourceUnitTest.java:112)
20:47:55.853 INFO  DAGScheduler - Parents of final stage: List()
20:47:55.853 INFO  DAGScheduler - Missing parents: List()
20:47:55.853 INFO  DAGScheduler - Submitting ResultStage 40 (MapPartitionsRDD[137] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:55.886 INFO  MemoryStore - Block broadcast_61 stored as values in memory (estimated size 425.0 KiB, free 1917.1 MiB)
20:47:55.889 INFO  MemoryStore - Block broadcast_61_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.0 MiB)
20:47:55.889 INFO  BlockManagerInfo - Added broadcast_61_piece0 in memory on localhost:39529 (size: 152.7 KiB, free: 1919.4 MiB)
20:47:55.890 INFO  SparkContext - Created broadcast 61 from broadcast at DAGScheduler.scala:1580
20:47:55.891 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))
20:47:55.891 INFO  TaskSchedulerImpl - Adding task set 40.0 with 1 tasks resource profile 0
20:47:55.892 INFO  TaskSetManager - Starting task 0.0 in stage 40.0 (TID 96) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
20:47:55.892 INFO  Executor - Running task 0.0 in stage 40.0 (TID 96)
20:47:55.943 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
20:47:55.953 INFO  Executor - Finished task 0.0 in stage 40.0 (TID 96). 159572 bytes result sent to driver
20:47:55.955 INFO  TaskSetManager - Finished task 0.0 in stage 40.0 (TID 96) in 64 ms on localhost (executor driver) (1/1)
20:47:55.955 INFO  TaskSchedulerImpl - Removed TaskSet 40.0, whose tasks have all completed, from pool 
20:47:55.955 INFO  DAGScheduler - ResultStage 40 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.101 s
20:47:55.956 INFO  DAGScheduler - Job 31 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:55.956 INFO  TaskSchedulerImpl - Killing all running tasks in stage 40: Stage finished
20:47:55.956 INFO  DAGScheduler - Job 31 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.103929 s
20:47:55.964 INFO  MemoryStore - Block broadcast_62 stored as values in memory (estimated size 528.0 B, free 1917.0 MiB)
20:47:55.965 INFO  MemoryStore - Block broadcast_62_piece0 stored as bytes in memory (estimated size 183.0 B, free 1917.0 MiB)
20:47:55.967 INFO  BlockManagerInfo - Added broadcast_62_piece0 in memory on localhost:39529 (size: 183.0 B, free: 1919.4 MiB)
20:47:55.967 INFO  SparkContext - Created broadcast 62 from broadcast at CramSource.java:114
20:47:55.970 INFO  MemoryStore - Block broadcast_63 stored as values in memory (estimated size 297.2 KiB, free 1916.7 MiB)
20:47:55.984 INFO  MemoryStore - Block broadcast_63_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.6 MiB)
20:47:55.985 INFO  BlockManagerInfo - Added broadcast_63_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.4 MiB)
20:47:55.986 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
20:47:56.041 INFO  MemoryStore - Block broadcast_64 stored as values in memory (estimated size 528.0 B, free 1916.6 MiB)
20:47:56.041 INFO  MemoryStore - Block broadcast_64_piece0 stored as bytes in memory (estimated size 183.0 B, free 1916.6 MiB)
20:47:56.042 INFO  BlockManagerInfo - Added broadcast_64_piece0 in memory on localhost:39529 (size: 183.0 B, free: 1919.4 MiB)
20:47:56.042 INFO  SparkContext - Created broadcast 64 from broadcast at CramSource.java:114
20:47:56.050 INFO  MemoryStore - Block broadcast_65 stored as values in memory (estimated size 297.2 KiB, free 1916.3 MiB)
20:47:56.063 INFO  MemoryStore - Block broadcast_65_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.3 MiB)
20:47:56.067 INFO  BlockManagerInfo - Added broadcast_65_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.3 MiB)
20:47:56.067 INFO  SparkContext - Created broadcast 65 from newAPIHadoopFile at PathSplitSource.java:96
20:47:56.099 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:47:56.100 INFO  DAGScheduler - Got job 32 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:47:56.100 INFO  DAGScheduler - Final stage: ResultStage 41 (collect at ReadsSparkSourceUnitTest.java:111)
20:47:56.100 INFO  DAGScheduler - Parents of final stage: List()
20:47:56.100 INFO  DAGScheduler - Missing parents: List()
20:47:56.100 INFO  DAGScheduler - Submitting ResultStage 41 (ParallelCollectionRDD[142] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:47:56.101 INFO  MemoryStore - Block broadcast_66 stored as values in memory (estimated size 3.0 KiB, free 1916.3 MiB)
20:47:56.105 INFO  MemoryStore - Block broadcast_66_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1916.3 MiB)
20:47:56.105 INFO  BlockManagerInfo - Added broadcast_66_piece0 in memory on localhost:39529 (size: 1780.0 B, free: 1919.3 MiB)
20:47:56.106 INFO  SparkContext - Created broadcast 66 from broadcast at DAGScheduler.scala:1580
20:47:56.106 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))
20:47:56.106 INFO  TaskSchedulerImpl - Adding task set 41.0 with 4 tasks resource profile 0
20:47:56.108 INFO  TaskSetManager - Starting task 0.0 in stage 41.0 (TID 97) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes) 
20:47:56.109 INFO  TaskSetManager - Starting task 1.0 in stage 41.0 (TID 98) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes) 
20:47:56.110 INFO  TaskSetManager - Starting task 2.0 in stage 41.0 (TID 99) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes) 
20:47:56.111 INFO  TaskSetManager - Starting task 3.0 in stage 41.0 (TID 100) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes) 
20:47:56.111 INFO  Executor - Running task 1.0 in stage 41.0 (TID 98)
20:47:56.111 INFO  Executor - Running task 3.0 in stage 41.0 (TID 100)
20:47:56.112 INFO  Executor - Running task 0.0 in stage 41.0 (TID 97)
20:47:56.114 INFO  Executor - Finished task 3.0 in stage 41.0 (TID 100). 39343 bytes result sent to driver
20:47:56.114 INFO  Executor - Finished task 1.0 in stage 41.0 (TID 98). 39130 bytes result sent to driver
20:47:56.116 INFO  TaskSetManager - Finished task 1.0 in stage 41.0 (TID 98) in 7 ms on localhost (executor driver) (1/4)
20:47:56.116 INFO  TaskSetManager - Finished task 3.0 in stage 41.0 (TID 100) in 6 ms on localhost (executor driver) (2/4)
20:47:56.117 INFO  Executor - Finished task 0.0 in stage 41.0 (TID 97). 38950 bytes result sent to driver
20:47:56.118 INFO  Executor - Running task 2.0 in stage 41.0 (TID 99)
20:47:56.119 INFO  Executor - Finished task 2.0 in stage 41.0 (TID 99). 39027 bytes result sent to driver
20:47:56.120 INFO  TaskSetManager - Finished task 2.0 in stage 41.0 (TID 99) in 11 ms on localhost (executor driver) (3/4)
