22:44:13.372 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
22:44:13.472 INFO Mutect2 - ------------------------------------------------------------
22:44:13.474 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:13.474 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:13.474 INFO Mutect2 - Executing as ?@nf-cd13c9f41e2be3e926123c9716640e6d-1c359-fz7lk on Linux v6.12.88 amd64
22:44:13.475 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:13.475 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:13 PM GMT
22:44:13.475 INFO Mutect2 - ------------------------------------------------------------
22:44:13.475 INFO Mutect2 - ------------------------------------------------------------
22:44:13.476 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:13.476 INFO Mutect2 - Picard Version: 3.1.1
22:44:13.476 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:13.476 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:13.476 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:13.476 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:13.477 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:13.477 INFO Mutect2 - Deflater: IntelDeflater
22:44:13.477 INFO Mutect2 - Inflater: IntelInflater
22:44:13.477 INFO Mutect2 - GCS max retries/reopens: 20
22:44:13.477 INFO Mutect2 - Requester pays: disabled
22:44:13.477 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.14KQXLxRaw/LS0916_tumor.bam.bai is older than BAM /tmp/nxf.14KQXLxRaw/LS0916_tumor.bam
22:44:13.652 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.14KQXLxRaw/af-only-gnomad.hg38.vcf.gz
22:44:13.775 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.14KQXLxRaw/TST500C_manifest.bed
22:44:13.810 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:13.839 INFO Mutect2 - Done initializing engine
22:44:13.849 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
22:44:13.851 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
22:44:13.852 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:13.852 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:13.865 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
22:44:13.874 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:13.874 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:13.875 INFO IntelPairHmm - Available threads: 384
22:44:13.875 INFO IntelPairHmm - Requested threads: 4
22:44:13.875 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:13.920 INFO ProgressMeter - Starting traversal
22:44:13.920 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:24.286 INFO ProgressMeter - chr1:11114811 0.2 60 347.3
22:44:34.450 INFO ProgressMeter - chr1:11259246 0.3 130 380.0
22:44:45.425 INFO ProgressMeter - chr1:15932411 0.5 180 342.8
22:44:56.691 INFO ProgressMeter - chr1:18744812 0.7 240 336.7
22:45:06.804 INFO ProgressMeter - chr1:26729790 0.9 290 329.0
22:45:17.612 INFO ProgressMeter - chr1:36472236 1.1 360 339.1
22:45:28.018 INFO ProgressMeter - chr1:43337847 1.2 430 348.2
22:45:38.424 INFO ProgressMeter - chr1:46273622 1.4 510 362.1
