WARNING 2025-03-28 22:32:12 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-03-28 22:32:12 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-03-28 22:32:12 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-03-28 22:32:12 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
22:32:12.880 INFO MemoryStore - Block broadcast_102 stored as values in memory (estimated size 81.1 KiB, free 1919.9 MiB)
22:32:12.883 INFO MemoryStore - Block broadcast_103 stored as values in memory (estimated size 81.1 KiB, free 1919.8 MiB)
22:32:12.885 INFO MemoryStore - Block broadcast_102_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1919.8 MiB)
22:32:12.886 INFO BlockManagerInfo - Added broadcast_102_piece0 in memory on localhost:35275 (size: 7.1 KiB, free: 1920.0 MiB)
22:32:12.886 INFO SparkContext - Created broadcast 102 from broadcast at VcfSource.java:129
22:32:12.889 INFO MemoryStore - Block broadcast_104 stored as values in memory (estimated size 326.3 KiB, free 1919.5 MiB)
22:32:12.893 INFO MemoryStore - Block broadcast_103_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.5 MiB)
22:32:12.893 INFO BlockManagerInfo - Added broadcast_103_piece0 in memory on localhost:35275 (size: 7.2 KiB, free: 1920.0 MiB)
22:32:12.893 INFO SparkContext - Created broadcast 103 from broadcast at VcfSource.java:129
22:32:12.895 INFO MemoryStore - Block broadcast_105 stored as values in memory (estimated size 326.3 KiB, free 1919.2 MiB)
22:32:12.902 INFO MemoryStore - Block broadcast_104_piece0 stored as bytes in memory (estimated size 55.7 KiB, free 1919.1 MiB)
22:32:12.903 INFO BlockManagerInfo - Added broadcast_104_piece0 in memory on localhost:35275 (size: 55.7 KiB, free: 1919.9 MiB)
22:32:12.903 INFO SparkContext - Created broadcast 104 from newAPIHadoopFile at VcfSource.java:168
22:32:12.913 INFO FileInputFormat - Total input files to process : 1
22:32:12.914 INFO MemoryStore - Block broadcast_105_piece0 stored as bytes in memory (estimated size 55.7 KiB, free 1919.1 MiB)
22:32:12.914 INFO BlockManagerInfo - Added broadcast_105_piece0 in memory on localhost:35275 (size: 55.7 KiB, free: 1919.9 MiB)
22:32:12.914 INFO SparkContext - Created broadcast 105 from newAPIHadoopFile at VcfSource.java:168
22:32:12.918 INFO FileInputFormat - Total input files to process : 1
22:32:12.922 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
22:32:12.947 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
22:32:12.970 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:78
22:32:12.972 INFO DAGScheduler - Got job 43 (collect at VariantsSparkSourceUnitTest.java:78) with 2 output partitions
22:32:12.972 INFO DAGScheduler - Final stage: ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78)
22:32:12.972 INFO DAGScheduler - Parents of final stage: List()
22:32:12.972 INFO DAGScheduler - Missing parents: List()
22:32:12.973 INFO DAGScheduler - Submitting ResultStage 52 (UnionRDD[266] at union at VariantsSparkSource.java:51), which has no missing parents
22:32:12.975 INFO MemoryStore - Block broadcast_106 stored as values in memory (estimated size 9.0 KiB, free 1919.1 MiB)
22:32:12.976 INFO MemoryStore - Block broadcast_106_piece0 stored as bytes in memory (estimated size 4.3 KiB, free 1919.1 MiB)
22:32:12.976 INFO BlockManagerInfo - Added broadcast_106_piece0 in memory on localhost:35275 (size: 4.3 KiB, free: 1919.9 MiB)
22:32:12.976 INFO SparkContext - Created broadcast 106 from broadcast at DAGScheduler.scala:1580
22:32:12.977 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))
22:32:12.977 INFO TaskSchedulerImpl - Adding task set 52.0 with 2 tasks resource profile 0
22:32:12.979 INFO TaskSetManager - Starting task 0.0 in stage 52.0 (TID 121) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7989 bytes)
