[May 27, 2025 at 2:05:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
[May 27, 2025 at 2:05:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
[May 27, 2025 at 2:05:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
14:05:52.474 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:05:52.474 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:05:52.474 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
14:05:52.474 INFO CollectMultipleMetricsSpark - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:05:52.474 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:05:52.474 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 2:05:52 PM GMT
14:05:52.474 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:05:52.474 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:05:52.474 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:05:52.474 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
14:05:52.474 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
14:05:52.474 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:05:52.474 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:05:52.474 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:05:52.474 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:05:52.474 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
14:05:52.474 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
14:05:52.474 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
14:05:52.474 INFO CollectMultipleMetricsSpark - Requester pays: disabled
14:05:52.474 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:05:52.474 INFO CollectMultipleMetricsSpark - Initializing engine
14:05:52.474 INFO CollectMultipleMetricsSpark - Done initializing engine
14:05:52.475 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
WARNING 2025-05-27 14:05:52 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-27 14:05:52 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
14:05:52.476 INFO MemoryStore - Block broadcast_3448 stored as values in memory (estimated size 37.8 KiB, free 1908.4 MiB)
14:05:52.477 INFO MemoryStore - Block broadcast_3448_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1908.4 MiB)
14:05:52.477 INFO BlockManagerInfo - Added broadcast_3448_piece0 in memory on localhost:46769 (size: 8.4 KiB, free: 1918.0 MiB)
14:05:52.477 INFO SparkContext - Created broadcast 3448 from broadcast at SamSource.java:78
14:05:52.478 INFO MemoryStore - Block broadcast_3449 stored as values in memory (estimated size 305.5 KiB, free 1908.1 MiB)
14:05:52.484 INFO MemoryStore - Block broadcast_3449_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1908.0 MiB)
14:05:52.484 INFO BlockManagerInfo - Added broadcast_3449_piece0 in memory on localhost:46769 (size: 64.1 KiB, free: 1917.9 MiB)
14:05:52.484 INFO SparkContext - Created broadcast 3449 from newAPIHadoopFile at SamSource.java:108
WARNING 2025-05-27 14:05:52 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-27 14:05:52 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
14:05:52.487 INFO MemoryStore - Block broadcast_3450 stored as values in memory (estimated size 37.8 KiB, free 1908.0 MiB)
14:05:52.487 INFO MemoryStore - Block broadcast_3450_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1907.9 MiB)
14:05:52.487 INFO BlockManagerInfo - Added broadcast_3450_piece0 in memory on localhost:46769 (size: 8.4 KiB, free: 1917.9 MiB)
14:05:52.487 INFO SparkContext - Created broadcast 3450 from broadcast at SamSource.java:78
14:05:52.488 INFO MemoryStore - Block broadcast_3451 stored as values in memory (estimated size 305.5 KiB, free 1907.6 MiB)
14:05:52.494 INFO MemoryStore - Block broadcast_3451_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1907.6 MiB)
14:05:52.494 INFO BlockManagerInfo - Added broadcast_3451_piece0 in memory on localhost:46769 (size: 64.1 KiB, free: 1917.8 MiB)
14:05:52.495 INFO SparkContext - Created broadcast 3451 from newAPIHadoopFile at SamSource.java:108
14:05:52.497 INFO FileInputFormat - Total input files to process : 1
14:05:52.500 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
14:05:52.500 INFO DAGScheduler - Got job 902 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
14:05:52.500 INFO DAGScheduler - Final stage: ResultStage 2491 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
14:05:52.500 INFO DAGScheduler - Parents of final stage: List()
14:05:52.500 INFO DAGScheduler - Missing parents: List()
