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 SRR7062655.md.recal.bam -O SRR7062655.md.recal.g.vcf -ERC GVCF 11:14:03.507 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 11:14:03.584 INFO HaplotypeCaller - ------------------------------------------------------------ 11:14:03.587 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.4.0.0 11:14:03.587 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 11:14:03.587 INFO HaplotypeCaller - Executing as formation@n024 on Linux v4.18.0-372.32.1.el8_6.x86_64 amd64 11:14:03.587 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.6+9-LTS-190 11:14:03.588 INFO HaplotypeCaller - Start Date/Time: November 7, 2023 at 11:14:03 AM CET 11:14:03.588 INFO HaplotypeCaller - ------------------------------------------------------------ 11:14:03.588 INFO HaplotypeCaller - ------------------------------------------------------------ 11:14:03.589 INFO HaplotypeCaller - HTSJDK Version: 3.0.5 11:14:03.589 INFO HaplotypeCaller - Picard Version: 3.0.0 11:14:03.589 INFO HaplotypeCaller - Built for Spark Version: 3.3.1 11:14:03.589 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 11:14:03.590 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 11:14:03.590 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 11:14:03.594 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 11:14:03.594 INFO HaplotypeCaller - Deflater: IntelDeflater 11:14:03.594 INFO HaplotypeCaller - Inflater: IntelInflater 11:14:03.595 INFO HaplotypeCaller - GCS max retries/reopens: 20 11:14:03.595 INFO HaplotypeCaller - Requester pays: disabled 11:14:03.595 INFO HaplotypeCaller - Initializing engine 11:14:03.828 INFO HaplotypeCaller - Done initializing engine 11:14:03.831 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 11:14:03.847 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to -0.0 for reference-model confidence output 11:14:03.847 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 11:14:03.865 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 11:14:03.868 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 11:14:03.885 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 11:14:03.885 INFO IntelPairHmm - Available threads: 1 11:14:03.886 INFO IntelPairHmm - Requested threads: 4 11:14:03.886 WARN IntelPairHmm - Using 1 available threads, but 4 were requested 11:14:03.887 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 11:14:03.957 INFO ProgressMeter - Starting traversal 11:14:03.957 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 11:14:05.300 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 25:2351 and possibly subsequent; at least 10 samples must have called genotypes 11:14:14.643 INFO ProgressMeter - 25:15071 0.2 110 618.5 11:14:24.655 INFO ProgressMeter - 25:39799 0.3 290 840.7 11:14:27.406 WARN DepthPerSampleHC - Annotation will not be calculated at position 25:72481 and possibly subsequent; genotype for sample SRR7062655 is not called 11:14:27.407 WARN StrandBiasBySample - Annotation will not be calculated at position 25:72481 and possibly subsequent; genotype for sample SRR7062655 is not called 11:14:35.066 INFO ProgressMeter - 25:103042 0.5 710 1369.4 11:14:45.230 INFO ProgressMeter - 25:146078 0.7 1060 1541.0 11:14:55.294 INFO ProgressMeter - 