18:52:54.283 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
18:52:54.404 INFO Mutect2 - ------------------------------------------------------------
18:52:54.406 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
18:52:54.406 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
18:52:54.406 INFO Mutect2 - Executing as ?@nf-51ed7eec2e89c63b24cbe4134c4aa126-dfb4e-8gdj7 on Linux v6.12.83 amd64
18:52:54.407 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
18:52:54.407 INFO Mutect2 - Start Date/Time: May 29, 2026 at 6:52:54 PM GMT
18:52:54.407 INFO Mutect2 - ------------------------------------------------------------
18:52:54.407 INFO Mutect2 - ------------------------------------------------------------
18:52:54.408 INFO Mutect2 - HTSJDK Version: 4.1.0
18:52:54.408 INFO Mutect2 - Picard Version: 3.1.1
18:52:54.408 INFO Mutect2 - Built for Spark Version: 3.5.0
18:52:54.408 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:52:54.408 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:52:54.408 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:52:54.408 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:52:54.408 INFO Mutect2 - Deflater: IntelDeflater
18:52:54.408 INFO Mutect2 - Inflater: IntelInflater
18:52:54.409 INFO Mutect2 - GCS max retries/reopens: 20
18:52:54.409 INFO Mutect2 - Requester pays: disabled
18:52:54.409 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.DDbGkBCjpL/LS0880.markdup.deduped.nosingletons.bam.bai is older than BAM /tmp/nxf.DDbGkBCjpL/LS0880.markdup.deduped.nosingletons.bam
18:52:54.537 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.DDbGkBCjpL/af-only-gnomad.hg38.vcf.gz
18:52:54.652 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.DDbGkBCjpL/TST500C_manifest.bed
18:52:54.684 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
18:52:54.712 INFO Mutect2 - Done initializing engine
18:52:54.721 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
18:52:54.723 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
18:52:54.723 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
18:52:54.723 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
18:52:54.735 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
18:52:54.743 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
18:52:54.743 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
18:52:54.744 INFO IntelPairHmm - Available threads: 192
18:52:54.744 INFO IntelPairHmm - Requested threads: 4
18:52:54.744 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
18:52:54.767 INFO ProgressMeter - Starting traversal
18:52:54.768 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
18:53:06.326 INFO ProgressMeter - chr1:11112850 0.2 50 259.6
18:53:17.844 INFO ProgressMeter - chr1:11241620 0.4 100 260.0
18:53:30.948 INFO ProgressMeter - chr1:15933155 0.6 140 232.2
18:53:41.104 INFO ProgressMeter - chr1:18735930 0.8 180 233.1
18:53:52.707 INFO ProgressMeter - chr1:26760854 1.0 220 227.8
18:54:04.446 INFO ProgressMeter - chr1:36472515 1.2 270 232.5
18:54:14.863 INFO ProgressMeter - chr1:43338540 1.3 320 239.7
