20:25:25.038 INFO MemoryStore - Block broadcast_34 stored as values in memory (estimated size 297.2 KiB, free 1919.6 MiB)
20:25:25.062 INFO MemoryStore - Block broadcast_34_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1919.5 MiB)
20:25:25.062 INFO BlockManagerInfo - Added broadcast_34_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.9 MiB)
20:25:25.063 INFO SparkContext - Created broadcast 34 from newAPIHadoopFile at PathSplitSource.java:96
20:25:25.109 INFO MemoryStore - Block broadcast_35 stored as values in memory (estimated size 297.2 KiB, free 1919.3 MiB)
20:25:25.121 INFO MemoryStore - Block broadcast_35_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1919.2 MiB)
20:25:25.121 INFO BlockManagerInfo - Added broadcast_35_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.9 MiB)
20:25:25.122 INFO SparkContext - Created broadcast 35 from newAPIHadoopFile at PathSplitSource.java:96
20:25:25.159 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:25:25.159 INFO DAGScheduler - Got job 20 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:25:25.159 INFO DAGScheduler - Final stage: ResultStage 29 (collect at ReadsSparkSourceUnitTest.java:111)
20:25:25.159 INFO DAGScheduler - Parents of final stage: List()
20:25:25.159 INFO DAGScheduler - Missing parents: List()
20:25:25.160 INFO DAGScheduler - Submitting ResultStage 29 (ParallelCollectionRDD[69] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:25:25.161 INFO MemoryStore - Block broadcast_36 stored as values in memory (estimated size 3.0 KiB, free 1919.2 MiB)
20:25:25.161 INFO MemoryStore - Block broadcast_36_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1919.2 MiB)
20:25:25.162 INFO BlockManagerInfo - Added broadcast_36_piece0 in memory on localhost:39477 (size: 1780.0 B, free: 1919.9 MiB)
20:25:25.162 INFO SparkContext - Created broadcast 36 from broadcast at DAGScheduler.scala:1580
20:25:25.162 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))
20:25:25.162 INFO TaskSchedulerImpl - Adding task set 29.0 with 4 tasks resource profile 0
20:25:25.164 INFO TaskSetManager - Starting task 0.0 in stage 29.0 (TID 67) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes)
20:25:25.165 INFO TaskSetManager - Starting task 1.0 in stage 29.0 (TID 68) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes)
20:25:25.165 INFO TaskSetManager - Starting task 2.0 in stage 29.0 (TID 69) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes)
20:25:25.166 INFO TaskSetManager - Starting task 3.0 in stage 29.0 (TID 70) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes)
20:25:25.166 INFO Executor - Running task 2.0 in stage 29.0 (TID 69)
20:25:25.166 INFO Executor - Running task 3.0 in stage 29.0 (TID 70)
20:25:25.167 INFO Executor - Running task 0.0 in stage 29.0 (TID 67)
20:25:25.167 INFO Executor - Running task 1.0 in stage 29.0 (TID 68)
20:25:25.173 INFO Executor - Finished task 2.0 in stage 29.0 (TID 69). 40380 bytes result sent to driver
20:25:25.173 INFO Executor - Finished task 3.0 in stage 29.0 (TID 70). 40805 bytes result sent to driver
20:25:25.175 INFO TaskSetManager - Finished task 2.0 in stage 29.0 (TID 69) in 9 ms on localhost (executor driver) (1/4)
20:25:25.176 INFO TaskSetManager - Finished task 3.0 in stage 29.0 (TID 70) in 11 ms on localhost (executor driver) (2/4)
20:25:25.178 INFO Executor - Finished task 1.0 in stage 29.0 (TID 68). 40512 bytes result sent to driver
20:25:25.178 INFO Executor - Finished task 0.0 in stage 29.0 (TID 67). 40355 bytes result sent to driver
20:25:25.179 INFO TaskSetManager - Finished task 1.0 in stage 29.0 (TID 68) in 15 ms on localhost (executor driver) (3/4)
20:25:25.180 INFO TaskSetManager - Finished task 0.0 in stage 29.0 (TID 67) in 17 ms on localhost (executor driver) (4/4)
20:25:25.180 INFO TaskSchedulerImpl - Removed TaskSet 29.0, whose tasks have all completed, from pool
20:25:25.180 INFO DAGScheduler - ResultStage 29 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.020 s
20:25:25.180 INFO DAGScheduler - Job 20 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:25.180 INFO TaskSchedulerImpl - Killing all running tasks in stage 29: Stage finished
20:25:25.180 INFO DAGScheduler - Job 20 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.021415 s
20:25:25.195 INFO FileInputFormat - Total input files to process : 1
20:25:25.247 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:25:25.247 INFO DAGScheduler - Got job 21 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:25:25.247 INFO DAGScheduler - Final stage: ResultStage 30 (collect at ReadsSparkSourceUnitTest.java:112)
20:25:25.247 INFO DAGScheduler - Parents of final stage: List()
20:25:25.248 INFO DAGScheduler - Missing parents: List()
20:25:25.248 INFO DAGScheduler - Submitting ResultStage 30 (MapPartitionsRDD[76] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:25.279 INFO MemoryStore - Block broadcast_37 stored as values in memory (estimated size 425.0 KiB, free 1918.8 MiB)
20:25:25.281 INFO MemoryStore - Block broadcast_37_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1918.6 MiB)
20:25:25.282 INFO BlockManagerInfo - Added broadcast_37_piece0 in memory on localhost:39477 (size: 152.7 KiB, free: 1919.7 MiB)
20:25:25.282 INFO SparkContext - Created broadcast 37 from broadcast at DAGScheduler.scala:1580
20:25:25.282 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))
20:25:25.282 INFO TaskSchedulerImpl - Adding task set 30.0 with 1 tasks resource profile 0
20:25:25.288 INFO TaskSetManager - Starting task 0.0 in stage 30.0 (TID 71) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes)
20:25:25.288 INFO Executor - Running task 0.0 in stage 30.0 (TID 71)
20:25:25.357 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
20:25:25.375 INFO Executor - Finished task 0.0 in stage 30.0 (TID 71). 159615 bytes result sent to driver
20:25:25.378 INFO TaskSetManager - Finished task 0.0 in stage 30.0 (TID 71) in 95 ms on localhost (executor driver) (1/1)
20:25:25.378 INFO TaskSchedulerImpl - Removed TaskSet 30.0, whose tasks have all completed, from pool
20:25:25.378 INFO DAGScheduler - ResultStage 30 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.128 s
20:25:25.378 INFO DAGScheduler - Job 21 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:25.378 INFO TaskSchedulerImpl - Killing all running tasks in stage 30: Stage finished
20:25:25.379 INFO DAGScheduler - Job 21 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.131781 s
20:25:25.389 INFO MemoryStore - Block broadcast_38 stored as values in memory (estimated size 297.3 KiB, free 1918.3 MiB)
20:25:25.398 INFO MemoryStore - Block broadcast_38_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.3 MiB)
20:25:25.398 INFO BlockManagerInfo - Added broadcast_38_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.7 MiB)
20:25:25.399 INFO SparkContext - Created broadcast 38 from newAPIHadoopFile at PathSplitSource.java:96
20:25:25.440 INFO MemoryStore - Block broadcast_39 stored as values in memory (estimated size 297.3 KiB, free 1918.0 MiB)
20:25:25.452 INFO MemoryStore - Block broadcast_39_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.0 MiB)
20:25:25.452 INFO BlockManagerInfo - Added broadcast_39_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.6 MiB)
20:25:25.453 INFO SparkContext - Created broadcast 39 from newAPIHadoopFile at PathSplitSource.java:96
20:25:25.487 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:25:25.488 INFO DAGScheduler - Got job 22 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:25:25.488 INFO DAGScheduler - Final stage: ResultStage 31 (collect at ReadsSparkSourceUnitTest.java:111)
20:25:25.488 INFO DAGScheduler - Parents of final stage: List()
20:25:25.488 INFO DAGScheduler - Missing parents: List()
20:25:25.489 INFO DAGScheduler - Submitting ResultStage 31 (ParallelCollectionRDD[82] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:25:25.490 INFO MemoryStore - Block broadcast_40 stored as values in memory (estimated size 3.0 KiB, free 1918.0 MiB)
20:25:25.490 INFO MemoryStore - Block broadcast_40_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1918.0 MiB)
20:25:25.491 INFO BlockManagerInfo - Added broadcast_40_piece0 in memory on localhost:39477 (size: 1780.0 B, free: 1919.6 MiB)
20:25:25.491 INFO SparkContext - Created broadcast 40 from broadcast at DAGScheduler.scala:1580
20:25:25.491 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))
20:25:25.491 INFO TaskSchedulerImpl - Adding task set 31.0 with 4 tasks resource profile 0
20:25:25.494 INFO TaskSetManager - Starting task 0.0 in stage 31.0 (TID 72) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes)
20:25:25.495 INFO TaskSetManager - Starting task 1.0 in stage 31.0 (TID 73) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes)
20:25:25.497 INFO TaskSetManager - Starting task 2.0 in stage 31.0 (TID 74) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes)
20:25:25.498 INFO TaskSetManager - Starting task 3.0 in stage 31.0 (TID 75) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes)
20:25:25.498 INFO Executor - Running task 2.0 in stage 31.0 (TID 74)
20:25:25.498 INFO Executor - Running task 0.0 in stage 31.0 (TID 72)
20:25:25.498 INFO Executor - Running task 3.0 in stage 31.0 (TID 75)
20:25:25.499 INFO Executor - Running task 1.0 in stage 31.0 (TID 73)
20:25:25.505 INFO Executor - Finished task 1.0 in stage 31.0 (TID 73). 163411 bytes result sent to driver
20:25:25.509 INFO Executor - Finished task 3.0 in stage 31.0 (TID 75). 162737 bytes result sent to driver
20:25:25.509 INFO TaskSetManager - Finished task 1.0 in stage 31.0 (TID 73) in 15 ms on localhost (executor driver) (1/4)
20:25:25.510 INFO Executor - Finished task 2.0 in stage 31.0 (TID 74). 163399 bytes result sent to driver
20:25:25.511 INFO Executor - Finished task 0.0 in stage 31.0 (TID 72). 163204 bytes result sent to driver
20:25:25.512 INFO TaskSetManager - Finished task 3.0 in stage 31.0 (TID 75) in 15 ms on localhost (executor driver) (2/4)
20:25:25.513 INFO TaskSetManager - Finished task 2.0 in stage 31.0 (TID 74) in 18 ms on localhost (executor driver) (3/4)
20:25:25.514 INFO TaskSetManager - Finished task 0.0 in stage 31.0 (TID 72) in 22 ms on localhost (executor driver) (4/4)
20:25:25.514 INFO TaskSchedulerImpl - Removed TaskSet 31.0, whose tasks have all completed, from pool
20:25:25.515 INFO DAGScheduler - ResultStage 31 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.025 s
20:25:25.515 INFO DAGScheduler - Job 22 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:25.515 INFO TaskSchedulerImpl - Killing all running tasks in stage 31: Stage finished
20:25:25.515 INFO DAGScheduler - Job 22 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.027309 s
20:25:25.517 INFO FileInputFormat - Total input files to process : 1
20:25:25.571 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:25:25.572 INFO DAGScheduler - Got job 23 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:25:25.572 INFO DAGScheduler - Final stage: ResultStage 32 (collect at ReadsSparkSourceUnitTest.java:112)
20:25:25.572 INFO DAGScheduler - Parents of final stage: List()
20:25:25.572 INFO DAGScheduler - Missing parents: List()
20:25:25.572 INFO DAGScheduler - Submitting ResultStage 32 (MapPartitionsRDD[89] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:25.598 INFO MemoryStore - Block broadcast_41 stored as values in memory (estimated size 425.0 KiB, free 1917.5 MiB)
20:25:25.600 INFO MemoryStore - Block broadcast_41_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.4 MiB)
