15:09:21.257 INFO BlockManagerInfo - Removed broadcast_6_piece0 on localhost:41569 in memory (size: 5.0 KiB, free: 1920.0 MiB)
15:09:21.261 INFO BlockManagerInfo - Removed broadcast_29_piece0 on localhost:41569 in memory (size: 3.8 KiB, free: 1920.0 MiB)
15:09:21.273 INFO BlockManager - Removing RDD 7
15:09:21.284 INFO BlockManagerInfo - Removed broadcast_10_piece0 on localhost:41569 in memory (size: 2.4 KiB, free: 1920.0 MiB)
15:09:21.289 INFO BlockManagerInfo - Removed broadcast_1_piece0 on localhost:41569 in memory (size: 143.0 B, free: 1920.0 MiB)
15:09:21.296 INFO BlockManagerInfo - Removed broadcast_26_piece0 on localhost:41569 in memory (size: 3.2 KiB, free: 1920.0 MiB)
15:09:21.307 INFO BlockManagerInfo - Removed broadcast_9_piece0 on localhost:41569 in memory (size: 4.7 KiB, free: 1920.0 MiB)
15:09:21.344 INFO BlockManagerInfo - Removed broadcast_17_piece0 on localhost:41569 in memory (size: 2.4 KiB, free: 1920.0 MiB)
15:09:21.351 INFO MemoryStore - Block broadcast_34 stored as values in memory (estimated size 297.2 KiB, free 1919.6 MiB)
15:09:21.351 INFO BlockManagerInfo - Removed broadcast_16_piece0 on localhost:41569 in memory (size: 2.4 KiB, free: 1920.0 MiB)
15:09:21.356 INFO BlockManagerInfo - Removed broadcast_15_piece0 on localhost:41569 in memory (size: 2.4 KiB, free: 1920.0 MiB)
15:09:21.360 INFO BlockManagerInfo - Removed broadcast_25_piece0 on localhost:41569 in memory (size: 4.5 KiB, free: 1920.0 MiB)
15:09:21.366 INFO BlockManagerInfo - Removed broadcast_5_piece0 on localhost:41569 in memory (size: 3.2 KiB, free: 1920.0 MiB)
15:09:21.381 INFO MemoryStore - Block broadcast_34_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1919.6 MiB)
15:09:21.381 INFO BlockManagerInfo - Added broadcast_34_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.9 MiB)
15:09:21.382 INFO SparkContext - Created broadcast 34 from newAPIHadoopFile at PathSplitSource.java:96
15:09:21.441 INFO MemoryStore - Block broadcast_35 stored as values in memory (estimated size 297.2 KiB, free 1919.3 MiB)
15:09:21.457 INFO MemoryStore - Block broadcast_35_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1919.3 MiB)
15:09:21.458 INFO BlockManagerInfo - Added broadcast_35_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.9 MiB)
15:09:21.458 INFO SparkContext - Created broadcast 35 from newAPIHadoopFile at PathSplitSource.java:96
15:09:21.504 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
15:09:21.505 INFO DAGScheduler - Got job 20 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
15:09:21.505 INFO DAGScheduler - Final stage: ResultStage 29 (collect at ReadsSparkSourceUnitTest.java:111)
15:09:21.505 INFO DAGScheduler - Parents of final stage: List()
15:09:21.505 INFO DAGScheduler - Missing parents: List()
15:09:21.505 INFO DAGScheduler - Submitting ResultStage 29 (ParallelCollectionRDD[69] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
15:09:21.506 INFO MemoryStore - Block broadcast_36 stored as values in memory (estimated size 3.0 KiB, free 1919.3 MiB)
15:09:21.507 INFO MemoryStore - Block broadcast_36_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1919.3 MiB)
15:09:21.507 INFO BlockManagerInfo - Added broadcast_36_piece0 in memory on localhost:41569 (size: 1780.0 B, free: 1919.9 MiB)
15:09:21.508 INFO SparkContext - Created broadcast 36 from broadcast at DAGScheduler.scala:1580
15:09:21.508 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))
15:09:21.508 INFO TaskSchedulerImpl - Adding task set 29.0 with 4 tasks resource profile 0
15:09:21.510 INFO TaskSetManager - Starting task 0.0 in stage 29.0 (TID 67) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes)
15:09:21.511 INFO TaskSetManager - Starting task 1.0 in stage 29.0 (TID 68) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes)
15:09:21.512 INFO TaskSetManager - Starting task 2.0 in stage 29.0 (TID 69) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes)
15:09:21.513 INFO TaskSetManager - Starting task 3.0 in stage 29.0 (TID 70) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes)
15:09:21.514 INFO Executor - Running task 1.0 in stage 29.0 (TID 68)
15:09:21.514 INFO Executor - Running task 0.0 in stage 29.0 (TID 67)
15:09:21.514 INFO Executor - Running task 3.0 in stage 29.0 (TID 70)
15:09:21.514 INFO Executor - Running task 2.0 in stage 29.0 (TID 69)
15:09:21.520 INFO Executor - Finished task 1.0 in stage 29.0 (TID 68). 40512 bytes result sent to driver
15:09:21.521 INFO Executor - Finished task 2.0 in stage 29.0 (TID 69). 40380 bytes result sent to driver
15:09:21.522 INFO Executor - Finished task 3.0 in stage 29.0 (TID 70). 40805 bytes result sent to driver
15:09:21.522 INFO TaskSetManager - Finished task 1.0 in stage 29.0 (TID 68) in 12 ms on localhost (executor driver) (1/4)
15:09:21.523 INFO TaskSetManager - Finished task 2.0 in stage 29.0 (TID 69) in 12 ms on localhost (executor driver) (2/4)
15:09:21.524 INFO Executor - Finished task 0.0 in stage 29.0 (TID 67). 40441 bytes result sent to driver
15:09:21.525 INFO TaskSetManager - Finished task 0.0 in stage 29.0 (TID 67) in 16 ms on localhost (executor driver) (3/4)
15:09:21.525 INFO TaskSetManager - Finished task 3.0 in stage 29.0 (TID 70) in 13 ms on localhost (executor driver) (4/4)
15:09:21.525 INFO TaskSchedulerImpl - Removed TaskSet 29.0, whose tasks have all completed, from pool
15:09:21.526 INFO DAGScheduler - ResultStage 29 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.021 s
15:09:21.526 INFO DAGScheduler - Job 20 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:21.526 INFO TaskSchedulerImpl - Killing all running tasks in stage 29: Stage finished
15:09:21.526 INFO DAGScheduler - Job 20 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.022043 s
15:09:21.542 INFO FileInputFormat - Total input files to process : 1
15:09:21.598 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
15:09:21.599 INFO DAGScheduler - Got job 21 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
15:09:21.599 INFO DAGScheduler - Final stage: ResultStage 30 (collect at ReadsSparkSourceUnitTest.java:112)
15:09:21.599 INFO DAGScheduler - Parents of final stage: List()
15:09:21.599 INFO DAGScheduler - Missing parents: List()
15:09:21.599 INFO DAGScheduler - Submitting ResultStage 30 (MapPartitionsRDD[76] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:21.626 INFO MemoryStore - Block broadcast_37 stored as values in memory (estimated size 425.0 KiB, free 1918.9 MiB)
15:09:21.628 INFO MemoryStore - Block broadcast_37_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1918.7 MiB)
15:09:21.628 INFO BlockManagerInfo - Added broadcast_37_piece0 in memory on localhost:41569 (size: 152.7 KiB, free: 1919.7 MiB)
15:09:21.629 INFO SparkContext - Created broadcast 37 from broadcast at DAGScheduler.scala:1580
15:09:21.629 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))
15:09:21.629 INFO TaskSchedulerImpl - Adding task set 30.0 with 1 tasks resource profile 0
15:09:21.635 INFO TaskSetManager - Starting task 0.0 in stage 30.0 (TID 71) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes)
15:09:21.636 INFO Executor - Running task 0.0 in stage 30.0 (TID 71)
15:09:21.711 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
15:09:21.727 INFO Executor - Finished task 0.0 in stage 30.0 (TID 71). 159615 bytes result sent to driver
15:09:21.729 INFO TaskSetManager - Finished task 0.0 in stage 30.0 (TID 71) in 99 ms on localhost (executor driver) (1/1)
15:09:21.729 INFO TaskSchedulerImpl - Removed TaskSet 30.0, whose tasks have all completed, from pool
15:09:21.730 INFO DAGScheduler - ResultStage 30 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.129 s
15:09:21.730 INFO DAGScheduler - Job 21 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:21.730 INFO TaskSchedulerImpl - Killing all running tasks in stage 30: Stage finished
15:09:21.730 INFO DAGScheduler - Job 21 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.131951 s
15:09:21.742 INFO MemoryStore - Block broadcast_38 stored as values in memory (estimated size 297.3 KiB, free 1918.4 MiB)
15:09:21.757 INFO MemoryStore - Block broadcast_38_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.4 MiB)
15:09:21.758 INFO BlockManagerInfo - Added broadcast_38_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.7 MiB)
15:09:21.758 INFO SparkContext - Created broadcast 38 from newAPIHadoopFile at PathSplitSource.java:96
15:09:21.814 INFO MemoryStore - Block broadcast_39 stored as values in memory (estimated size 297.3 KiB, free 1918.1 MiB)
15:09:21.823 INFO MemoryStore - Block broadcast_39_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.0 MiB)
15:09:21.824 INFO BlockManagerInfo - Added broadcast_39_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.6 MiB)
15:09:21.824 INFO SparkContext - Created broadcast 39 from newAPIHadoopFile at PathSplitSource.java:96
15:09:21.863 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
15:09:21.863 INFO DAGScheduler - Got job 22 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
15:09:21.863 INFO DAGScheduler - Final stage: ResultStage 31 (collect at ReadsSparkSourceUnitTest.java:111)
15:09:21.863 INFO DAGScheduler - Parents of final stage: List()
15:09:21.864 INFO DAGScheduler - Missing parents: List()
15:09:21.864 INFO DAGScheduler - Submitting ResultStage 31 (ParallelCollectionRDD[82] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
15:09:21.865 INFO MemoryStore - Block broadcast_40 stored as values in memory (estimated size 3.0 KiB, free 1918.0 MiB)
15:09:21.867 INFO MemoryStore - Block broadcast_40_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1918.0 MiB)
15:09:21.868 INFO BlockManagerInfo - Added broadcast_40_piece0 in memory on localhost:41569 (size: 1780.0 B, free: 1919.6 MiB)
15:09:21.868 INFO SparkContext - Created broadcast 40 from broadcast at DAGScheduler.scala:1580
15:09:21.868 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))
15:09:21.868 INFO TaskSchedulerImpl - Adding task set 31.0 with 4 tasks resource profile 0
15:09:21.870 INFO TaskSetManager - Starting task 0.0 in stage 31.0 (TID 72) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes)
15:09:21.871 INFO TaskSetManager - Starting task 1.0 in stage 31.0 (TID 73) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes)
15:09:21.872 INFO TaskSetManager - Starting task 2.0 in stage 31.0 (TID 74) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes)
15:09:21.873 INFO TaskSetManager - Starting task 3.0 in stage 31.0 (TID 75) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes)
15:09:21.873 INFO Executor - Running task 0.0 in stage 31.0 (TID 72)
15:09:21.873 INFO Executor - Running task 1.0 in stage 31.0 (TID 73)
15:09:21.874 INFO Executor - Running task 2.0 in stage 31.0 (TID 74)
15:09:21.878 INFO Executor - Running task 3.0 in stage 31.0 (TID 75)
15:09:21.883 INFO Executor - Finished task 0.0 in stage 31.0 (TID 72). 163247 bytes result sent to driver
15:09:21.884 INFO Executor - Finished task 2.0 in stage 31.0 (TID 74). 163442 bytes result sent to driver
15:09:21.885 INFO Executor - Finished task 3.0 in stage 31.0 (TID 75). 162737 bytes result sent to driver
15:09:21.886 INFO TaskSetManager - Finished task 0.0 in stage 31.0 (TID 72) in 17 ms on localhost (executor driver) (1/4)
15:09:21.887 INFO Executor - Finished task 1.0 in stage 31.0 (TID 73). 163411 bytes result sent to driver
15:09:21.888 INFO TaskSetManager - Finished task 2.0 in stage 31.0 (TID 74) in 17 ms on localhost (executor driver) (2/4)
15:09:21.889 INFO TaskSetManager - Finished task 1.0 in stage 31.0 (TID 73) in 19 ms on localhost (executor driver) (3/4)
15:09:21.889 INFO TaskSetManager - Finished task 3.0 in stage 31.0 (TID 75) in 17 ms on localhost (executor driver) (4/4)
15:09:21.890 INFO DAGScheduler - ResultStage 31 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.026 s
