22:44:13.364 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
22:44:13.453 INFO Mutect2 - ------------------------------------------------------------
22:44:13.455 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:13.455 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:13.455 INFO Mutect2 - Executing as ?@nf-f4eb19cbf9b96800eb144fcd9e79e3f3-f895d-2h2jq on Linux v6.12.88 amd64
22:44:13.455 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:13.455 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:13 PM GMT
22:44:13.456 INFO Mutect2 - ------------------------------------------------------------
22:44:13.456 INFO Mutect2 - ------------------------------------------------------------
22:44:13.456 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:13.456 INFO Mutect2 - Picard Version: 3.1.1
22:44:13.456 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:13.457 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:13.457 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:13.457 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:13.457 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:13.457 INFO Mutect2 - Deflater: IntelDeflater
22:44:13.457 INFO Mutect2 - Inflater: IntelInflater
22:44:13.457 INFO Mutect2 - GCS max retries/reopens: 20
22:44:13.457 INFO Mutect2 - Requester pays: disabled
22:44:13.458 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.UB8eGxhyKB/LS0881_tumor.bam.bai is older than BAM /tmp/nxf.UB8eGxhyKB/LS0881_tumor.bam
22:44:13.620 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.UB8eGxhyKB/af-only-gnomad.hg38.vcf.gz
22:44:13.731 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.UB8eGxhyKB/TST500C_manifest.bed
22:44:13.768 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:13.796 INFO Mutect2 - Done initializing engine
22:44:13.806 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
22:44:13.808 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
22:44:13.808 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:13.809 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:13.818 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
22:44:13.827 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:13.827 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:13.827 INFO IntelPairHmm - Available threads: 384
22:44:13.827 INFO IntelPairHmm - Requested threads: 4
22:44:13.827 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:13.866 INFO ProgressMeter - Starting traversal
22:44:13.866 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:25.190 INFO ProgressMeter - chr1:9723967 0.2 60 317.9
22:44:36.096 INFO ProgressMeter - chr1:11243127 0.4 130 350.9
22:44:48.314 INFO ProgressMeter - chr1:15933356 0.6 190 330.9
22:45:00.942 INFO ProgressMeter - chr1:18746274 0.8 250 318.6
22:45:12.296 INFO ProgressMeter - chr1:26775098 1.0 310 318.3
22:45:23.624 INFO ProgressMeter - chr1:39894023 1.2 370 318.2
22:45:35.101 INFO ProgressMeter - chr1:43340106 1.4 430 317.6
22:45:46.095 INFO ProgressMeter - chr1:46278266 1.5 500 325.3