14:05:52.500 INFO DAGScheduler - Submitting ResultStage 2491 (MapPartitionsRDD[10374] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
14:05:52.501 INFO MemoryStore - Block broadcast_3452 stored as values in memory (estimated size 34.8 KiB, free 1907.6 MiB)
14:05:52.501 INFO MemoryStore - Block broadcast_3452_piece0 stored as bytes in memory (estimated size 14.6 KiB, free 1907.5 MiB)
14:05:52.501 INFO BlockManagerInfo - Added broadcast_3452_piece0 in memory on localhost:46769 (size: 14.6 KiB, free: 1917.8 MiB)
14:05:52.501 INFO SparkContext - Created broadcast 3452 from broadcast at DAGScheduler.scala:1580
14:05:52.501 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 2491 (MapPartitionsRDD[10374] at filter at CollectMultipleMetricsSpark.java:193) (first 15 tasks are for partitions Vector(0))
14:05:52.501 INFO TaskSchedulerImpl - Adding task set 2491.0 with 1 tasks resource profile 0
14:05:52.502 INFO TaskSetManager - Starting task 0.0 in stage 2491.0 (TID 1910) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
14:05:52.502 INFO Executor - Running task 0.0 in stage 2491.0 (TID 1910)
14:05:52.503 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.sam:0+44008
14:05:52.504 INFO Executor - Finished task 0.0 in stage 2491.0 (TID 1910). 946 bytes result sent to driver
14:05:52.504 INFO TaskSetManager - Finished task 0.0 in stage 2491.0 (TID 1910) in 2 ms on localhost (executor driver) (1/1)
14:05:52.504 INFO TaskSchedulerImpl - Removed TaskSet 2491.0, whose tasks have all completed, from pool
14:05:52.504 INFO DAGScheduler - ResultStage 2491 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.004 s
14:05:52.504 INFO DAGScheduler - Job 902 is finished. Cancelling potential speculative or zombie tasks for this job
14:05:52.504 INFO TaskSchedulerImpl - Killing all running tasks in stage 2491: Stage finished
14:05:52.505 INFO DAGScheduler - Job 902 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.004594 s
14:05:52.505 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 2:05:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
14:05:52.518 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:05:52.518 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:05:52.518 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
14:05:52.518 INFO CollectMultipleMetricsSpark - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:05:52.518 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:05:52.518 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 2:05:52 PM GMT
14:05:52.518 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:05:52.518 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:05:52.518 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:05:52.518 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
14:05:52.518 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
14:05:52.518 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:05:52.518 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:05:52.518 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:05:52.518 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:05:52.518 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
14:05:52.518 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
14:05:52.518 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
14:05:52.518 INFO CollectMultipleMetricsSpark - Requester pays: disabled
14:05:52.518 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:05:52.518 INFO CollectMultipleMetricsSpark - Initializing engine
14:05:52.518 INFO CollectMultipleMetricsSpark - Done initializing engine
14:05:52.519 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
14:05:52.520 INFO MemoryStore - Block broadcast_3453 stored as values in memory (estimated size 305.5 KiB, free 1907.2 MiB)
14:05:52.527 INFO MemoryStore - Block broadcast_3453_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1907.2 MiB)
14:05:52.527 INFO BlockManagerInfo - Added broadcast_3453_piece0 in memory on localhost:46769 (size: 64.1 KiB, free: 1917.7 MiB)
14:05:52.527 INFO SparkContext - Created broadcast 3453 from newAPIHadoopFile at PathSplitSource.java:96
14:05:52.547 INFO MemoryStore - Block broadcast_3454 stored as values in memory (estimated size 305.5 KiB, free 1906.9 MiB)
14:05:52.553 INFO MemoryStore - Block broadcast_3454_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1906.8 MiB)
