22:44:17.650 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
22:44:17.766 INFO Mutect2 - ------------------------------------------------------------
22:44:17.769 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:17.769 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:17.769 INFO Mutect2 - Executing as ?@nf-d28bb16007c2238e054db97146a33ca3-b396a-lb9pr on Linux v6.12.88 amd64
22:44:17.769 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:17.769 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:17 PM GMT
22:44:17.769 INFO Mutect2 - ------------------------------------------------------------
22:44:17.769 INFO Mutect2 - ------------------------------------------------------------
22:44:17.770 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:17.770 INFO Mutect2 - Picard Version: 3.1.1
22:44:17.771 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:17.771 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:17.771 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:17.771 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:17.771 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:17.771 INFO Mutect2 - Deflater: IntelDeflater
22:44:17.771 INFO Mutect2 - Inflater: IntelInflater
22:44:17.771 INFO Mutect2 - GCS max retries/reopens: 20
22:44:17.771 INFO Mutect2 - Requester pays: disabled
22:44:17.772 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.EynWB9DPKW/LS0889_tumor.bam.bai is older than BAM /tmp/nxf.EynWB9DPKW/LS0889_tumor.bam
22:44:17.958 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.EynWB9DPKW/af-only-gnomad.hg38.vcf.gz
22:44:18.068 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.EynWB9DPKW/TST500C_manifest.bed
22:44:18.103 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:18.135 INFO Mutect2 - Done initializing engine
22:44:18.147 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
22:44:18.149 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
22:44:18.150 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:18.150 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:18.161 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
22:44:18.169 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:18.169 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:18.170 INFO IntelPairHmm - Available threads: 384
22:44:18.170 INFO IntelPairHmm - Requested threads: 4
22:44:18.170 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:18.213 INFO ProgressMeter - Starting traversal
22:44:18.213 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:28.417 INFO ProgressMeter - chr1:11121977 0.2 70 411.7
22:44:38.422 INFO ProgressMeter - chr1:15919402 0.3 150 445.4
22:44:49.201 INFO ProgressMeter - chr1:15939294 0.5 210 406.6
22:45:00.163 INFO ProgressMeter - chr1:18748777 0.7 270 386.2
22:45:10.947 INFO ProgressMeter - chr1:36344159 0.9 340 386.9
22:45:21.089 INFO ProgressMeter - chr1:39891923 1.0 380 362.6
22:45:31.689 INFO ProgressMeter - chr1:39902848 1.2 430 351.1
22:45:42.805 INFO ProgressMeter - chr1:46066052 1.4 490 347.6
22:45:54.753 INFO ProgressMeter - chr1:64838520 1.6 560 348.0
22:46:05.469 INFO ProgressMeter - chr1:85274399 1.8 630 352.4
22:46:17.468 INFO ProgressMeter - chr1:119511501 2.0 700 352.2