20:25:25.600 INFO BlockManagerInfo - Added broadcast_41_piece0 in memory on localhost:39477 (size: 152.7 KiB, free: 1919.5 MiB)
20:25:25.600 INFO SparkContext - Created broadcast 41 from broadcast at DAGScheduler.scala:1580
20:25:25.601 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))
20:25:25.601 INFO TaskSchedulerImpl - Adding task set 32.0 with 1 tasks resource profile 0
20:25:25.602 INFO TaskSetManager - Starting task 0.0 in stage 32.0 (TID 76) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7875 bytes)
20:25:25.602 INFO Executor - Running task 0.0 in stage 32.0 (TID 76)
20:25:25.650 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam:0+221635
20:25:25.680 INFO Executor - Finished task 0.0 in stage 32.0 (TID 76). 650184 bytes result sent to driver
20:25:25.683 INFO TaskSetManager - Finished task 0.0 in stage 32.0 (TID 76) in 81 ms on localhost (executor driver) (1/1)
20:25:25.683 INFO TaskSchedulerImpl - Removed TaskSet 32.0, whose tasks have all completed, from pool
20:25:25.683 INFO DAGScheduler - ResultStage 32 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.111 s
20:25:25.684 INFO DAGScheduler - Job 23 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:25.684 INFO TaskSchedulerImpl - Killing all running tasks in stage 32: Stage finished
20:25:25.684 INFO DAGScheduler - Job 23 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.112685 s
20:25:25.691 INFO MemoryStore - Block broadcast_42 stored as values in memory (estimated size 297.3 KiB, free 1917.1 MiB)
20:25:25.700 INFO MemoryStore - Block broadcast_42_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.1 MiB)
20:25:25.701 INFO BlockManagerInfo - Added broadcast_42_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.4 MiB)
20:25:25.701 INFO SparkContext - Created broadcast 42 from newAPIHadoopFile at PathSplitSource.java:96
20:25:25.741 INFO MemoryStore - Block broadcast_43 stored as values in memory (estimated size 297.3 KiB, free 1916.8 MiB)
20:25:25.749 INFO MemoryStore - Block broadcast_43_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.7 MiB)
20:25:25.749 INFO BlockManagerInfo - Added broadcast_43_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.4 MiB)
20:25:25.750 INFO SparkContext - Created broadcast 43 from newAPIHadoopFile at PathSplitSource.java:96
20:25:25.779 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:25:25.779 INFO DAGScheduler - Got job 24 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:25:25.779 INFO DAGScheduler - Final stage: ResultStage 33 (collect at ReadsSparkSourceUnitTest.java:111)
20:25:25.779 INFO DAGScheduler - Parents of final stage: List()
20:25:25.779 INFO DAGScheduler - Missing parents: List()
20:25:25.780 INFO DAGScheduler - Submitting ResultStage 33 (ParallelCollectionRDD[95] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:25:25.780 INFO MemoryStore - Block broadcast_44 stored as values in memory (estimated size 3.0 KiB, free 1916.7 MiB)
20:25:25.781 INFO MemoryStore - Block broadcast_44_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1916.7 MiB)
20:25:25.781 INFO BlockManagerInfo - Added broadcast_44_piece0 in memory on localhost:39477 (size: 1780.0 B, free: 1919.4 MiB)
20:25:25.782 INFO SparkContext - Created broadcast 44 from broadcast at DAGScheduler.scala:1580
20:25:25.782 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))
20:25:25.782 INFO TaskSchedulerImpl - Adding task set 33.0 with 4 tasks resource profile 0
20:25:25.783 INFO TaskSetManager - Starting task 0.0 in stage 33.0 (TID 77) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes)
20:25:25.784 INFO TaskSetManager - Starting task 1.0 in stage 33.0 (TID 78) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes)
20:25:25.785 INFO TaskSetManager - Starting task 2.0 in stage 33.0 (TID 79) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes)
20:25:25.786 INFO TaskSetManager - Starting task 3.0 in stage 33.0 (TID 80) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes)
20:25:25.786 INFO Executor - Running task 1.0 in stage 33.0 (TID 78)
20:25:25.786 INFO Executor - Running task 3.0 in stage 33.0 (TID 80)
20:25:25.786 INFO Executor - Running task 0.0 in stage 33.0 (TID 77)
20:25:25.789 INFO Executor - Running task 2.0 in stage 33.0 (TID 79)
20:25:25.792 INFO Executor - Finished task 3.0 in stage 33.0 (TID 80). 162737 bytes result sent to driver
20:25:25.794 INFO Executor - Finished task 1.0 in stage 33.0 (TID 78). 163411 bytes result sent to driver
20:25:25.794 INFO TaskSetManager - Finished task 3.0 in stage 33.0 (TID 80) in 9 ms on localhost (executor driver) (1/4)
20:25:25.795 INFO Executor - Finished task 2.0 in stage 33.0 (TID 79). 163399 bytes result sent to driver
20:25:25.795 INFO TaskSetManager - Finished task 1.0 in stage 33.0 (TID 78) in 12 ms on localhost (executor driver) (2/4)
20:25:25.795 INFO Executor - Finished task 0.0 in stage 33.0 (TID 77). 163204 bytes result sent to driver
20:25:25.797 INFO TaskSetManager - Finished task 0.0 in stage 33.0 (TID 77) in 14 ms on localhost (executor driver) (3/4)
20:25:25.798 INFO TaskSetManager - Finished task 2.0 in stage 33.0 (TID 79) in 14 ms on localhost (executor driver) (4/4)
20:25:25.798 INFO TaskSchedulerImpl - Removed TaskSet 33.0, whose tasks have all completed, from pool
20:25:25.798 INFO DAGScheduler - ResultStage 33 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.018 s
20:25:25.798 INFO DAGScheduler - Job 24 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:25.798 INFO TaskSchedulerImpl - Killing all running tasks in stage 33: Stage finished
20:25:25.799 INFO DAGScheduler - Job 24 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.019621 s
20:25:25.800 INFO FileInputFormat - Total input files to process : 1
20:25:25.841 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:25:25.842 INFO DAGScheduler - Got job 25 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:25:25.842 INFO DAGScheduler - Final stage: ResultStage 34 (collect at ReadsSparkSourceUnitTest.java:112)
20:25:25.842 INFO DAGScheduler - Parents of final stage: List()
20:25:25.842 INFO DAGScheduler - Missing parents: List()
20:25:25.843 INFO DAGScheduler - Submitting ResultStage 34 (MapPartitionsRDD[102] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:25.864 INFO MemoryStore - Block broadcast_45 stored as values in memory (estimated size 425.0 KiB, free 1916.3 MiB)
20:25:25.866 INFO MemoryStore - Block broadcast_45_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1916.1 MiB)
20:25:25.866 INFO BlockManagerInfo - Added broadcast_45_piece0 in memory on localhost:39477 (size: 152.7 KiB, free: 1919.2 MiB)
20:25:25.867 INFO SparkContext - Created broadcast 45 from broadcast at DAGScheduler.scala:1580
20:25:25.867 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))
20:25:25.867 INFO TaskSchedulerImpl - Adding task set 34.0 with 1 tasks resource profile 0
20:25:25.868 INFO TaskSetManager - Starting task 0.0 in stage 34.0 (TID 81) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7905 bytes)
20:25:25.868 INFO Executor - Running task 0.0 in stage 34.0 (TID 81)
20:25:25.916 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
20:25:25.958 INFO Executor - Finished task 0.0 in stage 34.0 (TID 81). 650184 bytes result sent to driver
20:25:25.960 INFO TaskSetManager - Finished task 0.0 in stage 34.0 (TID 81) in 92 ms on localhost (executor driver) (1/1)
20:25:25.960 INFO TaskSchedulerImpl - Removed TaskSet 34.0, whose tasks have all completed, from pool
20:25:25.960 INFO DAGScheduler - ResultStage 34 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.117 s
20:25:25.961 INFO DAGScheduler - Job 25 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:25.961 INFO TaskSchedulerImpl - Killing all running tasks in stage 34: Stage finished
20:25:25.961 INFO DAGScheduler - Job 25 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.119105 s
20:25:25.967 INFO MemoryStore - Block broadcast_46 stored as values in memory (estimated size 528.0 B, free 1916.1 MiB)
20:25:25.968 INFO MemoryStore - Block broadcast_46_piece0 stored as bytes in memory (estimated size 183.0 B, free 1916.1 MiB)
20:25:25.968 INFO BlockManagerInfo - Added broadcast_46_piece0 in memory on localhost:39477 (size: 183.0 B, free: 1919.2 MiB)
20:25:25.968 INFO SparkContext - Created broadcast 46 from broadcast at CramSource.java:114
20:25:25.971 INFO MemoryStore - Block broadcast_47 stored as values in memory (estimated size 297.2 KiB, free 1915.9 MiB)
20:25:25.977 INFO MemoryStore - Block broadcast_47_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.8 MiB)
20:25:25.978 INFO BlockManagerInfo - Added broadcast_47_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.2 MiB)
20:25:25.978 INFO SparkContext - Created broadcast 47 from newAPIHadoopFile at PathSplitSource.java:96
20:25:26.006 INFO MemoryStore - Block broadcast_48 stored as values in memory (estimated size 528.0 B, free 1915.8 MiB)
20:25:26.006 INFO MemoryStore - Block broadcast_48_piece0 stored as bytes in memory (estimated size 183.0 B, free 1915.8 MiB)
20:25:26.007 INFO BlockManagerInfo - Added broadcast_48_piece0 in memory on localhost:39477 (size: 183.0 B, free: 1919.2 MiB)
20:25:26.007 INFO SparkContext - Created broadcast 48 from broadcast at CramSource.java:114
20:25:26.010 INFO MemoryStore - Block broadcast_49 stored as values in memory (estimated size 297.2 KiB, free 1915.5 MiB)
20:25:26.016 INFO MemoryStore - Block broadcast_49_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.5 MiB)
20:25:26.016 INFO BlockManagerInfo - Added broadcast_49_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.1 MiB)
20:25:26.017 INFO SparkContext - Created broadcast 49 from newAPIHadoopFile at PathSplitSource.java:96
20:25:26.038 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:25:26.038 INFO DAGScheduler - Got job 26 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:25:26.038 INFO DAGScheduler - Final stage: ResultStage 35 (collect at ReadsSparkSourceUnitTest.java:111)
20:25:26.038 INFO DAGScheduler - Parents of final stage: List()
20:25:26.038 INFO DAGScheduler - Missing parents: List()
20:25:26.038 INFO DAGScheduler - Submitting ResultStage 35 (ParallelCollectionRDD[107] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:25:26.039 INFO MemoryStore - Block broadcast_50 stored as values in memory (estimated size 3.0 KiB, free 1915.5 MiB)
20:25:26.040 INFO MemoryStore - Block broadcast_50_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1915.5 MiB)
20:25:26.040 INFO BlockManagerInfo - Added broadcast_50_piece0 in memory on localhost:39477 (size: 1780.0 B, free: 1919.1 MiB)
20:25:26.040 INFO SparkContext - Created broadcast 50 from broadcast at DAGScheduler.scala:1580
20:25:26.041 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))
20:25:26.041 INFO TaskSchedulerImpl - Adding task set 35.0 with 4 tasks resource profile 0
20:25:26.044 INFO TaskSetManager - Starting task 0.0 in stage 35.0 (TID 82) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes)
20:25:26.046 INFO TaskSetManager - Starting task 1.0 in stage 35.0 (TID 83) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes)
20:25:26.047 INFO TaskSetManager - Starting task 2.0 in stage 35.0 (TID 84) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes)
20:25:26.048 INFO TaskSetManager - Starting task 3.0 in stage 35.0 (TID 85) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes)
20:25:26.049 INFO Executor - Running task 2.0 in stage 35.0 (TID 84)
20:25:26.049 INFO Executor - Running task 0.0 in stage 35.0 (TID 82)
