22:44:12.760 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
22:44:12.871 INFO Mutect2 - ------------------------------------------------------------
22:44:12.874 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:12.874 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:12.874 INFO Mutect2 - Executing as ?@nf-466d0b4e5f9bf71b05029889b21f82f1-91109-5flvs on Linux v6.12.88 amd64
22:44:12.874 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:12.874 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:12 PM GMT
22:44:12.874 INFO Mutect2 - ------------------------------------------------------------
22:44:12.875 INFO Mutect2 - ------------------------------------------------------------
22:44:12.875 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:12.875 INFO Mutect2 - Picard Version: 3.1.1
22:44:12.875 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:12.876 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:12.876 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:12.876 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:12.876 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:12.876 INFO Mutect2 - Deflater: IntelDeflater
22:44:12.876 INFO Mutect2 - Inflater: IntelInflater
22:44:12.876 INFO Mutect2 - GCS max retries/reopens: 20
22:44:12.876 INFO Mutect2 - Requester pays: disabled
22:44:12.877 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.wuZ9rSMrd2/LS0910_tumor.bam.bai is older than BAM /tmp/nxf.wuZ9rSMrd2/LS0910_tumor.bam
22:44:13.133 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.wuZ9rSMrd2/af-only-gnomad.hg38.vcf.gz
22:44:13.278 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.wuZ9rSMrd2/TST500C_manifest.bed
22:44:13.312 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:13.342 INFO Mutect2 - Done initializing engine
22:44:13.353 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
22:44:13.354 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
22:44:13.355 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:13.355 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:13.365 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
22:44:13.375 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:13.375 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:13.375 INFO IntelPairHmm - Available threads: 384
22:44:13.375 INFO IntelPairHmm - Requested threads: 4
22:44:13.375 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:13.413 INFO ProgressMeter - Starting traversal
22:44:13.413 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:24.035 INFO ProgressMeter - chr1:11139531 0.2 100 565.0
22:44:35.350 INFO ProgressMeter - chr1:15929764 0.4 180 492.3
22:44:45.351 INFO ProgressMeter - chr1:18735630 0.5 250 469.7
22:44:55.561 INFO ProgressMeter - chr1:26731569 0.7 320 455.5
22:45:06.586 INFO ProgressMeter - chr1:39890723 0.9 410 462.6
22:45:16.882 INFO ProgressMeter - chr1:45339974 1.1 510 482.1
22:45:27.496 INFO ProgressMeter - chr1:71698006 1.2 620 502.1
