WARNING 2025-05-19 19:02:03 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-19 19:02:03 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-19 19:02:03 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-19 19:02:03 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:02:03.955 INFO MemoryStore - Block broadcast_102 stored as values in memory (estimated size 81.1 KiB, free 1917.4 MiB)
19:02:03.958 INFO MemoryStore - Block broadcast_102_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1917.4 MiB)
19:02:03.958 INFO BlockManagerInfo - Added broadcast_102_piece0 in memory on localhost:45255 (size: 7.1 KiB, free: 1919.5 MiB)
19:02:03.959 INFO SparkContext - Created broadcast 102 from broadcast at VcfSource.java:129
19:02:03.962 INFO MemoryStore - Block broadcast_103 stored as values in memory (estimated size 81.1 KiB, free 1917.3 MiB)
19:02:03.962 INFO MemoryStore - Block broadcast_104 stored as values in memory (estimated size 297.9 KiB, free 1917.1 MiB)
19:02:03.963 INFO MemoryStore - Block broadcast_103_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1917.1 MiB)
19:02:03.965 INFO BlockManagerInfo - Added broadcast_103_piece0 in memory on localhost:45255 (size: 7.2 KiB, free: 1919.5 MiB)
19:02:03.965 INFO SparkContext - Created broadcast 103 from broadcast at VcfSource.java:129
19:02:03.968 INFO MemoryStore - Block broadcast_105 stored as values in memory (estimated size 297.9 KiB, free 1916.8 MiB)
19:02:03.975 INFO MemoryStore - Block broadcast_104_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1916.7 MiB)
19:02:03.975 INFO BlockManagerInfo - Added broadcast_104_piece0 in memory on localhost:45255 (size: 50.2 KiB, free: 1919.4 MiB)
19:02:03.975 INFO SparkContext - Created broadcast 104 from newAPIHadoopFile at VcfSource.java:168
19:02:03.977 INFO MemoryStore - Block broadcast_105_piece0 stored as bytes in memory (estimated size 50.2 KiB, free 1916.7 MiB)
19:02:03.977 INFO BlockManagerInfo - Added broadcast_105_piece0 in memory on localhost:45255 (size: 50.2 KiB, free: 1919.4 MiB)
19:02:03.978 INFO SparkContext - Created broadcast 105 from newAPIHadoopFile at VcfSource.java:168
19:02:03.985 INFO FileInputFormat - Total input files to process : 1
19:02:03.985 INFO FileInputFormat - Total input files to process : 1
19:02:03.992 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
19:02:04.003 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
19:02:04.020 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:78
19:02:04.021 INFO DAGScheduler - Got job 43 (collect at VariantsSparkSourceUnitTest.java:78) with 2 output partitions
19:02:04.021 INFO DAGScheduler - Final stage: ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78)
19:02:04.021 INFO DAGScheduler - Parents of final stage: List()
19:02:04.022 INFO DAGScheduler - Missing parents: List()
19:02:04.022 INFO DAGScheduler - Submitting ResultStage 52 (UnionRDD[266] at union at VariantsSparkSource.java:51), which has no missing parents
19:02:04.024 INFO MemoryStore - Block broadcast_106 stored as values in memory (estimated size 9.0 KiB, free 1916.7 MiB)
19:02:04.025 INFO MemoryStore - Block broadcast_106_piece0 stored as bytes in memory (estimated size 4.3 KiB, free 1916.6 MiB)
19:02:04.025 INFO BlockManagerInfo - Added broadcast_106_piece0 in memory on localhost:45255 (size: 4.3 KiB, free: 1919.4 MiB)
19:02:04.025 INFO SparkContext - Created broadcast 106 from broadcast at DAGScheduler.scala:1580
19:02:04.025 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))
