22:44:21.996 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
22:44:22.122 INFO Mutect2 - ------------------------------------------------------------
22:44:22.125 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:22.125 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:22.125 INFO Mutect2 - Executing as ?@nf-55c1c40812d6d7ec802dcffb45770b28-85249-hv4kk on Linux v6.12.88 amd64
22:44:22.125 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:22.126 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:21 PM GMT
22:44:22.126 INFO Mutect2 - ------------------------------------------------------------
22:44:22.126 INFO Mutect2 - ------------------------------------------------------------
22:44:22.127 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:22.127 INFO Mutect2 - Picard Version: 3.1.1
22:44:22.127 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:22.127 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:22.127 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:22.127 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:22.127 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:22.127 INFO Mutect2 - Deflater: IntelDeflater
22:44:22.127 INFO Mutect2 - Inflater: IntelInflater
22:44:22.127 INFO Mutect2 - GCS max retries/reopens: 20
22:44:22.128 INFO Mutect2 - Requester pays: disabled
22:44:22.128 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.xg2iB2Bx3l/LS0918_tumor.bam.bai is older than BAM /tmp/nxf.xg2iB2Bx3l/LS0918_tumor.bam
22:44:22.335 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.xg2iB2Bx3l/af-only-gnomad.hg38.vcf.gz
22:44:22.439 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.xg2iB2Bx3l/TST500C_manifest.bed
22:44:22.468 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:22.496 INFO Mutect2 - Done initializing engine
22:44:22.506 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
22:44:22.508 INFO NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
22:44:22.508 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:22.509 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:22.518 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
22:44:22.526 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:22.526 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:22.527 INFO IntelPairHmm - Available threads: 384
22:44:22.527 INFO IntelPairHmm - Requested threads: 4
22:44:22.527 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:22.563 INFO ProgressMeter - Starting traversal
22:44:22.564 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:33.301 INFO ProgressMeter - chr1:11129736 0.2 80 447.1
22:44:43.344 INFO ProgressMeter - chr1:15919402 0.3 150 433.1
22:44:54.322 INFO ProgressMeter - chr1:15938716 0.5 210 396.8
22:45:04.368 INFO ProgressMeter - chr1:18747261 0.7 270 387.5
22:45:14.395 INFO ProgressMeter - chr1:26779533 0.9 340 393.6
22:45:25.686 INFO ProgressMeter - chr1:39898101 1.1 420 399.2
22:45:36.074 INFO ProgressMeter - chr1:45334389 1.2 490 399.9
22:45:46.621 INFO ProgressMeter - chr1:64850802 1.4 580 414.0
22:45:57.409 INFO ProgressMeter - chr1:117210822 1.6 700 442.8