20:47:56.122 INFO  TaskSetManager - Finished task 0.0 in stage 41.0 (TID 97) in 15 ms on localhost (executor driver) (4/4)
20:47:56.122 INFO  TaskSchedulerImpl - Removed TaskSet 41.0, whose tasks have all completed, from pool 
20:47:56.123 INFO  DAGScheduler - ResultStage 41 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.021 s
20:47:56.123 INFO  DAGScheduler - Job 32 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:56.123 INFO  TaskSchedulerImpl - Killing all running tasks in stage 41: Stage finished
20:47:56.123 INFO  DAGScheduler - Job 32 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.024563 s
20:47:56.125 INFO  FileInputFormat - Total input files to process : 1
20:47:56.171 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:47:56.172 INFO  DAGScheduler - Got job 33 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:47:56.172 INFO  DAGScheduler - Final stage: ResultStage 42 (collect at ReadsSparkSourceUnitTest.java:112)
20:47:56.172 INFO  DAGScheduler - Parents of final stage: List()
20:47:56.172 INFO  DAGScheduler - Missing parents: List()
20:47:56.172 INFO  DAGScheduler - Submitting ResultStage 42 (MapPartitionsRDD[148] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:56.197 INFO  MemoryStore - Block broadcast_67 stored as values in memory (estimated size 286.0 KiB, free 1916.0 MiB)
20:47:56.199 INFO  MemoryStore - Block broadcast_67_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1915.9 MiB)
20:47:56.199 INFO  BlockManagerInfo - Added broadcast_67_piece0 in memory on localhost:39529 (size: 103.1 KiB, free: 1919.2 MiB)
20:47:56.200 INFO  SparkContext - Created broadcast 67 from broadcast at DAGScheduler.scala:1580
20:47:56.200 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))
20:47:56.200 INFO  TaskSchedulerImpl - Adding task set 42.0 with 1 tasks resource profile 0
20:47:56.201 INFO  TaskSetManager - Starting task 0.0 in stage 42.0 (TID 101) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes) 
20:47:56.202 INFO  Executor - Running task 0.0 in stage 42.0 (TID 101)
20:47:56.242 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
20:47:56.264 INFO  Executor - Finished task 0.0 in stage 42.0 (TID 101). 154101 bytes result sent to driver
20:47:56.265 INFO  TaskSetManager - Finished task 0.0 in stage 42.0 (TID 101) in 64 ms on localhost (executor driver) (1/1)
20:47:56.265 INFO  TaskSchedulerImpl - Removed TaskSet 42.0, whose tasks have all completed, from pool 
20:47:56.265 INFO  DAGScheduler - ResultStage 42 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.092 s
20:47:56.266 INFO  DAGScheduler - Job 33 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:56.266 INFO  TaskSchedulerImpl - Killing all running tasks in stage 42: Stage finished
20:47:56.266 INFO  DAGScheduler - Job 33 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.095260 s
20:47:56.274 INFO  MemoryStore - Block broadcast_68 stored as values in memory (estimated size 297.2 KiB, free 1915.6 MiB)
20:47:56.286 INFO  MemoryStore - Block broadcast_68_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.6 MiB)
20:47:56.286 INFO  BlockManagerInfo - Added broadcast_68_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.2 MiB)
20:47:56.287 INFO  SparkContext - Created broadcast 68 from newAPIHadoopFile at PathSplitSource.java:96
20:47:56.325 INFO  MemoryStore - Block broadcast_69 stored as values in memory (estimated size 297.2 KiB, free 1915.3 MiB)
20:47:56.336 INFO  MemoryStore - Block broadcast_69_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.2 MiB)
20:47:56.337 INFO  BlockManagerInfo - Added broadcast_69_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.1 MiB)
20:47:56.337 INFO  SparkContext - Created broadcast 69 from newAPIHadoopFile at PathSplitSource.java:96
20:47:56.376 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:47:56.376 INFO  DAGScheduler - Got job 34 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:47:56.376 INFO  DAGScheduler - Final stage: ResultStage 43 (collect at ReadsSparkSourceUnitTest.java:111)
20:47:56.376 INFO  DAGScheduler - Parents of final stage: List()
20:47:56.377 INFO  DAGScheduler - Missing parents: List()
20:47:56.377 INFO  DAGScheduler - Submitting ResultStage 43 (ParallelCollectionRDD[154] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:47:56.378 INFO  MemoryStore - Block broadcast_70 stored as values in memory (estimated size 3.0 KiB, free 1915.2 MiB)
20:47:56.378 INFO  MemoryStore - Block broadcast_70_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1915.2 MiB)
20:47:56.379 INFO  BlockManagerInfo - Added broadcast_70_piece0 in memory on localhost:39529 (size: 1780.0 B, free: 1919.1 MiB)
20:47:56.379 INFO  SparkContext - Created broadcast 70 from broadcast at DAGScheduler.scala:1580
20:47:56.379 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))
20:47:56.379 INFO  TaskSchedulerImpl - Adding task set 43.0 with 4 tasks resource profile 0
20:47:56.380 INFO  TaskSetManager - Starting task 0.0 in stage 43.0 (TID 102) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes) 
20:47:56.381 INFO  TaskSetManager - Starting task 1.0 in stage 43.0 (TID 103) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes) 
20:47:56.381 INFO  TaskSetManager - Starting task 2.0 in stage 43.0 (TID 104) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes) 
20:47:56.381 INFO  TaskSetManager - Starting task 3.0 in stage 43.0 (TID 105) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes) 
20:47:56.382 INFO  Executor - Running task 0.0 in stage 43.0 (TID 102)
20:47:56.383 INFO  Executor - Running task 2.0 in stage 43.0 (TID 104)
20:47:56.384 INFO  Executor - Finished task 0.0 in stage 43.0 (TID 102). 40355 bytes result sent to driver
20:47:56.384 INFO  Executor - Finished task 2.0 in stage 43.0 (TID 104). 40337 bytes result sent to driver
20:47:56.384 INFO  Executor - Running task 3.0 in stage 43.0 (TID 105)
20:47:56.385 INFO  Executor - Finished task 3.0 in stage 43.0 (TID 105). 40762 bytes result sent to driver
20:47:56.386 INFO  TaskSetManager - Finished task 0.0 in stage 43.0 (TID 102) in 6 ms on localhost (executor driver) (1/4)
20:47:56.387 INFO  TaskSetManager - Finished task 2.0 in stage 43.0 (TID 104) in 6 ms on localhost (executor driver) (2/4)
20:47:56.387 INFO  TaskSetManager - Finished task 3.0 in stage 43.0 (TID 105) in 6 ms on localhost (executor driver) (3/4)
20:47:56.387 INFO  Executor - Running task 1.0 in stage 43.0 (TID 103)