20:25:26.049 INFO Executor - Running task 3.0 in stage 35.0 (TID 85)
20:25:26.050 INFO Executor - Running task 1.0 in stage 35.0 (TID 83)
20:25:26.052 INFO Executor - Finished task 3.0 in stage 35.0 (TID 85). 39343 bytes result sent to driver
20:25:26.052 INFO Executor - Finished task 2.0 in stage 35.0 (TID 84). 39070 bytes result sent to driver
20:25:26.052 INFO Executor - Finished task 1.0 in stage 35.0 (TID 83). 39130 bytes result sent to driver
20:25:26.053 INFO TaskSetManager - Finished task 3.0 in stage 35.0 (TID 85) in 6 ms on localhost (executor driver) (1/4)
20:25:26.054 INFO Executor - Finished task 0.0 in stage 35.0 (TID 82). 38950 bytes result sent to driver
20:25:26.054 INFO TaskSetManager - Finished task 1.0 in stage 35.0 (TID 83) in 10 ms on localhost (executor driver) (2/4)
20:25:26.055 INFO TaskSetManager - Finished task 2.0 in stage 35.0 (TID 84) in 9 ms on localhost (executor driver) (3/4)
20:25:26.055 INFO TaskSetManager - Finished task 0.0 in stage 35.0 (TID 82) in 14 ms on localhost (executor driver) (4/4)
20:25:26.055 INFO TaskSchedulerImpl - Removed TaskSet 35.0, whose tasks have all completed, from pool
20:25:26.055 INFO DAGScheduler - ResultStage 35 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.016 s
20:25:26.055 INFO DAGScheduler - Job 26 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:26.055 INFO TaskSchedulerImpl - Killing all running tasks in stage 35: Stage finished
20:25:26.056 INFO DAGScheduler - Job 26 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.017830 s
20:25:26.057 INFO FileInputFormat - Total input files to process : 1
20:25:26.083 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:25:26.084 INFO DAGScheduler - Got job 27 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:25:26.084 INFO DAGScheduler - Final stage: ResultStage 36 (collect at ReadsSparkSourceUnitTest.java:112)
20:25:26.084 INFO DAGScheduler - Parents of final stage: List()
20:25:26.084 INFO DAGScheduler - Missing parents: List()
20:25:26.084 INFO DAGScheduler - Submitting ResultStage 36 (MapPartitionsRDD[113] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:26.097 INFO MemoryStore - Block broadcast_51 stored as values in memory (estimated size 286.0 KiB, free 1915.2 MiB)
20:25:26.098 INFO MemoryStore - Block broadcast_51_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1915.1 MiB)
20:25:26.098 INFO BlockManagerInfo - Added broadcast_51_piece0 in memory on localhost:39477 (size: 103.1 KiB, free: 1919.0 MiB)
20:25:26.099 INFO SparkContext - Created broadcast 51 from broadcast at DAGScheduler.scala:1580
20:25:26.099 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))
20:25:26.099 INFO TaskSchedulerImpl - Adding task set 36.0 with 1 tasks resource profile 0
20:25:26.100 INFO TaskSetManager - Starting task 0.0 in stage 36.0 (TID 86) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes)
20:25:26.100 INFO Executor - Running task 0.0 in stage 36.0 (TID 86)
20:25:26.134 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram:0+50619
20:25:26.154 INFO Executor - Finished task 0.0 in stage 36.0 (TID 86). 154101 bytes result sent to driver
20:25:26.155 INFO TaskSetManager - Finished task 0.0 in stage 36.0 (TID 86) in 55 ms on localhost (executor driver) (1/1)
20:25:26.155 INFO TaskSchedulerImpl - Removed TaskSet 36.0, whose tasks have all completed, from pool
20:25:26.155 INFO DAGScheduler - ResultStage 36 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.070 s
20:25:26.155 INFO DAGScheduler - Job 27 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:26.155 INFO TaskSchedulerImpl - Killing all running tasks in stage 36: Stage finished
20:25:26.155 INFO DAGScheduler - Job 27 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.071960 s
20:25:26.162 INFO MemoryStore - Block broadcast_52 stored as values in memory (estimated size 600.0 B, free 1915.1 MiB)
20:25:26.163 INFO MemoryStore - Block broadcast_52_piece0 stored as bytes in memory (estimated size 202.0 B, free 1915.1 MiB)
20:25:26.163 INFO BlockManagerInfo - Added broadcast_52_piece0 in memory on localhost:39477 (size: 202.0 B, free: 1919.0 MiB)
20:25:26.164 INFO SparkContext - Created broadcast 52 from broadcast at CramSource.java:114
20:25:26.168 INFO MemoryStore - Block broadcast_53 stored as values in memory (estimated size 297.3 KiB, free 1914.8 MiB)
20:25:26.178 INFO MemoryStore - Block broadcast_53_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1914.7 MiB)
20:25:26.179 INFO BlockManagerInfo - Added broadcast_53_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.0 MiB)
20:25:26.179 INFO SparkContext - Created broadcast 53 from newAPIHadoopFile at PathSplitSource.java:96
20:25:26.200 INFO MemoryStore - Block broadcast_54 stored as values in memory (estimated size 600.0 B, free 1914.7 MiB)
20:25:26.201 INFO MemoryStore - Block broadcast_54_piece0 stored as bytes in memory (estimated size 202.0 B, free 1914.7 MiB)
20:25:26.201 INFO BlockManagerInfo - Added broadcast_54_piece0 in memory on localhost:39477 (size: 202.0 B, free: 1919.0 MiB)
20:25:26.201 INFO SparkContext - Created broadcast 54 from broadcast at CramSource.java:114
20:25:26.204 INFO MemoryStore - Block broadcast_55 stored as values in memory (estimated size 297.3 KiB, free 1914.4 MiB)
20:25:26.216 INFO MemoryStore - Block broadcast_55_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1914.4 MiB)
20:25:26.216 INFO BlockManagerInfo - Added broadcast_55_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1918.9 MiB)
20:25:26.216 INFO SparkContext - Created broadcast 55 from newAPIHadoopFile at PathSplitSource.java:96
20:25:26.246 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:25:26.246 INFO DAGScheduler - Got job 28 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:25:26.246 INFO DAGScheduler - Final stage: ResultStage 37 (collect at ReadsSparkSourceUnitTest.java:111)
20:25:26.246 INFO DAGScheduler - Parents of final stage: List()
20:25:26.246 INFO DAGScheduler - Missing parents: List()
20:25:26.246 INFO DAGScheduler - Submitting ResultStage 37 (ParallelCollectionRDD[118] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:25:26.248 INFO MemoryStore - Block broadcast_56 stored as values in memory (estimated size 3.0 KiB, free 1914.4 MiB)
20:25:26.249 INFO MemoryStore - Block broadcast_56_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1914.4 MiB)
20:25:26.249 INFO BlockManagerInfo - Added broadcast_56_piece0 in memory on localhost:39477 (size: 1780.0 B, free: 1918.9 MiB)
20:25:26.249 INFO SparkContext - Created broadcast 56 from broadcast at DAGScheduler.scala:1580
20:25:26.249 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))
20:25:26.249 INFO TaskSchedulerImpl - Adding task set 37.0 with 4 tasks resource profile 0
20:25:26.251 INFO TaskSetManager - Starting task 0.0 in stage 37.0 (TID 87) (localhost, executor driver, partition 0, PROCESS_LOCAL, 8303 bytes)
20:25:26.251 INFO TaskSetManager - Starting task 1.0 in stage 37.0 (TID 88) (localhost, executor driver, partition 1, PROCESS_LOCAL, 8292 bytes)
20:25:26.251 INFO TaskSetManager - Starting task 2.0 in stage 37.0 (TID 89) (localhost, executor driver, partition 2, PROCESS_LOCAL, 8292 bytes)
20:25:26.251 INFO TaskSetManager - Starting task 3.0 in stage 37.0 (TID 90) (localhost, executor driver, partition 3, PROCESS_LOCAL, 8184 bytes)
20:25:26.252 INFO Executor - Running task 1.0 in stage 37.0 (TID 88)
20:25:26.252 INFO Executor - Running task 0.0 in stage 37.0 (TID 87)
20:25:26.252 INFO Executor - Running task 3.0 in stage 37.0 (TID 90)
20:25:26.252 INFO Executor - Running task 2.0 in stage 37.0 (TID 89)
20:25:26.254 INFO Executor - Finished task 0.0 in stage 37.0 (TID 87). 1578 bytes result sent to driver
20:25:26.254 INFO Executor - Finished task 3.0 in stage 37.0 (TID 90). 1459 bytes result sent to driver
20:25:26.255 INFO Executor - Finished task 1.0 in stage 37.0 (TID 88). 1567 bytes result sent to driver
20:25:26.255 INFO Executor - Finished task 2.0 in stage 37.0 (TID 89). 1567 bytes result sent to driver
20:25:26.256 INFO TaskSetManager - Finished task 3.0 in stage 37.0 (TID 90) in 5 ms on localhost (executor driver) (1/4)
20:25:26.256 INFO TaskSetManager - Finished task 2.0 in stage 37.0 (TID 89) in 5 ms on localhost (executor driver) (2/4)
20:25:26.256 INFO TaskSetManager - Finished task 0.0 in stage 37.0 (TID 87) in 6 ms on localhost (executor driver) (3/4)
20:25:26.257 INFO TaskSetManager - Finished task 1.0 in stage 37.0 (TID 88) in 6 ms on localhost (executor driver) (4/4)
20:25:26.257 INFO TaskSchedulerImpl - Removed TaskSet 37.0, whose tasks have all completed, from pool
20:25:26.257 INFO DAGScheduler - ResultStage 37 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.010 s
20:25:26.257 INFO DAGScheduler - Job 28 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:26.257 INFO TaskSchedulerImpl - Killing all running tasks in stage 37: Stage finished
20:25:26.258 INFO DAGScheduler - Job 28 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.011877 s
20:25:26.259 INFO FileInputFormat - Total input files to process : 1
20:25:26.292 INFO BlockManagerInfo - Removed broadcast_32_piece0 on localhost:39477 in memory (size: 3.8 KiB, free: 1918.9 MiB)
20:25:26.294 INFO BlockManagerInfo - Removed broadcast_34_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1919.0 MiB)
20:25:26.296 INFO BlockManagerInfo - Removed broadcast_37_piece0 on localhost:39477 in memory (size: 152.7 KiB, free: 1919.1 MiB)
20:25:26.299 INFO BlockManagerInfo - Removed broadcast_52_piece0 on localhost:39477 in memory (size: 202.0 B, free: 1919.1 MiB)
20:25:26.300 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:25:26.301 INFO BlockManagerInfo - Removed broadcast_22_piece0 on localhost:39477 in memory (size: 159.0 B, free: 1919.1 MiB)
20:25:26.301 INFO DAGScheduler - Got job 29 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:25:26.301 INFO DAGScheduler - Final stage: ResultStage 38 (collect at ReadsSparkSourceUnitTest.java:112)
20:25:26.301 INFO DAGScheduler - Parents of final stage: List()
20:25:26.301 INFO DAGScheduler - Missing parents: List()
20:25:26.301 INFO DAGScheduler - Submitting ResultStage 38 (MapPartitionsRDD[124] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:26.304 INFO BlockManagerInfo - Removed broadcast_25_piece0 on localhost:39477 in memory (size: 4.5 KiB, free: 1919.1 MiB)
20:25:26.306 INFO BlockManager - Removing RDD 47
20:25:26.309 INFO BlockManagerInfo - Removed broadcast_53_piece0 on localhost:39477 in memory (size: 50.1 KiB, free: 1919.2 MiB)
20:25:26.311 INFO BlockManagerInfo - Removed broadcast_33_piece0 on localhost:39477 in memory (size: 4.8 KiB, free: 1919.2 MiB)
20:25:26.312 INFO BlockManagerInfo - Removed broadcast_42_piece0 on localhost:39477 in memory (size: 50.1 KiB, free: 1919.2 MiB)
20:25:26.313 INFO BlockManagerInfo - Removed broadcast_30_piece0 on localhost:39477 in memory (size: 4.7 KiB, free: 1919.2 MiB)
20:25:26.314 INFO BlockManagerInfo - Removed broadcast_38_piece0 on localhost:39477 in memory (size: 50.1 KiB, free: 1919.3 MiB)
20:25:26.316 INFO BlockManagerInfo - Removed broadcast_41_piece0 on localhost:39477 in memory (size: 152.7 KiB, free: 1919.4 MiB)
20:25:26.317 INFO BlockManagerInfo - Removed broadcast_46_piece0 on localhost:39477 in memory (size: 183.0 B, free: 1919.4 MiB)
20:25:26.319 INFO BlockManagerInfo - Removed broadcast_50_piece0 on localhost:39477 in memory (size: 1780.0 B, free: 1919.4 MiB)
20:25:26.320 INFO BlockManagerInfo - Removed broadcast_21_piece0 on localhost:39477 in memory (size: 2.4 KiB, free: 1919.4 MiB)