18:54:25.558 INFO ProgressMeter - chr1:46274536 1.5 380 251.1
18:54:36.528 INFO ProgressMeter - chr1:77960342 1.7 440 259.4
18:54:47.878 INFO ProgressMeter - chr1:117623689 1.9 510 270.5
18:54:59.323 INFO ProgressMeter - chr1:119949005 2.1 550 264.9
18:55:09.926 INFO ProgressMeter - chr1:156874981 2.3 600 266.4
18:55:20.339 INFO ProgressMeter - chr1:158652465 2.4 650 267.9
18:55:30.512 INFO ProgressMeter - chr1:162778578 2.6 700 269.7
18:55:41.113 INFO ProgressMeter - chr1:204427646 2.8 770 277.7
18:55:51.719 INFO ProgressMeter - chr1:204537428 2.9 830 281.4
18:56:02.515 INFO ProgressMeter - chr1:226367564 3.1 890 284.4
18:56:13.502 INFO ProgressMeter - chr10:27005572 3.3 980 295.9
18:56:25.658 INFO ProgressMeter - chr10:32009064 3.5 1030 293.0
18:56:38.732 INFO ProgressMeter - chr10:43112953 3.7 1090 292.0
18:56:48.989 INFO ProgressMeter - chr10:43118099 3.9 1120 286.9
18:57:00.193 INFO ProgressMeter - chr10:68572937 4.1 1160 283.6
18:57:10.535 INFO ProgressMeter - chr10:86923592 4.3 1200 281.5
18:57:21.647 INFO ProgressMeter - chr10:101774501 4.4 1270 285.5
18:57:31.911 INFO ProgressMeter - chr10:110601945 4.6 1330 287.9
18:57:42.740 INFO ProgressMeter - chr10:121483174 4.8 1380 287.5
18:57:55.056 INFO ProgressMeter - chr11:22624686 5.0 1450 289.7
18:58:05.282 INFO ProgressMeter - chr11:67434196 5.2 1520 293.7
18:58:15.643 INFO ProgressMeter - chr11:69701108 5.3 1580 295.4
18:58:26.074 INFO ProgressMeter - chr11:69777915 5.5 1640 297.0
18:58:38.677 INFO ProgressMeter - chr11:76528266 5.7 1700 296.6
18:58:49.071 INFO ProgressMeter - chr11:77429651 5.9 1760 298.0
18:59:00.737 INFO ProgressMeter - chr11:102229700 6.1 1830 300.0
18:59:11.194 INFO ProgressMeter - chr11:108325308 6.3 1890 301.3
18:59:23.078 INFO ProgressMeter - chr11:118496259 6.5 1950 301.3
18:59:34.653 INFO ProgressMeter - chr11:119278164 6.7 1990 298.6
18:59:44.879 INFO ProgressMeter - chr11:128459578 6.8 2050 299.9
18:59:54.892 INFO ProgressMeter - chr11:128810457 7.0 2090 298.5
19:00:05.287 INFO ProgressMeter - chr12:913389 7.2 2140 298.2
19:00:16.948 INFO ProgressMeter - chr12:4434213 7.4 2200 298.5
19:00:28.019 INFO ProgressMeter - chr12:6591464 7.6 2250 297.8
19:00:41.720 INFO ProgressMeter - chr12:11857145 7.8 2300 295.5
19:00:53.646 INFO ProgressMeter - chr12:11865888 8.0 2340 293.2
19:01:03.948 INFO ProgressMeter - chr12:18488447 8.2 2390 293.1
19:01:14.265 INFO ProgressMeter - chr12:45817668 8.3 2460 295.5
19:01:25.868 INFO ProgressMeter - chr12:49028007 8.5 2500 293.5
19:01:36.307 INFO ProgressMeter - chr12:49039433 8.7 2530 291.1
19:01:47.557 INFO ProgressMeter - chr12:50087361 8.9 2580 290.5
19:01:58.690 INFO ProgressMeter - chr12:56099646 9.1 2640 291.2
19:02:09.948 INFO ProgressMeter - chr12:57470315 9.3 2680 289.6
19:02:20.396 INFO ProgressMeter - chr12:68836415 9.4 2750 291.7
19:02:30.816 INFO ProgressMeter - chr12:112486773 9.6 2810 292.7
19:02:41.441 INFO ProgressMeter - chr12:132632431 9.8 2860 292.5
19:02:51.907 INFO ProgressMeter - chr13:20974868 10.0 2910 292.4
19:03:02.639 INFO ProgressMeter - chr13:21699189 10.1 2960 292.2
