[May 19, 2025 at 4:02:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[May 19, 2025 at 4:02:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[May 19, 2025 at 4:02:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
16:02:42.350 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:02:42.350 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
16:02:42.350 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
16:02:42.350 INFO CollectMultipleMetricsSpark - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
16:02:42.350 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:02:42.350 INFO CollectMultipleMetricsSpark - Start Date/Time: May 19, 2025 at 4:02:42 PM GMT
16:02:42.350 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:02:42.350 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:02:42.350 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:02:42.350 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
16:02:42.350 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
16:02:42.351 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:02:42.351 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:02:42.351 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:02:42.351 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:02:42.351 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
16:02:42.351 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
16:02:42.351 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
16:02:42.351 INFO CollectMultipleMetricsSpark - Requester pays: disabled
16:02:42.351 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:02:42.351 INFO CollectMultipleMetricsSpark - Initializing engine
16:02:42.351 INFO CollectMultipleMetricsSpark - Done initializing engine
16:02:42.351 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
WARNING 2025-05-19 16:02:42 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-19 16:02:42 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
16:02:42.352 INFO MemoryStore - Block broadcast_3448 stored as values in memory (estimated size 37.8 KiB, free 1915.3 MiB)
16:02:42.353 INFO MemoryStore - Block broadcast_3448_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1915.3 MiB)
16:02:42.353 INFO BlockManagerInfo - Added broadcast_3448_piece0 in memory on localhost:42397 (size: 8.4 KiB, free: 1918.7 MiB)
16:02:42.353 INFO SparkContext - Created broadcast 3448 from broadcast at SamSource.java:78
16:02:42.354 INFO MemoryStore - Block broadcast_3449 stored as values in memory (estimated size 305.5 KiB, free 1915.0 MiB)
16:02:42.360 INFO MemoryStore - Block broadcast_3449_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1914.9 MiB)
16:02:42.361 INFO BlockManagerInfo - Added broadcast_3449_piece0 in memory on localhost:42397 (size: 64.1 KiB, free: 1918.6 MiB)
16:02:42.361 INFO SparkContext - Created broadcast 3449 from newAPIHadoopFile at SamSource.java:108
WARNING 2025-05-19 16:02:42 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-19 16:02:42 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
16:02:42.363 INFO MemoryStore - Block broadcast_3450 stored as values in memory (estimated size 37.8 KiB, free 1914.9 MiB)
16:02:42.363 INFO MemoryStore - Block broadcast_3450_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1914.8 MiB)
16:02:42.363 INFO BlockManagerInfo - Added broadcast_3450_piece0 in memory on localhost:42397 (size: 8.4 KiB, free: 1918.6 MiB)
16:02:42.364 INFO SparkContext - Created broadcast 3450 from broadcast at SamSource.java:78
16:02:42.364 INFO MemoryStore - Block broadcast_3451 stored as values in memory (estimated size 305.5 KiB, free 1914.5 MiB)
16:02:42.371 INFO MemoryStore - Block broadcast_3451_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1914.5 MiB)
16:02:42.371 INFO BlockManagerInfo - Added broadcast_3451_piece0 in memory on localhost:42397 (size: 64.1 KiB, free: 1918.6 MiB)
16:02:42.371 INFO SparkContext - Created broadcast 3451 from newAPIHadoopFile at SamSource.java:108
16:02:42.373 INFO FileInputFormat - Total input files to process : 1
16:02:42.376 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
16:02:42.376 INFO DAGScheduler - Got job 902 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
16:02:42.376 INFO DAGScheduler - Final stage: ResultStage 2491 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
16:02:42.376 INFO DAGScheduler - Parents of final stage: List()
16:02:42.376 INFO DAGScheduler - Missing parents: List()
16:02:42.376 INFO DAGScheduler - Submitting ResultStage 2491 (MapPartitionsRDD[10374] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
16:02:42.377 INFO MemoryStore - Block broadcast_3452 stored as values in memory (estimated size 34.8 KiB, free 1914.4 MiB)
16:02:42.377 INFO MemoryStore - Block broadcast_3452_piece0 stored as bytes in memory (estimated size 14.6 KiB, free 1914.4 MiB)