25:203267 0.9 1480 1729.7 11:15:05.296 INFO ProgressMeter - 25:795898 1.0 3730 3648.6 11:15:15.437 INFO ProgressMeter - 25:915865 1.2 4500 3777.3 11:15:25.920 INFO ProgressMeter - 25:1027888 1.4 5310 3887.1 11:15:37.849 INFO ProgressMeter - 25:1044855 1.6 5430 3469.9 11:15:48.254 INFO ProgressMeter - 25:1206650 1.7 6420 3693.3 11:15:58.427 INFO ProgressMeter - 25:1264404 1.9 6850 3590.5 11:16:08.433 INFO ProgressMeter - 25:1312363 2.1 7230 3485.0 11:16:18.555 INFO ProgressMeter - 25:1476418 2.2 8280 3691.0 11:16:28.769 INFO ProgressMeter - 25:1575573 2.4 9000 3729.0 11:16:38.796 INFO ProgressMeter - 25:1755224 2.6 10180 3944.7 11:16:49.080 INFO ProgressMeter - 25:1874751 2.8 10980 3989.8 11:16:59.089 INFO ProgressMeter - 25:1944319 2.9 11540 3953.6 11:17:09.383 INFO ProgressMeter - 25:2010322 3.1 12060 3902.4 11:17:19.472 INFO ProgressMeter - 25:2057545 3.3 12450 3820.7 11:17:30.120 INFO ProgressMeter - 25:2175306 3.4 13250 3856.2 11:17:40.315 INFO ProgressMeter - 25:2260594 3.6 13890 3851.9 11:17:50.388 INFO ProgressMeter - 25:2314450 3.8 14310 3791.9 11:18:00.635 INFO ProgressMeter - 25:2392846 3.9 14910 3779.8 11:18:10.747 INFO ProgressMeter - 25:2451155 4.1 15390 3741.6 11:18:20.778 INFO ProgressMeter - 25:2538921 4.3 16060 3752.0 11:18:30.830 INFO ProgressMeter - 25:2763668 4.4 17320 3894.0 11:18:40.854 INFO ProgressMeter - 26:102900 4.6 18690 4049.9 11:18:51.130 INFO ProgressMeter - 26:327236 4.8 19900 4157.8 11:19:01.248 INFO ProgressMeter - 26:412410 5.0 20560 4149.5 11:19:11.277 INFO ProgressMeter - 26:499152 5.1 21210 4141.0 11:19:21.591 INFO ProgressMeter - 26:575138 5.3 21820 4121.7 11:19:31.676 INFO ProgressMeter - 26:660064 5.5 22480 4115.7 11:19:41.973 INFO ProgressMeter - 26:704943 5.6 22860 4057.8 11:19:52.022 INFO ProgressMeter - 26:779574 5.8 23430 4038.9 11:20:02.152 INFO ProgressMeter - 26:836823 6.0 23900 4003.4 11:20:12.206 INFO ProgressMeter - 26:898835 6.1 24410 3977.2 11:20:22.331 INFO ProgressMeter - 26:970183 6.3 24980 3961.2 11:20:32.436 INFO ProgressMeter - 26:1019969 6.5 25400 3923.0 11:20:42.555 INFO ProgressMeter - 26:1103569 6.6 26010 3915.2 11:20:52.604 INFO ProgressMeter - 26:1235202 6.8 26960 3958.4 11:21:02.647 INFO ProgressMeter - 26:1327836 7.0 27610 3956.6 11:21:12.701 INFO ProgressMeter - 26:1396697 7.1 28160 3940.8 11:21:23.171 INFO ProgressMeter - 26:1457715 7.3 28640 3912.4 11:21:33.207 INFO ProgressMeter - 26:1528885 7.5 29180 3897.2 11:21:43.268 INFO ProgressMeter - 26:1590776 7.7 29680 3877.1 11:21:53.564 INFO ProgressMeter - 26:1670924 7.8 30280 3868.8 11:22:03.749 INFO ProgressMeter - 26:1742954 8.0 30840 3856.7 11:22:13.750 INFO ProgressMeter - 26:1805068 8.2 31340 3839.2 11:22:24.215 INFO ProgressMeter - 26:1863612 8.3 31790 3812.8 11:22:34.404 INFO ProgressMeter - 26:1895230 8.5 32060 3768.5 11:22:45.074 INFO ProgressMeter - 26:1970076 8.7 32650 3759.2 11:22:55.119 INFO ProgressMeter - 26:2040963 8.9 33210 3751.4 11:23:05.155 INFO ProgressMeter - 26:2107950 9.0 33710 3737.3 11:23:15.193 INFO ProgressMeter - 26:2170346 9.2 34200 3722.6 11:23:25.226 INFO ProgressMeter - 26:2249778 9.4 34800 3720.1 11:23:35.284 INFO ProgressMeter - 26:2324221 9.5 35420 3719.8 11:23:45.429 INFO ProgressMeter - 26:2380704 9.7 35860 3700.3 11:23:55.446 INFO ProgressMeter - 26:2438414 