22:45:38.545 INFO ProgressMeter - chr1:119915770 1.4 730 514.5
22:45:49.006 INFO ProgressMeter - chr1:156872113 1.6 820 514.7
22:46:00.168 INFO ProgressMeter - chr1:158644251 1.8 880 494.6
22:46:10.538 INFO ProgressMeter - chr1:176116661 2.0 980 502.0
22:46:21.803 INFO ProgressMeter - chr1:204469339 2.1 1090 509.4
22:46:33.055 INFO ProgressMeter - chr1:226379571 2.3 1200 515.6
22:46:43.102 INFO ProgressMeter - chr1:243503026 2.5 1270 509.1
22:46:53.757 INFO ProgressMeter - chr10:27035491 2.7 1340 501.4
22:47:03.820 INFO ProgressMeter - chr10:32056380 2.8 1430 503.5
22:47:14.866 INFO ProgressMeter - chr10:43115966 3.0 1490 492.7
22:47:26.618 INFO ProgressMeter - chr10:68574062 3.2 1560 484.5
22:47:36.619 INFO ProgressMeter - chr10:87938652 3.4 1640 484.2
22:47:47.051 INFO ProgressMeter - chr10:102599431 3.6 1730 485.9
22:47:58.729 INFO ProgressMeter - chr10:121480811 3.8 1820 484.7
22:48:10.692 INFO ProgressMeter - chr10:121565663 4.0 1890 477.9
22:48:21.563 INFO ProgressMeter - chr11:64807082 4.1 2000 483.6
22:48:32.740 INFO ProgressMeter - chr11:69701708 4.3 2100 485.9
22:48:47.948 INFO ProgressMeter - chr11:69810188 4.6 2180 476.4
22:48:58.490 INFO ProgressMeter - chr11:77336084 4.8 2260 475.7
22:49:09.034 INFO ProgressMeter - chr11:94437175 4.9 2350 477.0
22:49:21.474 INFO ProgressMeter - chr11:102325464 5.1 2420 471.3
22:49:33.618 INFO ProgressMeter - chr11:118472904 5.3 2530 474.1
22:49:45.464 INFO ProgressMeter - chr11:118505475 5.5 2600 469.8
22:49:56.537 INFO ProgressMeter - chr11:125633161 5.7 2660 465.1
22:50:06.832 INFO ProgressMeter - chr11:128459962 5.9 2710 460.1
22:50:17.116 INFO ProgressMeter - chr11:128811657 6.1 2770 457.0
22:50:28.085 INFO ProgressMeter - chr12:4370543 6.2 2870 459.6
22:50:38.887 INFO ProgressMeter - chr12:6570867 6.4 2960 460.7
22:50:50.151 INFO ProgressMeter - chr12:11854824 6.6 3030 458.2
22:51:02.152 INFO ProgressMeter - chr12:11860513 6.8 3080 452.1
22:51:14.815 INFO ProgressMeter - chr12:11868761 7.0 3130 445.7
22:51:25.320 INFO ProgressMeter - chr12:25226405 7.2 3230 448.7
22:51:35.333 INFO ProgressMeter - chr12:49022798 7.4 3310 449.4
22:51:45.579 INFO ProgressMeter - chr12:49037615 7.5 3360 445.9
22:51:57.603 INFO ProgressMeter - chr12:49052406 7.7 3440 444.6
22:52:08.580 INFO ProgressMeter - chr12:57092023 7.9 3550 448.3
22:52:19.580 INFO ProgressMeter - chr12:57750730 8.1 3630 448.0
22:52:30.114 INFO ProgressMeter - chr12:111418637 8.3 3740 451.8
22:52:40.175 INFO ProgressMeter - chr12:132632481 8.4 3830 453.5
22:52:51.557 INFO ProgressMeter - chr13:20988423 8.6 3920 453.9
22:53:02.157 INFO ProgressMeter - chr13:26400548 8.8 4000 453.9
22:53:13.614 INFO ProgressMeter - chr13:28385719 9.0 4070 452.1
22:53:24.651 INFO ProgressMeter - chr13:28430048 9.2 4110 447.4
22:53:36.486 INFO ProgressMeter - chr13:32338881 9.4 4170 444.3
22:53:47.182 INFO ProgressMeter - chr13:40560161 9.6 4220 441.3
