[June 2, 2025 at 2:36:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1065353216
[June 2, 2025 at 2:36:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1065353216
[June 2, 2025 at 2:36:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1065353216
14:36:40.693 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:36:40.693 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:36:40.693 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
14:36:40.693 INFO CollectMultipleMetricsSpark - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:36:40.693 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:36:40.693 INFO CollectMultipleMetricsSpark - Start Date/Time: June 2, 2025 at 2:36:40 PM GMT
14:36:40.693 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:36:40.693 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:36:40.693 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:36:40.693 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
14:36:40.693 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
14:36:40.693 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:36:40.693 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:36:40.693 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:36:40.693 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:36:40.693 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
14:36:40.693 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
14:36:40.693 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
14:36:40.693 INFO CollectMultipleMetricsSpark - Requester pays: disabled
14:36:40.693 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:36:40.693 INFO CollectMultipleMetricsSpark - Initializing engine
14:36:40.693 INFO CollectMultipleMetricsSpark - Done initializing engine
14:36:40.693 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
WARNING 2025-06-02 14:36:40 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-06-02 14:36:40 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
14:36:40.695 INFO MemoryStore - Block broadcast_3374 stored as values in memory (estimated size 37.8 KiB, free 1909.4 MiB)
14:36:40.695 INFO MemoryStore - Block broadcast_3374_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1909.4 MiB)
14:36:40.695 INFO BlockManagerInfo - Added broadcast_3374_piece0 in memory on localhost:34931 (size: 8.4 KiB, free: 1918.2 MiB)
14:36:40.696 INFO SparkContext - Created broadcast 3374 from broadcast at SamSource.java:78
14:36:40.696 INFO MemoryStore - Block broadcast_3375 stored as values in memory (estimated size 305.5 KiB, free 1909.1 MiB)
14:36:40.703 INFO MemoryStore - Block broadcast_3375_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1909.0 MiB)
14:36:40.703 INFO BlockManagerInfo - Added broadcast_3375_piece0 in memory on localhost:34931 (size: 64.1 KiB, free: 1918.1 MiB)
14:36:40.703 INFO SparkContext - Created broadcast 3375 from newAPIHadoopFile at SamSource.java:108
WARNING 2025-06-02 14:36:40 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-06-02 14:36:40 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
14:36:40.705 INFO MemoryStore - Block broadcast_3376 stored as values in memory (estimated size 37.8 KiB, free 1909.0 MiB)
14:36:40.705 INFO MemoryStore - Block broadcast_3376_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1909.0 MiB)
14:36:40.705 INFO BlockManagerInfo - Added broadcast_3376_piece0 in memory on localhost:34931 (size: 8.4 KiB, free: 1918.1 MiB)
14:36:40.706 INFO SparkContext - Created broadcast 3376 from broadcast at SamSource.java:78
14:36:40.706 INFO MemoryStore - Block broadcast_3377 stored as values in memory (estimated size 305.5 KiB, free 1908.7 MiB)
14:36:40.712 INFO MemoryStore - Block broadcast_3377_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1908.6 MiB)
14:36:40.713 INFO BlockManagerInfo - Added broadcast_3377_piece0 in memory on localhost:34931 (size: 64.1 KiB, free: 1918.1 MiB)
14:36:40.713 INFO SparkContext - Created broadcast 3377 from newAPIHadoopFile at SamSource.java:108
14:36:40.715 INFO FileInputFormat - Total input files to process : 1
14:36:40.718 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
14:36:40.718 INFO DAGScheduler - Got job 882 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
14:36:40.718 INFO DAGScheduler - Final stage: ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
14:36:40.718 INFO DAGScheduler - Parents of final stage: List()
14:36:40.718 INFO DAGScheduler - Missing parents: List()
14:36:40.718 INFO DAGScheduler - Submitting ResultStage 2471 (MapPartitionsRDD[10156] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
14:36:40.719 INFO MemoryStore - Block broadcast_3378 stored as values in memory (estimated size 34.8 KiB, free 1908.6 MiB)
14:36:40.724 INFO MemoryStore - Block broadcast_3378_piece0 stored as bytes in memory (estimated size 14.6 KiB, free 1909.0 MiB)