19:03:13.244 INFO ProgressMeter - chr13:28319421 10.3 3020 293.0
19:03:25.023 INFO ProgressMeter - chr13:28433817 10.5 3070 292.3
19:03:36.597 INFO ProgressMeter - chr13:32355213 10.7 3120 291.7
19:03:46.894 INFO ProgressMeter - chr13:48473358 10.9 3180 292.6
19:03:58.507 INFO ProgressMeter - chr13:102854286 11.1 3250 293.8
19:04:08.685 INFO ProgressMeter - chr13:113304396 11.2 3300 293.8
19:04:19.797 INFO ProgressMeter - chr14:37589377 11.4 3370 295.2
19:04:31.357 INFO ProgressMeter - chr14:81068252 11.6 3440 296.3
19:04:43.604 INFO ProgressMeter - chr14:95132513 11.8 3490 295.4
19:04:54.479 INFO ProgressMeter - chr15:34347741 12.0 3550 296.0
19:05:06.117 INFO ProgressMeter - chr15:41696373 12.2 3590 294.5
19:05:17.054 INFO ProgressMeter - chr15:41766302 12.4 3630 293.4
19:05:28.278 INFO ProgressMeter - chr15:73702253 12.6 3700 294.6
19:05:39.715 INFO ProgressMeter - chr15:88137491 12.7 3750 294.1
19:05:50.891 INFO ProgressMeter - chr15:90766908 12.9 3820 295.3
19:06:01.434 INFO ProgressMeter - chr15:98649580 13.1 3880 295.9
19:06:12.104 INFO ProgressMeter - chr16:2058745 13.3 3930 295.7
19:06:22.540 INFO ProgressMeter - chr16:2176558 13.5 3990 296.4
19:06:34.079 INFO ProgressMeter - chr16:3728316 13.7 4050 296.6
19:06:45.999 INFO ProgressMeter - chr16:9764947 13.9 4100 295.9
19:06:56.785 INFO ProgressMeter - chr16:23629638 14.0 4150 295.7
19:07:07.137 INFO ProgressMeter - chr16:55657899 14.2 4200 295.6
19:07:18.809 INFO ProgressMeter - chr16:68823576 14.4 4260 295.8
19:07:30.604 INFO ProgressMeter - chr16:72798274 14.6 4290 293.9
19:07:41.215 INFO ProgressMeter - chr16:81907683 14.8 4330 293.1
19:07:51.252 INFO ProgressMeter - chr16:89282913 14.9 4370 292.5
19:08:01.496 INFO ProgressMeter - chr16:89778941 15.1 4420 292.5
19:08:12.219 INFO ProgressMeter - chr17:7676117 15.3 4490 293.6
19:08:22.885 INFO ProgressMeter - chr17:16034763 15.5 4560 294.8
19:08:34.418 INFO ProgressMeter - chr17:17221539 15.7 4620 295.0
19:08:45.546 INFO ProgressMeter - chr17:31337817 15.8 4680 295.3
19:08:56.285 INFO ProgressMeter - chr17:39524672 16.0 4740 295.8
19:09:07.252 INFO ProgressMeter - chr17:40331217 16.2 4790 295.5
19:09:17.871 INFO ProgressMeter - chr17:42231998 16.4 4860 296.6
19:09:27.965 INFO ProgressMeter - chr17:43087706 16.6 4930 297.8
19:09:40.692 INFO ProgressMeter - chr17:43533185 16.8 4980 297.0
19:09:51.644 INFO ProgressMeter - chr17:43541967 16.9 5020 296.2
19:10:02.958 INFO ProgressMeter - chr17:49622731 17.1 5070 295.9
19:10:13.331 INFO ProgressMeter - chr17:59934432 17.3 5130 296.4
19:10:23.819 INFO ProgressMeter - chr17:63929432 17.5 5180 296.3
19:10:34.638 INFO ProgressMeter - chr17:80643726 17.7 5240 296.6
19:10:45.658 INFO ProgressMeter - chr18:41993268 17.8 5310 297.5
19:10:56.213 INFO ProgressMeter - chr18:45063358 18.0 5350 296.8
19:11:07.909 INFO ProgressMeter - chr19:1615583 18.2 5420 297.5
19:11:18.390 INFO ProgressMeter - chr19:3119204 18.4 5490 298.5
19:11:29.985 INFO ProgressMeter - chr19:5245998 18.6 5560 299.1
19:11:41.410 INFO ProgressMeter - chr19:10154291 18.8 5620 299.3
19:11:53.310 INFO ProgressMeter - chr19:11058786 19.0 5690 299.9
