16:12:18.427 INFO BlockManagerInfo - Removed broadcast_100_piece0 on localhost:40883 in memory (size: 50.1 KiB, free: 1919.9 MiB)
16:12:18.428 INFO BlockManagerInfo - Removed broadcast_89_piece0 on localhost:40883 in memory (size: 50.0 KiB, free: 1919.9 MiB)
16:12:18.429 INFO BlockManagerInfo - Removed broadcast_98_piece0 on localhost:40883 in memory (size: 50.1 KiB, free: 1920.0 MiB)
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
16:12:18.431 INFO BlockManagerInfo - Removed broadcast_82_piece0 on localhost:40883 in memory (size: 50.1 KiB, free: 1920.0 MiB)
16:12:18.435 INFO BlockManagerInfo - Removed broadcast_90_piece0 on localhost:40883 in memory (size: 202.0 B, free: 1920.0 MiB)
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
16:12:18.452 INFO MemoryStore - Block broadcast_102 stored as values in memory (estimated size 81.1 KiB, free 1919.9 MiB)
16:12:18.456 INFO MemoryStore - Block broadcast_102_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1919.9 MiB)
16:12:18.456 INFO BlockManagerInfo - Added broadcast_102_piece0 in memory on localhost:40883 (size: 7.1 KiB, free: 1920.0 MiB)
16:12:18.457 INFO MemoryStore - Block broadcast_103 stored as values in memory (estimated size 81.1 KiB, free 1919.8 MiB)
16:12:18.457 INFO SparkContext - Created broadcast 102 from broadcast at VcfSource.java:129
16:12:18.460 INFO MemoryStore - Block broadcast_103_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.8 MiB)
16:12:18.460 INFO MemoryStore - Block broadcast_104 stored as values in memory (estimated size 297.9 KiB, free 1919.5 MiB)
16:12:18.460 INFO BlockManagerInfo - Added broadcast_103_piece0 in memory on localhost:40883 (size: 7.2 KiB, free: 1920.0 MiB)
16:12:18.460 INFO SparkContext - Created broadcast 103 from broadcast at VcfSource.java:129
16:12:18.462 INFO MemoryStore - Block broadcast_105 stored as values in memory (estimated size 297.9 KiB, free 1919.2 MiB)
16:12:18.470 INFO MemoryStore - Block broadcast_105_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1919.2 MiB)
16:12:18.470 INFO BlockManagerInfo - Added broadcast_105_piece0 in memory on localhost:40883 (size: 50.2 KiB, free: 1919.9 MiB)
16:12:18.470 INFO SparkContext - Created broadcast 105 from newAPIHadoopFile at VcfSource.java:168
16:12:18.473 INFO MemoryStore - Block broadcast_104_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1919.1 MiB)
16:12:18.473 INFO BlockManagerInfo - Added broadcast_104_piece0 in memory on localhost:40883 (size: 50.2 KiB, free: 1919.9 MiB)
16:12:18.473 INFO SparkContext - Created broadcast 104 from newAPIHadoopFile at VcfSource.java:168
16:12:18.479 INFO FileInputFormat - Total input files to process : 1
16:12:18.481 INFO FileInputFormat - Total input files to process : 1
16:12:18.490 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
16:12:18.502 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
16:12:18.518 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:78
16:12:18.520 INFO DAGScheduler - Got job 43 (collect at VariantsSparkSourceUnitTest.java:78) with 2 output partitions
16:12:18.520 INFO DAGScheduler - Final stage: ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78)
16:12:18.520 INFO DAGScheduler - Parents of final stage: List()
16:12:18.520 INFO DAGScheduler - Missing parents: List()
16:12:18.520 INFO DAGScheduler - Submitting ResultStage 52 (UnionRDD[266] at union at VariantsSparkSource.java:51), which has no missing parents
16:12:18.522 INFO MemoryStore - Block broadcast_106 stored as values in memory (estimated size 9.0 KiB, free 1919.1 MiB)
16:12:18.523 INFO MemoryStore - Block broadcast_106_piece0 stored as bytes in memory (estimated size 4.3 KiB, free 1919.1 MiB)
16:12:18.523 INFO BlockManagerInfo - Added broadcast_106_piece0 in memory on localhost:40883 (size: 4.3 KiB, free: 1919.9 MiB)