22:45:56.949 INFO ProgressMeter - chr1:77949153 1.7 570 331.8
22:46:09.046 INFO ProgressMeter - chr1:119511501 1.9 670 349.0
22:46:19.116 INFO ProgressMeter - chr1:119953541 2.1 720 344.9
22:46:32.606 INFO ProgressMeter - chr1:156874818 2.3 790 341.6
22:46:44.233 INFO ProgressMeter - chr1:158652534 2.5 850 339.2
22:46:55.979 INFO ProgressMeter - chr1:175945151 2.7 920 340.5
22:47:06.337 INFO ProgressMeter - chr1:193236254 2.9 990 344.4
22:47:16.933 INFO ProgressMeter - chr1:204530682 3.1 1060 347.4
22:47:27.540 INFO ProgressMeter - chr1:226381066 3.2 1140 353.2
22:47:39.521 INFO ProgressMeter - chr1:243503148 3.4 1200 350.1
22:47:50.279 INFO ProgressMeter - chr10:27028874 3.6 1270 352.1
22:48:01.695 INFO ProgressMeter - chr10:32011360 3.8 1330 350.3
22:48:14.103 INFO ProgressMeter - chr10:43113508 4.0 1400 349.7
22:48:25.780 INFO ProgressMeter - chr10:43117842 4.2 1440 343.0
22:48:38.144 INFO ProgressMeter - chr10:68573461 4.4 1500 340.6
22:48:48.305 INFO ProgressMeter - chr10:87868680 4.6 1560 341.1
22:48:58.787 INFO ProgressMeter - chr10:101776032 4.7 1640 345.4
22:49:09.539 INFO ProgressMeter - chr10:110601026 4.9 1710 347.0
22:49:21.147 INFO ProgressMeter - chr10:121482427 5.1 1770 345.6
22:49:32.442 INFO ProgressMeter - chr11:2143771 5.3 1840 346.5
22:49:43.620 INFO ProgressMeter - chr11:64805048 5.5 1930 351.2
22:49:54.312 INFO ProgressMeter - chr11:69653909 5.7 2010 354.2
22:50:05.290 INFO ProgressMeter - chr11:69773356 5.9 2080 355.1
22:50:16.601 INFO ProgressMeter - chr11:69810603 6.0 2120 350.7
22:50:28.006 INFO ProgressMeter - chr11:76496213 6.2 2170 348.0
22:50:38.012 INFO ProgressMeter - chr11:77395651 6.4 2230 348.3
22:50:48.764 INFO ProgressMeter - chr11:101051422 6.6 2300 349.5
22:50:59.741 INFO ProgressMeter - chr11:102328050 6.8 2340 345.9
22:51:10.135 INFO ProgressMeter - chr11:108335927 6.9 2420 348.8
22:51:21.335 INFO ProgressMeter - chr11:118498517 7.1 2490 349.5
22:51:32.391 INFO ProgressMeter - chr11:119278508 7.3 2540 347.5
22:51:42.454 INFO ProgressMeter - chr11:125638675 7.5 2580 345.1
22:51:59.557 INFO ProgressMeter - chr11:128461863 7.8 2630 338.9
22:52:10.898 INFO ProgressMeter - chr12:293014 8.0 2690 338.3
22:52:22.253 INFO ProgressMeter - chr12:4372829 8.1 2770 340.3
22:52:33.157 INFO ProgressMeter - chr12:4444368 8.3 2840 341.3
22:52:43.391 INFO ProgressMeter - chr12:6601692 8.5 2900 341.5
22:52:54.779 INFO ProgressMeter - chr12:11857624 8.7 2940 338.6
22:53:06.484 INFO ProgressMeter - chr12:11864389 8.9 2980 335.7
22:53:17.414 INFO ProgressMeter - chr12:11869484 9.1 3010 332.3
22:53:28.193 INFO ProgressMeter - chr12:25231611 9.2 3090 334.5
22:53:39.345 INFO ProgressMeter - chr12:45852521 9.4 3150 334.2
22:53:51.084 INFO ProgressMeter - chr12:49033836 9.6 3200 332.6
22:54:02.451 INFO ProgressMeter - chr12:49046063 9.8 3260 332.3
22:54:13.395 INFO ProgressMeter - chr12:51982684 10.0 3320 332.3
22:54:24.754 INFO ProgressMeter - chr12:56102184 10.2 3400 333.9
22:54:36.738 INFO ProgressMeter - chr12:57470956 10.4 3460 333.3