19:12:03.573 INFO ProgressMeter - chr19:15179362 19.1 5740 299.8
19:12:14.054 INFO ProgressMeter - chr19:15265352 19.3 5790 299.7
19:12:24.430 INFO ProgressMeter - chr19:29815537 19.5 5870 301.1
19:12:36.239 INFO ProgressMeter - chr19:35732813 19.7 5940 301.7
19:12:46.734 INFO ProgressMeter - chr19:41221144 19.9 6000 302.0
19:12:57.518 INFO ProgressMeter - chr19:42291556 20.0 6050 301.8
19:13:07.898 INFO ProgressMeter - chr19:45370131 20.2 6110 302.2
19:13:18.047 INFO ProgressMeter - chr19:50409517 20.4 6180 303.1
19:13:29.666 INFO ProgressMeter - chr2:17761394 20.6 6250 303.7
19:13:43.438 INFO ProgressMeter - chr2:25744127 20.8 6310 303.2
19:13:53.858 INFO ProgressMeter - chr2:29223281 21.0 6350 302.6
19:14:05.382 INFO ProgressMeter - chr2:29448049 21.2 6390 301.7
19:14:16.720 INFO ProgressMeter - chr2:47375232 21.4 6450 301.9
19:14:27.029 INFO ProgressMeter - chr2:58161599 21.5 6500 301.8
19:14:38.272 INFO ProgressMeter - chr2:98566027 21.7 6580 302.9
19:14:50.177 INFO ProgressMeter - chr2:111124044 21.9 6640 302.9
19:15:03.209 INFO ProgressMeter - chr2:113224196 22.1 6690 302.2
19:15:14.378 INFO ProgressMeter - chr2:113230331 22.3 6720 301.0
19:15:25.072 INFO ProgressMeter - chr2:127257594 22.5 6770 300.8
19:15:35.882 INFO ProgressMeter - chr2:140485341 22.7 6830 301.1
19:15:47.239 INFO ProgressMeter - chr2:141015694 22.9 6890 301.2
19:15:58.587 INFO ProgressMeter - chr2:189854837 23.1 6950 301.3
19:16:10.474 INFO ProgressMeter - chr2:203872706 23.3 7030 302.2
19:16:23.921 INFO ProgressMeter - chr2:222200600 23.5 7100 302.3
19:16:34.253 INFO ProgressMeter - chr2:222208043 23.7 7140 301.8
19:16:47.143 INFO ProgressMeter - chr2:222217067 23.9 7180 300.8
19:16:57.368 INFO ProgressMeter - chr2:226755285 24.0 7230 300.7
19:17:07.843 INFO ProgressMeter - chr20:25297810 24.2 7280 300.6
19:17:18.345 INFO ProgressMeter - chr20:32798579 24.4 7330 300.5
19:17:29.297 INFO ProgressMeter - chr20:42350626 24.6 7400 301.1
19:17:40.624 INFO ProgressMeter - chr20:53576507 24.8 7450 300.8
19:17:50.624 INFO ProgressMeter - chr20:58891669 24.9 7490 300.4
19:18:02.535 INFO ProgressMeter - chr21:38402555 25.1 7550 300.4
19:18:14.966 INFO ProgressMeter - chr21:41489374 25.3 7600 300.0
19:18:27.341 INFO ProgressMeter - chr21:41499317 25.5 7640 299.1
19:18:39.362 INFO ProgressMeter - chr21:41505858 25.7 7670 297.9
19:18:51.096 INFO ProgressMeter - chr22:23261353 25.9 7750 298.8
19:19:02.177 INFO ProgressMeter - chr22:28704698 26.1 7820 299.3
19:19:13.320 INFO ProgressMeter - chr22:29639088 26.3 7900 300.3
19:19:26.176 INFO ProgressMeter - chr22:41178871 26.5 7970 300.5
19:19:37.556 INFO ProgressMeter - chr3:12353065 26.7 8040 301.0
19:19:49.291 INFO ProgressMeter - chr3:12359427 26.9 8080 300.3
19:20:02.936 INFO ProgressMeter - chr3:12366817 27.1 8120 299.2
19:20:13.679 INFO ProgressMeter - chr3:12374000 27.3 8150 298.4
19:20:24.084 INFO ProgressMeter - chr3:12434196 27.5 8190 297.9
19:20:35.339 INFO ProgressMeter - chr3:38139862 27.7 8270 298.8
19:20:46.427 INFO ProgressMeter - chr3:47121509 27.9 8320 298.6