16:12:18.523 INFO SparkContext - Created broadcast 106 from broadcast at DAGScheduler.scala:1580
16:12:18.523 INFO DAGScheduler - Submitting 2 missing tasks from ResultStage 52 (UnionRDD[266] at union at VariantsSparkSource.java:51) (first 15 tasks are for partitions Vector(0, 1))
16:12:18.524 INFO TaskSchedulerImpl - Adding task set 52.0 with 2 tasks resource profile 0
16:12:18.525 INFO TaskSetManager - Starting task 0.0 in stage 52.0 (TID 121) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7982 bytes)
16:12:18.525 INFO TaskSetManager - Starting task 1.0 in stage 52.0 (TID 122) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7973 bytes)
16:12:18.526 INFO Executor - Running task 0.0 in stage 52.0 (TID 121)
16:12:18.526 INFO Executor - Running task 1.0 in stage 52.0 (TID 122)
16:12:18.531 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
16:12:18.531 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
16:12:18.559 INFO Executor - Finished task 0.0 in stage 52.0 (TID 121). 12151 bytes result sent to driver
16:12:18.559 INFO Executor - Finished task 1.0 in stage 52.0 (TID 122). 12151 bytes result sent to driver
16:12:18.564 INFO TaskSetManager - Finished task 0.0 in stage 52.0 (TID 121) in 40 ms on localhost (executor driver) (1/2)
16:12:18.564 INFO TaskSetManager - Finished task 1.0 in stage 52.0 (TID 122) in 39 ms on localhost (executor driver) (2/2)
16:12:18.564 INFO TaskSchedulerImpl - Removed TaskSet 52.0, whose tasks have all completed, from pool
16:12:18.566 INFO DAGScheduler - ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78) finished in 0.045 s
16:12:18.566 INFO DAGScheduler - Job 43 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:18.566 INFO TaskSchedulerImpl - Killing all running tasks in stage 52: Stage finished
16:12:18.567 INFO DAGScheduler - Job 43 finished: collect at VariantsSparkSourceUnitTest.java:78, took 0.048870 s
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
16:12:18.581 INFO MemoryStore - Block broadcast_107 stored as values in memory (estimated size 81.1 KiB, free 1919.1 MiB)
16:12:18.582 INFO MemoryStore - Block broadcast_107_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.0 MiB)
16:12:18.583 INFO BlockManagerInfo - Added broadcast_107_piece0 in memory on localhost:40883 (size: 7.2 KiB, free: 1919.9 MiB)
16:12:18.583 INFO SparkContext - Created broadcast 107 from broadcast at VcfSource.java:129
16:12:18.585 INFO MemoryStore - Block broadcast_108 stored as values in memory (estimated size 298.2 KiB, free 1918.8 MiB)
16:12:18.592 INFO MemoryStore - Block broadcast_108_piece0 stored as bytes in memory (estimated size 50.4 KiB, free 1918.7 MiB)
16:12:18.592 INFO BlockManagerInfo - Added broadcast_108_piece0 in memory on localhost:40883 (size: 50.4 KiB, free: 1919.8 MiB)
16:12:18.593 INFO SparkContext - Created broadcast 108 from newAPIHadoopFile at VcfSource.java:168
16:12:18.595 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
16:12:18.602 INFO FileInputFormat - Total input files to process : 1
16:12:18.606 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
16:12:18.606 INFO DAGScheduler - Got job 44 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
16:12:18.606 INFO DAGScheduler - Final stage: ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43)
16:12:18.606 INFO DAGScheduler - Parents of final stage: List()
16:12:18.606 INFO DAGScheduler - Missing parents: List()
16:12:18.607 INFO DAGScheduler - Submitting ResultStage 53 (MapPartitionsRDD[271] at map at VariantsSparkSource.java:38), which has no missing parents
16:12:18.607 INFO MemoryStore - Block broadcast_109 stored as values in memory (estimated size 7.4 KiB, free 1918.7 MiB)
16:12:18.608 INFO MemoryStore - Block broadcast_109_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.7 MiB)
16:12:18.608 INFO BlockManagerInfo - Added broadcast_109_piece0 in memory on localhost:40883 (size: 3.7 KiB, free: 1919.8 MiB)
