20:25:28.330 INFO BlockManagerInfo - Removed broadcast_92_piece0 on localhost:39477 in memory (size: 50.1 KiB, free: 1919.6 MiB)
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
20:25:28.336 INFO BlockManagerInfo - Removed broadcast_94_piece0 on localhost:39477 in memory (size: 239.0 B, free: 1919.6 MiB)
20:25:28.337 INFO BlockManagerInfo - Removed broadcast_99_piece0 on localhost:39477 in memory (size: 152.8 KiB, free: 1919.7 MiB)
20:25:28.338 INFO BlockManagerInfo - Removed broadcast_85_piece0 on localhost:39477 in memory (size: 50.0 KiB, free: 1919.8 MiB)
20:25:28.339 INFO BlockManagerInfo - Removed broadcast_93_piece0 on localhost:39477 in memory (size: 152.7 KiB, free: 1919.9 MiB)
20:25:28.342 INFO BlockManagerInfo - Removed broadcast_90_piece0 on localhost:39477 in memory (size: 202.0 B, free: 1919.9 MiB)
20:25:28.343 INFO BlockManagerInfo - Removed broadcast_86_piece0 on localhost:39477 in memory (size: 50.1 KiB, free: 1920.0 MiB)
20:25:28.344 INFO BlockManagerInfo - Removed broadcast_100_piece0 on localhost:39477 in memory (size: 50.1 KiB, free: 1920.0 MiB)
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
20:25:28.357 INFO MemoryStore - Block broadcast_102 stored as values in memory (estimated size 81.1 KiB, free 1919.9 MiB)
20:25:28.361 INFO MemoryStore - Block broadcast_102_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.9 MiB)
20:25:28.361 INFO BlockManagerInfo - Added broadcast_102_piece0 in memory on localhost:39477 (size: 7.2 KiB, free: 1920.0 MiB)
20:25:28.361 INFO SparkContext - Created broadcast 102 from broadcast at VcfSource.java:129
20:25:28.362 INFO MemoryStore - Block broadcast_103 stored as values in memory (estimated size 81.1 KiB, free 1919.8 MiB)
20:25:28.364 INFO MemoryStore - Block broadcast_103_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1919.8 MiB)
20:25:28.365 INFO MemoryStore - Block broadcast_104 stored as values in memory (estimated size 297.9 KiB, free 1919.5 MiB)
20:25:28.366 INFO BlockManagerInfo - Added broadcast_103_piece0 in memory on localhost:39477 (size: 7.1 KiB, free: 1920.0 MiB)
20:25:28.367 INFO SparkContext - Created broadcast 103 from broadcast at VcfSource.java:129
20:25:28.371 INFO MemoryStore - Block broadcast_105 stored as values in memory (estimated size 297.9 KiB, free 1919.2 MiB)
20:25:28.383 INFO MemoryStore - Block broadcast_105_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1919.2 MiB)
20:25:28.383 INFO BlockManagerInfo - Added broadcast_105_piece0 in memory on localhost:39477 (size: 50.2 KiB, free: 1919.9 MiB)
20:25:28.384 INFO SparkContext - Created broadcast 105 from newAPIHadoopFile at VcfSource.java:168
20:25:28.386 INFO MemoryStore - Block broadcast_104_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1919.1 MiB)
20:25:28.386 INFO BlockManagerInfo - Added broadcast_104_piece0 in memory on localhost:39477 (size: 50.2 KiB, free: 1919.9 MiB)
20:25:28.387 INFO SparkContext - Created broadcast 104 from newAPIHadoopFile at VcfSource.java:168
20:25:28.393 INFO FileInputFormat - Total input files to process : 1
20:25:28.393 INFO FileInputFormat - Total input files to process : 1
20:25:28.400 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
20:25:28.412 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
20:25:28.431 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:78
20:25:28.433 INFO DAGScheduler - Got job 43 (collect at VariantsSparkSourceUnitTest.java:78) with 2 output partitions
20:25:28.433 INFO DAGScheduler - Final stage: ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78)
20:25:28.433 INFO DAGScheduler - Parents of final stage: List()
20:25:28.434 INFO DAGScheduler - Missing parents: List()
20:25:28.434 INFO DAGScheduler - Submitting ResultStage 52 (UnionRDD[266] at union at VariantsSparkSource.java:51), which has no missing parents