20:47:56.389 INFO  Executor - Finished task 1.0 in stage 43.0 (TID 103). 40426 bytes result sent to driver
20:47:56.389 INFO  TaskSetManager - Finished task 1.0 in stage 43.0 (TID 103) in 8 ms on localhost (executor driver) (4/4)
20:47:56.389 INFO  DAGScheduler - ResultStage 43 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.012 s
20:47:56.390 INFO  DAGScheduler - Job 34 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:56.390 INFO  TaskSchedulerImpl - Removed TaskSet 43.0, whose tasks have all completed, from pool 
20:47:56.390 INFO  TaskSchedulerImpl - Killing all running tasks in stage 43: Stage finished
20:47:56.390 INFO  DAGScheduler - Job 34 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.014049 s
20:47:56.391 INFO  FileInputFormat - Total input files to process : 1
20:47:56.454 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:47:56.455 INFO  DAGScheduler - Got job 35 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:47:56.455 INFO  DAGScheduler - Final stage: ResultStage 44 (collect at ReadsSparkSourceUnitTest.java:112)
20:47:56.455 INFO  DAGScheduler - Parents of final stage: List()
20:47:56.455 INFO  DAGScheduler - Missing parents: List()
20:47:56.455 INFO  DAGScheduler - Submitting ResultStage 44 (MapPartitionsRDD[161] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:56.476 INFO  MemoryStore - Block broadcast_71 stored as values in memory (estimated size 425.0 KiB, free 1914.8 MiB)
20:47:56.478 INFO  MemoryStore - Block broadcast_71_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1914.7 MiB)
20:47:56.478 INFO  BlockManagerInfo - Added broadcast_71_piece0 in memory on localhost:39529 (size: 152.7 KiB, free: 1919.0 MiB)
20:47:56.478 INFO  SparkContext - Created broadcast 71 from broadcast at DAGScheduler.scala:1580
20:47:56.479 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))
20:47:56.479 INFO  TaskSchedulerImpl - Adding task set 44.0 with 1 tasks resource profile 0
20:47:56.479 INFO  TaskSetManager - Starting task 0.0 in stage 44.0 (TID 106) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
20:47:56.480 INFO  Executor - Running task 0.0 in stage 44.0 (TID 106)
20:47:56.516 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
20:47:56.523 INFO  Executor - Finished task 0.0 in stage 44.0 (TID 106). 159572 bytes result sent to driver
20:47:56.524 INFO  TaskSetManager - Finished task 0.0 in stage 44.0 (TID 106) in 45 ms on localhost (executor driver) (1/1)
20:47:56.524 INFO  TaskSchedulerImpl - Removed TaskSet 44.0, whose tasks have all completed, from pool 
20:47:56.524 INFO  DAGScheduler - ResultStage 44 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.068 s
20:47:56.524 INFO  DAGScheduler - Job 35 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:56.524 INFO  TaskSchedulerImpl - Killing all running tasks in stage 44: Stage finished
20:47:56.525 INFO  DAGScheduler - Job 35 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.070287 s
20:47:56.530 INFO  MemoryStore - Block broadcast_72 stored as values in memory (estimated size 528.0 B, free 1914.7 MiB)
20:47:56.531 INFO  MemoryStore - Block broadcast_72_piece0 stored as bytes in memory (estimated size 183.0 B, free 1914.7 MiB)
20:47:56.531 INFO  BlockManagerInfo - Added broadcast_72_piece0 in memory on localhost:39529 (size: 183.0 B, free: 1919.0 MiB)
20:47:56.532 INFO  SparkContext - Created broadcast 72 from broadcast at CramSource.java:114
20:47:56.535 INFO  MemoryStore - Block broadcast_73 stored as values in memory (estimated size 297.2 KiB, free 1914.4 MiB)
20:47:56.542 INFO  MemoryStore - Block broadcast_73_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1914.3 MiB)
20:47:56.543 INFO  BlockManagerInfo - Added broadcast_73_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1918.9 MiB)
20:47:56.543 INFO  SparkContext - Created broadcast 73 from newAPIHadoopFile at PathSplitSource.java:96
20:47:56.572 INFO  MemoryStore - Block broadcast_74 stored as values in memory (estimated size 528.0 B, free 1914.3 MiB)
20:47:56.573 INFO  MemoryStore - Block broadcast_74_piece0 stored as bytes in memory (estimated size 183.0 B, free 1914.3 MiB)
20:47:56.573 INFO  BlockManagerInfo - Added broadcast_74_piece0 in memory on localhost:39529 (size: 183.0 B, free: 1918.9 MiB)
20:47:56.574 INFO  SparkContext - Created broadcast 74 from broadcast at CramSource.java:114
20:47:56.576 INFO  MemoryStore - Block broadcast_75 stored as values in memory (estimated size 297.2 KiB, free 1914.0 MiB)
20:47:56.583 INFO  MemoryStore - Block broadcast_75_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1914.0 MiB)
20:47:56.584 INFO  BlockManagerInfo - Added broadcast_75_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1918.9 MiB)
20:47:56.584 INFO  SparkContext - Created broadcast 75 from newAPIHadoopFile at PathSplitSource.java:96
20:47:56.611 INFO  BlockManagerInfo - Removed broadcast_68_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1918.9 MiB)
20:47:56.613 INFO  BlockManagerInfo - Removed broadcast_48_piece0 on localhost:39529 in memory (size: 183.0 B, free: 1918.9 MiB)
20:47:56.614 INFO  BlockManagerInfo - Removed broadcast_49_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.0 MiB)
20:47:56.615 INFO  BlockManagerInfo - Removed broadcast_70_piece0 on localhost:39529 in memory (size: 1780.0 B, free: 1919.0 MiB)
20:47:56.617 INFO  BlockManagerInfo - Removed broadcast_73_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.0 MiB)
20:47:56.618 INFO  BlockManagerInfo - Removed broadcast_55_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1919.1 MiB)
20:47:56.622 INFO  BlockManagerInfo - Removed broadcast_60_piece0 on localhost:39529 in memory (size: 1780.0 B, free: 1919.1 MiB)
20:47:56.623 INFO  BlockManagerInfo - Removed broadcast_72_piece0 on localhost:39529 in memory (size: 183.0 B, free: 1919.1 MiB)
20:47:56.625 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:47:56.625 INFO  BlockManagerInfo - Removed broadcast_63_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.1 MiB)
20:47:56.626 INFO  BlockManagerInfo - Removed broadcast_59_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.2 MiB)
20:47:56.627 INFO  DAGScheduler - Got job 36 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:47:56.627 INFO  DAGScheduler - Final stage: ResultStage 45 (collect at ReadsSparkSourceUnitTest.java:111)
20:47:56.627 INFO  DAGScheduler - Parents of final stage: List()
20:47:56.627 INFO  DAGScheduler - Missing parents: List()