16:12:18.608 INFO SparkContext - Created broadcast 109 from broadcast at DAGScheduler.scala:1580
16:12:18.609 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 53 (MapPartitionsRDD[271] at map at VariantsSparkSource.java:38) (first 15 tasks are for partitions Vector(0))
16:12:18.609 INFO TaskSchedulerImpl - Adding task set 53.0 with 1 tasks resource profile 0
16:12:18.609 INFO TaskSetManager - Starting task 0.0 in stage 53.0 (TID 123) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes)
16:12:18.610 INFO Executor - Running task 0.0 in stage 53.0 (TID 123)
16:12:18.612 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
16:12:18.621 INFO Executor - Finished task 0.0 in stage 53.0 (TID 123). 12108 bytes result sent to driver
16:12:18.623 INFO TaskSetManager - Finished task 0.0 in stage 53.0 (TID 123) in 14 ms on localhost (executor driver) (1/1)
16:12:18.623 INFO TaskSchedulerImpl - Removed TaskSet 53.0, whose tasks have all completed, from pool
16:12:18.623 INFO DAGScheduler - ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.016 s
16:12:18.623 INFO DAGScheduler - Job 44 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:18.623 INFO TaskSchedulerImpl - Killing all running tasks in stage 53: Stage finished
16:12:18.623 INFO DAGScheduler - Job 44 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.017476 s
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
16:12:18.635 INFO MemoryStore - Block broadcast_110 stored as values in memory (estimated size 81.1 KiB, free 1918.6 MiB)
16:12:18.637 INFO MemoryStore - Block broadcast_110_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1918.6 MiB)
16:12:18.637 INFO BlockManagerInfo - Added broadcast_110_piece0 in memory on localhost:40883 (size: 7.1 KiB, free: 1919.8 MiB)
16:12:18.637 INFO SparkContext - Created broadcast 110 from broadcast at VcfSource.java:129
16:12:18.639 INFO MemoryStore - Block broadcast_111 stored as values in memory (estimated size 298.5 KiB, free 1918.3 MiB)
16:12:18.646 INFO MemoryStore - Block broadcast_111_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1918.3 MiB)
16:12:18.646 INFO BlockManagerInfo - Added broadcast_111_piece0 in memory on localhost:40883 (size: 50.3 KiB, free: 1919.8 MiB)
16:12:18.646 INFO SparkContext - Created broadcast 111 from newAPIHadoopFile at VcfSource.java:168
16:12:18.649 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
16:12:18.655 INFO FileInputFormat - Total input files to process : 1
16:12:18.660 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
16:12:18.660 INFO DAGScheduler - Got job 45 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
16:12:18.660 INFO DAGScheduler - Final stage: ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43)
16:12:18.660 INFO DAGScheduler - Parents of final stage: List()
16:12:18.661 INFO DAGScheduler - Missing parents: List()
16:12:18.661 INFO DAGScheduler - Submitting ResultStage 54 (MapPartitionsRDD[276] at map at VariantsSparkSource.java:38), which has no missing parents
16:12:18.662 INFO MemoryStore - Block broadcast_112 stored as values in memory (estimated size 7.4 KiB, free 1918.3 MiB)
16:12:18.663 INFO MemoryStore - Block broadcast_112_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.3 MiB)
16:12:18.664 INFO BlockManagerInfo - Added broadcast_112_piece0 in memory on localhost:40883 (size: 3.7 KiB, free: 1919.8 MiB)
16:12:18.664 INFO SparkContext - Created broadcast 112 from broadcast at DAGScheduler.scala:1580
16:12:18.664 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 54 (MapPartitionsRDD[276] at map at VariantsSparkSource.java:38) (first 15 tasks are for partitions Vector(0))
16:12:18.664 INFO TaskSchedulerImpl - Adding task set 54.0 with 1 tasks resource profile 0
16:12:18.665 INFO TaskSetManager - Starting task 0.0 in stage 54.0 (TID 124) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes)