14:36:40.724 INFO BlockManagerInfo - Removed broadcast_3372_piece0 on localhost:34931 in memory (size: 147.5 KiB, free: 1918.2 MiB)
14:36:40.724 INFO BlockManagerInfo - Added broadcast_3378_piece0 in memory on localhost:34931 (size: 14.6 KiB, free: 1918.2 MiB)
14:36:40.725 INFO SparkContext - Created broadcast 3378 from broadcast at DAGScheduler.scala:1580
14:36:40.725 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))
14:36:40.725 INFO TaskSchedulerImpl - Adding task set 2471.0 with 1 tasks resource profile 0
14:36:40.725 INFO TaskSetManager - Starting task 0.0 in stage 2471.0 (TID 1890) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
14:36:40.725 INFO BlockManagerInfo - Removed broadcast_3367_piece0 on localhost:34931 in memory (size: 209.0 B, free: 1918.2 MiB)
14:36:40.725 INFO Executor - Running task 0.0 in stage 2471.0 (TID 1890)
14:36:40.726 INFO BlockManagerInfo - Removed broadcast_3362_piece0 on localhost:34931 in memory (size: 64.1 KiB, free: 1918.2 MiB)
14:36:40.726 INFO BlockManagerInfo - Removed broadcast_3373_piece0 on localhost:34931 in memory (size: 143.8 KiB, free: 1918.4 MiB)
14:36:40.726 INFO BlockManagerInfo - Removed broadcast_3371_piece0 on localhost:34931 in memory (size: 145.1 KiB, free: 1918.5 MiB)
14:36:40.726 INFO BlockManagerInfo - Removed broadcast_3375_piece0 on localhost:34931 in memory (size: 64.1 KiB, free: 1918.6 MiB)
14:36:40.727 INFO BlockManagerInfo - Removed broadcast_3370_piece0 on localhost:34931 in memory (size: 64.0 KiB, free: 1918.7 MiB)
14:36:40.727 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.sam:0+44008
14:36:40.727 INFO BlockManagerInfo - Removed broadcast_3363_piece0 on localhost:34931 in memory (size: 64.1 KiB, free: 1918.7 MiB)
14:36:40.727 INFO BlockManagerInfo - Removed broadcast_3365_piece0 on localhost:34931 in memory (size: 211.9 KiB, free: 1918.9 MiB)
14:36:40.728 INFO BlockManagerInfo - Removed broadcast_3369_piece0 on localhost:34931 in memory (size: 209.0 B, free: 1918.9 MiB)
14:36:40.728 INFO BlockManagerInfo - Removed broadcast_3374_piece0 on localhost:34931 in memory (size: 8.4 KiB, free: 1918.9 MiB)
14:36:40.728 INFO BlockManagerInfo - Removed broadcast_3368_piece0 on localhost:34931 in memory (size: 64.0 KiB, free: 1919.0 MiB)
14:36:40.728 INFO BlockManagerInfo - Removed broadcast_3366_piece0 on localhost:34931 in memory (size: 207.9 KiB, free: 1919.2 MiB)
14:36:40.728 INFO Executor - Finished task 0.0 in stage 2471.0 (TID 1890). 989 bytes result sent to driver
14:36:40.729 INFO TaskSetManager - Finished task 0.0 in stage 2471.0 (TID 1890) in 4 ms on localhost (executor driver) (1/1)
14:36:40.729 INFO TaskSchedulerImpl - Removed TaskSet 2471.0, whose tasks have all completed, from pool
14:36:40.729 INFO BlockManager - Removing RDD 10131
14:36:40.729 INFO DAGScheduler - ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.011 s
14:36:40.729 INFO DAGScheduler - Job 882 is finished. Cancelling potential speculative or zombie tasks for this job
14:36:40.729 INFO TaskSchedulerImpl - Killing all running tasks in stage 2471: Stage finished
14:36:40.729 INFO DAGScheduler - Job 882 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.010923 s
14:36:40.729 INFO CollectMultipleMetricsSpark - Shutting down engine
[June 2, 2025 at 2:36:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1065353216
14:36:40.729 INFO BlockManager - Removing RDD 10144
14:36:40.730 INFO BlockManagerInfo - Removed broadcast_3364_piece0 on localhost:34931 in memory (size: 209.3 KiB, free: 1919.5 MiB)
14:36:40.743 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:36:40.743 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:36:40.743 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
14:36:40.743 INFO CollectMultipleMetricsSpark - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:36:40.743 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:36:40.743 INFO CollectMultipleMetricsSpark - Start Date/Time: June 2, 2025 at 2:36:40 PM GMT
14:36:40.743 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:36:40.743 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:36:40.743 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:36:40.743 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
14:36:40.743 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
14:36:40.743 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:36:40.743 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:36:40.743 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:36:40.743 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:36:40.743 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
14:36:40.743 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
14:36:40.743 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