15:09:21.890 INFO DAGScheduler - Job 22 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:21.890 INFO TaskSchedulerImpl - Removed TaskSet 31.0, whose tasks have all completed, from pool
15:09:21.890 INFO TaskSchedulerImpl - Killing all running tasks in stage 31: Stage finished
15:09:21.890 INFO DAGScheduler - Job 22 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.027065 s
15:09:21.892 INFO FileInputFormat - Total input files to process : 1
15:09:21.951 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
15:09:21.951 INFO DAGScheduler - Got job 23 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
15:09:21.951 INFO DAGScheduler - Final stage: ResultStage 32 (collect at ReadsSparkSourceUnitTest.java:112)
15:09:21.952 INFO DAGScheduler - Parents of final stage: List()
15:09:21.952 INFO DAGScheduler - Missing parents: List()
15:09:21.952 INFO DAGScheduler - Submitting ResultStage 32 (MapPartitionsRDD[89] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:21.977 INFO MemoryStore - Block broadcast_41 stored as values in memory (estimated size 425.0 KiB, free 1917.6 MiB)
15:09:21.978 INFO MemoryStore - Block broadcast_41_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.5 MiB)
15:09:21.979 INFO BlockManagerInfo - Added broadcast_41_piece0 in memory on localhost:41569 (size: 152.7 KiB, free: 1919.5 MiB)
15:09:21.979 INFO SparkContext - Created broadcast 41 from broadcast at DAGScheduler.scala:1580
15:09:21.979 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))
15:09:21.979 INFO TaskSchedulerImpl - Adding task set 32.0 with 1 tasks resource profile 0
15:09:21.980 INFO TaskSetManager - Starting task 0.0 in stage 32.0 (TID 76) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7875 bytes)
15:09:21.981 INFO Executor - Running task 0.0 in stage 32.0 (TID 76)
15:09:22.026 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam:0+221635
15:09:22.063 INFO Executor - Finished task 0.0 in stage 32.0 (TID 76). 650184 bytes result sent to driver
15:09:22.069 INFO TaskSetManager - Finished task 0.0 in stage 32.0 (TID 76) in 89 ms on localhost (executor driver) (1/1)
15:09:22.069 INFO TaskSchedulerImpl - Removed TaskSet 32.0, whose tasks have all completed, from pool
15:09:22.069 INFO DAGScheduler - ResultStage 32 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.117 s
15:09:22.070 INFO DAGScheduler - Job 23 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:22.070 INFO TaskSchedulerImpl - Killing all running tasks in stage 32: Stage finished
15:09:22.070 INFO DAGScheduler - Job 23 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.118816 s
15:09:22.080 INFO MemoryStore - Block broadcast_42 stored as values in memory (estimated size 297.3 KiB, free 1917.2 MiB)
15:09:22.098 INFO MemoryStore - Block broadcast_42_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.1 MiB)
15:09:22.098 INFO BlockManagerInfo - Added broadcast_42_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.4 MiB)
15:09:22.099 INFO SparkContext - Created broadcast 42 from newAPIHadoopFile at PathSplitSource.java:96
15:09:22.144 INFO MemoryStore - Block broadcast_43 stored as values in memory (estimated size 297.3 KiB, free 1916.8 MiB)
15:09:22.156 INFO MemoryStore - Block broadcast_43_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.8 MiB)
15:09:22.156 INFO BlockManagerInfo - Added broadcast_43_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.4 MiB)
15:09:22.157 INFO SparkContext - Created broadcast 43 from newAPIHadoopFile at PathSplitSource.java:96
15:09:22.199 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
15:09:22.199 INFO DAGScheduler - Got job 24 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
15:09:22.199 INFO DAGScheduler - Final stage: ResultStage 33 (collect at ReadsSparkSourceUnitTest.java:111)
15:09:22.199 INFO DAGScheduler - Parents of final stage: List()
15:09:22.199 INFO DAGScheduler - Missing parents: List()
15:09:22.200 INFO DAGScheduler - Submitting ResultStage 33 (ParallelCollectionRDD[95] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
15:09:22.201 INFO MemoryStore - Block broadcast_44 stored as values in memory (estimated size 3.0 KiB, free 1916.8 MiB)
15:09:22.202 INFO MemoryStore - Block broadcast_44_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1916.8 MiB)
15:09:22.202 INFO BlockManagerInfo - Added broadcast_44_piece0 in memory on localhost:41569 (size: 1780.0 B, free: 1919.4 MiB)
15:09:22.202 INFO SparkContext - Created broadcast 44 from broadcast at DAGScheduler.scala:1580
15:09:22.203 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))
15:09:22.203 INFO TaskSchedulerImpl - Adding task set 33.0 with 4 tasks resource profile 0
15:09:22.205 INFO TaskSetManager - Starting task 0.0 in stage 33.0 (TID 77) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes)
15:09:22.207 INFO TaskSetManager - Starting task 1.0 in stage 33.0 (TID 78) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes)
15:09:22.208 INFO TaskSetManager - Starting task 2.0 in stage 33.0 (TID 79) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes)
15:09:22.209 INFO TaskSetManager - Starting task 3.0 in stage 33.0 (TID 80) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes)
15:09:22.209 INFO Executor - Running task 2.0 in stage 33.0 (TID 79)
15:09:22.209 INFO Executor - Running task 1.0 in stage 33.0 (TID 78)
15:09:22.209 INFO Executor - Running task 3.0 in stage 33.0 (TID 80)
15:09:22.210 INFO Executor - Running task 0.0 in stage 33.0 (TID 77)
15:09:22.215 INFO Executor - Finished task 1.0 in stage 33.0 (TID 78). 163411 bytes result sent to driver
15:09:22.216 INFO Executor - Finished task 3.0 in stage 33.0 (TID 80). 162737 bytes result sent to driver
15:09:22.217 INFO Executor - Finished task 2.0 in stage 33.0 (TID 79). 163399 bytes result sent to driver
15:09:22.218 INFO TaskSetManager - Finished task 1.0 in stage 33.0 (TID 78) in 13 ms on localhost (executor driver) (1/4)
15:09:22.219 INFO TaskSetManager - Finished task 3.0 in stage 33.0 (TID 80) in 11 ms on localhost (executor driver) (2/4)
15:09:22.220 INFO TaskSetManager - Finished task 2.0 in stage 33.0 (TID 79) in 13 ms on localhost (executor driver) (3/4)
15:09:22.223 INFO Executor - Finished task 0.0 in stage 33.0 (TID 77). 163161 bytes result sent to driver
15:09:22.224 INFO TaskSetManager - Finished task 0.0 in stage 33.0 (TID 77) in 21 ms on localhost (executor driver) (4/4)
15:09:22.224 INFO TaskSchedulerImpl - Removed TaskSet 33.0, whose tasks have all completed, from pool
15:09:22.224 INFO DAGScheduler - ResultStage 33 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.024 s
15:09:22.224 INFO DAGScheduler - Job 24 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:22.224 INFO TaskSchedulerImpl - Killing all running tasks in stage 33: Stage finished
15:09:22.224 INFO DAGScheduler - Job 24 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.025098 s
15:09:22.226 INFO FileInputFormat - Total input files to process : 1
15:09:22.286 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
15:09:22.287 INFO DAGScheduler - Got job 25 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
15:09:22.287 INFO DAGScheduler - Final stage: ResultStage 34 (collect at ReadsSparkSourceUnitTest.java:112)
15:09:22.287 INFO DAGScheduler - Parents of final stage: List()
15:09:22.287 INFO DAGScheduler - Missing parents: List()
15:09:22.287 INFO DAGScheduler - Submitting ResultStage 34 (MapPartitionsRDD[102] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:22.320 INFO MemoryStore - Block broadcast_45 stored as values in memory (estimated size 425.0 KiB, free 1916.4 MiB)
15:09:22.323 INFO MemoryStore - Block broadcast_45_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1916.2 MiB)
15:09:22.323 INFO BlockManagerInfo - Added broadcast_45_piece0 in memory on localhost:41569 (size: 152.7 KiB, free: 1919.2 MiB)
15:09:22.323 INFO SparkContext - Created broadcast 45 from broadcast at DAGScheduler.scala:1580
15:09:22.324 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))
15:09:22.324 INFO TaskSchedulerImpl - Adding task set 34.0 with 1 tasks resource profile 0
15:09:22.325 INFO TaskSetManager - Starting task 0.0 in stage 34.0 (TID 81) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7905 bytes)
15:09:22.325 INFO Executor - Running task 0.0 in stage 34.0 (TID 81)
15:09:22.370 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
15:09:22.398 INFO Executor - Finished task 0.0 in stage 34.0 (TID 81). 650184 bytes result sent to driver
15:09:22.400 INFO TaskSetManager - Finished task 0.0 in stage 34.0 (TID 81) in 75 ms on localhost (executor driver) (1/1)
15:09:22.400 INFO TaskSchedulerImpl - Removed TaskSet 34.0, whose tasks have all completed, from pool
15:09:22.401 INFO DAGScheduler - ResultStage 34 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.113 s
15:09:22.401 INFO DAGScheduler - Job 25 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:22.401 INFO TaskSchedulerImpl - Killing all running tasks in stage 34: Stage finished
15:09:22.401 INFO DAGScheduler - Job 25 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.115014 s
15:09:22.409 INFO MemoryStore - Block broadcast_46 stored as values in memory (estimated size 528.0 B, free 1916.2 MiB)
15:09:22.410 INFO MemoryStore - Block broadcast_46_piece0 stored as bytes in memory (estimated size 183.0 B, free 1916.2 MiB)
15:09:22.410 INFO BlockManagerInfo - Added broadcast_46_piece0 in memory on localhost:41569 (size: 183.0 B, free: 1919.2 MiB)
15:09:22.411 INFO SparkContext - Created broadcast 46 from broadcast at CramSource.java:114
15:09:22.415 INFO MemoryStore - Block broadcast_47 stored as values in memory (estimated size 297.2 KiB, free 1915.9 MiB)
15:09:22.423 INFO MemoryStore - Block broadcast_47_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.9 MiB)
15:09:22.423 INFO BlockManagerInfo - Added broadcast_47_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.2 MiB)
15:09:22.424 INFO SparkContext - Created broadcast 47 from newAPIHadoopFile at PathSplitSource.java:96
15:09:22.460 INFO BlockManagerInfo - Removed broadcast_41_piece0 on localhost:41569 in memory (size: 152.7 KiB, free: 1919.3 MiB)
15:09:22.463 INFO BlockManagerInfo - Removed broadcast_30_piece0 on localhost:41569 in memory (size: 4.7 KiB, free: 1919.3 MiB)
15:09:22.464 INFO BlockManagerInfo - Removed broadcast_39_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.4 MiB)
15:09:22.466 INFO BlockManagerInfo - Removed broadcast_45_piece0 on localhost:41569 in memory (size: 152.7 KiB, free: 1919.5 MiB)
15:09:22.467 INFO BlockManagerInfo - Removed broadcast_23_piece0 on localhost:41569 in memory (size: 465.0 B, free: 1919.5 MiB)
15:09:22.470 INFO BlockManagerInfo - Removed broadcast_44_piece0 on localhost:41569 in memory (size: 1780.0 B, free: 1919.5 MiB)
15:09:22.472 INFO BlockManager - Removing RDD 47
15:09:22.474 INFO BlockManagerInfo - Removed broadcast_28_piece0 on localhost:41569 in memory (size: 320.0 B, free: 1919.5 MiB)
15:09:22.474 INFO MemoryStore - Block broadcast_48 stored as values in memory (estimated size 528.0 B, free 1917.4 MiB)
15:09:22.475 INFO MemoryStore - Block broadcast_48_piece0 stored as bytes in memory (estimated size 183.0 B, free 1917.4 MiB)
15:09:22.475 INFO BlockManagerInfo - Added broadcast_48_piece0 in memory on localhost:41569 (size: 183.0 B, free: 1919.5 MiB)
15:09:22.476 INFO SparkContext - Created broadcast 48 from broadcast at CramSource.java:114
15:09:22.477 INFO BlockManagerInfo - Removed broadcast_43_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.6 MiB)
15:09:22.480 INFO BlockManagerInfo - Removed broadcast_36_piece0 on localhost:41569 in memory (size: 1780.0 B, free: 1919.6 MiB)
15:09:22.480 INFO MemoryStore - Block broadcast_49 stored as values in memory (estimated size 297.2 KiB, free 1917.4 MiB)
