WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
22:03:45.545 INFO MemoryStore - Block broadcast_102 stored as values in memory (estimated size 81.1 KiB, free 1919.9 MiB)
22:03:45.548 INFO MemoryStore - Block broadcast_102_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1919.9 MiB)
22:03:45.549 INFO BlockManagerInfo - Added broadcast_102_piece0 in memory on localhost:41281 (size: 7.1 KiB, free: 1920.0 MiB)
22:03:45.549 INFO SparkContext - Created broadcast 102 from broadcast at VcfSource.java:129
22:03:45.555 INFO MemoryStore - Block broadcast_104 stored as values in memory (estimated size 297.9 KiB, free 1919.6 MiB)
22:03:45.559 INFO MemoryStore - Block broadcast_103 stored as values in memory (estimated size 81.1 KiB, free 1919.5 MiB)
22:03:45.569 INFO MemoryStore - Block broadcast_103_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.5 MiB)
22:03:45.570 INFO BlockManagerInfo - Added broadcast_103_piece0 in memory on localhost:41281 (size: 7.2 KiB, free: 1920.0 MiB)
22:03:45.573 INFO SparkContext - Created broadcast 103 from broadcast at VcfSource.java:129
22:03:45.576 INFO MemoryStore - Block broadcast_104_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1919.5 MiB)
22:03:45.577 INFO MemoryStore - Block broadcast_105 stored as values in memory (estimated size 297.9 KiB, free 1919.2 MiB)
22:03:45.579 INFO BlockManagerInfo - Added broadcast_104_piece0 in memory on localhost:41281 (size: 50.2 KiB, free: 1919.9 MiB)
22:03:45.579 INFO SparkContext - Created broadcast 104 from newAPIHadoopFile at VcfSource.java:168
22:03:45.589 INFO FileInputFormat - Total input files to process : 1
22:03:45.589 INFO MemoryStore - Block broadcast_105_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1919.1 MiB)
22:03:45.590 INFO BlockManagerInfo - Added broadcast_105_piece0 in memory on localhost:41281 (size: 50.2 KiB, free: 1919.9 MiB)
22:03:45.590 INFO SparkContext - Created broadcast 105 from newAPIHadoopFile at VcfSource.java:168
22:03:45.595 INFO FileInputFormat - Total input files to process : 1
22:03:45.600 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
22:03:45.612 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
22:03:45.630 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:78
22:03:45.631 INFO DAGScheduler - Got job 43 (collect at VariantsSparkSourceUnitTest.java:78) with 2 output partitions
22:03:45.631 INFO DAGScheduler - Final stage: ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78)
22:03:45.631 INFO DAGScheduler - Parents of final stage: List()
22:03:45.631 INFO DAGScheduler - Missing parents: List()
22:03:45.631 INFO DAGScheduler - Submitting ResultStage 52 (UnionRDD[266] at union at VariantsSparkSource.java:51), which has no missing parents
22:03:45.633 INFO MemoryStore - Block broadcast_106 stored as values in memory (estimated size 9.0 KiB, free 1919.1 MiB)
22:03:45.634 INFO MemoryStore - Block broadcast_106_piece0 stored as bytes in memory (estimated size 4.3 KiB, free 1919.1 MiB)
22:03:45.634 INFO BlockManagerInfo - Added broadcast_106_piece0 in memory on localhost:41281 (size: 4.3 KiB, free: 1919.9 MiB)
22:03:45.634 INFO SparkContext - Created broadcast 106 from broadcast at DAGScheduler.scala:1580
22:03:45.635 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))
22:03:45.635 INFO TaskSchedulerImpl - Adding task set 52.0 with 2 tasks resource profile 0
22:03:45.636 INFO TaskSetManager - Starting task 0.0 in stage 52.0 (TID 121) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7982 bytes)
22:03:45.636 INFO TaskSetManager - Starting task 1.0 in stage 52.0 (TID 122) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7973 bytes)
22:03:45.637 INFO Executor - Running task 0.0 in stage 52.0 (TID 121)
22:03:45.637 INFO Executor - Running task 1.0 in stage 52.0 (TID 122)
22:03:45.641 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
22:03:45.641 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
22:03:45.667 INFO Executor - Finished task 1.0 in stage 52.0 (TID 122). 12151 bytes result sent to driver
22:03:45.668 INFO Executor - Finished task 0.0 in stage 52.0 (TID 121). 12151 bytes result sent to driver
22:03:45.672 INFO TaskSetManager - Finished task 1.0 in stage 52.0 (TID 122) in 36 ms on localhost (executor driver) (1/2)
22:03:45.672 INFO TaskSetManager - Finished task 0.0 in stage 52.0 (TID 121) in 37 ms on localhost (executor driver) (2/2)
22:03:45.672 INFO TaskSchedulerImpl - Removed TaskSet 52.0, whose tasks have all completed, from pool