22:46:07.860 INFO ProgressMeter - chr1:119963572 1.8 770 438.8
22:46:20.400 INFO ProgressMeter - chr1:156873917 2.0 830 422.6
22:46:31.952 INFO ProgressMeter - chr1:158657475 2.2 900 417.4
22:46:42.360 INFO ProgressMeter - chr1:179108272 2.3 990 424.9
22:46:52.551 INFO ProgressMeter - chr1:204519648 2.5 1090 436.0
22:47:03.032 INFO ProgressMeter - chr1:226368197 2.7 1190 444.9
22:47:14.900 INFO ProgressMeter - chr1:243503755 2.9 1270 442.2
22:47:25.276 INFO ProgressMeter - chr10:27037894 3.0 1340 440.0
22:47:36.354 INFO ProgressMeter - chr10:32034688 3.2 1410 436.6
22:47:46.802 INFO ProgressMeter - chr10:43115448 3.4 1480 434.8
22:47:58.345 INFO ProgressMeter - chr10:68573161 3.6 1550 431.0
22:48:09.043 INFO ProgressMeter - chr10:87958235 3.8 1650 437.1
22:48:19.693 INFO ProgressMeter - chr10:110589584 4.0 1750 442.8
22:48:31.039 INFO ProgressMeter - chr10:121482475 4.1 1820 439.5
22:48:42.160 INFO ProgressMeter - chr11:32391970 4.3 1920 443.8
22:48:53.023 INFO ProgressMeter - chr11:69651277 4.5 2040 452.6
22:49:03.922 INFO ProgressMeter - chr11:69773307 4.7 2120 452.1
22:49:14.794 INFO ProgressMeter - chr11:69814632 4.9 2170 445.5
22:49:25.005 INFO ProgressMeter - chr11:77355666 5.0 2250 446.4
22:49:35.877 INFO ProgressMeter - chr11:101039114 5.2 2340 448.1
22:49:46.859 INFO ProgressMeter - chr11:102336758 5.4 2390 442.2
22:49:58.582 INFO ProgressMeter - chr11:118476803 5.6 2510 448.2
22:50:08.779 INFO ProgressMeter - chr11:119284967 5.8 2590 448.9
22:50:21.204 INFO ProgressMeter - chr11:128460438 6.0 2670 446.7
22:50:31.475 INFO ProgressMeter - chr12:292757 6.1 2740 445.6
22:50:41.781 INFO ProgressMeter - chr12:4373770 6.3 2830 447.8
22:50:52.094 INFO ProgressMeter - chr12:4448469 6.5 2900 446.7
22:51:03.356 INFO ProgressMeter - chr12:11855322 6.7 2970 444.6
22:51:14.846 INFO ProgressMeter - chr12:11860751 6.9 3020 439.5
22:51:25.702 INFO ProgressMeter - chr12:11867068 7.1 3070 435.3
22:51:36.280 INFO ProgressMeter - chr12:18505290 7.2 3140 434.4
22:51:48.256 INFO ProgressMeter - chr12:45851239 7.4 3230 434.8
22:51:59.572 INFO ProgressMeter - chr12:49033421 7.6 3290 431.9
22:52:10.412 INFO ProgressMeter - chr12:49049980 7.8 3360 430.9
22:52:20.859 INFO ProgressMeter - chr12:56085478 8.0 3440 431.5
22:52:31.775 INFO ProgressMeter - chr12:57094778 8.2 3520 431.7
22:52:41.818 INFO ProgressMeter - chr12:68808623 8.3 3600 432.6
22:52:52.378 INFO ProgressMeter - chr12:111446751 8.5 3690 434.3
22:53:03.228 INFO ProgressMeter - chr12:132639123 8.7 3780 435.6
22:53:13.778 INFO ProgressMeter - chr13:21045984 8.9 3860 436.0
22:53:24.247 INFO ProgressMeter - chr13:28050093 9.0 3950 437.5
22:53:36.345 INFO ProgressMeter - chr13:28388492 9.2 4010 434.5
22:53:47.889 INFO ProgressMeter - chr13:32337664 9.4 4080 433.0
22:53:59.507 INFO ProgressMeter - chr13:40560121 9.6 4150 431.6
22:54:09.982 INFO ProgressMeter - chr13:102216390 9.8 4260 435.1
22:54:20.293 INFO ProgressMeter - chr13:113302627 10.0 4350 436.7
22:54:31.236 INFO ProgressMeter - chr14:36520051 10.1 4430 436.7
22:54:41.802 INFO ProgressMeter - chr14:52750043 10.3 4520 438.0
22:54:52.613 INFO ProgressMeter - chr14:95107912 10.5 4600 438.1