22:54:47.531 INFO ProgressMeter - chr12:68824553 10.6 3550 336.1
22:54:58.361 INFO ProgressMeter - chr12:111447328 10.7 3620 337.0
22:55:09.336 INFO ProgressMeter - chr12:130277079 10.9 3690 337.8
22:55:20.473 INFO ProgressMeter - chr13:20327548 11.1 3760 338.4
22:55:31.622 INFO ProgressMeter - chr13:21684046 11.3 3810 337.3
22:55:42.208 INFO ProgressMeter - chr13:28319421 11.5 3890 339.1
22:55:53.337 INFO ProgressMeter - chr13:28387751 11.7 3920 336.3
22:56:04.101 INFO ProgressMeter - chr13:32332515 11.8 3970 335.4
22:56:15.547 INFO ProgressMeter - chr13:32376668 12.0 4030 335.1
22:56:26.220 INFO ProgressMeter - chr13:72775994 12.2 4120 337.5
22:56:36.333 INFO ProgressMeter - chr13:102862658 12.4 4190 338.6
22:56:48.112 INFO ProgressMeter - chr13:113308031 12.6 4270 339.7
22:56:58.900 INFO ProgressMeter - chr14:36519069 12.8 4330 339.6
22:57:09.054 INFO ProgressMeter - chr14:37597203 12.9 4400 340.6
22:57:19.078 INFO ProgressMeter - chr14:95090496 13.1 4470 341.6
22:57:29.499 INFO ProgressMeter - chr14:104772876 13.3 4540 342.4
22:57:41.834 INFO ProgressMeter - chr15:34355974 13.5 4600 341.6
22:57:53.544 INFO ProgressMeter - chr15:41736683 13.7 4660 341.1
22:58:04.100 INFO ProgressMeter - chr15:49440215 13.8 4720 341.1
22:58:16.022 INFO ProgressMeter - chr15:87978087 14.0 4800 342.0
22:58:26.568 INFO ProgressMeter - chr15:89305603 14.2 4870 342.7
22:58:37.113 INFO ProgressMeter - chr15:92943053 14.4 4940 343.4
22:58:48.918 INFO ProgressMeter - chr15:98934822 14.6 5010 343.5
22:58:59.619 INFO ProgressMeter - chr16:2163919 14.8 5090 344.8
22:59:10.140 INFO ProgressMeter - chr16:3602160 14.9 5170 346.1
22:59:21.495 INFO ProgressMeter - chr16:3850354 15.1 5230 345.7
22:59:32.617 INFO ProgressMeter - chr16:13926559 15.3 5290 345.5
22:59:43.314 INFO ProgressMeter - chr16:50754459 15.5 5360 346.0
22:59:54.901 INFO ProgressMeter - chr16:68812133 15.7 5440 346.9
23:00:06.765 INFO ProgressMeter - chr16:72795254 15.9 5480 345.1
23:00:18.493 INFO ProgressMeter - chr16:72958782 16.1 5520 343.3
23:00:29.434 INFO ProgressMeter - chr16:89280100 16.3 5590 343.8
23:00:40.283 INFO ProgressMeter - chr16:89744957 16.4 5640 343.1
23:00:53.287 INFO ProgressMeter - chr17:7675290 16.7 5730 344.0
23:01:04.165 INFO ProgressMeter - chr17:16061480 16.8 5820 345.6
23:01:14.214 INFO ProgressMeter - chr17:31181720 17.0 5900 346.9
23:01:24.934 INFO ProgressMeter - chr17:35103452 17.2 5990 348.6
23:01:36.223 INFO ProgressMeter - chr17:39709811 17.4 6060 348.8
23:01:46.301 INFO ProgressMeter - chr17:40356118 17.5 6120 348.9
23:01:56.349 INFO ProgressMeter - chr17:42295617 17.7 6200 350.1
23:02:07.157 INFO ProgressMeter - chr17:43086706 17.9 6280 351.1
23:02:17.876 INFO ProgressMeter - chr17:43529502 18.1 6330 350.4
23:02:30.040 INFO ProgressMeter - chr17:43538513 18.3 6380 349.2
23:02:44.287 INFO ProgressMeter - chr17:43543406 18.5 6410 346.4
23:02:55.759 INFO ProgressMeter - chr17:49600376 18.7 6470 346.0
23:03:06.432 INFO ProgressMeter - chr17:59896877 18.9 6530 345.9
23:03:18.034 INFO ProgressMeter - chr17:60663514 19.1 6600 346.1