20:47:56.628 INFO  BlockManagerInfo - Removed broadcast_61_piece0 on localhost:39529 in memory (size: 152.7 KiB, free: 1919.3 MiB)
20:47:56.629 INFO  DAGScheduler - Submitting ResultStage 45 (ParallelCollectionRDD[166] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:47:56.630 INFO  BlockManagerInfo - Removed broadcast_71_piece0 on localhost:39529 in memory (size: 152.7 KiB, free: 1919.4 MiB)
20:47:56.630 INFO  MemoryStore - Block broadcast_76 stored as values in memory (estimated size 3.0 KiB, free 1917.1 MiB)
20:47:56.631 INFO  MemoryStore - Block broadcast_76_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1917.1 MiB)
20:47:56.631 INFO  BlockManagerInfo - Added broadcast_76_piece0 in memory on localhost:39529 (size: 1780.0 B, free: 1919.4 MiB)
20:47:56.632 INFO  BlockManagerInfo - Removed broadcast_62_piece0 on localhost:39529 in memory (size: 183.0 B, free: 1919.4 MiB)
20:47:56.633 INFO  BlockManagerInfo - Removed broadcast_52_piece0 on localhost:39529 in memory (size: 202.0 B, free: 1919.4 MiB)
20:47:56.634 INFO  BlockManagerInfo - Removed broadcast_69_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.5 MiB)
20:47:56.635 INFO  SparkContext - Created broadcast 76 from broadcast at DAGScheduler.scala:1580
20:47:56.635 INFO  BlockManagerInfo - Removed broadcast_57_piece0 on localhost:39529 in memory (size: 103.1 KiB, free: 1919.6 MiB)
20:47:56.635 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))
20:47:56.636 INFO  TaskSchedulerImpl - Adding task set 45.0 with 4 tasks resource profile 0
20:47:56.637 INFO  BlockManagerInfo - Removed broadcast_51_piece0 on localhost:39529 in memory (size: 103.1 KiB, free: 1919.7 MiB)
20:47:56.637 INFO  TaskSetManager - Starting task 0.0 in stage 45.0 (TID 107) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes) 
20:47:56.637 INFO  TaskSetManager - Starting task 1.0 in stage 45.0 (TID 108) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes) 
20:47:56.638 INFO  BlockManagerInfo - Removed broadcast_56_piece0 on localhost:39529 in memory (size: 1780.0 B, free: 1919.7 MiB)
20:47:56.638 INFO  TaskSetManager - Starting task 2.0 in stage 45.0 (TID 109) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes) 
20:47:56.638 INFO  TaskSetManager - Starting task 3.0 in stage 45.0 (TID 110) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes) 
20:47:56.639 INFO  Executor - Running task 0.0 in stage 45.0 (TID 107)
20:47:56.640 INFO  Executor - Running task 1.0 in stage 45.0 (TID 108)
20:47:56.641 INFO  Executor - Finished task 0.0 in stage 45.0 (TID 107). 38950 bytes result sent to driver
20:47:56.641 INFO  Executor - Finished task 1.0 in stage 45.0 (TID 108). 39087 bytes result sent to driver
20:47:56.641 INFO  Executor - Running task 3.0 in stage 45.0 (TID 110)
20:47:56.642 INFO  TaskSetManager - Finished task 0.0 in stage 45.0 (TID 107) in 6 ms on localhost (executor driver) (1/4)
20:47:56.643 INFO  Executor - Running task 2.0 in stage 45.0 (TID 109)
20:47:56.643 INFO  BlockManagerInfo - Removed broadcast_66_piece0 on localhost:39529 in memory (size: 1780.0 B, free: 1919.7 MiB)
20:47:56.645 INFO  Executor - Finished task 3.0 in stage 45.0 (TID 110). 39343 bytes result sent to driver
20:47:56.646 INFO  Executor - Finished task 2.0 in stage 45.0 (TID 109). 39027 bytes result sent to driver
20:47:56.646 INFO  TaskSetManager - Finished task 3.0 in stage 45.0 (TID 110) in 8 ms on localhost (executor driver) (2/4)
20:47:56.646 INFO  TaskSetManager - Finished task 1.0 in stage 45.0 (TID 108) in 9 ms on localhost (executor driver) (3/4)
20:47:56.647 INFO  TaskSetManager - Finished task 2.0 in stage 45.0 (TID 109) in 10 ms on localhost (executor driver) (4/4)
20:47:56.647 INFO  TaskSchedulerImpl - Removed TaskSet 45.0, whose tasks have all completed, from pool 
20:47:56.647 INFO  BlockManagerInfo - Removed broadcast_54_piece0 on localhost:39529 in memory (size: 202.0 B, free: 1919.7 MiB)
20:47:56.648 INFO  DAGScheduler - ResultStage 45 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.019 s
20:47:56.648 INFO  DAGScheduler - Job 36 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:56.648 INFO  TaskSchedulerImpl - Killing all running tasks in stage 45: Stage finished
20:47:56.648 INFO  DAGScheduler - Job 36 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.023405 s
20:47:56.649 INFO  BlockManagerInfo - Removed broadcast_65_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.8 MiB)
20:47:56.650 INFO  FileInputFormat - Total input files to process : 1
20:47:56.651 INFO  BlockManagerInfo - Removed broadcast_58_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.8 MiB)
20:47:56.653 INFO  BlockManagerInfo - Removed broadcast_64_piece0 on localhost:39529 in memory (size: 183.0 B, free: 1919.8 MiB)
20:47:56.654 INFO  BlockManagerInfo - Removed broadcast_53_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1919.8 MiB)
20:47:56.655 INFO  BlockManagerInfo - Removed broadcast_67_piece0 on localhost:39529 in memory (size: 103.1 KiB, free: 1919.9 MiB)
20:47:56.695 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:47:56.695 INFO  DAGScheduler - Got job 37 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:47:56.695 INFO  DAGScheduler - Final stage: ResultStage 46 (collect at ReadsSparkSourceUnitTest.java:112)
20:47:56.695 INFO  DAGScheduler - Parents of final stage: List()
20:47:56.696 INFO  DAGScheduler - Missing parents: List()
20:47:56.696 INFO  DAGScheduler - Submitting ResultStage 46 (MapPartitionsRDD[172] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:56.717 INFO  MemoryStore - Block broadcast_77 stored as values in memory (estimated size 286.0 KiB, free 1919.4 MiB)
20:47:56.719 INFO  MemoryStore - Block broadcast_77_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1919.3 MiB)
20:47:56.719 INFO  BlockManagerInfo - Added broadcast_77_piece0 in memory on localhost:39529 (size: 103.1 KiB, free: 1919.8 MiB)
20:47:56.720 INFO  SparkContext - Created broadcast 77 from broadcast at DAGScheduler.scala:1580
20:47:56.720 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))
20:47:56.720 INFO  TaskSchedulerImpl - Adding task set 46.0 with 1 tasks resource profile 0
20:47:56.721 INFO  TaskSetManager - Starting task 0.0 in stage 46.0 (TID 111) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes) 
20:47:56.721 INFO  Executor - Running task 0.0 in stage 46.0 (TID 111)
20:47:56.758 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram:0+50619