19:20:59.313 INFO ProgressMeter - chr3:49896727 28.1 8380 298.5
19:21:09.369 INFO ProgressMeter - chr3:52576539 28.2 8420 298.1
19:21:20.510 INFO ProgressMeter - chr3:70977641 28.4 8470 297.9
19:21:30.978 INFO ProgressMeter - chr3:89340914 28.6 8510 297.5
19:21:41.375 INFO ProgressMeter - chr3:135133012 28.8 8560 297.5
19:21:51.426 INFO ProgressMeter - chr3:136472392 28.9 8600 297.1
19:22:01.972 INFO ProgressMeter - chr3:142449452 29.1 8660 297.4
19:22:12.484 INFO ProgressMeter - chr3:170293381 29.3 8730 298.0
19:22:22.789 INFO ProgressMeter - chr3:183491925 29.5 8800 298.6
19:22:34.466 INFO ProgressMeter - chr3:186065811 29.7 8850 298.4
19:22:45.784 INFO ProgressMeter - chr3:196058572 29.9 8920 298.8
19:22:56.455 INFO ProgressMeter - chr4:10967473 30.0 8990 299.4
19:23:06.999 INFO ProgressMeter - chr4:41750984 30.2 9050 299.6
19:23:17.108 INFO ProgressMeter - chr4:54692213 30.4 9110 299.9
19:23:28.083 INFO ProgressMeter - chr4:55114872 30.6 9170 300.1
19:23:38.832 INFO ProgressMeter - chr4:80287299 30.7 9240 300.6
19:23:50.571 INFO ProgressMeter - chr4:105242598 30.9 9300 300.7
19:24:00.751 INFO ProgressMeter - chr4:142405204 31.1 9370 301.3
19:24:12.431 INFO ProgressMeter - chr4:186609181 31.3 9430 301.3
19:24:22.800 INFO ProgressMeter - chr4:186636777 31.5 9470 300.9
19:24:33.909 INFO ProgressMeter - chr5:1294991 31.7 9520 300.8
19:24:44.727 INFO ProgressMeter - chr5:44314662 31.8 9600 301.6
19:24:55.654 INFO ProgressMeter - chr5:58455537 32.0 9670 302.0
19:25:06.326 INFO ProgressMeter - chr5:87374161 32.2 9760 303.2
19:25:19.398 INFO ProgressMeter - chr5:112843312 32.4 9820 303.0
19:25:31.055 INFO ProgressMeter - chr5:138930828 32.6 9880 303.0
19:25:43.149 INFO ProgressMeter - chr5:150070460 32.8 9950 303.3
19:25:53.745 INFO ProgressMeter - chr5:150401935 33.0 10000 303.2
19:26:04.088 INFO ProgressMeter - chr5:177091683 33.2 10070 303.7
19:26:14.688 INFO ProgressMeter - chr5:177211813 33.3 10110 303.3
19:26:25.116 INFO ProgressMeter - chr5:180608279 33.5 10160 303.2
19:26:36.004 INFO ProgressMeter - chr6:20444963 33.7 10230 303.7
19:26:46.293 INFO ProgressMeter - chr6:26270972 33.9 10300 304.2
19:26:56.707 INFO ProgressMeter - chr6:42010290 34.0 10460 307.4
19:27:07.137 INFO ProgressMeter - chr6:106105723 34.2 10530 307.8
19:27:19.748 INFO ProgressMeter - chr6:117322360 34.4 10580 307.4
19:27:31.121 INFO ProgressMeter - chr6:117333673 34.6 10620 306.9
19:27:42.805 INFO ProgressMeter - chr6:117394675 34.8 10670 306.6
19:27:54.738 INFO ProgressMeter - chr6:135211000 35.0 10740 306.9
19:28:05.816 INFO ProgressMeter - chr6:137875994 35.2 10790 306.7
19:28:17.519 INFO ProgressMeter - chr6:151842595 35.4 10840 306.4
19:28:28.238 INFO ProgressMeter - chr6:157203864 35.6 10900 306.5
19:28:38.968 INFO ProgressMeter - chr6:163415192 35.7 10960 306.7
19:28:49.652 INFO ProgressMeter - chr7:6401866 35.9 11030 307.1
19:28:59.838 INFO ProgressMeter - chr7:13909491 36.1 11070 306.8
19:29:09.959 INFO ProgressMeter - chr7:13936107 36.3 11100 306.2
19:29:22.417 INFO ProgressMeter - chr7:13945498 36.5 11160 306.1
19:29:33.780 INFO ProgressMeter - chr7:13953074 36.7 11200 305.6