22:53:57.376 INFO ProgressMeter - chr13:101875184 9.7 4310 442.8
22:54:08.928 INFO ProgressMeter - chr13:106286100 9.9 4380 441.3
22:54:20.913 INFO ProgressMeter - chr14:23307822 10.1 4470 441.5
22:54:31.628 INFO ProgressMeter - chr14:65076556 10.3 4590 445.5
22:54:42.190 INFO ProgressMeter - chr14:102084950 10.5 4690 447.5
22:54:53.008 INFO ProgressMeter - chr15:34356759 10.7 4770 447.5
22:55:03.337 INFO ProgressMeter - chr15:41749852 10.8 4840 446.8
22:55:13.676 INFO ProgressMeter - chr15:73702339 11.0 4940 448.9
22:55:24.504 INFO ProgressMeter - chr15:89263901 11.2 5030 449.7
22:55:34.629 INFO ProgressMeter - chr15:92939705 11.4 5130 451.8
22:55:46.250 INFO ProgressMeter - chr16:346406 11.5 5230 452.9
22:55:56.570 INFO ProgressMeter - chr16:3582340 11.7 5350 456.5
22:56:07.199 INFO ProgressMeter - chr16:3728787 11.9 5400 453.9
22:56:18.868 INFO ProgressMeter - chr16:9938068 12.1 5480 453.2
22:56:29.036 INFO ProgressMeter - chr16:30121822 12.3 5560 453.5
22:56:39.378 INFO ProgressMeter - chr16:67629396 12.4 5650 454.4
22:56:50.004 INFO ProgressMeter - chr16:72797151 12.6 5720 453.6
22:57:00.838 INFO ProgressMeter - chr16:81923483 12.8 5790 452.7
22:57:11.368 INFO ProgressMeter - chr16:89744957 13.0 5870 452.7
22:57:21.997 INFO ProgressMeter - chr17:7685285 13.1 5990 455.8
22:57:32.149 INFO ProgressMeter - chr17:17221377 13.3 6110 459.0
22:57:42.933 INFO ProgressMeter - chr17:35101199 13.5 6230 461.8
22:57:53.716 INFO ProgressMeter - chr17:39724724 13.7 6330 463.0
22:58:03.792 INFO ProgressMeter - chr17:42307591 13.8 6460 466.8
22:58:16.008 INFO ProgressMeter - chr17:43094305 14.0 6560 467.1
22:58:26.012 INFO ProgressMeter - chr17:43538813 14.2 6650 468.0
22:58:37.032 INFO ProgressMeter - chr17:48728191 14.4 6720 466.9
22:58:48.546 INFO ProgressMeter - chr17:59947275 14.6 6830 468.3
22:58:59.366 INFO ProgressMeter - chr17:65558413 14.8 6930 469.3
22:59:10.109 INFO ProgressMeter - chr18:44949978 14.9 7080 473.7
22:59:20.269 INFO ProgressMeter - chr19:1625574 15.1 7200 476.4
22:59:30.374 INFO ProgressMeter - chr19:5220026 15.3 7320 479.0
22:59:41.446 INFO ProgressMeter - chr19:10154292 15.5 7430 480.4
22:59:51.851 INFO ProgressMeter - chr19:14517307 15.6 7550 482.7
23:00:02.548 INFO ProgressMeter - chr19:15265457 15.8 7660 484.2
23:00:12.862 INFO ProgressMeter - chr19:29819173 16.0 7760 485.3
23:00:22.992 INFO ProgressMeter - chr19:40231389 16.2 7870 487.0
23:00:33.229 INFO ProgressMeter - chr19:41260193 16.3 7950 486.8
23:00:43.548 INFO ProgressMeter - chr19:45364513 16.5 8040 487.2
23:00:54.147 INFO ProgressMeter - chr19:52219689 16.7 8170 489.8
23:01:04.590 INFO ProgressMeter - chr2:17773217 16.9 8240 488.9
23:01:15.920 INFO ProgressMeter - chr2:25749919 17.0 8310 487.6
23:01:27.050 INFO ProgressMeter - chr2:29225935 17.2 8380 486.4
23:01:38.887 INFO ProgressMeter - chr2:42261283 17.4 8450 484.9
23:01:49.671 INFO ProgressMeter - chr2:47429900 17.6 8520 484.0
23:02:00.228 INFO ProgressMeter - chr2:61499711 17.8 8620 484.8