20:47:56.773 INFO  Executor - Finished task 0.0 in stage 46.0 (TID 111). 154101 bytes result sent to driver
20:47:56.774 INFO  TaskSetManager - Finished task 0.0 in stage 46.0 (TID 111) in 53 ms on localhost (executor driver) (1/1)
20:47:56.774 INFO  TaskSchedulerImpl - Removed TaskSet 46.0, whose tasks have all completed, from pool 
20:47:56.774 INFO  DAGScheduler - ResultStage 46 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.077 s
20:47:56.774 INFO  DAGScheduler - Job 37 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:56.774 INFO  TaskSchedulerImpl - Killing all running tasks in stage 46: Stage finished
20:47:56.775 INFO  DAGScheduler - Job 37 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.079800 s
20:47:56.780 INFO  MemoryStore - Block broadcast_78 stored as values in memory (estimated size 297.2 KiB, free 1919.0 MiB)
20:47:56.791 INFO  MemoryStore - Block broadcast_78_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.9 MiB)
20:47:56.791 INFO  BlockManagerInfo - Added broadcast_78_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.8 MiB)
20:47:56.791 INFO  SparkContext - Created broadcast 78 from newAPIHadoopFile at PathSplitSource.java:96
20:47:56.831 INFO  MemoryStore - Block broadcast_79 stored as values in memory (estimated size 528.0 B, free 1918.9 MiB)
20:47:56.832 INFO  MemoryStore - Block broadcast_79_piece0 stored as bytes in memory (estimated size 183.0 B, free 1918.9 MiB)
20:47:56.832 INFO  BlockManagerInfo - Added broadcast_79_piece0 in memory on localhost:39529 (size: 183.0 B, free: 1919.8 MiB)
20:47:56.833 INFO  SparkContext - Created broadcast 79 from broadcast at CramSource.java:114
20:47:56.835 INFO  MemoryStore - Block broadcast_80 stored as values in memory (estimated size 297.2 KiB, free 1918.6 MiB)
20:47:56.846 INFO  MemoryStore - Block broadcast_80_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.6 MiB)
20:47:56.846 INFO  BlockManagerInfo - Added broadcast_80_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.8 MiB)
20:47:56.846 INFO  SparkContext - Created broadcast 80 from newAPIHadoopFile at PathSplitSource.java:96
20:47:56.985 WARN  FileSystem - Failed to initialize filesystem hdfs://bogus/path.bam: java.lang.IllegalArgumentException: java.net.UnknownHostException: bogus
20:47:56.991 INFO  MemoryStore - Block broadcast_81 stored as values in memory (estimated size 297.3 KiB, free 1918.3 MiB)
20:47:57.002 INFO  MemoryStore - Block broadcast_81_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.3 MiB)
20:47:57.002 INFO  BlockManagerInfo - Added broadcast_81_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.7 MiB)
20:47:57.003 INFO  SparkContext - Created broadcast 81 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.037 INFO  MemoryStore - Block broadcast_82 stored as values in memory (estimated size 297.3 KiB, free 1918.0 MiB)
20:47:57.048 INFO  MemoryStore - Block broadcast_82_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.9 MiB)
20:47:57.048 INFO  BlockManagerInfo - Added broadcast_82_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.7 MiB)
20:47:57.049 INFO  SparkContext - Created broadcast 82 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.076 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:154
20:47:57.076 INFO  DAGScheduler - Got job 38 (collect at ReadsSparkSourceUnitTest.java:154) with 4 output partitions
20:47:57.076 INFO  DAGScheduler - Final stage: ResultStage 47 (collect at ReadsSparkSourceUnitTest.java:154)
20:47:57.076 INFO  DAGScheduler - Parents of final stage: List()
20:47:57.076 INFO  DAGScheduler - Missing parents: List()
20:47:57.076 INFO  DAGScheduler - Submitting ResultStage 47 (ParallelCollectionRDD[187] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:47:57.077 INFO  MemoryStore - Block broadcast_83 stored as values in memory (estimated size 3.0 KiB, free 1917.9 MiB)
20:47:57.078 INFO  MemoryStore - Block broadcast_83_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1917.9 MiB)
20:47:57.078 INFO  BlockManagerInfo - Added broadcast_83_piece0 in memory on localhost:39529 (size: 1780.0 B, free: 1919.7 MiB)
20:47:57.079 INFO  SparkContext - Created broadcast 83 from broadcast at DAGScheduler.scala:1580
20:47:57.079 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))
20:47:57.079 INFO  TaskSchedulerImpl - Adding task set 47.0 with 4 tasks resource profile 0
20:47:57.080 INFO  TaskSetManager - Starting task 0.0 in stage 47.0 (TID 112) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes) 
20:47:57.081 INFO  TaskSetManager - Starting task 1.0 in stage 47.0 (TID 113) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes) 
20:47:57.081 INFO  TaskSetManager - Starting task 2.0 in stage 47.0 (TID 114) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes) 
20:47:57.082 INFO  TaskSetManager - Starting task 3.0 in stage 47.0 (TID 115) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes) 
20:47:57.082 INFO  Executor - Running task 0.0 in stage 47.0 (TID 112)
20:47:57.083 INFO  Executor - Running task 1.0 in stage 47.0 (TID 113)
20:47:57.083 INFO  Executor - Running task 3.0 in stage 47.0 (TID 115)
20:47:57.084 INFO  Executor - Running task 2.0 in stage 47.0 (TID 114)
20:47:57.086 INFO  Executor - Finished task 3.0 in stage 47.0 (TID 115). 162694 bytes result sent to driver
20:47:57.086 INFO  Executor - Finished task 2.0 in stage 47.0 (TID 114). 163313 bytes result sent to driver
20:47:57.087 INFO  Executor - Finished task 0.0 in stage 47.0 (TID 112). 163204 bytes result sent to driver
20:47:57.087 INFO  Executor - Finished task 1.0 in stage 47.0 (TID 113). 163368 bytes result sent to driver
20:47:57.087 INFO  TaskSetManager - Finished task 2.0 in stage 47.0 (TID 114) in 6 ms on localhost (executor driver) (1/4)
20:47:57.088 INFO  TaskSetManager - Finished task 0.0 in stage 47.0 (TID 112) in 8 ms on localhost (executor driver) (2/4)
20:47:57.088 INFO  TaskSetManager - Finished task 3.0 in stage 47.0 (TID 115) in 7 ms on localhost (executor driver) (3/4)
20:47:57.088 INFO  TaskSetManager - Finished task 1.0 in stage 47.0 (TID 113) in 8 ms on localhost (executor driver) (4/4)
20:47:57.088 INFO  TaskSchedulerImpl - Removed TaskSet 47.0, whose tasks have all completed, from pool 
20:47:57.089 INFO  DAGScheduler - ResultStage 47 (collect at ReadsSparkSourceUnitTest.java:154) finished in 0.012 s
20:47:57.089 INFO  DAGScheduler - Job 38 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:57.089 INFO  TaskSchedulerImpl - Killing all running tasks in stage 47: Stage finished