15:09:22.482 INFO BlockManagerInfo - Removed broadcast_47_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.6 MiB)
15:09:22.483 INFO BlockManagerInfo - Removed broadcast_38_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.7 MiB)
15:09:22.485 INFO BlockManagerInfo - Removed broadcast_32_piece0 on localhost:41569 in memory (size: 3.8 KiB, free: 1919.7 MiB)
15:09:22.487 INFO BlockManagerInfo - Removed broadcast_42_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.7 MiB)
15:09:22.489 INFO BlockManagerInfo - Removed broadcast_40_piece0 on localhost:41569 in memory (size: 1780.0 B, free: 1919.7 MiB)
15:09:22.490 INFO BlockManagerInfo - Removed broadcast_37_piece0 on localhost:41569 in memory (size: 152.7 KiB, free: 1919.9 MiB)
15:09:22.492 INFO BlockManagerInfo - Removed broadcast_35_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.9 MiB)
15:09:22.494 INFO BlockManagerInfo - Removed broadcast_31_piece0 on localhost:41569 in memory (size: 320.0 B, free: 1919.9 MiB)
15:09:22.494 INFO MemoryStore - Block broadcast_49_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1919.3 MiB)
15:09:22.495 INFO BlockManagerInfo - Removed broadcast_33_piece0 on localhost:41569 in memory (size: 4.8 KiB, free: 1920.0 MiB)
15:09:22.495 INFO BlockManagerInfo - Added broadcast_49_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.9 MiB)
15:09:22.496 INFO SparkContext - Created broadcast 49 from newAPIHadoopFile at PathSplitSource.java:96
15:09:22.496 INFO BlockManagerInfo - Removed broadcast_46_piece0 on localhost:41569 in memory (size: 183.0 B, free: 1919.9 MiB)
15:09:22.498 INFO BlockManagerInfo - Removed broadcast_22_piece0 on localhost:41569 in memory (size: 159.0 B, free: 1919.9 MiB)
15:09:22.499 INFO BlockManagerInfo - Removed broadcast_34_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1920.0 MiB)
15:09:22.525 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
15:09:22.526 INFO DAGScheduler - Got job 26 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
15:09:22.526 INFO DAGScheduler - Final stage: ResultStage 35 (collect at ReadsSparkSourceUnitTest.java:111)
15:09:22.526 INFO DAGScheduler - Parents of final stage: List()
15:09:22.526 INFO DAGScheduler - Missing parents: List()
15:09:22.527 INFO DAGScheduler - Submitting ResultStage 35 (ParallelCollectionRDD[107] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
15:09:22.528 INFO MemoryStore - Block broadcast_50 stored as values in memory (estimated size 3.0 KiB, free 1919.7 MiB)
15:09:22.529 INFO MemoryStore - Block broadcast_50_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1919.7 MiB)
15:09:22.529 INFO BlockManagerInfo - Added broadcast_50_piece0 in memory on localhost:41569 (size: 1780.0 B, free: 1919.9 MiB)
15:09:22.529 INFO SparkContext - Created broadcast 50 from broadcast at DAGScheduler.scala:1580
15:09:22.530 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))
15:09:22.530 INFO TaskSchedulerImpl - Adding task set 35.0 with 4 tasks resource profile 0
15:09:22.535 INFO TaskSetManager - Starting task 0.0 in stage 35.0 (TID 82) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes)
15:09:22.538 INFO TaskSetManager - Starting task 1.0 in stage 35.0 (TID 83) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes)
15:09:22.540 INFO TaskSetManager - Starting task 2.0 in stage 35.0 (TID 84) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes)
15:09:22.541 INFO TaskSetManager - Starting task 3.0 in stage 35.0 (TID 85) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes)
15:09:22.542 INFO Executor - Running task 1.0 in stage 35.0 (TID 83)
15:09:22.542 INFO Executor - Running task 2.0 in stage 35.0 (TID 84)
15:09:22.542 INFO Executor - Running task 0.0 in stage 35.0 (TID 82)
15:09:22.544 INFO Executor - Running task 3.0 in stage 35.0 (TID 85)
15:09:22.546 INFO Executor - Finished task 1.0 in stage 35.0 (TID 83). 39130 bytes result sent to driver
15:09:22.546 INFO Executor - Finished task 2.0 in stage 35.0 (TID 84). 39070 bytes result sent to driver
15:09:22.546 INFO Executor - Finished task 3.0 in stage 35.0 (TID 85). 39343 bytes result sent to driver
15:09:22.547 INFO TaskSetManager - Finished task 2.0 in stage 35.0 (TID 84) in 9 ms on localhost (executor driver) (1/4)
15:09:22.547 INFO Executor - Finished task 0.0 in stage 35.0 (TID 82). 38950 bytes result sent to driver
15:09:22.547 INFO TaskSetManager - Finished task 3.0 in stage 35.0 (TID 85) in 7 ms on localhost (executor driver) (2/4)
15:09:22.549 INFO TaskSetManager - Finished task 1.0 in stage 35.0 (TID 83) in 14 ms on localhost (executor driver) (3/4)
15:09:22.549 INFO TaskSetManager - Finished task 0.0 in stage 35.0 (TID 82) in 18 ms on localhost (executor driver) (4/4)
15:09:22.549 INFO TaskSchedulerImpl - Removed TaskSet 35.0, whose tasks have all completed, from pool
15:09:22.549 INFO DAGScheduler - ResultStage 35 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.021 s
15:09:22.549 INFO DAGScheduler - Job 26 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:22.549 INFO TaskSchedulerImpl - Killing all running tasks in stage 35: Stage finished
15:09:22.549 INFO DAGScheduler - Job 26 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.023804 s
15:09:22.551 INFO FileInputFormat - Total input files to process : 1
15:09:22.586 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
15:09:22.587 INFO DAGScheduler - Got job 27 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
15:09:22.587 INFO DAGScheduler - Final stage: ResultStage 36 (collect at ReadsSparkSourceUnitTest.java:112)
15:09:22.587 INFO DAGScheduler - Parents of final stage: List()
15:09:22.587 INFO DAGScheduler - Missing parents: List()
15:09:22.587 INFO DAGScheduler - Submitting ResultStage 36 (MapPartitionsRDD[113] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:22.612 INFO MemoryStore - Block broadcast_51 stored as values in memory (estimated size 286.0 KiB, free 1919.4 MiB)
15:09:22.614 INFO MemoryStore - Block broadcast_51_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1919.3 MiB)
15:09:22.614 INFO BlockManagerInfo - Added broadcast_51_piece0 in memory on localhost:41569 (size: 103.1 KiB, free: 1919.8 MiB)
15:09:22.614 INFO SparkContext - Created broadcast 51 from broadcast at DAGScheduler.scala:1580
15:09:22.615 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))
15:09:22.615 INFO TaskSchedulerImpl - Adding task set 36.0 with 1 tasks resource profile 0
15:09:22.616 INFO TaskSetManager - Starting task 0.0 in stage 36.0 (TID 86) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes)
15:09:22.616 INFO Executor - Running task 0.0 in stage 36.0 (TID 86)
15:09:22.647 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram:0+50619
15:09:22.668 INFO Executor - Finished task 0.0 in stage 36.0 (TID 86). 154101 bytes result sent to driver
15:09:22.669 INFO TaskSetManager - Finished task 0.0 in stage 36.0 (TID 86) in 53 ms on localhost (executor driver) (1/1)
15:09:22.669 INFO TaskSchedulerImpl - Removed TaskSet 36.0, whose tasks have all completed, from pool
15:09:22.670 INFO DAGScheduler - ResultStage 36 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.081 s
15:09:22.670 INFO DAGScheduler - Job 27 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:22.670 INFO TaskSchedulerImpl - Killing all running tasks in stage 36: Stage finished
15:09:22.670 INFO DAGScheduler - Job 27 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.083665 s
15:09:22.676 INFO MemoryStore - Block broadcast_52 stored as values in memory (estimated size 600.0 B, free 1919.3 MiB)
15:09:22.677 INFO MemoryStore - Block broadcast_52_piece0 stored as bytes in memory (estimated size 202.0 B, free 1919.3 MiB)
15:09:22.677 INFO BlockManagerInfo - Added broadcast_52_piece0 in memory on localhost:41569 (size: 202.0 B, free: 1919.8 MiB)
15:09:22.677 INFO SparkContext - Created broadcast 52 from broadcast at CramSource.java:114
15:09:22.681 INFO MemoryStore - Block broadcast_53 stored as values in memory (estimated size 297.3 KiB, free 1919.0 MiB)
15:09:22.689 INFO MemoryStore - Block broadcast_53_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.9 MiB)
15:09:22.689 INFO BlockManagerInfo - Added broadcast_53_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.8 MiB)
15:09:22.689 INFO SparkContext - Created broadcast 53 from newAPIHadoopFile at PathSplitSource.java:96
15:09:22.717 INFO MemoryStore - Block broadcast_54 stored as values in memory (estimated size 600.0 B, free 1918.9 MiB)
15:09:22.718 INFO MemoryStore - Block broadcast_54_piece0 stored as bytes in memory (estimated size 202.0 B, free 1918.9 MiB)
15:09:22.719 INFO BlockManagerInfo - Added broadcast_54_piece0 in memory on localhost:41569 (size: 202.0 B, free: 1919.8 MiB)
15:09:22.719 INFO SparkContext - Created broadcast 54 from broadcast at CramSource.java:114
15:09:22.722 INFO MemoryStore - Block broadcast_55 stored as values in memory (estimated size 297.3 KiB, free 1918.6 MiB)
15:09:22.731 INFO MemoryStore - Block broadcast_55_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.6 MiB)
15:09:22.732 INFO BlockManagerInfo - Added broadcast_55_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.8 MiB)
15:09:22.732 INFO SparkContext - Created broadcast 55 from newAPIHadoopFile at PathSplitSource.java:96
15:09:22.763 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
15:09:22.764 INFO DAGScheduler - Got job 28 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
15:09:22.764 INFO DAGScheduler - Final stage: ResultStage 37 (collect at ReadsSparkSourceUnitTest.java:111)
15:09:22.764 INFO DAGScheduler - Parents of final stage: List()
15:09:22.764 INFO DAGScheduler - Missing parents: List()
15:09:22.764 INFO DAGScheduler - Submitting ResultStage 37 (ParallelCollectionRDD[118] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
15:09:22.765 INFO MemoryStore - Block broadcast_56 stored as values in memory (estimated size 3.0 KiB, free 1918.6 MiB)
15:09:22.766 INFO MemoryStore - Block broadcast_56_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1918.6 MiB)
15:09:22.766 INFO BlockManagerInfo - Added broadcast_56_piece0 in memory on localhost:41569 (size: 1780.0 B, free: 1919.7 MiB)
15:09:22.766 INFO SparkContext - Created broadcast 56 from broadcast at DAGScheduler.scala:1580
15:09:22.767 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))
15:09:22.767 INFO TaskSchedulerImpl - Adding task set 37.0 with 4 tasks resource profile 0
15:09:22.768 INFO TaskSetManager - Starting task 0.0 in stage 37.0 (TID 87) (localhost, executor driver, partition 0, PROCESS_LOCAL, 8303 bytes)
15:09:22.768 INFO TaskSetManager - Starting task 1.0 in stage 37.0 (TID 88) (localhost, executor driver, partition 1, PROCESS_LOCAL, 8292 bytes)
15:09:22.769 INFO TaskSetManager - Starting task 2.0 in stage 37.0 (TID 89) (localhost, executor driver, partition 2, PROCESS_LOCAL, 8292 bytes)
15:09:22.769 INFO TaskSetManager - Starting task 3.0 in stage 37.0 (TID 90) (localhost, executor driver, partition 3, PROCESS_LOCAL, 8184 bytes)
15:09:22.769 INFO Executor - Running task 0.0 in stage 37.0 (TID 87)
15:09:22.772 INFO Executor - Finished task 0.0 in stage 37.0 (TID 87). 1578 bytes result sent to driver
15:09:22.772 INFO Executor - Running task 1.0 in stage 37.0 (TID 88)
15:09:22.773 INFO Executor - Running task 2.0 in stage 37.0 (TID 89)
15:09:22.773 INFO Executor - Finished task 1.0 in stage 37.0 (TID 88). 1524 bytes result sent to driver
15:09:22.774 INFO Executor - Running task 3.0 in stage 37.0 (TID 90)
15:09:22.774 INFO TaskSetManager - Finished task 0.0 in stage 37.0 (TID 87) in 6 ms on localhost (executor driver) (1/4)
15:09:22.775 INFO TaskSetManager - Finished task 1.0 in stage 37.0 (TID 88) in 7 ms on localhost (executor driver) (2/4)
15:09:22.776 INFO Executor - Finished task 2.0 in stage 37.0 (TID 89). 1567 bytes result sent to driver