22:03:45.673 INFO DAGScheduler - ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78) finished in 0.040 s
22:03:45.673 INFO DAGScheduler - Job 43 is finished. Cancelling potential speculative or zombie tasks for this job
22:03:45.673 INFO TaskSchedulerImpl - Killing all running tasks in stage 52: Stage finished
22:03:45.673 INFO DAGScheduler - Job 43 finished: collect at VariantsSparkSourceUnitTest.java:78, took 0.043142 s
WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
22:03:45.691 INFO MemoryStore - Block broadcast_107 stored as values in memory (estimated size 81.1 KiB, free 1919.1 MiB)
22:03:45.694 INFO MemoryStore - Block broadcast_107_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.0 MiB)
22:03:45.694 INFO BlockManagerInfo - Added broadcast_107_piece0 in memory on localhost:41281 (size: 7.2 KiB, free: 1919.9 MiB)
22:03:45.694 INFO SparkContext - Created broadcast 107 from broadcast at VcfSource.java:129
22:03:45.696 INFO MemoryStore - Block broadcast_108 stored as values in memory (estimated size 298.2 KiB, free 1918.8 MiB)
22:03:45.702 INFO MemoryStore - Block broadcast_108_piece0 stored as bytes in memory (estimated size 50.4 KiB, free 1918.7 MiB)
22:03:45.703 INFO BlockManagerInfo - Added broadcast_108_piece0 in memory on localhost:41281 (size: 50.4 KiB, free: 1919.8 MiB)
22:03:45.703 INFO SparkContext - Created broadcast 108 from newAPIHadoopFile at VcfSource.java:168
22:03:45.706 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
22:03:45.715 INFO FileInputFormat - Total input files to process : 1
22:03:45.719 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
22:03:45.719 INFO DAGScheduler - Got job 44 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
22:03:45.719 INFO DAGScheduler - Final stage: ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43)
22:03:45.719 INFO DAGScheduler - Parents of final stage: List()
22:03:45.720 INFO DAGScheduler - Missing parents: List()
22:03:45.720 INFO DAGScheduler - Submitting ResultStage 53 (MapPartitionsRDD[271] at map at VariantsSparkSource.java:38), which has no missing parents
22:03:45.721 INFO MemoryStore - Block broadcast_109 stored as values in memory (estimated size 7.4 KiB, free 1918.7 MiB)
22:03:45.721 INFO MemoryStore - Block broadcast_109_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.7 MiB)
22:03:45.721 INFO BlockManagerInfo - Added broadcast_109_piece0 in memory on localhost:41281 (size: 3.7 KiB, free: 1919.8 MiB)
22:03:45.722 INFO SparkContext - Created broadcast 109 from broadcast at DAGScheduler.scala:1580
22:03:45.722 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))
22:03:45.722 INFO TaskSchedulerImpl - Adding task set 53.0 with 1 tasks resource profile 0
22:03:45.723 INFO TaskSetManager - Starting task 0.0 in stage 53.0 (TID 123) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes)
22:03:45.723 INFO Executor - Running task 0.0 in stage 53.0 (TID 123)
22:03:45.725 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
22:03:45.742 INFO Executor - Finished task 0.0 in stage 53.0 (TID 123). 12108 bytes result sent to driver
22:03:45.744 INFO TaskSetManager - Finished task 0.0 in stage 53.0 (TID 123) in 22 ms on localhost (executor driver) (1/1)
22:03:45.744 INFO TaskSchedulerImpl - Removed TaskSet 53.0, whose tasks have all completed, from pool
22:03:45.744 INFO DAGScheduler - ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.024 s
22:03:45.745 INFO DAGScheduler - Job 44 is finished. Cancelling potential speculative or zombie tasks for this job
22:03:45.745 INFO TaskSchedulerImpl - Killing all running tasks in stage 53: Stage finished
22:03:45.745 INFO DAGScheduler - Job 44 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.025964 s
WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
22:03:45.758 INFO MemoryStore - Block broadcast_110 stored as values in memory (estimated size 81.1 KiB, free 1918.6 MiB)
22:03:45.759 INFO MemoryStore - Block broadcast_110_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1918.6 MiB)
22:03:45.759 INFO BlockManagerInfo - Added broadcast_110_piece0 in memory on localhost:41281 (size: 7.1 KiB, free: 1919.8 MiB)
22:03:45.759 INFO SparkContext - Created broadcast 110 from broadcast at VcfSource.java:129
22:03:45.761 INFO MemoryStore - Block broadcast_111 stored as values in memory (estimated size 298.5 KiB, free 1918.3 MiB)
22:03:45.767 INFO MemoryStore - Block broadcast_111_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1918.3 MiB)
22:03:45.767 INFO BlockManagerInfo - Added broadcast_111_piece0 in memory on localhost:41281 (size: 50.3 KiB, free: 1919.8 MiB)
