[May 27, 2025 at 4:50:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1702887424
[May 27, 2025 at 4:50:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1702887424
[May 27, 2025 at 4:50:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1702887424
16:50:48.077 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:50:48.077 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:50:48.077 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
16:50:48.077 INFO CollectMultipleMetricsSpark - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:50:48.077 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:50:48.077 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 4:50:48 PM GMT
16:50:48.077 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:50:48.077 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:50:48.077 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:50:48.077 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
16:50:48.077 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
16:50:48.077 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:50:48.077 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:50:48.077 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:50:48.077 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:50:48.078 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
16:50:48.078 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
16:50:48.078 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
16:50:48.078 INFO CollectMultipleMetricsSpark - Requester pays: disabled
16:50:48.078 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:50:48.078 INFO CollectMultipleMetricsSpark - Initializing engine
16:50:48.078 INFO CollectMultipleMetricsSpark - Done initializing engine
16:50:48.078 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
WARNING 2025-05-27 16:50:48 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-27 16:50:48 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
16:50:48.079 INFO MemoryStore - Block broadcast_3374 stored as values in memory (estimated size 37.8 KiB, free 1914.6 MiB)
16:50:48.080 INFO MemoryStore - Block broadcast_3374_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1914.6 MiB)
16:50:48.080 INFO BlockManagerInfo - Added broadcast_3374_piece0 in memory on localhost:37833 (size: 8.4 KiB, free: 1918.5 MiB)
16:50:48.080 INFO SparkContext - Created broadcast 3374 from broadcast at SamSource.java:78
16:50:48.081 INFO MemoryStore - Block broadcast_3375 stored as values in memory (estimated size 305.5 KiB, free 1914.3 MiB)
16:50:48.087 INFO MemoryStore - Block broadcast_3375_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1914.2 MiB)
16:50:48.087 INFO BlockManagerInfo - Added broadcast_3375_piece0 in memory on localhost:37833 (size: 64.1 KiB, free: 1918.4 MiB)
16:50:48.087 INFO SparkContext - Created broadcast 3375 from newAPIHadoopFile at SamSource.java:108
WARNING 2025-05-27 16:50:48 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-27 16:50:48 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
16:50:48.090 INFO MemoryStore - Block broadcast_3376 stored as values in memory (estimated size 37.8 KiB, free 1914.2 MiB)
16:50:48.090 INFO MemoryStore - Block broadcast_3376_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1914.2 MiB)
16:50:48.090 INFO BlockManagerInfo - Added broadcast_3376_piece0 in memory on localhost:37833 (size: 8.4 KiB, free: 1918.4 MiB)
16:50:48.090 INFO SparkContext - Created broadcast 3376 from broadcast at SamSource.java:78
16:50:48.091 INFO MemoryStore - Block broadcast_3377 stored as values in memory (estimated size 305.5 KiB, free 1913.9 MiB)
16:50:48.097 INFO MemoryStore - Block broadcast_3377_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1913.8 MiB)
16:50:48.098 INFO BlockManagerInfo - Added broadcast_3377_piece0 in memory on localhost:37833 (size: 64.1 KiB, free: 1918.4 MiB)
16:50:48.098 INFO SparkContext - Created broadcast 3377 from newAPIHadoopFile at SamSource.java:108
16:50:48.100 INFO FileInputFormat - Total input files to process : 1
16:50:48.103 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
16:50:48.103 INFO DAGScheduler - Got job 882 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
16:50:48.103 INFO DAGScheduler - Final stage: ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
16:50:48.103 INFO DAGScheduler - Parents of final stage: List()
16:50:48.103 INFO DAGScheduler - Missing parents: List()
16:50:48.103 INFO DAGScheduler - Submitting ResultStage 2471 (MapPartitionsRDD[10156] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
16:50:48.104 INFO MemoryStore - Block broadcast_3378 stored as values in memory (estimated size 34.8 KiB, free 1913.8 MiB)
16:50:48.104 INFO MemoryStore - Block broadcast_3378_piece0 stored as bytes in memory (estimated size 14.6 KiB, free 1913.8 MiB)
16:50:48.104 INFO BlockManagerInfo - Added broadcast_3378_piece0 in memory on localhost:37833 (size: 14.6 KiB, free: 1918.4 MiB)
16:50:48.105 INFO SparkContext - Created broadcast 3378 from broadcast at DAGScheduler.scala:1580
16:50:48.105 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))
16:50:48.105 INFO TaskSchedulerImpl - Adding task set 2471.0 with 1 tasks resource profile 0
16:50:48.105 INFO TaskSetManager - Starting task 0.0 in stage 2471.0 (TID 1890) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
16:50:48.105 INFO Executor - Running task 0.0 in stage 2471.0 (TID 1890)
16:50:48.106 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.sam:0+44008
16:50:48.107 INFO Executor - Finished task 0.0 in stage 2471.0 (TID 1890). 946 bytes result sent to driver
16:50:48.108 INFO TaskSetManager - Finished task 0.0 in stage 2471.0 (TID 1890) in 3 ms on localhost (executor driver) (1/1)