22:55:03.651 INFO ProgressMeter - chr15:34346592 10.7 4690 438.9
22:55:13.738 INFO ProgressMeter - chr15:41668893 10.9 4740 436.8
22:55:24.357 INFO ProgressMeter - chr15:44715421 11.0 4810 436.1
22:55:35.125 INFO ProgressMeter - chr15:73712932 11.2 4910 438.0
22:55:45.463 INFO ProgressMeter - chr15:89283134 11.4 4980 437.5
22:55:56.054 INFO ProgressMeter - chr15:90804297 11.6 5060 437.8
22:56:07.056 INFO ProgressMeter - chr15:98922146 11.7 5140 437.8
22:56:17.509 INFO ProgressMeter - chr16:2084443 11.9 5230 438.9
22:56:28.409 INFO ProgressMeter - chr16:3606530 12.1 5330 440.6
22:56:39.847 INFO ProgressMeter - chr16:9764139 12.3 5410 440.3
22:56:50.993 INFO ProgressMeter - chr16:23641108 12.5 5490 440.1
22:57:01.667 INFO ProgressMeter - chr16:67628368 12.7 5580 441.0
22:57:13.252 INFO ProgressMeter - chr16:72796133 12.8 5650 439.9
22:57:24.245 INFO ProgressMeter - chr16:72959989 13.0 5700 437.5
22:57:35.552 INFO ProgressMeter - chr16:89283481 13.2 5780 437.3
22:57:46.001 INFO ProgressMeter - chr17:5803341 13.4 5870 438.4
22:57:56.416 INFO ProgressMeter - chr17:12032264 13.6 5970 440.1
22:58:06.467 INFO ProgressMeter - chr17:18039463 13.7 6070 442.0
22:58:16.796 INFO ProgressMeter - chr17:35103540 13.9 6180 444.5
22:58:26.889 INFO ProgressMeter - chr17:39726560 14.1 6270 445.6
22:58:37.478 INFO ProgressMeter - chr17:42323317 14.2 6400 449.2
22:58:48.114 INFO ProgressMeter - chr17:43124227 14.4 6490 449.9
22:58:58.182 INFO ProgressMeter - chr17:43539607 14.6 6560 449.5
22:59:08.805 INFO ProgressMeter - chr17:48725137 14.8 6630 448.9
22:59:19.178 INFO ProgressMeter - chr17:59935191 14.9 6730 450.4
22:59:29.257 INFO ProgressMeter - chr17:65014328 15.1 6800 450.0
22:59:39.549 INFO ProgressMeter - chr17:80880413 15.3 6900 451.5
22:59:50.888 INFO ProgressMeter - chr18:44950326 15.5 7010 453.1
23:00:00.957 INFO ProgressMeter - chr18:58745772 15.6 7090 453.3
23:00:11.242 INFO ProgressMeter - chr19:3115053 15.8 7210 456.0
23:00:21.943 INFO ProgressMeter - chr19:7125404 16.0 7320 457.8
23:00:32.361 INFO ProgressMeter - chr19:10162665 16.2 7400 457.8
23:00:43.949 INFO ProgressMeter - chr19:14517487 16.4 7510 459.1
23:00:53.971 INFO ProgressMeter - chr19:15239057 16.5 7590 459.3
23:01:04.100 INFO ProgressMeter - chr19:18162200 16.7 7670 459.5
23:01:14.631 INFO ProgressMeter - chr19:35720137 16.9 7770 460.6
23:01:25.323 INFO ProgressMeter - chr19:40251162 17.0 7870 461.7
23:01:36.943 INFO ProgressMeter - chr19:41261585 17.2 7940 460.6
23:01:47.304 INFO ProgressMeter - chr19:45368311 17.4 8040 461.7
23:01:58.105 INFO ProgressMeter - chr19:52216527 17.6 8160 463.8
23:02:09.936 INFO ProgressMeter - chr2:17781589 17.8 8240 463.2
23:02:20.278 INFO ProgressMeter - chr2:25799502 18.0 8310 462.6
23:02:30.374 INFO ProgressMeter - chr2:29225235 18.1 8360 461.1
23:02:41.526 INFO ProgressMeter - chr2:42169545 18.3 8420 459.7
23:02:52.872 INFO ProgressMeter - chr2:47466656 18.5 8490 458.8
23:03:03.441 INFO ProgressMeter - chr2:61493892 18.7 8580 459.3
23:03:16.207 INFO ProgressMeter - chr2:108764848 18.9 8670 458.9
23:03:30.985 INFO ProgressMeter - chr2:111128793 19.1 8740 456.6