9.9 36320 3684.3 11:24:05.724 INFO ProgressMeter - 26:2529996 10.0 37060 3695.1 11:24:16.407 INFO ProgressMeter - 26:2589195 10.2 37540 3677.7 11:24:26.610 INFO ProgressMeter - 26:2634430 10.4 37940 3656.0 11:24:36.621 INFO ProgressMeter - 26:2694206 10.5 38420 3643.6 11:24:46.964 INFO ProgressMeter - 26:2728465 10.7 38680 3609.3 11:24:57.116 INFO ProgressMeter - 26:2762512 10.9 38950 3578.0 11:25:07.681 INFO ProgressMeter - 26:2821494 11.1 39440 3565.3 11:25:17.705 INFO ProgressMeter - 26:2881788 11.2 39930 3555.9 11:25:28.553 INFO ProgressMeter - 26:2935829 11.4 40360 3537.3 11:25:38.736 INFO ProgressMeter - 26:3003419 11.6 40860 3528.6 11:25:49.262 INFO ProgressMeter - 26:3051373 11.8 41250 3509.1 11:26:00.173 INFO ProgressMeter - 26:3096102 11.9 41620 3486.7 11:26:10.262 INFO ProgressMeter - 26:3151583 12.1 42060 3474.6 11:26:20.290 INFO ProgressMeter - 26:3207748 12.3 42520 3464.7 11:26:30.292 INFO ProgressMeter - 26:3283325 12.4 43150 3469.0 11:26:40.358 INFO ProgressMeter - 26:3341325 12.6 43600 3458.5 11:26:50.744 INFO ProgressMeter - 26:3412861 12.8 44160 3455.5 11:27:00.766 INFO ProgressMeter - 26:3463845 12.9 44570 3442.5 11:27:10.925 INFO ProgressMeter - 26:3540241 13.1 45160 3443.1 11:27:20.940 INFO ProgressMeter - 26:3631584 13.3 45890 3454.8 11:27:31.084 INFO ProgressMeter - 26:3697544 13.5 46420 3450.8 11:27:41.134 INFO ProgressMeter - 26:3748122 13.6 46810 3437.0 11:27:51.651 INFO ProgressMeter - 26:3817080 13.8 47300 3428.8 11:28:01.807 INFO ProgressMeter - 26:3890999 14.0 47860 3427.3 11:28:11.825 INFO ProgressMeter - 26:3947595 14.1 48250 3414.5 11:28:22.572 INFO ProgressMeter - 26:3985822 14.3 48570 3394.1 11:28:32.608 INFO ProgressMeter - 26:4074858 14.5 49220 3399.8 11:28:42.864 INFO ProgressMeter - 26:4202979 14.6 50150 3423.6 11:28:53.004 INFO ProgressMeter - 26:4352160 14.8 51100 3448.6 11:29:03.023 INFO ProgressMeter - 26:4413082 15.0 51550 3440.2 11:29:13.162 INFO ProgressMeter - 26:4469881 15.2 51980 3430.2 11:29:23.425 INFO ProgressMeter - 26:4533588 15.3 52500 3425.9 11:29:33.460 INFO ProgressMeter - 26:4629522 15.5 53230 3436.0 11:29:43.839 INFO ProgressMeter - 26:4758533 15.7 54120 3454.9 11:29:54.021 INFO ProgressMeter - 26:4858184 15.8 54900 3467.1 11:30:04.079 INFO ProgressMeter - 26:4928464 16.0 55460 3465.8 11:30:14.301 INFO ProgressMeter - 26:5009485 16.2 56130 3470.7 11:30:24.343 INFO ProgressMeter - 26:5108736 16.3 56860 3479.9 11:30:32.315 INFO HaplotypeCaller - 27657 read(s) filtered by: MappingQualityReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 86123 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 113780 total reads filtered out of 1921919 reads processed 11:30:32.316 INFO ProgressMeter - 26:5312296 16.5 57849 3511.8 11:30:32.316 INFO ProgressMeter - Traversal complete. Processed 57849 total regions in 16.5 minutes. 11:30:32.373 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.43754546600000005 11:30:32.373 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 166.039175879 11:30:32.374 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 498.83 sec 11:30:32.375 INFO HaplotypeCaller - Shutting down engine [November 7, 2023 at 11:30:32 AM CET] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 16.48 minutes. Runtime.totalMemory()=1013710848