14:05:52.553 INFO BlockManagerInfo - Added broadcast_3454_piece0 in memory on localhost:46769 (size: 64.1 KiB, free: 1917.7 MiB)
14:05:52.553 INFO SparkContext - Created broadcast 3454 from newAPIHadoopFile at PathSplitSource.java:96
14:05:52.573 INFO FileInputFormat - Total input files to process : 1
14:05:52.576 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
14:05:52.577 INFO DAGScheduler - Got job 903 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
14:05:52.577 INFO DAGScheduler - Final stage: ResultStage 2492 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
14:05:52.577 INFO DAGScheduler - Parents of final stage: List()
14:05:52.577 INFO DAGScheduler - Missing parents: List()
14:05:52.577 INFO DAGScheduler - Submitting ResultStage 2492 (MapPartitionsRDD[10387] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
14:05:52.593 INFO MemoryStore - Block broadcast_3455 stored as values in memory (estimated size 476.8 KiB, free 1906.3 MiB)
14:05:52.596 INFO MemoryStore - Block broadcast_3455_piece0 stored as bytes in memory (estimated size 207.4 KiB, free 1906.1 MiB)
14:05:52.596 INFO BlockManagerInfo - Added broadcast_3455_piece0 in memory on localhost:46769 (size: 207.4 KiB, free: 1917.5 MiB)
14:05:52.596 INFO SparkContext - Created broadcast 3455 from broadcast at DAGScheduler.scala:1580
14:05:52.596 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 2492 (MapPartitionsRDD[10387] at filter at CollectMultipleMetricsSpark.java:193) (first 15 tasks are for partitions Vector(0))
14:05:52.596 INFO TaskSchedulerImpl - Adding task set 2492.0 with 1 tasks resource profile 0
14:05:52.597 INFO TaskSetManager - Starting task 0.0 in stage 2492.0 (TID 1911) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
14:05:52.597 INFO Executor - Running task 0.0 in stage 2492.0 (TID 1911)
14:05:52.624 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.bam:0+8071
14:05:52.627 INFO Executor - Finished task 0.0 in stage 2492.0 (TID 1911). 989 bytes result sent to driver
14:05:52.627 INFO TaskSetManager - Finished task 0.0 in stage 2492.0 (TID 1911) in 31 ms on localhost (executor driver) (1/1)
14:05:52.628 INFO TaskSchedulerImpl - Removed TaskSet 2492.0, whose tasks have all completed, from pool
14:05:52.628 INFO DAGScheduler - ResultStage 2492 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.051 s
14:05:52.628 INFO DAGScheduler - Job 903 is finished. Cancelling potential speculative or zombie tasks for this job
14:05:52.628 INFO TaskSchedulerImpl - Killing all running tasks in stage 2492: Stage finished
14:05:52.628 INFO DAGScheduler - Job 903 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.051423 s
14:05:52.628 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 2:05:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
14:05:52.641 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:05:52.641 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:05:52.641 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
14:05:52.642 INFO CollectMultipleMetricsSpark - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:05:52.642 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:05:52.642 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 2:05:52 PM GMT
14:05:52.642 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:05:52.642 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:05:52.642 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:05:52.642 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
14:05:52.642 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
14:05:52.642 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:05:52.642 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:05:52.642 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:05:52.642 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:05:52.642 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
14:05:52.642 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
14:05:52.642 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
14:05:52.642 INFO CollectMultipleMetricsSpark - Requester pays: disabled
14:05:52.642 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:05:52.642 INFO CollectMultipleMetricsSpark - Initializing engine
14:05:52.642 INFO CollectMultipleMetricsSpark - Done initializing engine
14:05:52.642 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
