WARNING 2026-03-04 15:09:24 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2026-03-04 15:09:24 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2026-03-04 15:09:24 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2026-03-04 15:09:24 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:09:24.999 INFO MemoryStore - Block broadcast_102 stored as values in memory (estimated size 81.1 KiB, free 1919.9 MiB)
15:09:25.003 INFO MemoryStore - Block broadcast_102_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1919.9 MiB)
15:09:25.004 INFO BlockManagerInfo - Added broadcast_102_piece0 in memory on localhost:41569 (size: 7.1 KiB, free: 1920.0 MiB)
15:09:25.004 INFO SparkContext - Created broadcast 102 from broadcast at VcfSource.java:129
15:09:25.008 INFO MemoryStore - Block broadcast_104 stored as values in memory (estimated size 297.9 KiB, free 1919.6 MiB)
15:09:25.011 INFO MemoryStore - Block broadcast_103 stored as values in memory (estimated size 81.1 KiB, free 1919.5 MiB)
15:09:25.016 INFO MemoryStore - Block broadcast_103_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.5 MiB)
15:09:25.017 INFO BlockManagerInfo - Added broadcast_103_piece0 in memory on localhost:41569 (size: 7.2 KiB, free: 1920.0 MiB)
15:09:25.017 INFO SparkContext - Created broadcast 103 from broadcast at VcfSource.java:129
15:09:25.020 INFO MemoryStore - Block broadcast_105 stored as values in memory (estimated size 297.9 KiB, free 1919.2 MiB)
15:09:25.024 INFO MemoryStore - Block broadcast_104_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1919.2 MiB)
15:09:25.025 INFO BlockManagerInfo - Added broadcast_104_piece0 in memory on localhost:41569 (size: 50.2 KiB, free: 1919.9 MiB)
15:09:25.025 INFO SparkContext - Created broadcast 104 from newAPIHadoopFile at VcfSource.java:168
15:09:25.031 INFO MemoryStore - Block broadcast_105_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1919.1 MiB)
15:09:25.031 INFO BlockManagerInfo - Added broadcast_105_piece0 in memory on localhost:41569 (size: 50.2 KiB, free: 1919.9 MiB)
15:09:25.031 INFO SparkContext - Created broadcast 105 from newAPIHadoopFile at VcfSource.java:168
15:09:25.035 INFO FileInputFormat - Total input files to process : 1
15:09:25.035 INFO FileInputFormat - Total input files to process : 1
15:09:25.043 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
15:09:25.055 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
15:09:25.071 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:78
15:09:25.072 INFO DAGScheduler - Got job 43 (collect at VariantsSparkSourceUnitTest.java:78) with 2 output partitions
15:09:25.072 INFO DAGScheduler - Final stage: ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78)
15:09:25.073 INFO DAGScheduler - Parents of final stage: List()
15:09:25.073 INFO DAGScheduler - Missing parents: List()
15:09:25.073 INFO DAGScheduler - Submitting ResultStage 52 (UnionRDD[266] at union at VariantsSparkSource.java:51), which has no missing parents
15:09:25.075 INFO MemoryStore - Block broadcast_106 stored as values in memory (estimated size 9.0 KiB, free 1919.1 MiB)
15:09:25.076 INFO MemoryStore - Block broadcast_106_piece0 stored as bytes in memory (estimated size 4.3 KiB, free 1919.1 MiB)
15:09:25.076 INFO BlockManagerInfo - Added broadcast_106_piece0 in memory on localhost:41569 (size: 4.3 KiB, free: 1919.9 MiB)
15:09:25.077 INFO SparkContext - Created broadcast 106 from broadcast at DAGScheduler.scala:1580
15:09:25.077 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))
15:09:25.077 INFO TaskSchedulerImpl - Adding task set 52.0 with 2 tasks resource profile 0
15:09:25.079 INFO TaskSetManager - Starting task 0.0 in stage 52.0 (TID 121) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7982 bytes)
15:09:25.079 INFO TaskSetManager - Starting task 1.0 in stage 52.0 (TID 122) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7973 bytes)
15:09:25.080 INFO Executor - Running task 0.0 in stage 52.0 (TID 121)
15:09:25.080 INFO Executor - Running task 1.0 in stage 52.0 (TID 122)
15:09:25.084 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
15:09:25.084 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
15:09:25.110 INFO Executor - Finished task 0.0 in stage 52.0 (TID 121). 12151 bytes result sent to driver
15:09:25.114 INFO Executor - Finished task 1.0 in stage 52.0 (TID 122). 12151 bytes result sent to driver
15:09:25.114 INFO TaskSetManager - Finished task 0.0 in stage 52.0 (TID 121) in 36 ms on localhost (executor driver) (1/2)
15:09:25.118 INFO TaskSetManager - Finished task 1.0 in stage 52.0 (TID 122) in 39 ms on localhost (executor driver) (2/2)
