[May 27, 2025 at 3:13:00 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1480589312
[May 27, 2025 at 3:13:00 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1480589312
[May 27, 2025 at 3:13:01 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1480589312
15:13:01.240 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
15:13:01.240 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:13:01.240 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
15:13:01.240 INFO CollectMultipleMetricsSpark - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:13:01.240 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:13:01.240 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 3:13:01 PM GMT
15:13:01.241 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
15:13:01.241 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
15:13:01.241 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:13:01.241 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
15:13:01.241 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
15:13:01.241 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:13:01.241 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:13:01.241 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:13:01.241 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:13:01.241 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
15:13:01.241 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
15:13:01.241 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
15:13:01.241 INFO CollectMultipleMetricsSpark - Requester pays: disabled
15:13:01.241 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:13:01.241 INFO CollectMultipleMetricsSpark - Initializing engine
15:13:01.241 INFO CollectMultipleMetricsSpark - Done initializing engine
15:13:01.241 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
WARNING 2025-05-27 15:13:01 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-27 15:13:01 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
15:13:01.243 INFO MemoryStore - Block broadcast_3374 stored as values in memory (estimated size 37.8 KiB, free 1917.4 MiB)
15:13:01.243 INFO MemoryStore - Block broadcast_3374_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1917.3 MiB)
15:13:01.244 INFO BlockManagerInfo - Added broadcast_3374_piece0 in memory on localhost:36687 (size: 8.4 KiB, free: 1919.3 MiB)
15:13:01.244 INFO SparkContext - Created broadcast 3374 from broadcast at SamSource.java:78
15:13:01.245 INFO MemoryStore - Block broadcast_3375 stored as values in memory (estimated size 305.5 KiB, free 1917.1 MiB)
15:13:01.252 INFO MemoryStore - Block broadcast_3375_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1917.0 MiB)
15:13:01.252 INFO BlockManagerInfo - Added broadcast_3375_piece0 in memory on localhost:36687 (size: 64.1 KiB, free: 1919.2 MiB)
15:13:01.252 INFO SparkContext - Created broadcast 3375 from newAPIHadoopFile at SamSource.java:108
WARNING 2025-05-27 15:13:01 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-27 15:13:01 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
15:13:01.254 INFO MemoryStore - Block broadcast_3376 stored as values in memory (estimated size 37.8 KiB, free 1917.0 MiB)
15:13:01.255 INFO MemoryStore - Block broadcast_3376_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1916.9 MiB)
15:13:01.255 INFO BlockManagerInfo - Added broadcast_3376_piece0 in memory on localhost:36687 (size: 8.4 KiB, free: 1919.2 MiB)
15:13:01.255 INFO SparkContext - Created broadcast 3376 from broadcast at SamSource.java:78
15:13:01.256 INFO MemoryStore - Block broadcast_3377 stored as values in memory (estimated size 305.5 KiB, free 1916.6 MiB)
15:13:01.267 INFO MemoryStore - Block broadcast_3377_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1916.6 MiB)
15:13:01.267 INFO BlockManagerInfo - Added broadcast_3377_piece0 in memory on localhost:36687 (size: 64.1 KiB, free: 1919.1 MiB)
15:13:01.267 INFO SparkContext - Created broadcast 3377 from newAPIHadoopFile at SamSource.java:108
15:13:01.270 INFO FileInputFormat - Total input files to process : 1
15:13:01.274 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
15:13:01.275 INFO DAGScheduler - Got job 882 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
15:13:01.275 INFO DAGScheduler - Final stage: ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