23:02:10.754 INFO ProgressMeter - chr2:108764204 18.0 8710 485.1
23:02:21.766 INFO ProgressMeter - chr2:111127371 18.1 8770 483.5
23:02:35.000 INFO ProgressMeter - chr2:113226104 18.4 8830 480.9
23:02:45.659 INFO ProgressMeter - chr2:113232784 18.5 8880 479.0
23:02:56.277 INFO ProgressMeter - chr2:136118044 18.7 8950 478.2
23:03:07.044 INFO ProgressMeter - chr2:141013577 18.9 9060 479.5
23:03:17.995 INFO ProgressMeter - chr2:197396054 19.1 9170 480.7
23:03:28.634 INFO ProgressMeter - chr2:211725074 19.3 9280 482.0
23:03:39.718 INFO ProgressMeter - chr2:222203905 19.4 9350 481.0
23:03:51.386 INFO ProgressMeter - chr2:222210912 19.6 9410 479.3
23:04:02.714 INFO ProgressMeter - chr2:222217673 19.8 9450 476.8
23:04:13.616 INFO ProgressMeter - chr2:226795770 20.0 9530 476.4
23:04:24.396 INFO ProgressMeter - chr20:32431393 20.2 9610 476.1
23:04:34.661 INFO ProgressMeter - chr20:32792721 20.4 9650 474.1
23:04:45.350 INFO ProgressMeter - chr20:42141913 20.5 9730 473.9
23:04:58.228 INFO ProgressMeter - chr20:47652490 20.7 9800 472.4
23:05:08.644 INFO ProgressMeter - chr20:58840105 20.9 9850 470.8
23:05:18.964 INFO ProgressMeter - chr21:15313243 21.1 9910 469.8
23:05:29.238 INFO ProgressMeter - chr21:41043940 21.3 9980 469.3
23:05:42.008 INFO ProgressMeter - chr21:41491759 21.5 10040 467.5
23:05:52.276 INFO ProgressMeter - chr21:41503344 21.6 10090 466.1
23:06:02.702 INFO ProgressMeter - chr22:20949775 21.8 10160 465.6
23:06:14.066 INFO ProgressMeter - chr22:23292356 22.0 10250 465.7
23:06:25.813 INFO ProgressMeter - chr22:29285305 22.2 10360 466.5
23:06:35.842 INFO ProgressMeter - chr22:41141151 22.4 10440 466.6
23:06:46.113 INFO ProgressMeter - chr3:10088826 22.5 10540 467.5
23:06:56.877 INFO ProgressMeter - chr3:12358852 22.7 10610 466.9
23:07:08.227 INFO ProgressMeter - chr3:12366296 22.9 10660 465.2
23:07:18.419 INFO ProgressMeter - chr3:12375089 23.1 10720 464.4
23:07:28.902 INFO ProgressMeter - chr3:12653698 23.3 10800 464.4
23:07:39.199 INFO ProgressMeter - chr3:47097953 23.4 10900 465.2
23:07:50.287 INFO ProgressMeter - chr3:49896633 23.6 11000 465.8
23:08:00.522 INFO ProgressMeter - chr3:69959271 23.8 11100 466.7
23:08:10.597 INFO ProgressMeter - chr3:89413139 24.0 11180 466.7
23:08:20.610 INFO ProgressMeter - chr3:135201472 24.1 11240 466.0
23:08:30.936 INFO ProgressMeter - chr3:138700226 24.3 11320 466.0
23:08:41.721 INFO ProgressMeter - chr3:142553823 24.5 11410 466.3
23:08:52.001 INFO ProgressMeter - chr3:179210184 24.6 11490 466.3
23:09:02.538 INFO ProgressMeter - chr3:185447787 24.8 11560 465.8
23:09:13.222 INFO ProgressMeter - chr3:186057421 25.0 11600 464.1
23:09:24.554 INFO ProgressMeter - chr3:196058282 25.2 11690 464.2
23:09:35.277 INFO ProgressMeter - chr4:20598263 25.4 11820 466.0
23:09:45.527 INFO ProgressMeter - chr4:54287477 25.5 11920 466.8
23:09:56.144 INFO ProgressMeter - chr4:55092615 25.7 11990 466.3
23:10:06.463 INFO ProgressMeter - chr4:80286606 25.9 12090 467.1