15:09:22.776 INFO Executor - Finished task 3.0 in stage 37.0 (TID 90). 1416 bytes result sent to driver
15:09:22.778 INFO TaskSetManager - Finished task 2.0 in stage 37.0 (TID 89) in 9 ms on localhost (executor driver) (3/4)
15:09:22.778 INFO TaskSetManager - Finished task 3.0 in stage 37.0 (TID 90) in 9 ms on localhost (executor driver) (4/4)
15:09:22.779 INFO DAGScheduler - ResultStage 37 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.014 s
15:09:22.779 INFO DAGScheduler - Job 28 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:22.779 INFO TaskSchedulerImpl - Removed TaskSet 37.0, whose tasks have all completed, from pool
15:09:22.779 INFO TaskSchedulerImpl - Killing all running tasks in stage 37: Stage finished
15:09:22.780 INFO DAGScheduler - Job 28 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.016313 s
15:09:22.781 INFO FileInputFormat - Total input files to process : 1
15:09:22.844 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
15:09:22.845 INFO DAGScheduler - Got job 29 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
15:09:22.845 INFO DAGScheduler - Final stage: ResultStage 38 (collect at ReadsSparkSourceUnitTest.java:112)
15:09:22.845 INFO DAGScheduler - Parents of final stage: List()
15:09:22.845 INFO DAGScheduler - Missing parents: List()
15:09:22.845 INFO DAGScheduler - Submitting ResultStage 38 (MapPartitionsRDD[124] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:22.872 INFO MemoryStore - Block broadcast_57 stored as values in memory (estimated size 286.0 KiB, free 1918.3 MiB)
15:09:22.874 INFO MemoryStore - Block broadcast_57_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1918.2 MiB)
15:09:22.874 INFO BlockManagerInfo - Added broadcast_57_piece0 in memory on localhost:41569 (size: 103.1 KiB, free: 1919.6 MiB)
15:09:22.875 INFO SparkContext - Created broadcast 57 from broadcast at DAGScheduler.scala:1580
15:09:22.875 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))
15:09:22.875 INFO TaskSchedulerImpl - Adding task set 38.0 with 1 tasks resource profile 0
15:09:22.876 INFO TaskSetManager - Starting task 0.0 in stage 38.0 (TID 91) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7844 bytes)
15:09:22.877 INFO Executor - Running task 0.0 in stage 38.0 (TID 91)
15:09:22.922 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/valid.cram:0+13330
15:09:22.929 INFO Executor - Finished task 0.0 in stage 38.0 (TID 91). 3736 bytes result sent to driver
15:09:22.930 INFO TaskSetManager - Finished task 0.0 in stage 38.0 (TID 91) in 54 ms on localhost (executor driver) (1/1)
15:09:22.930 INFO TaskSchedulerImpl - Removed TaskSet 38.0, whose tasks have all completed, from pool
15:09:22.930 INFO DAGScheduler - ResultStage 38 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.084 s
15:09:22.930 INFO DAGScheduler - Job 29 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:22.930 INFO TaskSchedulerImpl - Killing all running tasks in stage 38: Stage finished
15:09:22.930 INFO DAGScheduler - Job 29 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.085987 s
15:09:22.938 INFO MemoryStore - Block broadcast_58 stored as values in memory (estimated size 297.2 KiB, free 1917.9 MiB)
15:09:22.952 INFO MemoryStore - Block broadcast_58_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.9 MiB)
15:09:22.952 INFO BlockManagerInfo - Added broadcast_58_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.6 MiB)
15:09:22.953 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
15:09:23.009 INFO MemoryStore - Block broadcast_59 stored as values in memory (estimated size 297.2 KiB, free 1917.6 MiB)
15:09:23.022 INFO MemoryStore - Block broadcast_59_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.5 MiB)
15:09:23.022 INFO BlockManagerInfo - Added broadcast_59_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.6 MiB)
15:09:23.022 INFO SparkContext - Created broadcast 59 from newAPIHadoopFile at PathSplitSource.java:96
15:09:23.063 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
15:09:23.064 INFO DAGScheduler - Got job 30 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
15:09:23.064 INFO DAGScheduler - Final stage: ResultStage 39 (collect at ReadsSparkSourceUnitTest.java:111)
15:09:23.064 INFO DAGScheduler - Parents of final stage: List()
15:09:23.064 INFO DAGScheduler - Missing parents: List()
15:09:23.064 INFO DAGScheduler - Submitting ResultStage 39 (ParallelCollectionRDD[130] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
15:09:23.065 INFO MemoryStore - Block broadcast_60 stored as values in memory (estimated size 3.0 KiB, free 1917.5 MiB)
15:09:23.067 INFO MemoryStore - Block broadcast_60_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1917.5 MiB)
15:09:23.067 INFO BlockManagerInfo - Added broadcast_60_piece0 in memory on localhost:41569 (size: 1780.0 B, free: 1919.5 MiB)
15:09:23.067 INFO SparkContext - Created broadcast 60 from broadcast at DAGScheduler.scala:1580
15:09:23.068 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))
15:09:23.068 INFO TaskSchedulerImpl - Adding task set 39.0 with 4 tasks resource profile 0
15:09:23.069 INFO TaskSetManager - Starting task 0.0 in stage 39.0 (TID 92) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes)
15:09:23.069 INFO TaskSetManager - Starting task 1.0 in stage 39.0 (TID 93) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes)
15:09:23.070 INFO TaskSetManager - Starting task 2.0 in stage 39.0 (TID 94) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes)
15:09:23.070 INFO TaskSetManager - Starting task 3.0 in stage 39.0 (TID 95) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes)
15:09:23.070 INFO Executor - Running task 0.0 in stage 39.0 (TID 92)
15:09:23.071 INFO Executor - Running task 2.0 in stage 39.0 (TID 94)
15:09:23.071 INFO Executor - Running task 3.0 in stage 39.0 (TID 95)
15:09:23.072 INFO Executor - Running task 1.0 in stage 39.0 (TID 93)
15:09:23.074 INFO Executor - Finished task 2.0 in stage 39.0 (TID 94). 40380 bytes result sent to driver
15:09:23.075 INFO Executor - Finished task 1.0 in stage 39.0 (TID 93). 40512 bytes result sent to driver
15:09:23.075 INFO Executor - Finished task 0.0 in stage 39.0 (TID 92). 40355 bytes result sent to driver
15:09:23.075 INFO Executor - Finished task 3.0 in stage 39.0 (TID 95). 40805 bytes result sent to driver
15:09:23.075 INFO TaskSetManager - Finished task 2.0 in stage 39.0 (TID 94) in 6 ms on localhost (executor driver) (1/4)
15:09:23.076 INFO TaskSetManager - Finished task 3.0 in stage 39.0 (TID 95) in 6 ms on localhost (executor driver) (2/4)
15:09:23.076 INFO TaskSetManager - Finished task 0.0 in stage 39.0 (TID 92) in 8 ms on localhost (executor driver) (3/4)
15:09:23.077 INFO TaskSetManager - Finished task 1.0 in stage 39.0 (TID 93) in 8 ms on localhost (executor driver) (4/4)
15:09:23.077 INFO TaskSchedulerImpl - Removed TaskSet 39.0, whose tasks have all completed, from pool
15:09:23.077 INFO DAGScheduler - ResultStage 39 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.013 s
15:09:23.077 INFO DAGScheduler - Job 30 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:23.077 INFO TaskSchedulerImpl - Killing all running tasks in stage 39: Stage finished
15:09:23.077 INFO DAGScheduler - Job 30 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.014122 s
15:09:23.079 INFO FileInputFormat - Total input files to process : 1
15:09:23.127 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
15:09:23.127 INFO DAGScheduler - Got job 31 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
15:09:23.127 INFO DAGScheduler - Final stage: ResultStage 40 (collect at ReadsSparkSourceUnitTest.java:112)
15:09:23.127 INFO DAGScheduler - Parents of final stage: List()
15:09:23.127 INFO DAGScheduler - Missing parents: List()
15:09:23.128 INFO DAGScheduler - Submitting ResultStage 40 (MapPartitionsRDD[137] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:23.152 INFO MemoryStore - Block broadcast_61 stored as values in memory (estimated size 425.0 KiB, free 1917.1 MiB)
15:09:23.153 INFO MemoryStore - Block broadcast_61_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1917.0 MiB)
15:09:23.154 INFO BlockManagerInfo - Added broadcast_61_piece0 in memory on localhost:41569 (size: 152.7 KiB, free: 1919.4 MiB)
15:09:23.154 INFO SparkContext - Created broadcast 61 from broadcast at DAGScheduler.scala:1580
15:09:23.154 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))
15:09:23.154 INFO TaskSchedulerImpl - Adding task set 40.0 with 1 tasks resource profile 0
15:09:23.155 INFO TaskSetManager - Starting task 0.0 in stage 40.0 (TID 96) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes)
15:09:23.155 INFO Executor - Running task 0.0 in stage 40.0 (TID 96)
15:09:23.205 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
15:09:23.214 INFO Executor - Finished task 0.0 in stage 40.0 (TID 96). 159615 bytes result sent to driver
15:09:23.216 INFO TaskSetManager - Finished task 0.0 in stage 40.0 (TID 96) in 61 ms on localhost (executor driver) (1/1)
15:09:23.216 INFO TaskSchedulerImpl - Removed TaskSet 40.0, whose tasks have all completed, from pool
15:09:23.216 INFO DAGScheduler - ResultStage 40 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.088 s
15:09:23.216 INFO DAGScheduler - Job 31 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:23.216 INFO TaskSchedulerImpl - Killing all running tasks in stage 40: Stage finished
15:09:23.216 INFO DAGScheduler - Job 31 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.089588 s
15:09:23.221 INFO MemoryStore - Block broadcast_62 stored as values in memory (estimated size 528.0 B, free 1917.0 MiB)
15:09:23.222 INFO MemoryStore - Block broadcast_62_piece0 stored as bytes in memory (estimated size 183.0 B, free 1917.0 MiB)
15:09:23.223 INFO BlockManagerInfo - Added broadcast_62_piece0 in memory on localhost:41569 (size: 183.0 B, free: 1919.4 MiB)
15:09:23.223 INFO SparkContext - Created broadcast 62 from broadcast at CramSource.java:114
15:09:23.226 INFO MemoryStore - Block broadcast_63 stored as values in memory (estimated size 297.2 KiB, free 1916.7 MiB)
15:09:23.234 INFO MemoryStore - Block broadcast_63_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.6 MiB)
15:09:23.234 INFO BlockManagerInfo - Added broadcast_63_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.4 MiB)
15:09:23.234 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
15:09:23.267 INFO MemoryStore - Block broadcast_64 stored as values in memory (estimated size 528.0 B, free 1916.6 MiB)
15:09:23.267 INFO MemoryStore - Block broadcast_64_piece0 stored as bytes in memory (estimated size 183.0 B, free 1916.6 MiB)
15:09:23.268 INFO BlockManagerInfo - Added broadcast_64_piece0 in memory on localhost:41569 (size: 183.0 B, free: 1919.4 MiB)
15:09:23.268 INFO SparkContext - Created broadcast 64 from broadcast at CramSource.java:114
15:09:23.272 INFO MemoryStore - Block broadcast_65 stored as values in memory (estimated size 297.2 KiB, free 1916.3 MiB)
15:09:23.281 INFO MemoryStore - Block broadcast_65_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1916.3 MiB)
15:09:23.281 INFO BlockManagerInfo - Added broadcast_65_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.3 MiB)
15:09:23.281 INFO SparkContext - Created broadcast 65 from newAPIHadoopFile at PathSplitSource.java:96
15:09:23.301 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
15:09:23.302 INFO DAGScheduler - Got job 32 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
15:09:23.302 INFO DAGScheduler - Final stage: ResultStage 41 (collect at ReadsSparkSourceUnitTest.java:111)
15:09:23.302 INFO DAGScheduler - Parents of final stage: List()
15:09:23.302 INFO DAGScheduler - Missing parents: List()
15:09:23.302 INFO DAGScheduler - Submitting ResultStage 41 (ParallelCollectionRDD[142] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