22:45:48.541 INFO ProgressMeter - chr1:77956570 1.6 590 374.1
22:46:00.663 INFO ProgressMeter - chr1:117627377 1.8 690 387.9
22:46:11.844 INFO ProgressMeter - chr1:119967464 2.0 750 381.6
22:46:22.610 INFO ProgressMeter - chr1:156874381 2.1 810 377.7
22:46:33.373 INFO ProgressMeter - chr1:158666314 2.3 880 378.6
22:46:44.358 INFO ProgressMeter - chr1:179108451 2.5 970 386.9
22:46:54.607 INFO ProgressMeter - chr1:204464010 2.7 1060 395.8
22:47:05.453 INFO ProgressMeter - chr1:206478941 2.9 1140 398.8
22:47:16.704 INFO ProgressMeter - chr1:243499979 3.0 1230 403.8
22:47:26.838 INFO ProgressMeter - chr1:243615094 3.2 1270 395.0
22:47:37.284 INFO ProgressMeter - chr10:27077394 3.4 1340 395.4
22:47:47.415 INFO ProgressMeter - chr10:43100457 3.6 1410 396.3
22:47:59.226 INFO ProgressMeter - chr10:43117950 3.8 1460 388.8
22:48:11.176 INFO ProgressMeter - chr10:68600979 4.0 1520 384.4
22:48:21.209 INFO ProgressMeter - chr10:87892778 4.1 1580 383.4
22:48:32.461 INFO ProgressMeter - chr10:101771571 4.3 1650 382.9
22:48:42.832 INFO ProgressMeter - chr10:110589871 4.5 1730 386.0
22:48:53.075 INFO ProgressMeter - chr10:121480878 4.7 1790 384.7
22:49:05.366 INFO ProgressMeter - chr10:121565436 4.9 1850 380.9
22:49:16.152 INFO ProgressMeter - chr11:64360174 5.0 1930 383.1
22:49:27.005 INFO ProgressMeter - chr11:69648873 5.2 2020 387.1
22:49:37.385 INFO ProgressMeter - chr11:69702961 5.4 2070 384.0
22:49:52.180 INFO ProgressMeter - chr11:69809468 5.6 2140 379.6
22:50:02.199 INFO ProgressMeter - chr11:69819063 5.8 2180 375.6
22:50:14.055 INFO ProgressMeter - chr11:77358896 6.0 2250 374.9
22:50:24.213 INFO ProgressMeter - chr11:94445808 6.2 2320 375.9
22:50:36.786 INFO ProgressMeter - chr11:102322618 6.4 2370 371.4
22:50:47.343 INFO ProgressMeter - chr11:108310271 6.6 2440 372.1
22:50:58.728 INFO ProgressMeter - chr11:118484181 6.7 2520 373.5
22:51:09.491 INFO ProgressMeter - chr11:118506285 6.9 2570 371.1
22:51:21.086 INFO ProgressMeter - chr11:125635445 7.1 2630 369.4
22:51:35.037 INFO ProgressMeter - chr11:128460832 7.4 2680 364.5
22:51:45.656 INFO ProgressMeter - chr11:128812453 7.5 2730 362.6
22:51:56.152 INFO ProgressMeter - chr12:4368324 7.7 2810 364.8
22:52:06.382 INFO ProgressMeter - chr12:4439592 7.9 2880 365.7
22:52:16.565 INFO ProgressMeter - chr12:6599771 8.0 2950 366.7
22:52:27.915 INFO ProgressMeter - chr12:11857686 8.2 3000 364.4
22:52:41.281 INFO ProgressMeter - chr12:11864389 8.5 3040 359.5
22:52:51.930 INFO ProgressMeter - chr12:11869878 8.6 3080 356.8
22:53:02.586 INFO ProgressMeter - chr12:25236077 8.8 3170 359.8
22:53:13.546 INFO ProgressMeter - chr12:49022047 9.0 3240 360.3
22:53:23.739 INFO ProgressMeter - chr12:49033414 9.2 3290 359.0
22:53:33.769 INFO ProgressMeter - chr12:49044441 9.3 3350 359.0
22:53:44.262 INFO ProgressMeter - chr12:51993983 9.5 3430 360.8
22:53:54.912 INFO ProgressMeter - chr12:57092574 9.7 3510 362.5
22:54:05.909 INFO ProgressMeter - chr12:57750654 9.9 3580 362.8
22:54:16.358 INFO ProgressMeter - chr12:92144378 10.0 3660 364.5
