[October 27, 2025 at 5:48:16 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1631584256
[October 27, 2025 at 5:48:16 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1631584256
[October 27, 2025 at 5:48:16 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1631584256
17:48:16.702 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:48:16.705 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression7597791375769883507.so: /tmp/local16469784102307886954/libgkl_compression7597791375769883507.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:48:16.705 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:48:16.708 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression6297357276860915237.so: /tmp/local16469784102307886954/libgkl_compression6297357276860915237.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:48:16.709 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
17:48:16.709 INFO CollectMultipleMetricsSpark - org.broadinstitute.hellbender.tools.spark.pipelines.metrics vUnavailable
17:48:16.709 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
17:48:16.709 INFO CollectMultipleMetricsSpark - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:48:16.709 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:48:16.709 INFO CollectMultipleMetricsSpark - Start Date/Time: October 27, 2025 at 5:48:16 PM UTC
17:48:16.709 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
17:48:16.709 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
17:48:16.709 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:48:16.709 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:48:16.709 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:48:16.709 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:48:16.709 INFO CollectMultipleMetricsSpark - Deflater: JdkDeflater
17:48:16.709 INFO CollectMultipleMetricsSpark - Inflater: JdkInflater
17:48:16.709 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
17:48:16.709 INFO CollectMultipleMetricsSpark - Requester pays: disabled
17:48:16.709 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
17:48:16.709 INFO CollectMultipleMetricsSpark - Initializing engine
17:48:16.709 INFO CollectMultipleMetricsSpark - Done initializing engine
17:48:16.709 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
WARNING 2025-10-27 17:48:16 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-10-27 17:48:16 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
17:48:16.711 INFO MemoryStore - Block broadcast_3317 stored as values in memory (estimated size 37.8 KiB, free 1911.2 MiB)
17:48:16.712 INFO MemoryStore - Block broadcast_3317_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1911.2 MiB)
17:48:16.712 INFO BlockManagerInfo - Added broadcast_3317_piece0 in memory on localhost:42685 (size: 8.4 KiB, free: 1917.7 MiB)
17:48:16.712 INFO SparkContext - Created broadcast 3317 from broadcast at SamSource.java:78
17:48:16.713 INFO MemoryStore - Block broadcast_3318 stored as values in memory (estimated size 306.3 KiB, free 1910.9 MiB)
17:48:16.719 INFO MemoryStore - Block broadcast_3318_piece0 stored as bytes in memory (estimated size 64.4 KiB, free 1910.8 MiB)
17:48:16.719 INFO BlockManagerInfo - Added broadcast_3318_piece0 in memory on localhost:42685 (size: 64.4 KiB, free: 1917.7 MiB)
17:48:16.719 INFO SparkContext - Created broadcast 3318 from newAPIHadoopFile at SamSource.java:108
WARNING 2025-10-27 17:48:16 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-10-27 17:48:16 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
17:48:16.722 INFO MemoryStore - Block broadcast_3319 stored as values in memory (estimated size 37.8 KiB, free 1910.8 MiB)
17:48:16.722 INFO MemoryStore - Block broadcast_3319_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1910.8 MiB)
17:48:16.722 INFO BlockManagerInfo - Added broadcast_3319_piece0 in memory on localhost:42685 (size: 8.4 KiB, free: 1917.7 MiB)
17:48:16.723 INFO SparkContext - Created broadcast 3319 from broadcast at SamSource.java:78
17:48:16.723 INFO MemoryStore - Block broadcast_3320 stored as values in memory (estimated size 306.3 KiB, free 1910.5 MiB)
17:48:16.729 INFO MemoryStore - Block broadcast_3320_piece0 stored as bytes in memory (estimated size 64.4 KiB, free 1910.4 MiB)
17:48:16.729 INFO BlockManagerInfo - Added broadcast_3320_piece0 in memory on localhost:42685 (size: 64.4 KiB, free: 1917.6 MiB)
17:48:16.729 INFO SparkContext - Created broadcast 3320 from newAPIHadoopFile at SamSource.java:108
17:48:16.732 INFO FileInputFormat - Total input files to process : 1
17:48:16.735 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
17:48:16.735 INFO DAGScheduler - Got job 850 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
17:48:16.735 INFO DAGScheduler - Final stage: ResultStage 2285 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
17:48:16.735 INFO DAGScheduler - Parents of final stage: List()