15:09:23.303 INFO MemoryStore - Block broadcast_66 stored as values in memory (estimated size 3.0 KiB, free 1916.3 MiB)
15:09:23.303 INFO MemoryStore - Block broadcast_66_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1916.3 MiB)
15:09:23.304 INFO BlockManagerInfo - Added broadcast_66_piece0 in memory on localhost:41569 (size: 1780.0 B, free: 1919.3 MiB)
15:09:23.304 INFO SparkContext - Created broadcast 66 from broadcast at DAGScheduler.scala:1580
15:09:23.304 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))
15:09:23.304 INFO TaskSchedulerImpl - Adding task set 41.0 with 4 tasks resource profile 0
15:09:23.306 INFO TaskSetManager - Starting task 0.0 in stage 41.0 (TID 97) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes)
15:09:23.307 INFO TaskSetManager - Starting task 1.0 in stage 41.0 (TID 98) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes)
15:09:23.308 INFO TaskSetManager - Starting task 2.0 in stage 41.0 (TID 99) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes)
15:09:23.309 INFO TaskSetManager - Starting task 3.0 in stage 41.0 (TID 100) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes)
15:09:23.309 INFO Executor - Running task 1.0 in stage 41.0 (TID 98)
15:09:23.309 INFO Executor - Running task 3.0 in stage 41.0 (TID 100)
15:09:23.310 INFO Executor - Running task 0.0 in stage 41.0 (TID 97)
15:09:23.310 INFO Executor - Running task 2.0 in stage 41.0 (TID 99)
15:09:23.313 INFO Executor - Finished task 2.0 in stage 41.0 (TID 99). 39070 bytes result sent to driver
15:09:23.313 INFO Executor - Finished task 1.0 in stage 41.0 (TID 98). 39130 bytes result sent to driver
15:09:23.314 INFO Executor - Finished task 3.0 in stage 41.0 (TID 100). 39386 bytes result sent to driver
15:09:23.314 INFO Executor - Finished task 0.0 in stage 41.0 (TID 97). 38950 bytes result sent to driver
15:09:23.315 INFO TaskSetManager - Finished task 2.0 in stage 41.0 (TID 99) in 7 ms on localhost (executor driver) (1/4)
15:09:23.315 INFO TaskSetManager - Finished task 3.0 in stage 41.0 (TID 100) in 7 ms on localhost (executor driver) (2/4)
15:09:23.315 INFO TaskSetManager - Finished task 1.0 in stage 41.0 (TID 98) in 9 ms on localhost (executor driver) (3/4)
15:09:23.315 INFO TaskSetManager - Finished task 0.0 in stage 41.0 (TID 97) in 10 ms on localhost (executor driver) (4/4)
15:09:23.315 INFO TaskSchedulerImpl - Removed TaskSet 41.0, whose tasks have all completed, from pool
15:09:23.316 INFO DAGScheduler - ResultStage 41 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.014 s
15:09:23.316 INFO DAGScheduler - Job 32 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:23.316 INFO TaskSchedulerImpl - Killing all running tasks in stage 41: Stage finished
15:09:23.316 INFO DAGScheduler - Job 32 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.015103 s
15:09:23.317 INFO FileInputFormat - Total input files to process : 1
15:09:23.351 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
15:09:23.352 INFO DAGScheduler - Got job 33 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
15:09:23.352 INFO DAGScheduler - Final stage: ResultStage 42 (collect at ReadsSparkSourceUnitTest.java:112)
15:09:23.352 INFO DAGScheduler - Parents of final stage: List()
15:09:23.352 INFO DAGScheduler - Missing parents: List()
15:09:23.352 INFO DAGScheduler - Submitting ResultStage 42 (MapPartitionsRDD[148] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:23.372 INFO MemoryStore - Block broadcast_67 stored as values in memory (estimated size 286.0 KiB, free 1916.0 MiB)
15:09:23.374 INFO MemoryStore - Block broadcast_67_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1915.9 MiB)
15:09:23.374 INFO BlockManagerInfo - Added broadcast_67_piece0 in memory on localhost:41569 (size: 103.1 KiB, free: 1919.2 MiB)
15:09:23.374 INFO SparkContext - Created broadcast 67 from broadcast at DAGScheduler.scala:1580
15:09:23.375 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))
15:09:23.375 INFO TaskSchedulerImpl - Adding task set 42.0 with 1 tasks resource profile 0
15:09:23.376 INFO TaskSetManager - Starting task 0.0 in stage 42.0 (TID 101) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes)
15:09:23.376 INFO Executor - Running task 0.0 in stage 42.0 (TID 101)
15:09:23.404 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
15:09:23.418 INFO Executor - Finished task 0.0 in stage 42.0 (TID 101). 154101 bytes result sent to driver
15:09:23.419 INFO TaskSetManager - Finished task 0.0 in stage 42.0 (TID 101) in 44 ms on localhost (executor driver) (1/1)
15:09:23.419 INFO TaskSchedulerImpl - Removed TaskSet 42.0, whose tasks have all completed, from pool
15:09:23.419 INFO DAGScheduler - ResultStage 42 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.066 s
15:09:23.419 INFO DAGScheduler - Job 33 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:23.419 INFO TaskSchedulerImpl - Killing all running tasks in stage 42: Stage finished
15:09:23.419 INFO DAGScheduler - Job 33 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.067971 s
15:09:23.425 INFO MemoryStore - Block broadcast_68 stored as values in memory (estimated size 297.2 KiB, free 1915.6 MiB)
15:09:23.431 INFO MemoryStore - Block broadcast_68_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.6 MiB)
15:09:23.432 INFO BlockManagerInfo - Added broadcast_68_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.2 MiB)
15:09:23.432 INFO SparkContext - Created broadcast 68 from newAPIHadoopFile at PathSplitSource.java:96
15:09:23.458 INFO MemoryStore - Block broadcast_69 stored as values in memory (estimated size 297.2 KiB, free 1915.3 MiB)
15:09:23.465 INFO MemoryStore - Block broadcast_69_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.2 MiB)
15:09:23.465 INFO BlockManagerInfo - Added broadcast_69_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.1 MiB)
15:09:23.465 INFO SparkContext - Created broadcast 69 from newAPIHadoopFile at PathSplitSource.java:96
15:09:23.490 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
15:09:23.491 INFO DAGScheduler - Got job 34 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
15:09:23.491 INFO DAGScheduler - Final stage: ResultStage 43 (collect at ReadsSparkSourceUnitTest.java:111)
15:09:23.491 INFO DAGScheduler - Parents of final stage: List()
15:09:23.491 INFO DAGScheduler - Missing parents: List()
15:09:23.491 INFO DAGScheduler - Submitting ResultStage 43 (ParallelCollectionRDD[154] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
15:09:23.492 INFO MemoryStore - Block broadcast_70 stored as values in memory (estimated size 3.0 KiB, free 1915.2 MiB)
15:09:23.492 INFO MemoryStore - Block broadcast_70_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1915.2 MiB)
15:09:23.493 INFO BlockManagerInfo - Added broadcast_70_piece0 in memory on localhost:41569 (size: 1780.0 B, free: 1919.1 MiB)
15:09:23.493 INFO SparkContext - Created broadcast 70 from broadcast at DAGScheduler.scala:1580
15:09:23.494 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))
15:09:23.494 INFO TaskSchedulerImpl - Adding task set 43.0 with 4 tasks resource profile 0
15:09:23.495 INFO TaskSetManager - Starting task 0.0 in stage 43.0 (TID 102) (localhost, executor driver, partition 0, PROCESS_LOCAL, 47080 bytes)
15:09:23.496 INFO TaskSetManager - Starting task 1.0 in stage 43.0 (TID 103) (localhost, executor driver, partition 1, PROCESS_LOCAL, 47194 bytes)
15:09:23.496 INFO TaskSetManager - Starting task 2.0 in stage 43.0 (TID 104) (localhost, executor driver, partition 2, PROCESS_LOCAL, 47105 bytes)
15:09:23.497 INFO TaskSetManager - Starting task 3.0 in stage 43.0 (TID 105) (localhost, executor driver, partition 3, PROCESS_LOCAL, 47530 bytes)
15:09:23.497 INFO Executor - Running task 0.0 in stage 43.0 (TID 102)
15:09:23.497 INFO Executor - Running task 1.0 in stage 43.0 (TID 103)
15:09:23.498 INFO Executor - Running task 3.0 in stage 43.0 (TID 105)
15:09:23.499 INFO Executor - Running task 2.0 in stage 43.0 (TID 104)
15:09:23.501 INFO Executor - Finished task 0.0 in stage 43.0 (TID 102). 40355 bytes result sent to driver
15:09:23.501 INFO Executor - Finished task 2.0 in stage 43.0 (TID 104). 40380 bytes result sent to driver
15:09:23.502 INFO Executor - Finished task 1.0 in stage 43.0 (TID 103). 40469 bytes result sent to driver
15:09:23.502 INFO Executor - Finished task 3.0 in stage 43.0 (TID 105). 40848 bytes result sent to driver
15:09:23.502 INFO TaskSetManager - Finished task 0.0 in stage 43.0 (TID 102) in 8 ms on localhost (executor driver) (1/4)
15:09:23.503 INFO TaskSetManager - Finished task 2.0 in stage 43.0 (TID 104) in 7 ms on localhost (executor driver) (2/4)
15:09:23.503 INFO TaskSetManager - Finished task 1.0 in stage 43.0 (TID 103) in 8 ms on localhost (executor driver) (3/4)
15:09:23.504 INFO TaskSetManager - Finished task 3.0 in stage 43.0 (TID 105) in 8 ms on localhost (executor driver) (4/4)
15:09:23.504 INFO TaskSchedulerImpl - Removed TaskSet 43.0, whose tasks have all completed, from pool
15:09:23.504 INFO DAGScheduler - ResultStage 43 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.013 s
15:09:23.504 INFO DAGScheduler - Job 34 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:23.504 INFO TaskSchedulerImpl - Killing all running tasks in stage 43: Stage finished
15:09:23.504 INFO DAGScheduler - Job 34 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.014001 s
15:09:23.505 INFO FileInputFormat - Total input files to process : 1
15:09:23.542 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
15:09:23.543 INFO DAGScheduler - Got job 35 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
15:09:23.543 INFO DAGScheduler - Final stage: ResultStage 44 (collect at ReadsSparkSourceUnitTest.java:112)
15:09:23.543 INFO DAGScheduler - Parents of final stage: List()
15:09:23.543 INFO DAGScheduler - Missing parents: List()
15:09:23.544 INFO DAGScheduler - Submitting ResultStage 44 (MapPartitionsRDD[161] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:23.562 INFO MemoryStore - Block broadcast_71 stored as values in memory (estimated size 425.0 KiB, free 1914.8 MiB)
15:09:23.564 INFO MemoryStore - Block broadcast_71_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1914.7 MiB)
15:09:23.564 INFO BlockManagerInfo - Added broadcast_71_piece0 in memory on localhost:41569 (size: 152.7 KiB, free: 1919.0 MiB)
15:09:23.564 INFO SparkContext - Created broadcast 71 from broadcast at DAGScheduler.scala:1580
15:09:23.565 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))
15:09:23.565 INFO TaskSchedulerImpl - Adding task set 44.0 with 1 tasks resource profile 0
15:09:23.566 INFO TaskSetManager - Starting task 0.0 in stage 44.0 (TID 106) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes)
15:09:23.566 INFO Executor - Running task 0.0 in stage 44.0 (TID 106)
15:09:23.621 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
15:09:23.640 INFO BlockManagerInfo - Removed broadcast_48_piece0 on localhost:41569 in memory (size: 183.0 B, free: 1919.0 MiB)
15:09:23.642 INFO Executor - Finished task 0.0 in stage 44.0 (TID 106). 159615 bytes result sent to driver
15:09:23.642 INFO BlockManagerInfo - Removed broadcast_65_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.0 MiB)
15:09:23.643 INFO BlockManagerInfo - Removed broadcast_56_piece0 on localhost:41569 in memory (size: 1780.0 B, free: 1919.0 MiB)
15:09:23.644 INFO BlockManagerInfo - Removed broadcast_60_piece0 on localhost:41569 in memory (size: 1780.0 B, free: 1919.0 MiB)
15:09:23.645 INFO TaskSetManager - Finished task 0.0 in stage 44.0 (TID 106) in 80 ms on localhost (executor driver) (1/1)
15:09:23.645 INFO TaskSchedulerImpl - Removed TaskSet 44.0, whose tasks have all completed, from pool
15:09:23.645 INFO BlockManagerInfo - Removed broadcast_49_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.1 MiB)