22:46:28.908 INFO ProgressMeter - chr1:119949005 2.2 750 344.3
22:46:47.389 INFO ProgressMeter - chr1:156874381 2.5 820 329.8
22:46:58.115 INFO ProgressMeter - chr1:158642484 2.7 870 326.5
22:47:09.825 INFO ProgressMeter - chr1:162776134 2.9 940 328.7
22:47:20.497 INFO ProgressMeter - chr1:204427646 3.0 1020 335.7
22:47:31.326 INFO ProgressMeter - chr1:204532377 3.2 1090 338.7
22:47:41.606 INFO ProgressMeter - chr1:206493918 3.4 1150 339.2
22:47:53.172 INFO ProgressMeter - chr1:243500729 3.6 1230 343.3
22:48:03.529 INFO ProgressMeter - chr10:8055759 3.8 1280 340.9
22:48:14.067 INFO ProgressMeter - chr10:32010250 3.9 1350 343.4
22:48:25.932 INFO ProgressMeter - chr10:43113308 4.1 1430 346.4
22:48:37.350 INFO ProgressMeter - chr10:43126883 4.3 1480 342.7
22:48:48.162 INFO ProgressMeter - chr10:68686354 4.5 1550 344.5
22:48:59.207 INFO ProgressMeter - chr10:101773503 4.7 1650 352.3
22:49:09.780 INFO ProgressMeter - chr10:113089398 4.9 1740 358.1
22:49:20.006 INFO ProgressMeter - chr10:121503144 5.0 1800 357.9
22:49:30.719 INFO ProgressMeter - chr11:64360161 5.2 1910 366.7
22:49:40.934 INFO ProgressMeter - chr11:69650543 5.4 2010 373.7
22:49:50.963 INFO ProgressMeter - chr11:69703108 5.5 2060 371.5
22:50:04.508 INFO ProgressMeter - chr11:69810603 5.8 2130 369.1
22:50:15.465 INFO ProgressMeter - chr11:76546209 6.0 2190 367.8
22:50:26.501 INFO ProgressMeter - chr11:77452651 6.1 2260 368.2
22:50:41.075 INFO ProgressMeter - chr11:102324879 6.4 2340 366.7
22:50:51.683 INFO ProgressMeter - chr11:118471960 6.6 2440 372.1
22:51:02.894 INFO ProgressMeter - chr11:118505475 6.7 2500 370.7
22:51:12.970 INFO ProgressMeter - chr11:125627605 6.9 2550 368.9
22:51:25.204 INFO ProgressMeter - chr11:128460928 7.1 2610 366.8
22:51:36.983 INFO ProgressMeter - chr12:310883 7.3 2670 365.1
22:51:47.679 INFO ProgressMeter - chr12:4373770 7.5 2750 367.1
22:51:59.234 INFO ProgressMeter - chr12:4450501 7.7 2820 367.0
22:52:10.408 INFO ProgressMeter - chr12:11853593 7.9 2890 367.2
22:52:22.618 INFO ProgressMeter - chr12:11859830 8.1 2940 364.2
22:52:35.031 INFO ProgressMeter - chr12:11866872 8.3 2980 359.9
22:52:48.248 INFO ProgressMeter - chr12:11869466 8.5 3000 352.9
22:52:58.650 INFO ProgressMeter - chr12:25226405 8.7 3080 355.1
22:53:09.104 INFO ProgressMeter - chr12:45851134 8.8 3140 354.9
22:53:19.223 INFO ProgressMeter - chr12:49032689 9.0 3190 353.8
22:53:29.872 INFO ProgressMeter - chr12:49040567 9.2 3220 350.2
22:53:41.406 INFO ProgressMeter - chr12:49053976 9.4 3280 349.4
22:53:52.459 INFO ProgressMeter - chr12:56097043 9.6 3360 351.1
22:54:02.916 INFO ProgressMeter - chr12:57095053 9.7 3410 349.9
22:54:13.143 INFO ProgressMeter - chr12:57751868 9.9 3470 350.0
22:54:24.113 INFO ProgressMeter - chr12:102417816 10.1 3550 351.5
22:54:36.010 INFO ProgressMeter - chr12:120994271 10.3 3630 352.5
22:54:47.326 INFO ProgressMeter - chr12:132673573 10.5 3700 352.9
22:54:57.347 INFO ProgressMeter - chr13:21701188 10.7 3780 354.9
22:55:09.167 INFO ProgressMeter - chr13:28387751 10.8 3880 357.6
22:55:22.216 INFO ProgressMeter - chr13:32339505 11.1 3950 356.9
22:55:32.767 INFO ProgressMeter - chr13:72761644 11.2 4050 360.2
22:55:42.952 INFO ProgressMeter - chr13:106286025 11.4 4150 363.6