17:48:16.736 INFO DAGScheduler - Missing parents: List()
17:48:16.736 INFO DAGScheduler - Submitting ResultStage 2285 (MapPartitionsRDD[10069] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
17:48:16.736 INFO MemoryStore - Block broadcast_3321 stored as values in memory (estimated size 34.8 KiB, free 1910.4 MiB)
17:48:16.736 INFO MemoryStore - Block broadcast_3321_piece0 stored as bytes in memory (estimated size 14.6 KiB, free 1910.4 MiB)
17:48:16.737 INFO BlockManagerInfo - Added broadcast_3321_piece0 in memory on localhost:42685 (size: 14.6 KiB, free: 1917.6 MiB)
17:48:16.737 INFO SparkContext - Created broadcast 3321 from broadcast at DAGScheduler.scala:1580
17:48:16.737 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 2285 (MapPartitionsRDD[10069] at filter at CollectMultipleMetricsSpark.java:193) (first 15 tasks are for partitions Vector(0))
17:48:16.737 INFO TaskSchedulerImpl - Adding task set 2285.0 with 1 tasks resource profile 0
17:48:16.737 INFO TaskSetManager - Starting task 0.0 in stage 2285.0 (TID 1798) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9772 bytes)
17:48:16.738 INFO Executor - Running task 0.0 in stage 2285.0 (TID 1798)
17:48:16.739 INFO NewHadoopRDD - Input split: file:/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.sam:0+44008
17:48:16.741 INFO Executor - Finished task 0.0 in stage 2285.0 (TID 1798). 989 bytes result sent to driver
17:48:16.741 INFO TaskSetManager - Finished task 0.0 in stage 2285.0 (TID 1798) in 4 ms on localhost (executor driver) (1/1)
17:48:16.741 INFO TaskSchedulerImpl - Removed TaskSet 2285.0, whose tasks have all completed, from pool
17:48:16.741 INFO DAGScheduler - ResultStage 2285 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.005 s
17:48:16.741 INFO DAGScheduler - Job 850 is finished. Cancelling potential speculative or zombie tasks for this job
17:48:16.741 INFO TaskSchedulerImpl - Killing all running tasks in stage 2285: Stage finished
17:48:16.741 INFO DAGScheduler - Job 850 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.006082 s
17:48:16.741 INFO CollectMultipleMetricsSpark - Shutting down engine
[October 27, 2025 at 5:48:16 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1631584256
17:48:16.746 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:48:16.749 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression16885937931283891896.so: /tmp/local16469784102307886954/libgkl_compression16885937931283891896.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:48:16.749 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:48:16.752 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression2560186857777002454.so: /tmp/local16469784102307886954/libgkl_compression2560186857777002454.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:48:16.753 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
17:48:16.753 INFO CollectMultipleMetricsSpark - org.broadinstitute.hellbender.tools.spark.pipelines.metrics vUnavailable
17:48:16.753 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
17:48:16.753 INFO CollectMultipleMetricsSpark - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:48:16.753 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:48:16.753 INFO CollectMultipleMetricsSpark - Start Date/Time: October 27, 2025 at 5:48:16 PM UTC
17:48:16.753 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
17:48:16.753 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
17:48:16.753 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:48:16.753 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:48:16.753 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:48:16.753 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:48:16.753 INFO CollectMultipleMetricsSpark - Deflater: JdkDeflater
17:48:16.753 INFO CollectMultipleMetricsSpark - Inflater: JdkInflater
17:48:16.753 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
17:48:16.753 INFO CollectMultipleMetricsSpark - Requester pays: disabled
17:48:16.753 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
17:48:16.753 INFO CollectMultipleMetricsSpark - Initializing engine
17:48:16.753 INFO CollectMultipleMetricsSpark - Done initializing engine
17:48:16.753 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
17:48:16.754 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:48:16.756 INFO MemoryStore - Block broadcast_3322 stored as values in memory (estimated size 306.3 KiB, free 1910.1 MiB)
17:48:16.761 INFO MemoryStore - Block broadcast_3322_piece0 stored as bytes in memory (estimated size 64.4 KiB, free 1910.0 MiB)
17:48:16.762 INFO BlockManagerInfo - Added broadcast_3322_piece0 in memory on localhost:42685 (size: 64.4 KiB, free: 1917.5 MiB)
17:48:16.762 INFO SparkContext - Created broadcast 3322 from newAPIHadoopFile at PathSplitSource.java:96
17:48:16.780 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:48:16.781 INFO MemoryStore - Block broadcast_3323 stored as values in memory (estimated size 306.3 KiB, free 1909.7 MiB)
