13:19:26.276 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 1:19:26 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:19:26.422 INFO HaplotypeCaller - ------------------------------------------------------------ 13:19:26.423 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.0.0 13:19:26.423 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:19:26.423 INFO HaplotypeCaller - Executing as yshen16@scc-pi1.scc.bu.edu on Linux v3.10.0-1160.15.2.el7.x86_64 amd64 13:19:26.423 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_172-b11 13:19:26.423 INFO HaplotypeCaller - Start Date/Time: May 7, 2021 1:19:26 PM EDT 13:19:26.423 INFO HaplotypeCaller - ------------------------------------------------------------ 13:19:26.423 INFO HaplotypeCaller - ------------------------------------------------------------ 13:19:26.424 INFO HaplotypeCaller - HTSJDK Version: 2.24.0 13:19:26.424 INFO HaplotypeCaller - Picard Version: 2.25.0 13:19:26.424 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:19:26.424 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:19:26.424 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:19:26.424 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:19:26.424 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:19:26.424 INFO HaplotypeCaller - Deflater: IntelDeflater 13:19:26.424 INFO HaplotypeCaller - Inflater: IntelInflater 13:19:26.424 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:19:26.425 INFO HaplotypeCaller - Requester pays: disabled 13:19:26.425 INFO HaplotypeCaller - Initializing engine 13:19:27.226 INFO FeatureManager - Using codec VCFCodec to read file file:///project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.dbsnp138.vcf 13:19:27.580 INFO HaplotypeCaller - Done initializing engine 13:19:27.718 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output 13:19:27.756 INFO NativeLibraryLoader - Loading libgkl_utils.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_utils.so 13:19:27.801 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.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_pairhmm_omp.so 13:19:27.912 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:19:27.912 INFO IntelPairHmm - Available threads: 1 13:19:27.912 INFO IntelPairHmm - Requested threads: 4 13:19:27.913 WARN IntelPairHmm - Using 1 available threads, but 4 were requested 13:19:27.913 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:19:27.964 INFO ProgressMeter - Starting traversal 13:19:27.964 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:19:37.966 INFO ProgressMeter - chr1:53072281 0.2 176910 1061460.0 13:19:47.964 INFO ProgressMeter - chr1:120005281 0.3 400020 1200060.0 13:19:57.964 INFO ProgressMeter - chr1:187364281 0.5 624550 1249100.0 13:20:07.964 INFO ProgressMeter - chr1:246332281 0.7 821110 1231665.0 13:20:17.964 INFO ProgressMeter - chr2:59154601 0.8 1027040 1232448.0 13:20:27.964 INFO ProgressMeter - chr2:126510601 1.0 1251560 1251560.0 13:20:37.964 INFO ProgressMeter - chr2:193401601 1.2 1474530 1263882.9 13:20:47.964 INFO ProgressMeter - chr3:17375712 1.3 1695090 1271317.5 13:20:57.964 INFO ProgressMeter - chr3:85988712 1.5 1923800 1282533.3 13:21:07.964 INFO ProgressMeter - chr3:153593712 1.7 2149150 1289490.0 13:21:17.964 INFO ProgressMeter - chr4:7422901 1.8 2322900 1267036.4 13:21:27.964 INFO ProgressMeter - chr4:72963901 2.0 2541370 1270685.0 13:21:37.964 INFO ProgressMeter - chr4:140958901 2.2 2768020 1277547.7 