22:55:53.918 INFO ProgressMeter - chr14:23307766 11.6 4230 364.8
22:56:04.177 INFO ProgressMeter - chr14:37597843 11.8 4330 368.0
22:56:15.031 INFO ProgressMeter - chr14:95095770 11.9 4400 368.3
22:56:26.464 INFO ProgressMeter - chr14:104772363 12.1 4470 368.3
22:56:37.943 INFO ProgressMeter - chr15:34355716 12.3 4530 367.4
22:56:49.428 INFO ProgressMeter - chr15:41749590 12.5 4590 366.6
22:57:00.677 INFO ProgressMeter - chr15:66435151 12.7 4670 367.5
22:57:11.738 INFO ProgressMeter - chr15:88127160 12.9 4740 367.7
22:57:22.252 INFO ProgressMeter - chr15:90749850 13.1 4830 369.6
22:57:32.796 INFO ProgressMeter - chr15:93014694 13.2 4910 370.8
22:57:43.479 INFO ProgressMeter - chr16:2072239 13.4 5000 372.5
22:57:53.855 INFO ProgressMeter - chr16:3602116 13.6 5110 375.9
22:58:04.852 INFO ProgressMeter - chr16:9764789 13.8 5190 376.7
22:58:14.944 INFO ProgressMeter - chr16:31135456 13.9 5280 378.6
22:58:25.703 INFO ProgressMeter - chr16:68833350 14.1 5380 380.9
22:58:36.025 INFO ProgressMeter - chr16:72797875 14.3 5420 379.1
22:58:46.658 INFO ProgressMeter - chr16:81946173 14.5 5500 380.0
22:58:56.660 INFO ProgressMeter - chr16:89752136 14.6 5570 380.4
22:59:08.840 INFO ProgressMeter - chr17:7676192 14.8 5660 381.3
22:59:18.891 INFO ProgressMeter - chr17:16065645 15.0 5750 383.0
22:59:30.044 INFO ProgressMeter - chr17:31222626 15.2 5850 384.9
22:59:40.490 INFO ProgressMeter - chr17:35118621 15.4 5950 387.1
22:59:51.131 INFO ProgressMeter - chr17:39727293 15.5 6040 388.5
23:00:01.400 INFO ProgressMeter - chr17:42323258 15.7 6150 391.2
23:00:14.391 INFO ProgressMeter - chr17:43093795 15.9 6230 390.9
23:00:28.094 INFO ProgressMeter - chr17:43535246 16.2 6290 389.1
23:00:39.393 INFO ProgressMeter - chr17:43541983 16.4 6340 387.7
23:00:50.179 INFO ProgressMeter - chr17:45290743 16.5 6390 386.5
23:01:01.432 INFO ProgressMeter - chr17:59921649 16.7 6480 387.6
23:01:11.831 INFO ProgressMeter - chr17:61861445 16.9 6550 387.7
23:01:22.881 INFO ProgressMeter - chr17:80880413 17.1 6640 388.8
23:01:34.251 INFO ProgressMeter - chr18:44950069 17.3 6740 390.3
23:01:44.543 INFO ProgressMeter - chr18:58696364 17.4 6800 389.9
23:01:54.771 INFO ProgressMeter - chr19:2223398 17.6 6910 392.4
23:02:05.194 INFO ProgressMeter - chr19:5273523 17.8 7020 394.8
23:02:16.277 INFO ProgressMeter - chr19:10154903 18.0 7100 395.2
23:02:27.026 INFO ProgressMeter - chr19:11058253 18.1 7180 395.7
23:02:38.010 INFO ProgressMeter - chr19:15187103 18.3 7260 396.1
23:02:48.079 INFO ProgressMeter - chr19:17835922 18.5 7330 396.3
23:03:01.180 INFO ProgressMeter - chr19:29817404 18.7 7410 395.9
23:03:11.383 INFO ProgressMeter - chr19:35727721 18.9 7490 396.6
23:03:21.382 INFO ProgressMeter - chr19:40260271 19.1 7560 396.8
23:03:31.673 INFO ProgressMeter - chr19:41260245 19.2 7610 395.9
23:03:42.461 INFO ProgressMeter - chr19:45352744 19.4 7680 395.8
23:03:53.018 INFO ProgressMeter - chr19:45416592 19.6 7760 396.3
23:04:04.108 INFO ProgressMeter - chr19:50409517 19.8 7810 395.1
23:04:15.256 INFO ProgressMeter - chr2:15942743 20.0 7870 394.5
23:04:26.282 INFO ProgressMeter - chr2:25247589 20.1 7940 394.3
23:04:36.854 INFO ProgressMeter - chr2:25878164 20.3 7990 393.4