19:02:04.025 INFO TaskSchedulerImpl - Adding task set 52.0 with 2 tasks resource profile 0
19:02:04.027 INFO TaskSetManager - Starting task 0.0 in stage 52.0 (TID 121) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7982 bytes)
19:02:04.027 INFO TaskSetManager - Starting task 1.0 in stage 52.0 (TID 122) (localhost, executor driver, partition 1, PROCESS_LOCAL, 7973 bytes)
19:02:04.028 INFO Executor - Running task 1.0 in stage 52.0 (TID 122)
19:02:04.028 INFO Executor - Running task 0.0 in stage 52.0 (TID 121)
19:02:04.035 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
19:02:04.036 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
19:02:04.084 INFO Executor - Finished task 0.0 in stage 52.0 (TID 121). 12151 bytes result sent to driver
19:02:04.084 INFO Executor - Finished task 1.0 in stage 52.0 (TID 122). 12108 bytes result sent to driver
19:02:04.089 INFO TaskSetManager - Finished task 0.0 in stage 52.0 (TID 121) in 63 ms on localhost (executor driver) (1/2)
19:02:04.090 INFO TaskSetManager - Finished task 1.0 in stage 52.0 (TID 122) in 63 ms on localhost (executor driver) (2/2)
19:02:04.090 INFO TaskSchedulerImpl - Removed TaskSet 52.0, whose tasks have all completed, from pool
19:02:04.090 INFO DAGScheduler - ResultStage 52 (collect at VariantsSparkSourceUnitTest.java:78) finished in 0.067 s
19:02:04.090 INFO DAGScheduler - Job 43 is finished. Cancelling potential speculative or zombie tasks for this job
19:02:04.090 INFO TaskSchedulerImpl - Killing all running tasks in stage 52: Stage finished
19:02:04.090 INFO DAGScheduler - Job 43 finished: collect at VariantsSparkSourceUnitTest.java:78, took 0.070388 s
WARNING 2025-05-19 19:02:04 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-19 19:02:04 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:02:04.103 INFO MemoryStore - Block broadcast_107 stored as values in memory (estimated size 81.1 KiB, free 1916.6 MiB)
19:02:04.105 INFO MemoryStore - Block broadcast_107_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1916.6 MiB)
19:02:04.105 INFO BlockManagerInfo - Added broadcast_107_piece0 in memory on localhost:45255 (size: 7.2 KiB, free: 1919.4 MiB)
19:02:04.105 INFO SparkContext - Created broadcast 107 from broadcast at VcfSource.java:129
19:02:04.107 INFO MemoryStore - Block broadcast_108 stored as values in memory (estimated size 298.2 KiB, free 1916.3 MiB)
19:02:04.115 INFO MemoryStore - Block broadcast_108_piece0 stored as bytes in memory (estimated size 50.4 KiB, free 1916.2 MiB)
19:02:04.115 INFO BlockManagerInfo - Added broadcast_108_piece0 in memory on localhost:45255 (size: 50.4 KiB, free: 1919.3 MiB)
19:02:04.115 INFO SparkContext - Created broadcast 108 from newAPIHadoopFile at VcfSource.java:168
19:02:04.118 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
19:02:04.124 INFO FileInputFormat - Total input files to process : 1
19:02:04.128 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
19:02:04.128 INFO DAGScheduler - Got job 44 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
19:02:04.128 INFO DAGScheduler - Final stage: ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43)
19:02:04.128 INFO DAGScheduler - Parents of final stage: List()
19:02:04.129 INFO DAGScheduler - Missing parents: List()
19:02:04.129 INFO DAGScheduler - Submitting ResultStage 53 (MapPartitionsRDD[271] at map at VariantsSparkSource.java:38), which has no missing parents
19:02:04.130 INFO MemoryStore - Block broadcast_109 stored as values in memory (estimated size 7.4 KiB, free 1916.2 MiB)