22:32:12.979 INFO TaskSetManager - Starting task 1.0 in stage 52.0 (TID 122) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7980 bytes)
22:32:12.980 INFO Executor - Running task 0.0 in stage 52.0 (TID 121)
22:32:12.980 INFO Executor - Running task 1.0 in stage 52.0 (TID 122)
22:32:12.987 INFO NewHadoopRDD - Input split: file:/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
22:32:12.989 INFO NewHadoopRDD - Input split: file:/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
22:32:13.023 INFO Executor - Finished task 1.0 in stage 52.0 (TID 122). 12151 bytes result sent to driver
22:32:13.029 INFO TaskSetManager - Finished task 1.0 in stage 52.0 (TID 122) in 50 ms on localhost (executor driver) (1/2)
22:32:13.032 INFO Executor - Finished task 0.0 in stage 52.0 (TID 121). 12151 bytes result sent to driver
22:32:13.037 INFO TaskSetManager - Finished task 0.0 in stage 52.0 (TID 121) in 60 ms on localhost (executor driver) (2/2)
22:32:13.038 INFO DAGScheduler - ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78) finished in 0.065 s
22:32:13.038 INFO DAGScheduler - Job 43 is finished. Cancelling potential speculative or zombie tasks for this job
22:32:13.038 INFO TaskSchedulerImpl - Removed TaskSet 52.0, whose tasks have all completed, from pool
22:32:13.038 INFO TaskSchedulerImpl - Killing all running tasks in stage 52: Stage finished
22:32:13.038 INFO DAGScheduler - Job 43 finished: collect at VariantsSparkSourceUnitTest.java:78, took 0.067841 s
WARNING 2025-03-28 22:32:13 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-03-28 22:32:13 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
22:32:13.058 INFO MemoryStore - Block broadcast_107 stored as values in memory (estimated size 81.1 KiB, free 1919.0 MiB)
22:32:13.060 INFO MemoryStore - Block broadcast_107_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.0 MiB)
22:32:13.062 INFO BlockManagerInfo - Added broadcast_107_piece0 in memory on localhost:35275 (size: 7.2 KiB, free: 1919.9 MiB)
22:32:13.062 INFO SparkContext - Created broadcast 107 from broadcast at VcfSource.java:129
22:32:13.064 INFO MemoryStore - Block broadcast_108 stored as values in memory (estimated size 326.6 KiB, free 1918.7 MiB)
22:32:13.076 INFO MemoryStore - Block broadcast_108_piece0 stored as bytes in memory (estimated size 55.7 KiB, free 1918.6 MiB)
22:32:13.076 INFO BlockManagerInfo - Added broadcast_108_piece0 in memory on localhost:35275 (size: 55.7 KiB, free: 1919.8 MiB)
22:32:13.077 INFO SparkContext - Created broadcast 108 from newAPIHadoopFile at VcfSource.java:168
22:32:13.081 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
22:32:13.092 INFO FileInputFormat - Total input files to process : 1
22:32:13.098 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
22:32:13.099 INFO DAGScheduler - Got job 44 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
22:32:13.099 INFO DAGScheduler - Final stage: ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43)
22:32:13.099 INFO DAGScheduler - Parents of final stage: List()
22:32:13.099 INFO DAGScheduler - Missing parents: List()
22:32:13.100 INFO DAGScheduler - Submitting ResultStage 53 (MapPartitionsRDD[271] at map at VariantsSparkSource.java:38), which has no missing parents
22:32:13.101 INFO MemoryStore - Block broadcast_109 stored as values in memory (estimated size 7.4 KiB, free 1918.6 MiB)
22:32:13.102 INFO MemoryStore - Block broadcast_109_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.6 MiB)
22:32:13.102 INFO BlockManagerInfo - Added broadcast_109_piece0 in memory on localhost:35275 (size: 3.7 KiB, free: 1919.8 MiB)
22:32:13.103 INFO SparkContext - Created broadcast 109 from broadcast at DAGScheduler.scala:1580
22:32:13.103 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))
22:32:13.103 INFO TaskSchedulerImpl - Adding task set 53.0 with 1 tasks resource profile 0