23:10:17.340 INFO ProgressMeter - chr4:105241728 26.1 12170 466.9
23:10:27.611 INFO ProgressMeter - chr4:142260490 26.2 12270 467.7
23:10:38.592 INFO ProgressMeter - chr4:186617003 26.4 12370 468.2
23:10:48.727 INFO ProgressMeter - chr4:186709449 26.6 12430 467.5
23:11:00.114 INFO ProgressMeter - chr5:38950519 26.8 12510 467.2
23:11:10.944 INFO ProgressMeter - chr5:56856598 27.0 12610 467.7
23:11:21.258 INFO ProgressMeter - chr5:87333265 27.1 12740 469.6
23:11:32.045 INFO ProgressMeter - chr5:112843025 27.3 12830 469.8
23:11:42.263 INFO ProgressMeter - chr5:142600700 27.5 12920 470.1
23:11:52.415 INFO ProgressMeter - chr5:149509858 27.7 12980 469.4
23:12:02.518 INFO ProgressMeter - chr5:150123108 27.8 13050 469.1
23:12:13.276 INFO ProgressMeter - chr5:161689252 28.0 13120 468.6
23:12:23.699 INFO ProgressMeter - chr5:177092319 28.2 13180 467.8
23:12:33.950 INFO ProgressMeter - chr5:177211943 28.3 13230 466.8
23:12:44.373 INFO ProgressMeter - chr5:180611329 28.5 13300 466.4
23:12:54.814 INFO ProgressMeter - chr6:20463065 28.7 13400 467.1
23:13:06.323 INFO ProgressMeter - chr6:29945057 28.9 13500 467.4
23:13:16.542 INFO ProgressMeter - chr6:32200943 29.1 13560 466.7
23:13:26.718 INFO ProgressMeter - chr6:33322860 29.2 13630 466.4
23:13:37.592 INFO ProgressMeter - chr6:93246844 29.4 13760 468.0
23:13:48.594 INFO ProgressMeter - chr6:117318210 29.6 13850 468.1
23:13:59.360 INFO ProgressMeter - chr6:117325281 29.8 13900 467.0
23:14:10.380 INFO ProgressMeter - chr6:117335887 29.9 13960 466.1
23:14:21.390 INFO ProgressMeter - chr6:117387837 30.1 14020 465.3
23:14:31.446 INFO ProgressMeter - chr6:135207622 30.3 14090 465.0
23:14:47.860 INFO ProgressMeter - chr6:135213422 30.6 14130 462.2
23:14:59.632 INFO ProgressMeter - chr6:137879061 30.8 14190 461.2
23:15:10.377 INFO ProgressMeter - chr6:151857551 30.9 14260 460.8
23:15:20.778 INFO ProgressMeter - chr6:157206238 31.1 14340 460.8
23:15:31.122 INFO ProgressMeter - chr6:163563418 31.3 14430 461.1
23:15:41.379 INFO ProgressMeter - chr7:13893614 31.5 14510 461.1
23:15:52.521 INFO ProgressMeter - chr7:13909408 31.7 14550 459.7
23:16:03.905 INFO ProgressMeter - chr7:13939555 31.8 14600 458.5
23:16:14.576 INFO ProgressMeter - chr7:13946613 32.0 14640 457.2
23:16:25.180 INFO ProgressMeter - chr7:13950893 32.2 14670 455.6
23:16:35.365 INFO ProgressMeter - chr7:13956265 32.4 14710 454.5
23:16:46.551 INFO ProgressMeter - chr7:13963073 32.6 14760 453.4
23:17:03.106 INFO ProgressMeter - chr7:13971386 32.8 14810 451.1
23:17:15.163 INFO ProgressMeter - chr7:13975520 33.0 14850 449.6
23:17:25.372 INFO ProgressMeter - chr7:13981756 33.2 14900 448.8
23:17:38.056 INFO ProgressMeter - chr7:13988517 33.4 14940 447.2
23:17:48.805 INFO ProgressMeter - chr7:55153925 33.6 15010 446.9
23:18:01.576 INFO ProgressMeter - chr7:55169406 33.8 15060 445.5
23:18:11.749 INFO ProgressMeter - chr7:55178474 34.0 15110 444.8
23:18:21.943 INFO ProgressMeter - chr7:55201420 34.1 15160 444.0