19:02:04.131 INFO MemoryStore - Block broadcast_109_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1916.2 MiB)
19:02:04.131 INFO BlockManagerInfo - Added broadcast_109_piece0 in memory on localhost:45255 (size: 3.7 KiB, free: 1919.3 MiB)
19:02:04.131 INFO SparkContext - Created broadcast 109 from broadcast at DAGScheduler.scala:1580
19:02:04.131 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))
19:02:04.131 INFO TaskSchedulerImpl - Adding task set 53.0 with 1 tasks resource profile 0
19:02:04.132 INFO TaskSetManager - Starting task 0.0 in stage 53.0 (TID 123) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes)
19:02:04.132 INFO Executor - Running task 0.0 in stage 53.0 (TID 123)
19:02:04.135 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
19:02:04.148 INFO Executor - Finished task 0.0 in stage 53.0 (TID 123). 12108 bytes result sent to driver
19:02:04.149 INFO TaskSetManager - Finished task 0.0 in stage 53.0 (TID 123) in 17 ms on localhost (executor driver) (1/1)
19:02:04.149 INFO TaskSchedulerImpl - Removed TaskSet 53.0, whose tasks have all completed, from pool
19:02:04.150 INFO DAGScheduler - ResultStage 53 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.021 s
19:02:04.150 INFO DAGScheduler - Job 44 is finished. Cancelling potential speculative or zombie tasks for this job
19:02:04.150 INFO TaskSchedulerImpl - Killing all running tasks in stage 53: Stage finished
19:02:04.150 INFO DAGScheduler - Job 44 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.021868 s
WARNING 2025-05-19 19:02:04 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-19 19:02:04 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:02:04.159 INFO MemoryStore - Block broadcast_110 stored as values in memory (estimated size 81.1 KiB, free 1916.1 MiB)
19:02:04.171 INFO MemoryStore - Block broadcast_110_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1916.1 MiB)
19:02:04.172 INFO BlockManagerInfo - Added broadcast_110_piece0 in memory on localhost:45255 (size: 7.1 KiB, free: 1919.3 MiB)
19:02:04.172 INFO BlockManagerInfo - Removed broadcast_98_piece0 on localhost:45255 in memory (size: 50.1 KiB, free: 1919.4 MiB)
19:02:04.173 INFO SparkContext - Created broadcast 110 from broadcast at VcfSource.java:129
19:02:04.173 INFO BlockManagerInfo - Removed broadcast_104_piece0 on localhost:45255 in memory (size: 50.2 KiB, free: 1919.4 MiB)
19:02:04.174 INFO BlockManagerInfo - Removed broadcast_95_piece0 on localhost:45255 in memory (size: 50.0 KiB, free: 1919.5 MiB)
19:02:04.174 INFO BlockManagerInfo - Removed broadcast_94_piece0 on localhost:45255 in memory (size: 239.0 B, free: 1919.5 MiB)
19:02:04.175 INFO BlockManagerInfo - Removed broadcast_100_piece0 on localhost:45255 in memory (size: 50.1 KiB, free: 1919.5 MiB)
19:02:04.175 INFO MemoryStore - Block broadcast_111 stored as values in memory (estimated size 298.5 KiB, free 1917.2 MiB)
19:02:04.176 INFO BlockManagerInfo - Removed broadcast_108_piece0 on localhost:45255 in memory (size: 50.4 KiB, free: 1919.6 MiB)
19:02:04.177 INFO BlockManagerInfo - Removed broadcast_103_piece0 on localhost:45255 in memory (size: 7.2 KiB, free: 1919.6 MiB)
19:02:04.177 INFO BlockManagerInfo - Removed broadcast_107_piece0 on localhost:45255 in memory (size: 7.2 KiB, free: 1919.6 MiB)
19:02:04.178 INFO BlockManagerInfo - Removed broadcast_105_piece0 on localhost:45255 in memory (size: 50.2 KiB, free: 1919.6 MiB)