20:25:26.321 INFO BlockManagerInfo - Removed broadcast_24_piece0 on localhost:39477 in memory (size: 4.3 KiB, free: 1919.4 MiB)
20:25:26.322 INFO BlockManagerInfo - Removed broadcast_49_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1919.5 MiB)
20:25:26.323 INFO BlockManagerInfo - Removed broadcast_43_piece0 on localhost:39477 in memory (size: 50.1 KiB, free: 1919.5 MiB)
20:25:26.324 INFO MemoryStore - Block broadcast_57 stored as values in memory (estimated size 286.0 KiB, free 1917.4 MiB)
20:25:26.324 INFO BlockManagerInfo - Removed broadcast_26_piece0 on localhost:39477 in memory (size: 3.2 KiB, free: 1919.5 MiB)
20:25:26.326 INFO MemoryStore - Block broadcast_57_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1917.3 MiB)
20:25:26.326 INFO BlockManagerInfo - Added broadcast_57_piece0 in memory on localhost:39477 (size: 103.1 KiB, free: 1919.4 MiB)
20:25:26.326 INFO SparkContext - Created broadcast 57 from broadcast at DAGScheduler.scala:1580
20:25:26.326 INFO BlockManagerInfo - Removed broadcast_28_piece0 on localhost:39477 in memory (size: 320.0 B, free: 1919.4 MiB)
20:25:26.327 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))
20:25:26.327 INFO TaskSchedulerImpl - Adding task set 38.0 with 1 tasks resource profile 0
20:25:26.327 INFO BlockManagerInfo - Removed broadcast_23_piece0 on localhost:39477 in memory (size: 465.0 B, free: 1919.4 MiB)
20:25:26.328 INFO TaskSetManager - Starting task 0.0 in stage 38.0 (TID 91) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7844 bytes)
20:25:26.329 INFO Executor - Running task 0.0 in stage 38.0 (TID 91)
20:25:26.329 INFO BlockManagerInfo - Removed broadcast_51_piece0 on localhost:39477 in memory (size: 103.1 KiB, free: 1919.5 MiB)
20:25:26.331 INFO BlockManagerInfo - Removed broadcast_20_piece0 on localhost:39477 in memory (size: 2.4 KiB, free: 1919.5 MiB)
20:25:26.332 INFO BlockManagerInfo - Removed broadcast_27_piece0 on localhost:39477 in memory (size: 5.1 KiB, free: 1919.5 MiB)
20:25:26.334 INFO BlockManagerInfo - Removed broadcast_39_piece0 on localhost:39477 in memory (size: 50.1 KiB, free: 1919.6 MiB)
20:25:26.335 INFO BlockManagerInfo - Removed broadcast_45_piece0 on localhost:39477 in memory (size: 152.7 KiB, free: 1919.7 MiB)
20:25:26.335 INFO BlockManagerInfo - Removed broadcast_29_piece0 on localhost:39477 in memory (size: 3.8 KiB, free: 1919.7 MiB)
20:25:26.336 INFO BlockManagerInfo - Removed broadcast_40_piece0 on localhost:39477 in memory (size: 1780.0 B, free: 1919.7 MiB)
20:25:26.337 INFO BlockManagerInfo - Removed broadcast_56_piece0 on localhost:39477 in memory (size: 1780.0 B, free: 1919.7 MiB)
20:25:26.338 INFO BlockManagerInfo - Removed broadcast_35_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1919.8 MiB)
20:25:26.339 INFO BlockManagerInfo - Removed broadcast_47_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1919.8 MiB)
20:25:26.340 INFO BlockManagerInfo - Removed broadcast_44_piece0 on localhost:39477 in memory (size: 1780.0 B, free: 1919.8 MiB)
20:25:26.341 INFO BlockManagerInfo - Removed broadcast_31_piece0 on localhost:39477 in memory (size: 320.0 B, free: 1919.8 MiB)
20:25:26.342 INFO BlockManagerInfo - Removed broadcast_48_piece0 on localhost:39477 in memory (size: 183.0 B, free: 1919.8 MiB)
20:25:26.343 INFO BlockManagerInfo - Removed broadcast_36_piece0 on localhost:39477 in memory (size: 1780.0 B, free: 1919.9 MiB)
20:25:26.369 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.cram:0+13330
20:25:26.375 INFO Executor - Finished task 0.0 in stage 38.0 (TID 91). 3736 bytes result sent to driver
20:25:26.376 INFO TaskSetManager - Finished task 0.0 in stage 38.0 (TID 91) in 48 ms on localhost (executor driver) (1/1)
20:25:26.376 INFO TaskSchedulerImpl - Removed TaskSet 38.0, whose tasks have all completed, from pool
20:25:26.377 INFO DAGScheduler - ResultStage 38 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.075 s
20:25:26.377 INFO DAGScheduler - Job 29 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:26.377 INFO TaskSchedulerImpl - Killing all running tasks in stage 38: Stage finished
20:25:26.377 INFO DAGScheduler - Job 29 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.076910 s
20:25:26.384 INFO MemoryStore - Block broadcast_58 stored as values in memory (estimated size 297.2 KiB, free 1919.0 MiB)
20:25:26.396 INFO MemoryStore - Block broadcast_58_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.9 MiB)
20:25:26.396 INFO BlockManagerInfo - Added broadcast_58_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.8 MiB)
20:25:26.396 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
20:25:26.433 INFO MemoryStore - Block broadcast_59 stored as values in memory (estimated size 297.2 KiB, free 1918.7 MiB)
20:25:26.440 INFO MemoryStore - Block broadcast_59_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.6 MiB)
20:25:26.440 INFO BlockManagerInfo - Added broadcast_59_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.8 MiB)
20:25:26.440 INFO SparkContext - Created broadcast 59 from newAPIHadoopFile at PathSplitSource.java:96
20:25:26.465 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:25:26.465 INFO DAGScheduler - Got job 30 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:25:26.465 INFO DAGScheduler - Final stage: ResultStage 39 (collect at ReadsSparkSourceUnitTest.java:111)
20:25:26.465 INFO DAGScheduler - Parents of final stage: List()
20:25:26.465 INFO DAGScheduler - Missing parents: List()
20:25:26.465 INFO DAGScheduler - Submitting ResultStage 39 (ParallelCollectionRDD[130] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:25:26.466 INFO MemoryStore - Block broadcast_60 stored as values in memory (estimated size 3.0 KiB, free 1918.6 MiB)
20:25:26.467 INFO MemoryStore - Block broadcast_60_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1918.6 MiB)
20:25:26.467 INFO BlockManagerInfo - Added broadcast_60_piece0 in memory on localhost:39477 (size: 1780.0 B, free: 1919.8 MiB)
20:25:26.467 INFO SparkContext - Created broadcast 60 from broadcast at DAGScheduler.scala:1580
20:25:26.467 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))
20:25:26.468 INFO TaskSchedulerImpl - Adding task set 39.0 with 4 tasks resource profile 0
20:25:26.469 INFO TaskSetManager - Starting task 0.0 in stage 39.0 (TID 92) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes)
20:25:26.469 INFO TaskSetManager - Starting task 1.0 in stage 39.0 (TID 93) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes)
20:25:26.470 INFO TaskSetManager - Starting task 2.0 in stage 39.0 (TID 94) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes)
20:25:26.470 INFO TaskSetManager - Starting task 3.0 in stage 39.0 (TID 95) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes)
20:25:26.470 INFO Executor - Running task 0.0 in stage 39.0 (TID 92)
20:25:26.470 INFO Executor - Running task 1.0 in stage 39.0 (TID 93)
20:25:26.471 INFO Executor - Running task 3.0 in stage 39.0 (TID 95)
20:25:26.472 INFO Executor - Running task 2.0 in stage 39.0 (TID 94)
20:25:26.474 INFO Executor - Finished task 2.0 in stage 39.0 (TID 94). 40380 bytes result sent to driver
20:25:26.475 INFO Executor - Finished task 0.0 in stage 39.0 (TID 92). 40355 bytes result sent to driver
20:25:26.476 INFO TaskSetManager - Finished task 2.0 in stage 39.0 (TID 94) in 6 ms on localhost (executor driver) (1/4)
20:25:26.476 INFO Executor - Finished task 3.0 in stage 39.0 (TID 95). 40805 bytes result sent to driver
20:25:26.477 INFO Executor - Finished task 1.0 in stage 39.0 (TID 93). 40469 bytes result sent to driver
20:25:26.477 INFO TaskSetManager - Finished task 0.0 in stage 39.0 (TID 92) in 9 ms on localhost (executor driver) (2/4)
20:25:26.477 INFO TaskSetManager - Finished task 3.0 in stage 39.0 (TID 95) in 7 ms on localhost (executor driver) (3/4)
20:25:26.478 INFO TaskSetManager - Finished task 1.0 in stage 39.0 (TID 93) in 9 ms on localhost (executor driver) (4/4)
20:25:26.478 INFO TaskSchedulerImpl - Removed TaskSet 39.0, whose tasks have all completed, from pool
20:25:26.478 INFO DAGScheduler - ResultStage 39 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.012 s
20:25:26.478 INFO DAGScheduler - Job 30 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:26.479 INFO TaskSchedulerImpl - Killing all running tasks in stage 39: Stage finished
20:25:26.479 INFO DAGScheduler - Job 30 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.013977 s
20:25:26.480 INFO FileInputFormat - Total input files to process : 1
20:25:26.520 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:25:26.520 INFO DAGScheduler - Got job 31 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:25:26.520 INFO DAGScheduler - Final stage: ResultStage 40 (collect at ReadsSparkSourceUnitTest.java:112)
20:25:26.520 INFO DAGScheduler - Parents of final stage: List()
20:25:26.520 INFO DAGScheduler - Missing parents: List()
20:25:26.521 INFO DAGScheduler - Submitting ResultStage 40 (MapPartitionsRDD[137] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:26.545 INFO MemoryStore - Block broadcast_61 stored as values in memory (estimated size 425.0 KiB, free 1918.2 MiB)
20:25:26.546 INFO MemoryStore - Block broadcast_61_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1918.0 MiB)
20:25:26.547 INFO BlockManagerInfo - Added broadcast_61_piece0 in memory on localhost:39477 (size: 152.7 KiB, free: 1919.6 MiB)
20:25:26.547 INFO SparkContext - Created broadcast 61 from broadcast at DAGScheduler.scala:1580
20:25:26.547 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))
20:25:26.547 INFO TaskSchedulerImpl - Adding task set 40.0 with 1 tasks resource profile 0
20:25:26.548 INFO TaskSetManager - Starting task 0.0 in stage 40.0 (TID 96) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes)
20:25:26.549 INFO Executor - Running task 0.0 in stage 40.0 (TID 96)
20:25:26.587 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
20:25:26.596 INFO Executor - Finished task 0.0 in stage 40.0 (TID 96). 159572 bytes result sent to driver
20:25:26.598 INFO TaskSetManager - Finished task 0.0 in stage 40.0 (TID 96) in 50 ms on localhost (executor driver) (1/1)
20:25:26.598 INFO TaskSchedulerImpl - Removed TaskSet 40.0, whose tasks have all completed, from pool
20:25:26.598 INFO DAGScheduler - ResultStage 40 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.077 s
20:25:26.598 INFO DAGScheduler - Job 31 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:26.598 INFO TaskSchedulerImpl - Killing all running tasks in stage 40: Stage finished
20:25:26.599 INFO DAGScheduler - Job 31 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.078912 s
20:25:26.603 INFO MemoryStore - Block broadcast_62 stored as values in memory (estimated size 528.0 B, free 1918.0 MiB)
20:25:26.604 INFO MemoryStore - Block broadcast_62_piece0 stored as bytes in memory (estimated size 183.0 B, free 1918.0 MiB)
20:25:26.605 INFO BlockManagerInfo - Added broadcast_62_piece0 in memory on localhost:39477 (size: 183.0 B, free: 1919.6 MiB)
20:25:26.605 INFO SparkContext - Created broadcast 62 from broadcast at CramSource.java:114
20:25:26.608 INFO MemoryStore - Block broadcast_63 stored as values in memory (estimated size 297.2 KiB, free 1917.7 MiB)
20:25:26.615 INFO MemoryStore - Block broadcast_63_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.7 MiB)
20:25:26.615 INFO BlockManagerInfo - Added broadcast_63_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.6 MiB)
20:25:26.616 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
20:25:26.645 INFO MemoryStore - Block broadcast_64 stored as values in memory (estimated size 528.0 B, free 1917.7 MiB)