17:48:16.787 INFO MemoryStore - Block broadcast_3323_piece0 stored as bytes in memory (estimated size 64.4 KiB, free 1909.6 MiB)
17:48:16.787 INFO BlockManagerInfo - Added broadcast_3323_piece0 in memory on localhost:42685 (size: 64.4 KiB, free: 1917.5 MiB)
17:48:16.787 INFO SparkContext - Created broadcast 3323 from newAPIHadoopFile at PathSplitSource.java:96
17:48:16.806 INFO FileInputFormat - Total input files to process : 1
17:48:16.809 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
17:48:16.809 INFO DAGScheduler - Got job 851 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
17:48:16.809 INFO DAGScheduler - Final stage: ResultStage 2286 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
17:48:16.809 INFO DAGScheduler - Parents of final stage: List()
17:48:16.809 INFO DAGScheduler - Missing parents: List()
17:48:16.809 INFO DAGScheduler - Submitting ResultStage 2286 (MapPartitionsRDD[10082] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
17:48:16.824 INFO MemoryStore - Block broadcast_3324 stored as values in memory (estimated size 478.0 KiB, free 1909.2 MiB)
17:48:16.826 INFO MemoryStore - Block broadcast_3324_piece0 stored as bytes in memory (estimated size 208.0 KiB, free 1909.0 MiB)
17:48:16.826 INFO BlockManagerInfo - Added broadcast_3324_piece0 in memory on localhost:42685 (size: 208.0 KiB, free: 1917.3 MiB)
17:48:16.826 INFO SparkContext - Created broadcast 3324 from broadcast at DAGScheduler.scala:1580
17:48:16.827 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 2286 (MapPartitionsRDD[10082] at filter at CollectMultipleMetricsSpark.java:193) (first 15 tasks are for partitions Vector(0))
17:48:16.827 INFO TaskSchedulerImpl - Adding task set 2286.0 with 1 tasks resource profile 0
17:48:16.827 INFO TaskSetManager - Starting task 0.0 in stage 2286.0 (TID 1799) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9772 bytes)
17:48:16.827 INFO Executor - Running task 0.0 in stage 2286.0 (TID 1799)
17:48:16.861 INFO NewHadoopRDD - Input split: file:/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.bam:0+8071
17:48:16.862 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:48:16.862 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:48:16.865 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:48:16.865 INFO Executor - Finished task 0.0 in stage 2286.0 (TID 1799). 989 bytes result sent to driver
17:48:16.866 INFO TaskSetManager - Finished task 0.0 in stage 2286.0 (TID 1799) in 39 ms on localhost (executor driver) (1/1)
17:48:16.866 INFO TaskSchedulerImpl - Removed TaskSet 2286.0, whose tasks have all completed, from pool
17:48:16.866 INFO DAGScheduler - ResultStage 2286 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.057 s
17:48:16.866 INFO DAGScheduler - Job 851 is finished. Cancelling potential speculative or zombie tasks for this job
17:48:16.866 INFO TaskSchedulerImpl - Killing all running tasks in stage 2286: Stage finished
17:48:16.866 INFO DAGScheduler - Job 851 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.057396 s
17:48:16.866 INFO CollectMultipleMetricsSpark - Shutting down engine
[October 27, 2025 at 5:48:16 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1631584256
17:48:16.871 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:48:16.873 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression11255113914393285939.so: /tmp/local16469784102307886954/libgkl_compression11255113914393285939.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:48:16.873 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:48:16.876 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression15613099438502149686.so: /tmp/local16469784102307886954/libgkl_compression15613099438502149686.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:48:16.877 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
17:48:16.877 INFO CollectMultipleMetricsSpark - org.broadinstitute.hellbender.tools.spark.pipelines.metrics vUnavailable
17:48:16.877 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
17:48:16.877 INFO CollectMultipleMetricsSpark - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:48:16.877 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:48:16.877 INFO CollectMultipleMetricsSpark - Start Date/Time: October 27, 2025 at 5:48:16 PM UTC
17:48:16.877 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
17:48:16.877 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
17:48:16.878 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:48:16.878 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:48:16.878 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:48:16.878 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:48:16.878 INFO CollectMultipleMetricsSpark - Deflater: JdkDeflater
17:48:16.878 INFO CollectMultipleMetricsSpark - Inflater: JdkInflater
17:48:16.878 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