14:36:40.743 INFO CollectMultipleMetricsSpark - Requester pays: disabled
14:36:40.743 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:36:40.743 INFO CollectMultipleMetricsSpark - Initializing engine
14:36:40.743 INFO CollectMultipleMetricsSpark - Done initializing engine
14:36:40.743 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
14:36:40.746 INFO MemoryStore - Block broadcast_3379 stored as values in memory (estimated size 305.5 KiB, free 1913.6 MiB)
14:36:40.755 INFO MemoryStore - Block broadcast_3379_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1913.5 MiB)
14:36:40.755 INFO BlockManagerInfo - Added broadcast_3379_piece0 in memory on localhost:34931 (size: 64.1 KiB, free: 1919.4 MiB)
14:36:40.755 INFO SparkContext - Created broadcast 3379 from newAPIHadoopFile at PathSplitSource.java:96
14:36:40.775 INFO MemoryStore - Block broadcast_3380 stored as values in memory (estimated size 305.5 KiB, free 1913.2 MiB)
14:36:40.781 INFO MemoryStore - Block broadcast_3380_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1913.2 MiB)
14:36:40.781 INFO BlockManagerInfo - Added broadcast_3380_piece0 in memory on localhost:34931 (size: 64.1 KiB, free: 1919.3 MiB)
14:36:40.782 INFO SparkContext - Created broadcast 3380 from newAPIHadoopFile at PathSplitSource.java:96
14:36:40.801 INFO FileInputFormat - Total input files to process : 1
14:36:40.804 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
14:36:40.804 INFO DAGScheduler - Got job 883 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
14:36:40.804 INFO DAGScheduler - Final stage: ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
14:36:40.804 INFO DAGScheduler - Parents of final stage: List()
14:36:40.804 INFO DAGScheduler - Missing parents: List()
14:36:40.804 INFO DAGScheduler - Submitting ResultStage 2472 (MapPartitionsRDD[10169] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
14:36:40.828 INFO MemoryStore - Block broadcast_3381 stored as values in memory (estimated size 476.8 KiB, free 1912.7 MiB)
14:36:40.830 INFO MemoryStore - Block broadcast_3381_piece0 stored as bytes in memory (estimated size 207.4 KiB, free 1912.5 MiB)
14:36:40.830 INFO BlockManagerInfo - Added broadcast_3381_piece0 in memory on localhost:34931 (size: 207.4 KiB, free: 1919.1 MiB)
14:36:40.830 INFO SparkContext - Created broadcast 3381 from broadcast at DAGScheduler.scala:1580
14:36:40.830 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))
14:36:40.830 INFO TaskSchedulerImpl - Adding task set 2472.0 with 1 tasks resource profile 0
14:36:40.831 INFO TaskSetManager - Starting task 0.0 in stage 2472.0 (TID 1891) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
14:36:40.831 INFO Executor - Running task 0.0 in stage 2472.0 (TID 1891)
14:36:40.859 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.bam:0+8071
14:36:40.862 INFO Executor - Finished task 0.0 in stage 2472.0 (TID 1891). 989 bytes result sent to driver
14:36:40.862 INFO TaskSetManager - Finished task 0.0 in stage 2472.0 (TID 1891) in 32 ms on localhost (executor driver) (1/1)
14:36:40.862 INFO TaskSchedulerImpl - Removed TaskSet 2472.0, whose tasks have all completed, from pool
14:36:40.862 INFO DAGScheduler - ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.057 s
14:36:40.862 INFO DAGScheduler - Job 883 is finished. Cancelling potential speculative or zombie tasks for this job
14:36:40.862 INFO TaskSchedulerImpl - Killing all running tasks in stage 2472: Stage finished
14:36:40.862 INFO DAGScheduler - Job 883 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.058372 s
14:36:40.862 INFO CollectMultipleMetricsSpark - Shutting down engine
[June 2, 2025 at 2:36:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1065353216
14:36:40.876 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:36:40.876 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:36:40.876 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
14:36:40.876 INFO CollectMultipleMetricsSpark - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:36:40.876 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:36:40.876 INFO CollectMultipleMetricsSpark - Start Date/Time: June 2, 2025 at 2:36:40 PM GMT
14:36:40.876 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:36:40.876 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
14:36:40.876 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:36:40.876 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
14:36:40.876 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
14:36:40.876 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:36:40.876 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:36:40.876 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:36:40.876 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:36:40.876 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