23:04:48.938 INFO ProgressMeter - chr2:29225940 20.5 8040 392.0
23:04:59.157 INFO ProgressMeter - chr2:29920245 20.7 8090 391.2
23:05:10.027 INFO ProgressMeter - chr2:47379872 20.9 8150 390.6
23:05:21.033 INFO ProgressMeter - chr2:47806777 21.0 8200 389.6
23:05:34.009 INFO ProgressMeter - chr2:96262363 21.3 8270 388.9
23:05:44.552 INFO ProgressMeter - chr2:108767287 21.4 8350 389.5
23:05:54.627 INFO ProgressMeter - chr2:111153778 21.6 8400 388.8
23:06:04.936 INFO ProgressMeter - chr2:113225069 21.8 8440 387.5
23:06:15.559 INFO ProgressMeter - chr2:113230538 22.0 8480 386.2
23:06:27.340 INFO ProgressMeter - chr2:113234356 22.2 8510 384.2
23:06:37.942 INFO ProgressMeter - chr2:140247084 22.3 8590 384.7
23:06:48.729 INFO ProgressMeter - chr2:140907875 22.5 8680 385.6
23:06:59.121 INFO ProgressMeter - chr2:189854537 22.7 8770 386.7
23:07:09.281 INFO ProgressMeter - chr2:201285136 22.9 8860 387.7
23:07:21.464 INFO ProgressMeter - chr2:222200404 23.1 8960 388.6
23:07:31.592 INFO ProgressMeter - chr2:222204265 23.2 8990 387.1
23:07:44.060 INFO ProgressMeter - chr2:222214580 23.4 9040 385.8
23:07:55.010 INFO ProgressMeter - chr2:222293628 23.6 9080 384.5
23:08:06.008 INFO ProgressMeter - chr2:241852919 23.8 9150 384.5
23:08:16.131 INFO ProgressMeter - chr20:32435967 24.0 9210 384.3
23:08:26.967 INFO ProgressMeter - chr20:42081880 24.1 9290 384.7
23:08:37.341 INFO ProgressMeter - chr20:47652404 24.3 9360 384.9
23:08:47.387 INFO ProgressMeter - chr20:63700675 24.5 9440 385.5
23:08:57.886 INFO ProgressMeter - chr21:38471877 24.7 9520 386.0
23:09:08.335 INFO ProgressMeter - chr21:41490942 24.8 9570 385.3
23:09:20.423 INFO ProgressMeter - chr21:41499242 25.0 9610 383.8
23:09:30.801 INFO ProgressMeter - chr21:41507939 25.2 9660 383.2
23:09:43.121 INFO ProgressMeter - chr22:23290002 25.4 9760 384.0
23:09:53.655 INFO ProgressMeter - chr22:23791754 25.6 9800 383.0
23:10:05.045 INFO ProgressMeter - chr22:29284601 25.8 9900 384.0
23:10:15.712 INFO ProgressMeter - chr22:29287104 26.0 9920 382.2
23:10:26.884 INFO ProgressMeter - chr22:41147845 26.1 10000 382.5
23:10:37.083 INFO ProgressMeter - chr3:10049372 26.3 10070 382.7
23:10:47.639 INFO ProgressMeter - chr3:12357455 26.5 10150 383.2
23:10:58.991 INFO ProgressMeter - chr3:12363241 26.7 10190 381.9
23:11:09.295 INFO ProgressMeter - chr3:12371254 26.9 10240 381.4
23:11:20.673 INFO ProgressMeter - chr3:12405880 27.0 10300 380.9
23:11:31.197 INFO ProgressMeter - chr3:37040184 27.2 10390 381.8
23:11:42.787 INFO ProgressMeter - chr3:47124274 27.4 10480 382.3
23:11:53.463 INFO ProgressMeter - chr3:52550745 27.6 10580 383.5
23:12:03.988 INFO ProgressMeter - chr3:89209864 27.8 10690 385.0
23:12:15.280 INFO ProgressMeter - chr3:136338236 28.0 10770 385.3
23:12:25.574 INFO ProgressMeter - chr3:138704226 28.1 10840 385.5
23:12:35.950 INFO ProgressMeter - chr3:142519667 28.3 10910 385.6
23:12:47.275 INFO ProgressMeter - chr3:179185522 28.5 10990 385.8
23:12:58.450 INFO ProgressMeter - chr3:185447810 28.7 11060 385.8
23:13:08.824 INFO ProgressMeter - chr3:186105623 28.8 11100 384.8
23:13:20.953 INFO ProgressMeter - chr3:196057867 29.0 11180 384.9
23:13:31.348 INFO ProgressMeter - chr4:20550850 29.2 11290 386.4
23:13:42.076 INFO ProgressMeter - chr4:54672213 29.4 11390 387.4
