Class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSourceUnitTest

5

tests

0

failures

0

ignored

0.474s

duration

100%

successful

Tests

Test Duration Result
getMultipleParallelVCFsTest[0]([/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, /gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf]) 0.170s passed
pairReadsAndVariantsTest[0](/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf) 0.056s passed
pairReadsAndVariantsTest[1](/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf) 0.063s passed
pairReadsAndVariantsTest_variantContexts[0](/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf) 0.104s passed
pairReadsAndVariantsTest_variantContexts[1](/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf) 0.081s passed

Standard error

WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
21:18:00.086 INFO  MemoryStore - Block broadcast_103 stored as values in memory (estimated size 81.1 KiB, free 1919.8 MiB)
21:18:00.086 INFO  MemoryStore - Block broadcast_102 stored as values in memory (estimated size 81.1 KiB, free 1919.9 MiB)
21:18:00.090 INFO  MemoryStore - Block broadcast_102_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.8 MiB)
21:18:00.090 INFO  BlockManagerInfo - Added broadcast_102_piece0 in memory on localhost:40577 (size: 7.2 KiB, free: 1920.0 MiB)
21:18:00.091 INFO  SparkContext - Created broadcast 102 from broadcast at VcfSource.java:129
21:18:00.091 INFO  MemoryStore - Block broadcast_103_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1919.8 MiB)
21:18:00.091 INFO  BlockManagerInfo - Added broadcast_103_piece0 in memory on localhost:40577 (size: 7.1 KiB, free: 1920.0 MiB)
21:18:00.093 INFO  MemoryStore - Block broadcast_104 stored as values in memory (estimated size 297.9 KiB, free 1919.5 MiB)
21:18:00.094 INFO  SparkContext - Created broadcast 103 from broadcast at VcfSource.java:129
21:18:00.095 INFO  MemoryStore - Block broadcast_105 stored as values in memory (estimated size 297.9 KiB, free 1919.2 MiB)
21:18:00.107 INFO  MemoryStore - Block broadcast_104_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1919.2 MiB)
21:18:00.108 INFO  BlockManagerInfo - Added broadcast_104_piece0 in memory on localhost:40577 (size: 50.2 KiB, free: 1919.9 MiB)
21:18:00.108 INFO  SparkContext - Created broadcast 104 from newAPIHadoopFile at VcfSource.java:168
21:18:00.111 INFO  MemoryStore - Block broadcast_105_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1919.1 MiB)
21:18:00.111 INFO  BlockManagerInfo - Added broadcast_105_piece0 in memory on localhost:40577 (size: 50.2 KiB, free: 1919.9 MiB)
21:18:00.111 INFO  SparkContext - Created broadcast 105 from newAPIHadoopFile at VcfSource.java:168
21:18:00.119 INFO  FileInputFormat - Total input files to process : 1
21:18:00.119 INFO  FileInputFormat - Total input files to process : 1
21:18:00.127 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
21:18:00.139 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
21:18:00.166 INFO  SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:78
21:18:00.168 INFO  DAGScheduler - Got job 43 (collect at VariantsSparkSourceUnitTest.java:78) with 2 output partitions
21:18:00.168 INFO  DAGScheduler - Final stage: ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78)
21:18:00.168 INFO  DAGScheduler - Parents of final stage: List()
21:18:00.169 INFO  DAGScheduler - Missing parents: List()
21:18:00.169 INFO  DAGScheduler - Submitting ResultStage 52 (UnionRDD[266] at union at VariantsSparkSource.java:51), which has no missing parents
21:18:00.171 INFO  MemoryStore - Block broadcast_106 stored as values in memory (estimated size 9.0 KiB, free 1919.1 MiB)
21:18:00.172 INFO  MemoryStore - Block broadcast_106_piece0 stored as bytes in memory (estimated size 4.3 KiB, free 1919.1 MiB)
