13:19:11.292 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 1:19:11 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:19:11.443 INFO BaseRecalibrator - ------------------------------------------------------------ 13:19:11.444 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.0.0 13:19:11.444 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:19:11.444 INFO BaseRecalibrator - Executing as yshen16@scc-pi1.scc.bu.edu on Linux v3.10.0-1160.15.2.el7.x86_64 amd64 13:19:11.444 INFO BaseRecalibrator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_172-b11 13:19:11.444 INFO BaseRecalibrator - Start Date/Time: May 7, 2021 1:19:11 PM EDT 13:19:11.444 INFO BaseRecalibrator - ------------------------------------------------------------ 13:19:11.444 INFO BaseRecalibrator - ------------------------------------------------------------ 13:19:11.445 INFO BaseRecalibrator - HTSJDK Version: 2.24.0 13:19:11.445 INFO BaseRecalibrator - Picard Version: 2.25.0 13:19:11.445 INFO BaseRecalibrator - Built for Spark Version: 2.4.5 13:19:11.445 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:19:11.445 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:19:11.445 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:19:11.445 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:19:11.445 INFO BaseRecalibrator - Deflater: IntelDeflater 13:19:11.445 INFO BaseRecalibrator - Inflater: IntelInflater 13:19:11.445 INFO BaseRecalibrator - GCS max retries/reopens: 20 13:19:11.445 INFO BaseRecalibrator - Requester pays: disabled 13:19:11.445 INFO BaseRecalibrator - Initializing engine 13:19:12.392 INFO FeatureManager - Using codec VCFCodec to read file file:///project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.dbsnp138.vcf 13:19:12.597 INFO FeatureManager - Using codec VCFCodec to read file file:///project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.known_indels.vcf.gz 13:19:12.860 INFO BaseRecalibrator - Done initializing engine 13:19:12.864 INFO BaseRecalibrationEngine - The covariates being used here: 13:19:12.864 INFO BaseRecalibrationEngine - ReadGroupCovariate 13:19:12.864 INFO BaseRecalibrationEngine - QualityScoreCovariate 13:19:12.864 INFO BaseRecalibrationEngine - ContextCovariate 13:19:12.864 INFO BaseRecalibrationEngine - CycleCovariate 13:19:12.939 INFO ProgressMeter - Starting traversal 13:19:12.940 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute 13:19:16.950 INFO BaseRecalibrator - 33 read(s) filtered by: MappingQualityNotZeroReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 1 read(s) filtered by: NotSecondaryAlignmentReadFilter 2 read(s) filtered by: NotDuplicateReadFilter 0 read(s) filtered by: PassesVendorQualityCheckReadFilter 0 read(s) filtered by: WellformedReadFilter 36 total reads filtered 13:19:16.951 INFO ProgressMeter - unmapped 0.1 367 5491.3 13:19:16.951 INFO ProgressMeter - Traversal complete. Processed 367 total reads in 0.1 minutes. 13:19:17.023 INFO BaseRecalibrator - Calculating quantized quality scores... 13:19:17.033 INFO BaseRecalibrator - Writing recalibration report... 13:19:17.694 INFO BaseRecalibrator - ...done! 13:19:17.695 INFO BaseRecalibrator - BaseRecalibrator was able to recalibrate 367 reads 13:19:17.695 INFO BaseRecalibrator - Shutting down engine [May 7, 2021 1:19:17 PM EDT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=2371878912