20:47:57.090 INFO  DAGScheduler - Job 38 finished: collect at ReadsSparkSourceUnitTest.java:154, took 0.014077 s
20:47:57.101 INFO  FileInputFormat - Total input files to process : 2
20:47:57.155 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:155
20:47:57.156 INFO  DAGScheduler - Got job 39 (collect at ReadsSparkSourceUnitTest.java:155) with 2 output partitions
20:47:57.156 INFO  DAGScheduler - Final stage: ResultStage 48 (collect at ReadsSparkSourceUnitTest.java:155)
20:47:57.156 INFO  DAGScheduler - Parents of final stage: List()
20:47:57.156 INFO  DAGScheduler - Missing parents: List()
20:47:57.156 INFO  DAGScheduler - Submitting ResultStage 48 (MapPartitionsRDD[194] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:57.182 INFO  MemoryStore - Block broadcast_84 stored as values in memory (estimated size 425.0 KiB, free 1917.5 MiB)
20:47:57.184 INFO  MemoryStore - Block broadcast_84_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.3 MiB)
20:47:57.185 INFO  BlockManagerInfo - Added broadcast_84_piece0 in memory on localhost:39529 (size: 152.7 KiB, free: 1919.5 MiB)
20:47:57.185 INFO  SparkContext - Created broadcast 84 from broadcast at DAGScheduler.scala:1580
20:47:57.185 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))
20:47:57.185 INFO  TaskSchedulerImpl - Adding task set 48.0 with 2 tasks resource profile 0
20:47:57.186 INFO  TaskSetManager - Starting task 0.0 in stage 48.0 (TID 116) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7921 bytes) 
20:47:57.187 INFO  TaskSetManager - Starting task 1.0 in stage 48.0 (TID 117) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7921 bytes) 
20:47:57.187 INFO  Executor - Running task 0.0 in stage 48.0 (TID 116)
20:47:57.187 INFO  Executor - Running task 1.0 in stage 48.0 (TID 117)
20:47:57.238 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
20:47:57.247 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
20:47:57.260 INFO  Executor - Finished task 0.0 in stage 48.0 (TID 116). 325590 bytes result sent to driver
20:47:57.261 INFO  TaskSetManager - Finished task 0.0 in stage 48.0 (TID 116) in 75 ms on localhost (executor driver) (1/2)
20:47:57.270 INFO  Executor - Finished task 1.0 in stage 48.0 (TID 117). 325590 bytes result sent to driver
20:47:57.271 INFO  TaskSetManager - Finished task 1.0 in stage 48.0 (TID 117) in 85 ms on localhost (executor driver) (2/2)
20:47:57.271 INFO  TaskSchedulerImpl - Removed TaskSet 48.0, whose tasks have all completed, from pool 
20:47:57.271 INFO  DAGScheduler - ResultStage 48 (collect at ReadsSparkSourceUnitTest.java:155) finished in 0.114 s
20:47:57.271 INFO  DAGScheduler - Job 39 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:57.271 INFO  TaskSchedulerImpl - Killing all running tasks in stage 48: Stage finished
20:47:57.272 INFO  DAGScheduler - Job 39 finished: collect at ReadsSparkSourceUnitTest.java:155, took 0.116333 s
20:47:57.277 INFO  MemoryStore - Block broadcast_85 stored as values in memory (estimated size 297.2 KiB, free 1917.1 MiB)
20:47:57.287 INFO  MemoryStore - Block broadcast_85_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.0 MiB)
20:47:57.287 INFO  BlockManagerInfo - Added broadcast_85_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.5 MiB)
20:47:57.287 INFO  SparkContext - Created broadcast 85 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.316 INFO  MemoryStore - Block broadcast_86 stored as values in memory (estimated size 297.3 KiB, free 1916.7 MiB)
20:47:57.323 INFO  MemoryStore - Block broadcast_86_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.7 MiB)
20:47:57.323 INFO  BlockManagerInfo - Added broadcast_86_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.4 MiB)
20:47:57.323 INFO  SparkContext - Created broadcast 86 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.348 INFO  MemoryStore - Block broadcast_87 stored as values in memory (estimated size 297.3 KiB, free 1916.4 MiB)
20:47:57.357 INFO  MemoryStore - Block broadcast_87_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.3 MiB)
20:47:57.357 INFO  BlockManagerInfo - Added broadcast_87_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.4 MiB)
20:47:57.358 INFO  SparkContext - Created broadcast 87 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.382 INFO  MemoryStore - Block broadcast_88 stored as values in memory (estimated size 528.0 B, free 1916.3 MiB)
20:47:57.383 INFO  MemoryStore - Block broadcast_88_piece0 stored as bytes in memory (estimated size 183.0 B, free 1916.3 MiB)
20:47:57.383 INFO  BlockManagerInfo - Added broadcast_88_piece0 in memory on localhost:39529 (size: 183.0 B, free: 1919.4 MiB)
20:47:57.384 INFO  SparkContext - Created broadcast 88 from broadcast at CramSource.java:114
20:47:57.386 INFO  MemoryStore - Block broadcast_89 stored as values in memory (estimated size 297.2 KiB, free 1916.0 MiB)
20:47:57.393 INFO  MemoryStore - Block broadcast_89_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.0 MiB)
20:47:57.393 INFO  BlockManagerInfo - Added broadcast_89_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.3 MiB)
20:47:57.394 INFO  SparkContext - Created broadcast 89 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.412 INFO  MemoryStore - Block broadcast_90 stored as values in memory (estimated size 600.0 B, free 1916.0 MiB)
20:47:57.412 INFO  MemoryStore - Block broadcast_90_piece0 stored as bytes in memory (estimated size 202.0 B, free 1916.0 MiB)
20:47:57.413 INFO  BlockManagerInfo - Added broadcast_90_piece0 in memory on localhost:39529 (size: 202.0 B, free: 1919.3 MiB)
20:47:57.413 INFO  SparkContext - Created broadcast 90 from broadcast at CramSource.java:114
20:47:57.415 INFO  MemoryStore - Block broadcast_91 stored as values in memory (estimated size 297.3 KiB, free 1915.7 MiB)
20:47:57.422 INFO  MemoryStore - Block broadcast_91_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1915.7 MiB)
20:47:57.423 INFO  BlockManagerInfo - Added broadcast_91_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.3 MiB)
20:47:57.423 INFO  SparkContext - Created broadcast 91 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.442 INFO  MemoryStore - Block broadcast_92 stored as values in memory (estimated size 297.3 KiB, free 1915.4 MiB)
20:47:57.449 INFO  MemoryStore - Block broadcast_92_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1915.3 MiB)
20:47:57.450 INFO  BlockManagerInfo - Added broadcast_92_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.2 MiB)