19:02:04.179 INFO BlockManagerInfo - Removed broadcast_106_piece0 on localhost:45255 in memory (size: 4.3 KiB, free: 1919.6 MiB)
19:02:04.180 INFO BlockManagerInfo - Removed broadcast_101_piece0 on localhost:45255 in memory (size: 50.1 KiB, free: 1919.7 MiB)
19:02:04.181 INFO BlockManagerInfo - Removed broadcast_96_piece0 on localhost:45255 in memory (size: 152.8 KiB, free: 1919.8 MiB)
19:02:04.182 INFO BlockManagerInfo - Removed broadcast_102_piece0 on localhost:45255 in memory (size: 7.1 KiB, free: 1919.8 MiB)
19:02:04.182 INFO BlockManagerInfo - Removed broadcast_97_piece0 on localhost:45255 in memory (size: 229.0 B, free: 1919.8 MiB)
19:02:04.183 INFO BlockManagerInfo - Removed broadcast_99_piece0 on localhost:45255 in memory (size: 152.8 KiB, free: 1920.0 MiB)
19:02:04.184 INFO BlockManagerInfo - Removed broadcast_109_piece0 on localhost:45255 in memory (size: 3.7 KiB, free: 1920.0 MiB)
19:02:04.186 INFO MemoryStore - Block broadcast_111_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1919.6 MiB)
19:02:04.186 INFO BlockManagerInfo - Added broadcast_111_piece0 in memory on localhost:45255 (size: 50.3 KiB, free: 1919.9 MiB)
19:02:04.186 INFO SparkContext - Created broadcast 111 from newAPIHadoopFile at VcfSource.java:168
19:02:04.189 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
19:02:04.195 INFO FileInputFormat - Total input files to process : 1
19:02:04.200 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:43
19:02:04.200 INFO DAGScheduler - Got job 45 (collect at VariantsSparkSourceUnitTest.java:43) with 1 output partitions
19:02:04.200 INFO DAGScheduler - Final stage: ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43)
19:02:04.200 INFO DAGScheduler - Parents of final stage: List()
19:02:04.200 INFO DAGScheduler - Missing parents: List()
19:02:04.201 INFO DAGScheduler - Submitting ResultStage 54 (MapPartitionsRDD[276] at map at VariantsSparkSource.java:38), which has no missing parents
19:02:04.203 INFO MemoryStore - Block broadcast_112 stored as values in memory (estimated size 7.4 KiB, free 1919.6 MiB)
19:02:04.204 INFO MemoryStore - Block broadcast_112_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1919.6 MiB)
19:02:04.204 INFO BlockManagerInfo - Added broadcast_112_piece0 in memory on localhost:45255 (size: 3.7 KiB, free: 1919.9 MiB)
19:02:04.204 INFO SparkContext - Created broadcast 112 from broadcast at DAGScheduler.scala:1580
19:02:04.205 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))
19:02:04.205 INFO TaskSchedulerImpl - Adding task set 54.0 with 1 tasks resource profile 0
19:02:04.206 INFO TaskSetManager - Starting task 0.0 in stage 54.0 (TID 124) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes)
19:02:04.206 INFO Executor - Running task 0.0 in stage 54.0 (TID 124)
19:02:04.208 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
19:02:04.217 INFO Executor - Finished task 0.0 in stage 54.0 (TID 124). 12108 bytes result sent to driver
19:02:04.219 INFO TaskSetManager - Finished task 0.0 in stage 54.0 (TID 124) in 13 ms on localhost (executor driver) (1/1)
19:02:04.220 INFO DAGScheduler - ResultStage 54 (collect at VariantsSparkSourceUnitTest.java:43) finished in 0.018 s
19:02:04.220 INFO DAGScheduler - Job 45 is finished. Cancelling potential speculative or zombie tasks for this job
19:02:04.220 INFO TaskSchedulerImpl - Removed TaskSet 54.0, whose tasks have all completed, from pool
19:02:04.220 INFO TaskSchedulerImpl - Killing all running tasks in stage 54: Stage finished
