[March 28, 2025 at 10:46:05 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[March 28, 2025 at 10:46:05 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[March 28, 2025 at 10:46:06 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
22:46:06.272 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
22:46:06.272 INFO CollectMultipleMetricsSpark - org.broadinstitute.hellbender.tools.spark.pipelines.metrics vUnavailable
22:46:06.272 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
22:46:06.272 INFO CollectMultipleMetricsSpark - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:46:06.272 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:46:06.272 INFO CollectMultipleMetricsSpark - Start Date/Time: March 28, 2025 at 10:46:06 PM UTC
22:46:06.273 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
22:46:06.273 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
22:46:06.273 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:46:06.273 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:46:06.273 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:46:06.273 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:46:06.273 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
22:46:06.273 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
22:46:06.273 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
22:46:06.273 INFO CollectMultipleMetricsSpark - Requester pays: disabled
22:46:06.273 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
22:46:06.273 INFO CollectMultipleMetricsSpark - Initializing engine
22:46:06.273 INFO CollectMultipleMetricsSpark - Done initializing engine
22:46:06.273 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
WARNING 2025-03-28 22:46:06 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-03-28 22:46:06 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
22:46:06.274 INFO MemoryStore - Block broadcast_3374 stored as values in memory (estimated size 37.8 KiB, free 1916.4 MiB)
22:46:06.275 INFO MemoryStore - Block broadcast_3374_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1916.4 MiB)
22:46:06.275 INFO BlockManagerInfo - Added broadcast_3374_piece0 in memory on localhost:46727 (size: 8.4 KiB, free: 1919.1 MiB)
22:46:06.275 INFO SparkContext - Created broadcast 3374 from broadcast at SamSource.java:78
22:46:06.276 INFO MemoryStore - Block broadcast_3375 stored as values in memory (estimated size 333.6 KiB, free 1916.1 MiB)
22:46:06.283 INFO MemoryStore - Block broadcast_3375_piece0 stored as bytes in memory (estimated size 71.2 KiB, free 1916.0 MiB)
22:46:06.283 INFO BlockManagerInfo - Added broadcast_3375_piece0 in memory on localhost:46727 (size: 71.2 KiB, free: 1919.0 MiB)
22:46:06.283 INFO SparkContext - Created broadcast 3375 from newAPIHadoopFile at SamSource.java:108
WARNING 2025-03-28 22:46:06 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
WARNING 2025-03-28 22:46:06 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format.
22:46:06.285 INFO MemoryStore - Block broadcast_3376 stored as values in memory (estimated size 37.8 KiB, free 1916.0 MiB)
22:46:06.286 INFO MemoryStore - Block broadcast_3376_piece0 stored as bytes in memory (estimated size 8.4 KiB, free 1916.0 MiB)
22:46:06.286 INFO BlockManagerInfo - Added broadcast_3376_piece0 in memory on localhost:46727 (size: 8.4 KiB, free: 1919.0 MiB)
22:46:06.286 INFO SparkContext - Created broadcast 3376 from broadcast at SamSource.java:78
22:46:06.287 INFO MemoryStore - Block broadcast_3377 stored as values in memory (estimated size 333.6 KiB, free 1915.6 MiB)
22:46:06.299 INFO MemoryStore - Block broadcast_3377_piece0 stored as bytes in memory (estimated size 71.2 KiB, free 1915.6 MiB)
22:46:06.299 INFO BlockManagerInfo - Added broadcast_3377_piece0 in memory on localhost:46727 (size: 71.2 KiB, free: 1919.0 MiB)
22:46:06.299 INFO SparkContext - Created broadcast 3377 from newAPIHadoopFile at SamSource.java:108
22:46:06.302 INFO FileInputFormat - Total input files to process : 1