22:54:27.190 INFO ProgressMeter - chr12:120993518 10.2 3750 366.9
22:54:37.584 INFO ProgressMeter - chr12:132679952 10.4 3830 368.5
22:54:48.624 INFO ProgressMeter - chr13:21695796 10.6 3890 367.7
22:54:59.579 INFO ProgressMeter - chr13:28322788 10.8 3970 368.9
22:55:10.759 INFO ProgressMeter - chr13:28387968 10.9 4010 366.3
22:55:21.681 INFO ProgressMeter - chr13:28434135 11.1 4040 363.0
22:55:31.975 INFO ProgressMeter - chr13:32339256 11.3 4090 361.9
22:55:42.300 INFO ProgressMeter - chr13:48342597 11.5 4150 361.7
22:55:53.158 INFO ProgressMeter - chr13:102199777 11.7 4240 363.8
22:56:04.048 INFO ProgressMeter - chr13:109782792 11.8 4300 363.3
22:56:16.879 INFO ProgressMeter - chr14:23183219 12.0 4380 363.5
22:56:27.042 INFO ProgressMeter - chr14:37592575 12.2 4450 364.2
22:56:37.582 INFO ProgressMeter - chr14:81091067 12.4 4530 365.5
22:56:48.260 INFO ProgressMeter - chr14:102082409 12.6 4590 365.1
22:57:02.862 INFO ProgressMeter - chr15:34348140 12.8 4660 363.6
22:57:13.853 INFO ProgressMeter - chr15:41729162 13.0 4730 363.9
22:57:24.521 INFO ProgressMeter - chr15:49424531 13.2 4790 363.5
22:57:36.433 INFO ProgressMeter - chr15:73704174 13.4 4880 364.9
22:57:47.115 INFO ProgressMeter - chr15:88256133 13.6 4940 364.5
22:57:57.984 INFO ProgressMeter - chr15:90751785 13.7 5020 365.5
22:58:08.376 INFO ProgressMeter - chr15:93002175 13.9 5090 366.0
22:58:19.708 INFO ProgressMeter - chr16:2048705 14.1 5160 366.0
22:58:30.024 INFO ProgressMeter - chr16:2597705 14.3 5260 368.6
22:58:40.824 INFO ProgressMeter - chr16:3728256 14.4 5320 368.2
22:58:52.232 INFO ProgressMeter - chr16:9764173 14.6 5390 368.2
22:59:03.717 INFO ProgressMeter - chr16:23630193 14.8 5460 368.2
22:59:14.574 INFO ProgressMeter - chr16:56830535 15.0 5540 369.1
22:59:26.129 INFO ProgressMeter - chr16:72788024 15.2 5610 369.0
22:59:37.403 INFO ProgressMeter - chr16:72811903 15.4 5660 367.7
22:59:48.031 INFO ProgressMeter - chr16:81919482 15.6 5720 367.4
22:59:59.000 INFO ProgressMeter - chr16:89283518 15.8 5780 367.0
23:00:09.594 INFO ProgressMeter - chr16:89808292 15.9 5860 367.9
23:00:20.424 INFO ProgressMeter - chr17:7687308 16.1 5950 369.4
23:00:30.472 INFO ProgressMeter - chr17:16108784 16.3 6040 371.1
23:00:41.395 INFO ProgressMeter - chr17:31259030 16.5 6130 372.5
23:00:51.823 INFO ProgressMeter - chr17:39470877 16.6 6210 373.4
23:01:03.253 INFO ProgressMeter - chr17:39726560 16.8 6280 373.3
23:01:14.796 INFO ProgressMeter - chr17:42224794 17.0 6370 374.4
23:01:25.474 INFO ProgressMeter - chr17:43078745 17.2 6460 375.7
23:01:35.526 INFO ProgressMeter - chr17:43530105 17.4 6520 375.6
23:01:48.203 INFO ProgressMeter - chr17:43540153 17.6 6580 374.5
23:02:00.138 INFO ProgressMeter - chr17:43546183 17.8 6620 372.5
23:02:12.024 INFO ProgressMeter - chr17:58363273 18.0 6690 372.3
23:02:23.776 INFO ProgressMeter - chr17:60600413 18.2 6780 373.3
23:02:34.345 INFO ProgressMeter - chr17:65014626 18.3 6840 372.9
23:02:45.216 INFO ProgressMeter - chr17:80791448 18.5 6920 373.6