23:03:42.086 INFO ProgressMeter - chr2:113224745 19.3 8790 454.8
23:03:55.258 INFO ProgressMeter - chr2:113229771 19.5 8830 451.8
23:04:05.286 INFO ProgressMeter - chr2:113233532 19.7 8860 449.5
23:04:15.517 INFO ProgressMeter - chr2:140234784 19.9 8930 449.1
23:04:26.218 INFO ProgressMeter - chr2:140989530 20.1 9030 450.1
23:04:37.239 INFO ProgressMeter - chr2:189863780 20.2 9120 450.5
23:04:48.435 INFO ProgressMeter - chr2:211383770 20.4 9230 451.8
23:04:58.658 INFO ProgressMeter - chr2:222200687 20.6 9310 451.9
23:05:09.355 INFO ProgressMeter - chr2:222206113 20.8 9350 450.0
23:05:23.329 INFO ProgressMeter - chr2:222212687 21.0 9400 447.3
23:05:34.385 INFO ProgressMeter - chr2:222217845 21.2 9440 445.3
23:05:45.227 INFO ProgressMeter - chr2:224514610 21.4 9500 444.4
23:05:58.684 INFO ProgressMeter - chr20:9580590 21.6 9570 443.0
23:06:08.685 INFO ProgressMeter - chr20:32435925 21.8 9620 441.9
23:06:19.953 INFO ProgressMeter - chr20:41100054 22.0 9700 441.8
23:06:30.038 INFO ProgressMeter - chr20:47627000 22.1 9760 441.1
23:06:41.963 INFO ProgressMeter - chr20:53576251 22.3 9800 439.0
23:06:54.118 INFO ProgressMeter - chr20:58855115 22.5 9850 437.3
23:07:04.727 INFO ProgressMeter - chr21:38470775 22.7 9940 437.8
23:07:19.837 INFO ProgressMeter - chr21:41492284 23.0 10000 435.6
23:07:31.608 INFO ProgressMeter - chr21:41503558 23.2 10060 434.5
23:07:42.450 INFO ProgressMeter - chr22:20988787 23.3 10140 434.6
23:07:52.640 INFO ProgressMeter - chr22:23290774 23.5 10210 434.4
23:08:02.680 INFO ProgressMeter - chr22:28724975 23.7 10290 434.8
23:08:13.806 INFO ProgressMeter - chr22:29286932 23.9 10360 434.3
23:08:24.722 INFO ProgressMeter - chr22:41176771 24.0 10460 435.2
23:08:34.942 INFO ProgressMeter - chr3:12353566 24.2 10550 435.8
23:08:46.471 INFO ProgressMeter - chr3:12360366 24.4 10590 434.0
23:08:57.378 INFO ProgressMeter - chr3:12367590 24.6 10640 432.9
23:09:09.459 INFO ProgressMeter - chr3:12377151 24.8 10710 432.2
23:09:20.058 INFO ProgressMeter - chr3:30650268 25.0 10790 432.3
23:09:31.664 INFO ProgressMeter - chr3:47120763 25.2 10890 433.0
23:09:41.957 INFO ProgressMeter - chr3:49897278 25.3 10970 433.2
23:09:52.657 INFO ProgressMeter - chr3:69949129 25.5 11070 434.1
23:10:02.856 INFO ProgressMeter - chr3:89472613 25.7 11160 434.7
23:10:13.593 INFO ProgressMeter - chr3:136452112 25.9 11250 435.2
23:10:24.228 INFO ProgressMeter - chr3:142497011 26.0 11350 436.1
23:10:34.282 INFO ProgressMeter - chr3:179173622 26.2 11440 436.7
23:10:44.324 INFO ProgressMeter - chr3:183555426 26.4 11530 437.4
23:10:55.378 INFO ProgressMeter - chr3:187728461 26.5 11610 437.3
23:11:05.887 INFO ProgressMeter - chr4:1801383 26.7 11720 438.6
23:11:16.751 INFO ProgressMeter - chr4:54262543 26.9 11850 440.5
23:11:30.037 INFO ProgressMeter - chr4:54732108 27.1 11930 439.8
23:11:40.938 INFO ProgressMeter - chr4:80272867 27.3 12030 440.6
23:11:51.522 INFO ProgressMeter - chr4:105237877 27.5 12110 440.6
23:12:01.891 INFO ProgressMeter - chr4:122859484 27.7 12180 440.4
23:12:12.530 INFO ProgressMeter - chr4:186598090 27.8 12280 441.2
23:12:22.659 INFO ProgressMeter - chr4:186706601 28.0 12350 441.0