22:32:13.104 INFO TaskSetManager - Starting task 0.0 in stage 53.0 (TID 123) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7865 bytes)
22:32:13.104 INFO Executor - Running task 0.0 in stage 53.0 (TID 123)
22:32:13.107 INFO NewHadoopRDD - Input split: file:/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
22:32:13.123 INFO Executor - Finished task 0.0 in stage 53.0 (TID 123). 12108 bytes result sent to driver
22:32:13.126 INFO TaskSetManager - Finished task 0.0 in stage 53.0 (TID 123) in 22 ms on localhost (executor driver) (1/1)
22:32:13.126 INFO TaskSchedulerImpl - Removed TaskSet 53.0, whose tasks have all completed, from pool
22:32:13.127 INFO DAGScheduler - ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.027 s
22:32:13.127 INFO DAGScheduler - Job 44 is finished. Cancelling potential speculative or zombie tasks for this job
22:32:13.127 INFO TaskSchedulerImpl - Killing all running tasks in stage 53: Stage finished
22:32:13.127 INFO DAGScheduler - Job 44 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.028574 s
WARNING 2025-03-28 22:32:13 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-03-28 22:32:13 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
22:32:13.136 INFO MemoryStore - Block broadcast_110 stored as values in memory (estimated size 81.1 KiB, free 1918.5 MiB)
22:32:13.139 INFO MemoryStore - Block broadcast_110_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1918.5 MiB)
22:32:13.139 INFO BlockManagerInfo - Added broadcast_110_piece0 in memory on localhost:35275 (size: 7.1 KiB, free: 1919.8 MiB)
22:32:13.139 INFO SparkContext - Created broadcast 110 from broadcast at VcfSource.java:129
22:32:13.141 INFO MemoryStore - Block broadcast_111 stored as values in memory (estimated size 326.9 KiB, free 1918.2 MiB)
22:32:13.155 INFO MemoryStore - Block broadcast_111_piece0 stored as bytes in memory (estimated size 55.7 KiB, free 1918.1 MiB)
22:32:13.155 INFO BlockManagerInfo - Added broadcast_111_piece0 in memory on localhost:35275 (size: 55.7 KiB, free: 1919.7 MiB)
22:32:13.155 INFO SparkContext - Created broadcast 111 from newAPIHadoopFile at VcfSource.java:168
22:32:13.160 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
22:32:13.170 INFO FileInputFormat - Total input files to process : 1
22:32:13.178 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
22:32:13.178 INFO DAGScheduler - Got job 45 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
22:32:13.178 INFO DAGScheduler - Final stage: ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43)
22:32:13.179 INFO DAGScheduler - Parents of final stage: List()
22:32:13.179 INFO DAGScheduler - Missing parents: List()
22:32:13.180 INFO DAGScheduler - Submitting ResultStage 54 (MapPartitionsRDD[276] at map at VariantsSparkSource.java:38), which has no missing parents
22:32:13.181 INFO MemoryStore - Block broadcast_112 stored as values in memory (estimated size 7.4 KiB, free 1918.1 MiB)
22:32:13.184 INFO MemoryStore - Block broadcast_112_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1918.1 MiB)
22:32:13.184 INFO BlockManagerInfo - Added broadcast_112_piece0 in memory on localhost:35275 (size: 3.7 KiB, free: 1919.7 MiB)
22:32:13.186 INFO SparkContext - Created broadcast 112 from broadcast at DAGScheduler.scala:1580
22:32:13.186 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))
22:32:13.186 INFO TaskSchedulerImpl - Adding task set 54.0 with 1 tasks resource profile 0
22:32:13.190 INFO TaskSetManager - Starting task 0.0 in stage 54.0 (TID 124) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7856 bytes)
22:32:13.190 INFO Executor - Running task 0.0 in stage 54.0 (TID 124)
22:32:13.193 INFO NewHadoopRDD - Input split: file:/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