14:36:40.876 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
14:36:40.876 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
14:36:40.876 INFO CollectMultipleMetricsSpark - Requester pays: disabled
14:36:40.876 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:36:40.876 INFO CollectMultipleMetricsSpark - Initializing engine
14:36:40.876 INFO CollectMultipleMetricsSpark - Done initializing engine
14:36:40.876 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
14:36:40.879 INFO MemoryStore - Block broadcast_3382 stored as values in memory (estimated size 592.0 B, free 1912.5 MiB)
14:36:40.879 INFO MemoryStore - Block broadcast_3382_piece0 stored as bytes in memory (estimated size 209.0 B, free 1912.5 MiB)
14:36:40.879 INFO BlockManagerInfo - Added broadcast_3382_piece0 in memory on localhost:34931 (size: 209.0 B, free: 1919.1 MiB)
14:36:40.879 INFO SparkContext - Created broadcast 3382 from broadcast at CramSource.java:114
14:36:40.880 INFO MemoryStore - Block broadcast_3383 stored as values in memory (estimated size 305.5 KiB, free 1912.2 MiB)
14:36:40.886 INFO MemoryStore - Block broadcast_3383_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1912.2 MiB)
14:36:40.886 INFO BlockManagerInfo - Added broadcast_3383_piece0 in memory on localhost:34931 (size: 64.0 KiB, free: 1919.1 MiB)
14:36:40.887 INFO SparkContext - Created broadcast 3383 from newAPIHadoopFile at PathSplitSource.java:96
14:36:40.901 INFO MemoryStore - Block broadcast_3384 stored as values in memory (estimated size 592.0 B, free 1912.2 MiB)
14:36:40.901 INFO MemoryStore - Block broadcast_3384_piece0 stored as bytes in memory (estimated size 209.0 B, free 1912.2 MiB)
14:36:40.901 INFO BlockManagerInfo - Added broadcast_3384_piece0 in memory on localhost:34931 (size: 209.0 B, free: 1919.1 MiB)
14:36:40.901 INFO SparkContext - Created broadcast 3384 from broadcast at CramSource.java:114
14:36:40.902 INFO MemoryStore - Block broadcast_3385 stored as values in memory (estimated size 305.5 KiB, free 1911.9 MiB)
14:36:40.908 INFO MemoryStore - Block broadcast_3385_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1911.8 MiB)
14:36:40.908 INFO BlockManagerInfo - Added broadcast_3385_piece0 in memory on localhost:34931 (size: 64.0 KiB, free: 1919.0 MiB)
14:36:40.908 INFO SparkContext - Created broadcast 3385 from newAPIHadoopFile at PathSplitSource.java:96
14:36:40.922 INFO FileInputFormat - Total input files to process : 1
14:36:40.925 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
14:36:40.925 INFO DAGScheduler - Got job 884 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
14:36:40.925 INFO DAGScheduler - Final stage: ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
14:36:40.925 INFO DAGScheduler - Parents of final stage: List()
14:36:40.925 INFO DAGScheduler - Missing parents: List()
14:36:40.925 INFO DAGScheduler - Submitting ResultStage 2473 (MapPartitionsRDD[10180] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
14:36:40.937 INFO MemoryStore - Block broadcast_3386 stored as values in memory (estimated size 329.7 KiB, free 1911.5 MiB)
14:36:40.939 INFO MemoryStore - Block broadcast_3386_piece0 stored as bytes in memory (estimated size 143.3 KiB, free 1911.3 MiB)
14:36:40.939 INFO BlockManagerInfo - Added broadcast_3386_piece0 in memory on localhost:34931 (size: 143.3 KiB, free: 1918.9 MiB)
14:36:40.939 INFO SparkContext - Created broadcast 3386 from broadcast at DAGScheduler.scala:1580
14:36:40.939 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))
14:36:40.939 INFO TaskSchedulerImpl - Adding task set 2473.0 with 1 tasks resource profile 0
14:36:40.940 INFO TaskSetManager - Starting task 0.0 in stage 2473.0 (TID 1892) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9689 bytes)
14:36:40.940 INFO Executor - Running task 0.0 in stage 2473.0 (TID 1892)
14:36:40.960 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.cram:0+8617
14:36:40.964 INFO Executor - Finished task 0.0 in stage 2473.0 (TID 1892). 989 bytes result sent to driver
14:36:40.964 INFO TaskSetManager - Finished task 0.0 in stage 2473.0 (TID 1892) in 24 ms on localhost (executor driver) (1/1)
14:36:40.964 INFO TaskSchedulerImpl - Removed TaskSet 2473.0, whose tasks have all completed, from pool
14:36:40.964 INFO DAGScheduler - ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.038 s
14:36:40.964 INFO DAGScheduler - Job 884 is finished. Cancelling potential speculative or zombie tasks for this job
14:36:40.964 INFO TaskSchedulerImpl - Killing all running tasks in stage 2473: Stage finished
14:36:40.964 INFO DAGScheduler - Job 884 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.039063 s
14:36:40.964 INFO CollectMultipleMetricsSpark - Shutting down engine
[June 2, 2025 at 2:36:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1065353216