13:21:47.964 INFO ProgressMeter - chr5:16753201 2.3 2988050 1280592.9 13:21:57.964 INFO ProgressMeter - chr5:80434201 2.5 3200320 1280128.0 13:22:07.964 INFO ProgressMeter - chr5:146899201 2.7 3421870 1283201.3 13:22:17.964 INFO ProgressMeter - chr6:27814801 2.8 3630050 1281194.1 13:22:27.964 INFO ProgressMeter - chr6:94600801 3.0 3852670 1284223.3 13:22:37.964 INFO ProgressMeter - chr6:160021801 3.2 4070740 1285496.8 13:22:47.964 INFO ProgressMeter - chr7:54495601 3.3 4288340 1286502.0 13:22:57.964 INFO ProgressMeter - chr7:121011601 3.5 4510060 1288588.6 13:23:07.964 INFO ProgressMeter - chr8:26293908 3.7 4725490 1288770.0 13:23:17.964 INFO ProgressMeter - chr8:94738908 3.8 4953640 1292253.9 13:23:27.964 INFO ProgressMeter - chr9:16776001 4.0 5177560 1294390.0 13:23:37.964 INFO ProgressMeter - chr9:83844001 4.2 5401120 1296268.8 13:23:47.964 INFO ProgressMeter - chr10:12028201 4.3 5623050 1297626.9 13:23:57.964 INFO ProgressMeter - chr10:80122201 4.5 5850030 1300006.7 13:24:07.964 INFO ProgressMeter - chr11:12363301 4.7 6070160 1300748.6 13:24:17.964 INFO ProgressMeter - chr11:79752301 4.8 6294790 1302370.3 13:24:27.964 INFO ProgressMeter - chr12:7740601 5.0 6505040 1301008.0 13:24:37.964 INFO ProgressMeter - chr12:76047268 5.2 6732730 1303109.0 13:24:47.964 INFO ProgressMeter - chr13:9674701 5.3 6955740 1304201.3 13:24:57.964 INFO ProgressMeter - chr13:77375701 5.5 7181410 1305710.9 13:25:07.964 INFO ProgressMeter - chr14:29502701 5.7 7403050 1306420.6 13:25:17.964 INFO ProgressMeter - chr14:97824701 5.8 7630790 1308135.4 13:25:27.964 INFO ProgressMeter - chr15:58067701 6.0 7855080 1309180.0 13:25:37.964 INFO ProgressMeter - chr16:22430401 6.2 8076260 1309663.8 13:25:47.964 INFO ProgressMeter - chr16:87439938 6.3 8292960 1309414.7 13:25:57.964 INFO ProgressMeter - chr17:64904401 6.5 8518970 1310610.8 13:26:07.964 INFO ProgressMeter - chr18:48669301 6.7 8742380 1311357.0 13:26:17.964 INFO ProgressMeter - chr19:36030001 6.8 8968160 1312413.7 13:26:27.964 INFO ProgressMeter - chr20:43817101 7.0 9189510 1312787.1 13:26:37.964 INFO ProgressMeter - chr21:40665615 7.2 9393820 1310765.6 13:26:47.964 INFO ProgressMeter - chrX:10271101 7.3 9617600 1311490.9 13:26:57.964 INFO ProgressMeter - chrX:78821101 7.5 9846100 1312813.3 13:27:07.964 INFO ProgressMeter - chrX:141917101 7.7 10056420 1311707.0 13:27:17.964 INFO ProgressMeter - chrY:46557001 7.8 10258690 1309620.0 13:27:27.964 INFO ProgressMeter - chr16_KI270854v1_alt:42901 8.0 10456500 1307062.5 13:27:37.964 INFO ProgressMeter - chr6_GL000254v2_alt:4584301 8.2 10647500 1303775.5 13:27:42.120 INFO HaplotypeCaller - 38 read(s) filtered by: MappingQualityReadFilter 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: NonZeroReferenceLengthAlignmentReadFilter 0 read(s) filtered by: GoodCigarReadFilter 0 read(s) filtered by: WellformedReadFilter 41 total reads filtered 13:27:42.120 INFO ProgressMeter - HLA-DRB1*16:02:01:9601 8.2 10726184 1302364.1 13:27:42.120 INFO ProgressMeter - Traversal complete. Processed 10726184 total regions in 8.2 minutes. 13:27:42.140 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 2.3774600000000002E-4 13:27:42.140 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 7.2212E-4 13:27:42.141 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec 13:27:42.141 INFO HaplotypeCaller - Shutting down engine [May 7, 2021 1:27:42 PM EDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 8.26 minutes. Runtime.totalMemory()=1750073344