15:09:23.645 INFO DAGScheduler - ResultStage 44 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.101 s
15:09:23.645 INFO DAGScheduler - Job 35 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:23.645 INFO TaskSchedulerImpl - Killing all running tasks in stage 44: Stage finished
15:09:23.646 INFO BlockManagerInfo - Removed broadcast_54_piece0 on localhost:41569 in memory (size: 202.0 B, free: 1919.1 MiB)
15:09:23.646 INFO DAGScheduler - Job 35 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.103267 s
15:09:23.647 INFO BlockManagerInfo - Removed broadcast_61_piece0 on localhost:41569 in memory (size: 152.7 KiB, free: 1919.2 MiB)
15:09:23.647 INFO BlockManagerInfo - Removed broadcast_68_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.2 MiB)
15:09:23.648 INFO BlockManagerInfo - Removed broadcast_55_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.3 MiB)
15:09:23.649 INFO BlockManagerInfo - Removed broadcast_66_piece0 on localhost:41569 in memory (size: 1780.0 B, free: 1919.3 MiB)
15:09:23.650 INFO BlockManagerInfo - Removed broadcast_57_piece0 on localhost:41569 in memory (size: 103.1 KiB, free: 1919.4 MiB)
15:09:23.651 INFO BlockManagerInfo - Removed broadcast_53_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.5 MiB)
15:09:23.652 INFO MemoryStore - Block broadcast_72 stored as values in memory (estimated size 528.0 B, free 1917.4 MiB)
15:09:23.652 INFO BlockManagerInfo - Removed broadcast_67_piece0 on localhost:41569 in memory (size: 103.1 KiB, free: 1919.6 MiB)
15:09:23.653 INFO MemoryStore - Block broadcast_72_piece0 stored as bytes in memory (estimated size 183.0 B, free 1917.7 MiB)
15:09:23.653 INFO BlockManagerInfo - Added broadcast_72_piece0 in memory on localhost:41569 (size: 183.0 B, free: 1919.6 MiB)
15:09:23.653 INFO BlockManagerInfo - Removed broadcast_59_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.6 MiB)
15:09:23.654 INFO SparkContext - Created broadcast 72 from broadcast at CramSource.java:114
15:09:23.654 INFO BlockManagerInfo - Removed broadcast_64_piece0 on localhost:41569 in memory (size: 183.0 B, free: 1919.6 MiB)
15:09:23.655 INFO BlockManagerInfo - Removed broadcast_63_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.6 MiB)
15:09:23.656 INFO BlockManagerInfo - Removed broadcast_62_piece0 on localhost:41569 in memory (size: 183.0 B, free: 1919.6 MiB)
15:09:23.657 INFO BlockManagerInfo - Removed broadcast_51_piece0 on localhost:41569 in memory (size: 103.1 KiB, free: 1919.7 MiB)
15:09:23.658 INFO BlockManagerInfo - Removed broadcast_58_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.8 MiB)
15:09:23.658 INFO MemoryStore - Block broadcast_73 stored as values in memory (estimated size 297.2 KiB, free 1918.8 MiB)
15:09:23.658 INFO BlockManagerInfo - Removed broadcast_70_piece0 on localhost:41569 in memory (size: 1780.0 B, free: 1919.8 MiB)
15:09:23.659 INFO BlockManagerInfo - Removed broadcast_52_piece0 on localhost:41569 in memory (size: 202.0 B, free: 1919.8 MiB)
15:09:23.660 INFO BlockManagerInfo - Removed broadcast_50_piece0 on localhost:41569 in memory (size: 1780.0 B, free: 1919.8 MiB)
15:09:23.666 INFO MemoryStore - Block broadcast_73_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.8 MiB)
15:09:23.666 INFO BlockManagerInfo - Added broadcast_73_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.8 MiB)
15:09:23.666 INFO SparkContext - Created broadcast 73 from newAPIHadoopFile at PathSplitSource.java:96
15:09:23.693 INFO MemoryStore - Block broadcast_74 stored as values in memory (estimated size 528.0 B, free 1918.8 MiB)
15:09:23.694 INFO MemoryStore - Block broadcast_74_piece0 stored as bytes in memory (estimated size 183.0 B, free 1918.8 MiB)
15:09:23.694 INFO BlockManagerInfo - Added broadcast_74_piece0 in memory on localhost:41569 (size: 183.0 B, free: 1919.8 MiB)
15:09:23.694 INFO SparkContext - Created broadcast 74 from broadcast at CramSource.java:114
15:09:23.697 INFO MemoryStore - Block broadcast_75 stored as values in memory (estimated size 297.2 KiB, free 1918.5 MiB)
15:09:23.704 INFO MemoryStore - Block broadcast_75_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1918.4 MiB)
15:09:23.704 INFO BlockManagerInfo - Added broadcast_75_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.7 MiB)
15:09:23.704 INFO SparkContext - Created broadcast 75 from newAPIHadoopFile at PathSplitSource.java:96
15:09:23.724 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:111
15:09:23.724 INFO DAGScheduler - Got job 36 (collect at ReadsSparkSourceUnitTest.java:111) with 4 output partitions
15:09:23.724 INFO DAGScheduler - Final stage: ResultStage 45 (collect at ReadsSparkSourceUnitTest.java:111)
15:09:23.724 INFO DAGScheduler - Parents of final stage: List()
15:09:23.725 INFO DAGScheduler - Missing parents: List()
15:09:23.725 INFO DAGScheduler - Submitting ResultStage 45 (ParallelCollectionRDD[166] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
15:09:23.726 INFO MemoryStore - Block broadcast_76 stored as values in memory (estimated size 3.0 KiB, free 1918.4 MiB)
15:09:23.727 INFO MemoryStore - Block broadcast_76_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1918.4 MiB)
15:09:23.727 INFO BlockManagerInfo - Added broadcast_76_piece0 in memory on localhost:41569 (size: 1780.0 B, free: 1919.7 MiB)
15:09:23.728 INFO SparkContext - Created broadcast 76 from broadcast at DAGScheduler.scala:1580
15:09:23.728 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))
15:09:23.728 INFO TaskSchedulerImpl - Adding task set 45.0 with 4 tasks resource profile 0
15:09:23.730 INFO TaskSetManager - Starting task 0.0 in stage 45.0 (TID 107) (localhost, executor driver, partition 0, PROCESS_LOCAL, 45675 bytes)
15:09:23.732 INFO TaskSetManager - Starting task 1.0 in stage 45.0 (TID 108) (localhost, executor driver, partition 1, PROCESS_LOCAL, 45855 bytes)
15:09:23.733 INFO TaskSetManager - Starting task 2.0 in stage 45.0 (TID 109) (localhost, executor driver, partition 2, PROCESS_LOCAL, 45795 bytes)
15:09:23.735 INFO TaskSetManager - Starting task 3.0 in stage 45.0 (TID 110) (localhost, executor driver, partition 3, PROCESS_LOCAL, 46068 bytes)
15:09:23.736 INFO Executor - Running task 1.0 in stage 45.0 (TID 108)
15:09:23.736 INFO Executor - Running task 0.0 in stage 45.0 (TID 107)
15:09:23.738 INFO Executor - Running task 2.0 in stage 45.0 (TID 109)
15:09:23.740 INFO Executor - Running task 3.0 in stage 45.0 (TID 110)
15:09:23.740 INFO Executor - Finished task 2.0 in stage 45.0 (TID 109). 39027 bytes result sent to driver
15:09:23.742 INFO Executor - Finished task 1.0 in stage 45.0 (TID 108). 39130 bytes result sent to driver
15:09:23.742 INFO Executor - Finished task 0.0 in stage 45.0 (TID 107). 38950 bytes result sent to driver
15:09:23.743 INFO TaskSetManager - Finished task 2.0 in stage 45.0 (TID 109) in 11 ms on localhost (executor driver) (1/4)
15:09:23.744 INFO TaskSetManager - Finished task 1.0 in stage 45.0 (TID 108) in 14 ms on localhost (executor driver) (2/4)
15:09:23.744 INFO TaskSetManager - Finished task 0.0 in stage 45.0 (TID 107) in 15 ms on localhost (executor driver) (3/4)
15:09:23.742 INFO Executor - Finished task 3.0 in stage 45.0 (TID 110). 39343 bytes result sent to driver
15:09:23.745 INFO TaskSetManager - Finished task 3.0 in stage 45.0 (TID 110) in 11 ms on localhost (executor driver) (4/4)
15:09:23.745 INFO TaskSchedulerImpl - Removed TaskSet 45.0, whose tasks have all completed, from pool
15:09:23.745 INFO DAGScheduler - ResultStage 45 (collect at ReadsSparkSourceUnitTest.java:111) finished in 0.020 s
15:09:23.746 INFO DAGScheduler - Job 36 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:23.746 INFO TaskSchedulerImpl - Killing all running tasks in stage 45: Stage finished
15:09:23.746 INFO DAGScheduler - Job 36 finished: collect at ReadsSparkSourceUnitTest.java:111, took 0.021916 s
15:09:23.747 INFO FileInputFormat - Total input files to process : 1
15:09:23.785 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:112
15:09:23.786 INFO DAGScheduler - Got job 37 (collect at ReadsSparkSourceUnitTest.java:112) with 1 output partitions
15:09:23.786 INFO DAGScheduler - Final stage: ResultStage 46 (collect at ReadsSparkSourceUnitTest.java:112)
15:09:23.786 INFO DAGScheduler - Parents of final stage: List()
15:09:23.786 INFO DAGScheduler - Missing parents: List()
15:09:23.786 INFO DAGScheduler - Submitting ResultStage 46 (MapPartitionsRDD[172] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:23.804 INFO MemoryStore - Block broadcast_77 stored as values in memory (estimated size 286.0 KiB, free 1918.1 MiB)
15:09:23.805 INFO MemoryStore - Block broadcast_77_piece0 stored as bytes in memory (estimated size 103.1 KiB, free 1918.0 MiB)
15:09:23.805 INFO BlockManagerInfo - Added broadcast_77_piece0 in memory on localhost:41569 (size: 103.1 KiB, free: 1919.6 MiB)
15:09:23.805 INFO SparkContext - Created broadcast 77 from broadcast at DAGScheduler.scala:1580
15:09:23.806 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))
15:09:23.806 INFO TaskSchedulerImpl - Adding task set 46.0 with 1 tasks resource profile 0
15:09:23.807 INFO TaskSetManager - Starting task 0.0 in stage 46.0 (TID 111) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7832 bytes)
15:09:23.807 INFO Executor - Running task 0.0 in stage 46.0 (TID 111)
15:09:23.841 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.cram:0+50619
15:09:23.853 INFO Executor - Finished task 0.0 in stage 46.0 (TID 111). 154101 bytes result sent to driver
15:09:23.855 INFO TaskSetManager - Finished task 0.0 in stage 46.0 (TID 111) in 49 ms on localhost (executor driver) (1/1)
15:09:23.855 INFO TaskSchedulerImpl - Removed TaskSet 46.0, whose tasks have all completed, from pool
15:09:23.855 INFO DAGScheduler - ResultStage 46 (collect at ReadsSparkSourceUnitTest.java:112) finished in 0.069 s
15:09:23.855 INFO DAGScheduler - Job 37 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:23.855 INFO TaskSchedulerImpl - Killing all running tasks in stage 46: Stage finished
15:09:23.856 INFO DAGScheduler - Job 37 finished: collect at ReadsSparkSourceUnitTest.java:112, took 0.070580 s
15:09:23.861 INFO MemoryStore - Block broadcast_78 stored as values in memory (estimated size 297.2 KiB, free 1917.7 MiB)
15:09:23.868 INFO MemoryStore - Block broadcast_78_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.7 MiB)
15:09:23.868 INFO BlockManagerInfo - Added broadcast_78_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.6 MiB)
15:09:23.869 INFO SparkContext - Created broadcast 78 from newAPIHadoopFile at PathSplitSource.java:96
15:09:23.899 INFO MemoryStore - Block broadcast_79 stored as values in memory (estimated size 528.0 B, free 1917.7 MiB)
15:09:23.901 INFO MemoryStore - Block broadcast_79_piece0 stored as bytes in memory (estimated size 183.0 B, free 1917.7 MiB)
15:09:23.901 INFO BlockManagerInfo - Added broadcast_79_piece0 in memory on localhost:41569 (size: 183.0 B, free: 1919.6 MiB)
15:09:23.901 INFO SparkContext - Created broadcast 79 from broadcast at CramSource.java:114
15:09:23.903 INFO MemoryStore - Block broadcast_80 stored as values in memory (estimated size 297.2 KiB, free 1917.4 MiB)
15:09:23.910 INFO MemoryStore - Block broadcast_80_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1917.4 MiB)
15:09:23.910 INFO BlockManagerInfo - Added broadcast_80_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.5 MiB)
15:09:23.911 INFO SparkContext - Created broadcast 80 from newAPIHadoopFile at PathSplitSource.java:96
15:09:23.970 WARN FileSystem - Failed to initialize filesystem hdfs://bogus/path.bam: java.lang.IllegalArgumentException: java.net.UnknownHostException: bogus
15:09:23.977 INFO MemoryStore - Block broadcast_81 stored as values in memory (estimated size 297.3 KiB, free 1917.1 MiB)