16:02:42.377 INFO BlockManagerInfo - Added broadcast_3452_piece0 in memory on localhost:42397 (size: 14.6 KiB, free: 1918.6 MiB)
16:02:42.378 INFO SparkContext - Created broadcast 3452 from broadcast at DAGScheduler.scala:1580
16:02:42.378 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))
16:02:42.378 INFO TaskSchedulerImpl - Adding task set 2491.0 with 1 tasks resource profile 0
16:02:42.378 INFO TaskSetManager - Starting task 0.0 in stage 2491.0 (TID 1910) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
16:02:42.378 INFO Executor - Running task 0.0 in stage 2491.0 (TID 1910)
16:02:42.379 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.sam:0+44008
16:02:42.381 INFO Executor - Finished task 0.0 in stage 2491.0 (TID 1910). 946 bytes result sent to driver
16:02:42.381 INFO TaskSetManager - Finished task 0.0 in stage 2491.0 (TID 1910) in 3 ms on localhost (executor driver) (1/1)
16:02:42.381 INFO TaskSchedulerImpl - Removed TaskSet 2491.0, whose tasks have all completed, from pool
16:02:42.381 INFO DAGScheduler - ResultStage 2491 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.004 s
16:02:42.381 INFO DAGScheduler - Job 902 is finished. Cancelling potential speculative or zombie tasks for this job
16:02:42.381 INFO TaskSchedulerImpl - Killing all running tasks in stage 2491: Stage finished
16:02:42.381 INFO DAGScheduler - Job 902 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.004877 s
16:02:42.381 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 19, 2025 at 4:02:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
16:02:42.395 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:02:42.395 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
16:02:42.395 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
16:02:42.395 INFO CollectMultipleMetricsSpark - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
16:02:42.395 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:02:42.395 INFO CollectMultipleMetricsSpark - Start Date/Time: May 19, 2025 at 4:02:42 PM GMT
16:02:42.395 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:02:42.395 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:02:42.395 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:02:42.395 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
16:02:42.395 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
16:02:42.395 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:02:42.395 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:02:42.395 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:02:42.395 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:02:42.395 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
16:02:42.395 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
16:02:42.395 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
16:02:42.395 INFO CollectMultipleMetricsSpark - Requester pays: disabled
16:02:42.395 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:02:42.396 INFO CollectMultipleMetricsSpark - Initializing engine
16:02:42.396 INFO CollectMultipleMetricsSpark - Done initializing engine
16:02:42.396 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
16:02:42.397 INFO MemoryStore - Block broadcast_3453 stored as values in memory (estimated size 305.5 KiB, free 1914.1 MiB)
16:02:42.404 INFO MemoryStore - Block broadcast_3453_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1914.1 MiB)
16:02:42.404 INFO BlockManagerInfo - Added broadcast_3453_piece0 in memory on localhost:42397 (size: 64.1 KiB, free: 1918.5 MiB)
16:02:42.404 INFO SparkContext - Created broadcast 3453 from newAPIHadoopFile at PathSplitSource.java:96
16:02:42.425 INFO MemoryStore - Block broadcast_3454 stored as values in memory (estimated size 305.5 KiB, free 1913.8 MiB)
16:02:42.432 INFO MemoryStore - Block broadcast_3454_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1913.7 MiB)
16:02:42.432 INFO BlockManagerInfo - Added broadcast_3454_piece0 in memory on localhost:42397 (size: 64.1 KiB, free: 1918.4 MiB)
16:02:42.432 INFO SparkContext - Created broadcast 3454 from newAPIHadoopFile at PathSplitSource.java:96
16:02:42.452 INFO FileInputFormat - Total input files to process : 1
16:02:42.455 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
16:02:42.455 INFO DAGScheduler - Got job 903 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
16:02:42.455 INFO DAGScheduler - Final stage: ResultStage 2492 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
16:02:42.455 INFO DAGScheduler - Parents of final stage: List()
16:02:42.455 INFO DAGScheduler - Missing parents: List()
16:02:42.455 INFO DAGScheduler - Submitting ResultStage 2492 (MapPartitionsRDD[10387] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
16:02:42.471 INFO MemoryStore - Block broadcast_3455 stored as values in memory (estimated size 476.8 KiB, free 1913.2 MiB)