23:03:29.607 INFO ProgressMeter - chr17:65549518 19.3 6660 345.8
23:03:39.862 INFO ProgressMeter - chr17:80957622 19.4 6740 346.8
23:03:51.125 INFO ProgressMeter - chr18:44951376 19.6 6830 348.1
23:04:01.540 INFO ProgressMeter - chr18:58735284 19.8 6900 348.6
23:04:12.011 INFO ProgressMeter - chr19:2213861 20.0 6990 350.0
23:04:23.452 INFO ProgressMeter - chr19:5214649 20.2 7070 350.7
23:04:35.092 INFO ProgressMeter - chr19:7267760 20.4 7150 351.3
23:04:46.471 INFO ProgressMeter - chr19:10987664 20.5 7230 351.9
23:04:57.112 INFO ProgressMeter - chr19:14517151 20.7 7300 352.3
23:05:08.140 INFO ProgressMeter - chr19:15191598 20.9 7360 352.1
23:05:18.393 INFO ProgressMeter - chr19:17835984 21.1 7420 352.1
23:05:28.471 INFO ProgressMeter - chr19:29815169 21.2 7490 352.6
23:05:40.120 INFO ProgressMeter - chr19:35722716 21.4 7560 352.7
23:05:50.640 INFO ProgressMeter - chr19:40241936 21.6 7640 353.5
23:06:05.670 INFO ProgressMeter - chr19:41261105 21.9 7710 352.6
23:06:16.641 INFO ProgressMeter - chr19:45352304 22.0 7780 352.9
23:06:27.816 INFO ProgressMeter - chr19:45418828 22.2 7860 353.5
23:06:42.261 INFO ProgressMeter - chr2:15940905 22.5 7950 353.8
23:06:52.895 INFO ProgressMeter - chr2:17781661 22.7 8010 353.6
23:07:03.146 INFO ProgressMeter - chr2:25743350 22.8 8060 353.2
23:07:16.099 INFO ProgressMeter - chr2:29223374 23.0 8120 352.5
23:07:26.827 INFO ProgressMeter - chr2:29227572 23.2 8150 351.1
23:07:37.221 INFO ProgressMeter - chr2:42169620 23.4 8200 350.6
23:07:48.069 INFO ProgressMeter - chr2:47410318 23.6 8270 350.9
23:08:00.460 INFO ProgressMeter - chr2:47803458 23.8 8310 349.5
23:08:12.503 INFO ProgressMeter - chr2:95183683 24.0 8380 349.5
23:08:22.901 INFO ProgressMeter - chr2:108764297 24.2 8450 349.9
23:08:37.357 INFO ProgressMeter - chr2:111127773 24.4 8500 348.5
23:08:48.716 INFO ProgressMeter - chr2:113223156 24.6 8540 347.4
23:09:01.153 INFO ProgressMeter - chr2:113226838 24.8 8570 345.7
23:09:13.569 INFO ProgressMeter - chr2:113232491 25.0 8610 344.5
23:09:23.753 INFO ProgressMeter - chr2:113234875 25.2 8630 342.9
23:09:34.791 INFO ProgressMeter - chr2:140334456 25.3 8710 343.6
23:09:45.640 INFO ProgressMeter - chr2:140883815 25.5 8780 343.9
23:09:58.012 INFO ProgressMeter - chr2:177233176 25.7 8850 343.9
23:10:08.161 INFO ProgressMeter - chr2:197420503 25.9 8930 344.7
23:10:18.395 INFO ProgressMeter - chr2:211725074 26.1 9000 345.2
23:10:28.929 INFO ProgressMeter - chr2:222201363 26.3 9050 344.7
23:10:41.196 INFO ProgressMeter - chr2:222206843 26.5 9090 343.6
23:10:52.044 INFO ProgressMeter - chr2:222212528 26.6 9130 342.8
23:11:04.864 INFO ProgressMeter - chr2:222218323 26.8 9160 341.2
23:11:14.899 INFO ProgressMeter - chr2:224506856 27.0 9210 340.9
23:11:26.802 INFO ProgressMeter - chr20:9566037 27.2 9270 340.6
23:11:38.343 INFO ProgressMeter - chr20:32437142 27.4 9330 340.4
23:11:49.522 INFO ProgressMeter - chr20:41122004 27.6 9410 341.0
23:12:01.530 INFO ProgressMeter - chr20:47639030 27.8 9470 340.7
23:12:13.049 INFO ProgressMeter - chr20:53581804 28.0 9510 339.8
