[May 27, 2025 at 6:32:51 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1199570944
[May 27, 2025 at 6:32:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1199570944
[May 27, 2025 at 6:32:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1199570944
18:32:52.683 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
18:32:52.683 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:32:52.683 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
18:32:52.683 INFO CollectMultipleMetricsSpark - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:32:52.683 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:32:52.683 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 6:32:52 PM GMT
18:32:52.683 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
18:32:52.683 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
18:32:52.683 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
18:32:52.683 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
18:32:52.683 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
18:32:52.683 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:32:52.683 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:32:52.683 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:32:52.683 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:32:52.683 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
18:32:52.683 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
18:32:52.683 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
18:32:52.683 INFO CollectMultipleMetricsSpark - Requester pays: disabled
18:32:52.683 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
18:32:52.683 INFO CollectMultipleMetricsSpark - Initializing engine
18:32:52.684 INFO CollectMultipleMetricsSpark - Done initializing engine
18:32:52.684 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
WARNING 2025-05-27 18:32:52 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-27 18:32:52 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
18:32:52.685 INFO MemoryStore - Block broadcast_3374 stored as values in memory (estimated size 37.8 KiB, free 1912.6 MiB)
18:32:52.686 INFO MemoryStore - Block broadcast_3374_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1912.6 MiB)
18:32:52.686 INFO BlockManagerInfo - Added broadcast_3374_piece0 in memory on localhost:38805 (size: 8.4 KiB, free: 1919.1 MiB)
18:32:52.686 INFO SparkContext - Created broadcast 3374 from broadcast at SamSource.java:78
18:32:52.687 INFO MemoryStore - Block broadcast_3375 stored as values in memory (estimated size 305.5 KiB, free 1912.3 MiB)
18:32:52.694 INFO MemoryStore - Block broadcast_3375_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1912.2 MiB)
18:32:52.694 INFO BlockManagerInfo - Added broadcast_3375_piece0 in memory on localhost:38805 (size: 64.1 KiB, free: 1919.0 MiB)
18:32:52.694 INFO SparkContext - Created broadcast 3375 from newAPIHadoopFile at SamSource.java:108
WARNING 2025-05-27 18:32:52 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-05-27 18:32:52 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
18:32:52.697 INFO MemoryStore - Block broadcast_3376 stored as values in memory (estimated size 37.8 KiB, free 1912.2 MiB)
18:32:52.698 INFO MemoryStore - Block broadcast_3376_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1912.1 MiB)
18:32:52.698 INFO BlockManagerInfo - Added broadcast_3376_piece0 in memory on localhost:38805 (size: 8.4 KiB, free: 1919.0 MiB)
18:32:52.698 INFO SparkContext - Created broadcast 3376 from broadcast at SamSource.java:78
18:32:52.699 INFO MemoryStore - Block broadcast_3377 stored as values in memory (estimated size 305.5 KiB, free 1911.9 MiB)
18:32:52.706 INFO MemoryStore - Block broadcast_3377_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1911.8 MiB)
18:32:52.706 INFO BlockManagerInfo - Added broadcast_3377_piece0 in memory on localhost:38805 (size: 64.1 KiB, free: 1918.9 MiB)
18:32:52.706 INFO SparkContext - Created broadcast 3377 from newAPIHadoopFile at SamSource.java:108
18:32:52.708 INFO FileInputFormat - Total input files to process : 1
18:32:52.712 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
18:32:52.712 INFO DAGScheduler - Got job 882 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
18:32:52.712 INFO DAGScheduler - Final stage: ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