16:12:18.666 INFO Executor - Running task 0.0 in stage 54.0 (TID 124)
16:12:18.668 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
16:12:18.679 INFO Executor - Finished task 0.0 in stage 54.0 (TID 124). 12108 bytes result sent to driver
16:12:18.681 INFO TaskSetManager - Finished task 0.0 in stage 54.0 (TID 124) in 16 ms on localhost (executor driver) (1/1)
16:12:18.681 INFO TaskSchedulerImpl - Removed TaskSet 54.0, whose tasks have all completed, from pool
16:12:18.681 INFO DAGScheduler - ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.019 s
16:12:18.681 INFO DAGScheduler - Job 45 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:18.681 INFO TaskSchedulerImpl - Killing all running tasks in stage 54: Stage finished
16:12:18.682 INFO DAGScheduler - Job 45 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.021723 s
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
16:12:18.694 INFO MemoryStore - Block broadcast_113 stored as values in memory (estimated size 81.1 KiB, free 1918.2 MiB)
16:12:18.696 INFO MemoryStore - Block broadcast_113_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1918.2 MiB)
16:12:18.696 INFO BlockManagerInfo - Added broadcast_113_piece0 in memory on localhost:40883 (size: 7.2 KiB, free: 1919.8 MiB)
16:12:18.696 INFO SparkContext - Created broadcast 113 from broadcast at VcfSource.java:129
16:12:18.698 INFO MemoryStore - Block broadcast_114 stored as values in memory (estimated size 298.8 KiB, free 1917.9 MiB)
16:12:18.704 INFO MemoryStore - Block broadcast_114_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1917.8 MiB)
16:12:18.705 INFO BlockManagerInfo - Added broadcast_114_piece0 in memory on localhost:40883 (size: 50.3 KiB, free: 1919.7 MiB)
16:12:18.705 INFO SparkContext - Created broadcast 114 from newAPIHadoopFile at VcfSource.java:168
16:12:18.708 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
16:12:18.714 INFO FileInputFormat - Total input files to process : 1
16:12:18.718 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
16:12:18.719 INFO DAGScheduler - Got job 46 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
16:12:18.719 INFO DAGScheduler - Final stage: ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55)
16:12:18.719 INFO DAGScheduler - Parents of final stage: List()
16:12:18.719 INFO DAGScheduler - Missing parents: List()
16:12:18.719 INFO DAGScheduler - Submitting ResultStage 55 (MapPartitionsRDD[279] at mapPartitions at VcfSource.java:134), which has no missing parents
16:12:18.720 INFO MemoryStore - Block broadcast_115 stored as values in memory (estimated size 6.3 KiB, free 1917.8 MiB)
16:12:18.720 INFO MemoryStore - Block broadcast_115_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.8 MiB)
16:12:18.721 INFO BlockManagerInfo - Added broadcast_115_piece0 in memory on localhost:40883 (size: 3.4 KiB, free: 1919.7 MiB)
16:12:18.721 INFO SparkContext - Created broadcast 115 from broadcast at DAGScheduler.scala:1580
16:12:18.721 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 55 (MapPartitionsRDD[279] at mapPartitions at VcfSource.java:134) (first 15 tasks are for partitions Vector(0))
16:12:18.721 INFO TaskSchedulerImpl - Adding task set 55.0 with 1 tasks resource profile 0
16:12:18.722 INFO TaskSetManager - Starting task 0.0 in stage 55.0 (TID 125) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes)
16:12:18.723 INFO Executor - Running task 0.0 in stage 55.0 (TID 125)
16:12:18.725 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
16:12:18.751 INFO Executor - Finished task 0.0 in stage 55.0 (TID 125). 153274 bytes result sent to driver
16:12:18.765 INFO TaskSetManager - Finished task 0.0 in stage 55.0 (TID 125) in 43 ms on localhost (executor driver) (1/1)
16:12:18.765 INFO TaskSchedulerImpl - Removed TaskSet 55.0, whose tasks have all completed, from pool