23:12:34.453 INFO ProgressMeter - chr5:38942302 28.2 12420 440.5
23:12:45.531 INFO ProgressMeter - chr5:44332026 28.4 12500 440.4
23:12:55.957 INFO ProgressMeter - chr5:66082613 28.6 12590 440.9
23:13:06.125 INFO ProgressMeter - chr5:112838558 28.7 12710 442.5
23:13:16.402 INFO ProgressMeter - chr5:132591222 28.9 12780 442.3
23:13:27.675 INFO ProgressMeter - chr5:142692614 29.1 12870 442.5
23:13:38.814 INFO ProgressMeter - chr5:150403435 29.3 12970 443.1
23:13:49.847 INFO ProgressMeter - chr5:177093284 29.5 13050 443.1
23:14:00.189 INFO ProgressMeter - chr5:177294535 29.6 13120 442.8
23:14:10.632 INFO ProgressMeter - chr6:20428076 29.8 13230 443.9
23:14:20.800 INFO ProgressMeter - chr6:26271355 30.0 13340 445.1
23:14:31.144 INFO ProgressMeter - chr6:30711665 30.1 13390 444.2
23:14:41.667 INFO ProgressMeter - chr6:33319593 30.3 13470 444.3
23:14:52.101 INFO ProgressMeter - chr6:41964050 30.5 13550 444.4
23:15:02.648 INFO ProgressMeter - chr6:93258097 30.7 13620 444.1
23:15:12.866 INFO ProgressMeter - chr6:117318802 30.8 13710 444.6
23:15:23.140 INFO ProgressMeter - chr6:117326228 31.0 13750 443.4
23:15:34.605 INFO ProgressMeter - chr6:117337404 31.2 13820 442.9
23:15:45.773 INFO ProgressMeter - chr6:135197259 31.4 13900 442.9
23:15:56.402 INFO ProgressMeter - chr6:135208288 31.6 13940 441.6
23:16:09.932 INFO ProgressMeter - chr6:135213737 31.8 13980 439.8
23:16:21.540 INFO ProgressMeter - chr6:137198254 32.0 14010 438.0
23:16:33.282 INFO ProgressMeter - chr6:151365850 32.2 14070 437.2
23:16:43.906 INFO ProgressMeter - chr6:156777985 32.4 14130 436.7
23:16:56.315 INFO ProgressMeter - chr6:161048786 32.6 14200 436.1
23:17:07.471 INFO ProgressMeter - chr7:2924260 32.7 14290 436.4
23:17:18.992 INFO ProgressMeter - chr7:13894115 32.9 14360 435.9
23:17:30.894 INFO ProgressMeter - chr7:13932108 33.1 14400 434.5
23:17:40.920 INFO ProgressMeter - chr7:13938789 33.3 14440 433.6
23:17:51.639 INFO ProgressMeter - chr7:13945256 33.5 14480 432.4
23:18:03.632 INFO ProgressMeter - chr7:13949469 33.7 14510 430.8
23:18:14.120 INFO ProgressMeter - chr7:13952911 33.9 14530 429.1
23:18:24.432 INFO ProgressMeter - chr7:13958778 34.0 14570 428.1
23:18:38.199 INFO ProgressMeter - chr7:13964066 34.3 14610 426.4
23:18:51.587 INFO ProgressMeter - chr7:13971461 34.5 14660 425.1
23:19:07.569 INFO ProgressMeter - chr7:13976586 34.8 14700 423.0
23:19:18.328 INFO ProgressMeter - chr7:13980861 34.9 14740 422.0
23:19:29.349 INFO ProgressMeter - chr7:13988084 35.1 14780 420.9
23:19:40.899 INFO ProgressMeter - chr7:50391727 35.3 14820 419.8
23:19:50.960 INFO ProgressMeter - chr7:55163731 35.5 14870 419.2
23:20:03.120 INFO ProgressMeter - chr7:55170892 35.7 14910 417.9
23:20:14.852 INFO ProgressMeter - chr7:55179380 35.9 14950 416.8
23:20:26.086 INFO ProgressMeter - chr7:78127370 36.1 15000 416.0
23:20:36.340 INFO ProgressMeter - chr7:86786611 36.2 15070 416.0
23:20:46.474 INFO ProgressMeter - chr7:102193907 36.4 15140 416.0
23:20:57.191 INFO ProgressMeter - chr7:106868913 36.6 15200 415.6
23:21:07.829 INFO ProgressMeter - chr7:116771678 36.8 15260 415.2
23:21:17.976 INFO ProgressMeter - chr7:140739810 36.9 15310 414.6