19:02:04.220 INFO DAGScheduler - Job 45 finished: collect at VariantsSparkSourceUnitTest.java:43, took 0.020712 s
WARNING 2025-05-19 19:02:04 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-19 19:02:04 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:02:04.232 INFO MemoryStore - Block broadcast_113 stored as values in memory (estimated size 81.1 KiB, free 1919.5 MiB)
19:02:04.234 INFO MemoryStore - Block broadcast_113_piece0 stored as bytes in memory (estimated size 7.2 KiB, free 1919.5 MiB)
19:02:04.234 INFO BlockManagerInfo - Added broadcast_113_piece0 in memory on localhost:45255 (size: 7.2 KiB, free: 1919.9 MiB)
19:02:04.234 INFO SparkContext - Created broadcast 113 from broadcast at VcfSource.java:129
19:02:04.236 INFO MemoryStore - Block broadcast_114 stored as values in memory (estimated size 298.8 KiB, free 1919.2 MiB)
19:02:04.243 INFO MemoryStore - Block broadcast_114_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1919.1 MiB)
19:02:04.243 INFO BlockManagerInfo - Added broadcast_114_piece0 in memory on localhost:45255 (size: 50.3 KiB, free: 1919.9 MiB)
19:02:04.243 INFO SparkContext - Created broadcast 114 from newAPIHadoopFile at VcfSource.java:168
19:02:04.247 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
19:02:04.252 INFO FileInputFormat - Total input files to process : 1
19:02:04.257 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
19:02:04.257 INFO DAGScheduler - Got job 46 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
19:02:04.258 INFO DAGScheduler - Final stage: ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55)
19:02:04.258 INFO DAGScheduler - Parents of final stage: List()
19:02:04.258 INFO DAGScheduler - Missing parents: List()
19:02:04.258 INFO DAGScheduler - Submitting ResultStage 55 (MapPartitionsRDD[279] at mapPartitions at VcfSource.java:134), which has no missing parents
19:02:04.259 INFO MemoryStore - Block broadcast_115 stored as values in memory (estimated size 6.3 KiB, free 1919.1 MiB)
19:02:04.260 INFO MemoryStore - Block broadcast_115_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1919.1 MiB)
19:02:04.260 INFO BlockManagerInfo - Added broadcast_115_piece0 in memory on localhost:45255 (size: 3.4 KiB, free: 1919.9 MiB)
19:02:04.261 INFO SparkContext - Created broadcast 115 from broadcast at DAGScheduler.scala:1580
19:02:04.261 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))
19:02:04.261 INFO TaskSchedulerImpl - Adding task set 55.0 with 1 tasks resource profile 0
19:02:04.262 INFO TaskSetManager - Starting task 0.0 in stage 55.0 (TID 125) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7858 bytes)
19:02:04.262 INFO Executor - Running task 0.0 in stage 55.0 (TID 125)
19:02:04.264 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf:0+111531
19:02:04.283 INFO Executor - Finished task 0.0 in stage 55.0 (TID 125). 153274 bytes result sent to driver
19:02:04.298 INFO TaskSetManager - Finished task 0.0 in stage 55.0 (TID 125) in 36 ms on localhost (executor driver) (1/1)
19:02:04.298 INFO TaskSchedulerImpl - Removed TaskSet 55.0, whose tasks have all completed, from pool
19:02:04.298 INFO DAGScheduler - ResultStage 55 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.040 s
19:02:04.299 INFO DAGScheduler - Job 46 is finished. Cancelling potential speculative or zombie tasks for this job
19:02:04.299 INFO TaskSchedulerImpl - Killing all running tasks in stage 55: Stage finished
19:02:04.299 INFO DAGScheduler - Job 46 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.041934 s