15:13:01.275 INFO DAGScheduler - Parents of final stage: List()
15:13:01.275 INFO DAGScheduler - Missing parents: List()
15:13:01.275 INFO DAGScheduler - Submitting ResultStage 2471 (MapPartitionsRDD[10156] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
15:13:01.275 INFO MemoryStore - Block broadcast_3378 stored as values in memory (estimated size 34.8 KiB, free 1916.5 MiB)
15:13:01.276 INFO MemoryStore - Block broadcast_3378_piece0 stored as bytes in memory (estimated size 14.6 KiB, free 1916.5 MiB)
15:13:01.276 INFO BlockManagerInfo - Added broadcast_3378_piece0 in memory on localhost:36687 (size: 14.6 KiB, free: 1919.1 MiB)
15:13:01.276 INFO SparkContext - Created broadcast 3378 from broadcast at DAGScheduler.scala:1580
15:13:01.276 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))
15:13:01.276 INFO TaskSchedulerImpl - Adding task set 2471.0 with 1 tasks resource profile 0
15:13:01.277 INFO TaskSetManager - Starting task 0.0 in stage 2471.0 (TID 1890) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
15:13:01.277 INFO Executor - Running task 0.0 in stage 2471.0 (TID 1890)
15:13:01.278 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.sam:0+44008
15:13:01.280 INFO Executor - Finished task 0.0 in stage 2471.0 (TID 1890). 989 bytes result sent to driver
15:13:01.280 INFO TaskSetManager - Finished task 0.0 in stage 2471.0 (TID 1890) in 3 ms on localhost (executor driver) (1/1)
15:13:01.280 INFO TaskSchedulerImpl - Removed TaskSet 2471.0, whose tasks have all completed, from pool
15:13:01.280 INFO DAGScheduler - ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.005 s
15:13:01.280 INFO DAGScheduler - Job 882 is finished. Cancelling potential speculative or zombie tasks for this job
15:13:01.280 INFO TaskSchedulerImpl - Killing all running tasks in stage 2471: Stage finished
15:13:01.280 INFO DAGScheduler - Job 882 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.005609 s
15:13:01.280 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 3:13:01 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1480589312
15:13:01.294 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
15:13:01.294 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:13:01.294 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
15:13:01.294 INFO CollectMultipleMetricsSpark - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:13:01.294 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:13:01.294 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 3:13:01 PM GMT
15:13:01.294 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
15:13:01.294 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
15:13:01.294 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:13:01.294 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
15:13:01.294 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
15:13:01.294 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:13:01.294 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:13:01.294 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:13:01.294 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:13:01.294 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
15:13:01.294 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
15:13:01.294 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
15:13:01.294 INFO CollectMultipleMetricsSpark - Requester pays: disabled
15:13:01.294 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:13:01.294 INFO CollectMultipleMetricsSpark - Initializing engine
15:13:01.294 INFO CollectMultipleMetricsSpark - Done initializing engine
15:13:01.294 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
15:13:01.296 INFO MemoryStore - Block broadcast_3379 stored as values in memory (estimated size 305.5 KiB, free 1916.2 MiB)
15:13:01.305 INFO MemoryStore - Block broadcast_3379_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1916.2 MiB)
15:13:01.305 INFO BlockManagerInfo - Added broadcast_3379_piece0 in memory on localhost:36687 (size: 64.1 KiB, free: 1919.1 MiB)
15:13:01.306 INFO SparkContext - Created broadcast 3379 from newAPIHadoopFile at PathSplitSource.java:96
15:13:01.326 INFO MemoryStore - Block broadcast_3380 stored as values in memory (estimated size 305.5 KiB, free 1915.9 MiB)