16:02:42.474 INFO MemoryStore - Block broadcast_3455_piece0 stored as bytes in memory (estimated size 207.4 KiB, free 1913.0 MiB)
16:02:42.474 INFO BlockManagerInfo - Added broadcast_3455_piece0 in memory on localhost:42397 (size: 207.4 KiB, free: 1918.2 MiB)
16:02:42.474 INFO SparkContext - Created broadcast 3455 from broadcast at DAGScheduler.scala:1580
16:02:42.474 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))
16:02:42.474 INFO TaskSchedulerImpl - Adding task set 2492.0 with 1 tasks resource profile 0
16:02:42.475 INFO TaskSetManager - Starting task 0.0 in stage 2492.0 (TID 1911) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
16:02:42.475 INFO Executor - Running task 0.0 in stage 2492.0 (TID 1911)
16:02:42.503 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.bam:0+8071
16:02:42.506 INFO Executor - Finished task 0.0 in stage 2492.0 (TID 1911). 989 bytes result sent to driver
16:02:42.506 INFO TaskSetManager - Finished task 0.0 in stage 2492.0 (TID 1911) in 32 ms on localhost (executor driver) (1/1)
16:02:42.506 INFO TaskSchedulerImpl - Removed TaskSet 2492.0, whose tasks have all completed, from pool
16:02:42.506 INFO DAGScheduler - ResultStage 2492 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.051 s
16:02:42.506 INFO DAGScheduler - Job 903 is finished. Cancelling potential speculative or zombie tasks for this job
16:02:42.507 INFO TaskSchedulerImpl - Killing all running tasks in stage 2492: Stage finished
16:02:42.507 INFO DAGScheduler - Job 903 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.051953 s
16:02:42.507 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 19, 2025 at 4:02:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
16:02:42.520 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:02:42.520 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
16:02:42.520 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
16:02:42.520 INFO CollectMultipleMetricsSpark - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
16:02:42.520 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:02:42.520 INFO CollectMultipleMetricsSpark - Start Date/Time: May 19, 2025 at 4:02:42 PM GMT
16:02:42.520 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:02:42.520 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
16:02:42.520 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:02:42.520 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
16:02:42.521 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
16:02:42.521 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:02:42.521 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:02:42.521 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:02:42.521 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:02:42.521 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
16:02:42.521 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
16:02:42.521 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
16:02:42.521 INFO CollectMultipleMetricsSpark - Requester pays: disabled
16:02:42.521 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:02:42.521 INFO CollectMultipleMetricsSpark - Initializing engine
16:02:42.521 INFO CollectMultipleMetricsSpark - Done initializing engine
16:02:42.521 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
16:02:42.523 INFO MemoryStore - Block broadcast_3456 stored as values in memory (estimated size 592.0 B, free 1913.0 MiB)
16:02:42.523 INFO MemoryStore - Block broadcast_3456_piece0 stored as bytes in memory (estimated size 209.0 B, free 1913.0 MiB)
16:02:42.523 INFO BlockManagerInfo - Added broadcast_3456_piece0 in memory on localhost:42397 (size: 209.0 B, free: 1918.2 MiB)
16:02:42.523 INFO SparkContext - Created broadcast 3456 from broadcast at CramSource.java:114
16:02:42.524 INFO MemoryStore - Block broadcast_3457 stored as values in memory (estimated size 305.5 KiB, free 1912.7 MiB)
16:02:42.530 INFO MemoryStore - Block broadcast_3457_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1912.7 MiB)
16:02:42.530 INFO BlockManagerInfo - Added broadcast_3457_piece0 in memory on localhost:42397 (size: 64.0 KiB, free: 1918.2 MiB)
16:02:42.531 INFO SparkContext - Created broadcast 3457 from newAPIHadoopFile at PathSplitSource.java:96
16:02:42.545 INFO MemoryStore - Block broadcast_3458 stored as values in memory (estimated size 592.0 B, free 1912.7 MiB)
16:02:42.545 INFO MemoryStore - Block broadcast_3458_piece0 stored as bytes in memory (estimated size 209.0 B, free 1912.7 MiB)
16:02:42.545 INFO BlockManagerInfo - Added broadcast_3458_piece0 in memory on localhost:42397 (size: 209.0 B, free: 1918.2 MiB)
16:02:42.545 INFO SparkContext - Created broadcast 3458 from broadcast at CramSource.java:114
16:02:42.546 INFO MemoryStore - Block broadcast_3459 stored as values in memory (estimated size 305.5 KiB, free 1912.4 MiB)