22:46:06.306 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
22:46:06.307 INFO DAGScheduler - Got job 882 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
22:46:06.307 INFO DAGScheduler - Final stage: ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
22:46:06.307 INFO DAGScheduler - Parents of final stage: List()
22:46:06.307 INFO DAGScheduler - Missing parents: List()
22:46:06.307 INFO DAGScheduler - Submitting ResultStage 2471 (MapPartitionsRDD[10156] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
22:46:06.307 INFO MemoryStore - Block broadcast_3378 stored as values in memory (estimated size 34.8 KiB, free 1915.5 MiB)
22:46:06.308 INFO MemoryStore - Block broadcast_3378_piece0 stored as bytes in memory (estimated size 14.6 KiB, free 1915.5 MiB)
22:46:06.308 INFO BlockManagerInfo - Added broadcast_3378_piece0 in memory on localhost:46727 (size: 14.6 KiB, free: 1918.9 MiB)
22:46:06.308 INFO SparkContext - Created broadcast 3378 from broadcast at DAGScheduler.scala:1580
22:46:06.308 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))
22:46:06.308 INFO TaskSchedulerImpl - Adding task set 2471.0 with 1 tasks resource profile 0
22:46:06.308 INFO TaskSetManager - Starting task 0.0 in stage 2471.0 (TID 1890) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9772 bytes)
22:46:06.308 INFO Executor - Running task 0.0 in stage 2471.0 (TID 1890)
22:46:06.309 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
22:46:06.311 INFO Executor - Finished task 0.0 in stage 2471.0 (TID 1890). 946 bytes result sent to driver
22:46:06.311 INFO TaskSetManager - Finished task 0.0 in stage 2471.0 (TID 1890) in 3 ms on localhost (executor driver) (1/1)
22:46:06.311 INFO TaskSchedulerImpl - Removed TaskSet 2471.0, whose tasks have all completed, from pool
22:46:06.311 INFO DAGScheduler - ResultStage 2471 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.004 s
22:46:06.311 INFO DAGScheduler - Job 882 is finished. Cancelling potential speculative or zombie tasks for this job
22:46:06.311 INFO TaskSchedulerImpl - Killing all running tasks in stage 2471: Stage finished
22:46:06.311 INFO DAGScheduler - Job 882 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.004716 s
22:46:06.311 INFO CollectMultipleMetricsSpark - Shutting down engine
[March 28, 2025 at 10:46:06 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
22:46:06.316 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
22:46:06.316 INFO CollectMultipleMetricsSpark - org.broadinstitute.hellbender.tools.spark.pipelines.metrics vUnavailable
22:46:06.316 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
22:46:06.316 INFO CollectMultipleMetricsSpark - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:46:06.316 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:46:06.316 INFO CollectMultipleMetricsSpark - Start Date/Time: March 28, 2025 at 10:46:06 PM UTC
22:46:06.316 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
22:46:06.316 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
22:46:06.316 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:46:06.316 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:46:06.316 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:46:06.316 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:46:06.316 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
22:46:06.316 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
22:46:06.316 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
22:46:06.316 INFO CollectMultipleMetricsSpark - Requester pays: disabled
22:46:06.317 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
22:46:06.317 INFO CollectMultipleMetricsSpark - Initializing engine
22:46:06.317 INFO CollectMultipleMetricsSpark - Done initializing engine
22:46:06.317 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
22:46:06.319 INFO MemoryStore - Block broadcast_3379 stored as values in memory (estimated size 333.6 KiB, free 1915.2 MiB)