15:13:01.333 INFO MemoryStore - Block broadcast_3380_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1915.8 MiB)
15:13:01.333 INFO BlockManagerInfo - Added broadcast_3380_piece0 in memory on localhost:36687 (size: 64.1 KiB, free: 1919.0 MiB)
15:13:01.333 INFO SparkContext - Created broadcast 3380 from newAPIHadoopFile at PathSplitSource.java:96
15:13:01.354 INFO FileInputFormat - Total input files to process : 1
15:13:01.357 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
15:13:01.357 INFO DAGScheduler - Got job 883 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
15:13:01.357 INFO DAGScheduler - Final stage: ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
15:13:01.357 INFO DAGScheduler - Parents of final stage: List()
15:13:01.357 INFO DAGScheduler - Missing parents: List()
15:13:01.357 INFO DAGScheduler - Submitting ResultStage 2472 (MapPartitionsRDD[10169] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
15:13:01.375 INFO MemoryStore - Block broadcast_3381 stored as values in memory (estimated size 476.8 KiB, free 1915.3 MiB)
15:13:01.377 INFO MemoryStore - Block broadcast_3381_piece0 stored as bytes in memory (estimated size 207.4 KiB, free 1915.1 MiB)
15:13:01.378 INFO BlockManagerInfo - Added broadcast_3381_piece0 in memory on localhost:36687 (size: 207.4 KiB, free: 1918.8 MiB)
15:13:01.378 INFO SparkContext - Created broadcast 3381 from broadcast at DAGScheduler.scala:1580
15:13:01.378 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))
15:13:01.378 INFO TaskSchedulerImpl - Adding task set 2472.0 with 1 tasks resource profile 0
15:13:01.378 INFO TaskSetManager - Starting task 0.0 in stage 2472.0 (TID 1891) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
15:13:01.378 INFO Executor - Running task 0.0 in stage 2472.0 (TID 1891)
15:13:01.406 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.bam:0+8071
15:13:01.410 INFO Executor - Finished task 0.0 in stage 2472.0 (TID 1891). 989 bytes result sent to driver
15:13:01.410 INFO TaskSetManager - Finished task 0.0 in stage 2472.0 (TID 1891) in 32 ms on localhost (executor driver) (1/1)
15:13:01.410 INFO TaskSchedulerImpl - Removed TaskSet 2472.0, whose tasks have all completed, from pool
15:13:01.410 INFO DAGScheduler - ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.053 s
15:13:01.410 INFO DAGScheduler - Job 883 is finished. Cancelling potential speculative or zombie tasks for this job
15:13:01.410 INFO TaskSchedulerImpl - Killing all running tasks in stage 2472: Stage finished
15:13:01.410 INFO DAGScheduler - Job 883 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.053339 s
15:13:01.410 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 3:13:01 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1480589312
15:13:01.424 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
15:13:01.424 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:13:01.424 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
15:13:01.424 INFO CollectMultipleMetricsSpark - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:13:01.424 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:13:01.424 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 3:13:01 PM GMT
15:13:01.424 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
15:13:01.424 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
15:13:01.424 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:13:01.424 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
15:13:01.424 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
15:13:01.424 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:13:01.424 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:13:01.425 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:13:01.425 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:13:01.425 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
15:13:01.425 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
15:13:01.425 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
15:13:01.425 INFO CollectMultipleMetricsSpark - Requester pays: disabled
15:13:01.425 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:13:01.425 INFO CollectMultipleMetricsSpark - Initializing engine
15:13:01.425 INFO CollectMultipleMetricsSpark - Done initializing engine
15:13:01.425 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