20:47:57.450 INFO  SparkContext - Created broadcast 92 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.473 INFO  FileInputFormat - Total input files to process : 1
20:47:57.509 INFO  SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:163
20:47:57.509 INFO  DAGScheduler - Got job 40 (collect at ReadsSparkSourceUnitTest.java:163) with 1 output partitions
20:47:57.509 INFO  DAGScheduler - Final stage: ResultStage 49 (collect at ReadsSparkSourceUnitTest.java:163)
20:47:57.510 INFO  DAGScheduler - Parents of final stage: List()
20:47:57.510 INFO  DAGScheduler - Missing parents: List()
20:47:57.510 INFO  DAGScheduler - Submitting ResultStage 49 (MapPartitionsRDD[224] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:57.528 INFO  MemoryStore - Block broadcast_93 stored as values in memory (estimated size 425.0 KiB, free 1914.9 MiB)
20:47:57.530 INFO  MemoryStore - Block broadcast_93_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1914.7 MiB)
20:47:57.530 INFO  BlockManagerInfo - Added broadcast_93_piece0 in memory on localhost:39529 (size: 152.7 KiB, free: 1919.1 MiB)
20:47:57.530 INFO  SparkContext - Created broadcast 93 from broadcast at DAGScheduler.scala:1580
20:47:57.530 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))
20:47:57.530 INFO  TaskSchedulerImpl - Adding task set 49.0 with 1 tasks resource profile 0
20:47:57.531 INFO  TaskSetManager - Starting task 0.0 in stage 49.0 (TID 118) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7875 bytes) 
20:47:57.532 INFO  Executor - Running task 0.0 in stage 49.0 (TID 118)
20:47:57.568 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam:0+221635
20:47:57.583 INFO  Executor - Finished task 0.0 in stage 49.0 (TID 118). 650184 bytes result sent to driver
20:47:57.585 INFO  TaskSetManager - Finished task 0.0 in stage 49.0 (TID 118) in 54 ms on localhost (executor driver) (1/1)
20:47:57.585 INFO  TaskSchedulerImpl - Removed TaskSet 49.0, whose tasks have all completed, from pool 
20:47:57.585 INFO  DAGScheduler - ResultStage 49 (collect at ReadsSparkSourceUnitTest.java:163) finished in 0.075 s
20:47:57.585 INFO  DAGScheduler - Job 40 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:57.585 INFO  TaskSchedulerImpl - Killing all running tasks in stage 49: Stage finished
20:47:57.585 INFO  DAGScheduler - Job 40 finished: collect at ReadsSparkSourceUnitTest.java:163, took 0.076544 s
20:47:57.589 INFO  MemoryStore - Block broadcast_94 stored as values in memory (estimated size 208.0 B, free 1914.7 MiB)
20:47:57.591 INFO  MemoryStore - Block broadcast_94_piece0 stored as bytes in memory (estimated size 239.0 B, free 1914.7 MiB)
20:47:57.591 INFO  BlockManagerInfo - Added broadcast_94_piece0 in memory on localhost:39529 (size: 239.0 B, free: 1919.1 MiB)
20:47:57.592 INFO  SparkContext - Created broadcast 94 from broadcast at AbstractBinarySamSource.java:82
20:47:57.593 INFO  MemoryStore - Block broadcast_95 stored as values in memory (estimated size 297.2 KiB, free 1914.5 MiB)
20:47:57.599 INFO  MemoryStore - Block broadcast_95_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1914.4 MiB)
20:47:57.600 INFO  BlockManagerInfo - Added broadcast_95_piece0 in memory on localhost:39529 (size: 50.0 KiB, free: 1919.0 MiB)
20:47:57.600 INFO  SparkContext - Created broadcast 95 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.622 INFO  FileInputFormat - Total input files to process : 1
20:47:57.627 INFO  SparkContext - Starting job: count at ReadsSparkSourceUnitTest.java:265
20:47:57.628 INFO  DAGScheduler - Got job 41 (count at ReadsSparkSourceUnitTest.java:265) with 1 output partitions
20:47:57.628 INFO  DAGScheduler - Final stage: ResultStage 50 (count at ReadsSparkSourceUnitTest.java:265)
20:47:57.628 INFO  DAGScheduler - Parents of final stage: List()
20:47:57.628 INFO  DAGScheduler - Missing parents: List()
20:47:57.628 INFO  DAGScheduler - Submitting ResultStage 50 (MapPartitionsRDD[231] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:57.646 INFO  MemoryStore - Block broadcast_96 stored as values in memory (estimated size 424.9 KiB, free 1914.0 MiB)
20:47:57.648 INFO  MemoryStore - Block broadcast_96_piece0 stored as bytes in memory (estimated size 152.8 KiB, free 1913.8 MiB)
20:47:57.648 INFO  BlockManagerInfo - Added broadcast_96_piece0 in memory on localhost:39529 (size: 152.8 KiB, free: 1918.9 MiB)
20:47:57.648 INFO  SparkContext - Created broadcast 96 from broadcast at DAGScheduler.scala:1580
20:47:57.648 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))
20:47:57.648 INFO  TaskSchedulerImpl - Adding task set 50.0 with 1 tasks resource profile 0
20:47:57.649 INFO  TaskSetManager - Starting task 0.0 in stage 50.0 (TID 119) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes) 
20:47:57.650 INFO  Executor - Running task 0.0 in stage 50.0 (TID 119)
20:47:57.688 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
20:47:57.694 INFO  Executor - Finished task 0.0 in stage 50.0 (TID 119). 989 bytes result sent to driver
20:47:57.695 INFO  TaskSetManager - Finished task 0.0 in stage 50.0 (TID 119) in 46 ms on localhost (executor driver) (1/1)
20:47:57.695 INFO  TaskSchedulerImpl - Removed TaskSet 50.0, whose tasks have all completed, from pool 
20:47:57.695 INFO  DAGScheduler - ResultStage 50 (count at ReadsSparkSourceUnitTest.java:265) finished in 0.067 s
20:47:57.696 INFO  DAGScheduler - Job 41 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:57.696 INFO  TaskSchedulerImpl - Killing all running tasks in stage 50: Stage finished
20:47:57.696 INFO  DAGScheduler - Job 41 finished: count at ReadsSparkSourceUnitTest.java:265, took 0.069068 s
20:47:57.710 INFO  MemoryStore - Block broadcast_97 stored as values in memory (estimated size 160.0 B, free 1913.8 MiB)
20:47:57.711 INFO  MemoryStore - Block broadcast_97_piece0 stored as bytes in memory (estimated size 229.0 B, free 1913.8 MiB)
20:47:57.712 INFO  BlockManagerInfo - Removed broadcast_78_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1918.9 MiB)
20:47:57.712 INFO  BlockManagerInfo - Added broadcast_97_piece0 in memory on localhost:39529 (size: 229.0 B, free: 1918.9 MiB)
20:47:57.712 INFO  SparkContext - Created broadcast 97 from broadcast at AbstractBinarySamSource.java:82
20:47:57.713 INFO  BlockManagerInfo - Removed broadcast_75_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.0 MiB)
20:47:57.714 INFO  MemoryStore - Block broadcast_98 stored as values in memory (estimated size 297.3 KiB, free 1914.3 MiB)
