13:20:19.148 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/pkg.7/gatk/4.2.0.0/install/bin/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
May 07, 2021 1:20:19 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
13:20:19.321 INFO  ApplyBQSR - ------------------------------------------------------------
13:20:19.322 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.2.0.0
13:20:19.322 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
13:20:19.322 INFO  ApplyBQSR - Executing as yshen16@scc-mc2.scc.bu.edu on Linux v3.10.0-1160.15.2.el7.x86_64 amd64
13:20:19.322 INFO  ApplyBQSR - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_172-b11
13:20:19.322 INFO  ApplyBQSR - Start Date/Time: May 7, 2021 1:20:19 PM EDT
13:20:19.322 INFO  ApplyBQSR - ------------------------------------------------------------
13:20:19.322 INFO  ApplyBQSR - ------------------------------------------------------------
13:20:19.323 INFO  ApplyBQSR - HTSJDK Version: 2.24.0
13:20:19.323 INFO  ApplyBQSR - Picard Version: 2.25.0
13:20:19.323 INFO  ApplyBQSR - Built for Spark Version: 2.4.5
13:20:19.323 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:20:19.323 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:20:19.323 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:20:19.323 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:20:19.323 INFO  ApplyBQSR - Deflater: IntelDeflater
13:20:19.323 INFO  ApplyBQSR - Inflater: IntelInflater
13:20:19.323 INFO  ApplyBQSR - GCS max retries/reopens: 20
13:20:19.324 INFO  ApplyBQSR - Requester pays: disabled
13:20:19.324 INFO  ApplyBQSR - Initializing engine
13:20:20.035 INFO  ApplyBQSR - Done initializing engine
13:20:20.125 INFO  ProgressMeter - Starting traversal
13:20:20.126 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
13:20:21.070 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

13:20:21.070 INFO  ProgressMeter -             unmapped              0.0                   803          51038.1
13:20:21.070 INFO  ProgressMeter - Traversal complete. Processed 803 total reads in 0.0 minutes.
13:20:21.298 INFO  ApplyBQSR - Shutting down engine
[May 7, 2021 1:20:21 PM EDT] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=2764570624