Using GATK jar /usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx10g -Xms1000m -jar /usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar HaplotypeCaller -R Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa -I SRR7062654.md.recal.bam -O SRR7062654.md.recal.g.vcf -ERC GVCF 11:13:48.798 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 11:13:48.858 INFO HaplotypeCaller - ------------------------------------------------------------ 11:13:48.861 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.4.0.0 11:13:48.861 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 11:13:48.861 INFO HaplotypeCaller - Executing as formation@n002 on Linux v4.18.0-372.32.1.el8_6.x86_64 amd64 11:13:48.861 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.6+9-LTS-190 11:13:48.862 INFO HaplotypeCaller - Start Date/Time: November 7, 2023 at 11:13:48 AM CET 11:13:48.862 INFO HaplotypeCaller - ------------------------------------------------------------ 11:13:48.862 INFO HaplotypeCaller - ------------------------------------------------------------ 11:13:48.862 INFO HaplotypeCaller - HTSJDK Version: 3.0.5 11:13:48.863 INFO HaplotypeCaller - Picard Version: 3.0.0 11:13:48.863 INFO HaplotypeCaller - Built for Spark Version: 3.3.1 11:13:48.863 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 11:13:48.864 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 11:13:48.864 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 11:13:48.865 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 11:13:48.866 INFO HaplotypeCaller - Deflater: IntelDeflater 11:13:48.866 INFO HaplotypeCaller - Inflater: IntelInflater 11:13:48.866 INFO HaplotypeCaller - GCS max retries/reopens: 20 11:13:48.866 INFO HaplotypeCaller - Requester pays: disabled 11:13:48.866 INFO HaplotypeCaller - Initializing engine 11:13:49.069 INFO HaplotypeCaller - Done initializing engine 11:13:49.084 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 11:13:49.093 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to -0.0 for reference-model confidence output 11:13:49.093 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 11:13:49.120 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 11:13:49.122 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 11:13:49.151 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 11:13:49.151 INFO IntelPairHmm - Available threads: 1 11:13:49.152 INFO IntelPairHmm - Requested threads: 4 11:13:49.152 WARN IntelPairHmm - Using 1 available threads, but 4 were requested 11:13:49.152 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 11:13:49.227 INFO ProgressMeter - Starting traversal 11:13:49.229 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 11:13:49.956 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 25:71 and possibly subsequent; at least 10 samples must have called genotypes 11:13:50.757 WARN DepthPerSampleHC - Annotation will not be calculated at position 25:2332 and possibly subsequent; genotype for sample SRR7062654 is not called 11:13:50.757 WARN StrandBiasBySample - Annotation will not be calculated at position 25:2332 and possibly subsequent; genotype for sample SRR7062654 is not called 11:13:59.907 INFO ProgressMeter - 25:14135 0.2 120 674.3 11:14:09.973 INFO ProgressMeter - 25:55021 0.3 390 1128.0 11:14:20.041 INFO ProgressMeter - 25:112910 0.5 790 1538.4 11:14:30.059 INFO ProgressMeter - 25:170459 0.7 1240 1822.2 11:14:40.513 INFO ProgressMeter - 25:270090 0.9 1900 2222.9 11:14:50.520 INFO ProgressMeter - 25:875520 1.0 4230 4140.9 11:15:00.578 INFO ProgressMeter - 25:956160 1.2 4850 4078.5 11:15:10.670 INFO ProgressMeter - 25:1009367 1.4 5320 3919.4 11:15:20.820 INFO ProgressMeter - 25:1035306 1.5 5540 3629.2 11:15:31.218 INFO ProgressMeter - 25:1065728 1.7 5790 3406.3 11:15:41.428 INFO ProgressMeter - 25:1169348 1.9 6550 3502.7 11:15:51.455 INFO ProgressMeter - 25:1330067 2.0 7670 3765.2 11:16:01.460 INFO ProgressMeter - 25:1520771 2.2 9020 4092.8 11:16:11.885 INFO ProgressMeter - 25:1724839 2.4 10410 4378.4 11:16:21.888 INFO ProgressMeter - 25:1804670 2.5 10990 4319.4 11:16:31.901 INFO ProgressMeter - 25:1906199 2.7 11710 4319.1 11:16:42.330 INFO ProgressMeter - 25:1964416 2.9 12170 4218.3 11:16:52.514 INFO ProgressMeter - 25:2004039 3.1 12500 4092.0 11:17:02.516 INFO ProgressMeter - 25:2048875 3.2 12870 3995.1 11:17:12.544 INFO ProgressMeter - 25:2135209 3.4 13470 3975.1 11:17:23.018 INFO ProgressMeter - 25:2237232 3.6 14210 3988.0 11:17:33.041 INFO ProgressMeter - 