23:13:53.151 INFO ProgressMeter - chr4:55113302 29.6 11460 387.4
23:14:03.494 INFO ProgressMeter - chr4:98929093 29.8 11570 388.8
23:14:13.714 INFO ProgressMeter - chr4:105275079 29.9 11630 388.6
23:14:23.952 INFO ProgressMeter - chr4:186596746 30.1 11740 390.1
23:14:36.174 INFO ProgressMeter - chr4:186708654 30.3 11820 390.1
23:14:46.655 INFO ProgressMeter - chr5:38966639 30.5 11910 390.8
23:14:57.141 INFO ProgressMeter - chr5:56882557 30.6 12010 391.9
23:15:07.787 INFO ProgressMeter - chr5:112827195 30.8 12150 394.1
23:15:18.359 INFO ProgressMeter - chr5:122451506 31.0 12210 393.8
23:15:29.670 INFO ProgressMeter - chr5:142685259 31.2 12310 394.7
23:15:40.251 INFO ProgressMeter - chr5:150129755 31.4 12380 394.7
23:15:50.926 INFO ProgressMeter - chr5:171390049 31.5 12450 394.7
23:16:01.053 INFO ProgressMeter - chr5:177098470 31.7 12520 394.8
23:16:11.565 INFO ProgressMeter - chr5:177295135 31.9 12580 394.5
23:16:22.041 INFO ProgressMeter - chr6:20419963 32.1 12680 395.5
23:16:32.533 INFO ProgressMeter - chr6:20481557 32.2 12730 394.9
23:16:47.398 INFO ProgressMeter - chr6:30700563 32.5 12810 394.3
23:16:57.635 INFO ProgressMeter - chr6:32200829 32.7 12870 394.1
23:17:08.317 INFO ProgressMeter - chr6:36684095 32.8 12950 394.4
23:17:18.757 INFO ProgressMeter - chr6:93269475 33.0 13060 395.6
23:17:29.920 INFO ProgressMeter - chr6:117318294 33.2 13140 395.8
23:17:41.820 INFO ProgressMeter - chr6:117323916 33.4 13180 394.7
23:17:52.779 INFO ProgressMeter - chr6:117331662 33.6 13230 394.0
23:18:04.670 INFO ProgressMeter - chr6:117339256 33.8 13290 393.5
23:18:14.698 INFO ProgressMeter - chr6:135200083 33.9 13360 393.6
23:18:31.014 INFO ProgressMeter - chr6:135208939 34.2 13400 391.7
23:18:42.002 INFO ProgressMeter - chr6:135212371 34.4 13430 390.4
23:18:52.953 INFO ProgressMeter - chr6:135217539 34.6 13470 389.5
23:19:03.063 INFO ProgressMeter - chr6:149684572 34.7 13530 389.4
23:19:14.446 INFO ProgressMeter - chr6:156778133 34.9 13600 389.3
23:19:25.953 INFO ProgressMeter - chr6:161049499 35.1 13660 388.9
23:19:36.952 INFO ProgressMeter - chr7:2938692 35.3 13750 389.4
23:19:47.464 INFO ProgressMeter - chr7:13906728 35.5 13810 389.2
23:19:57.938 INFO ProgressMeter - chr7:13933578 35.7 13840 388.1
23:20:09.826 INFO ProgressMeter - chr7:13940868 35.9 13890 387.3
23:20:20.443 INFO ProgressMeter - chr7:13946371 36.0 13930 386.5
23:20:30.504 INFO ProgressMeter - chr7:13950689 36.2 13960 385.6
23:20:42.364 INFO ProgressMeter - chr7:13956182 36.4 13990 384.3
23:20:54.348 INFO ProgressMeter - chr7:13962143 36.6 14030 383.3
23:21:05.884 INFO ProgressMeter - chr7:13969039 36.8 14070 382.4
23:21:18.539 INFO ProgressMeter - chr7:13974711 37.0 14110 381.3
23:21:29.176 INFO ProgressMeter - chr7:13979314 37.2 14140 380.3
23:21:39.811 INFO ProgressMeter - chr7:13985866 37.4 14180 379.6
23:21:49.964 INFO ProgressMeter - chr7:41689816 37.5 14210 378.6
23:22:01.332 INFO ProgressMeter - chr7:55157661 37.7 14270 378.3
23:22:15.871 INFO ProgressMeter - chr7:55170231 38.0 14310 377.0
23:22:27.908 INFO ProgressMeter - chr7:55178490 38.2 14360 376.3
23:22:38.992 INFO ProgressMeter - chr7:55204756 38.3 14410 375.8
23:22:50.167 INFO ProgressMeter - chr7:86850368 38.5 14490 376.0