20:25:28.436 INFO MemoryStore - Block broadcast_106 stored as values in memory (estimated size 9.0 KiB, free 1919.1 MiB)
20:25:28.437 INFO MemoryStore - Block broadcast_106_piece0 stored as bytes in memory (estimated size 4.3 KiB, free 1919.1 MiB)
20:25:28.437 INFO BlockManagerInfo - Added broadcast_106_piece0 in memory on localhost:39477 (size: 4.3 KiB, free: 1919.9 MiB)
20:25:28.437 INFO SparkContext - Created broadcast 106 from broadcast at DAGScheduler.scala:1580
20:25:28.438 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))
20:25:28.438 INFO TaskSchedulerImpl - Adding task set 52.0 with 2 tasks resource profile 0
20:25:28.439 INFO TaskSetManager - Starting task 0.0 in stage 52.0 (TID 121) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7982 bytes)
20:25:28.440 INFO TaskSetManager - Starting task 1.0 in stage 52.0 (TID 122) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7973 bytes)
20:25:28.440 INFO Executor - Running task 0.0 in stage 52.0 (TID 121)
20:25:28.440 INFO Executor - Running task 1.0 in stage 52.0 (TID 122)
20:25:28.444 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
20:25:28.445 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
20:25:28.474 INFO Executor - Finished task 0.0 in stage 52.0 (TID 121). 12151 bytes result sent to driver
20:25:28.474 INFO Executor - Finished task 1.0 in stage 52.0 (TID 122). 12151 bytes result sent to driver
20:25:28.481 INFO TaskSetManager - Finished task 0.0 in stage 52.0 (TID 121) in 43 ms on localhost (executor driver) (1/2)
20:25:28.482 INFO TaskSetManager - Finished task 1.0 in stage 52.0 (TID 122) in 43 ms on localhost (executor driver) (2/2)
20:25:28.482 INFO TaskSchedulerImpl - Removed TaskSet 52.0, whose tasks have all completed, from pool
20:25:28.482 INFO DAGScheduler - ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78) finished in 0.047 s
20:25:28.482 INFO DAGScheduler - Job 43 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:28.482 INFO TaskSchedulerImpl - Killing all running tasks in stage 52: Stage finished
20:25:28.483 INFO DAGScheduler - Job 43 finished: collect at VariantsSparkSourceUnitTest.java:78, took 0.050833 s
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
20:25:28.497 INFO MemoryStore - Block broadcast_107 stored as values in memory (estimated size 81.1 KiB, free 1919.1 MiB)
20:25:28.499 INFO MemoryStore - Block broadcast_107_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.0 MiB)
20:25:28.499 INFO BlockManagerInfo - Added broadcast_107_piece0 in memory on localhost:39477 (size: 7.2 KiB, free: 1919.9 MiB)
20:25:28.499 INFO SparkContext - Created broadcast 107 from broadcast at VcfSource.java:129
20:25:28.501 INFO MemoryStore - Block broadcast_108 stored as values in memory (estimated size 298.2 KiB, free 1918.8 MiB)
20:25:28.513 INFO MemoryStore - Block broadcast_108_piece0 stored as bytes in memory (estimated size 50.4 KiB, free 1918.7 MiB)
20:25:28.513 INFO BlockManagerInfo - Added broadcast_108_piece0 in memory on localhost:39477 (size: 50.4 KiB, free: 1919.8 MiB)
20:25:28.513 INFO SparkContext - Created broadcast 108 from newAPIHadoopFile at VcfSource.java:168
20:25:28.517 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
20:25:28.527 INFO FileInputFormat - Total input files to process : 1
20:25:28.531 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
20:25:28.531 INFO DAGScheduler - Got job 44 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
20:25:28.531 INFO DAGScheduler - Final stage: ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43)
20:25:28.531 INFO DAGScheduler - Parents of final stage: List()
20:25:28.531 INFO DAGScheduler - Missing parents: List()
20:25:28.531 INFO DAGScheduler - Submitting ResultStage 53 (MapPartitionsRDD[271] at map at VariantsSparkSource.java:38), which has no missing parents