22:32:13.212 INFO Executor - Finished task 0.0 in stage 54.0 (TID 124). 12151 bytes result sent to driver
22:32:13.214 INFO TaskSetManager - Finished task 0.0 in stage 54.0 (TID 124) in 23 ms on localhost (executor driver) (1/1)
22:32:13.214 INFO TaskSchedulerImpl - Removed TaskSet 54.0, whose tasks have all completed, from pool
22:32:13.214 INFO DAGScheduler - ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.034 s
22:32:13.214 INFO DAGScheduler - Job 45 is finished. Cancelling potential speculative or zombie tasks for this job
22:32:13.214 INFO TaskSchedulerImpl - Killing all running tasks in stage 54: Stage finished
22:32:13.216 INFO DAGScheduler - Job 45 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.037817 s
WARNING 2025-03-28 22:32:13 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-03-28 22:32:13 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
22:32:13.227 INFO MemoryStore - Block broadcast_113 stored as values in memory (estimated size 81.1 KiB, free 1918.0 MiB)
22:32:13.231 INFO MemoryStore - Block broadcast_113_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1918.0 MiB)
22:32:13.232 INFO BlockManagerInfo - Added broadcast_113_piece0 in memory on localhost:35275 (size: 7.2 KiB, free: 1919.7 MiB)
22:32:13.232 INFO SparkContext - Created broadcast 113 from broadcast at VcfSource.java:129
22:32:13.234 INFO MemoryStore - Block broadcast_114 stored as values in memory (estimated size 327.2 KiB, free 1917.7 MiB)
22:32:13.249 INFO MemoryStore - Block broadcast_114_piece0 stored as bytes in memory (estimated size 55.7 KiB, free 1917.7 MiB)
22:32:13.250 INFO BlockManagerInfo - Added broadcast_114_piece0 in memory on localhost:35275 (size: 55.7 KiB, free: 1919.7 MiB)
22:32:13.250 INFO SparkContext - Created broadcast 114 from newAPIHadoopFile at VcfSource.java:168
22:32:13.254 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
22:32:13.265 INFO FileInputFormat - Total input files to process : 1
22:32:13.272 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
22:32:13.273 INFO DAGScheduler - Got job 46 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
22:32:13.273 INFO DAGScheduler - Final stage: ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55)
22:32:13.273 INFO DAGScheduler - Parents of final stage: List()
22:32:13.273 INFO DAGScheduler - Missing parents: List()
22:32:13.274 INFO DAGScheduler - Submitting ResultStage 55 (MapPartitionsRDD[279] at mapPartitions at VcfSource.java:134), which has no missing parents
22:32:13.275 INFO MemoryStore - Block broadcast_115 stored as values in memory (estimated size 6.3 KiB, free 1917.7 MiB)
22:32:13.278 INFO MemoryStore - Block broadcast_115_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.7 MiB)
22:32:13.278 INFO BlockManagerInfo - Added broadcast_115_piece0 in memory on localhost:35275 (size: 3.4 KiB, free: 1919.7 MiB)
22:32:13.279 INFO SparkContext - Created broadcast 115 from broadcast at DAGScheduler.scala:1580
22:32:13.279 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))
22:32:13.279 INFO TaskSchedulerImpl - Adding task set 55.0 with 1 tasks resource profile 0
22:32:13.280 INFO TaskSetManager - Starting task 0.0 in stage 55.0 (TID 125) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7865 bytes)
22:32:13.280 INFO Executor - Running task 0.0 in stage 55.0 (TID 125)
22:32:13.282 INFO NewHadoopRDD - Input split: file:/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
22:32:13.314 INFO Executor - Finished task 0.0 in stage 55.0 (TID 125). 153274 bytes result sent to driver
22:32:13.335 INFO TaskSetManager - Finished task 0.0 in stage 55.0 (TID 125) in 54 ms on localhost (executor driver) (1/1)
22:32:13.335 INFO TaskSchedulerImpl - Removed TaskSet 55.0, whose tasks have all completed, from pool