23:02:55.523 INFO ProgressMeter - chr18:22182755 18.7 7000 374.5
23:03:06.705 INFO ProgressMeter - chr18:51054881 18.9 7080 375.0
23:03:17.164 INFO ProgressMeter - chr19:1625574 19.1 7170 376.3
23:03:27.419 INFO ProgressMeter - chr19:4117564 19.2 7260 377.6
23:03:37.678 INFO ProgressMeter - chr19:7142814 19.4 7340 378.4
23:03:48.572 INFO ProgressMeter - chr19:10180776 19.6 7420 379.0
23:03:59.655 INFO ProgressMeter - chr19:12940539 19.8 7500 379.5
23:04:10.481 INFO ProgressMeter - chr19:15184293 19.9 7560 379.1
23:04:20.825 INFO ProgressMeter - chr19:15265352 20.1 7630 379.3
23:04:31.639 INFO ProgressMeter - chr19:29812967 20.3 7710 379.9
23:04:41.651 INFO ProgressMeter - chr19:35720006 20.5 7770 379.7
23:04:52.458 INFO ProgressMeter - chr19:35737857 20.6 7840 379.8
23:05:02.617 INFO ProgressMeter - chr19:41242881 20.8 7910 380.1
23:05:13.696 INFO ProgressMeter - chr19:42287318 21.0 7950 378.6
23:05:24.424 INFO ProgressMeter - chr19:45364428 21.2 8030 379.2
23:05:36.273 INFO ProgressMeter - chr19:50403491 21.4 8120 379.9
23:05:47.777 INFO ProgressMeter - chr2:15940892 21.6 8180 379.3
23:05:58.766 INFO ProgressMeter - chr2:17781670 21.7 8240 378.9
23:06:09.837 INFO ProgressMeter - chr2:25749694 21.9 8300 378.4
23:06:21.824 INFO ProgressMeter - chr2:29224425 22.1 8360 377.7
23:06:33.055 INFO ProgressMeter - chr2:29328348 22.3 8400 376.4
23:06:44.158 INFO ProgressMeter - chr2:42331274 22.5 8460 375.9
23:06:54.594 INFO ProgressMeter - chr2:47798637 22.7 8510 375.3
23:07:04.995 INFO ProgressMeter - chr2:61492033 22.9 8580 375.5
23:07:15.926 INFO ProgressMeter - chr2:99465080 23.0 8640 375.1
23:07:27.176 INFO ProgressMeter - chr2:111123744 23.2 8710 375.1
23:07:39.603 INFO ProgressMeter - chr2:111144486 23.4 8740 373.1
23:07:50.334 INFO ProgressMeter - chr2:113225653 23.6 8780 371.9
23:08:02.106 INFO ProgressMeter - chr2:113230730 23.8 8820 370.5
23:08:12.607 INFO ProgressMeter - chr2:113234805 24.0 8850 369.1
23:08:22.987 INFO ProgressMeter - chr2:140274557 24.2 8920 369.3
23:08:33.346 INFO ProgressMeter - chr2:140840916 24.3 9000 370.0
23:08:43.509 INFO ProgressMeter - chr2:172566854 24.5 9070 370.3
23:08:54.377 INFO ProgressMeter - chr2:197400250 24.7 9150 370.8
23:09:04.970 INFO ProgressMeter - chr2:211424153 24.9 9230 371.4
23:09:17.313 INFO ProgressMeter - chr2:222201089 25.1 9310 371.6
23:09:29.177 INFO ProgressMeter - chr2:222207804 25.3 9350 370.2
23:09:40.075 INFO ProgressMeter - chr2:222214621 25.4 9390 369.2
23:09:51.553 INFO ProgressMeter - chr2:222232076 25.6 9430 368.0
23:10:02.557 INFO ProgressMeter - chr2:226797176 25.8 9490 367.7
23:10:13.732 INFO ProgressMeter - chr20:32428323 26.0 9560 367.7
23:10:23.803 INFO ProgressMeter - chr20:32787276 26.2 9600 366.9
23:10:34.704 INFO ProgressMeter - chr20:42081880 26.3 9670 367.0
23:10:45.784 INFO ProgressMeter - chr20:47636189 26.5 9730 366.7
23:10:57.546 INFO ProgressMeter - chr20:53582167 26.7 9780 365.9
23:11:07.761 INFO ProgressMeter - chr20:58903715 26.9 9830 365.5
23:11:18.862 INFO ProgressMeter - chr21:38383223 27.1 9900 365.6