22:03:45.768 INFO SparkContext - Created broadcast 111 from newAPIHadoopFile at VcfSource.java:168
22:03:45.771 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
22:03:45.776 INFO FileInputFormat - Total input files to process : 1
22:03:45.780 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
22:03:45.781 INFO DAGScheduler - Got job 45 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
22:03:45.781 INFO DAGScheduler - Final stage: ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43)
22:03:45.781 INFO DAGScheduler - Parents of final stage: List()
22:03:45.781 INFO DAGScheduler - Missing parents: List()
22:03:45.781 INFO DAGScheduler - Submitting ResultStage 54 (MapPartitionsRDD[276] at map at VariantsSparkSource.java:38), which has no missing parents
22:03:45.782 INFO MemoryStore - Block broadcast_112 stored as values in memory (estimated size 7.4 KiB, free 1918.3 MiB)
22:03:45.783 INFO MemoryStore - Block broadcast_112_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.3 MiB)
22:03:45.783 INFO BlockManagerInfo - Added broadcast_112_piece0 in memory on localhost:41281 (size: 3.7 KiB, free: 1919.8 MiB)
22:03:45.783 INFO SparkContext - Created broadcast 112 from broadcast at DAGScheduler.scala:1580
22:03:45.783 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))
22:03:45.783 INFO TaskSchedulerImpl - Adding task set 54.0 with 1 tasks resource profile 0
22:03:45.784 INFO TaskSetManager - Starting task 0.0 in stage 54.0 (TID 124) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes)
22:03:45.785 INFO Executor - Running task 0.0 in stage 54.0 (TID 124)
22:03:45.787 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
22:03:45.801 INFO Executor - Finished task 0.0 in stage 54.0 (TID 124). 12108 bytes result sent to driver
22:03:45.803 INFO TaskSetManager - Finished task 0.0 in stage 54.0 (TID 124) in 19 ms on localhost (executor driver) (1/1)
22:03:45.803 INFO TaskSchedulerImpl - Removed TaskSet 54.0, whose tasks have all completed, from pool
22:03:45.804 INFO DAGScheduler - ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.022 s
22:03:45.804 INFO DAGScheduler - Job 45 is finished. Cancelling potential speculative or zombie tasks for this job
22:03:45.804 INFO TaskSchedulerImpl - Killing all running tasks in stage 54: Stage finished
22:03:45.804 INFO DAGScheduler - Job 45 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.023521 s
WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
22:03:45.815 INFO MemoryStore - Block broadcast_113 stored as values in memory (estimated size 81.1 KiB, free 1918.2 MiB)
22:03:45.816 INFO MemoryStore - Block broadcast_113_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1918.2 MiB)
22:03:45.816 INFO BlockManagerInfo - Added broadcast_113_piece0 in memory on localhost:41281 (size: 7.2 KiB, free: 1919.8 MiB)
22:03:45.817 INFO SparkContext - Created broadcast 113 from broadcast at VcfSource.java:129
22:03:45.818 INFO MemoryStore - Block broadcast_114 stored as values in memory (estimated size 298.8 KiB, free 1917.9 MiB)
22:03:45.824 INFO MemoryStore - Block broadcast_114_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1917.8 MiB)
22:03:45.825 INFO BlockManagerInfo - Added broadcast_114_piece0 in memory on localhost:41281 (size: 50.3 KiB, free: 1919.7 MiB)
22:03:45.825 INFO SparkContext - Created broadcast 114 from newAPIHadoopFile at VcfSource.java:168
22:03:45.827 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
22:03:45.832 INFO FileInputFormat - Total input files to process : 1
22:03:45.836 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
22:03:45.837 INFO DAGScheduler - Got job 46 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
22:03:45.837 INFO DAGScheduler - Final stage: ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55)
22:03:45.837 INFO DAGScheduler - Parents of final stage: List()
22:03:45.837 INFO DAGScheduler - Missing parents: List()
22:03:45.837 INFO DAGScheduler - Submitting ResultStage 55 (MapPartitionsRDD[279] at mapPartitions at VcfSource.java:134), which has no missing parents
22:03:45.838 INFO MemoryStore - Block broadcast_115 stored as values in memory (estimated size 6.3 KiB, free 1917.8 MiB)
22:03:45.839 INFO MemoryStore - Block broadcast_115_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.8 MiB)
22:03:45.839 INFO BlockManagerInfo - Added broadcast_115_piece0 in memory on localhost:41281 (size: 3.4 KiB, free: 1919.7 MiB)
22:03:45.839 INFO SparkContext - Created broadcast 115 from broadcast at DAGScheduler.scala:1580