19:29:44.651 INFO ProgressMeter - chr7:13962469 36.8 11250 305.4
19:29:54.817 INFO ProgressMeter - chr7:13969764 37.0 11290 305.1
19:30:06.245 INFO ProgressMeter - chr7:13976586 37.2 11340 304.9
19:30:18.062 INFO ProgressMeter - chr7:13988660 37.4 11390 304.6
19:30:29.350 INFO ProgressMeter - chr7:55156060 37.6 11440 304.4
19:30:40.731 INFO ProgressMeter - chr7:55170572 37.8 11480 304.0
19:30:51.080 INFO ProgressMeter - chr7:55180501 37.9 11510 303.4
19:31:01.867 INFO ProgressMeter - chr7:78255941 38.1 11560 303.3
19:31:12.093 INFO ProgressMeter - chr7:92706436 38.3 11620 303.5
19:31:23.901 INFO ProgressMeter - chr7:106867959 38.5 11690 303.8
19:31:34.786 INFO ProgressMeter - chr7:116778774 38.7 11740 303.6
19:31:44.816 INFO ProgressMeter - chr7:140790920 38.8 11800 303.9
19:31:54.990 INFO ProgressMeter - chr7:148827162 39.0 11880 304.6
19:32:06.002 INFO ProgressMeter - chr7:152177376 39.2 11930 304.4
19:32:16.057 INFO ProgressMeter - chr7:152250851 39.4 11970 304.2
19:32:26.063 INFO ProgressMeter - chr8:32262204 39.5 12040 304.6
19:32:37.881 INFO ProgressMeter - chr8:37698343 39.7 12090 304.4
19:32:49.542 INFO ProgressMeter - chr8:38432079 39.9 12140 304.2
19:33:01.247 INFO ProgressMeter - chr8:47778726 40.1 12190 303.9
19:33:11.658 INFO ProgressMeter - chr8:47913899 40.3 12250 304.1
19:33:22.839 INFO ProgressMeter - chr8:68118548 40.5 12330 304.7
19:33:33.828 INFO ProgressMeter - chr8:127734368 40.7 12410 305.3
19:33:44.003 INFO ProgressMeter - chr8:144517699 40.8 12480 305.7
19:33:54.065 INFO ProgressMeter - chr9:8389230 41.0 12550 306.2
19:34:05.019 INFO ProgressMeter - chr9:35074925 41.2 12620 306.5
19:34:16.368 INFO ProgressMeter - chr9:84743090 41.4 12690 306.8
19:34:28.724 INFO ProgressMeter - chr9:84862627 41.6 12730 306.3
19:34:41.769 INFO ProgressMeter - chr9:84877008 41.8 12770 305.6
19:34:52.172 INFO ProgressMeter - chr9:90862204 42.0 12810 305.3
19:35:03.013 INFO ProgressMeter - chr9:95485683 42.1 12870 305.4
19:35:13.235 INFO ProgressMeter - chr9:130884567 42.3 12930 305.6
19:35:25.293 INFO ProgressMeter - chr9:136496369 42.5 12980 305.3
19:35:36.180 INFO ProgressMeter - chr9:136900420 42.7 13040 305.5
19:35:46.600 INFO ProgressMeter - chrX:40074124 42.9 13100 305.6
19:35:57.616 INFO ProgressMeter - chrX:47566984 43.0 13170 305.9
19:36:09.689 INFO ProgressMeter - chrX:53195229 43.2 13240 306.1
19:36:22.177 INFO ProgressMeter - chrX:64185119 43.5 13290 305.8
19:36:33.131 INFO ProgressMeter - chrX:67658808 43.6 13340 305.7
19:36:44.084 INFO ProgressMeter - chrX:71366384 43.8 13400 305.8
19:36:54.269 INFO ProgressMeter - chrX:77635913 44.0 13460 306.0
19:37:05.605 INFO ProgressMeter - chrX:123885661 44.2 13530 306.2
19:37:16.605 INFO ProgressMeter - chrX:130015924 44.4 13590 306.3
19:37:20.872 INFO Mutect2 - 1177794 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
251 read(s) filtered by: ReadLengthReadFilter
0 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
1178045 total reads filtered out of 84912896 reads processed
19:37:20.872 INFO ProgressMeter - chrY:20819373 44.4 13652 307.2