21:18:00.172 INFO  BlockManagerInfo - Added broadcast_106_piece0 in memory on localhost:40577 (size: 4.3 KiB, free: 1919.9 MiB)
21:18:00.172 INFO  SparkContext - Created broadcast 106 from broadcast at DAGScheduler.scala:1580
21:18:00.173 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))
21:18:00.173 INFO  TaskSchedulerImpl - Adding task set 52.0 with 2 tasks resource profile 0
21:18:00.174 INFO  TaskSetManager - Starting task 0.0 in stage 52.0 (TID 121) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7982 bytes) 
21:18:00.175 INFO  TaskSetManager - Starting task 1.0 in stage 52.0 (TID 122) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7973 bytes) 
21:18:00.175 INFO  Executor - Running task 0.0 in stage 52.0 (TID 121)
21:18:00.175 INFO  Executor - Running task 1.0 in stage 52.0 (TID 122)
21:18:00.180 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
21:18:00.181 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
21:18:00.212 INFO  Executor - Finished task 1.0 in stage 52.0 (TID 122). 12151 bytes result sent to driver
21:18:00.217 INFO  Executor - Finished task 0.0 in stage 52.0 (TID 121). 12151 bytes result sent to driver
21:18:00.221 INFO  TaskSetManager - Finished task 1.0 in stage 52.0 (TID 122) in 47 ms on localhost (executor driver) (1/2)
21:18:00.222 INFO  TaskSetManager - Finished task 0.0 in stage 52.0 (TID 121) in 49 ms on localhost (executor driver) (2/2)
21:18:00.222 INFO  TaskSchedulerImpl - Removed TaskSet 52.0, whose tasks have all completed, from pool 
21:18:00.223 INFO  DAGScheduler - ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78) finished in 0.053 s
21:18:00.223 INFO  DAGScheduler - Job 43 is finished. Cancelling potential speculative or zombie tasks for this job
21:18:00.223 INFO  TaskSchedulerImpl - Killing all running tasks in stage 52: Stage finished
21:18:00.223 INFO  DAGScheduler - Job 43 finished: collect at VariantsSparkSourceUnitTest.java:78, took 0.056797 s
WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
21:18:00.236 INFO  MemoryStore - Block broadcast_107 stored as values in memory (estimated size 81.1 KiB, free 1919.1 MiB)
21:18:00.238 INFO  MemoryStore - Block broadcast_107_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.0 MiB)
21:18:00.238 INFO  BlockManagerInfo - Added broadcast_107_piece0 in memory on localhost:40577 (size: 7.2 KiB, free: 1919.9 MiB)
21:18:00.239 INFO  SparkContext - Created broadcast 107 from broadcast at VcfSource.java:129
21:18:00.240 INFO  MemoryStore - Block broadcast_108 stored as values in memory (estimated size 298.2 KiB, free 1918.8 MiB)
21:18:00.246 INFO  MemoryStore - Block broadcast_108_piece0 stored as bytes in memory (estimated size 50.4 KiB, free 1918.7 MiB)
21:18:00.247 INFO  BlockManagerInfo - Added broadcast_108_piece0 in memory on localhost:40577 (size: 50.4 KiB, free: 1919.8 MiB)
21:18:00.247 INFO  SparkContext - Created broadcast 108 from newAPIHadoopFile at VcfSource.java:168
21:18:00.251 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
21:18:00.258 INFO  FileInputFormat - Total input files to process : 1
21:18:00.262 INFO  SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
21:18:00.263 INFO  DAGScheduler - Got job 44 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
21:18:00.263 INFO  DAGScheduler - Final stage: ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43)
21:18:00.263 INFO  DAGScheduler - Parents of final stage: List()
21:18:00.263 INFO  DAGScheduler - Missing parents: List()
21:18:00.263 INFO  DAGScheduler - Submitting ResultStage 53 (MapPartitionsRDD[271] at map at VariantsSparkSource.java:38), which has no missing parents
21:18:00.264 INFO  MemoryStore - Block broadcast_109 stored as values in memory (estimated size 7.4 KiB, free 1918.7 MiB)
21:18:00.265 INFO  MemoryStore - Block broadcast_109_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.7 MiB)