15:09:23.984 INFO MemoryStore - Block broadcast_81_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.0 MiB)
15:09:23.984 INFO BlockManagerInfo - Added broadcast_81_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.5 MiB)
15:09:23.985 INFO SparkContext - Created broadcast 81 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.021 INFO MemoryStore - Block broadcast_82 stored as values in memory (estimated size 297.3 KiB, free 1916.7 MiB)
15:09:24.028 INFO MemoryStore - Block broadcast_82_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1916.7 MiB)
15:09:24.028 INFO BlockManagerInfo - Added broadcast_82_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.4 MiB)
15:09:24.028 INFO SparkContext - Created broadcast 82 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.054 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:154
15:09:24.055 INFO DAGScheduler - Got job 38 (collect at ReadsSparkSourceUnitTest.java:154) with 4 output partitions
15:09:24.055 INFO DAGScheduler - Final stage: ResultStage 47 (collect at ReadsSparkSourceUnitTest.java:154)
15:09:24.055 INFO DAGScheduler - Parents of final stage: List()
15:09:24.055 INFO DAGScheduler - Missing parents: List()
15:09:24.056 INFO DAGScheduler - Submitting ResultStage 47 (ParallelCollectionRDD[187] at parallelize at ReadsSparkSourceUnitTest.java:310), which has no missing parents
15:09:24.056 INFO MemoryStore - Block broadcast_83 stored as values in memory (estimated size 3.0 KiB, free 1916.7 MiB)
15:09:24.057 INFO MemoryStore - Block broadcast_83_piece0 stored as bytes in memory (estimated size 1780.0 B, free 1916.7 MiB)
15:09:24.057 INFO BlockManagerInfo - Added broadcast_83_piece0 in memory on localhost:41569 (size: 1780.0 B, free: 1919.4 MiB)
15:09:24.058 INFO SparkContext - Created broadcast 83 from broadcast at DAGScheduler.scala:1580
15:09:24.058 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))
15:09:24.058 INFO TaskSchedulerImpl - Adding task set 47.0 with 4 tasks resource profile 0
15:09:24.059 INFO TaskSetManager - Starting task 0.0 in stage 47.0 (TID 112) (localhost, executor driver, partition 0, PROCESS_LOCAL, 169886 bytes)
15:09:24.060 INFO TaskSetManager - Starting task 1.0 in stage 47.0 (TID 113) (localhost, executor driver, partition 1, PROCESS_LOCAL, 170093 bytes)
15:09:24.061 INFO TaskSetManager - Starting task 2.0 in stage 47.0 (TID 114) (localhost, executor driver, partition 2, PROCESS_LOCAL, 170081 bytes)
15:09:24.061 INFO TaskSetManager - Starting task 3.0 in stage 47.0 (TID 115) (localhost, executor driver, partition 3, PROCESS_LOCAL, 169419 bytes)
15:09:24.062 INFO Executor - Running task 0.0 in stage 47.0 (TID 112)
15:09:24.062 INFO Executor - Running task 1.0 in stage 47.0 (TID 113)
15:09:24.062 INFO Executor - Running task 2.0 in stage 47.0 (TID 114)
15:09:24.064 INFO Executor - Running task 3.0 in stage 47.0 (TID 115)
15:09:24.067 INFO Executor - Finished task 0.0 in stage 47.0 (TID 112). 163204 bytes result sent to driver
15:09:24.067 INFO Executor - Finished task 1.0 in stage 47.0 (TID 113). 163368 bytes result sent to driver
15:09:24.068 INFO Executor - Finished task 3.0 in stage 47.0 (TID 115). 162737 bytes result sent to driver
15:09:24.069 INFO TaskSetManager - Finished task 0.0 in stage 47.0 (TID 112) in 10 ms on localhost (executor driver) (1/4)
15:09:24.070 INFO Executor - Finished task 2.0 in stage 47.0 (TID 114). 163356 bytes result sent to driver
15:09:24.070 INFO TaskSetManager - Finished task 1.0 in stage 47.0 (TID 113) in 11 ms on localhost (executor driver) (2/4)
15:09:24.070 INFO TaskSetManager - Finished task 3.0 in stage 47.0 (TID 115) in 9 ms on localhost (executor driver) (3/4)
15:09:24.071 INFO TaskSetManager - Finished task 2.0 in stage 47.0 (TID 114) in 11 ms on localhost (executor driver) (4/4)
15:09:24.071 INFO TaskSchedulerImpl - Removed TaskSet 47.0, whose tasks have all completed, from pool
15:09:24.071 INFO DAGScheduler - ResultStage 47 (collect at ReadsSparkSourceUnitTest.java:154) finished in 0.015 s
15:09:24.071 INFO DAGScheduler - Job 38 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:24.071 INFO TaskSchedulerImpl - Killing all running tasks in stage 47: Stage finished
15:09:24.071 INFO DAGScheduler - Job 38 finished: collect at ReadsSparkSourceUnitTest.java:154, took 0.016779 s
15:09:24.081 INFO FileInputFormat - Total input files to process : 2
15:09:24.125 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:155
15:09:24.126 INFO DAGScheduler - Got job 39 (collect at ReadsSparkSourceUnitTest.java:155) with 2 output partitions
15:09:24.126 INFO DAGScheduler - Final stage: ResultStage 48 (collect at ReadsSparkSourceUnitTest.java:155)
15:09:24.126 INFO DAGScheduler - Parents of final stage: List()
15:09:24.126 INFO DAGScheduler - Missing parents: List()
15:09:24.126 INFO DAGScheduler - Submitting ResultStage 48 (MapPartitionsRDD[194] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:24.144 INFO MemoryStore - Block broadcast_84 stored as values in memory (estimated size 425.0 KiB, free 1916.3 MiB)
15:09:24.145 INFO MemoryStore - Block broadcast_84_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1916.1 MiB)
15:09:24.146 INFO BlockManagerInfo - Added broadcast_84_piece0 in memory on localhost:41569 (size: 152.7 KiB, free: 1919.3 MiB)
15:09:24.146 INFO SparkContext - Created broadcast 84 from broadcast at DAGScheduler.scala:1580
15:09:24.146 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))
15:09:24.146 INFO TaskSchedulerImpl - Adding task set 48.0 with 2 tasks resource profile 0
15:09:24.147 INFO TaskSetManager - Starting task 0.0 in stage 48.0 (TID 116) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7921 bytes)
15:09:24.147 INFO TaskSetManager - Starting task 1.0 in stage 48.0 (TID 117) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7921 bytes)
15:09:24.148 INFO Executor - Running task 1.0 in stage 48.0 (TID 117)
15:09:24.148 INFO Executor - Running task 0.0 in stage 48.0 (TID 116)
15:09:24.187 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
15:09:24.201 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
15:09:24.203 INFO Executor - Finished task 0.0 in stage 48.0 (TID 116). 325633 bytes result sent to driver
15:09:24.205 INFO TaskSetManager - Finished task 0.0 in stage 48.0 (TID 116) in 58 ms on localhost (executor driver) (1/2)
15:09:24.219 INFO Executor - Finished task 1.0 in stage 48.0 (TID 117). 325633 bytes result sent to driver
15:09:24.221 INFO TaskSetManager - Finished task 1.0 in stage 48.0 (TID 117) in 74 ms on localhost (executor driver) (2/2)
15:09:24.221 INFO TaskSchedulerImpl - Removed TaskSet 48.0, whose tasks have all completed, from pool
15:09:24.221 INFO DAGScheduler - ResultStage 48 (collect at ReadsSparkSourceUnitTest.java:155) finished in 0.094 s
15:09:24.221 INFO DAGScheduler - Job 39 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:24.221 INFO TaskSchedulerImpl - Killing all running tasks in stage 48: Stage finished
15:09:24.221 INFO DAGScheduler - Job 39 finished: collect at ReadsSparkSourceUnitTest.java:155, took 0.096069 s
15:09:24.228 INFO MemoryStore - Block broadcast_85 stored as values in memory (estimated size 297.2 KiB, free 1915.8 MiB)
15:09:24.239 INFO MemoryStore - Block broadcast_85_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1915.8 MiB)
15:09:24.240 INFO BlockManagerInfo - Added broadcast_85_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.2 MiB)
15:09:24.240 INFO SparkContext - Created broadcast 85 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.265 INFO MemoryStore - Block broadcast_86 stored as values in memory (estimated size 297.3 KiB, free 1915.5 MiB)
15:09:24.271 INFO MemoryStore - Block broadcast_86_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1915.4 MiB)
15:09:24.272 INFO BlockManagerInfo - Added broadcast_86_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.2 MiB)
15:09:24.272 INFO SparkContext - Created broadcast 86 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.297 INFO MemoryStore - Block broadcast_87 stored as values in memory (estimated size 297.3 KiB, free 1915.1 MiB)
15:09:24.304 INFO MemoryStore - Block broadcast_87_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1915.1 MiB)
15:09:24.304 INFO BlockManagerInfo - Added broadcast_87_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.1 MiB)
15:09:24.304 INFO SparkContext - Created broadcast 87 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.330 INFO MemoryStore - Block broadcast_88 stored as values in memory (estimated size 528.0 B, free 1915.1 MiB)
15:09:24.332 INFO MemoryStore - Block broadcast_88_piece0 stored as bytes in memory (estimated size 183.0 B, free 1915.1 MiB)
15:09:24.332 INFO BlockManagerInfo - Added broadcast_88_piece0 in memory on localhost:41569 (size: 183.0 B, free: 1919.1 MiB)
15:09:24.332 INFO SparkContext - Created broadcast 88 from broadcast at CramSource.java:114
15:09:24.334 INFO MemoryStore - Block broadcast_89 stored as values in memory (estimated size 297.2 KiB, free 1914.8 MiB)
15:09:24.341 INFO MemoryStore - Block broadcast_89_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1914.7 MiB)
15:09:24.341 INFO BlockManagerInfo - Added broadcast_89_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1919.1 MiB)
15:09:24.342 INFO SparkContext - Created broadcast 89 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.359 INFO MemoryStore - Block broadcast_90 stored as values in memory (estimated size 600.0 B, free 1914.7 MiB)
15:09:24.359 INFO MemoryStore - Block broadcast_90_piece0 stored as bytes in memory (estimated size 202.0 B, free 1914.7 MiB)
15:09:24.359 INFO BlockManagerInfo - Added broadcast_90_piece0 in memory on localhost:41569 (size: 202.0 B, free: 1919.1 MiB)
15:09:24.360 INFO SparkContext - Created broadcast 90 from broadcast at CramSource.java:114
15:09:24.361 INFO MemoryStore - Block broadcast_91 stored as values in memory (estimated size 297.3 KiB, free 1914.5 MiB)
15:09:24.368 INFO MemoryStore - Block broadcast_91_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1914.4 MiB)
15:09:24.368 INFO BlockManagerInfo - Added broadcast_91_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.0 MiB)
15:09:24.368 INFO SparkContext - Created broadcast 91 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.386 INFO MemoryStore - Block broadcast_92 stored as values in memory (estimated size 297.3 KiB, free 1914.1 MiB)
15:09:24.392 INFO MemoryStore - Block broadcast_92_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1914.1 MiB)
15:09:24.392 INFO BlockManagerInfo - Added broadcast_92_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.0 MiB)
15:09:24.393 INFO SparkContext - Created broadcast 92 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.414 INFO FileInputFormat - Total input files to process : 1
15:09:24.450 INFO SparkContext - Starting job: collect at ReadsSparkSourceUnitTest.java:163
15:09:24.451 INFO DAGScheduler - Got job 40 (collect at ReadsSparkSourceUnitTest.java:163) with 1 output partitions
15:09:24.451 INFO DAGScheduler - Final stage: ResultStage 49 (collect at ReadsSparkSourceUnitTest.java:163)
15:09:24.451 INFO DAGScheduler - Parents of final stage: List()
15:09:24.451 INFO DAGScheduler - Missing parents: List()
15:09:24.451 INFO DAGScheduler - Submitting ResultStage 49 (MapPartitionsRDD[224] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:24.469 INFO MemoryStore - Block broadcast_93 stored as values in memory (estimated size 425.0 KiB, free 1913.7 MiB)
15:09:24.470 INFO MemoryStore - Block broadcast_93_piece0 stored as bytes in memory (estimated size 152.7 KiB, free 1913.5 MiB)
15:09:24.470 INFO BlockManagerInfo - Added broadcast_93_piece0 in memory on localhost:41569 (size: 152.7 KiB, free: 1918.8 MiB)
15:09:24.471 INFO SparkContext - Created broadcast 93 from broadcast at DAGScheduler.scala:1580