23:21:30.330 INFO ProgressMeter - chr7:140792977 37.1 15370 414.0
23:21:41.383 INFO ProgressMeter - chr7:142957865 37.3 15450 414.1
23:21:51.561 INFO ProgressMeter - chr7:152162415 37.5 15520 414.1
23:22:02.033 INFO ProgressMeter - chr7:152182972 37.7 15560 413.2
23:22:12.580 INFO ProgressMeter - chr8:26293664 37.8 15650 413.7
23:22:22.905 INFO ProgressMeter - chr8:32759304 38.0 15730 413.9
23:22:33.552 INFO ProgressMeter - chr8:38454504 38.2 15830 414.6
23:22:44.130 INFO ProgressMeter - chr8:47789149 38.4 15900 414.5
23:22:54.335 INFO ProgressMeter - chr8:47918285 38.5 15970 414.5
23:23:04.713 INFO ProgressMeter - chr8:68044485 38.7 16040 414.4
23:23:17.689 INFO ProgressMeter - chr8:89964408 38.9 16110 413.9
23:23:31.292 INFO ProgressMeter - chr8:127732334 39.1 16170 413.1
23:23:42.456 INFO ProgressMeter - chr8:144511919 39.3 16230 412.6
23:23:52.934 INFO ProgressMeter - chr9:5080227 39.5 16310 412.8
23:24:03.057 INFO ProgressMeter - chr9:8733778 39.7 16400 413.4
23:24:14.228 INFO ProgressMeter - chr9:83973881 39.9 16490 413.7
23:24:25.105 INFO ProgressMeter - chr9:84743712 40.0 16530 412.8
23:24:35.406 INFO ProgressMeter - chr9:84813843 40.2 16570 412.0
23:24:45.712 INFO ProgressMeter - chr9:84864311 40.4 16610 411.3
23:24:56.008 INFO ProgressMeter - chr9:84873729 40.6 16640 410.3
23:25:06.729 INFO ProgressMeter - chr9:85023158 40.7 16690 409.7
23:25:17.929 INFO ProgressMeter - chr9:90864587 40.9 16720 408.6
23:25:28.077 INFO ProgressMeter - chr9:95516739 41.1 16810 409.1
23:25:38.559 INFO ProgressMeter - chr9:130886024 41.3 16890 409.3
23:25:49.049 INFO ProgressMeter - chr9:136498930 41.4 16960 409.3
23:25:59.337 INFO ProgressMeter - chrX:40054015 41.6 17080 410.4
23:26:09.434 INFO ProgressMeter - chrX:47569891 41.8 17200 411.7
23:26:19.660 INFO ProgressMeter - chrX:53218274 42.0 17320 412.9
23:26:30.098 INFO ProgressMeter - chrX:67604654 42.1 17420 413.5
23:26:40.391 INFO ProgressMeter - chrX:77589832 42.3 17570 415.4
23:26:50.933 INFO ProgressMeter - chrX:130014096 42.5 17720 417.2
23:26:55.067 INFO Mutect2 - 553174 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappingQualityNotZeroReadFilter
0 read(s) filtered by: MappedReadFilter
0 read(s) filtered by: NotSecondaryAlignmentReadFilter
0 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
0 read(s) filtered by: NonChimericOriginalAlignmentReadFilter
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
3 read(s) filtered by: ReadLengthReadFilter
153 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
553330 total reads filtered out of 71696078 reads processed
23:26:55.067 INFO ProgressMeter - chrY:20398623 42.5 17805 418.5
23:26:55.067 INFO ProgressMeter - Traversal complete. Processed 17805 total regions in 42.5 minutes.
23:26:55.084 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 5.517565514
23:26:55.085 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 219.351686475
23:26:55.085 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 8.99 sec
23:26:55.085 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:26:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 42.55 minutes.