15:09:25.118 INFO TaskSchedulerImpl - Removed TaskSet 52.0, whose tasks have all completed, from pool
15:09:25.118 INFO DAGScheduler - ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78) finished in 0.044 s
15:09:25.118 INFO DAGScheduler - Job 43 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:25.118 INFO TaskSchedulerImpl - Killing all running tasks in stage 52: Stage finished
15:09:25.119 INFO DAGScheduler - Job 43 finished: collect at VariantsSparkSourceUnitTest.java:78, took 0.047681 s
WARNING 2026-03-04 15:09:25 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2026-03-04 15:09:25 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:09:25.138 INFO MemoryStore - Block broadcast_107 stored as values in memory (estimated size 81.1 KiB, free 1919.1 MiB)
15:09:25.139 INFO MemoryStore - Block broadcast_107_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.0 MiB)
15:09:25.140 INFO BlockManagerInfo - Added broadcast_107_piece0 in memory on localhost:41569 (size: 7.2 KiB, free: 1919.9 MiB)
15:09:25.140 INFO SparkContext - Created broadcast 107 from broadcast at VcfSource.java:129
15:09:25.143 INFO MemoryStore - Block broadcast_108 stored as values in memory (estimated size 298.2 KiB, free 1918.8 MiB)
15:09:25.155 INFO MemoryStore - Block broadcast_108_piece0 stored as bytes in memory (estimated size 50.4 KiB, free 1918.7 MiB)
15:09:25.155 INFO BlockManagerInfo - Added broadcast_108_piece0 in memory on localhost:41569 (size: 50.4 KiB, free: 1919.8 MiB)
15:09:25.156 INFO SparkContext - Created broadcast 108 from newAPIHadoopFile at VcfSource.java:168
15:09:25.159 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
15:09:25.165 INFO FileInputFormat - Total input files to process : 1
15:09:25.169 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
15:09:25.170 INFO DAGScheduler - Got job 44 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
15:09:25.170 INFO DAGScheduler - Final stage: ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43)
15:09:25.170 INFO DAGScheduler - Parents of final stage: List()
15:09:25.170 INFO DAGScheduler - Missing parents: List()
15:09:25.170 INFO DAGScheduler - Submitting ResultStage 53 (MapPartitionsRDD[271] at map at VariantsSparkSource.java:38), which has no missing parents
15:09:25.171 INFO MemoryStore - Block broadcast_109 stored as values in memory (estimated size 7.4 KiB, free 1918.7 MiB)
15:09:25.172 INFO MemoryStore - Block broadcast_109_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.7 MiB)
15:09:25.172 INFO BlockManagerInfo - Added broadcast_109_piece0 in memory on localhost:41569 (size: 3.7 KiB, free: 1919.8 MiB)
15:09:25.173 INFO SparkContext - Created broadcast 109 from broadcast at DAGScheduler.scala:1580
15:09:25.173 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))
15:09:25.173 INFO TaskSchedulerImpl - Adding task set 53.0 with 1 tasks resource profile 0
15:09:25.174 INFO TaskSetManager - Starting task 0.0 in stage 53.0 (TID 123) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes)
15:09:25.174 INFO Executor - Running task 0.0 in stage 53.0 (TID 123)
15:09:25.177 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
15:09:25.191 INFO Executor - Finished task 0.0 in stage 53.0 (TID 123). 12151 bytes result sent to driver
15:09:25.193 INFO TaskSetManager - Finished task 0.0 in stage 53.0 (TID 123) in 20 ms on localhost (executor driver) (1/1)
15:09:25.194 INFO TaskSchedulerImpl - Removed TaskSet 53.0, whose tasks have all completed, from pool
15:09:25.194 INFO DAGScheduler - ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.023 s
15:09:25.194 INFO DAGScheduler - Job 44 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:25.194 INFO TaskSchedulerImpl - Killing all running tasks in stage 53: Stage finished
15:09:25.194 INFO DAGScheduler - Job 44 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.024818 s
WARNING 2026-03-04 15:09:25 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2026-03-04 15:09:25 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:09:25.212 INFO MemoryStore - Block broadcast_110 stored as values in memory (estimated size 81.1 KiB, free 1918.6 MiB)
15:09:25.214 INFO MemoryStore - Block broadcast_110_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1918.6 MiB)
15:09:25.214 INFO BlockManagerInfo - Added broadcast_110_piece0 in memory on localhost:41569 (size: 7.1 KiB, free: 1919.8 MiB)
15:09:25.215 INFO SparkContext - Created broadcast 110 from broadcast at VcfSource.java:129
15:09:25.217 INFO MemoryStore - Block broadcast_111 stored as values in memory (estimated size 298.5 KiB, free 1918.3 MiB)
15:09:25.226 INFO MemoryStore - Block broadcast_111_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1918.3 MiB)