23:23:01.466 INFO ProgressMeter - chr7:102201833 38.7 14570 376.3
23:23:11.801 INFO ProgressMeter - chr7:116699683 38.9 14630 376.2
23:23:24.097 INFO ProgressMeter - chr7:140739008 39.1 14700 376.0
23:23:35.404 INFO ProgressMeter - chr7:140805691 39.3 14760 375.7
23:23:45.671 INFO ProgressMeter - chr7:152144711 39.5 14850 376.4
23:23:57.068 INFO ProgressMeter - chr7:152180794 39.6 14900 375.8
23:24:07.726 INFO ProgressMeter - chr8:11750201 39.8 14980 376.1
23:24:18.475 INFO ProgressMeter - chr8:32634041 40.0 15050 376.2
23:24:29.648 INFO ProgressMeter - chr8:37831548 40.2 15120 376.2
23:24:40.515 INFO ProgressMeter - chr8:38437079 40.4 15180 376.0
23:24:51.678 INFO ProgressMeter - chr8:41955294 40.6 15240 375.8
23:25:01.812 INFO ProgressMeter - chr8:47849152 40.7 15310 375.9
23:25:12.414 INFO ProgressMeter - chr8:55969715 40.9 15400 376.5
23:25:22.515 INFO ProgressMeter - chr8:89955348 41.1 15480 376.9
23:25:32.574 INFO ProgressMeter - chr8:127735568 41.2 15550 377.1
23:25:43.012 INFO ProgressMeter - chr8:144514934 41.4 15630 377.4
23:25:53.048 INFO ProgressMeter - chr9:8492860 41.6 15740 378.5
23:26:03.282 INFO ProgressMeter - chr9:35079439 41.8 15830 379.2
23:26:16.366 INFO ProgressMeter - chr9:84744616 42.0 15910 379.1
23:26:29.713 INFO ProgressMeter - chr9:84861467 42.2 15950 378.0
23:26:40.281 INFO ProgressMeter - chr9:84866417 42.4 15980 377.2
23:26:50.440 INFO ProgressMeter - chr9:84877541 42.5 16020 376.6
23:27:04.356 INFO ProgressMeter - chr9:90844065 42.8 16070 375.7
23:27:15.100 INFO ProgressMeter - chr9:99137986 42.9 16160 376.3
23:27:25.533 INFO ProgressMeter - chr9:132896233 43.1 16230 376.4
23:27:36.866 INFO ProgressMeter - chr9:136517902 43.3 16310 376.6
23:27:47.966 INFO ProgressMeter - chrX:40073617 43.5 16400 377.0
23:27:58.475 INFO ProgressMeter - chrX:47186171 43.7 16480 377.4
23:28:14.006 INFO ProgressMeter - chrX:49036096 43.9 16540 376.5
23:28:25.111 INFO ProgressMeter - chrX:53195914 44.1 16580 375.8
23:28:36.864 INFO ProgressMeter - chrX:64191134 44.3 16650 375.8
23:28:47.903 INFO ProgressMeter - chrX:67574654 44.5 16690 375.1
23:28:58.287 INFO ProgressMeter - chrX:71132071 44.7 16760 375.2
23:29:09.698 INFO ProgressMeter - chrX:71463822 44.9 16830 375.2
23:29:20.310 INFO ProgressMeter - chrX:101356782 45.0 16900 375.3
23:29:30.503 INFO ProgressMeter - chrX:124066354 45.2 16980 375.6
23:29:41.156 INFO ProgressMeter - chrX:134413802 45.4 17040 375.5
23:29:41.644 INFO Mutect2 - 555723 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
12 read(s) filtered by: ReadLengthReadFilter
147 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
555882 total reads filtered out of 80124382 reads processed
23:29:41.645 INFO ProgressMeter - chrY:20398623 45.4 17085 376.4
23:29:41.645 INFO ProgressMeter - Traversal complete. Processed 17085 total regions in 45.4 minutes.
23:29:41.660 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 5.998248487000001
23:29:41.661 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 271.30059264
23:29:41.661 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 9.21 sec
23:29:41.661 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:29:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 45.40 minutes.