15:09:24.471 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))
15:09:24.471 INFO TaskSchedulerImpl - Adding task set 49.0 with 1 tasks resource profile 0
15:09:24.472 INFO TaskSetManager - Starting task 0.0 in stage 49.0 (TID 118) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7875 bytes)
15:09:24.472 INFO Executor - Running task 0.0 in stage 49.0 (TID 118)
15:09:24.508 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate.bam:0+221635
15:09:24.524 INFO Executor - Finished task 0.0 in stage 49.0 (TID 118). 650184 bytes result sent to driver
15:09:24.526 INFO TaskSetManager - Finished task 0.0 in stage 49.0 (TID 118) in 54 ms on localhost (executor driver) (1/1)
15:09:24.526 INFO TaskSchedulerImpl - Removed TaskSet 49.0, whose tasks have all completed, from pool
15:09:24.526 INFO DAGScheduler - ResultStage 49 (collect at ReadsSparkSourceUnitTest.java:163) finished in 0.074 s
15:09:24.526 INFO DAGScheduler - Job 40 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:24.526 INFO TaskSchedulerImpl - Killing all running tasks in stage 49: Stage finished
15:09:24.527 INFO DAGScheduler - Job 40 finished: collect at ReadsSparkSourceUnitTest.java:163, took 0.075977 s
15:09:24.530 INFO MemoryStore - Block broadcast_94 stored as values in memory (estimated size 208.0 B, free 1913.5 MiB)
15:09:24.532 INFO MemoryStore - Block broadcast_94_piece0 stored as bytes in memory (estimated size 239.0 B, free 1913.5 MiB)
15:09:24.532 INFO BlockManagerInfo - Added broadcast_94_piece0 in memory on localhost:41569 (size: 239.0 B, free: 1918.8 MiB)
15:09:24.533 INFO SparkContext - Created broadcast 94 from broadcast at AbstractBinarySamSource.java:82
15:09:24.534 INFO MemoryStore - Block broadcast_95 stored as values in memory (estimated size 297.2 KiB, free 1913.2 MiB)
15:09:24.541 INFO MemoryStore - Block broadcast_95_piece0 stored as bytes in memory (estimated size 50.0 KiB, free 1913.2 MiB)
15:09:24.541 INFO BlockManagerInfo - Added broadcast_95_piece0 in memory on localhost:41569 (size: 50.0 KiB, free: 1918.8 MiB)
15:09:24.541 INFO SparkContext - Created broadcast 95 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.572 INFO BlockManagerInfo - Removed broadcast_84_piece0 on localhost:41569 in memory (size: 152.7 KiB, free: 1918.9 MiB)
15:09:24.572 INFO BlockManagerInfo - Removed broadcast_86_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.0 MiB)
15:09:24.573 INFO BlockManagerInfo - Removed broadcast_80_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.0 MiB)
15:09:24.574 INFO BlockManagerInfo - Removed broadcast_81_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.1 MiB)
15:09:24.575 INFO BlockManagerInfo - Removed broadcast_85_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.1 MiB)
15:09:24.575 INFO BlockManagerInfo - Removed broadcast_73_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.2 MiB)
15:09:24.576 INFO BlockManagerInfo - Removed broadcast_88_piece0 on localhost:41569 in memory (size: 183.0 B, free: 1919.2 MiB)
15:09:24.577 INFO BlockManagerInfo - Removed broadcast_72_piece0 on localhost:41569 in memory (size: 183.0 B, free: 1919.2 MiB)
15:09:24.578 INFO BlockManagerInfo - Removed broadcast_71_piece0 on localhost:41569 in memory (size: 152.7 KiB, free: 1919.3 MiB)
15:09:24.579 INFO BlockManagerInfo - Removed broadcast_78_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.4 MiB)
15:09:24.579 INFO FileInputFormat - Total input files to process : 1
15:09:24.579 INFO BlockManagerInfo - Removed broadcast_77_piece0 on localhost:41569 in memory (size: 103.1 KiB, free: 1919.5 MiB)
15:09:24.580 INFO BlockManagerInfo - Removed broadcast_83_piece0 on localhost:41569 in memory (size: 1780.0 B, free: 1919.5 MiB)
15:09:24.581 INFO BlockManagerInfo - Removed broadcast_92_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.5 MiB)
15:09:24.582 INFO BlockManagerInfo - Removed broadcast_75_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.6 MiB)
15:09:24.583 INFO BlockManagerInfo - Removed broadcast_91_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.6 MiB)
15:09:24.584 INFO SparkContext - Starting job: count at ReadsSparkSourceUnitTest.java:265
15:09:24.584 INFO BlockManagerInfo - Removed broadcast_69_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1919.7 MiB)
15:09:24.585 INFO DAGScheduler - Got job 41 (count at ReadsSparkSourceUnitTest.java:265) with 1 output partitions
15:09:24.585 INFO DAGScheduler - Final stage: ResultStage 50 (count at ReadsSparkSourceUnitTest.java:265)
15:09:24.585 INFO DAGScheduler - Parents of final stage: List()
15:09:24.585 INFO DAGScheduler - Missing parents: List()
15:09:24.585 INFO DAGScheduler - Submitting ResultStage 50 (MapPartitionsRDD[231] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:24.587 INFO BlockManagerInfo - Removed broadcast_90_piece0 on localhost:41569 in memory (size: 202.0 B, free: 1919.7 MiB)
15:09:24.588 INFO BlockManagerInfo - Removed broadcast_87_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.7 MiB)
15:09:24.588 INFO BlockManagerInfo - Removed broadcast_79_piece0 on localhost:41569 in memory (size: 183.0 B, free: 1919.7 MiB)
15:09:24.589 INFO BlockManagerInfo - Removed broadcast_82_piece0 on localhost:41569 in memory (size: 50.1 KiB, free: 1919.8 MiB)
15:09:24.590 INFO BlockManagerInfo - Removed broadcast_74_piece0 on localhost:41569 in memory (size: 183.0 B, free: 1919.8 MiB)
15:09:24.591 INFO BlockManagerInfo - Removed broadcast_76_piece0 on localhost:41569 in memory (size: 1780.0 B, free: 1919.8 MiB)
15:09:24.592 INFO BlockManagerInfo - Removed broadcast_93_piece0 on localhost:41569 in memory (size: 152.7 KiB, free: 1919.9 MiB)
15:09:24.592 INFO BlockManagerInfo - Removed broadcast_89_piece0 on localhost:41569 in memory (size: 50.0 KiB, free: 1920.0 MiB)
15:09:24.605 INFO MemoryStore - Block broadcast_96 stored as values in memory (estimated size 424.9 KiB, free 1919.2 MiB)
15:09:24.607 INFO MemoryStore - Block broadcast_96_piece0 stored as bytes in memory (estimated size 152.8 KiB, free 1919.1 MiB)
15:09:24.607 INFO BlockManagerInfo - Added broadcast_96_piece0 in memory on localhost:41569 (size: 152.8 KiB, free: 1919.8 MiB)
15:09:24.607 INFO SparkContext - Created broadcast 96 from broadcast at DAGScheduler.scala:1580
15:09:24.608 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))
15:09:24.608 INFO TaskSchedulerImpl - Adding task set 50.0 with 1 tasks resource profile 0
15:09:24.609 INFO TaskSetManager - Starting task 0.0 in stage 50.0 (TID 119) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7831 bytes)
15:09:24.609 INFO Executor - Running task 0.0 in stage 50.0 (TID 119)
15:09:24.642 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/NA12878.chr17_69k_70k.dictFix.bam:0+57538
15:09:24.647 INFO Executor - Finished task 0.0 in stage 50.0 (TID 119). 989 bytes result sent to driver
15:09:24.648 INFO TaskSetManager - Finished task 0.0 in stage 50.0 (TID 119) in 40 ms on localhost (executor driver) (1/1)
15:09:24.648 INFO TaskSchedulerImpl - Removed TaskSet 50.0, whose tasks have all completed, from pool
15:09:24.648 INFO DAGScheduler - ResultStage 50 (count at ReadsSparkSourceUnitTest.java:265) finished in 0.063 s
15:09:24.649 INFO DAGScheduler - Job 41 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:24.649 INFO TaskSchedulerImpl - Killing all running tasks in stage 50: Stage finished
15:09:24.649 INFO DAGScheduler - Job 41 finished: count at ReadsSparkSourceUnitTest.java:265, took 0.064713 s
15:09:24.652 INFO MemoryStore - Block broadcast_97 stored as values in memory (estimated size 160.0 B, free 1919.1 MiB)
15:09:24.653 INFO MemoryStore - Block broadcast_97_piece0 stored as bytes in memory (estimated size 229.0 B, free 1919.1 MiB)
15:09:24.653 INFO BlockManagerInfo - Added broadcast_97_piece0 in memory on localhost:41569 (size: 229.0 B, free: 1919.8 MiB)
15:09:24.653 INFO SparkContext - Created broadcast 97 from broadcast at AbstractBinarySamSource.java:82
15:09:24.655 INFO MemoryStore - Block broadcast_98 stored as values in memory (estimated size 297.3 KiB, free 1918.8 MiB)
15:09:24.661 INFO MemoryStore - Block broadcast_98_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1918.8 MiB)
15:09:24.661 INFO BlockManagerInfo - Added broadcast_98_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.8 MiB)
15:09:24.662 INFO SparkContext - Created broadcast 98 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.684 INFO FileInputFormat - Total input files to process : 1
15:09:24.687 INFO SparkContext - Starting job: count at ReadsSparkSourceUnitTest.java:286
15:09:24.688 INFO DAGScheduler - Got job 42 (count at ReadsSparkSourceUnitTest.java:286) with 1 output partitions
15:09:24.688 INFO DAGScheduler - Final stage: ResultStage 51 (count at ReadsSparkSourceUnitTest.java:286)
15:09:24.688 INFO DAGScheduler - Parents of final stage: List()
15:09:24.688 INFO DAGScheduler - Missing parents: List()
15:09:24.688 INFO DAGScheduler - Submitting ResultStage 51 (MapPartitionsRDD[238] at filter at ReadsSparkSource.java:96), which has no missing parents
15:09:24.720 INFO MemoryStore - Block broadcast_99 stored as values in memory (estimated size 424.9 KiB, free 1918.3 MiB)
15:09:24.722 INFO MemoryStore - Block broadcast_99_piece0 stored as bytes in memory (estimated size 152.8 KiB, free 1918.2 MiB)
15:09:24.722 INFO BlockManagerInfo - Added broadcast_99_piece0 in memory on localhost:41569 (size: 152.8 KiB, free: 1919.6 MiB)
15:09:24.722 INFO SparkContext - Created broadcast 99 from broadcast at DAGScheduler.scala:1580
15:09:24.723 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))
15:09:24.723 INFO TaskSchedulerImpl - Adding task set 51.0 with 1 tasks resource profile 0
15:09:24.724 INFO TaskSetManager - Starting task 0.0 in stage 51.0 (TID 120) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7891 bytes)
15:09:24.724 INFO Executor - Running task 0.0 in stage 51.0 (TID 120)
15:09:24.775 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam:0+2184
15:09:24.783 INFO Executor - Finished task 0.0 in stage 51.0 (TID 120). 989 bytes result sent to driver
15:09:24.784 INFO TaskSetManager - Finished task 0.0 in stage 51.0 (TID 120) in 61 ms on localhost (executor driver) (1/1)
15:09:24.784 INFO TaskSchedulerImpl - Removed TaskSet 51.0, whose tasks have all completed, from pool
15:09:24.785 INFO DAGScheduler - ResultStage 51 (count at ReadsSparkSourceUnitTest.java:286) finished in 0.096 s
15:09:24.785 INFO DAGScheduler - Job 42 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:24.785 INFO TaskSchedulerImpl - Killing all running tasks in stage 51: Stage finished
15:09:24.785 INFO DAGScheduler - Job 42 finished: count at ReadsSparkSourceUnitTest.java:286, took 0.097927 s
15:09:24.791 INFO MemoryStore - Block broadcast_100 stored as values in memory (estimated size 297.3 KiB, free 1917.9 MiB)
15:09:24.798 INFO MemoryStore - Block broadcast_100_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.9 MiB)
15:09:24.798 INFO BlockManagerInfo - Added broadcast_100_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.6 MiB)
15:09:24.799 INFO SparkContext - Created broadcast 100 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.824 INFO MemoryStore - Block broadcast_101 stored as values in memory (estimated size 297.4 KiB, free 1917.6 MiB)
15:09:24.830 INFO MemoryStore - Block broadcast_101_piece0 stored as bytes in memory (estimated size 50.1 KiB, free 1917.5 MiB)
15:09:24.831 INFO BlockManagerInfo - Added broadcast_101_piece0 in memory on localhost:41569 (size: 50.1 KiB, free: 1919.5 MiB)
15:09:24.831 INFO SparkContext - Created broadcast 101 from newAPIHadoopFile at PathSplitSource.java:96
15:09:24.858 INFO FileInputFormat - Total input files to process : 1
15:09:24.858 INFO FileInputFormat - Total input files to process : 1