15:09:25.226 INFO BlockManagerInfo - Added broadcast_111_piece0 in memory on localhost:41569 (size: 50.3 KiB, free: 1919.8 MiB)
15:09:25.226 INFO SparkContext - Created broadcast 111 from newAPIHadoopFile at VcfSource.java:168
15:09:25.230 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
15:09:25.235 INFO FileInputFormat - Total input files to process : 1
15:09:25.240 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
15:09:25.241 INFO DAGScheduler - Got job 45 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
15:09:25.241 INFO DAGScheduler - Final stage: ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43)
15:09:25.241 INFO DAGScheduler - Parents of final stage: List()
15:09:25.241 INFO DAGScheduler - Missing parents: List()
15:09:25.241 INFO DAGScheduler - Submitting ResultStage 54 (MapPartitionsRDD[276] at map at VariantsSparkSource.java:38), which has no missing parents
15:09:25.242 INFO MemoryStore - Block broadcast_112 stored as values in memory (estimated size 7.4 KiB, free 1918.3 MiB)
15:09:25.243 INFO MemoryStore - Block broadcast_112_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.3 MiB)
15:09:25.243 INFO BlockManagerInfo - Added broadcast_112_piece0 in memory on localhost:41569 (size: 3.7 KiB, free: 1919.8 MiB)
15:09:25.243 INFO SparkContext - Created broadcast 112 from broadcast at DAGScheduler.scala:1580
15:09:25.244 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))
15:09:25.244 INFO TaskSchedulerImpl - Adding task set 54.0 with 1 tasks resource profile 0
15:09:25.245 INFO TaskSetManager - Starting task 0.0 in stage 54.0 (TID 124) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes)
15:09:25.245 INFO Executor - Running task 0.0 in stage 54.0 (TID 124)
15:09:25.247 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
15:09:25.257 INFO Executor - Finished task 0.0 in stage 54.0 (TID 124). 12108 bytes result sent to driver
15:09:25.259 INFO TaskSetManager - Finished task 0.0 in stage 54.0 (TID 124) in 15 ms on localhost (executor driver) (1/1)
15:09:25.259 INFO TaskSchedulerImpl - Removed TaskSet 54.0, whose tasks have all completed, from pool
15:09:25.259 INFO DAGScheduler - ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.017 s
15:09:25.259 INFO DAGScheduler - Job 45 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:25.259 INFO TaskSchedulerImpl - Killing all running tasks in stage 54: Stage finished
15:09:25.259 INFO DAGScheduler - Job 45 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.019156 s
WARNING 2026-03-04 15:09:25 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2026-03-04 15:09:25 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:09:25.271 INFO MemoryStore - Block broadcast_113 stored as values in memory (estimated size 81.1 KiB, free 1918.2 MiB)
15:09:25.273 INFO MemoryStore - Block broadcast_113_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1918.2 MiB)
15:09:25.273 INFO BlockManagerInfo - Added broadcast_113_piece0 in memory on localhost:41569 (size: 7.2 KiB, free: 1919.8 MiB)
15:09:25.273 INFO SparkContext - Created broadcast 113 from broadcast at VcfSource.java:129
15:09:25.275 INFO MemoryStore - Block broadcast_114 stored as values in memory (estimated size 298.8 KiB, free 1917.9 MiB)
15:09:25.282 INFO MemoryStore - Block broadcast_114_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1917.8 MiB)
15:09:25.283 INFO BlockManagerInfo - Added broadcast_114_piece0 in memory on localhost:41569 (size: 50.3 KiB, free: 1919.7 MiB)
15:09:25.283 INFO SparkContext - Created broadcast 114 from newAPIHadoopFile at VcfSource.java:168
15:09:25.286 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
15:09:25.292 INFO FileInputFormat - Total input files to process : 1
15:09:25.297 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
15:09:25.298 INFO DAGScheduler - Got job 46 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
15:09:25.298 INFO DAGScheduler - Final stage: ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55)
15:09:25.298 INFO DAGScheduler - Parents of final stage: List()
15:09:25.298 INFO DAGScheduler - Missing parents: List()
15:09:25.299 INFO DAGScheduler - Submitting ResultStage 55 (MapPartitionsRDD[279] at mapPartitions at VcfSource.java:134), which has no missing parents
15:09:25.299 INFO MemoryStore - Block broadcast_115 stored as values in memory (estimated size 6.3 KiB, free 1917.8 MiB)
15:09:25.300 INFO MemoryStore - Block broadcast_115_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.8 MiB)
15:09:25.300 INFO BlockManagerInfo - Added broadcast_115_piece0 in memory on localhost:41569 (size: 3.4 KiB, free: 1919.7 MiB)