22:46:06.326 INFO MemoryStore - Block broadcast_3379_piece0 stored as bytes in memory (estimated size 71.2 KiB, free 1915.1 MiB)
22:46:06.326 INFO BlockManagerInfo - Added broadcast_3379_piece0 in memory on localhost:46727 (size: 71.2 KiB, free: 1918.9 MiB)
22:46:06.326 INFO SparkContext - Created broadcast 3379 from newAPIHadoopFile at PathSplitSource.java:96
22:46:06.347 INFO MemoryStore - Block broadcast_3380 stored as values in memory (estimated size 333.6 KiB, free 1914.8 MiB)
22:46:06.354 INFO MemoryStore - Block broadcast_3380_piece0 stored as bytes in memory (estimated size 71.2 KiB, free 1914.7 MiB)
22:46:06.354 INFO BlockManagerInfo - Added broadcast_3380_piece0 in memory on localhost:46727 (size: 71.2 KiB, free: 1918.8 MiB)
22:46:06.354 INFO SparkContext - Created broadcast 3380 from newAPIHadoopFile at PathSplitSource.java:96
22:46:06.375 INFO FileInputFormat - Total input files to process : 1
22:46:06.379 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
22:46:06.379 INFO DAGScheduler - Got job 883 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
22:46:06.379 INFO DAGScheduler - Final stage: ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
22:46:06.379 INFO DAGScheduler - Parents of final stage: List()
22:46:06.379 INFO DAGScheduler - Missing parents: List()
22:46:06.379 INFO DAGScheduler - Submitting ResultStage 2472 (MapPartitionsRDD[10169] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
22:46:06.397 INFO MemoryStore - Block broadcast_3381 stored as values in memory (estimated size 522.3 KiB, free 1914.2 MiB)
22:46:06.400 INFO MemoryStore - Block broadcast_3381_piece0 stored as bytes in memory (estimated size 228.9 KiB, free 1914.0 MiB)
22:46:06.400 INFO BlockManagerInfo - Added broadcast_3381_piece0 in memory on localhost:46727 (size: 228.9 KiB, free: 1918.6 MiB)
22:46:06.400 INFO SparkContext - Created broadcast 3381 from broadcast at DAGScheduler.scala:1580
22:46:06.400 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))
22:46:06.400 INFO TaskSchedulerImpl - Adding task set 2472.0 with 1 tasks resource profile 0
22:46:06.400 INFO TaskSetManager - Starting task 0.0 in stage 2472.0 (TID 1891) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9772 bytes)
22:46:06.401 INFO Executor - Running task 0.0 in stage 2472.0 (TID 1891)
22:46:06.432 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
22:46:06.436 INFO Executor - Finished task 0.0 in stage 2472.0 (TID 1891). 989 bytes result sent to driver
22:46:06.436 INFO TaskSetManager - Finished task 0.0 in stage 2472.0 (TID 1891) in 36 ms on localhost (executor driver) (1/1)
22:46:06.436 INFO TaskSchedulerImpl - Removed TaskSet 2472.0, whose tasks have all completed, from pool
22:46:06.436 INFO DAGScheduler - ResultStage 2472 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.057 s
22:46:06.436 INFO DAGScheduler - Job 883 is finished. Cancelling potential speculative or zombie tasks for this job
22:46:06.436 INFO TaskSchedulerImpl - Killing all running tasks in stage 2472: Stage finished
22:46:06.436 INFO DAGScheduler - Job 883 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.057449 s
22:46:06.436 INFO CollectMultipleMetricsSpark - Shutting down engine
[March 28, 2025 at 10:46:06 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
22:46:06.440 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
22:46:06.441 INFO CollectMultipleMetricsSpark - org.broadinstitute.hellbender.tools.spark.pipelines.metrics vUnavailable
22:46:06.441 INFO CollectMultipleMetricsSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
22:46:06.441 INFO CollectMultipleMetricsSpark - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:46:06.441 INFO CollectMultipleMetricsSpark - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:46:06.441 INFO CollectMultipleMetricsSpark - Start Date/Time: March 28, 2025 at 10:46:06 PM UTC
22:46:06.441 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
