13:20:25.558 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 1:20:25 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 13:20:25.722 INFO HaplotypeCaller - ------------------------------------------------------------ 13:20:25.722 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.0.0 13:20:25.722 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 13:20:25.722 INFO HaplotypeCaller - Executing as yshen16@scc-mc2.scc.bu.edu on Linux v3.10.0-1160.15.2.el7.x86_64 amd64 13:20:25.722 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_172-b11 13:20:25.722 INFO HaplotypeCaller - Start Date/Time: May 7, 2021 1:20:25 PM EDT 13:20:25.722 INFO HaplotypeCaller - ------------------------------------------------------------ 13:20:25.722 INFO HaplotypeCaller - ------------------------------------------------------------ 13:20:25.723 INFO HaplotypeCaller - HTSJDK Version: 2.24.0 13:20:25.723 INFO HaplotypeCaller - Picard Version: 2.25.0 13:20:25.723 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 13:20:25.723 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 13:20:25.723 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 13:20:25.723 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 13:20:25.723 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 13:20:25.723 INFO HaplotypeCaller - Deflater: IntelDeflater 13:20:25.723 INFO HaplotypeCaller - Inflater: IntelInflater 13:20:25.723 INFO HaplotypeCaller - GCS max retries/reopens: 20 13:20:25.723 INFO HaplotypeCaller - Requester pays: disabled 13:20:25.724 INFO HaplotypeCaller - Initializing engine 13:20:26.474 INFO FeatureManager - Using codec VCFCodec to read file file:///project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.dbsnp138.vcf 13:20:26.808 INFO HaplotypeCaller - Done initializing engine 13:20:26.881 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output 13:20:26.909 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 13:20:26.913 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 13:20:26.974 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 13:20:26.974 INFO IntelPairHmm - Available threads: 1 13:20:26.974 INFO IntelPairHmm - Requested threads: 4 13:20:26.974 WARN IntelPairHmm - Using 1 available threads, but 4 were requested 13:20:26.974 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 13:20:27.058 INFO ProgressMeter - Starting traversal 13:20:27.059 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 13:20:36.764 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position chr1:50703143 and possibly subsequent; at least 10 samples must have called genotypes 13:20:37.059 INFO ProgressMeter - chr1:52121281 0.2 173740 1042440.0 13:20:47.059 INFO ProgressMeter - chr1:114035281 0.3 380120 1140360.0 13:20:57.060 INFO ProgressMeter - chr1:177470281 0.5 591570 1183140.0 13:21:07.059 INFO ProgressMeter - chr1:239603281 0.7 798680 1198020.0 13:21:17.059 INFO ProgressMeter - chr2:48411601 0.8 991230 1189476.0 13:21:27.059 INFO ProgressMeter - chr2:111513601 1.0 1201570 1201570.0 13:21:37.059 INFO ProgressMeter - chr2:173424125 1.2 1407940 1206805.7 13:21:47.059 INFO ProgressMeter - chr2:235911125 1.3 1616230 1212172.5 13:21:57.059 INFO ProgressMeter - chr3:55910112 1.5 1823540 1215693.3 13:22:07.059 INFO ProgressMeter - chr3:118928112 1.7 2033600 1220160.0 13:22:17.059 INFO ProgressMeter - chr3:179447112 1.8 2235330 1219270.9 13:22:27.059 INFO ProgressMeter - chr4:41907301 2.0 2437850 1218925.0 13:22:37.059 INFO ProgressMeter - chr4:105834301 2.2 2650940 1223510.8 13:22:47.059 INFO ProgressMeter - chr4:169809301 2.3 2864190 1227510.0 13:22:57.059 INFO ProgressMeter - chr5:42876601 2.5 3075130 1230052.0 13:23:07.059 INFO ProgressMeter - chr5:107004601 2.7 3288890 1233333.8 13:23:17.059 INFO ProgressMeter - chr5:170853601 2.8 3501720 1235901.2 13:23:27.059 INFO ProgressMeter - chr6:52264201 3.0 3711550 1237183.3 13:23:37.059 INFO ProgressMeter - chr6:115894201 3.2 3923650 1239047.4 13:23:47.059 INFO ProgressMeter - chr7:6312001 3.3 4127730 1238319.0 13:23:57.059 INFO ProgressMeter - chr7:69930001 3.5 4339790 1239940.0 13:24:07.059 INFO ProgressMeter - chr7:133866001 3.7 4552910 1241702.7 13:24:17.059 INFO ProgressMeter - chr8:38170308 3.8 4765080 1243064.3 13:24:27.059 INFO ProgressMeter - chr8:101068308 4.0 4974740 1243685.0 13:24:37.059 INFO ProgressMeter - chr9:18677401 4.2 5183900 1244136.0 13:24:47.059 INFO ProgressMeter - chr9:82154401 4.3 5395490 1245113.1 13:24:57.059 INFO ProgressMeter - chr10:6924601 4.5 5606040 1245786.7 13:25:07.059 INFO ProgressMeter - chr10:71322601 4.7 5820700 1247292.9 13:25:17.059 INFO ProgressMeter - chr11:194701 4.8 6029600 1247503.4 13:25:27.059 INFO ProgressMeter - chr11:64421701 5.0 6243690 1248738.0 13:25:37.059 INFO ProgressMeter - chr11:125204456 5.2 6446300 1247671.0 13:25:47.059 INFO ProgressMeter - chr12:52052368 5.3 6652750 1247390.6 13:25:57.059 INFO ProgressMeter - chr12:116108368 5.5 6866270 1248412.7 13:26:07.059 INFO ProgressMeter - chr13:46345801 5.7 7077980 1249055.3 13:26:17.059 INFO ProgressMeter - chr13:109642374 5.8 7288970 1249537.7 13:26:27.059 INFO ProgressMeter - chr14:58154501 6.0 7498560 1249760.0 13:26:37.059 INFO ProgressMeter - chr15:15298501 6.2 7712520 1250678.9 13:26:47.059 INFO ProgressMeter - chr15:78880501 6.3 7924460 1251230.5 13:26:57.059 INFO ProgressMeter - chr16:39408738 6.5 8132860 1251209.2 13:27:07.059 INFO ProgressMeter - chr17:11925961 6.7 8342380 1251357.0 13:27:17.059 INFO ProgressMeter - chr17:75636493 6.8 8554750 1251914.6 13:27:27.059 INFO ProgressMeter - chr18:56950801 7.0 8769990 1252855.7 13:27:37.059 INFO ProgressMeter - chr19:40687501 7.2 8983690 1253538.1 13:27:47.059 INFO ProgressMeter - chr20:44691601 7.3 9192430 1253513.2 13:27:57.059 INFO ProgressMeter - chr21:40877115 7.5 9394530 1252604.0 13:28:07.059 INFO ProgressMeter - chrX:5199601 7.7 9600700 1252265.2 13:28:17.059 INFO ProgressMeter - chrX:69450601 7.8 9814870 1252962.1 13:28:27.059 INFO ProgressMeter - chrX:133593601 8.0 10028680 1253585.0 13:28:37.059 INFO ProgressMeter - chrY:35182501 8.2 10220780 1251524.1 13:28:47.059 INFO ProgressMeter - chr7_KI270805v1_alt:86701 8.3 10402510 1248301.2 13:28:57.059 INFO ProgressMeter - chr19_KI270921v1_alt:246301 8.5 10583280 1245091.8 13:29:05.134 INFO HaplotypeCaller - 73 read(s) filtered by: MappingQualityReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 1 read(s) filtered by: NotSecondaryAlignmentReadFilter 4 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 78 total reads filtered 13:29:05.134 INFO ProgressMeter - HLA-DRB1*16:02:01:8101 8.6 10726189 1242235.9 13:29:05.134 INFO ProgressMeter - Traversal complete. Processed 10726189 total regions in 8.6 minutes. 13:29:05.212 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 3.10165E-4 13:29:05.212 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 7.884070000000001E-4 13:29:05.212 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.01 sec 13:29:05.212 INFO HaplotypeCaller - Shutting down engine [May 7, 2021 1:29:05 PM EDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 8.66 minutes. Runtime.totalMemory()=3416260608