[May 19, 2025 at 7:14:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1713373184
[May 19, 2025 at 7:14:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1713373184
[May 19, 2025 at 7:14:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1713373184
19:14:53.990 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
19:14:53.990 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:14:53.990 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
19:14:53.990 INFO CollectMultipleMetricsSpark - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:14:53.990 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:14:53.990 INFO CollectMultipleMetricsSpark - Start Date/Time: May 19, 2025 at 7:14:53 PM GMT
19:14:53.990 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
19:14:53.990 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
19:14:53.990 INFO CollectMultipleMetricsSpark - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:14:53.990 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
19:14:53.990 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
19:14:53.990 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:14:53.990 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:14:53.990 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:14:53.990 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:14:53.990 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
19:14:53.990 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
19:14:53.990 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
19:14:53.990 INFO CollectMultipleMetricsSpark - Requester pays: disabled
19:14:53.990 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
19:14:53.990 INFO CollectMultipleMetricsSpark - Initializing engine
19:14:53.990 INFO CollectMultipleMetricsSpark - Done initializing engine
19:14:53.990 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
WARNING 2025-05-19 19:14:53 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-19 19:14:53 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
19:14:53.992 INFO MemoryStore - Block broadcast_3374 stored as values in memory (estimated size 37.8 KiB, free 1914.2 MiB)
19:14:53.992 INFO MemoryStore - Block broadcast_3374_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1914.2 MiB)
19:14:53.993 INFO BlockManagerInfo - Added broadcast_3374_piece0 in memory on localhost:36441 (size: 8.4 KiB, free: 1918.4 MiB)
19:14:53.993 INFO SparkContext - Created broadcast 3374 from broadcast at SamSource.java:78
19:14:53.993 INFO MemoryStore - Block broadcast_3375 stored as values in memory (estimated size 305.5 KiB, free 1913.9 MiB)
19:14:54.000 INFO MemoryStore - Block broadcast_3375_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1913.9 MiB)
19:14:54.000 INFO BlockManagerInfo - Added broadcast_3375_piece0 in memory on localhost:36441 (size: 64.1 KiB, free: 1918.4 MiB)
19:14:54.001 INFO SparkContext - Created broadcast 3375 from newAPIHadoopFile at SamSource.java:108
WARNING 2025-05-19 19:14:54 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-19 19:14:54 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
19:14:54.003 INFO MemoryStore - Block broadcast_3376 stored as values in memory (estimated size 37.8 KiB, free 1913.8 MiB)
19:14:54.004 INFO MemoryStore - Block broadcast_3376_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1913.8 MiB)
19:14:54.004 INFO BlockManagerInfo - Added broadcast_3376_piece0 in memory on localhost:36441 (size: 8.4 KiB, free: 1918.4 MiB)
19:14:54.004 INFO SparkContext - Created broadcast 3376 from broadcast at SamSource.java:78
19:14:54.004 INFO MemoryStore - Block broadcast_3377 stored as values in memory (estimated size 305.5 KiB, free 1913.5 MiB)
19:14:54.011 INFO MemoryStore - Block broadcast_3377_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1913.4 MiB)
19:14:54.011 INFO BlockManagerInfo - Added broadcast_3377_piece0 in memory on localhost:36441 (size: 64.1 KiB, free: 1918.3 MiB)
19:14:54.011 INFO SparkContext - Created broadcast 3377 from newAPIHadoopFile at SamSource.java:108
19:14:54.013 INFO FileInputFormat - Total input files to process : 1
19:14:54.016 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
19:14:54.016 INFO DAGScheduler - Got job 882 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
19:14:54.016 INFO DAGScheduler - Final stage: ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
19:14:54.016 INFO DAGScheduler - Parents of final stage: List()