22:46:06.441 INFO CollectMultipleMetricsSpark - ------------------------------------------------------------
22:46:06.441 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:46:06.441 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:46:06.441 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:46:06.441 INFO CollectMultipleMetricsSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:46:06.441 INFO CollectMultipleMetricsSpark - Deflater: IntelDeflater
22:46:06.441 INFO CollectMultipleMetricsSpark - Inflater: IntelInflater
22:46:06.441 INFO CollectMultipleMetricsSpark - GCS max retries/reopens: 20
22:46:06.441 INFO CollectMultipleMetricsSpark - Requester pays: disabled
22:46:06.441 WARN CollectMultipleMetricsSpark -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: CollectMultipleMetricsSpark is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
22:46:06.441 INFO CollectMultipleMetricsSpark - Initializing engine
22:46:06.441 INFO CollectMultipleMetricsSpark - Done initializing engine
22:46:06.441 INFO CollectMultipleMetricsSpark - Spark verbosity set to INFO (see --spark-verbosity argument)
22:46:06.443 INFO MemoryStore - Block broadcast_3382 stored as values in memory (estimated size 600.0 B, free 1914.0 MiB)
22:46:06.443 INFO MemoryStore - Block broadcast_3382_piece0 stored as bytes in memory (estimated size 211.0 B, free 1914.0 MiB)
22:46:06.443 INFO BlockManagerInfo - Added broadcast_3382_piece0 in memory on localhost:46727 (size: 211.0 B, free: 1918.6 MiB)
22:46:06.444 INFO SparkContext - Created broadcast 3382 from broadcast at CramSource.java:114
22:46:06.444 INFO MemoryStore - Block broadcast_3383 stored as values in memory (estimated size 333.6 KiB, free 1913.7 MiB)
22:46:06.451 INFO MemoryStore - Block broadcast_3383_piece0 stored as bytes in memory (estimated size 71.2 KiB, free 1913.6 MiB)
22:46:06.451 INFO BlockManagerInfo - Added broadcast_3383_piece0 in memory on localhost:46727 (size: 71.2 KiB, free: 1918.5 MiB)
22:46:06.452 INFO SparkContext - Created broadcast 3383 from newAPIHadoopFile at PathSplitSource.java:96
22:46:06.467 INFO MemoryStore - Block broadcast_3384 stored as values in memory (estimated size 600.0 B, free 1913.6 MiB)
22:46:06.467 INFO MemoryStore - Block broadcast_3384_piece0 stored as bytes in memory (estimated size 211.0 B, free 1913.6 MiB)
22:46:06.467 INFO BlockManagerInfo - Added broadcast_3384_piece0 in memory on localhost:46727 (size: 211.0 B, free: 1918.5 MiB)
22:46:06.467 INFO SparkContext - Created broadcast 3384 from broadcast at CramSource.java:114
22:46:06.468 INFO MemoryStore - Block broadcast_3385 stored as values in memory (estimated size 333.6 KiB, free 1913.3 MiB)
22:46:06.473 INFO BlockManagerInfo - Removed broadcast_3378_piece0 on localhost:46727 in memory (size: 14.6 KiB, free: 1918.5 MiB)
22:46:06.473 INFO BlockManagerInfo - Removed broadcast_3372_piece0 on localhost:46727 in memory (size: 162.6 KiB, free: 1918.7 MiB)
22:46:06.474 INFO BlockManagerInfo - Removed broadcast_3374_piece0 on localhost:46727 in memory (size: 8.4 KiB, free: 1918.7 MiB)
22:46:06.474 INFO BlockManagerInfo - Removed broadcast_3373_piece0 on localhost:46727 in memory (size: 158.6 KiB, free: 1918.8 MiB)
22:46:06.474 INFO BlockManagerInfo - Removed broadcast_3381_piece0 on localhost:46727 in memory (size: 228.9 KiB, free: 1919.1 MiB)
22:46:06.474 INFO BlockManagerInfo - Removed broadcast_3379_piece0 on localhost:46727 in memory (size: 71.2 KiB, free: 1919.1 MiB)
22:46:06.475 INFO BlockManagerInfo - Removed broadcast_3376_piece0 on localhost:46727 in memory (size: 8.4 KiB, free: 1919.1 MiB)
22:46:06.475 INFO BlockManagerInfo - Removed broadcast_3380_piece0 on localhost:46727 in memory (size: 71.2 KiB, free: 1919.2 MiB)
22:46:06.475 INFO BlockManagerInfo - Removed broadcast_3367_piece0 on localhost:46727 in memory (size: 211.0 B, free: 1919.2 MiB)
22:46:06.475 INFO BlockManagerInfo - Removed broadcast_3370_piece0 on localhost:46727 in memory (size: 71.2 KiB, free: 1919.3 MiB)