19:37:20.872 INFO ProgressMeter - Traversal complete. Processed 13652 total regions in 44.4 minutes.
19:37:20.885 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 3.688662223
19:37:20.885 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 22.516678719
19:37:20.885 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 0.93 sec
19:37:20.886 INFO Mutect2 - Shutting down engine
[May 29, 2026 at 7:37:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 44.44 minutes.
Runtime.totalMemory()=1226309632
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar Mutect2 -R hg38.fa -I LS0880.markdup.deduped.nosingletons.bam --tumor-sample LS0880 -L TST500C_manifest.bed -O LS0880.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 20 --germline-resource af-only-gnomad.hg38.vcf.gz
19:37:22.039 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
19:37:22.118 INFO FilterMutectCalls - ------------------------------------------------------------
19:37:22.119 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
19:37:22.119 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
19:37:22.120 INFO FilterMutectCalls - Executing as ?@nf-51ed7eec2e89c63b24cbe4134c4aa126-dfb4e-8gdj7 on Linux v6.12.83 amd64
19:37:22.120 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
19:37:22.120 INFO FilterMutectCalls - Start Date/Time: May 29, 2026 at 7:37:22 PM GMT
19:37:22.120 INFO FilterMutectCalls - ------------------------------------------------------------
19:37:22.120 INFO FilterMutectCalls - ------------------------------------------------------------
19:37:22.120 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
19:37:22.120 INFO FilterMutectCalls - Picard Version: 3.1.1
19:37:22.120 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
19:37:22.120 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:37:22.121 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:37:22.121 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:37:22.121 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:37:22.121 INFO FilterMutectCalls - Deflater: IntelDeflater
19:37:22.121 INFO FilterMutectCalls - Inflater: IntelInflater
19:37:22.121 INFO FilterMutectCalls - GCS max retries/reopens: 20
19:37:22.121 INFO FilterMutectCalls - Requester pays: disabled
19:37:22.122 INFO FilterMutectCalls - Initializing engine
19:37:22.200 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.DDbGkBCjpL/LS0880.mutect2.raw.vcf.gz
19:37:22.244 INFO FilterMutectCalls - Done initializing engine
19:37:22.288 INFO ProgressMeter - Starting traversal
19:37:22.289 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:37:22.290 INFO FilterMutectCalls - Starting pass 0 through the variants
19:37:23.779 INFO FilterMutectCalls - Finished pass 0 through the variants
19:37:30.359 INFO FilterMutectCalls - Starting pass 1 through the variants
19:37:32.049 INFO FilterMutectCalls - Finished pass 1 through the variants
19:37:33.449 INFO FilterMutectCalls - Starting pass 2 through the variants
19:37:34.458 INFO ProgressMeter - chr3:72750552 0.2 4000 19725.5
19:37:35.081 INFO FilterMutectCalls - Finished pass 2 through the variants