23:18:32.271 INFO ProgressMeter - chr7:86786259 34.3 15250 444.4
23:18:42.341 INFO ProgressMeter - chr7:102193821 34.5 15330 444.6
23:18:52.712 INFO ProgressMeter - chr7:106882185 34.7 15400 444.4
23:19:03.857 INFO ProgressMeter - chr7:129210963 34.8 15480 444.3
23:19:14.090 INFO ProgressMeter - chr7:140792577 35.0 15540 443.9
23:19:24.252 INFO ProgressMeter - chr7:142953878 35.2 15620 444.0
23:19:34.356 INFO ProgressMeter - chr7:152162982 35.3 15700 444.1
23:19:45.527 INFO ProgressMeter - chr7:152238709 35.5 15770 443.8
23:19:55.658 INFO ProgressMeter - chr8:32083130 35.7 15870 444.5
23:20:07.082 INFO ProgressMeter - chr8:32742986 35.9 15920 443.5
23:20:17.473 INFO ProgressMeter - chr8:37835556 36.1 15980 443.1
23:20:28.347 INFO ProgressMeter - chr8:38431186 36.2 16040 442.5
23:20:39.318 INFO ProgressMeter - chr8:41940840 36.4 16080 441.4
23:20:50.457 INFO ProgressMeter - chr8:47837338 36.6 16150 441.0
23:21:00.539 INFO ProgressMeter - chr8:54459328 36.8 16230 441.2
23:21:11.088 INFO ProgressMeter - chr8:73959763 37.0 16310 441.3
23:21:21.717 INFO ProgressMeter - chr8:127731999 37.1 16380 441.1
23:21:32.680 INFO ProgressMeter - chr8:144514187 37.3 16450 440.8
23:21:43.131 INFO ProgressMeter - chr9:8486060 37.5 16560 441.7
23:21:53.428 INFO ProgressMeter - chr9:36846841 37.7 16650 442.0
23:22:04.857 INFO ProgressMeter - chr9:84752044 37.9 16740 442.2
23:22:16.351 INFO ProgressMeter - chr9:84863686 38.0 16790 441.3
23:22:26.380 INFO ProgressMeter - chr9:84874271 38.2 16830 440.4
23:22:37.598 INFO ProgressMeter - chr9:85024895 38.4 16890 439.8
23:22:48.559 INFO ProgressMeter - chr9:95468780 38.6 16960 439.5
23:22:59.083 INFO ProgressMeter - chr9:130885577 38.8 17060 440.1
23:23:09.919 INFO ProgressMeter - chr9:136510696 38.9 17150 440.4
23:23:19.963 INFO ProgressMeter - chrX:44873550 39.1 17270 441.6
23:23:30.649 INFO ProgressMeter - chrX:49035180 39.3 17400 442.9
23:23:41.415 INFO ProgressMeter - chrX:53404991 39.5 17500 443.4
23:23:52.172 INFO ProgressMeter - chrX:67682851 39.6 17590 443.7
23:24:02.366 INFO ProgressMeter - chrX:77520786 39.8 17710 444.8
23:24:13.490 INFO ProgressMeter - chrX:124071147 40.0 17860 446.5
23:24:21.895 INFO Mutect2 - 496104 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
0 read(s) filtered by: ReadLengthReadFilter
87 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
496191 total reads filtered out of 67409657 reads processed
23:24:21.895 INFO ProgressMeter - chrY:20489365 40.1 17984 448.0
23:24:21.895 INFO ProgressMeter - Traversal complete. Processed 17984 total regions in 40.1 minutes.
23:24:21.913 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 5.288646325
23:24:21.913 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 195.95499715300002
23:24:21.913 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 8.00 sec
23:24:21.914 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:24:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 40.15 minutes.