23:12:23.732 INFO ProgressMeter - chr20:58855195 28.2 9550 339.1
23:12:35.566 INFO ProgressMeter - chr21:38383701 28.4 9630 339.5
23:12:47.252 INFO ProgressMeter - chr21:41488587 28.6 9680 339.0
23:12:57.652 INFO ProgressMeter - chr21:41491353 28.7 9700 337.6
23:13:09.356 INFO ProgressMeter - chr21:41500674 28.9 9740 336.7
23:13:20.150 INFO ProgressMeter - chr21:41506237 29.1 9780 336.0
23:13:30.733 INFO ProgressMeter - chr22:20992212 29.3 9840 336.1
23:13:41.921 INFO ProgressMeter - chr22:23291793 29.5 9900 336.0
23:13:52.295 INFO ProgressMeter - chr22:28729886 29.6 9980 336.7
23:14:03.746 INFO ProgressMeter - chr22:29287017 29.8 10030 336.2
23:14:14.156 INFO ProgressMeter - chr22:41117485 30.0 10100 336.6
23:14:24.332 INFO ProgressMeter - chr3:10032875 30.2 10170 337.0
23:14:35.327 INFO ProgressMeter - chr3:12352901 30.4 10240 337.3
23:14:45.892 INFO ProgressMeter - chr3:12358291 30.5 10270 336.3
23:14:58.825 INFO ProgressMeter - chr3:12365531 30.7 10310 335.3
23:15:09.436 INFO ProgressMeter - chr3:12371197 30.9 10350 334.7
23:15:21.703 INFO ProgressMeter - chr3:12377271 31.1 10390 333.8
23:15:33.685 INFO ProgressMeter - chr3:12629648 31.3 10450 333.5
23:15:44.459 INFO ProgressMeter - chr3:41239132 31.5 10530 334.2
23:15:54.901 INFO ProgressMeter - chr3:47123220 31.7 10580 333.9
23:16:05.786 INFO ProgressMeter - chr3:49899191 31.9 10650 334.2
23:16:16.571 INFO ProgressMeter - chr3:52662131 32.0 10720 334.5
23:16:27.295 INFO ProgressMeter - chr3:89107794 32.2 10800 335.2
23:16:37.588 INFO ProgressMeter - chr3:135192574 32.4 10870 335.5
23:16:47.808 INFO ProgressMeter - chr3:138700226 32.6 10940 335.9
23:16:58.937 INFO ProgressMeter - chr3:142553823 32.8 11030 336.8
23:17:10.459 INFO ProgressMeter - chr3:179210696 32.9 11110 337.2
23:17:21.936 INFO ProgressMeter - chr3:185449898 33.1 11180 337.4
23:17:32.507 INFO ProgressMeter - chr3:186081044 33.3 11220 336.8
23:17:44.172 INFO ProgressMeter - chr3:196055078 33.5 11290 337.0
23:17:55.472 INFO ProgressMeter - chr4:10967371 33.7 11380 337.8
23:18:06.695 INFO ProgressMeter - chr4:54258096 33.9 11460 338.2
23:18:16.774 INFO ProgressMeter - chr4:54693213 34.0 11520 338.3
23:18:28.371 INFO ProgressMeter - chr4:54738686 34.2 11560 337.6
23:18:39.833 INFO ProgressMeter - chr4:80268263 34.4 11640 338.1
23:18:51.762 INFO ProgressMeter - chr4:105236600 34.6 11720 338.4
23:19:02.402 INFO ProgressMeter - chr4:105259617 34.8 11760 337.8
23:19:12.654 INFO ProgressMeter - chr4:152326004 35.0 11840 338.5
23:19:24.448 INFO ProgressMeter - chr4:186619668 35.2 11920 338.9
23:19:35.227 INFO ProgressMeter - chr5:236426 35.4 11980 338.8
23:19:45.390 INFO ProgressMeter - chr5:38981865 35.5 12060 339.5
23:19:56.370 INFO ProgressMeter - chr5:56881654 35.7 12150 340.3
23:20:06.842 INFO ProgressMeter - chr5:80792731 35.9 12240 341.1
23:20:19.224 INFO ProgressMeter - chr5:112841437 36.1 12330 341.7
23:20:29.983 INFO ProgressMeter - chr5:138783175 36.3 12400 341.9
23:20:40.066 INFO ProgressMeter - chr5:142692528 36.4 12460 342.0