20:25:28.532 INFO MemoryStore - Block broadcast_109 stored as values in memory (estimated size 7.4 KiB, free 1918.7 MiB)
20:25:28.533 INFO MemoryStore - Block broadcast_109_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.7 MiB)
20:25:28.533 INFO BlockManagerInfo - Added broadcast_109_piece0 in memory on localhost:39477 (size: 3.7 KiB, free: 1919.8 MiB)
20:25:28.533 INFO SparkContext - Created broadcast 109 from broadcast at DAGScheduler.scala:1580
20:25:28.534 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))
20:25:28.534 INFO TaskSchedulerImpl - Adding task set 53.0 with 1 tasks resource profile 0
20:25:28.534 INFO TaskSetManager - Starting task 0.0 in stage 53.0 (TID 123) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes)
20:25:28.535 INFO Executor - Running task 0.0 in stage 53.0 (TID 123)
20:25:28.536 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
20:25:28.547 INFO Executor - Finished task 0.0 in stage 53.0 (TID 123). 12108 bytes result sent to driver
20:25:28.549 INFO TaskSetManager - Finished task 0.0 in stage 53.0 (TID 123) in 15 ms on localhost (executor driver) (1/1)
20:25:28.549 INFO TaskSchedulerImpl - Removed TaskSet 53.0, whose tasks have all completed, from pool
20:25:28.549 INFO DAGScheduler - ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.017 s
20:25:28.549 INFO DAGScheduler - Job 44 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:28.549 INFO TaskSchedulerImpl - Killing all running tasks in stage 53: Stage finished
20:25:28.549 INFO DAGScheduler - Job 44 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.018323 s
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
20:25:28.562 INFO MemoryStore - Block broadcast_110 stored as values in memory (estimated size 81.1 KiB, free 1918.6 MiB)
20:25:28.564 INFO MemoryStore - Block broadcast_110_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1918.6 MiB)
20:25:28.564 INFO BlockManagerInfo - Added broadcast_110_piece0 in memory on localhost:39477 (size: 7.1 KiB, free: 1919.8 MiB)
20:25:28.564 INFO SparkContext - Created broadcast 110 from broadcast at VcfSource.java:129
20:25:28.566 INFO MemoryStore - Block broadcast_111 stored as values in memory (estimated size 298.5 KiB, free 1918.3 MiB)
20:25:28.577 INFO MemoryStore - Block broadcast_111_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1918.3 MiB)
20:25:28.577 INFO BlockManagerInfo - Added broadcast_111_piece0 in memory on localhost:39477 (size: 50.3 KiB, free: 1919.8 MiB)
20:25:28.578 INFO SparkContext - Created broadcast 111 from newAPIHadoopFile at VcfSource.java:168
20:25:28.582 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
20:25:28.593 INFO FileInputFormat - Total input files to process : 1
20:25:28.599 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
20:25:28.599 INFO DAGScheduler - Got job 45 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
20:25:28.599 INFO DAGScheduler - Final stage: ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43)
20:25:28.599 INFO DAGScheduler - Parents of final stage: List()
20:25:28.599 INFO DAGScheduler - Missing parents: List()
20:25:28.600 INFO DAGScheduler - Submitting ResultStage 54 (MapPartitionsRDD[276] at map at VariantsSparkSource.java:38), which has no missing parents
20:25:28.601 INFO MemoryStore - Block broadcast_112 stored as values in memory (estimated size 7.4 KiB, free 1918.3 MiB)
20:25:28.601 INFO MemoryStore - Block broadcast_112_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.3 MiB)
20:25:28.601 INFO BlockManagerInfo - Added broadcast_112_piece0 in memory on localhost:39477 (size: 3.7 KiB, free: 1919.8 MiB)
20:25:28.602 INFO SparkContext - Created broadcast 112 from broadcast at DAGScheduler.scala:1580
20:25:28.602 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))