20:25:26.646 INFO MemoryStore - Block broadcast_64_piece0 stored as bytes in memory (estimated size 183.0 B, free 1917.7 MiB)
20:25:26.646 INFO BlockManagerInfo - Added broadcast_64_piece0 in memory on localhost:39477 (size: 183.0 B, free: 1919.6 MiB)
20:25:26.647 INFO SparkContext - Created broadcast 64 from broadcast at CramSource.java:114
20:25:26.650 INFO MemoryStore - Block broadcast_65 stored as values in memory (estimated size 297.2 KiB, free 1917.4 MiB)
20:25:26.658 INFO MemoryStore - Block broadcast_65_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.4 MiB)
20:25:26.658 INFO BlockManagerInfo - Added broadcast_65_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.5 MiB)
20:25:26.658 INFO SparkContext - Created broadcast 65 from newAPIHadoopFile at PathSplitSource.java:96
20:25:26.676 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:25:26.677 INFO DAGScheduler - Got job 32 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:25:26.677 INFO DAGScheduler - Final stage: ResultStage 41 (collect at ReadsSparkSourceUnitTest.java:111)
20:25:26.677 INFO DAGScheduler - Parents of final stage: List()
20:25:26.677 INFO DAGScheduler - Missing parents: List()
20:25:26.677 INFO DAGScheduler - Submitting ResultStage 41 (ParallelCollectionRDD[142] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:25:26.678 INFO MemoryStore - Block broadcast_66 stored as values in memory (estimated size 3.0 KiB, free 1917.4 MiB)
20:25:26.678 INFO MemoryStore - Block broadcast_66_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1917.3 MiB)
20:25:26.679 INFO BlockManagerInfo - Added broadcast_66_piece0 in memory on localhost:39477 (size: 1780.0 B, free: 1919.5 MiB)
20:25:26.679 INFO SparkContext - Created broadcast 66 from broadcast at DAGScheduler.scala:1580
20:25:26.679 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))
20:25:26.679 INFO TaskSchedulerImpl - Adding task set 41.0 with 4 tasks resource profile 0
20:25:26.682 INFO TaskSetManager - Starting task 0.0 in stage 41.0 (TID 97) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes)
20:25:26.683 INFO TaskSetManager - Starting task 1.0 in stage 41.0 (TID 98) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes)
20:25:26.684 INFO TaskSetManager - Starting task 2.0 in stage 41.0 (TID 99) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes)
20:25:26.686 INFO TaskSetManager - Starting task 3.0 in stage 41.0 (TID 100) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes)
20:25:26.686 INFO Executor - Running task 0.0 in stage 41.0 (TID 97)
20:25:26.687 INFO Executor - Running task 1.0 in stage 41.0 (TID 98)
20:25:26.688 INFO Executor - Running task 2.0 in stage 41.0 (TID 99)
20:25:26.689 INFO Executor - Finished task 0.0 in stage 41.0 (TID 97). 38950 bytes result sent to driver
20:25:26.689 INFO Executor - Running task 3.0 in stage 41.0 (TID 100)
20:25:26.690 INFO Executor - Finished task 2.0 in stage 41.0 (TID 99). 39070 bytes result sent to driver
20:25:26.691 INFO Executor - Finished task 3.0 in stage 41.0 (TID 100). 39300 bytes result sent to driver
20:25:26.692 INFO TaskSetManager - Finished task 2.0 in stage 41.0 (TID 99) in 9 ms on localhost (executor driver) (1/4)
20:25:26.693 INFO TaskSetManager - Finished task 0.0 in stage 41.0 (TID 97) in 13 ms on localhost (executor driver) (2/4)
20:25:26.693 INFO TaskSetManager - Finished task 3.0 in stage 41.0 (TID 100) in 9 ms on localhost (executor driver) (3/4)
20:25:26.692 INFO Executor - Finished task 1.0 in stage 41.0 (TID 98). 39130 bytes result sent to driver
20:25:26.694 INFO TaskSetManager - Finished task 1.0 in stage 41.0 (TID 98) in 12 ms on localhost (executor driver) (4/4)
20:25:26.694 INFO TaskSchedulerImpl - Removed TaskSet 41.0, whose tasks have all completed, from pool
20:25:26.694 INFO DAGScheduler - ResultStage 41 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.017 s
20:25:26.694 INFO DAGScheduler - Job 32 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:26.694 INFO TaskSchedulerImpl - Killing all running tasks in stage 41: Stage finished
20:25:26.695 INFO DAGScheduler - Job 32 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.018654 s
20:25:26.696 INFO FileInputFormat - Total input files to process : 1
20:25:26.734 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:25:26.734 INFO DAGScheduler - Got job 33 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:25:26.734 INFO DAGScheduler - Final stage: ResultStage 42 (collect at ReadsSparkSourceUnitTest.java:112)
20:25:26.734 INFO DAGScheduler - Parents of final stage: List()
20:25:26.735 INFO DAGScheduler - Missing parents: List()
20:25:26.735 INFO DAGScheduler - Submitting ResultStage 42 (MapPartitionsRDD[148] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:26.753 INFO MemoryStore - Block broadcast_67 stored as values in memory (estimated size 286.0 KiB, free 1917.1 MiB)
20:25:26.755 INFO MemoryStore - Block broadcast_67_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1917.0 MiB)
20:25:26.755 INFO BlockManagerInfo - Added broadcast_67_piece0 in memory on localhost:39477 (size: 103.1 KiB, free: 1919.4 MiB)
20:25:26.755 INFO SparkContext - Created broadcast 67 from broadcast at DAGScheduler.scala:1580
20:25:26.756 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))
20:25:26.756 INFO TaskSchedulerImpl - Adding task set 42.0 with 1 tasks resource profile 0
20:25:26.756 INFO TaskSetManager - Starting task 0.0 in stage 42.0 (TID 101) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes)
20:25:26.757 INFO Executor - Running task 0.0 in stage 42.0 (TID 101)
20:25:26.787 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
20:25:26.804 INFO Executor - Finished task 0.0 in stage 42.0 (TID 101). 154101 bytes result sent to driver
20:25:26.805 INFO TaskSetManager - Finished task 0.0 in stage 42.0 (TID 101) in 49 ms on localhost (executor driver) (1/1)
20:25:26.805 INFO TaskSchedulerImpl - Removed TaskSet 42.0, whose tasks have all completed, from pool
20:25:26.806 INFO DAGScheduler - ResultStage 42 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.071 s
20:25:26.806 INFO DAGScheduler - Job 33 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:26.806 INFO TaskSchedulerImpl - Killing all running tasks in stage 42: Stage finished
20:25:26.806 INFO DAGScheduler - Job 33 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.072237 s
20:25:26.813 INFO MemoryStore - Block broadcast_68 stored as values in memory (estimated size 297.2 KiB, free 1916.7 MiB)
20:25:26.823 INFO MemoryStore - Block broadcast_68_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.6 MiB)
20:25:26.824 INFO BlockManagerInfo - Added broadcast_68_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.4 MiB)
20:25:26.824 INFO SparkContext - Created broadcast 68 from newAPIHadoopFile at PathSplitSource.java:96
20:25:26.863 INFO MemoryStore - Block broadcast_69 stored as values in memory (estimated size 297.2 KiB, free 1916.3 MiB)
20:25:26.870 INFO MemoryStore - Block broadcast_69_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.3 MiB)
20:25:26.871 INFO BlockManagerInfo - Added broadcast_69_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.3 MiB)
20:25:26.871 INFO SparkContext - Created broadcast 69 from newAPIHadoopFile at PathSplitSource.java:96
20:25:26.895 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:25:26.895 INFO DAGScheduler - Got job 34 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:25:26.896 INFO DAGScheduler - Final stage: ResultStage 43 (collect at ReadsSparkSourceUnitTest.java:111)
20:25:26.896 INFO DAGScheduler - Parents of final stage: List()
20:25:26.896 INFO DAGScheduler - Missing parents: List()
20:25:26.896 INFO DAGScheduler - Submitting ResultStage 43 (ParallelCollectionRDD[154] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:25:26.897 INFO MemoryStore - Block broadcast_70 stored as values in memory (estimated size 3.0 KiB, free 1916.3 MiB)
20:25:26.897 INFO MemoryStore - Block broadcast_70_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1916.3 MiB)
20:25:26.897 INFO BlockManagerInfo - Added broadcast_70_piece0 in memory on localhost:39477 (size: 1780.0 B, free: 1919.3 MiB)
20:25:26.898 INFO SparkContext - Created broadcast 70 from broadcast at DAGScheduler.scala:1580
20:25:26.898 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))
20:25:26.898 INFO TaskSchedulerImpl - Adding task set 43.0 with 4 tasks resource profile 0
20:25:26.899 INFO TaskSetManager - Starting task 0.0 in stage 43.0 (TID 102) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes)
20:25:26.899 INFO TaskSetManager - Starting task 1.0 in stage 43.0 (TID 103) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes)
20:25:26.900 INFO TaskSetManager - Starting task 2.0 in stage 43.0 (TID 104) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes)
20:25:26.900 INFO TaskSetManager - Starting task 3.0 in stage 43.0 (TID 105) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes)
20:25:26.900 INFO Executor - Running task 1.0 in stage 43.0 (TID 103)
20:25:26.900 INFO Executor - Running task 0.0 in stage 43.0 (TID 102)
20:25:26.900 INFO Executor - Running task 3.0 in stage 43.0 (TID 105)
20:25:26.902 INFO Executor - Running task 2.0 in stage 43.0 (TID 104)
20:25:26.904 INFO Executor - Finished task 3.0 in stage 43.0 (TID 105). 40805 bytes result sent to driver
20:25:26.904 INFO Executor - Finished task 0.0 in stage 43.0 (TID 102). 40355 bytes result sent to driver
20:25:26.905 INFO Executor - Finished task 1.0 in stage 43.0 (TID 103). 40469 bytes result sent to driver
20:25:26.905 INFO Executor - Finished task 2.0 in stage 43.0 (TID 104). 40337 bytes result sent to driver
20:25:26.905 INFO TaskSetManager - Finished task 3.0 in stage 43.0 (TID 105) in 5 ms on localhost (executor driver) (1/4)
20:25:26.906 INFO TaskSetManager - Finished task 0.0 in stage 43.0 (TID 102) in 7 ms on localhost (executor driver) (2/4)
20:25:26.906 INFO TaskSetManager - Finished task 1.0 in stage 43.0 (TID 103) in 7 ms on localhost (executor driver) (3/4)
20:25:26.906 INFO TaskSetManager - Finished task 2.0 in stage 43.0 (TID 104) in 6 ms on localhost (executor driver) (4/4)
20:25:26.906 INFO TaskSchedulerImpl - Removed TaskSet 43.0, whose tasks have all completed, from pool
20:25:26.906 INFO DAGScheduler - ResultStage 43 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.010 s
20:25:26.906 INFO DAGScheduler - Job 34 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:26.906 INFO TaskSchedulerImpl - Killing all running tasks in stage 43: Stage finished
20:25:26.906 INFO DAGScheduler - Job 34 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.011281 s
20:25:26.908 INFO FileInputFormat - Total input files to process : 1
20:25:26.946 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:25:26.947 INFO DAGScheduler - Got job 35 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:25:26.947 INFO DAGScheduler - Final stage: ResultStage 44 (collect at ReadsSparkSourceUnitTest.java:112)
20:25:26.947 INFO DAGScheduler - Parents of final stage: List()
20:25:26.947 INFO DAGScheduler - Missing parents: List()
20:25:26.947 INFO DAGScheduler - Submitting ResultStage 44 (MapPartitionsRDD[161] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:26.977 INFO MemoryStore - Block broadcast_71 stored as values in memory (estimated size 425.0 KiB, free 1915.9 MiB)
20:25:26.979 INFO MemoryStore - Block broadcast_71_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1915.7 MiB)