20:47:57.715 INFO  BlockManagerInfo - Removed broadcast_86_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1919.0 MiB)
20:47:57.716 INFO  BlockManagerInfo - Removed broadcast_79_piece0 on localhost:39529 in memory (size: 183.0 B, free: 1919.0 MiB)
20:47:57.717 INFO  BlockManagerInfo - Removed broadcast_89_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.1 MiB)
20:47:57.718 INFO  BlockManagerInfo - Removed broadcast_80_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.1 MiB)
20:47:57.722 INFO  BlockManagerInfo - Removed broadcast_82_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1919.2 MiB)
20:47:57.725 INFO  MemoryStore - Block broadcast_98_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1915.5 MiB)
20:47:57.725 INFO  BlockManagerInfo - Added broadcast_98_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.1 MiB)
20:47:57.726 INFO  BlockManagerInfo - Removed broadcast_93_piece0 on localhost:39529 in memory (size: 152.7 KiB, free: 1919.3 MiB)
20:47:57.726 INFO  SparkContext - Created broadcast 98 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.729 INFO  BlockManagerInfo - Removed broadcast_88_piece0 on localhost:39529 in memory (size: 183.0 B, free: 1919.3 MiB)
20:47:57.733 INFO  BlockManagerInfo - Removed broadcast_96_piece0 on localhost:39529 in memory (size: 152.8 KiB, free: 1919.4 MiB)
20:47:57.734 INFO  BlockManagerInfo - Removed broadcast_76_piece0 on localhost:39529 in memory (size: 1780.0 B, free: 1919.4 MiB)
20:47:57.734 INFO  BlockManagerInfo - Removed broadcast_83_piece0 on localhost:39529 in memory (size: 1780.0 B, free: 1919.4 MiB)
20:47:57.735 INFO  BlockManagerInfo - Removed broadcast_85_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.5 MiB)
20:47:57.737 INFO  BlockManagerInfo - Removed broadcast_95_piece0 on localhost:39529 in memory (size: 50.0 KiB, free: 1919.5 MiB)
20:47:57.741 INFO  BlockManagerInfo - Removed broadcast_81_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1919.6 MiB)
20:47:57.742 INFO  BlockManagerInfo - Removed broadcast_77_piece0 on localhost:39529 in memory (size: 103.1 KiB, free: 1919.7 MiB)
20:47:57.744 INFO  BlockManagerInfo - Removed broadcast_74_piece0 on localhost:39529 in memory (size: 183.0 B, free: 1919.7 MiB)
20:47:57.745 INFO  BlockManagerInfo - Removed broadcast_94_piece0 on localhost:39529 in memory (size: 239.0 B, free: 1919.7 MiB)
20:47:57.745 INFO  BlockManagerInfo - Removed broadcast_92_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1919.7 MiB)
20:47:57.746 INFO  BlockManagerInfo - Removed broadcast_91_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1919.8 MiB)
20:47:57.747 INFO  BlockManagerInfo - Removed broadcast_84_piece0 on localhost:39529 in memory (size: 152.7 KiB, free: 1919.9 MiB)
20:47:57.747 INFO  BlockManagerInfo - Removed broadcast_90_piece0 on localhost:39529 in memory (size: 202.0 B, free: 1919.9 MiB)
20:47:57.748 INFO  BlockManagerInfo - Removed broadcast_87_piece0 on localhost:39529 in memory (size: 50.1 KiB, free: 1920.0 MiB)
20:47:57.764 INFO  FileInputFormat - Total input files to process : 1
20:47:57.769 INFO  SparkContext - Starting job: count at ReadsSparkSourceUnitTest.java:286
20:47:57.769 INFO  DAGScheduler - Got job 42 (count at ReadsSparkSourceUnitTest.java:286) with 1 output partitions
20:47:57.769 INFO  DAGScheduler - Final stage: ResultStage 51 (count at ReadsSparkSourceUnitTest.java:286)
20:47:57.769 INFO  DAGScheduler - Parents of final stage: List()
20:47:57.770 INFO  DAGScheduler - Missing parents: List()
20:47:57.770 INFO  DAGScheduler - Submitting ResultStage 51 (MapPartitionsRDD[238] at filter at ReadsSparkSource.java:96), which has no missing parents
20:47:57.789 INFO  MemoryStore - Block broadcast_99 stored as values in memory (estimated size 424.9 KiB, free 1919.2 MiB)
20:47:57.791 INFO  MemoryStore - Block broadcast_99_piece0 stored as bytes in memory (estimated size 152.8 KiB, free 1919.1 MiB)
20:47:57.791 INFO  BlockManagerInfo - Added broadcast_99_piece0 in memory on localhost:39529 (size: 152.8 KiB, free: 1919.8 MiB)
20:47:57.791 INFO  SparkContext - Created broadcast 99 from broadcast at DAGScheduler.scala:1580
20:47:57.791 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))
20:47:57.791 INFO  TaskSchedulerImpl - Adding task set 51.0 with 1 tasks resource profile 0
20:47:57.792 INFO  TaskSetManager - Starting task 0.0 in stage 51.0 (TID 120) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7891 bytes) 
20:47:57.793 INFO  Executor - Running task 0.0 in stage 51.0 (TID 120)
20:47:57.832 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam:0+2184
20:47:57.838 INFO  Executor - Finished task 0.0 in stage 51.0 (TID 120). 989 bytes result sent to driver
20:47:57.839 INFO  TaskSetManager - Finished task 0.0 in stage 51.0 (TID 120) in 47 ms on localhost (executor driver) (1/1)
20:47:57.839 INFO  TaskSchedulerImpl - Removed TaskSet 51.0, whose tasks have all completed, from pool 
20:47:57.839 INFO  DAGScheduler - ResultStage 51 (count at ReadsSparkSourceUnitTest.java:286) finished in 0.069 s
20:47:57.839 INFO  DAGScheduler - Job 42 is finished. Cancelling potential speculative or zombie tasks for this job
20:47:57.839 INFO  TaskSchedulerImpl - Killing all running tasks in stage 51: Stage finished
20:47:57.839 INFO  DAGScheduler - Job 42 finished: count at ReadsSparkSourceUnitTest.java:286, took 0.070454 s
20:47:57.844 INFO  MemoryStore - Block broadcast_100 stored as values in memory (estimated size 297.3 KiB, free 1918.8 MiB)
20:47:57.851 INFO  MemoryStore - Block broadcast_100_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.8 MiB)
20:47:57.851 INFO  BlockManagerInfo - Added broadcast_100_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.8 MiB)
20:47:57.851 INFO  SparkContext - Created broadcast 100 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.880 INFO  MemoryStore - Block broadcast_101 stored as values in memory (estimated size 297.4 KiB, free 1918.5 MiB)
20:47:57.887 INFO  MemoryStore - Block broadcast_101_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.4 MiB)
20:47:57.887 INFO  BlockManagerInfo - Added broadcast_101_piece0 in memory on localhost:39529 (size: 50.1 KiB, free: 1919.7 MiB)
20:47:57.887 INFO  SparkContext - Created broadcast 101 from newAPIHadoopFile at PathSplitSource.java:96
20:47:57.909 INFO  FileInputFormat - Total input files to process : 1
20:47:57.910 INFO  FileInputFormat - Total input files to process : 1