23:11:34.044 INFO ProgressMeter - chr21:41490463 27.3 9970 364.7
23:11:45.068 INFO ProgressMeter - chr21:41494122 27.5 10000 363.4
23:11:57.385 INFO ProgressMeter - chr21:41505322 27.7 10050 362.5
23:12:07.980 INFO ProgressMeter - chr22:20992896 27.9 10120 362.7
23:12:23.846 INFO ProgressMeter - chr22:23309422 28.2 10190 361.8
23:12:34.007 INFO ProgressMeter - chr22:29273739 28.3 10280 362.8
23:12:46.325 INFO ProgressMeter - chr22:29286852 28.5 10320 361.6
23:12:57.215 INFO ProgressMeter - chr22:41131386 28.7 10390 361.7
23:13:08.610 INFO ProgressMeter - chr3:10063790 28.9 10470 362.1
23:13:20.769 INFO ProgressMeter - chr3:12355011 29.1 10530 361.7
23:13:33.012 INFO ProgressMeter - chr3:12360938 29.3 10570 360.5
23:13:44.435 INFO ProgressMeter - chr3:12368032 29.5 10620 359.9
23:13:55.561 INFO ProgressMeter - chr3:12373655 29.7 10660 359.0
23:14:06.606 INFO ProgressMeter - chr3:12417002 29.9 10710 358.5
23:14:17.607 INFO ProgressMeter - chr3:30671997 30.1 10780 358.6
23:14:27.715 INFO ProgressMeter - chr3:47062161 30.2 10860 359.2
23:14:38.938 INFO ProgressMeter - chr3:47126646 30.4 10920 359.0
23:14:50.513 INFO ProgressMeter - chr3:52402286 30.6 11000 359.4
23:15:01.813 INFO ProgressMeter - chr3:69959271 30.8 11090 360.1
23:15:11.983 INFO ProgressMeter - chr3:89472477 31.0 11160 360.4
23:15:22.096 INFO ProgressMeter - chr3:136363345 31.1 11230 360.7
23:15:32.365 INFO ProgressMeter - chr3:138721850 31.3 11310 361.3
23:15:42.991 INFO ProgressMeter - chr3:142560261 31.5 11390 361.8
23:15:54.230 INFO ProgressMeter - chr3:179234280 31.7 11480 362.5
23:16:07.701 INFO ProgressMeter - chr3:186046856 31.9 11550 362.1
23:16:18.117 INFO ProgressMeter - chr3:189789799 32.1 11620 362.3
23:16:28.657 INFO ProgressMeter - chr4:1799252 32.2 11710 363.2
23:16:40.173 INFO ProgressMeter - chr4:24542919 32.4 11800 363.8
23:16:50.590 INFO ProgressMeter - chr4:54662213 32.6 11870 364.0
23:17:00.994 INFO ProgressMeter - chr4:54731910 32.8 11910 363.3
23:17:11.704 INFO ProgressMeter - chr4:65601639 33.0 11990 363.7
23:17:22.288 INFO ProgressMeter - chr4:98928893 33.1 12070 364.2
23:17:32.842 INFO ProgressMeter - chr4:105241251 33.3 12120 363.8
23:17:42.982 INFO ProgressMeter - chr4:122890556 33.5 12180 363.8
23:17:53.456 INFO ProgressMeter - chr4:186588590 33.7 12260 364.2
23:18:04.008 INFO ProgressMeter - chr4:186619042 33.8 12320 364.1
23:18:14.973 INFO ProgressMeter - chr4:186707207 34.0 12370 363.6
23:18:25.355 INFO ProgressMeter - chr5:38944911 34.2 12440 363.8
23:18:35.988 INFO ProgressMeter - chr5:44370662 34.4 12530 364.6
23:18:46.077 INFO ProgressMeter - chr5:66918650 34.5 12610 365.1
23:18:56.892 INFO ProgressMeter - chr5:112792444 34.7 12720 366.4
23:19:07.816 INFO ProgressMeter - chr5:112842243 34.9 12770 365.9
23:19:18.408 INFO ProgressMeter - chr5:132603918 35.1 12830 365.8
23:19:29.243 INFO ProgressMeter - chr5:142687528 35.3 12910 366.2
23:19:39.631 INFO ProgressMeter - chr5:150120928 35.4 12970 366.1
23:19:49.959 INFO ProgressMeter - chr5:161688947 35.6 13040 366.3