20:25:26.979 INFO BlockManagerInfo - Added broadcast_71_piece0 in memory on localhost:39477 (size: 152.7 KiB, free: 1919.2 MiB)
20:25:26.980 INFO SparkContext - Created broadcast 71 from broadcast at DAGScheduler.scala:1580
20:25:26.980 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))
20:25:26.980 INFO TaskSchedulerImpl - Adding task set 44.0 with 1 tasks resource profile 0
20:25:26.981 INFO TaskSetManager - Starting task 0.0 in stage 44.0 (TID 106) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes)
20:25:26.981 INFO Executor - Running task 0.0 in stage 44.0 (TID 106)
20:25:27.017 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
20:25:27.022 INFO Executor - Finished task 0.0 in stage 44.0 (TID 106). 159572 bytes result sent to driver
20:25:27.024 INFO TaskSetManager - Finished task 0.0 in stage 44.0 (TID 106) in 43 ms on localhost (executor driver) (1/1)
20:25:27.024 INFO TaskSchedulerImpl - Removed TaskSet 44.0, whose tasks have all completed, from pool
20:25:27.024 INFO DAGScheduler - ResultStage 44 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.077 s
20:25:27.024 INFO DAGScheduler - Job 35 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:27.024 INFO TaskSchedulerImpl - Killing all running tasks in stage 44: Stage finished
20:25:27.024 INFO DAGScheduler - Job 35 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.078475 s
20:25:27.028 INFO MemoryStore - Block broadcast_72 stored as values in memory (estimated size 528.0 B, free 1915.7 MiB)
20:25:27.030 INFO MemoryStore - Block broadcast_72_piece0 stored as bytes in memory (estimated size 183.0 B, free 1915.7 MiB)
20:25:27.030 INFO BlockManagerInfo - Added broadcast_72_piece0 in memory on localhost:39477 (size: 183.0 B, free: 1919.2 MiB)
20:25:27.030 INFO SparkContext - Created broadcast 72 from broadcast at CramSource.java:114
20:25:27.032 INFO MemoryStore - Block broadcast_73 stored as values in memory (estimated size 297.2 KiB, free 1915.4 MiB)
20:25:27.039 INFO MemoryStore - Block broadcast_73_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.4 MiB)
20:25:27.039 INFO BlockManagerInfo - Added broadcast_73_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.1 MiB)
20:25:27.039 INFO SparkContext - Created broadcast 73 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.063 INFO MemoryStore - Block broadcast_74 stored as values in memory (estimated size 528.0 B, free 1915.4 MiB)
20:25:27.064 INFO MemoryStore - Block broadcast_74_piece0 stored as bytes in memory (estimated size 183.0 B, free 1915.4 MiB)
20:25:27.064 INFO BlockManagerInfo - Added broadcast_74_piece0 in memory on localhost:39477 (size: 183.0 B, free: 1919.1 MiB)
20:25:27.065 INFO SparkContext - Created broadcast 74 from broadcast at CramSource.java:114
20:25:27.067 INFO MemoryStore - Block broadcast_75 stored as values in memory (estimated size 297.2 KiB, free 1915.1 MiB)
20:25:27.074 INFO MemoryStore - Block broadcast_75_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.0 MiB)
20:25:27.074 INFO BlockManagerInfo - Added broadcast_75_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.1 MiB)
20:25:27.074 INFO SparkContext - Created broadcast 75 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.093 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
20:25:27.093 INFO DAGScheduler - Got job 36 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
20:25:27.093 INFO DAGScheduler - Final stage: ResultStage 45 (collect at ReadsSparkSourceUnitTest.java:111)
20:25:27.093 INFO DAGScheduler - Parents of final stage: List()
20:25:27.093 INFO DAGScheduler - Missing parents: List()
20:25:27.094 INFO DAGScheduler - Submitting ResultStage 45 (ParallelCollectionRDD[166] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:25:27.094 INFO MemoryStore - Block broadcast_76 stored as values in memory (estimated size 3.0 KiB, free 1915.0 MiB)
20:25:27.095 INFO MemoryStore - Block broadcast_76_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1915.0 MiB)
20:25:27.096 INFO BlockManagerInfo - Added broadcast_76_piece0 in memory on localhost:39477 (size: 1780.0 B, free: 1919.1 MiB)
20:25:27.096 INFO SparkContext - Created broadcast 76 from broadcast at DAGScheduler.scala:1580
20:25:27.096 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))
20:25:27.096 INFO TaskSchedulerImpl - Adding task set 45.0 with 4 tasks resource profile 0
20:25:27.098 INFO TaskSetManager - Starting task 0.0 in stage 45.0 (TID 107) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes)
20:25:27.099 INFO TaskSetManager - Starting task 1.0 in stage 45.0 (TID 108) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes)
20:25:27.100 INFO TaskSetManager - Starting task 2.0 in stage 45.0 (TID 109) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes)
20:25:27.100 INFO TaskSetManager - Starting task 3.0 in stage 45.0 (TID 110) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes)
20:25:27.101 INFO Executor - Running task 0.0 in stage 45.0 (TID 107)
20:25:27.101 INFO Executor - Running task 2.0 in stage 45.0 (TID 109)
20:25:27.102 INFO Executor - Running task 1.0 in stage 45.0 (TID 108)
20:25:27.103 INFO Executor - Running task 3.0 in stage 45.0 (TID 110)
20:25:27.104 INFO Executor - Finished task 0.0 in stage 45.0 (TID 107). 38950 bytes result sent to driver
20:25:27.104 INFO Executor - Finished task 1.0 in stage 45.0 (TID 108). 39087 bytes result sent to driver
20:25:27.105 INFO TaskSetManager - Finished task 1.0 in stage 45.0 (TID 108) in 7 ms on localhost (executor driver) (1/4)
20:25:27.105 INFO Executor - Finished task 2.0 in stage 45.0 (TID 109). 39070 bytes result sent to driver
20:25:27.105 INFO Executor - Finished task 3.0 in stage 45.0 (TID 110). 39300 bytes result sent to driver
20:25:27.106 INFO TaskSetManager - Finished task 0.0 in stage 45.0 (TID 107) in 9 ms on localhost (executor driver) (2/4)
20:25:27.106 INFO TaskSetManager - Finished task 2.0 in stage 45.0 (TID 109) in 7 ms on localhost (executor driver) (3/4)
20:25:27.106 INFO TaskSetManager - Finished task 3.0 in stage 45.0 (TID 110) in 6 ms on localhost (executor driver) (4/4)
20:25:27.106 INFO TaskSchedulerImpl - Removed TaskSet 45.0, whose tasks have all completed, from pool
20:25:27.106 INFO DAGScheduler - ResultStage 45 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.012 s
20:25:27.107 INFO DAGScheduler - Job 36 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:27.107 INFO TaskSchedulerImpl - Killing all running tasks in stage 45: Stage finished
20:25:27.107 INFO DAGScheduler - Job 36 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.013929 s
20:25:27.108 INFO FileInputFormat - Total input files to process : 1
20:25:27.135 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
20:25:27.135 INFO DAGScheduler - Got job 37 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
20:25:27.135 INFO DAGScheduler - Final stage: ResultStage 46 (collect at ReadsSparkSourceUnitTest.java:112)
20:25:27.135 INFO DAGScheduler - Parents of final stage: List()
20:25:27.136 INFO DAGScheduler - Missing parents: List()
20:25:27.136 INFO DAGScheduler - Submitting ResultStage 46 (MapPartitionsRDD[172] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:27.155 INFO MemoryStore - Block broadcast_77 stored as values in memory (estimated size 286.0 KiB, free 1914.8 MiB)
20:25:27.156 INFO MemoryStore - Block broadcast_77_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1914.7 MiB)
20:25:27.156 INFO BlockManagerInfo - Added broadcast_77_piece0 in memory on localhost:39477 (size: 103.1 KiB, free: 1919.0 MiB)
20:25:27.157 INFO SparkContext - Created broadcast 77 from broadcast at DAGScheduler.scala:1580
20:25:27.157 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))
20:25:27.157 INFO TaskSchedulerImpl - Adding task set 46.0 with 1 tasks resource profile 0
20:25:27.158 INFO TaskSetManager - Starting task 0.0 in stage 46.0 (TID 111) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes)
20:25:27.158 INFO Executor - Running task 0.0 in stage 46.0 (TID 111)
20:25:27.188 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram:0+50619
20:25:27.199 INFO Executor - Finished task 0.0 in stage 46.0 (TID 111). 154101 bytes result sent to driver
20:25:27.200 INFO TaskSetManager - Finished task 0.0 in stage 46.0 (TID 111) in 42 ms on localhost (executor driver) (1/1)
20:25:27.201 INFO TaskSchedulerImpl - Removed TaskSet 46.0, whose tasks have all completed, from pool
20:25:27.201 INFO DAGScheduler - ResultStage 46 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.065 s
20:25:27.201 INFO DAGScheduler - Job 37 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:27.201 INFO TaskSchedulerImpl - Killing all running tasks in stage 46: Stage finished
20:25:27.201 INFO DAGScheduler - Job 37 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.066565 s
20:25:27.207 INFO MemoryStore - Block broadcast_78 stored as values in memory (estimated size 297.2 KiB, free 1914.4 MiB)
20:25:27.218 INFO MemoryStore - Block broadcast_78_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1914.3 MiB)
20:25:27.218 INFO BlockManagerInfo - Added broadcast_78_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1918.9 MiB)
20:25:27.218 INFO SparkContext - Created broadcast 78 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.259 INFO MemoryStore - Block broadcast_79 stored as values in memory (estimated size 528.0 B, free 1914.3 MiB)
20:25:27.259 INFO MemoryStore - Block broadcast_79_piece0 stored as bytes in memory (estimated size 183.0 B, free 1914.3 MiB)
20:25:27.260 INFO BlockManagerInfo - Added broadcast_79_piece0 in memory on localhost:39477 (size: 183.0 B, free: 1918.9 MiB)
20:25:27.260 INFO SparkContext - Created broadcast 79 from broadcast at CramSource.java:114
20:25:27.263 INFO MemoryStore - Block broadcast_80 stored as values in memory (estimated size 297.2 KiB, free 1914.0 MiB)
20:25:27.274 INFO MemoryStore - Block broadcast_80_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1914.0 MiB)
20:25:27.274 INFO BlockManagerInfo - Added broadcast_80_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1918.9 MiB)
20:25:27.275 INFO SparkContext - Created broadcast 80 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.374 WARN FileSystem - Failed to initialize filesystem hdfs://bogus/path.bam: java.lang.IllegalArgumentException: java.net.UnknownHostException: bogus
20:25:27.382 INFO MemoryStore - Block broadcast_81 stored as values in memory (estimated size 297.3 KiB, free 1913.7 MiB)
20:25:27.392 INFO MemoryStore - Block broadcast_81_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1913.6 MiB)
20:25:27.393 INFO BlockManagerInfo - Added broadcast_81_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1918.8 MiB)
20:25:27.395 INFO SparkContext - Created broadcast 81 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.434 INFO MemoryStore - Block broadcast_82 stored as values in memory (estimated size 297.3 KiB, free 1913.3 MiB)
20:25:27.440 INFO MemoryStore - Block broadcast_82_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1913.3 MiB)
20:25:27.441 INFO BlockManagerInfo - Added broadcast_82_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1918.8 MiB)
20:25:27.441 INFO SparkContext - Created broadcast 82 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.467 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:154
20:25:27.467 INFO DAGScheduler - Got job 38 (collect at ReadsSparkSourceUnitTest.java:154) with 4 output partitions
20:25:27.467 INFO DAGScheduler - Final stage: ResultStage 47 (collect at ReadsSparkSourceUnitTest.java:154)