16:12:18.766 INFO DAGScheduler - ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.047 s
16:12:18.766 INFO DAGScheduler - Job 46 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:18.766 INFO TaskSchedulerImpl - Killing all running tasks in stage 55: Stage finished
16:12:18.766 INFO DAGScheduler - Job 46 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.048056 s
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-05 16:12:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
16:12:18.792 INFO MemoryStore - Block broadcast_116 stored as values in memory (estimated size 81.1 KiB, free 1917.7 MiB)
16:12:18.793 INFO MemoryStore - Block broadcast_116_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1917.7 MiB)
16:12:18.793 INFO BlockManagerInfo - Added broadcast_116_piece0 in memory on localhost:40883 (size: 7.1 KiB, free: 1919.7 MiB)
16:12:18.794 INFO SparkContext - Created broadcast 116 from broadcast at VcfSource.java:129
16:12:18.796 INFO MemoryStore - Block broadcast_117 stored as values in memory (estimated size 299.0 KiB, free 1917.4 MiB)
16:12:18.802 INFO MemoryStore - Block broadcast_117_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1917.4 MiB)
16:12:18.802 INFO BlockManagerInfo - Added broadcast_117_piece0 in memory on localhost:40883 (size: 50.3 KiB, free: 1919.6 MiB)
16:12:18.803 INFO SparkContext - Created broadcast 117 from newAPIHadoopFile at VcfSource.java:168
16:12:18.805 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
16:12:18.811 INFO FileInputFormat - Total input files to process : 1
16:12:18.815 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
16:12:18.815 INFO DAGScheduler - Got job 47 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
16:12:18.816 INFO DAGScheduler - Final stage: ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55)
16:12:18.816 INFO DAGScheduler - Parents of final stage: List()
16:12:18.816 INFO DAGScheduler - Missing parents: List()
16:12:18.816 INFO DAGScheduler - Submitting ResultStage 56 (MapPartitionsRDD[282] at mapPartitions at VcfSource.java:134), which has no missing parents
16:12:18.817 INFO MemoryStore - Block broadcast_118 stored as values in memory (estimated size 6.3 KiB, free 1917.4 MiB)
16:12:18.817 INFO MemoryStore - Block broadcast_118_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.4 MiB)
16:12:18.817 INFO BlockManagerInfo - Added broadcast_118_piece0 in memory on localhost:40883 (size: 3.4 KiB, free: 1919.6 MiB)
16:12:18.818 INFO SparkContext - Created broadcast 118 from broadcast at DAGScheduler.scala:1580
16:12:18.818 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 56 (MapPartitionsRDD[282] at mapPartitions at VcfSource.java:134) (first 15 tasks are for partitions Vector(0))
16:12:18.818 INFO TaskSchedulerImpl - Adding task set 56.0 with 1 tasks resource profile 0
16:12:18.818 INFO TaskSetManager - Starting task 0.0 in stage 56.0 (TID 126) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes)
16:12:18.819 INFO Executor - Running task 0.0 in stage 56.0 (TID 126)
16:12:18.821 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
16:12:18.848 INFO Executor - Finished task 0.0 in stage 56.0 (TID 126). 153274 bytes result sent to driver
16:12:18.857 INFO TaskSetManager - Finished task 0.0 in stage 56.0 (TID 126) in 39 ms on localhost (executor driver) (1/1)
16:12:18.857 INFO TaskSchedulerImpl - Removed TaskSet 56.0, whose tasks have all completed, from pool
16:12:18.857 INFO DAGScheduler - ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.041 s
16:12:18.857 INFO DAGScheduler - Job 47 is finished. Cancelling potential speculative or zombie tasks for this job
16:12:18.857 INFO TaskSchedulerImpl - Killing all running tasks in stage 56: Stage finished
16:12:18.857 INFO DAGScheduler - Job 47 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.042085 s