Runtime.totalMemory()=6291456000
Using GATK jar /gatk/gatk-package-4.5.0.0-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 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar Mutect2 -R hg38.fa -I LS0918_tumor.bam --tumor-sample LS0918 -L TST500C_manifest.bed -O LS0918.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:26:56.794 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:26:56.910 INFO FilterMutectCalls - ------------------------------------------------------------
23:26:56.914 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:26:56.914 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:26:56.914 INFO FilterMutectCalls - Executing as ?@nf-55c1c40812d6d7ec802dcffb45770b28-85249-hv4kk on Linux v6.12.88 amd64
23:26:56.914 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:26:56.914 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:26:56 PM GMT
23:26:56.914 INFO FilterMutectCalls - ------------------------------------------------------------
23:26:56.914 INFO FilterMutectCalls - ------------------------------------------------------------
23:26:56.915 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:26:56.915 INFO FilterMutectCalls - Picard Version: 3.1.1
23:26:56.915 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:26:56.915 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:26:56.915 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:26:56.915 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:26:56.915 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:26:56.915 INFO FilterMutectCalls - Deflater: IntelDeflater
23:26:56.915 INFO FilterMutectCalls - Inflater: IntelInflater
23:26:56.916 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:26:56.916 INFO FilterMutectCalls - Requester pays: disabled
23:26:56.916 INFO FilterMutectCalls - Initializing engine
23:26:57.037 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.xg2iB2Bx3l/LS0918.mutect2.raw.vcf.gz
23:26:57.143 INFO FilterMutectCalls - Done initializing engine
23:26:57.200 INFO ProgressMeter - Starting traversal
23:26:57.201 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:26:57.201 INFO FilterMutectCalls - Starting pass 0 through the variants
23:26:58.273 INFO FilterMutectCalls - Finished pass 0 through the variants
23:26:59.910 INFO FilterMutectCalls - Starting pass 1 through the variants
23:27:00.843 INFO FilterMutectCalls - Finished pass 1 through the variants
23:27:01.322 INFO FilterMutectCalls - Starting pass 2 through the variants
23:27:02.224 INFO FilterMutectCalls - Finished pass 2 through the variants
23:27:02.226 INFO FilterMutectCalls - Starting pass 3 through the variants
23:27:03.090 INFO FilterMutectCalls - Finished pass 3 through the variants
23:27:03.098 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:27:03.098 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:27:03.099 INFO ProgressMeter - chr6:135203378 0.1 10632 108177.0
23:27:03.099 INFO ProgressMeter - Traversal complete. Processed 10632 total variants in 0.1 minutes.
23:27:03.111 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:27:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=587202560
Using GATK jar /gatk/gatk-package-4.5.0.0-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 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R hg38.fa -V LS0918.mutect2.raw.vcf.gz --stats LS0918.mutect2.raw.vcf.gz.stats -O LS0918.mutect2.filtered.vcf.gz
23:27:04.327 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:27:04.434 INFO SelectVariants - ------------------------------------------------------------
23:27:04.436 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:27:04.436 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:27:04.436 INFO SelectVariants - Executing as ?@nf-55c1c40812d6d7ec802dcffb45770b28-85249-hv4kk on Linux v6.12.88 amd64
23:27:04.436 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:27:04.436 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:27:04 PM GMT
23:27:04.436 INFO SelectVariants - ------------------------------------------------------------
23:27:04.436 INFO SelectVariants - ------------------------------------------------------------
23:27:04.437 INFO SelectVariants - HTSJDK Version: 4.1.0
23:27:04.437 INFO SelectVariants - Picard Version: 3.1.1
23:27:04.437 INFO SelectVariants - Built for Spark Version: 3.5.0
23:27:04.437 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:27:04.437 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:27:04.437 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:27:04.437 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:27:04.437 INFO SelectVariants - Deflater: IntelDeflater
23:27:04.437 INFO SelectVariants - Inflater: IntelInflater
23:27:04.438 INFO SelectVariants - GCS max retries/reopens: 20
23:27:04.438 INFO SelectVariants - Requester pays: disabled
23:27:04.438 INFO SelectVariants - Initializing engine
23:27:04.552 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.xg2iB2Bx3l/LS0918.mutect2.filtered.vcf.gz
23:27:04.653 INFO SelectVariants - Done initializing engine
23:27:04.689 INFO ProgressMeter - Starting traversal
23:27:04.689 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:27:04.764 INFO ProgressMeter - chr6:111714367 0.0 2658 2184657.5
23:27:04.765 INFO ProgressMeter - Traversal complete. Processed 2658 total variants in 0.0 minutes.
23:27:04.775 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:27:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=469762048
Using GATK jar /gatk/gatk-package-4.5.0.0-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 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar SelectVariants -R hg38.fa -V LS0918.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0918.mutect2.pass.vcf.gz