20:25:28.602 INFO TaskSchedulerImpl - Adding task set 54.0 with 1 tasks resource profile 0
20:25:28.603 INFO TaskSetManager - Starting task 0.0 in stage 54.0 (TID 124) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes)
20:25:28.603 INFO Executor - Running task 0.0 in stage 54.0 (TID 124)
20:25:28.605 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
20:25:28.621 INFO Executor - Finished task 0.0 in stage 54.0 (TID 124). 12108 bytes result sent to driver
20:25:28.623 INFO TaskSetManager - Finished task 0.0 in stage 54.0 (TID 124) in 21 ms on localhost (executor driver) (1/1)
20:25:28.623 INFO TaskSchedulerImpl - Removed TaskSet 54.0, whose tasks have all completed, from pool
20:25:28.624 INFO DAGScheduler - ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.024 s
20:25:28.624 INFO DAGScheduler - Job 45 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:28.624 INFO TaskSchedulerImpl - Killing all running tasks in stage 54: Stage finished
20:25:28.624 INFO DAGScheduler - Job 45 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.025175 s
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
20:25:28.631 INFO MemoryStore - Block broadcast_113 stored as values in memory (estimated size 81.1 KiB, free 1918.2 MiB)
20:25:28.634 INFO MemoryStore - Block broadcast_113_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1918.2 MiB)
20:25:28.634 INFO BlockManagerInfo - Added broadcast_113_piece0 in memory on localhost:39477 (size: 7.2 KiB, free: 1919.8 MiB)
20:25:28.634 INFO SparkContext - Created broadcast 113 from broadcast at VcfSource.java:129
20:25:28.635 INFO MemoryStore - Block broadcast_114 stored as values in memory (estimated size 298.8 KiB, free 1917.9 MiB)
20:25:28.642 INFO MemoryStore - Block broadcast_114_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1917.8 MiB)
20:25:28.642 INFO BlockManagerInfo - Added broadcast_114_piece0 in memory on localhost:39477 (size: 50.3 KiB, free: 1919.7 MiB)
20:25:28.642 INFO SparkContext - Created broadcast 114 from newAPIHadoopFile at VcfSource.java:168
20:25:28.645 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
20:25:28.650 INFO FileInputFormat - Total input files to process : 1
20:25:28.654 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
20:25:28.655 INFO DAGScheduler - Got job 46 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
20:25:28.655 INFO DAGScheduler - Final stage: ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55)
20:25:28.655 INFO DAGScheduler - Parents of final stage: List()
20:25:28.655 INFO DAGScheduler - Missing parents: List()
20:25:28.655 INFO DAGScheduler - Submitting ResultStage 55 (MapPartitionsRDD[279] at mapPartitions at VcfSource.java:134), which has no missing parents
20:25:28.656 INFO MemoryStore - Block broadcast_115 stored as values in memory (estimated size 6.3 KiB, free 1917.8 MiB)
20:25:28.657 INFO MemoryStore - Block broadcast_115_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.8 MiB)
20:25:28.657 INFO BlockManagerInfo - Added broadcast_115_piece0 in memory on localhost:39477 (size: 3.4 KiB, free: 1919.7 MiB)
20:25:28.657 INFO SparkContext - Created broadcast 115 from broadcast at DAGScheduler.scala:1580
20:25:28.657 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))
20:25:28.657 INFO TaskSchedulerImpl - Adding task set 55.0 with 1 tasks resource profile 0
20:25:28.658 INFO TaskSetManager - Starting task 0.0 in stage 55.0 (TID 125) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes)
20:25:28.658 INFO Executor - Running task 0.0 in stage 55.0 (TID 125)
20:25:28.660 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
20:25:28.681 INFO Executor - Finished task 0.0 in stage 55.0 (TID 125). 153274 bytes result sent to driver
20:25:28.692 INFO TaskSetManager - Finished task 0.0 in stage 55.0 (TID 125) in 34 ms on localhost (executor driver) (1/1)