21:18:00.265 INFO  BlockManagerInfo - Added broadcast_109_piece0 in memory on localhost:40577 (size: 3.7 KiB, free: 1919.8 MiB)
21:18:00.265 INFO  SparkContext - Created broadcast 109 from broadcast at DAGScheduler.scala:1580
21:18:00.265 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))
21:18:00.265 INFO  TaskSchedulerImpl - Adding task set 53.0 with 1 tasks resource profile 0
21:18:00.266 INFO  TaskSetManager - Starting task 0.0 in stage 53.0 (TID 123) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes) 
21:18:00.266 INFO  Executor - Running task 0.0 in stage 53.0 (TID 123)
21:18:00.268 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
21:18:00.280 INFO  Executor - Finished task 0.0 in stage 53.0 (TID 123). 12108 bytes result sent to driver
21:18:00.281 INFO  TaskSetManager - Finished task 0.0 in stage 53.0 (TID 123) in 15 ms on localhost (executor driver) (1/1)
21:18:00.281 INFO  TaskSchedulerImpl - Removed TaskSet 53.0, whose tasks have all completed, from pool 
21:18:00.281 INFO  DAGScheduler - ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.018 s
21:18:00.281 INFO  DAGScheduler - Job 44 is finished. Cancelling potential speculative or zombie tasks for this job
21:18:00.282 INFO  TaskSchedulerImpl - Killing all running tasks in stage 53: Stage finished
21:18:00.282 INFO  DAGScheduler - Job 44 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.019535 s
WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
21:18:00.291 INFO  MemoryStore - Block broadcast_110 stored as values in memory (estimated size 81.1 KiB, free 1918.6 MiB)
21:18:00.293 INFO  MemoryStore - Block broadcast_110_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1918.6 MiB)
21:18:00.293 INFO  BlockManagerInfo - Added broadcast_110_piece0 in memory on localhost:40577 (size: 7.1 KiB, free: 1919.8 MiB)
21:18:00.293 INFO  SparkContext - Created broadcast 110 from broadcast at VcfSource.java:129
21:18:00.295 INFO  MemoryStore - Block broadcast_111 stored as values in memory (estimated size 298.5 KiB, free 1918.3 MiB)
21:18:00.304 INFO  MemoryStore - Block broadcast_111_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1918.3 MiB)
21:18:00.304 INFO  BlockManagerInfo - Added broadcast_111_piece0 in memory on localhost:40577 (size: 50.3 KiB, free: 1919.8 MiB)
21:18:00.304 INFO  SparkContext - Created broadcast 111 from newAPIHadoopFile at VcfSource.java:168
21:18:00.307 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
21:18:00.313 INFO  FileInputFormat - Total input files to process : 1
21:18:00.318 INFO  SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
21:18:00.318 INFO  DAGScheduler - Got job 45 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
21:18:00.318 INFO  DAGScheduler - Final stage: ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43)
21:18:00.319 INFO  DAGScheduler - Parents of final stage: List()
21:18:00.319 INFO  DAGScheduler - Missing parents: List()
21:18:00.319 INFO  DAGScheduler - Submitting ResultStage 54 (MapPartitionsRDD[276] at map at VariantsSparkSource.java:38), which has no missing parents
21:18:00.320 INFO  MemoryStore - Block broadcast_112 stored as values in memory (estimated size 7.4 KiB, free 1918.3 MiB)
21:18:00.320 INFO  MemoryStore - Block broadcast_112_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.3 MiB)
21:18:00.321 INFO  BlockManagerInfo - Added broadcast_112_piece0 in memory on localhost:40577 (size: 3.7 KiB, free: 1919.8 MiB)
21:18:00.321 INFO  SparkContext - Created broadcast 112 from broadcast at DAGScheduler.scala:1580
21:18:00.321 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))
21:18:00.321 INFO  TaskSchedulerImpl - Adding task set 54.0 with 1 tasks resource profile 0
21:18:00.325 INFO  TaskSetManager - Starting task 0.0 in stage 54.0 (TID 124) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes) 