22:03:45.839 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))
22:03:45.839 INFO TaskSchedulerImpl - Adding task set 55.0 with 1 tasks resource profile 0
22:03:45.840 INFO TaskSetManager - Starting task 0.0 in stage 55.0 (TID 125) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes)
22:03:45.841 INFO Executor - Running task 0.0 in stage 55.0 (TID 125)
22:03:45.842 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
22:03:45.868 INFO Executor - Finished task 0.0 in stage 55.0 (TID 125). 153274 bytes result sent to driver
22:03:45.880 INFO TaskSetManager - Finished task 0.0 in stage 55.0 (TID 125) in 40 ms on localhost (executor driver) (1/1)
22:03:45.880 INFO TaskSchedulerImpl - Removed TaskSet 55.0, whose tasks have all completed, from pool
22:03:45.881 INFO DAGScheduler - ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.043 s
22:03:45.881 INFO DAGScheduler - Job 46 is finished. Cancelling potential speculative or zombie tasks for this job
22:03:45.881 INFO TaskSchedulerImpl - Killing all running tasks in stage 55: Stage finished
22:03:45.881 INFO DAGScheduler - Job 46 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.044819 s
WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-04-22 22:03:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
22:03:45.904 INFO MemoryStore - Block broadcast_116 stored as values in memory (estimated size 81.1 KiB, free 1917.7 MiB)
22:03:45.905 INFO MemoryStore - Block broadcast_116_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1917.7 MiB)
22:03:45.906 INFO BlockManagerInfo - Added broadcast_116_piece0 in memory on localhost:41281 (size: 7.1 KiB, free: 1919.7 MiB)
22:03:45.906 INFO SparkContext - Created broadcast 116 from broadcast at VcfSource.java:129
22:03:45.907 INFO MemoryStore - Block broadcast_117 stored as values in memory (estimated size 299.0 KiB, free 1917.4 MiB)
22:03:45.914 INFO MemoryStore - Block broadcast_117_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1917.4 MiB)
22:03:45.914 INFO BlockManagerInfo - Added broadcast_117_piece0 in memory on localhost:41281 (size: 50.3 KiB, free: 1919.6 MiB)
22:03:45.914 INFO SparkContext - Created broadcast 117 from newAPIHadoopFile at VcfSource.java:168
22:03:45.916 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
22:03:45.923 INFO FileInputFormat - Total input files to process : 1
22:03:45.927 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
22:03:45.928 INFO DAGScheduler - Got job 47 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
22:03:45.928 INFO DAGScheduler - Final stage: ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55)
22:03:45.928 INFO DAGScheduler - Parents of final stage: List()
22:03:45.928 INFO DAGScheduler - Missing parents: List()
22:03:45.928 INFO DAGScheduler - Submitting ResultStage 56 (MapPartitionsRDD[282] at mapPartitions at VcfSource.java:134), which has no missing parents
22:03:45.929 INFO MemoryStore - Block broadcast_118 stored as values in memory (estimated size 6.3 KiB, free 1917.4 MiB)
22:03:45.930 INFO MemoryStore - Block broadcast_118_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.4 MiB)
22:03:45.930 INFO BlockManagerInfo - Added broadcast_118_piece0 in memory on localhost:41281 (size: 3.4 KiB, free: 1919.6 MiB)
22:03:45.930 INFO SparkContext - Created broadcast 118 from broadcast at DAGScheduler.scala:1580
22:03:45.930 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))
22:03:45.930 INFO TaskSchedulerImpl - Adding task set 56.0 with 1 tasks resource profile 0
22:03:45.931 INFO TaskSetManager - Starting task 0.0 in stage 56.0 (TID 126) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes)
22:03:45.932 INFO Executor - Running task 0.0 in stage 56.0 (TID 126)
22:03:45.933 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
22:03:45.960 INFO Executor - Finished task 0.0 in stage 56.0 (TID 126). 153274 bytes result sent to driver
22:03:45.968 INFO TaskSetManager - Finished task 0.0 in stage 56.0 (TID 126) in 36 ms on localhost (executor driver) (1/1)
22:03:45.968 INFO TaskSchedulerImpl - Removed TaskSet 56.0, whose tasks have all completed, from pool
22:03:45.968 INFO DAGScheduler - ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.039 s
22:03:45.968 INFO DAGScheduler - Job 47 is finished. Cancelling potential speculative or zombie tasks for this job
22:03:45.968 INFO TaskSchedulerImpl - Killing all running tasks in stage 56: Stage finished
22:03:45.968 INFO DAGScheduler - Job 47 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.040550 s