19:14:54.016 INFO DAGScheduler - Missing parents: List()
19:14:54.016 INFO DAGScheduler - Submitting ResultStage 2471 (MapPartitionsRDD[10156] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
19:14:54.017 INFO MemoryStore - Block broadcast_3378 stored as values in memory (estimated size 34.8 KiB, free 1913.4 MiB)
19:14:54.017 INFO MemoryStore - Block broadcast_3378_piece0 stored as bytes in memory (estimated size 14.6 KiB, free 1913.4 MiB)
19:14:54.018 INFO BlockManagerInfo - Added broadcast_3378_piece0 in memory on localhost:36441 (size: 14.6 KiB, free: 1918.3 MiB)
19:14:54.018 INFO SparkContext - Created broadcast 3378 from broadcast at DAGScheduler.scala:1580
19:14:54.018 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 2471 (MapPartitionsRDD[10156] at filter at CollectMultipleMetricsSpark.java:193) (first 15 tasks are for partitions Vector(0))
19:14:54.018 INFO TaskSchedulerImpl - Adding task set 2471.0 with 1 tasks resource profile 0
19:14:54.018 INFO TaskSetManager - Starting task 0.0 in stage 2471.0 (TID 1890) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
19:14:54.018 INFO Executor - Running task 0.0 in stage 2471.0 (TID 1890)
19:14:54.019 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.sam:0+44008
19:14:54.020 INFO Executor - Finished task 0.0 in stage 2471.0 (TID 1890). 946 bytes result sent to driver
19:14:54.021 INFO TaskSetManager - Finished task 0.0 in stage 2471.0 (TID 1890) in 3 ms on localhost (executor driver) (1/1)
19:14:54.021 INFO TaskSchedulerImpl - Removed TaskSet 2471.0, whose tasks have all completed, from pool
19:14:54.021 INFO DAGScheduler - ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.004 s
19:14:54.021 INFO DAGScheduler - Job 882 is finished. Cancelling potential speculative or zombie tasks for this job
19:14:54.021 INFO TaskSchedulerImpl - Killing all running tasks in stage 2471: Stage finished
19:14:54.021 INFO DAGScheduler - Job 882 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.004670 s
19:14:54.021 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 19, 2025 at 7:14:54 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1713373184
19:14:54.034 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
19:14:54.034 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:14:54.034 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
19:14:54.034 INFO CollectMultipleMetricsSpark - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:14:54.034 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:14:54.035 INFO CollectMultipleMetricsSpark - Start Date/Time: May 19, 2025 at 7:14:54 PM GMT
19:14:54.035 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
19:14:54.035 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
19:14:54.035 INFO CollectMultipleMetricsSpark - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:14:54.035 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
19:14:54.035 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
19:14:54.035 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:14:54.035 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:14:54.035 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:14:54.035 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:14:54.035 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
19:14:54.035 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
19:14:54.035 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
19:14:54.035 INFO CollectMultipleMetricsSpark - Requester pays: disabled
19:14:54.035 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
19:14:54.035 INFO CollectMultipleMetricsSpark - Initializing engine
19:14:54.035 INFO CollectMultipleMetricsSpark - Done initializing engine
19:14:54.035 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
19:14:54.036 INFO MemoryStore - Block broadcast_3379 stored as values in memory (estimated size 305.5 KiB, free 1913.1 MiB)
19:14:54.043 INFO MemoryStore - Block broadcast_3379_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1913.0 MiB)
19:14:54.043 INFO BlockManagerInfo - Added broadcast_3379_piece0 in memory on localhost:36441 (size: 64.1 KiB, free: 1918.2 MiB)
19:14:54.043 INFO SparkContext - Created broadcast 3379 from newAPIHadoopFile at PathSplitSource.java:96
19:14:54.062 INFO MemoryStore - Block broadcast_3380 stored as values in memory (estimated size 305.5 KiB, free 1912.7 MiB)
19:14:54.068 INFO MemoryStore - Block broadcast_3380_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1912.7 MiB)