18:32:52.712 INFO DAGScheduler - Parents of final stage: List()
18:32:52.712 INFO DAGScheduler - Missing parents: List()
18:32:52.712 INFO DAGScheduler - Submitting ResultStage 2471 (MapPartitionsRDD[10156] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
18:32:52.713 INFO MemoryStore - Block broadcast_3378 stored as values in memory (estimated size 34.8 KiB, free 1911.8 MiB)
18:32:52.713 INFO MemoryStore - Block broadcast_3378_piece0 stored as bytes in memory (estimated size 14.6 KiB, free 1911.7 MiB)
18:32:52.713 INFO BlockManagerInfo - Added broadcast_3378_piece0 in memory on localhost:38805 (size: 14.6 KiB, free: 1918.9 MiB)
18:32:52.714 INFO SparkContext - Created broadcast 3378 from broadcast at DAGScheduler.scala:1580
18:32:52.714 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))
18:32:52.714 INFO TaskSchedulerImpl - Adding task set 2471.0 with 1 tasks resource profile 0
18:32:52.714 INFO TaskSetManager - Starting task 0.0 in stage 2471.0 (TID 1890) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
18:32:52.715 INFO Executor - Running task 0.0 in stage 2471.0 (TID 1890)
18:32:52.717 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.sam:0+44008
18:32:52.719 INFO Executor - Finished task 0.0 in stage 2471.0 (TID 1890). 989 bytes result sent to driver
18:32:52.720 INFO TaskSetManager - Finished task 0.0 in stage 2471.0 (TID 1890) in 6 ms on localhost (executor driver) (1/1)
18:32:52.720 INFO TaskSchedulerImpl - Removed TaskSet 2471.0, whose tasks have all completed, from pool
18:32:52.720 INFO DAGScheduler - ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.008 s
18:32:52.720 INFO DAGScheduler - Job 882 is finished. Cancelling potential speculative or zombie tasks for this job
18:32:52.720 INFO TaskSchedulerImpl - Killing all running tasks in stage 2471: Stage finished
18:32:52.720 INFO DAGScheduler - Job 882 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.008249 s
18:32:52.720 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 6:32:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1199570944
18:32:52.735 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
18:32:52.735 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:32:52.735 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
18:32:52.735 INFO CollectMultipleMetricsSpark - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:32:52.735 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:32:52.735 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 6:32:52 PM GMT
18:32:52.735 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
18:32:52.735 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
18:32:52.735 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
18:32:52.735 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
18:32:52.735 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
18:32:52.735 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:32:52.735 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:32:52.735 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:32:52.735 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:32:52.735 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
18:32:52.735 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
18:32:52.735 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
18:32:52.735 INFO CollectMultipleMetricsSpark - Requester pays: disabled
18:32:52.735 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
18:32:52.735 INFO CollectMultipleMetricsSpark - Initializing engine
18:32:52.735 INFO CollectMultipleMetricsSpark - Done initializing engine
18:32:52.735 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
18:32:52.738 INFO MemoryStore - Block broadcast_3379 stored as values in memory (estimated size 305.5 KiB, free 1911.4 MiB)
18:32:52.749 INFO MemoryStore - Block broadcast_3379_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1911.4 MiB)
18:32:52.749 INFO BlockManagerInfo - Added broadcast_3379_piece0 in memory on localhost:38805 (size: 64.1 KiB, free: 1918.9 MiB)
18:32:52.750 INFO SparkContext - Created broadcast 3379 from newAPIHadoopFile at PathSplitSource.java:96
18:32:52.778 INFO MemoryStore - Block broadcast_3380 stored as values in memory (estimated size 305.5 KiB, free 1911.1 MiB)
18:32:52.785 INFO MemoryStore - Block broadcast_3380_piece0 stored as bytes in memory (estimated size 64.1 KiB, free 1911.0 MiB)