22:32:13.335 INFO DAGScheduler - ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.060 s
22:32:13.335 INFO DAGScheduler - Job 46 is finished. Cancelling potential speculative or zombie tasks for this job
22:32:13.335 INFO TaskSchedulerImpl - Killing all running tasks in stage 55: Stage finished
22:32:13.335 INFO DAGScheduler - Job 46 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.062834 s
WARNING 2025-03-28 22:32:13 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-03-28 22:32:13 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
22:32:13.363 INFO MemoryStore - Block broadcast_116 stored as values in memory (estimated size 81.1 KiB, free 1917.6 MiB)
22:32:13.367 INFO MemoryStore - Block broadcast_116_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1917.6 MiB)
22:32:13.367 INFO BlockManagerInfo - Added broadcast_116_piece0 in memory on localhost:35275 (size: 7.1 KiB, free: 1919.7 MiB)
22:32:13.367 INFO SparkContext - Created broadcast 116 from broadcast at VcfSource.java:129
22:32:13.369 INFO MemoryStore - Block broadcast_117 stored as values in memory (estimated size 327.5 KiB, free 1917.3 MiB)
22:32:13.385 INFO MemoryStore - Block broadcast_117_piece0 stored as bytes in memory (estimated size 55.6 KiB, free 1917.2 MiB)
22:32:13.385 INFO BlockManagerInfo - Added broadcast_117_piece0 in memory on localhost:35275 (size: 55.6 KiB, free: 1919.6 MiB)
22:32:13.386 INFO SparkContext - Created broadcast 117 from newAPIHadoopFile at VcfSource.java:168
22:32:13.389 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
22:32:13.401 INFO FileInputFormat - Total input files to process : 1
22:32:13.408 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
22:32:13.409 INFO DAGScheduler - Got job 47 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
22:32:13.409 INFO DAGScheduler - Final stage: ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55)
22:32:13.409 INFO DAGScheduler - Parents of final stage: List()
22:32:13.409 INFO DAGScheduler - Missing parents: List()
22:32:13.409 INFO DAGScheduler - Submitting ResultStage 56 (MapPartitionsRDD[282] at mapPartitions at VcfSource.java:134), which has no missing parents
22:32:13.410 INFO MemoryStore - Block broadcast_118 stored as values in memory (estimated size 6.3 KiB, free 1917.2 MiB)
22:32:13.413 INFO MemoryStore - Block broadcast_118_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1917.2 MiB)
22:32:13.413 INFO BlockManagerInfo - Added broadcast_118_piece0 in memory on localhost:35275 (size: 3.4 KiB, free: 1919.6 MiB)
22:32:13.413 INFO SparkContext - Created broadcast 118 from broadcast at DAGScheduler.scala:1580
22:32:13.414 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))
22:32:13.414 INFO TaskSchedulerImpl - Adding task set 56.0 with 1 tasks resource profile 0
22:32:13.415 INFO TaskSetManager - Starting task 0.0 in stage 56.0 (TID 126) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7856 bytes)
22:32:13.415 INFO Executor - Running task 0.0 in stage 56.0 (TID 126)
22:32:13.417 INFO NewHadoopRDD - Input split: file:/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
22:32:13.443 INFO Executor - Finished task 0.0 in stage 56.0 (TID 126). 153274 bytes result sent to driver
22:32:13.458 INFO TaskSetManager - Finished task 0.0 in stage 56.0 (TID 126) in 44 ms on localhost (executor driver) (1/1)
22:32:13.458 INFO TaskSchedulerImpl - Removed TaskSet 56.0, whose tasks have all completed, from pool
22:32:13.458 INFO DAGScheduler - ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.048 s
22:32:13.459 INFO DAGScheduler - Job 47 is finished. Cancelling potential speculative or zombie tasks for this job
22:32:13.459 INFO TaskSchedulerImpl - Killing all running tasks in stage 56: Stage finished
22:32:13.459 INFO DAGScheduler - Job 47 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.050519 s