23:20:00.616 INFO ProgressMeter - chr5:177093205 35.8 13100 366.1
23:20:12.136 INFO ProgressMeter - chr5:177210954 36.0 13140 365.3
23:20:22.650 INFO ProgressMeter - chr5:180619251 36.1 13220 365.7
23:20:34.187 INFO ProgressMeter - chr6:20462963 36.3 13300 366.0
23:20:45.449 INFO ProgressMeter - chr6:26250582 36.5 13380 366.3
23:20:57.145 INFO ProgressMeter - chr6:30705989 36.7 13430 365.7
23:21:08.101 INFO ProgressMeter - chr6:32214108 36.9 13490 365.6
23:21:18.128 INFO ProgressMeter - chr6:35466242 37.1 13550 365.5
23:21:29.268 INFO ProgressMeter - chr6:93245296 37.3 13650 366.4
23:21:39.997 INFO ProgressMeter - chr6:111719832 37.4 13720 366.5
23:21:54.582 INFO ProgressMeter - chr6:117322459 37.7 13770 365.5
23:22:04.952 INFO ProgressMeter - chr6:117328863 37.9 13810 364.9
23:22:15.160 INFO ProgressMeter - chr6:117336442 38.0 13860 364.5
23:22:25.566 INFO ProgressMeter - chr6:117385681 38.2 13910 364.2
23:22:38.179 INFO ProgressMeter - chr6:135206139 38.4 13980 364.0
23:22:48.358 INFO ProgressMeter - chr6:135211640 38.6 14020 363.5
23:23:00.545 INFO ProgressMeter - chr6:135214296 38.8 14040 362.1
23:23:11.047 INFO ProgressMeter - chr6:137878590 39.0 14090 361.7
23:23:23.287 INFO ProgressMeter - chr6:151880703 39.2 14150 361.4
23:23:34.220 INFO ProgressMeter - chr6:157184385 39.3 14210 361.2
23:23:45.382 INFO ProgressMeter - chr6:161101953 39.5 14270 361.0
23:23:55.935 INFO ProgressMeter - chr7:2922697 39.7 14340 361.2
23:24:07.017 INFO ProgressMeter - chr7:13893194 39.9 14410 361.3
23:24:17.668 INFO ProgressMeter - chr7:13908517 40.1 14450 360.7
23:24:30.370 INFO ProgressMeter - chr7:13933941 40.3 14480 359.5
23:24:42.126 INFO ProgressMeter - chr7:13939916 40.5 14520 358.8
23:24:54.739 INFO ProgressMeter - chr7:13944586 40.7 14550 357.7
23:25:07.538 INFO ProgressMeter - chr7:13948554 40.9 14580 356.5
23:25:20.621 INFO ProgressMeter - chr7:13953533 41.1 14620 355.6
23:25:32.554 INFO ProgressMeter - chr7:13959454 41.3 14660 354.9
23:25:42.730 INFO ProgressMeter - chr7:13963948 41.5 14690 354.1
23:25:53.154 INFO ProgressMeter - chr7:13969833 41.7 14730 353.6
23:26:03.317 INFO ProgressMeter - chr7:13973865 41.8 14760 352.9
23:26:15.344 INFO ProgressMeter - chr7:13977766 42.0 14790 351.9
23:26:26.273 INFO ProgressMeter - chr7:13981948 42.2 14830 351.4
23:26:37.179 INFO ProgressMeter - chr7:13986055 42.4 14860 350.6
23:26:47.827 INFO ProgressMeter - chr7:13989634 42.6 14880 349.6
23:27:00.118 INFO ProgressMeter - chr7:55153922 42.8 14940 349.3
23:27:12.900 INFO ProgressMeter - chr7:55170157 43.0 14990 348.7
23:27:23.749 INFO ProgressMeter - chr7:55179588 43.2 15030 348.2
23:27:34.810 INFO ProgressMeter - chr7:78160115 43.3 15080 347.9
23:27:44.926 INFO ProgressMeter - chr7:86786765 43.5 15140 347.9
23:27:56.233 INFO ProgressMeter - chr7:102195486 43.7 15210 348.0
23:28:08.809 INFO ProgressMeter - chr7:106869224 43.9 15270 347.7
23:28:19.232 INFO ProgressMeter - chr7:116765399 44.1 15320 347.5
23:28:34.529 INFO ProgressMeter - chr7:140752633 44.3 15380 346.8