18:32:52.786 INFO BlockManagerInfo - Added broadcast_3380_piece0 in memory on localhost:38805 (size: 64.1 KiB, free: 1918.8 MiB)
18:32:52.786 INFO SparkContext - Created broadcast 3380 from newAPIHadoopFile at PathSplitSource.java:96
18:32:52.809 INFO FileInputFormat - Total input files to process : 1
18:32:52.812 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
18:32:52.813 INFO DAGScheduler - Got job 883 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
18:32:52.813 INFO DAGScheduler - Final stage: ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
18:32:52.813 INFO DAGScheduler - Parents of final stage: List()
18:32:52.813 INFO DAGScheduler - Missing parents: List()
18:32:52.813 INFO DAGScheduler - Submitting ResultStage 2472 (MapPartitionsRDD[10169] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
18:32:52.832 INFO MemoryStore - Block broadcast_3381 stored as values in memory (estimated size 476.8 KiB, free 1910.6 MiB)
18:32:52.834 INFO MemoryStore - Block broadcast_3381_piece0 stored as bytes in memory (estimated size 207.4 KiB, free 1910.4 MiB)
18:32:52.835 INFO BlockManagerInfo - Added broadcast_3381_piece0 in memory on localhost:38805 (size: 207.4 KiB, free: 1918.6 MiB)
18:32:52.835 INFO SparkContext - Created broadcast 3381 from broadcast at DAGScheduler.scala:1580
18:32:52.835 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))
18:32:52.835 INFO TaskSchedulerImpl - Adding task set 2472.0 with 1 tasks resource profile 0
18:32:52.836 INFO TaskSetManager - Starting task 0.0 in stage 2472.0 (TID 1891) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9688 bytes)
18:32:52.836 INFO Executor - Running task 0.0 in stage 2472.0 (TID 1891)
18:32:52.869 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.bam:0+8071
18:32:52.873 INFO Executor - Finished task 0.0 in stage 2472.0 (TID 1891). 989 bytes result sent to driver
18:32:52.874 INFO TaskSetManager - Finished task 0.0 in stage 2472.0 (TID 1891) in 37 ms on localhost (executor driver) (1/1)
18:32:52.874 INFO TaskSchedulerImpl - Removed TaskSet 2472.0, whose tasks have all completed, from pool
18:32:52.874 INFO DAGScheduler - ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.061 s
18:32:52.874 INFO DAGScheduler - Job 883 is finished. Cancelling potential speculative or zombie tasks for this job
18:32:52.874 INFO TaskSchedulerImpl - Killing all running tasks in stage 2472: Stage finished
18:32:52.874 INFO DAGScheduler - Job 883 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.061366 s
18:32:52.874 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 6:32:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1199570944
18:32:52.889 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
18:32:52.889 INFO CollectMultipleMetricsSpark - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:32:52.889 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
18:32:52.889 INFO CollectMultipleMetricsSpark - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:32:52.889 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:32:52.890 INFO CollectMultipleMetricsSpark - Start Date/Time: May 27, 2025 at 6:32:52 PM GMT
18:32:52.890 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
18:32:52.890 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
18:32:52.890 INFO CollectMultipleMetricsSpark - HTSJDK Version: test_cram_wiring-SNAPSHOT
18:32:52.890 INFO CollectMultipleMetricsSpark - Picard Version: 3.4.0
18:32:52.890 INFO CollectMultipleMetricsSpark - Built for Spark Version: 3.5.0
18:32:52.890 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:32:52.890 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:32:52.890 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:32:52.890 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:32:52.890 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
18:32:52.890 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
18:32:52.890 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
18:32:52.890 INFO CollectMultipleMetricsSpark - Requester pays: disabled
18:32:52.890 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
18:32:52.890 INFO CollectMultipleMetricsSpark - Initializing engine
18:32:52.890 INFO CollectMultipleMetricsSpark - Done initializing engine
18:32:52.890 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