16:50:48.108 INFO TaskSchedulerImpl - Removed TaskSet 2471.0, whose tasks have all completed, from pool
16:50:48.108 INFO DAGScheduler - ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.004 s
16:50:48.108 INFO DAGScheduler - Job 882 is finished. Cancelling potential speculative or zombie tasks for this job
16:50:48.108 INFO TaskSchedulerImpl - Killing all running tasks in stage 2471: Stage finished
16:50:48.108 INFO DAGScheduler - Job 882 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.004795 s
16:50:48.108 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 4:50:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1702887424
16:50:48.122 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:50:48.122 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:50:48.122 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
16:50:48.122 INFO CollectMultipleMetricsSpark - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:50:48.122 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:50:48.122 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 4:50:48 PM GMT
16:50:48.122 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:50:48.122 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:50:48.122 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:50:48.122 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
16:50:48.122 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
16:50:48.122 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:50:48.122 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:50:48.122 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:50:48.122 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:50:48.122 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
16:50:48.122 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
16:50:48.122 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
16:50:48.122 INFO CollectMultipleMetricsSpark - Requester pays: disabled
16:50:48.122 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:50:48.122 INFO CollectMultipleMetricsSpark - Initializing engine
16:50:48.122 INFO CollectMultipleMetricsSpark - Done initializing engine
16:50:48.122 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
16:50:48.124 INFO MemoryStore - Block broadcast_3379 stored as values in memory (estimated size 305.5 KiB, free 1913.5 MiB)
16:50:48.130 INFO MemoryStore - Block broadcast_3379_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1913.4 MiB)
16:50:48.130 INFO BlockManagerInfo - Added broadcast_3379_piece0 in memory on localhost:37833 (size: 64.1 KiB, free: 1918.3 MiB)
16:50:48.131 INFO SparkContext - Created broadcast 3379 from newAPIHadoopFile at PathSplitSource.java:96
16:50:48.150 INFO MemoryStore - Block broadcast_3380 stored as values in memory (estimated size 305.5 KiB, free 1913.1 MiB)
16:50:48.157 INFO MemoryStore - Block broadcast_3380_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1913.0 MiB)
16:50:48.157 INFO BlockManagerInfo - Added broadcast_3380_piece0 in memory on localhost:37833 (size: 64.1 KiB, free: 1918.2 MiB)
16:50:48.157 INFO SparkContext - Created broadcast 3380 from newAPIHadoopFile at PathSplitSource.java:96
16:50:48.176 INFO FileInputFormat - Total input files to process : 1
16:50:48.179 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
16:50:48.180 INFO DAGScheduler - Got job 883 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
16:50:48.180 INFO DAGScheduler - Final stage: ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
16:50:48.180 INFO DAGScheduler - Parents of final stage: List()
16:50:48.180 INFO DAGScheduler - Missing parents: List()
16:50:48.180 INFO DAGScheduler - Submitting ResultStage 2472 (MapPartitionsRDD[10169] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
16:50:48.197 INFO MemoryStore - Block broadcast_3381 stored as values in memory (estimated size 476.8 KiB, free 1912.6 MiB)
16:50:48.199 INFO MemoryStore - Block broadcast_3381_piece0 stored as bytes in memory (estimated size 207.4 KiB, free 1912.4 MiB)
16:50:48.199 INFO BlockManagerInfo - Added broadcast_3381_piece0 in memory on localhost:37833 (size: 207.4 KiB, free: 1918.0 MiB)
16:50:48.200 INFO SparkContext - Created broadcast 3381 from broadcast at DAGScheduler.scala:1580
16:50:48.200 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))
16:50:48.200 INFO TaskSchedulerImpl - Adding task set 2472.0 with 1 tasks resource profile 0
16:50:48.200 INFO TaskSetManager - Starting task 0.0 in stage 2472.0 (TID 1891) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
16:50:48.200 INFO Executor - Running task 0.0 in stage 2472.0 (TID 1891)
16:50:48.228 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.bam:0+8071
16:50:48.232 INFO Executor - Finished task 0.0 in stage 2472.0 (TID 1891). 989 bytes result sent to driver
16:50:48.232 INFO TaskSetManager - Finished task 0.0 in stage 2472.0 (TID 1891) in 32 ms on localhost (executor driver) (1/1)
16:50:48.232 INFO TaskSchedulerImpl - Removed TaskSet 2472.0, whose tasks have all completed, from pool
16:50:48.232 INFO DAGScheduler - ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.052 s
16:50:48.232 INFO DAGScheduler - Job 883 is finished. Cancelling potential speculative or zombie tasks for this job
16:50:48.232 INFO TaskSchedulerImpl - Killing all running tasks in stage 2472: Stage finished
16:50:48.232 INFO DAGScheduler - Job 883 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.052670 s
16:50:48.232 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 4:50:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1702887424
16:50:48.246 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:50:48.246 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:50:48.246 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