Runtime.totalMemory()=2105540608
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 LS0910_tumor.bam --tumor-sample LS0910 -L TST500C_manifest.bed -O LS0910.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:24:23.368 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
23:24:23.492 INFO FilterMutectCalls - ------------------------------------------------------------
23:24:23.495 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:24:23.495 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:24:23.495 INFO FilterMutectCalls - Executing as ?@nf-466d0b4e5f9bf71b05029889b21f82f1-91109-5flvs on Linux v6.12.88 amd64
23:24:23.495 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:24:23.496 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:24:23 PM GMT
23:24:23.496 INFO FilterMutectCalls - ------------------------------------------------------------
23:24:23.496 INFO FilterMutectCalls - ------------------------------------------------------------
23:24:23.496 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:24:23.497 INFO FilterMutectCalls - Picard Version: 3.1.1
23:24:23.497 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:24:23.497 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:24:23.497 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:24:23.497 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:24:23.497 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:24:23.497 INFO FilterMutectCalls - Deflater: IntelDeflater
23:24:23.497 INFO FilterMutectCalls - Inflater: IntelInflater
23:24:23.498 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:24:23.498 INFO FilterMutectCalls - Requester pays: disabled
23:24:23.501 INFO FilterMutectCalls - Initializing engine
23:24:23.615 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.wuZ9rSMrd2/LS0910.mutect2.raw.vcf.gz
23:24:23.731 INFO FilterMutectCalls - Done initializing engine
23:24:23.785 INFO ProgressMeter - Starting traversal
23:24:23.786 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:24:23.787 INFO FilterMutectCalls - Starting pass 0 through the variants
23:24:24.932 INFO FilterMutectCalls - Finished pass 0 through the variants
23:24:27.321 INFO FilterMutectCalls - Starting pass 1 through the variants
23:24:28.492 INFO FilterMutectCalls - Finished pass 1 through the variants
23:24:29.065 INFO FilterMutectCalls - Starting pass 2 through the variants
23:24:30.219 INFO FilterMutectCalls - Finished pass 2 through the variants
23:24:30.221 INFO FilterMutectCalls - Starting pass 3 through the variants
23:24:31.253 INFO FilterMutectCalls - Finished pass 3 through the variants
23:24:31.261 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:24:31.261 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:24:31.262 INFO ProgressMeter - chrX:111196526 0.1 11012 88378.8
23:24:31.262 INFO ProgressMeter - Traversal complete. Processed 11012 total variants in 0.1 minutes.
23:24:31.273 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:24:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=335544320
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 LS0910.mutect2.raw.vcf.gz --stats LS0910.mutect2.raw.vcf.gz.stats -O LS0910.mutect2.filtered.vcf.gz
23:24:32.520 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
23:24:32.628 INFO SelectVariants - ------------------------------------------------------------
23:24:32.635 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:24:32.635 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:24:32.635 INFO SelectVariants - Executing as ?@nf-466d0b4e5f9bf71b05029889b21f82f1-91109-5flvs on Linux v6.12.88 amd64
23:24:32.635 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:24:32.636 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:24:32 PM GMT
23:24:32.636 INFO SelectVariants - ------------------------------------------------------------
23:24:32.636 INFO SelectVariants - ------------------------------------------------------------
23:24:32.637 INFO SelectVariants - HTSJDK Version: 4.1.0
23:24:32.637 INFO SelectVariants - Picard Version: 3.1.1
23:24:32.637 INFO SelectVariants - Built for Spark Version: 3.5.0
23:24:32.637 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:24:32.637 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:24:32.637 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:24:32.637 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:24:32.637 INFO SelectVariants - Deflater: IntelDeflater
23:24:32.637 INFO SelectVariants - Inflater: IntelInflater
23:24:32.638 INFO SelectVariants - GCS max retries/reopens: 20
23:24:32.638 INFO SelectVariants - Requester pays: disabled
23:24:32.638 INFO SelectVariants - Initializing engine
23:24:32.764 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.wuZ9rSMrd2/LS0910.mutect2.filtered.vcf.gz
23:24:32.866 INFO SelectVariants - Done initializing engine
23:24:32.900 INFO ProgressMeter - Starting traversal
23:24:32.901 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:24:32.977 INFO ProgressMeter - chr6:35456196 0.0 2753 2262739.7
23:24:32.977 INFO ProgressMeter - Traversal complete. Processed 2753 total variants in 0.0 minutes.
23:24:32.987 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:24:32 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 LS0910.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0910.mutect2.pass.vcf.gz