20:25:28.692 INFO TaskSchedulerImpl - Removed TaskSet 55.0, whose tasks have all completed, from pool
20:25:28.692 INFO DAGScheduler - ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.036 s
20:25:28.692 INFO DAGScheduler - Job 46 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:28.692 INFO TaskSchedulerImpl - Killing all running tasks in stage 55: Stage finished
20:25:28.693 INFO DAGScheduler - Job 46 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.038172 s
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-02-10 20:25:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
20:25:28.709 INFO MemoryStore - Block broadcast_116 stored as values in memory (estimated size 81.1 KiB, free 1917.7 MiB)
20:25:28.710 INFO MemoryStore - Block broadcast_116_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1917.7 MiB)
20:25:28.710 INFO BlockManagerInfo - Added broadcast_116_piece0 in memory on localhost:39477 (size: 7.1 KiB, free: 1919.7 MiB)
20:25:28.711 INFO SparkContext - Created broadcast 116 from broadcast at VcfSource.java:129
20:25:28.712 INFO MemoryStore - Block broadcast_117 stored as values in memory (estimated size 299.0 KiB, free 1917.4 MiB)
20:25:28.718 INFO MemoryStore - Block broadcast_117_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1917.4 MiB)
20:25:28.718 INFO BlockManagerInfo - Added broadcast_117_piece0 in memory on localhost:39477 (size: 50.3 KiB, free: 1919.6 MiB)
20:25:28.719 INFO SparkContext - Created broadcast 117 from newAPIHadoopFile at VcfSource.java:168
20:25:28.721 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
20:25:28.726 INFO FileInputFormat - Total input files to process : 1
20:25:28.730 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
20:25:28.730 INFO DAGScheduler - Got job 47 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
20:25:28.730 INFO DAGScheduler - Final stage: ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55)
20:25:28.730 INFO DAGScheduler - Parents of final stage: List()
20:25:28.730 INFO DAGScheduler - Missing parents: List()
20:25:28.731 INFO DAGScheduler - Submitting ResultStage 56 (MapPartitionsRDD[282] at mapPartitions at VcfSource.java:134), which has no missing parents
20:25:28.731 INFO MemoryStore - Block broadcast_118 stored as values in memory (estimated size 6.3 KiB, free 1917.4 MiB)
20:25:28.732 INFO MemoryStore - Block broadcast_118_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.4 MiB)
20:25:28.732 INFO BlockManagerInfo - Added broadcast_118_piece0 in memory on localhost:39477 (size: 3.4 KiB, free: 1919.6 MiB)
20:25:28.732 INFO SparkContext - Created broadcast 118 from broadcast at DAGScheduler.scala:1580
20:25:28.732 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))
20:25:28.732 INFO TaskSchedulerImpl - Adding task set 56.0 with 1 tasks resource profile 0
20:25:28.733 INFO TaskSetManager - Starting task 0.0 in stage 56.0 (TID 126) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes)
20:25:28.734 INFO Executor - Running task 0.0 in stage 56.0 (TID 126)
20:25:28.735 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
20:25:28.754 INFO Executor - Finished task 0.0 in stage 56.0 (TID 126). 153274 bytes result sent to driver
20:25:28.760 INFO TaskSetManager - Finished task 0.0 in stage 56.0 (TID 126) in 27 ms on localhost (executor driver) (1/1)
20:25:28.760 INFO TaskSchedulerImpl - Removed TaskSet 56.0, whose tasks have all completed, from pool
20:25:28.760 INFO DAGScheduler - ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.029 s
20:25:28.760 INFO DAGScheduler - Job 47 is finished. Cancelling potential speculative or zombie tasks for this job
20:25:28.760 INFO TaskSchedulerImpl - Killing all running tasks in stage 56: Stage finished
20:25:28.760 INFO DAGScheduler - Job 47 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.030517 s