23:20:51.602 INFO ProgressMeter - chr5:150120072 36.6 12520 341.8
23:21:02.463 INFO ProgressMeter - chr5:161685988 36.8 12580 341.8
23:21:14.197 INFO ProgressMeter - chr5:177090498 37.0 12630 341.3
23:21:26.709 INFO ProgressMeter - chr5:177135162 37.2 12670 340.5
23:21:37.186 INFO ProgressMeter - chr5:177294235 37.4 12720 340.2
23:21:47.279 INFO ProgressMeter - chr5:180620607 37.6 12780 340.3
23:21:57.859 INFO ProgressMeter - chr6:20443020 37.7 12860 340.8
23:22:09.039 INFO ProgressMeter - chr6:26158168 37.9 12940 341.2
23:22:21.444 INFO ProgressMeter - chr6:30704701 38.1 12990 340.7
23:22:32.540 INFO ProgressMeter - chr6:32203768 38.3 13040 340.4
23:22:42.546 INFO ProgressMeter - chr6:35457554 38.5 13100 340.5
23:22:52.796 INFO ProgressMeter - chr6:89080893 38.6 13190 341.3
23:23:04.268 INFO ProgressMeter - chr6:112054302 38.8 13270 341.7
23:23:18.571 INFO ProgressMeter - chr6:117323094 39.1 13320 340.9
23:23:29.146 INFO ProgressMeter - chr6:117331143 39.3 13360 340.3
23:23:39.492 INFO ProgressMeter - chr6:117339309 39.4 13410 340.1
23:23:50.717 INFO ProgressMeter - chr6:117416256 39.6 13470 340.0
23:24:02.225 INFO ProgressMeter - chr6:135207622 39.8 13520 339.6
23:24:19.647 INFO ProgressMeter - chr6:135213648 40.1 13560 338.2
23:24:30.799 INFO ProgressMeter - chr6:137198414 40.3 13590 337.4
23:24:43.714 INFO ProgressMeter - chr6:151366382 40.5 13650 337.1
23:24:54.191 INFO ProgressMeter - chr6:156777985 40.7 13710 337.1
23:25:05.522 INFO ProgressMeter - chr6:161048844 40.9 13770 337.0
23:25:15.739 INFO ProgressMeter - chr7:2917288 41.0 13850 337.5
23:25:26.872 INFO ProgressMeter - chr7:13893974 41.2 13920 337.7
23:25:38.558 INFO ProgressMeter - chr7:13931689 41.4 13960 337.1
23:25:50.869 INFO ProgressMeter - chr7:13940173 41.6 14010 336.6
23:26:03.660 INFO ProgressMeter - chr7:13946638 41.8 14050 335.9
23:26:16.403 INFO ProgressMeter - chr7:13951536 42.0 14080 334.9
23:26:28.112 INFO ProgressMeter - chr7:13958911 42.2 14120 334.3
23:26:38.718 INFO ProgressMeter - chr7:13963680 42.4 14150 333.6
23:26:49.456 INFO ProgressMeter - chr7:13970147 42.6 14190 333.2
23:27:05.377 INFO ProgressMeter - chr7:13977275 42.9 14240 332.3
23:27:15.500 INFO ProgressMeter - chr7:13981756 43.0 14280 331.9
23:27:25.625 INFO ProgressMeter - chr7:13985655 43.2 14310 331.3
23:27:36.728 INFO ProgressMeter - chr7:41700246 43.4 14350 330.8
23:27:50.582 INFO ProgressMeter - chr7:55167237 43.6 14410 330.4
23:28:02.151 INFO ProgressMeter - chr7:55176777 43.8 14450 329.9
23:28:13.317 INFO ProgressMeter - chr7:55192764 44.0 14500 329.6
23:28:24.139 INFO ProgressMeter - chr7:81742940 44.2 14570 329.9
23:28:35.346 INFO ProgressMeter - chr7:102189792 44.4 14650 330.3
23:28:45.692 INFO ProgressMeter - chr7:106872535 44.5 14710 330.3
23:28:56.104 INFO ProgressMeter - chr7:116796081 44.7 14770 330.4
23:29:07.584 INFO ProgressMeter - chr7:140789750 44.9 14830 330.3
23:29:18.095 INFO ProgressMeter - chr7:140920344 45.1 14900 330.6
23:29:28.901 INFO ProgressMeter - chr7:152154324 45.3 14980 331.0
23:29:40.175 INFO ProgressMeter - chr7:152187392 45.4 15030 330.8