19:14:54.068 INFO BlockManagerInfo - Added broadcast_3380_piece0 in memory on localhost:36441 (size: 64.1 KiB, free: 1918.2 MiB)
19:14:54.069 INFO SparkContext - Created broadcast 3380 from newAPIHadoopFile at PathSplitSource.java:96
19:14:54.088 INFO FileInputFormat - Total input files to process : 1
19:14:54.091 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
19:14:54.091 INFO DAGScheduler - Got job 883 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
19:14:54.091 INFO DAGScheduler - Final stage: ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
19:14:54.091 INFO DAGScheduler - Parents of final stage: List()
19:14:54.091 INFO DAGScheduler - Missing parents: List()
19:14:54.091 INFO DAGScheduler - Submitting ResultStage 2472 (MapPartitionsRDD[10169] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
19:14:54.115 INFO MemoryStore - Block broadcast_3381 stored as values in memory (estimated size 476.8 KiB, free 1912.2 MiB)
19:14:54.117 INFO MemoryStore - Block broadcast_3381_piece0 stored as bytes in memory (estimated size 207.4 KiB, free 1912.0 MiB)
19:14:54.117 INFO BlockManagerInfo - Added broadcast_3381_piece0 in memory on localhost:36441 (size: 207.4 KiB, free: 1918.0 MiB)
19:14:54.117 INFO SparkContext - Created broadcast 3381 from broadcast at DAGScheduler.scala:1580
19:14:54.118 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 2472 (MapPartitionsRDD[10169] at filter at CollectMultipleMetricsSpark.java:193) (first 15 tasks are for partitions Vector(0))
19:14:54.118 INFO TaskSchedulerImpl - Adding task set 2472.0 with 1 tasks resource profile 0
19:14:54.118 INFO TaskSetManager - Starting task 0.0 in stage 2472.0 (TID 1891) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
19:14:54.118 INFO Executor - Running task 0.0 in stage 2472.0 (TID 1891)
19:14:54.152 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.bam:0+8071
19:14:54.155 INFO Executor - Finished task 0.0 in stage 2472.0 (TID 1891). 989 bytes result sent to driver
19:14:54.155 INFO TaskSetManager - Finished task 0.0 in stage 2472.0 (TID 1891) in 37 ms on localhost (executor driver) (1/1)
19:14:54.155 INFO TaskSchedulerImpl - Removed TaskSet 2472.0, whose tasks have all completed, from pool
19:14:54.155 INFO DAGScheduler - ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.064 s
19:14:54.156 INFO DAGScheduler - Job 883 is finished. Cancelling potential speculative or zombie tasks for this job
19:14:54.156 INFO TaskSchedulerImpl - Killing all running tasks in stage 2472: Stage finished
19:14:54.156 INFO DAGScheduler - Job 883 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.064963 s
19:14:54.156 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 19, 2025 at 7:14:54 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1713373184
19:14:54.170 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
19:14:54.170 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:14:54.170 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
19:14:54.170 INFO CollectMultipleMetricsSpark - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:14:54.170 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:14:54.170 INFO CollectMultipleMetricsSpark - Start Date/Time: May 19, 2025 at 7:14:54 PM GMT
19:14:54.170 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
19:14:54.170 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
19:14:54.170 INFO CollectMultipleMetricsSpark - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:14:54.170 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
19:14:54.170 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
19:14:54.170 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:14:54.170 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:14:54.170 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:14:54.170 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:14:54.170 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
19:14:54.170 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
19:14:54.170 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
19:14:54.170 INFO CollectMultipleMetricsSpark - Requester pays: disabled
19:14:54.170 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
19:14:54.170 INFO CollectMultipleMetricsSpark - Initializing engine
19:14:54.170 INFO CollectMultipleMetricsSpark - Done initializing engine
19:14:54.170 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