25:2283984 3.7 14590 3911.3 11:17:43.609 INFO ProgressMeter - 25:2357676 3.9 15200 3891.1 11:17:54.105 INFO ProgressMeter - 25:2428459 4.1 15760 3861.5 11:18:04.222 INFO ProgressMeter - 25:2488154 4.2 16210 3814.2 11:18:14.290 INFO ProgressMeter - 25:2619784 4.4 17180 3888.9 11:18:24.423 INFO ProgressMeter - 26:1067 4.6 18800 4099.2 11:18:34.469 INFO ProgressMeter - 26:326990 4.8 20370 4284.8 11:18:44.536 INFO ProgressMeter - 26:412750 4.9 21050 4276.9 11:18:54.680 INFO ProgressMeter - 26:461919 5.1 21440 4211.5 11:19:04.712 INFO ProgressMeter - 26:518598 5.3 21900 4165.0 11:19:14.824 INFO ProgressMeter - 26:573552 5.4 22320 4113.1 11:19:24.825 INFO ProgressMeter - 26:642492 5.6 22850 4085.3 11:19:34.894 INFO ProgressMeter - 26:725212 5.8 23500 4079.1 11:19:45.086 INFO ProgressMeter - 26:810526 5.9 24170 4075.2 11:19:55.098 INFO ProgressMeter - 26:848619 6.1 24490 4016.2 11:20:05.112 INFO ProgressMeter - 26:933209 6.3 25140 4013.0 11:20:15.242 INFO ProgressMeter - 26:994104 6.4 25680 3991.6 11:20:25.250 INFO ProgressMeter - 26:1039666 6.6 26050 3946.8 11:20:35.420 INFO ProgressMeter - 26:1102048 6.8 26510 3915.9 11:20:45.549 INFO ProgressMeter - 26:1285184 6.9 27750 3999.3 11:20:55.774 INFO ProgressMeter - 26:1340617 7.1 28200 3966.8 11:21:06.142 INFO ProgressMeter - 26:1379452 7.3 28510 3915.2 11:21:16.998 INFO ProgressMeter - 26:1431907 7.5 28910 3873.9 11:21:27.280 INFO ProgressMeter - 26:1453874 7.6 29090 3810.5 11:21:37.351 INFO ProgressMeter - 26:1533140 7.8 29710 3808.0 11:21:47.388 INFO ProgressMeter - 26:1590888 8.0 30150 3783.3 11:21:57.473 INFO ProgressMeter - 26:1671608 8.1 30780 3782.5 11:22:07.496 INFO ProgressMeter - 26:1763135 8.3 31510 3794.4 11:22:17.936 INFO ProgressMeter - 26:1842386 8.5 32120 3788.4 11:22:28.150 INFO ProgressMeter - 26:1887716 8.6 32480 3755.5 11:22:38.225 INFO ProgressMeter - 26:1969997 8.8 33150 3760.0 11:22:48.349 INFO ProgressMeter - 26:2042916 9.0 33720 3752.8 11:22:58.563 INFO ProgressMeter - 26:2114313 9.2 34250 3740.9 11:23:08.980 INFO ProgressMeter - 26:2175364 9.3 34750 3724.9 11:23:19.003 INFO ProgressMeter - 26:2248800 9.5 35300 3717.3 11:23:29.977 INFO ProgressMeter - 26:2318593 9.7 35880 3706.9 11:23:40.025 INFO ProgressMeter - 26:2373032 9.8 36330 3689.6 11:23:50.079 INFO ProgressMeter - 26:2435178 10.0 36800 3674.8 11:24:00.366 INFO ProgressMeter - 26:2539599 10.2 37590 3690.5 11:24:10.734 INFO ProgressMeter - 26:2589097 10.4 38000 3668.5 11:24:21.000 INFO ProgressMeter - 26:2640532 10.5 38470 3653.5 11:24:31.286 INFO ProgressMeter - 26:2711109 10.7 39040 3648.3 11:24:41.387 INFO ProgressMeter - 26:2734726 10.9 39220 3608.3 11:24:51.416 INFO ProgressMeter - 26:2796334 11.0 39700 3597.2 11:25:01.520 INFO ProgressMeter - 26:2863813 11.2 40250 3592.2 11:25:11.541 INFO ProgressMeter - 26:2999742 11.4 41120 3615.9 11:25:21.837 INFO ProgressMeter - 26:3092829 11.5 41800 3621.1 11:25:32.750 INFO ProgressMeter - 26:3286570 11.7 43100 3675.8 11:25:42.860 INFO ProgressMeter - 26:3414184 11.9 43970 3696.9 11:25:52.926 INFO ProgressMeter - 26:3561863 12.1 45010 3731.7 11:26:03.073 INFO ProgressMeter - 26:3737630 12.2 46140 3772.5 11:26:13.077 INFO ProgressMeter - 26:3857403 12.4 46990 3790.3 11:26:23.093 INFO ProgressMeter - 26:3989222 12.6 47850 3808.4 11:26:33.130 INFO ProgressMeter - 26:4114694 12.7 48830 3835.3 11:26:43.264 INFO ProgressMeter - 26:4304333 12.9 50040 3878.9 11:26:53.305 INFO ProgressMeter - 26:4448015 13.1 51120 3911.9 11:27:03.350 INFO ProgressMeter - 26:4592479 13.2 52180 3942.5 11:27:13.443 INFO ProgressMeter - 26:4786575 13.4 53500 3991.5 11:27:23.504 INFO ProgressMeter - 26:5010700 13.6 55170 4065.2 11:27:30.550 INFO HaplotypeCaller - 27947 read(s) filtered by: MappingQualityReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 54976 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 82923 total reads filtered out of 1988606 reads processed 11:27:30.551 INFO ProgressMeter - 26:5312941 13.7 56704 4142.4 11:27:30.551 INFO ProgressMeter - Traversal complete. Processed 56704 total regions in 13.7 minutes. 11:27:30.613 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.41367174900000003 11:27:30.613 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 150.259271979 11:27:30.613 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 410.84 sec 11:27:30.614 INFO HaplotypeCaller - Shutting down engine [November 7, 2023 at 11:27:30 AM CET] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 13.70 minutes. Runtime.totalMemory()=1013710848