19:37:35.083 INFO FilterMutectCalls - Starting pass 3 through the variants
19:37:36.468 INFO FilterMutectCalls - Finished pass 3 through the variants
19:37:36.473 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
19:37:36.474 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
19:37:36.474 INFO ProgressMeter - chr7:55201335 0.2 6188 26174.1
19:37:36.474 INFO ProgressMeter - Traversal complete. Processed 6188 total variants in 0.2 minutes.
19:37:36.484 INFO FilterMutectCalls - Shutting down engine
[May 29, 2026 at 7:37:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.24 minutes.
Runtime.totalMemory()=806354944
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R hg38.fa -V LS0880.mutect2.raw.vcf.gz --stats LS0880.mutect2.raw.vcf.gz.stats -O LS0880.mutect2.filtered.vcf.gz
19:37:37.537 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
19:37:37.611 INFO SelectVariants - ------------------------------------------------------------
19:37:37.612 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
19:37:37.613 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
19:37:37.613 INFO SelectVariants - Executing as ?@nf-51ed7eec2e89c63b24cbe4134c4aa126-dfb4e-8gdj7 on Linux v6.12.83 amd64
19:37:37.613 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
19:37:37.613 INFO SelectVariants - Start Date/Time: May 29, 2026 at 7:37:37 PM GMT
19:37:37.613 INFO SelectVariants - ------------------------------------------------------------
19:37:37.613 INFO SelectVariants - ------------------------------------------------------------
19:37:37.613 INFO SelectVariants - HTSJDK Version: 4.1.0
19:37:37.613 INFO SelectVariants - Picard Version: 3.1.1
19:37:37.613 INFO SelectVariants - Built for Spark Version: 3.5.0
19:37:37.613 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:37:37.614 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:37:37.614 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:37:37.614 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:37:37.614 INFO SelectVariants - Deflater: IntelDeflater
19:37:37.614 INFO SelectVariants - Inflater: IntelInflater
19:37:37.614 INFO SelectVariants - GCS max retries/reopens: 20
19:37:37.614 INFO SelectVariants - Requester pays: disabled
19:37:37.614 INFO SelectVariants - Initializing engine
19:37:37.694 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.DDbGkBCjpL/LS0880.mutect2.filtered.vcf.gz
19:37:37.737 INFO SelectVariants - Done initializing engine
19:37:37.764 INFO ProgressMeter - Starting traversal
19:37:37.764 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:37:37.823 INFO ProgressMeter - chr4:152411228 0.0 1547 1628421.1
19:37:37.823 INFO ProgressMeter - Traversal complete. Processed 1547 total variants in 0.0 minutes.
19:37:37.835 INFO SelectVariants - Shutting down engine
[May 29, 2026 at 7:37:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=567803904
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar SelectVariants -R hg38.fa -V LS0880.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0880.mutect2.pass.vcf.gz