19:14:54.173 INFO MemoryStore - Block broadcast_3382 stored as values in memory (estimated size 592.0 B, free 1912.0 MiB)
19:14:54.173 INFO MemoryStore - Block broadcast_3382_piece0 stored as bytes in memory (estimated size 209.0 B, free 1912.0 MiB)
19:14:54.173 INFO BlockManagerInfo - Added broadcast_3382_piece0 in memory on localhost:36441 (size: 209.0 B, free: 1918.0 MiB)
19:14:54.173 INFO SparkContext - Created broadcast 3382 from broadcast at CramSource.java:114
19:14:54.174 INFO MemoryStore - Block broadcast_3383 stored as values in memory (estimated size 305.5 KiB, free 1911.7 MiB)
19:14:54.181 INFO MemoryStore - Block broadcast_3383_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1911.6 MiB)
19:14:54.181 INFO BlockManagerInfo - Added broadcast_3383_piece0 in memory on localhost:36441 (size: 64.0 KiB, free: 1917.9 MiB)
19:14:54.181 INFO SparkContext - Created broadcast 3383 from newAPIHadoopFile at PathSplitSource.java:96
19:14:54.195 INFO MemoryStore - Block broadcast_3384 stored as values in memory (estimated size 592.0 B, free 1911.6 MiB)
19:14:54.196 INFO MemoryStore - Block broadcast_3384_piece0 stored as bytes in memory (estimated size 209.0 B, free 1911.6 MiB)
19:14:54.196 INFO BlockManagerInfo - Added broadcast_3384_piece0 in memory on localhost:36441 (size: 209.0 B, free: 1917.9 MiB)
19:14:54.196 INFO SparkContext - Created broadcast 3384 from broadcast at CramSource.java:114
19:14:54.197 INFO MemoryStore - Block broadcast_3385 stored as values in memory (estimated size 305.5 KiB, free 1911.3 MiB)
19:14:54.203 INFO MemoryStore - Block broadcast_3385_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1911.3 MiB)
19:14:54.203 INFO BlockManagerInfo - Added broadcast_3385_piece0 in memory on localhost:36441 (size: 64.0 KiB, free: 1917.8 MiB)
19:14:54.203 INFO SparkContext - Created broadcast 3385 from newAPIHadoopFile at PathSplitSource.java:96
19:14:54.217 INFO FileInputFormat - Total input files to process : 1
19:14:54.220 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
19:14:54.220 INFO DAGScheduler - Got job 884 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
19:14:54.220 INFO DAGScheduler - Final stage: ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
19:14:54.220 INFO DAGScheduler - Parents of final stage: List()
19:14:54.220 INFO DAGScheduler - Missing parents: List()
19:14:54.220 INFO DAGScheduler - Submitting ResultStage 2473 (MapPartitionsRDD[10180] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
19:14:54.237 INFO MemoryStore - Block broadcast_3386 stored as values in memory (estimated size 329.7 KiB, free 1911.0 MiB)
19:14:54.239 INFO MemoryStore - Block broadcast_3386_piece0 stored as bytes in memory (estimated size 143.3 KiB, free 1910.8 MiB)
19:14:54.239 INFO BlockManagerInfo - Added broadcast_3386_piece0 in memory on localhost:36441 (size: 143.3 KiB, free: 1917.7 MiB)
19:14:54.239 INFO SparkContext - Created broadcast 3386 from broadcast at DAGScheduler.scala:1580
19:14:54.239 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 2473 (MapPartitionsRDD[10180] at filter at CollectMultipleMetricsSpark.java:193) (first 15 tasks are for partitions Vector(0))
19:14:54.239 INFO TaskSchedulerImpl - Adding task set 2473.0 with 1 tasks resource profile 0
19:14:54.240 INFO TaskSetManager - Starting task 0.0 in stage 2473.0 (TID 1892) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9689 bytes)
19:14:54.240 INFO Executor - Running task 0.0 in stage 2473.0 (TID 1892)
19:14:54.265 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.cram:0+8617
19:14:54.269 INFO Executor - Finished task 0.0 in stage 2473.0 (TID 1892). 989 bytes result sent to driver
19:14:54.269 INFO TaskSetManager - Finished task 0.0 in stage 2473.0 (TID 1892) in 29 ms on localhost (executor driver) (1/1)
19:14:54.269 INFO TaskSchedulerImpl - Removed TaskSet 2473.0, whose tasks have all completed, from pool
19:14:54.269 INFO DAGScheduler - ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.049 s
19:14:54.269 INFO DAGScheduler - Job 884 is finished. Cancelling potential speculative or zombie tasks for this job
19:14:54.269 INFO TaskSchedulerImpl - Killing all running tasks in stage 2473: Stage finished
19:14:54.269 INFO DAGScheduler - Job 884 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.049238 s
19:14:54.269 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 19, 2025 at 7:14:54 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1713373184