20:25:27.467 INFO DAGScheduler - Parents of final stage: List()
20:25:27.467 INFO DAGScheduler - Missing parents: List()
20:25:27.468 INFO DAGScheduler - Submitting ResultStage 47 (ParallelCollectionRDD[187] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
20:25:27.468 INFO MemoryStore - Block broadcast_83 stored as values in memory (estimated size 3.0 KiB, free 1913.3 MiB)
20:25:27.469 INFO MemoryStore - Block broadcast_83_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1913.3 MiB)
20:25:27.469 INFO BlockManagerInfo - Added broadcast_83_piece0 in memory on localhost:39477 (size: 1780.0 B, free: 1918.8 MiB)
20:25:27.469 INFO SparkContext - Created broadcast 83 from broadcast at DAGScheduler.scala:1580
20:25:27.469 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))
20:25:27.470 INFO TaskSchedulerImpl - Adding task set 47.0 with 4 tasks resource profile 0
20:25:27.471 INFO TaskSetManager - Starting task 0.0 in stage 47.0 (TID 112) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes)
20:25:27.472 INFO TaskSetManager - Starting task 1.0 in stage 47.0 (TID 113) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes)
20:25:27.472 INFO TaskSetManager - Starting task 2.0 in stage 47.0 (TID 114) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes)
20:25:27.473 INFO TaskSetManager - Starting task 3.0 in stage 47.0 (TID 115) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes)
20:25:27.474 INFO Executor - Running task 1.0 in stage 47.0 (TID 113)
20:25:27.474 INFO Executor - Running task 0.0 in stage 47.0 (TID 112)
20:25:27.474 INFO Executor - Running task 2.0 in stage 47.0 (TID 114)
20:25:27.475 INFO Executor - Running task 3.0 in stage 47.0 (TID 115)
20:25:27.477 INFO Executor - Finished task 0.0 in stage 47.0 (TID 112). 163161 bytes result sent to driver
20:25:27.478 INFO Executor - Finished task 3.0 in stage 47.0 (TID 115). 162694 bytes result sent to driver
20:25:27.478 INFO Executor - Finished task 2.0 in stage 47.0 (TID 114). 163356 bytes result sent to driver
20:25:27.480 INFO TaskSetManager - Finished task 2.0 in stage 47.0 (TID 114) in 8 ms on localhost (executor driver) (1/4)
20:25:27.480 INFO TaskSetManager - Finished task 0.0 in stage 47.0 (TID 112) in 10 ms on localhost (executor driver) (2/4)
20:25:27.480 INFO Executor - Finished task 1.0 in stage 47.0 (TID 113). 163411 bytes result sent to driver
20:25:27.481 INFO TaskSetManager - Finished task 3.0 in stage 47.0 (TID 115) in 8 ms on localhost (executor driver) (3/4)
20:25:27.482 INFO TaskSetManager - Finished task 1.0 in stage 47.0 (TID 113) in 11 ms on localhost (executor driver) (4/4)
20:25:27.482 INFO TaskSchedulerImpl - Removed TaskSet 47.0, whose tasks have all completed, from pool
20:25:27.482 INFO DAGScheduler - ResultStage 47 (collect at ReadsSparkSourceUnitTest.java:154) finished in 0.014 s
20:25:27.482 INFO DAGScheduler - Job 38 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:27.482 INFO TaskSchedulerImpl - Killing all running tasks in stage 47: Stage finished
20:25:27.482 INFO DAGScheduler - Job 38 finished: collect at ReadsSparkSourceUnitTest.java:154, took 0.015480 s
20:25:27.491 INFO FileInputFormat - Total input files to process : 2
20:25:27.528 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:155
20:25:27.529 INFO DAGScheduler - Got job 39 (collect at ReadsSparkSourceUnitTest.java:155) with 2 output partitions
20:25:27.529 INFO DAGScheduler - Final stage: ResultStage 48 (collect at ReadsSparkSourceUnitTest.java:155)
20:25:27.529 INFO DAGScheduler - Parents of final stage: List()
20:25:27.529 INFO DAGScheduler - Missing parents: List()
20:25:27.529 INFO DAGScheduler - Submitting ResultStage 48 (MapPartitionsRDD[194] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:27.547 INFO MemoryStore - Block broadcast_84 stored as values in memory (estimated size 425.0 KiB, free 1912.9 MiB)
20:25:27.549 INFO MemoryStore - Block broadcast_84_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1912.7 MiB)
20:25:27.549 INFO BlockManagerInfo - Added broadcast_84_piece0 in memory on localhost:39477 (size: 152.7 KiB, free: 1918.6 MiB)
20:25:27.549 INFO SparkContext - Created broadcast 84 from broadcast at DAGScheduler.scala:1580
20:25:27.549 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))
20:25:27.549 INFO TaskSchedulerImpl - Adding task set 48.0 with 2 tasks resource profile 0
20:25:27.550 INFO TaskSetManager - Starting task 0.0 in stage 48.0 (TID 116) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7921 bytes)
20:25:27.550 INFO TaskSetManager - Starting task 1.0 in stage 48.0 (TID 117) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7921 bytes)
20:25:27.551 INFO Executor - Running task 1.0 in stage 48.0 (TID 117)
20:25:27.551 INFO Executor - Running task 0.0 in stage 48.0 (TID 116)
20:25:27.589 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
20:25:27.601 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
20:25:27.605 INFO Executor - Finished task 0.0 in stage 48.0 (TID 116). 325633 bytes result sent to driver
20:25:27.607 INFO TaskSetManager - Finished task 0.0 in stage 48.0 (TID 116) in 57 ms on localhost (executor driver) (1/2)
20:25:27.619 INFO Executor - Finished task 1.0 in stage 48.0 (TID 117). 325633 bytes result sent to driver
20:25:27.621 INFO TaskSetManager - Finished task 1.0 in stage 48.0 (TID 117) in 71 ms on localhost (executor driver) (2/2)
20:25:27.621 INFO TaskSchedulerImpl - Removed TaskSet 48.0, whose tasks have all completed, from pool
20:25:27.621 INFO DAGScheduler - ResultStage 48 (collect at ReadsSparkSourceUnitTest.java:155) finished in 0.092 s
20:25:27.621 INFO DAGScheduler - Job 39 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:27.622 INFO TaskSchedulerImpl - Killing all running tasks in stage 48: Stage finished
20:25:27.622 INFO DAGScheduler - Job 39 finished: collect at ReadsSparkSourceUnitTest.java:155, took 0.093570 s
20:25:27.639 INFO BlockManagerInfo - Removed broadcast_72_piece0 on localhost:39477 in memory (size: 183.0 B, free: 1918.6 MiB)
20:25:27.640 INFO BlockManagerInfo - Removed broadcast_83_piece0 on localhost:39477 in memory (size: 1780.0 B, free: 1918.6 MiB)
20:25:27.641 INFO BlockManagerInfo - Removed broadcast_60_piece0 on localhost:39477 in memory (size: 1780.0 B, free: 1918.6 MiB)
20:25:27.641 INFO MemoryStore - Block broadcast_85 stored as values in memory (estimated size 297.2 KiB, free 1912.5 MiB)
20:25:27.641 INFO BlockManagerInfo - Removed broadcast_79_piece0 on localhost:39477 in memory (size: 183.0 B, free: 1918.6 MiB)
20:25:27.642 INFO BlockManagerInfo - Removed broadcast_70_piece0 on localhost:39477 in memory (size: 1780.0 B, free: 1918.6 MiB)
20:25:27.643 INFO BlockManagerInfo - Removed broadcast_69_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1918.7 MiB)
20:25:27.644 INFO BlockManagerInfo - Removed broadcast_63_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1918.7 MiB)
20:25:27.645 INFO BlockManagerInfo - Removed broadcast_57_piece0 on localhost:39477 in memory (size: 103.1 KiB, free: 1918.8 MiB)
20:25:27.645 INFO BlockManagerInfo - Removed broadcast_78_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1918.9 MiB)
20:25:27.646 INFO BlockManagerInfo - Removed broadcast_65_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1918.9 MiB)
20:25:27.647 INFO BlockManagerInfo - Removed broadcast_81_piece0 on localhost:39477 in memory (size: 50.1 KiB, free: 1919.0 MiB)
20:25:27.648 INFO BlockManagerInfo - Removed broadcast_59_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1919.0 MiB)
20:25:27.648 INFO BlockManagerInfo - Removed broadcast_64_piece0 on localhost:39477 in memory (size: 183.0 B, free: 1919.0 MiB)
20:25:27.649 INFO BlockManagerInfo - Removed broadcast_84_piece0 on localhost:39477 in memory (size: 152.7 KiB, free: 1919.2 MiB)
20:25:27.650 INFO BlockManagerInfo - Removed broadcast_80_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1919.2 MiB)
20:25:27.651 INFO BlockManagerInfo - Removed broadcast_71_piece0 on localhost:39477 in memory (size: 152.7 KiB, free: 1919.4 MiB)
20:25:27.651 INFO MemoryStore - Block broadcast_85_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.3 MiB)
20:25:27.651 INFO BlockManagerInfo - Removed broadcast_73_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1919.4 MiB)
20:25:27.652 INFO BlockManagerInfo - Added broadcast_85_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.4 MiB)
20:25:27.652 INFO SparkContext - Created broadcast 85 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.653 INFO BlockManagerInfo - Removed broadcast_61_piece0 on localhost:39477 in memory (size: 152.7 KiB, free: 1919.5 MiB)
20:25:27.654 INFO BlockManagerInfo - Removed broadcast_55_piece0 on localhost:39477 in memory (size: 50.1 KiB, free: 1919.6 MiB)
20:25:27.655 INFO BlockManagerInfo - Removed broadcast_66_piece0 on localhost:39477 in memory (size: 1780.0 B, free: 1919.6 MiB)
20:25:27.655 INFO BlockManagerInfo - Removed broadcast_58_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1919.6 MiB)
20:25:27.656 INFO BlockManagerInfo - Removed broadcast_62_piece0 on localhost:39477 in memory (size: 183.0 B, free: 1919.6 MiB)
20:25:27.657 INFO BlockManagerInfo - Removed broadcast_76_piece0 on localhost:39477 in memory (size: 1780.0 B, free: 1919.6 MiB)
20:25:27.659 INFO BlockManagerInfo - Removed broadcast_74_piece0 on localhost:39477 in memory (size: 183.0 B, free: 1919.6 MiB)
20:25:27.660 INFO BlockManagerInfo - Removed broadcast_68_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1919.7 MiB)
20:25:27.661 INFO BlockManagerInfo - Removed broadcast_67_piece0 on localhost:39477 in memory (size: 103.1 KiB, free: 1919.8 MiB)
20:25:27.662 INFO BlockManagerInfo - Removed broadcast_77_piece0 on localhost:39477 in memory (size: 103.1 KiB, free: 1919.9 MiB)
20:25:27.663 INFO BlockManagerInfo - Removed broadcast_82_piece0 on localhost:39477 in memory (size: 50.1 KiB, free: 1919.9 MiB)
20:25:27.664 INFO BlockManagerInfo - Removed broadcast_75_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1920.0 MiB)
20:25:27.665 INFO BlockManagerInfo - Removed broadcast_54_piece0 on localhost:39477 in memory (size: 202.0 B, free: 1920.0 MiB)
20:25:27.685 INFO MemoryStore - Block broadcast_86 stored as values in memory (estimated size 297.3 KiB, free 1919.4 MiB)
20:25:27.692 INFO MemoryStore - Block broadcast_86_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1919.3 MiB)
20:25:27.693 INFO BlockManagerInfo - Added broadcast_86_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.9 MiB)
20:25:27.693 INFO SparkContext - Created broadcast 86 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.719 INFO MemoryStore - Block broadcast_87 stored as values in memory (estimated size 297.3 KiB, free 1919.0 MiB)
20:25:27.726 INFO MemoryStore - Block broadcast_87_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1919.0 MiB)
20:25:27.726 INFO BlockManagerInfo - Added broadcast_87_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.9 MiB)
20:25:27.727 INFO SparkContext - Created broadcast 87 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.750 INFO MemoryStore - Block broadcast_88 stored as values in memory (estimated size 528.0 B, free 1919.0 MiB)
20:25:27.751 INFO MemoryStore - Block broadcast_88_piece0 stored as bytes in memory (estimated size 183.0 B, free 1919.0 MiB)
20:25:27.751 INFO BlockManagerInfo - Added broadcast_88_piece0 in memory on localhost:39477 (size: 183.0 B, free: 1919.9 MiB)
20:25:27.751 INFO SparkContext - Created broadcast 88 from broadcast at CramSource.java:114