21:18:00.326 INFO  Executor - Running task 0.0 in stage 54.0 (TID 124)
21:18:00.328 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
21:18:00.342 INFO  Executor - Finished task 0.0 in stage 54.0 (TID 124). 12108 bytes result sent to driver
21:18:00.344 INFO  TaskSetManager - Finished task 0.0 in stage 54.0 (TID 124) in 19 ms on localhost (executor driver) (1/1)
21:18:00.344 INFO  TaskSchedulerImpl - Removed TaskSet 54.0, whose tasks have all completed, from pool 
21:18:00.345 INFO  DAGScheduler - ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.025 s
21:18:00.345 INFO  DAGScheduler - Job 45 is finished. Cancelling potential speculative or zombie tasks for this job
21:18:00.345 INFO  TaskSchedulerImpl - Killing all running tasks in stage 54: Stage finished
21:18:00.346 INFO  DAGScheduler - Job 45 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.027608 s
WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
21:18:00.355 INFO  MemoryStore - Block broadcast_113 stored as values in memory (estimated size 81.1 KiB, free 1918.2 MiB)
21:18:00.357 INFO  MemoryStore - Block broadcast_113_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1918.2 MiB)
21:18:00.357 INFO  BlockManagerInfo - Added broadcast_113_piece0 in memory on localhost:40577 (size: 7.2 KiB, free: 1919.8 MiB)
21:18:00.357 INFO  SparkContext - Created broadcast 113 from broadcast at VcfSource.java:129
21:18:00.359 INFO  MemoryStore - Block broadcast_114 stored as values in memory (estimated size 298.8 KiB, free 1917.9 MiB)
21:18:00.370 INFO  MemoryStore - Block broadcast_114_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1917.8 MiB)
21:18:00.370 INFO  BlockManagerInfo - Added broadcast_114_piece0 in memory on localhost:40577 (size: 50.3 KiB, free: 1919.7 MiB)
21:18:00.370 INFO  SparkContext - Created broadcast 114 from newAPIHadoopFile at VcfSource.java:168
21:18:00.373 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
21:18:00.382 INFO  FileInputFormat - Total input files to process : 1
21:18:00.387 INFO  SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
21:18:00.388 INFO  DAGScheduler - Got job 46 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
21:18:00.388 INFO  DAGScheduler - Final stage: ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55)
21:18:00.388 INFO  DAGScheduler - Parents of final stage: List()
21:18:00.388 INFO  DAGScheduler - Missing parents: List()
21:18:00.388 INFO  DAGScheduler - Submitting ResultStage 55 (MapPartitionsRDD[279] at mapPartitions at VcfSource.java:134), which has no missing parents
21:18:00.389 INFO  MemoryStore - Block broadcast_115 stored as values in memory (estimated size 6.3 KiB, free 1917.8 MiB)
21:18:00.389 INFO  MemoryStore - Block broadcast_115_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.8 MiB)
21:18:00.390 INFO  BlockManagerInfo - Added broadcast_115_piece0 in memory on localhost:40577 (size: 3.4 KiB, free: 1919.7 MiB)
21:18:00.390 INFO  SparkContext - Created broadcast 115 from broadcast at DAGScheduler.scala:1580
21:18:00.390 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))
21:18:00.390 INFO  TaskSchedulerImpl - Adding task set 55.0 with 1 tasks resource profile 0
21:18:00.391 INFO  TaskSetManager - Starting task 0.0 in stage 55.0 (TID 125) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes) 
21:18:00.392 INFO  Executor - Running task 0.0 in stage 55.0 (TID 125)
21:18:00.394 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
21:18:00.421 INFO  Executor - Finished task 0.0 in stage 55.0 (TID 125). 153274 bytes result sent to driver
21:18:00.436 INFO  TaskSetManager - Finished task 0.0 in stage 55.0 (TID 125) in 45 ms on localhost (executor driver) (1/1)
21:18:00.436 INFO  TaskSchedulerImpl - Removed TaskSet 55.0, whose tasks have all completed, from pool 