17:48:16.878 INFO CollectMultipleMetricsSpark - Requester pays: disabled
17:48:16.878 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
17:48:16.878 INFO CollectMultipleMetricsSpark - Initializing engine
17:48:16.878 INFO CollectMultipleMetricsSpark - Done initializing engine
17:48:16.878 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
17:48:16.880 INFO MemoryStore - Block broadcast_3325 stored as values in memory (estimated size 600.0 B, free 1909.0 MiB)
17:48:16.881 INFO MemoryStore - Block broadcast_3325_piece0 stored as bytes in memory (estimated size 211.0 B, free 1909.0 MiB)
17:48:16.881 INFO BlockManagerInfo - Added broadcast_3325_piece0 in memory on localhost:42685 (size: 211.0 B, free: 1917.3 MiB)
17:48:16.881 INFO SparkContext - Created broadcast 3325 from broadcast at CramSource.java:114
17:48:16.882 INFO MemoryStore - Block broadcast_3326 stored as values in memory (estimated size 306.3 KiB, free 1908.7 MiB)
17:48:16.888 INFO MemoryStore - Block broadcast_3326_piece0 stored as bytes in memory (estimated size 64.4 KiB, free 1908.6 MiB)
17:48:16.888 INFO BlockManagerInfo - Added broadcast_3326_piece0 in memory on localhost:42685 (size: 64.4 KiB, free: 1917.2 MiB)
17:48:16.888 INFO SparkContext - Created broadcast 3326 from newAPIHadoopFile at PathSplitSource.java:96
17:48:16.902 INFO MemoryStore - Block broadcast_3327 stored as values in memory (estimated size 600.0 B, free 1908.6 MiB)
17:48:16.902 INFO MemoryStore - Block broadcast_3327_piece0 stored as bytes in memory (estimated size 211.0 B, free 1908.6 MiB)
17:48:16.902 INFO BlockManagerInfo - Added broadcast_3327_piece0 in memory on localhost:42685 (size: 211.0 B, free: 1917.2 MiB)
17:48:16.903 INFO SparkContext - Created broadcast 3327 from broadcast at CramSource.java:114
17:48:16.903 INFO MemoryStore - Block broadcast_3328 stored as values in memory (estimated size 306.3 KiB, free 1908.3 MiB)
17:48:16.909 INFO MemoryStore - Block broadcast_3328_piece0 stored as bytes in memory (estimated size 64.4 KiB, free 1908.2 MiB)
17:48:16.909 INFO BlockManagerInfo - Added broadcast_3328_piece0 in memory on localhost:42685 (size: 64.4 KiB, free: 1917.1 MiB)
17:48:16.909 INFO SparkContext - Created broadcast 3328 from newAPIHadoopFile at PathSplitSource.java:96
17:48:16.922 INFO FileInputFormat - Total input files to process : 1
17:48:16.925 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
17:48:16.926 INFO DAGScheduler - Got job 852 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
17:48:16.926 INFO DAGScheduler - Final stage: ResultStage 2287 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
17:48:16.926 INFO DAGScheduler - Parents of final stage: List()
17:48:16.926 INFO DAGScheduler - Missing parents: List()
17:48:16.926 INFO DAGScheduler - Submitting ResultStage 2287 (MapPartitionsRDD[10093] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
17:48:16.936 INFO MemoryStore - Block broadcast_3329 stored as values in memory (estimated size 330.5 KiB, free 1907.9 MiB)
17:48:16.937 INFO MemoryStore - Block broadcast_3329_piece0 stored as bytes in memory (estimated size 143.8 KiB, free 1907.8 MiB)
17:48:16.938 INFO BlockManagerInfo - Added broadcast_3329_piece0 in memory on localhost:42685 (size: 143.8 KiB, free: 1917.0 MiB)
17:48:16.938 INFO SparkContext - Created broadcast 3329 from broadcast at DAGScheduler.scala:1580
17:48:16.938 INFO DAGScheduler - Submitting 1 missing tasks from ResultStage 2287 (MapPartitionsRDD[10093] at filter at CollectMultipleMetricsSpark.java:193) (first 15 tasks are for partitions Vector(0))
17:48:16.938 INFO TaskSchedulerImpl - Adding task set 2287.0 with 1 tasks resource profile 0
17:48:16.938 INFO TaskSetManager - Starting task 0.0 in stage 2287.0 (TID 1800) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9773 bytes)
17:48:16.939 INFO Executor - Running task 0.0 in stage 2287.0 (TID 1800)
17:48:16.962 INFO NewHadoopRDD - Input split: file:/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectInsertSizeMetrics/insert_size_metrics_test.cram:0+8617
17:48:16.966 INFO Executor - Finished task 0.0 in stage 2287.0 (TID 1800). 989 bytes result sent to driver
17:48:16.967 INFO TaskSetManager - Finished task 0.0 in stage 2287.0 (TID 1800) in 29 ms on localhost (executor driver) (1/1)
17:48:16.967 INFO TaskSchedulerImpl - Removed TaskSet 2287.0, whose tasks have all completed, from pool
17:48:16.967 INFO DAGScheduler - ResultStage 2287 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.041 s
17:48:16.967 INFO DAGScheduler - Job 852 is finished. Cancelling potential speculative or zombie tasks for this job
17:48:16.967 INFO TaskSchedulerImpl - Killing all running tasks in stage 2287: Stage finished
17:48:16.967 INFO DAGScheduler - Job 852 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.041577 s
17:48:16.967 INFO CollectMultipleMetricsSpark - Shutting down engine
[October 27, 2025 at 5:48:16 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1631584256