20:25:27.754 INFO MemoryStore - Block broadcast_89 stored as values in memory (estimated size 297.2 KiB, free 1918.7 MiB)
20:25:27.760 INFO MemoryStore - Block broadcast_89_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.6 MiB)
20:25:27.761 INFO BlockManagerInfo - Added broadcast_89_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.8 MiB)
20:25:27.761 INFO SparkContext - Created broadcast 89 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.778 INFO MemoryStore - Block broadcast_90 stored as values in memory (estimated size 600.0 B, free 1918.6 MiB)
20:25:27.779 INFO MemoryStore - Block broadcast_90_piece0 stored as bytes in memory (estimated size 202.0 B, free 1918.6 MiB)
20:25:27.779 INFO BlockManagerInfo - Added broadcast_90_piece0 in memory on localhost:39477 (size: 202.0 B, free: 1919.8 MiB)
20:25:27.779 INFO SparkContext - Created broadcast 90 from broadcast at CramSource.java:114
20:25:27.781 INFO MemoryStore - Block broadcast_91 stored as values in memory (estimated size 297.3 KiB, free 1918.4 MiB)
20:25:27.788 INFO MemoryStore - Block broadcast_91_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.3 MiB)
20:25:27.788 INFO BlockManagerInfo - Added broadcast_91_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.8 MiB)
20:25:27.788 INFO SparkContext - Created broadcast 91 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.806 INFO MemoryStore - Block broadcast_92 stored as values in memory (estimated size 297.3 KiB, free 1918.0 MiB)
20:25:27.813 INFO MemoryStore - Block broadcast_92_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.0 MiB)
20:25:27.814 INFO BlockManagerInfo - Added broadcast_92_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.7 MiB)
20:25:27.814 INFO SparkContext - Created broadcast 92 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.837 INFO FileInputFormat - Total input files to process : 1
20:25:27.874 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:163
20:25:27.875 INFO DAGScheduler - Got job 40 (collect at ReadsSparkSourceUnitTest.java:163) with 1 output partitions
20:25:27.875 INFO DAGScheduler - Final stage: ResultStage 49 (collect at ReadsSparkSourceUnitTest.java:163)
20:25:27.875 INFO DAGScheduler - Parents of final stage: List()
20:25:27.875 INFO DAGScheduler - Missing parents: List()
20:25:27.875 INFO DAGScheduler - Submitting ResultStage 49 (MapPartitionsRDD[224] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:27.894 INFO MemoryStore - Block broadcast_93 stored as values in memory (estimated size 425.0 KiB, free 1917.5 MiB)
20:25:27.895 INFO MemoryStore - Block broadcast_93_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.4 MiB)
20:25:27.896 INFO BlockManagerInfo - Added broadcast_93_piece0 in memory on localhost:39477 (size: 152.7 KiB, free: 1919.6 MiB)
20:25:27.896 INFO SparkContext - Created broadcast 93 from broadcast at DAGScheduler.scala:1580
20:25:27.896 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))
20:25:27.896 INFO TaskSchedulerImpl - Adding task set 49.0 with 1 tasks resource profile 0
20:25:27.897 INFO TaskSetManager - Starting task 0.0 in stage 49.0 (TID 118) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7875 bytes)
20:25:27.898 INFO Executor - Running task 0.0 in stage 49.0 (TID 118)
20:25:27.933 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam:0+221635
20:25:27.950 INFO Executor - Finished task 0.0 in stage 49.0 (TID 118). 650184 bytes result sent to driver
20:25:27.953 INFO TaskSetManager - Finished task 0.0 in stage 49.0 (TID 118) in 56 ms on localhost (executor driver) (1/1)
20:25:27.953 INFO TaskSchedulerImpl - Removed TaskSet 49.0, whose tasks have all completed, from pool
20:25:27.953 INFO DAGScheduler - ResultStage 49 (collect at ReadsSparkSourceUnitTest.java:163) finished in 0.077 s
20:25:27.953 INFO DAGScheduler - Job 40 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:27.953 INFO TaskSchedulerImpl - Killing all running tasks in stage 49: Stage finished
20:25:27.953 INFO DAGScheduler - Job 40 finished: collect at ReadsSparkSourceUnitTest.java:163, took 0.078873 s
20:25:27.958 INFO MemoryStore - Block broadcast_94 stored as values in memory (estimated size 208.0 B, free 1917.4 MiB)
20:25:27.960 INFO MemoryStore - Block broadcast_94_piece0 stored as bytes in memory (estimated size 239.0 B, free 1917.4 MiB)
20:25:27.960 INFO BlockManagerInfo - Added broadcast_94_piece0 in memory on localhost:39477 (size: 239.0 B, free: 1919.6 MiB)
20:25:27.960 INFO SparkContext - Created broadcast 94 from broadcast at AbstractBinarySamSource.java:82
20:25:27.962 INFO MemoryStore - Block broadcast_95 stored as values in memory (estimated size 297.2 KiB, free 1917.1 MiB)
20:25:27.969 INFO MemoryStore - Block broadcast_95_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.1 MiB)
20:25:27.969 INFO BlockManagerInfo - Added broadcast_95_piece0 in memory on localhost:39477 (size: 50.0 KiB, free: 1919.5 MiB)
20:25:27.970 INFO SparkContext - Created broadcast 95 from newAPIHadoopFile at PathSplitSource.java:96
20:25:27.992 INFO FileInputFormat - Total input files to process : 1
20:25:27.996 INFO SparkContext - Starting job: count at ReadsSparkSourceUnitTest.java:265
20:25:27.997 INFO DAGScheduler - Got job 41 (count at ReadsSparkSourceUnitTest.java:265) with 1 output partitions
20:25:27.997 INFO DAGScheduler - Final stage: ResultStage 50 (count at ReadsSparkSourceUnitTest.java:265)
20:25:27.997 INFO DAGScheduler - Parents of final stage: List()
20:25:27.997 INFO DAGScheduler - Missing parents: List()
20:25:27.997 INFO DAGScheduler - Submitting ResultStage 50 (MapPartitionsRDD[231] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:28.016 INFO MemoryStore - Block broadcast_96 stored as values in memory (estimated size 424.9 KiB, free 1916.6 MiB)
20:25:28.018 INFO MemoryStore - Block broadcast_96_piece0 stored as bytes in memory (estimated size 152.8 KiB, free 1916.5 MiB)
20:25:28.019 INFO BlockManagerInfo - Added broadcast_96_piece0 in memory on localhost:39477 (size: 152.8 KiB, free: 1919.4 MiB)
20:25:28.019 INFO SparkContext - Created broadcast 96 from broadcast at DAGScheduler.scala:1580
20:25:28.019 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))
20:25:28.019 INFO TaskSchedulerImpl - Adding task set 50.0 with 1 tasks resource profile 0
20:25:28.020 INFO TaskSetManager - Starting task 0.0 in stage 50.0 (TID 119) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes)
20:25:28.021 INFO Executor - Running task 0.0 in stage 50.0 (TID 119)
20:25:28.054 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
20:25:28.060 INFO Executor - Finished task 0.0 in stage 50.0 (TID 119). 989 bytes result sent to driver
20:25:28.060 INFO TaskSetManager - Finished task 0.0 in stage 50.0 (TID 119) in 40 ms on localhost (executor driver) (1/1)
20:25:28.060 INFO DAGScheduler - ResultStage 50 (count at ReadsSparkSourceUnitTest.java:265) finished in 0.063 s
20:25:28.061 INFO DAGScheduler - Job 41 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:28.061 INFO TaskSchedulerImpl - Removed TaskSet 50.0, whose tasks have all completed, from pool
20:25:28.061 INFO TaskSchedulerImpl - Killing all running tasks in stage 50: Stage finished
20:25:28.061 INFO DAGScheduler - Job 41 finished: count at ReadsSparkSourceUnitTest.java:265, took 0.064476 s
20:25:28.064 INFO MemoryStore - Block broadcast_97 stored as values in memory (estimated size 160.0 B, free 1916.5 MiB)
20:25:28.066 INFO MemoryStore - Block broadcast_97_piece0 stored as bytes in memory (estimated size 229.0 B, free 1916.5 MiB)
20:25:28.066 INFO BlockManagerInfo - Added broadcast_97_piece0 in memory on localhost:39477 (size: 229.0 B, free: 1919.4 MiB)
20:25:28.066 INFO SparkContext - Created broadcast 97 from broadcast at AbstractBinarySamSource.java:82
20:25:28.068 INFO MemoryStore - Block broadcast_98 stored as values in memory (estimated size 297.3 KiB, free 1916.2 MiB)
20:25:28.075 INFO MemoryStore - Block broadcast_98_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.2 MiB)
20:25:28.075 INFO BlockManagerInfo - Added broadcast_98_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.3 MiB)
20:25:28.076 INFO SparkContext - Created broadcast 98 from newAPIHadoopFile at PathSplitSource.java:96
20:25:28.102 INFO FileInputFormat - Total input files to process : 1
20:25:28.105 INFO SparkContext - Starting job: count at ReadsSparkSourceUnitTest.java:286
20:25:28.105 INFO DAGScheduler - Got job 42 (count at ReadsSparkSourceUnitTest.java:286) with 1 output partitions
20:25:28.105 INFO DAGScheduler - Final stage: ResultStage 51 (count at ReadsSparkSourceUnitTest.java:286)
20:25:28.105 INFO DAGScheduler - Parents of final stage: List()
20:25:28.105 INFO DAGScheduler - Missing parents: List()
20:25:28.106 INFO DAGScheduler - Submitting ResultStage 51 (MapPartitionsRDD[238] at filter at ReadsSparkSource.java:96), which has no missing parents
20:25:28.124 INFO MemoryStore - Block broadcast_99 stored as values in memory (estimated size 424.9 KiB, free 1915.7 MiB)
20:25:28.125 INFO MemoryStore - Block broadcast_99_piece0 stored as bytes in memory (estimated size 152.8 KiB, free 1915.6 MiB)
20:25:28.125 INFO BlockManagerInfo - Added broadcast_99_piece0 in memory on localhost:39477 (size: 152.8 KiB, free: 1919.2 MiB)
20:25:28.125 INFO SparkContext - Created broadcast 99 from broadcast at DAGScheduler.scala:1580
20:25:28.126 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))
20:25:28.126 INFO TaskSchedulerImpl - Adding task set 51.0 with 1 tasks resource profile 0
20:25:28.126 INFO TaskSetManager - Starting task 0.0 in stage 51.0 (TID 120) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7891 bytes)
20:25:28.127 INFO Executor - Running task 0.0 in stage 51.0 (TID 120)
20:25:28.159 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam:0+2184
20:25:28.165 INFO Executor - Finished task 0.0 in stage 51.0 (TID 120). 989 bytes result sent to driver
20:25:28.166 INFO TaskSetManager - Finished task 0.0 in stage 51.0 (TID 120) in 40 ms on localhost (executor driver) (1/1)
20:25:28.166 INFO TaskSchedulerImpl - Removed TaskSet 51.0, whose tasks have all completed, from pool
20:25:28.166 INFO DAGScheduler - ResultStage 51 (count at ReadsSparkSourceUnitTest.java:286) finished in 0.060 s
20:25:28.166 INFO DAGScheduler - Job 42 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:28.166 INFO TaskSchedulerImpl - Killing all running tasks in stage 51: Stage finished
20:25:28.166 INFO DAGScheduler - Job 42 finished: count at ReadsSparkSourceUnitTest.java:286, took 0.061505 s
20:25:28.171 INFO MemoryStore - Block broadcast_100 stored as values in memory (estimated size 297.3 KiB, free 1915.3 MiB)
20:25:28.177 INFO MemoryStore - Block broadcast_100_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1915.3 MiB)
20:25:28.177 INFO BlockManagerInfo - Added broadcast_100_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.1 MiB)
20:25:28.178 INFO SparkContext - Created broadcast 100 from newAPIHadoopFile at PathSplitSource.java:96
20:25:28.201 INFO MemoryStore - Block broadcast_101 stored as values in memory (estimated size 297.4 KiB, free 1915.0 MiB)
20:25:28.208 INFO MemoryStore - Block broadcast_101_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1914.9 MiB)
20:25:28.209 INFO BlockManagerInfo - Added broadcast_101_piece0 in memory on localhost:39477 (size: 50.1 KiB, free: 1919.1 MiB)
20:25:28.209 INFO SparkContext - Created broadcast 101 from newAPIHadoopFile at PathSplitSource.java:96
20:25:28.230 INFO FileInputFormat - Total input files to process : 1
20:25:28.230 INFO FileInputFormat - Total input files to process : 1