14:05:52.644 INFO MemoryStore - Block broadcast_3456 stored as values in memory (estimated size 592.0 B, free 1906.1 MiB)
14:05:52.644 INFO MemoryStore - Block broadcast_3456_piece0 stored as bytes in memory (estimated size 209.0 B, free 1906.1 MiB)
14:05:52.644 INFO BlockManagerInfo - Added broadcast_3456_piece0 in memory on localhost:46769 (size: 209.0 B, free: 1917.5 MiB)
14:05:52.644 INFO SparkContext - Created broadcast 3456 from broadcast at CramSource.java:114
14:05:52.645 INFO MemoryStore - Block broadcast_3457 stored as values in memory (estimated size 305.5 KiB, free 1905.8 MiB)
14:05:52.651 INFO MemoryStore - Block broadcast_3457_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1905.8 MiB)
14:05:52.652 INFO BlockManagerInfo - Added broadcast_3457_piece0 in memory on localhost:46769 (size: 64.0 KiB, free: 1917.4 MiB)
14:05:52.652 INFO SparkContext - Created broadcast 3457 from newAPIHadoopFile at PathSplitSource.java:96
14:05:52.665 INFO MemoryStore - Block broadcast_3458 stored as values in memory (estimated size 592.0 B, free 1905.8 MiB)
14:05:52.666 INFO MemoryStore - Block broadcast_3458_piece0 stored as bytes in memory (estimated size 209.0 B, free 1905.8 MiB)
14:05:52.666 INFO BlockManagerInfo - Added broadcast_3458_piece0 in memory on localhost:46769 (size: 209.0 B, free: 1917.4 MiB)
14:05:52.666 INFO SparkContext - Created broadcast 3458 from broadcast at CramSource.java:114
14:05:52.667 INFO MemoryStore - Block broadcast_3459 stored as values in memory (estimated size 305.5 KiB, free 1905.5 MiB)
14:05:52.673 INFO MemoryStore - Block broadcast_3459_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1905.4 MiB)
14:05:52.673 INFO BlockManagerInfo - Added broadcast_3459_piece0 in memory on localhost:46769 (size: 64.0 KiB, free: 1917.4 MiB)
14:05:52.673 INFO SparkContext - Created broadcast 3459 from newAPIHadoopFile at PathSplitSource.java:96
14:05:52.687 INFO FileInputFormat - Total input files to process : 1
14:05:52.690 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
14:05:52.690 INFO DAGScheduler - Got job 904 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
14:05:52.690 INFO DAGScheduler - Final stage: ResultStage 2493 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
14:05:52.690 INFO DAGScheduler - Parents of final stage: List()
14:05:52.690 INFO DAGScheduler - Missing parents: List()
14:05:52.690 INFO DAGScheduler - Submitting ResultStage 2493 (MapPartitionsRDD[10398] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
14:05:52.702 INFO MemoryStore - Block broadcast_3460 stored as values in memory (estimated size 329.7 KiB, free 1905.1 MiB)
14:05:52.703 INFO MemoryStore - Block broadcast_3460_piece0 stored as bytes in memory (estimated size 143.3 KiB, free 1905.0 MiB)
14:05:52.703 INFO BlockManagerInfo - Added broadcast_3460_piece0 in memory on localhost:46769 (size: 143.3 KiB, free: 1917.2 MiB)
14:05:52.704 INFO SparkContext - Created broadcast 3460 from broadcast at DAGScheduler.scala:1580
14:05:52.704 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 2493 (MapPartitionsRDD[10398] at filter at CollectMultipleMetricsSpark.java:193) (first 15 tasks are for partitions Vector(0))
14:05:52.704 INFO TaskSchedulerImpl - Adding task set 2493.0 with 1 tasks resource profile 0
14:05:52.704 INFO TaskSetManager - Starting task 0.0 in stage 2493.0 (TID 1912) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9689 bytes)
14:05:52.704 INFO Executor - Running task 0.0 in stage 2493.0 (TID 1912)
14:05:52.723 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.cram:0+8617
14:05:52.727 INFO Executor - Finished task 0.0 in stage 2493.0 (TID 1912). 989 bytes result sent to driver
14:05:52.727 INFO TaskSetManager - Finished task 0.0 in stage 2493.0 (TID 1912) in 23 ms on localhost (executor driver) (1/1)
14:05:52.727 INFO TaskSchedulerImpl - Removed TaskSet 2493.0, whose tasks have all completed, from pool
14:05:52.727 INFO DAGScheduler - ResultStage 2493 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.036 s
14:05:52.727 INFO DAGScheduler - Job 904 is finished. Cancelling potential speculative or zombie tasks for this job
14:05:52.727 INFO TaskSchedulerImpl - Killing all running tasks in stage 2493: Stage finished
14:05:52.727 INFO DAGScheduler - Job 904 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.036882 s
14:05:52.727 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 2:05:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808