22:46:06.476 INFO BlockManagerInfo - Removed broadcast_3368_piece0 on localhost:46727 in memory (size: 71.2 KiB, free: 1919.4 MiB)
22:46:06.476 INFO BlockManagerInfo - Removed broadcast_3382_piece0 on localhost:46727 in memory (size: 211.0 B, free: 1919.4 MiB)
22:46:06.476 INFO BlockManagerInfo - Removed broadcast_3375_piece0 on localhost:46727 in memory (size: 71.2 KiB, free: 1919.4 MiB)
22:46:06.476 INFO BlockManagerInfo - Removed broadcast_3371_piece0 on localhost:46727 in memory (size: 159.9 KiB, free: 1919.6 MiB)
22:46:06.477 INFO BlockManagerInfo - Removed broadcast_3383_piece0 on localhost:46727 in memory (size: 71.2 KiB, free: 1919.6 MiB)
22:46:06.477 INFO BlockManagerInfo - Removed broadcast_3377_piece0 on localhost:46727 in memory (size: 71.2 KiB, free: 1919.7 MiB)
22:46:06.477 INFO BlockManagerInfo - Removed broadcast_3369_piece0 on localhost:46727 in memory (size: 211.0 B, free: 1919.7 MiB)
22:46:06.477 INFO BlockManager - Removing RDD 10144
22:46:06.481 INFO MemoryStore - Block broadcast_3385_piece0 stored as bytes in memory (estimated size 71.2 KiB, free 1918.4 MiB)
22:46:06.481 INFO BlockManagerInfo - Added broadcast_3385_piece0 in memory on localhost:46727 (size: 71.2 KiB, free: 1919.7 MiB)
22:46:06.481 INFO SparkContext - Created broadcast 3385 from newAPIHadoopFile at PathSplitSource.java:96
22:46:06.496 INFO FileInputFormat - Total input files to process : 1
22:46:06.499 INFO SparkContext - Starting job: count at CollectMultipleMetricsSparkIntegrationTest.java:130
22:46:06.500 INFO DAGScheduler - Got job 884 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) with 1 output partitions
22:46:06.500 INFO DAGScheduler - Final stage: ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130)
22:46:06.500 INFO DAGScheduler - Parents of final stage: List()
22:46:06.500 INFO DAGScheduler - Missing parents: List()
22:46:06.500 INFO DAGScheduler - Submitting ResultStage 2473 (MapPartitionsRDD[10180] at filter at CollectMultipleMetricsSpark.java:193), which has no missing parents
22:46:06.512 INFO MemoryStore - Block broadcast_3386 stored as values in memory (estimated size 360.1 KiB, free 1918.1 MiB)
22:46:06.514 INFO MemoryStore - Block broadcast_3386_piece0 stored as bytes in memory (estimated size 157.9 KiB, free 1917.9 MiB)
22:46:06.514 INFO BlockManagerInfo - Added broadcast_3386_piece0 in memory on localhost:46727 (size: 157.9 KiB, free: 1919.5 MiB)
22:46:06.514 INFO SparkContext - Created broadcast 3386 from broadcast at DAGScheduler.scala:1580
22:46:06.514 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))
22:46:06.514 INFO TaskSchedulerImpl - Adding task set 2473.0 with 1 tasks resource profile 0
22:46:06.515 INFO TaskSetManager - Starting task 0.0 in stage 2473.0 (TID 1892) (localhost, executor driver, partition 0, PROCESS_LOCAL, 9773 bytes)
22:46:06.515 INFO Executor - Running task 0.0 in stage 2473.0 (TID 1892)
22:46:06.539 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
22:46:06.543 INFO Executor - Finished task 0.0 in stage 2473.0 (TID 1892). 989 bytes result sent to driver
22:46:06.544 INFO TaskSetManager - Finished task 0.0 in stage 2473.0 (TID 1892) in 29 ms on localhost (executor driver) (1/1)
22:46:06.544 INFO TaskSchedulerImpl - Removed TaskSet 2473.0, whose tasks have all completed, from pool
22:46:06.544 INFO DAGScheduler - ResultStage 2473 (count at CollectMultipleMetricsSparkIntegrationTest.java:130) finished in 0.044 s
22:46:06.544 INFO DAGScheduler - Job 884 is finished. Cancelling potential speculative or zombie tasks for this job
22:46:06.544 INFO TaskSchedulerImpl - Killing all running tasks in stage 2473: Stage finished
22:46:06.544 INFO DAGScheduler - Job 884 finished: count at CollectMultipleMetricsSparkIntegrationTest.java:130, took 0.044559 s
22:46:06.544 INFO CollectMultipleMetricsSpark - Shutting down engine
[March 28, 2025 at 10:46:06 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000