23:29:50.300 INFO ProgressMeter - chr8:23681311 45.6 15110 331.3
23:30:01.427 INFO ProgressMeter - chr8:32647913 45.8 15180 331.5
23:30:12.779 INFO ProgressMeter - chr8:37842003 46.0 15250 331.7
23:30:24.004 INFO ProgressMeter - chr8:41934677 46.2 15310 331.6
23:30:34.967 INFO ProgressMeter - chr8:47858847 46.4 15380 331.8
23:30:45.797 INFO ProgressMeter - chr8:68053095 46.5 15470 332.5
23:30:55.959 INFO ProgressMeter - chr8:91960240 46.7 15540 332.8
23:31:06.481 INFO ProgressMeter - chr8:127733768 46.9 15590 332.6
23:31:16.774 INFO ProgressMeter - chr8:144512640 47.0 15650 332.6
23:31:27.036 INFO ProgressMeter - chr9:5126682 47.2 15730 333.1
23:31:38.136 INFO ProgressMeter - chr9:21974402 47.4 15820 333.7
23:31:49.313 INFO ProgressMeter - chr9:84702346 47.6 15910 334.3
23:32:00.017 INFO ProgressMeter - chr9:84811379 47.8 15940 333.7
23:32:12.390 INFO ProgressMeter - chr9:84861751 48.0 15970 332.9
23:32:24.138 INFO ProgressMeter - chr9:84865595 48.2 16000 332.1
23:32:34.711 INFO ProgressMeter - chr9:84874833 48.3 16040 331.8
23:32:45.392 INFO ProgressMeter - chr9:85023268 48.5 16080 331.4
23:32:55.543 INFO ProgressMeter - chr9:90867129 48.7 16110 330.8
23:33:05.688 INFO ProgressMeter - chr9:95477545 48.9 16170 330.9
23:33:16.575 INFO ProgressMeter - chr9:130880498 49.0 16250 331.3
23:33:27.618 INFO ProgressMeter - chr9:132925585 49.2 16310 331.3
23:33:38.901 INFO ProgressMeter - chr9:136523846 49.4 16380 331.5
23:33:49.575 INFO ProgressMeter - chrX:40072629 49.6 16460 331.9
23:33:59.611 INFO ProgressMeter - chrX:47176498 49.8 16520 332.0
23:34:10.834 INFO ProgressMeter - chrX:49031527 49.9 16590 332.1
23:34:22.169 INFO ProgressMeter - chrX:49037536 50.1 16620 331.5
23:34:33.060 INFO ProgressMeter - chrX:53220837 50.3 16680 331.5
23:34:43.509 INFO ProgressMeter - chrX:64191455 50.5 16730 331.3
23:34:54.784 INFO ProgressMeter - chrX:67689378 50.7 16790 331.3
23:35:05.646 INFO ProgressMeter - chrX:71141228 50.9 16860 331.5
23:35:16.612 INFO ProgressMeter - chrX:77654096 51.0 16950 332.1
23:35:26.656 INFO ProgressMeter - chrX:111162913 51.2 17020 332.3
23:35:37.580 INFO ProgressMeter - chrX:124371349 51.4 17090 332.5
23:35:48.769 INFO ProgressMeter - chrX:134377984 51.6 17130 332.1
23:35:50.268 INFO Mutect2 - 669245 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
2 read(s) filtered by: ReadLengthReadFilter
178 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
669425 total reads filtered out of 93896928 reads processed
23:35:50.268 INFO ProgressMeter - chrY:19567332 51.6 17178 332.9
23:35:50.268 INFO ProgressMeter - Traversal complete. Processed 17178 total regions in 51.6 minutes.
23:35:50.283 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 6.0296129
23:35:50.283 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 269.73644780800004
23:35:50.283 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 10.78 sec
23:35:50.284 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:35:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 51.62 minutes.