15:13:01.427 INFO MemoryStore - Block broadcast_3382 stored as values in memory (estimated size 592.0 B, free 1915.1 MiB)
15:13:01.427 INFO MemoryStore - Block broadcast_3382_piece0 stored as bytes in memory (estimated size 209.0 B, free 1915.1 MiB)
15:13:01.427 INFO BlockManagerInfo - Added broadcast_3382_piece0 in memory on localhost:36687 (size: 209.0 B, free: 1918.8 MiB)
15:13:01.427 INFO SparkContext - Created broadcast 3382 from broadcast at CramSource.java:114
15:13:01.428 INFO MemoryStore - Block broadcast_3383 stored as values in memory (estimated size 305.5 KiB, free 1914.8 MiB)
15:13:01.435 INFO MemoryStore - Block broadcast_3383_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1914.8 MiB)
15:13:01.435 INFO BlockManagerInfo - Added broadcast_3383_piece0 in memory on localhost:36687 (size: 64.0 KiB, free: 1918.7 MiB)
15:13:01.435 INFO SparkContext - Created broadcast 3383 from newAPIHadoopFile at PathSplitSource.java:96
15:13:01.449 INFO MemoryStore - Block broadcast_3384 stored as values in memory (estimated size 592.0 B, free 1914.8 MiB)
15:13:01.450 INFO MemoryStore - Block broadcast_3384_piece0 stored as bytes in memory (estimated size 209.0 B, free 1914.8 MiB)
15:13:01.450 INFO BlockManagerInfo - Added broadcast_3384_piece0 in memory on localhost:36687 (size: 209.0 B, free: 1918.7 MiB)
15:13:01.450 INFO SparkContext - Created broadcast 3384 from broadcast at CramSource.java:114
15:13:01.451 INFO MemoryStore - Block broadcast_3385 stored as values in memory (estimated size 305.5 KiB, free 1914.5 MiB)
15:13:01.457 INFO MemoryStore - Block broadcast_3385_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1914.4 MiB)
15:13:01.457 INFO BlockManagerInfo - Added broadcast_3385_piece0 in memory on localhost:36687 (size: 64.0 KiB, free: 1918.7 MiB)
15:13:01.457 INFO SparkContext - Created broadcast 3385 from newAPIHadoopFile at PathSplitSource.java:96
15:13:01.472 INFO FileInputFormat - Total input files to process : 1
15:13:01.475 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
15:13:01.475 INFO DAGScheduler - Got job 884 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
15:13:01.475 INFO DAGScheduler - Final stage: ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
15:13:01.475 INFO DAGScheduler - Parents of final stage: List()
15:13:01.475 INFO DAGScheduler - Missing parents: List()
15:13:01.475 INFO DAGScheduler - Submitting ResultStage 2473 (MapPartitionsRDD[10180] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
15:13:01.487 INFO MemoryStore - Block broadcast_3386 stored as values in memory (estimated size 329.7 KiB, free 1914.1 MiB)
15:13:01.489 INFO MemoryStore - Block broadcast_3386_piece0 stored as bytes in memory (estimated size 143.3 KiB, free 1914.0 MiB)
15:13:01.489 INFO BlockManagerInfo - Added broadcast_3386_piece0 in memory on localhost:36687 (size: 143.3 KiB, free: 1918.5 MiB)
15:13:01.489 INFO SparkContext - Created broadcast 3386 from broadcast at DAGScheduler.scala:1580
15:13:01.489 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))
15:13:01.489 INFO TaskSchedulerImpl - Adding task set 2473.0 with 1 tasks resource profile 0
15:13:01.489 INFO TaskSetManager - Starting task 0.0 in stage 2473.0 (TID 1892) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9689 bytes)
15:13:01.489 INFO Executor - Running task 0.0 in stage 2473.0 (TID 1892)
15:13:01.511 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.cram:0+8617
15:13:01.515 INFO Executor - Finished task 0.0 in stage 2473.0 (TID 1892). 989 bytes result sent to driver
15:13:01.515 INFO TaskSetManager - Finished task 0.0 in stage 2473.0 (TID 1892) in 26 ms on localhost (executor driver) (1/1)
15:13:01.515 INFO TaskSchedulerImpl - Removed TaskSet 2473.0, whose tasks have all completed, from pool
15:13:01.515 INFO DAGScheduler - ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.040 s
15:13:01.515 INFO DAGScheduler - Job 884 is finished. Cancelling potential speculative or zombie tasks for this job
15:13:01.515 INFO TaskSchedulerImpl - Killing all running tasks in stage 2473: Stage finished
15:13:01.515 INFO DAGScheduler - Job 884 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.040579 s
15:13:01.515 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 3:13:01 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1480589312