21:18:00.436 INFO  DAGScheduler - ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.048 s
21:18:00.437 INFO  DAGScheduler - Job 46 is finished. Cancelling potential speculative or zombie tasks for this job
21:18:00.437 INFO  TaskSchedulerImpl - Killing all running tasks in stage 55: Stage finished
21:18:00.437 INFO  DAGScheduler - Job 46 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.050016 s
WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 21:18:00	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
21:18:00.460 INFO  MemoryStore - Block broadcast_116 stored as values in memory (estimated size 81.1 KiB, free 1917.7 MiB)
21:18:00.461 INFO  MemoryStore - Block broadcast_116_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1917.7 MiB)
21:18:00.462 INFO  BlockManagerInfo - Added broadcast_116_piece0 in memory on localhost:40577 (size: 7.1 KiB, free: 1919.7 MiB)
21:18:00.462 INFO  SparkContext - Created broadcast 116 from broadcast at VcfSource.java:129
21:18:00.463 INFO  MemoryStore - Block broadcast_117 stored as values in memory (estimated size 299.0 KiB, free 1917.4 MiB)
21:18:00.474 INFO  MemoryStore - Block broadcast_117_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1917.4 MiB)
21:18:00.474 INFO  BlockManagerInfo - Added broadcast_117_piece0 in memory on localhost:40577 (size: 50.3 KiB, free: 1919.6 MiB)
21:18:00.475 INFO  SparkContext - Created broadcast 117 from newAPIHadoopFile at VcfSource.java:168
21:18:00.478 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
21:18:00.485 INFO  FileInputFormat - Total input files to process : 1
21:18:00.490 INFO  SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
21:18:00.491 INFO  DAGScheduler - Got job 47 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
21:18:00.491 INFO  DAGScheduler - Final stage: ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55)
21:18:00.491 INFO  DAGScheduler - Parents of final stage: List()
21:18:00.491 INFO  DAGScheduler - Missing parents: List()
21:18:00.492 INFO  DAGScheduler - Submitting ResultStage 56 (MapPartitionsRDD[282] at mapPartitions at VcfSource.java:134), which has no missing parents
21:18:00.492 INFO  MemoryStore - Block broadcast_118 stored as values in memory (estimated size 6.3 KiB, free 1917.4 MiB)
21:18:00.493 INFO  MemoryStore - Block broadcast_118_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.4 MiB)
21:18:00.493 INFO  BlockManagerInfo - Added broadcast_118_piece0 in memory on localhost:40577 (size: 3.4 KiB, free: 1919.6 MiB)
21:18:00.493 INFO  SparkContext - Created broadcast 118 from broadcast at DAGScheduler.scala:1580
21:18:00.494 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))
21:18:00.494 INFO  TaskSchedulerImpl - Adding task set 56.0 with 1 tasks resource profile 0
21:18:00.495 INFO  TaskSetManager - Starting task 0.0 in stage 56.0 (TID 126) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes) 
21:18:00.495 INFO  Executor - Running task 0.0 in stage 56.0 (TID 126)
21:18:00.496 INFO  NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
21:18:00.518 INFO  Executor - Finished task 0.0 in stage 56.0 (TID 126). 153274 bytes result sent to driver
21:18:00.524 INFO  TaskSetManager - Finished task 0.0 in stage 56.0 (TID 126) in 30 ms on localhost (executor driver) (1/1)
21:18:00.524 INFO  TaskSchedulerImpl - Removed TaskSet 56.0, whose tasks have all completed, from pool 
21:18:00.524 INFO  DAGScheduler - ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.032 s
21:18:00.524 INFO  DAGScheduler - Job 47 is finished. Cancelling potential speculative or zombie tasks for this job
21:18:00.524 INFO  TaskSchedulerImpl - Killing all running tasks in stage 56: Stage finished
21:18:00.525 INFO  DAGScheduler - Job 47 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.034220 s