15:09:25.300 INFO SparkContext - Created broadcast 115 from broadcast at DAGScheduler.scala:1580
15:09:25.301 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))
15:09:25.301 INFO TaskSchedulerImpl - Adding task set 55.0 with 1 tasks resource profile 0
15:09:25.302 INFO TaskSetManager - Starting task 0.0 in stage 55.0 (TID 125) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes)
15:09:25.302 INFO Executor - Running task 0.0 in stage 55.0 (TID 125)
15:09:25.304 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
15:09:25.332 INFO Executor - Finished task 0.0 in stage 55.0 (TID 125). 153274 bytes result sent to driver
15:09:25.343 INFO TaskSetManager - Finished task 0.0 in stage 55.0 (TID 125) in 42 ms on localhost (executor driver) (1/1)
15:09:25.343 INFO TaskSchedulerImpl - Removed TaskSet 55.0, whose tasks have all completed, from pool
15:09:25.343 INFO DAGScheduler - ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.044 s
15:09:25.343 INFO DAGScheduler - Job 46 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:25.343 INFO TaskSchedulerImpl - Killing all running tasks in stage 55: Stage finished
15:09:25.343 INFO DAGScheduler - Job 46 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.046249 s
WARNING 2026-03-04 15:09:25 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2026-03-04 15:09:25 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
15:09:25.370 INFO MemoryStore - Block broadcast_116 stored as values in memory (estimated size 81.1 KiB, free 1917.7 MiB)
15:09:25.371 INFO MemoryStore - Block broadcast_116_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1917.7 MiB)
15:09:25.372 INFO BlockManagerInfo - Added broadcast_116_piece0 in memory on localhost:41569 (size: 7.1 KiB, free: 1919.7 MiB)
15:09:25.372 INFO SparkContext - Created broadcast 116 from broadcast at VcfSource.java:129
15:09:25.374 INFO MemoryStore - Block broadcast_117 stored as values in memory (estimated size 299.0 KiB, free 1917.4 MiB)
15:09:25.384 INFO MemoryStore - Block broadcast_117_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1917.4 MiB)
15:09:25.385 INFO BlockManagerInfo - Added broadcast_117_piece0 in memory on localhost:41569 (size: 50.3 KiB, free: 1919.6 MiB)
15:09:25.385 INFO SparkContext - Created broadcast 117 from newAPIHadoopFile at VcfSource.java:168
15:09:25.387 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
15:09:25.395 INFO FileInputFormat - Total input files to process : 1
15:09:25.400 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
15:09:25.400 INFO DAGScheduler - Got job 47 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
15:09:25.400 INFO DAGScheduler - Final stage: ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55)
15:09:25.400 INFO DAGScheduler - Parents of final stage: List()
15:09:25.400 INFO DAGScheduler - Missing parents: List()
15:09:25.400 INFO DAGScheduler - Submitting ResultStage 56 (MapPartitionsRDD[282] at mapPartitions at VcfSource.java:134), which has no missing parents
15:09:25.402 INFO MemoryStore - Block broadcast_118 stored as values in memory (estimated size 6.3 KiB, free 1917.4 MiB)
15:09:25.402 INFO MemoryStore - Block broadcast_118_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.4 MiB)
15:09:25.402 INFO BlockManagerInfo - Added broadcast_118_piece0 in memory on localhost:41569 (size: 3.4 KiB, free: 1919.6 MiB)
15:09:25.403 INFO SparkContext - Created broadcast 118 from broadcast at DAGScheduler.scala:1580
15:09:25.403 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))
15:09:25.403 INFO TaskSchedulerImpl - Adding task set 56.0 with 1 tasks resource profile 0
15:09:25.404 INFO TaskSetManager - Starting task 0.0 in stage 56.0 (TID 126) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes)
15:09:25.404 INFO Executor - Running task 0.0 in stage 56.0 (TID 126)
15:09:25.406 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
15:09:25.434 INFO Executor - Finished task 0.0 in stage 56.0 (TID 126). 153274 bytes result sent to driver
15:09:25.440 INFO TaskSetManager - Finished task 0.0 in stage 56.0 (TID 126) in 37 ms on localhost (executor driver) (1/1)
15:09:25.440 INFO TaskSchedulerImpl - Removed TaskSet 56.0, whose tasks have all completed, from pool
15:09:25.440 INFO DAGScheduler - ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.039 s
15:09:25.440 INFO DAGScheduler - Job 47 is finished. Cancelling potential speculative or zombie tasks for this job
15:09:25.440 INFO TaskSchedulerImpl - Killing all running tasks in stage 56: Stage finished
15:09:25.441 INFO DAGScheduler - Job 47 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.040808 s