Runtime.totalMemory()=5326766080
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 LS0889_tumor.bam --tumor-sample LS0889 -L TST500C_manifest.bed -O LS0889.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:29:43.337 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
23:29:43.455 INFO FilterMutectCalls - ------------------------------------------------------------
23:29:43.458 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:29:43.458 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:29:43.458 INFO FilterMutectCalls - Executing as ?@nf-d28bb16007c2238e054db97146a33ca3-b396a-lb9pr on Linux v6.12.88 amd64
23:29:43.458 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:29:43.458 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:29:43 PM GMT
23:29:43.458 INFO FilterMutectCalls - ------------------------------------------------------------
23:29:43.459 INFO FilterMutectCalls - ------------------------------------------------------------
23:29:43.459 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:29:43.459 INFO FilterMutectCalls - Picard Version: 3.1.1
23:29:43.460 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:29:43.460 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:29:43.460 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:29:43.460 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:29:43.460 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:29:43.460 INFO FilterMutectCalls - Deflater: IntelDeflater
23:29:43.460 INFO FilterMutectCalls - Inflater: IntelInflater
23:29:43.460 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:29:43.460 INFO FilterMutectCalls - Requester pays: disabled
23:29:43.461 INFO FilterMutectCalls - Initializing engine
23:29:43.605 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.EynWB9DPKW/LS0889.mutect2.raw.vcf.gz
23:29:43.708 INFO FilterMutectCalls - Done initializing engine
23:29:43.762 INFO ProgressMeter - Starting traversal
23:29:43.762 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:29:43.763 INFO FilterMutectCalls - Starting pass 0 through the variants
23:29:44.964 INFO FilterMutectCalls - Finished pass 0 through the variants
23:29:49.640 INFO FilterMutectCalls - Starting pass 1 through the variants
23:29:50.937 INFO FilterMutectCalls - Finished pass 1 through the variants
23:29:51.740 INFO FilterMutectCalls - Starting pass 2 through the variants
23:29:53.011 INFO FilterMutectCalls - Finished pass 2 through the variants
23:29:53.013 INFO FilterMutectCalls - Starting pass 3 through the variants
23:29:53.985 INFO ProgressMeter - chr7:55169102 0.2 10000 58714.2
23:29:54.128 INFO FilterMutectCalls - Finished pass 3 through the variants
23:29:54.134 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:29:54.135 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:29:54.135 INFO ProgressMeter - chr7:55169102 0.2 10344 59838.0
23:29:54.135 INFO ProgressMeter - Traversal complete. Processed 10344 total variants in 0.2 minutes.
23:29:54.146 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:29:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.18 minutes.
Runtime.totalMemory()=226492416
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 LS0889.mutect2.raw.vcf.gz --stats LS0889.mutect2.raw.vcf.gz.stats -O LS0889.mutect2.filtered.vcf.gz
23:29:55.339 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
23:29:55.446 INFO SelectVariants - ------------------------------------------------------------
23:29:55.448 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:29:55.448 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:29:55.448 INFO SelectVariants - Executing as ?@nf-d28bb16007c2238e054db97146a33ca3-b396a-lb9pr on Linux v6.12.88 amd64
23:29:55.448 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:29:55.448 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:29:55 PM GMT
23:29:55.448 INFO SelectVariants - ------------------------------------------------------------
23:29:55.449 INFO SelectVariants - ------------------------------------------------------------
23:29:55.449 INFO SelectVariants - HTSJDK Version: 4.1.0
23:29:55.449 INFO SelectVariants - Picard Version: 3.1.1
23:29:55.449 INFO SelectVariants - Built for Spark Version: 3.5.0
23:29:55.449 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:29:55.449 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:29:55.449 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:29:55.450 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:29:55.450 INFO SelectVariants - Deflater: IntelDeflater
23:29:55.450 INFO SelectVariants - Inflater: IntelInflater
23:29:55.450 INFO SelectVariants - GCS max retries/reopens: 20
23:29:55.450 INFO SelectVariants - Requester pays: disabled
23:29:55.450 INFO SelectVariants - Initializing engine
23:29:55.635 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.EynWB9DPKW/LS0889.mutect2.filtered.vcf.gz
23:29:55.751 INFO SelectVariants - Done initializing engine
23:29:55.790 INFO ProgressMeter - Starting traversal
23:29:55.790 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:29:55.872 INFO ProgressMeter - chr6:137878546 0.0 2586 1939500.0
23:29:55.872 INFO ProgressMeter - Traversal complete. Processed 2586 total variants in 0.0 minutes.
23:29:55.882 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:29:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=427819008
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 LS0889.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0889.mutect2.pass.vcf.gz