23:28:45.893 INFO ProgressMeter - chr7:140805691 44.5 15430 346.5
23:28:56.830 INFO ProgressMeter - chr7:148811623 44.7 15500 346.6
23:29:08.206 INFO ProgressMeter - chr7:152162559 44.9 15570 346.7
23:29:19.906 INFO ProgressMeter - chr7:152182557 45.1 15610 346.1
23:29:31.427 INFO ProgressMeter - chr7:156198157 45.3 15680 346.2
23:29:41.834 INFO ProgressMeter - chr8:32648209 45.5 15770 346.9
23:29:52.451 INFO ProgressMeter - chr8:38414150 45.6 15850 347.3
23:30:03.475 INFO ProgressMeter - chr8:41933941 45.8 15910 347.2
23:30:14.172 INFO ProgressMeter - chr8:47799208 46.0 15970 347.1
23:30:25.797 INFO ProgressMeter - chr8:47888646 46.2 16030 347.0
23:30:36.315 INFO ProgressMeter - chr8:56009940 46.4 16100 347.2
23:30:47.645 INFO ProgressMeter - chr8:73955909 46.6 16160 347.1
23:30:58.111 INFO ProgressMeter - chr8:116854243 46.7 16220 347.1
23:31:08.714 INFO ProgressMeter - chr8:127737856 46.9 16260 346.6
23:31:19.297 INFO ProgressMeter - chr8:127745289 47.1 16290 345.9
23:31:30.543 INFO ProgressMeter - chr9:5072183 47.3 16360 346.0
23:31:41.221 INFO ProgressMeter - chr9:8500828 47.5 16430 346.2
23:31:51.749 INFO ProgressMeter - chr9:22005985 47.6 16490 346.2
23:32:01.831 INFO ProgressMeter - chr9:83972842 47.8 16560 346.5
23:32:12.732 INFO ProgressMeter - chr9:84742886 48.0 16600 346.0
23:32:24.399 INFO ProgressMeter - chr9:84813594 48.2 16640 345.4
23:32:35.727 INFO ProgressMeter - chr9:84862697 48.4 16670 344.7
23:32:48.528 INFO ProgressMeter - chr9:84872687 48.6 16710 344.0
23:33:00.193 INFO ProgressMeter - chr9:85022236 48.8 16750 343.4
23:33:10.565 INFO ProgressMeter - chr9:90865046 48.9 16790 343.0
23:33:21.393 INFO ProgressMeter - chr9:95507932 49.1 16860 343.2
23:33:31.723 INFO ProgressMeter - chr9:130883967 49.3 16930 343.4
23:33:42.181 INFO ProgressMeter - chr9:132905579 49.5 16970 343.0
23:33:52.243 INFO ProgressMeter - chr9:136515481 49.6 17040 343.3
23:34:02.450 INFO ProgressMeter - chrX:40074388 49.8 17150 344.3
23:34:13.074 INFO ProgressMeter - chrX:49031395 50.0 17270 345.5
23:34:23.712 INFO ProgressMeter - chrX:53394757 50.2 17370 346.3
23:34:34.125 INFO ProgressMeter - chrX:67689257 50.3 17460 346.9
23:34:44.988 INFO ProgressMeter - chrX:77681560 50.5 17610 348.6
23:34:55.513 INFO ProgressMeter - chrX:130015346 50.7 17750 350.1
23:35:02.039 INFO Mutect2 - 631106 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
94 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
631200 total reads filtered out of 88227009 reads processed
23:35:02.039 INFO ProgressMeter - chrY:20960482 50.8 17831 351.0
23:35:02.039 INFO ProgressMeter - Traversal complete. Processed 17831 total regions in 50.8 minutes.
23:35:02.057 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 5.867226603000001
23:35:02.058 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 265.929633162
23:35:02.058 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 9.08 sec
23:35:02.058 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:35:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 50.81 minutes.