18:32:52.893 INFO MemoryStore - Block broadcast_3382 stored as values in memory (estimated size 592.0 B, free 1910.3 MiB)
18:32:52.893 INFO MemoryStore - Block broadcast_3382_piece0 stored as bytes in memory (estimated size 209.0 B, free 1910.3 MiB)
18:32:52.893 INFO BlockManagerInfo - Added broadcast_3382_piece0 in memory on localhost:38805 (size: 209.0 B, free: 1918.6 MiB)
18:32:52.893 INFO SparkContext - Created broadcast 3382 from broadcast at CramSource.java:114
18:32:52.894 INFO MemoryStore - Block broadcast_3383 stored as values in memory (estimated size 305.5 KiB, free 1910.1 MiB)
18:32:52.901 INFO MemoryStore - Block broadcast_3383_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1910.0 MiB)
18:32:52.902 INFO BlockManagerInfo - Added broadcast_3383_piece0 in memory on localhost:38805 (size: 64.0 KiB, free: 1918.5 MiB)
18:32:52.902 INFO SparkContext - Created broadcast 3383 from newAPIHadoopFile at PathSplitSource.java:96
18:32:52.917 INFO MemoryStore - Block broadcast_3384 stored as values in memory (estimated size 592.0 B, free 1910.0 MiB)
18:32:52.918 INFO MemoryStore - Block broadcast_3384_piece0 stored as bytes in memory (estimated size 209.0 B, free 1910.0 MiB)
18:32:52.918 INFO BlockManagerInfo - Added broadcast_3384_piece0 in memory on localhost:38805 (size: 209.0 B, free: 1918.5 MiB)
18:32:52.918 INFO SparkContext - Created broadcast 3384 from broadcast at CramSource.java:114
18:32:52.919 INFO MemoryStore - Block broadcast_3385 stored as values in memory (estimated size 305.5 KiB, free 1909.7 MiB)
18:32:52.925 INFO MemoryStore - Block broadcast_3385_piece0 stored as bytes in memory (estimated size 64.0 KiB, free 1909.6 MiB)
18:32:52.926 INFO BlockManagerInfo - Added broadcast_3385_piece0 in memory on localhost:38805 (size: 64.0 KiB, free: 1918.5 MiB)
18:32:52.926 INFO SparkContext - Created broadcast 3385 from newAPIHadoopFile at PathSplitSource.java:96
18:32:52.940 INFO FileInputFormat - Total input files to process : 1
18:32:52.943 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
18:32:52.944 INFO DAGScheduler - Got job 884 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
18:32:52.944 INFO DAGScheduler - Final stage: ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
18:32:52.944 INFO DAGScheduler - Parents of final stage: List()
18:32:52.944 INFO DAGScheduler - Missing parents: List()
18:32:52.944 INFO DAGScheduler - Submitting ResultStage 2473 (MapPartitionsRDD[10180] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
18:32:52.955 INFO MemoryStore - Block broadcast_3386 stored as values in memory (estimated size 329.7 KiB, free 1909.3 MiB)
18:32:52.957 INFO MemoryStore - Block broadcast_3386_piece0 stored as bytes in memory (estimated size 143.3 KiB, free 1909.2 MiB)
18:32:52.957 INFO BlockManagerInfo - Added broadcast_3386_piece0 in memory on localhost:38805 (size: 143.3 KiB, free: 1918.3 MiB)
18:32:52.958 INFO SparkContext - Created broadcast 3386 from broadcast at DAGScheduler.scala:1580
18:32:52.958 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))
18:32:52.958 INFO TaskSchedulerImpl - Adding task set 2473.0 with 1 tasks resource profile 0
18:32:52.958 INFO TaskSetManager - Starting task 0.0 in stage 2473.0 (TID 1892) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9689 bytes)
18:32:52.959 INFO Executor - Running task 0.0 in stage 2473.0 (TID 1892)
18:32:52.979 INFO NewHadoopRDD - Input split: file:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.cram:0+8617
18:32:52.984 INFO Executor - Finished task 0.0 in stage 2473.0 (TID 1892). 989 bytes result sent to driver
18:32:52.984 INFO TaskSetManager - Finished task 0.0 in stage 2473.0 (TID 1892) in 26 ms on localhost (executor driver) (1/1)
18:32:52.984 INFO TaskSchedulerImpl - Removed TaskSet 2473.0, whose tasks have all completed, from pool
18:32:52.985 INFO DAGScheduler - ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.040 s
18:32:52.985 INFO DAGScheduler - Job 884 is finished. Cancelling potential speculative or zombie tasks for this job
18:32:52.985 INFO TaskSchedulerImpl - Killing all running tasks in stage 2473: Stage finished
18:32:52.985 INFO DAGScheduler - Job 884 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.041294 s
18:32:52.985 INFO CollectMultipleMetricsSpark - Shutting down engine
[May 27, 2025 at 6:32:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1199570944