Runtime.totalMemory()=4143972352
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 LS0881_tumor.bam --tumor-sample LS0881 -L TST500C_manifest.bed -O LS0881.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:35:51.695 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
23:35:51.831 INFO FilterMutectCalls - ------------------------------------------------------------
23:35:51.834 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:35:51.834 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:35:51.834 INFO FilterMutectCalls - Executing as ?@nf-f4eb19cbf9b96800eb144fcd9e79e3f3-f895d-2h2jq on Linux v6.12.88 amd64
23:35:51.834 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:35:51.834 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:35:51 PM GMT
23:35:51.835 INFO FilterMutectCalls - ------------------------------------------------------------
23:35:51.835 INFO FilterMutectCalls - ------------------------------------------------------------
23:35:51.835 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:35:51.836 INFO FilterMutectCalls - Picard Version: 3.1.1
23:35:51.836 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:35:51.836 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:35:51.836 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:35:51.836 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:35:51.836 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:35:51.836 INFO FilterMutectCalls - Deflater: IntelDeflater
23:35:51.836 INFO FilterMutectCalls - Inflater: IntelInflater
23:35:51.836 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:35:51.836 INFO FilterMutectCalls - Requester pays: disabled
23:35:51.837 INFO FilterMutectCalls - Initializing engine
23:35:52.019 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.UB8eGxhyKB/LS0881.mutect2.raw.vcf.gz
23:35:52.123 INFO FilterMutectCalls - Done initializing engine
23:35:52.179 INFO ProgressMeter - Starting traversal
23:35:52.179 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:35:52.180 INFO FilterMutectCalls - Starting pass 0 through the variants
23:35:53.380 INFO FilterMutectCalls - Finished pass 0 through the variants
23:35:55.084 INFO FilterMutectCalls - Starting pass 1 through the variants
23:35:56.313 INFO FilterMutectCalls - Finished pass 1 through the variants
23:35:56.696 INFO FilterMutectCalls - Starting pass 2 through the variants
23:35:57.909 INFO FilterMutectCalls - Finished pass 2 through the variants
23:35:57.911 INFO FilterMutectCalls - Starting pass 3 through the variants
23:35:58.977 INFO FilterMutectCalls - Finished pass 3 through the variants
23:35:58.985 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:35:58.986 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:35:58.986 INFO ProgressMeter - chr7:13970263 0.1 10464 92234.5
23:35:58.986 INFO ProgressMeter - Traversal complete. Processed 10464 total variants in 0.1 minutes.
23:35:58.999 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:35:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.12 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 LS0881.mutect2.raw.vcf.gz --stats LS0881.mutect2.raw.vcf.gz.stats -O LS0881.mutect2.filtered.vcf.gz
23:36:00.186 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
23:36:00.299 INFO SelectVariants - ------------------------------------------------------------
23:36:00.302 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:36:00.302 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:36:00.302 INFO SelectVariants - Executing as ?@nf-f4eb19cbf9b96800eb144fcd9e79e3f3-f895d-2h2jq on Linux v6.12.88 amd64
23:36:00.302 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:36:00.302 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:36:00 PM GMT
23:36:00.303 INFO SelectVariants - ------------------------------------------------------------
23:36:00.303 INFO SelectVariants - ------------------------------------------------------------
23:36:00.303 INFO SelectVariants - HTSJDK Version: 4.1.0
23:36:00.303 INFO SelectVariants - Picard Version: 3.1.1
23:36:00.303 INFO SelectVariants - Built for Spark Version: 3.5.0
23:36:00.303 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:36:00.303 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:36:00.303 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:36:00.304 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:36:00.304 INFO SelectVariants - Deflater: IntelDeflater
23:36:00.304 INFO SelectVariants - Inflater: IntelInflater
23:36:00.304 INFO SelectVariants - GCS max retries/reopens: 20
23:36:00.304 INFO SelectVariants - Requester pays: disabled
23:36:00.304 INFO SelectVariants - Initializing engine
23:36:00.428 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.UB8eGxhyKB/LS0881.mutect2.filtered.vcf.gz
23:36:00.526 INFO SelectVariants - Done initializing engine
23:36:00.565 INFO ProgressMeter - Starting traversal
23:36:00.565 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:36:00.645 INFO ProgressMeter - chr6:151944387 0.0 2616 2038441.6
23:36:00.645 INFO ProgressMeter - Traversal complete. Processed 2616 total variants in 0.0 minutes.
23:36:00.658 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:36:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=486539264
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 LS0881.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0881.mutect2.pass.vcf.gz