16:50:48.246 INFO CollectMultipleMetricsSpark - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:50:48.246 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:50:48.246 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 4:50:48 PM GMT
16:50:48.246 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:50:48.246 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:50:48.246 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:50:48.246 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
16:50:48.246 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
16:50:48.246 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:50:48.246 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:50:48.246 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:50:48.246 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:50:48.246 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
16:50:48.246 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
16:50:48.246 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
16:50:48.247 INFO CollectMultipleMetricsSpark - Requester pays: disabled
16:50:48.247 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:50:48.247 INFO CollectMultipleMetricsSpark - Initializing engine
16:50:48.247 INFO CollectMultipleMetricsSpark - Done initializing engine
16:50:48.247 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
16:50:48.249 INFO MemoryStore - Block broadcast_3382 stored as values in memory (estimated size 592.0 B, free 1912.4 MiB)
16:50:48.249 INFO MemoryStore - Block broadcast_3382_piece0 stored as bytes in memory (estimated size 209.0 B, free 1912.4 MiB)
16:50:48.249 INFO BlockManagerInfo - Added broadcast_3382_piece0 in memory on localhost:37833 (size: 209.0 B, free: 1918.0 MiB)
16:50:48.249 INFO SparkContext - Created broadcast 3382 from broadcast at CramSource.java:114
16:50:48.250 INFO MemoryStore - Block broadcast_3383 stored as values in memory (estimated size 305.5 KiB, free 1912.1 MiB)
16:50:48.256 INFO MemoryStore - Block broadcast_3383_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1912.0 MiB)
16:50:48.257 INFO BlockManagerInfo - Added broadcast_3383_piece0 in memory on localhost:37833 (size: 64.0 KiB, free: 1918.0 MiB)
16:50:48.257 INFO SparkContext - Created broadcast 3383 from newAPIHadoopFile at PathSplitSource.java:96
16:50:48.271 INFO MemoryStore - Block broadcast_3384 stored as values in memory (estimated size 592.0 B, free 1912.0 MiB)
16:50:48.271 INFO MemoryStore - Block broadcast_3384_piece0 stored as bytes in memory (estimated size 209.0 B, free 1912.0 MiB)
16:50:48.271 INFO BlockManagerInfo - Added broadcast_3384_piece0 in memory on localhost:37833 (size: 209.0 B, free: 1918.0 MiB)
16:50:48.271 INFO SparkContext - Created broadcast 3384 from broadcast at CramSource.java:114
16:50:48.272 INFO MemoryStore - Block broadcast_3385 stored as values in memory (estimated size 305.5 KiB, free 1911.7 MiB)
16:50:48.279 INFO MemoryStore - Block broadcast_3385_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1911.6 MiB)
16:50:48.279 INFO BlockManagerInfo - Added broadcast_3385_piece0 in memory on localhost:37833 (size: 64.0 KiB, free: 1917.9 MiB)
16:50:48.279 INFO SparkContext - Created broadcast 3385 from newAPIHadoopFile at PathSplitSource.java:96
16:50:48.293 INFO FileInputFormat - Total input files to process : 1
16:50:48.296 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
16:50:48.296 INFO DAGScheduler - Got job 884 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
16:50:48.296 INFO DAGScheduler - Final stage: ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
16:50:48.296 INFO DAGScheduler - Parents of final stage: List()
16:50:48.296 INFO DAGScheduler - Missing parents: List()
16:50:48.296 INFO DAGScheduler - Submitting ResultStage 2473 (MapPartitionsRDD[10180] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
16:50:48.308 INFO MemoryStore - Block broadcast_3386 stored as values in memory (estimated size 329.7 KiB, free 1911.3 MiB)
16:50:48.309 INFO MemoryStore - Block broadcast_3386_piece0 stored as bytes in memory (estimated size 143.3 KiB, free 1911.2 MiB)
16:50:48.309 INFO BlockManagerInfo - Added broadcast_3386_piece0 in memory on localhost:37833 (size: 143.3 KiB, free: 1917.8 MiB)
16:50:48.309 INFO SparkContext - Created broadcast 3386 from broadcast at DAGScheduler.scala:1580
16:50:48.310 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))
16:50:48.310 INFO TaskSchedulerImpl - Adding task set 2473.0 with 1 tasks resource profile 0
16:50:48.310 INFO TaskSetManager - Starting task 0.0 in stage 2473.0 (TID 1892) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9689 bytes)
16:50:48.310 INFO Executor - Running task 0.0 in stage 2473.0 (TID 1892)
16:50:48.329 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.cram:0+8617
16:50:48.333 INFO Executor - Finished task 0.0 in stage 2473.0 (TID 1892). 989 bytes result sent to driver
16:50:48.333 INFO TaskSetManager - Finished task 0.0 in stage 2473.0 (TID 1892) in 23 ms on localhost (executor driver) (1/1)
16:50:48.333 INFO TaskSchedulerImpl - Removed TaskSet 2473.0, whose tasks have all completed, from pool
16:50:48.333 INFO DAGScheduler - ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.037 s
16:50:48.334 INFO DAGScheduler - Job 884 is finished. Cancelling potential speculative or zombie tasks for this job
16:50:48.334 INFO TaskSchedulerImpl - Killing all running tasks in stage 2473: Stage finished
16:50:48.334 INFO DAGScheduler - Job 884 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.038065 s
16:50:48.334 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 4:50:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1702887424