Runtime.totalMemory()=3321888768
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 LS0916_tumor.bam --tumor-sample LS0916 -L TST500C_manifest.bed -O LS0916.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:35:03.408 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
23:35:03.515 INFO FilterMutectCalls - ------------------------------------------------------------
23:35:03.520 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:35:03.520 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:35:03.520 INFO FilterMutectCalls - Executing as ?@nf-cd13c9f41e2be3e926123c9716640e6d-1c359-fz7lk on Linux v6.12.88 amd64
23:35:03.520 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:35:03.521 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:35:03 PM GMT
23:35:03.521 INFO FilterMutectCalls - ------------------------------------------------------------
23:35:03.521 INFO FilterMutectCalls - ------------------------------------------------------------
23:35:03.521 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:35:03.521 INFO FilterMutectCalls - Picard Version: 3.1.1
23:35:03.521 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:35:03.522 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:35:03.522 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:35:03.522 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:35:03.522 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:35:03.522 INFO FilterMutectCalls - Deflater: IntelDeflater
23:35:03.522 INFO FilterMutectCalls - Inflater: IntelInflater
23:35:03.522 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:35:03.522 INFO FilterMutectCalls - Requester pays: disabled
23:35:03.523 INFO FilterMutectCalls - Initializing engine
23:35:03.723 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.14KQXLxRaw/LS0916.mutect2.raw.vcf.gz
23:35:03.836 INFO FilterMutectCalls - Done initializing engine
23:35:03.894 INFO ProgressMeter - Starting traversal
23:35:03.894 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:35:03.895 INFO FilterMutectCalls - Starting pass 0 through the variants
23:35:05.215 INFO FilterMutectCalls - Finished pass 0 through the variants
23:35:07.317 INFO FilterMutectCalls - Starting pass 1 through the variants
23:35:08.680 INFO FilterMutectCalls - Finished pass 1 through the variants
23:35:09.203 INFO FilterMutectCalls - Starting pass 2 through the variants
23:35:10.534 INFO FilterMutectCalls - Finished pass 2 through the variants
23:35:10.536 INFO FilterMutectCalls - Starting pass 3 through the variants
23:35:11.679 INFO FilterMutectCalls - Finished pass 3 through the variants
23:35:11.687 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:35:11.688 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:35:11.688 INFO ProgressMeter - chr4:54738774 0.1 9976 76797.5
23:35:11.688 INFO ProgressMeter - Traversal complete. Processed 9976 total variants in 0.1 minutes.
23:35:11.699 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:35:11 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=478150656
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 LS0916.mutect2.raw.vcf.gz --stats LS0916.mutect2.raw.vcf.gz.stats -O LS0916.mutect2.filtered.vcf.gz
23:35:12.925 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
23:35:13.039 INFO SelectVariants - ------------------------------------------------------------
23:35:13.042 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:35:13.042 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:35:13.042 INFO SelectVariants - Executing as ?@nf-cd13c9f41e2be3e926123c9716640e6d-1c359-fz7lk on Linux v6.12.88 amd64
23:35:13.043 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:35:13.043 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:35:12 PM GMT
23:35:13.043 INFO SelectVariants - ------------------------------------------------------------
23:35:13.043 INFO SelectVariants - ------------------------------------------------------------
23:35:13.044 INFO SelectVariants - HTSJDK Version: 4.1.0
23:35:13.044 INFO SelectVariants - Picard Version: 3.1.1
23:35:13.044 INFO SelectVariants - Built for Spark Version: 3.5.0
23:35:13.044 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:35:13.044 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:35:13.044 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:35:13.044 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:35:13.044 INFO SelectVariants - Deflater: IntelDeflater
23:35:13.044 INFO SelectVariants - Inflater: IntelInflater
23:35:13.044 INFO SelectVariants - GCS max retries/reopens: 20
23:35:13.044 INFO SelectVariants - Requester pays: disabled
23:35:13.045 INFO SelectVariants - Initializing engine
23:35:13.245 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.14KQXLxRaw/LS0916.mutect2.filtered.vcf.gz
23:35:13.352 INFO SelectVariants - Done initializing engine
23:35:13.389 INFO ProgressMeter - Starting traversal
23:35:13.390 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:35:13.466 INFO ProgressMeter - chr7:13948622 0.0 2494 2022162.2
23:35:13.466 INFO ProgressMeter - Traversal complete. Processed 2494 total variants in 0.0 minutes.
23:35:13.477 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:35:13 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 LS0916.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0916.mutect2.pass.vcf.gz