16:02:42.552 INFO MemoryStore - Block broadcast_3459_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1912.3 MiB)
16:02:42.552 INFO BlockManagerInfo - Added broadcast_3459_piece0 in memory on localhost:42397 (size: 64.0 KiB, free: 1918.1 MiB)
16:02:42.552 INFO SparkContext - Created broadcast 3459 from newAPIHadoopFile at PathSplitSource.java:96
16:02:42.566 INFO FileInputFormat - Total input files to process : 1
16:02:42.569 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
16:02:42.569 INFO DAGScheduler - Got job 904 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
16:02:42.569 INFO DAGScheduler - Final stage: ResultStage 2493 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
16:02:42.569 INFO DAGScheduler - Parents of final stage: List()
16:02:42.569 INFO DAGScheduler - Missing parents: List()
16:02:42.569 INFO DAGScheduler - Submitting ResultStage 2493 (MapPartitionsRDD[10398] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
16:02:42.581 INFO MemoryStore - Block broadcast_3460 stored as values in memory (estimated size 329.7 KiB, free 1912.0 MiB)
16:02:42.582 INFO MemoryStore - Block broadcast_3460_piece0 stored as bytes in memory (estimated size 143.3 KiB, free 1911.9 MiB)
16:02:42.582 INFO BlockManagerInfo - Added broadcast_3460_piece0 in memory on localhost:42397 (size: 143.3 KiB, free: 1918.0 MiB)
16:02:42.583 INFO SparkContext - Created broadcast 3460 from broadcast at DAGScheduler.scala:1580
16:02:42.583 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))
16:02:42.583 INFO TaskSchedulerImpl - Adding task set 2493.0 with 1 tasks resource profile 0
16:02:42.583 INFO TaskSetManager - Starting task 0.0 in stage 2493.0 (TID 1912) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9689 bytes)
16:02:42.583 INFO Executor - Running task 0.0 in stage 2493.0 (TID 1912)
16:02:42.602 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.cram:0+8617
16:02:42.608 INFO BlockManagerInfo - Removed broadcast_3454_piece0 on localhost:42397 in memory (size: 64.1 KiB, free: 1918.0 MiB)
16:02:42.608 INFO BlockManagerInfo - Removed broadcast_3451_piece0 on localhost:42397 in memory (size: 64.1 KiB, free: 1918.1 MiB)
16:02:42.608 INFO BlockManagerInfo - Removed broadcast_3455_piece0 on localhost:42397 in memory (size: 207.4 KiB, free: 1918.3 MiB)
16:02:42.608 INFO BlockManagerInfo - Removed broadcast_3442_piece0 on localhost:42397 in memory (size: 64.0 KiB, free: 1918.4 MiB)
16:02:42.609 INFO BlockManagerInfo - Removed broadcast_3446_piece0 on localhost:42397 in memory (size: 147.5 KiB, free: 1918.5 MiB)
16:02:42.609 INFO BlockManager - Removing RDD 10362
16:02:42.610 INFO BlockManagerInfo - Removed broadcast_3453_piece0 on localhost:42397 in memory (size: 64.1 KiB, free: 1918.6 MiB)
16:02:42.610 INFO BlockManagerInfo - Removed broadcast_3456_piece0 on localhost:42397 in memory (size: 209.0 B, free: 1918.6 MiB)
16:02:42.610 INFO BlockManagerInfo - Removed broadcast_3448_piece0 on localhost:42397 in memory (size: 8.4 KiB, free: 1918.6 MiB)
16:02:42.611 INFO BlockManagerInfo - Removed broadcast_3447_piece0 on localhost:42397 in memory (size: 143.8 KiB, free: 1918.7 MiB)
16:02:42.611 INFO BlockManagerInfo - Removed broadcast_3439_piece0 on localhost:42397 in memory (size: 211.9 KiB, free: 1919.0 MiB)
16:02:42.611 INFO BlockManagerInfo - Removed broadcast_3445_piece0 on localhost:42397 in memory (size: 145.1 KiB, free: 1919.1 MiB)
16:02:42.611 INFO BlockManagerInfo - Removed broadcast_3441_piece0 on localhost:42397 in memory (size: 209.0 B, free: 1919.1 MiB)
16:02:42.612 INFO BlockManagerInfo - Removed broadcast_3450_piece0 on localhost:42397 in memory (size: 8.4 KiB, free: 1919.1 MiB)
16:02:42.612 INFO BlockManagerInfo - Removed broadcast_3443_piece0 on localhost:42397 in memory (size: 209.0 B, free: 1919.1 MiB)
16:02:42.612 INFO Executor - Finished task 0.0 in stage 2493.0 (TID 1912). 1032 bytes result sent to driver
16:02:42.612 INFO BlockManager - Removing RDD 10349
16:02:42.612 INFO TaskSetManager - Finished task 0.0 in stage 2493.0 (TID 1912) in 29 ms on localhost (executor driver) (1/1)
16:02:42.612 INFO TaskSchedulerImpl - Removed TaskSet 2493.0, whose tasks have all completed, from pool
16:02:42.612 INFO DAGScheduler - ResultStage 2493 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.043 s
16:02:42.613 INFO DAGScheduler - Job 904 is finished. Cancelling potential speculative or zombie tasks for this job
16:02:42.613 INFO TaskSchedulerImpl - Killing all running tasks in stage 2493: Stage finished
16:02:42.613 INFO DAGScheduler - Job 904 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.043897 s
16:02:42.613 INFO CollectMultipleMetricsSpark - Shutting down engine
16:02:42.613 INFO BlockManagerInfo - Removed broadcast_3452_piece0 on localhost:42397 in memory (size: 14.6 KiB, free: 1919.1 MiB)
[May 19, 2025 at 4:02:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744