WARNING 2025-05-19 19:02:04 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2025-05-19 19:02:04 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
19:02:04.325 INFO MemoryStore - Block broadcast_116 stored as values in memory (estimated size 81.1 KiB, free 1919.0 MiB)
19:02:04.327 INFO MemoryStore - Block broadcast_116_piece0 stored as bytes in memory (estimated size 7.1 KiB, free 1919.0 MiB)
19:02:04.327 INFO BlockManagerInfo - Added broadcast_116_piece0 in memory on localhost:45255 (size: 7.1 KiB, free: 1919.9 MiB)
19:02:04.327 INFO SparkContext - Created broadcast 116 from broadcast at VcfSource.java:129
19:02:04.330 INFO MemoryStore - Block broadcast_117 stored as values in memory (estimated size 299.0 KiB, free 1918.7 MiB)
19:02:04.340 INFO MemoryStore - Block broadcast_117_piece0 stored as bytes in memory (estimated size 50.3 KiB, free 1918.7 MiB)
19:02:04.340 INFO BlockManagerInfo - Added broadcast_117_piece0 in memory on localhost:45255 (size: 50.3 KiB, free: 1919.8 MiB)
19:02:04.341 INFO SparkContext - Created broadcast 117 from newAPIHadoopFile at VcfSource.java:168
19:02:04.344 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
19:02:04.351 INFO FileInputFormat - Total input files to process : 1
19:02:04.356 INFO SparkContext - Starting job: collect at VariantsSparkSourceUnitTest.java:55
19:02:04.356 INFO DAGScheduler - Got job 47 (collect at VariantsSparkSourceUnitTest.java:55) with 1 output partitions
19:02:04.356 INFO DAGScheduler - Final stage: ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55)
19:02:04.356 INFO DAGScheduler - Parents of final stage: List()
19:02:04.356 INFO DAGScheduler - Missing parents: List()
19:02:04.357 INFO DAGScheduler - Submitting ResultStage 56 (MapPartitionsRDD[282] at mapPartitions at VcfSource.java:134), which has no missing parents
19:02:04.358 INFO MemoryStore - Block broadcast_118 stored as values in memory (estimated size 6.3 KiB, free 1918.7 MiB)
19:02:04.359 INFO MemoryStore - Block broadcast_118_piece0 stored as bytes in memory (estimated size 3.4 KiB, free 1918.7 MiB)
19:02:04.359 INFO BlockManagerInfo - Added broadcast_118_piece0 in memory on localhost:45255 (size: 3.4 KiB, free: 1919.8 MiB)
19:02:04.359 INFO SparkContext - Created broadcast 118 from broadcast at DAGScheduler.scala:1580
19:02:04.359 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))
19:02:04.359 INFO TaskSchedulerImpl - Adding task set 56.0 with 1 tasks resource profile 0
19:02:04.360 INFO TaskSetManager - Starting task 0.0 in stage 56.0 (TID 126) (localhost, executor driver, partition 0, PROCESS_LOCAL, 7849 bytes)
19:02:04.360 INFO Executor - Running task 0.0 in stage 56.0 (TID 126)
19:02:04.362 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf:0+111529
19:02:04.387 INFO Executor - Finished task 0.0 in stage 56.0 (TID 126). 153274 bytes result sent to driver
19:02:04.397 INFO TaskSetManager - Finished task 0.0 in stage 56.0 (TID 126) in 37 ms on localhost (executor driver) (1/1)
19:02:04.397 INFO TaskSchedulerImpl - Removed TaskSet 56.0, whose tasks have all completed, from pool
19:02:04.398 INFO DAGScheduler - ResultStage 56 (collect at VariantsSparkSourceUnitTest.java:55) finished in 0.041 s
19:02:04.398 INFO DAGScheduler - Job 47 is finished. Cancelling potential speculative or zombie tasks for this job
19:02:04.398 INFO TaskSchedulerImpl - Killing all running tasks in stage 56: Stage finished
19:02:04.398 INFO DAGScheduler - Job 47 finished: collect at VariantsSparkSourceUnitTest.java:55, took 0.042368 s