22:44:21.197 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 22:44:21.309 INFO Mutect2 - ------------------------------------------------------------ 22:44:21.311 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0 22:44:21.312 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 22:44:21.312 INFO Mutect2 - Executing as ?@nf-2ec2b10517a2ec509a1cb61374f4eb49-a65b7-ssrz2 on Linux v6.12.88 amd64 22:44:21.312 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04 22:44:21.312 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:21 PM GMT 22:44:21.312 INFO Mutect2 - ------------------------------------------------------------ 22:44:21.312 INFO Mutect2 - ------------------------------------------------------------ 22:44:21.313 INFO Mutect2 - HTSJDK Version: 4.1.0 22:44:21.313 INFO Mutect2 - Picard Version: 3.1.1 22:44:21.313 INFO Mutect2 - Built for Spark Version: 3.5.0 22:44:21.313 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 22:44:21.313 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 22:44:21.313 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 22:44:21.314 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 22:44:21.314 INFO Mutect2 - Deflater: IntelDeflater 22:44:21.314 INFO Mutect2 - Inflater: IntelInflater 22:44:21.314 INFO Mutect2 - GCS max retries/reopens: 20 22:44:21.314 INFO Mutect2 - Requester pays: disabled 22:44:21.314 INFO Mutect2 - Initializing engine WARNING: BAM index file /tmp/nxf.RicrL5aqwA/LS0909_tumor.bam.bai is older than BAM /tmp/nxf.RicrL5aqwA/LS0909_tumor.bam 22:44:21.481 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.RicrL5aqwA/af-only-gnomad.hg38.vcf.gz 22:44:21.600 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.RicrL5aqwA/TST500C_manifest.bed 22:44:21.635 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals 22:44:21.665 INFO Mutect2 - Done initializing engine 22:44:21.677 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 22:44:21.679 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 22:44:21.680 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions 22:44:21.680 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation 22:44:21.691 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 22:44:21.700 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions 22:44:21.700 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 22:44:21.701 INFO IntelPairHmm - Available threads: 384 22:44:21.701 INFO IntelPairHmm - Requested threads: 4 22:44:21.701 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 22:44:21.740 INFO ProgressMeter - Starting traversal 22:44:21.741 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 22:44:32.689 INFO ProgressMeter - chr1:11134349 0.2 80 438.5 22:44:43.236 INFO ProgressMeter - chr1:15929475 0.4 160 446.6 22:44:53.468 INFO ProgressMeter - chr1:18631035 0.5 220 416.0 22:45:04.509 INFO ProgressMeter - chr1:26731312 0.7 290 406.9 22:45:14.842 INFO ProgressMeter - chr1:36472236 0.9 370 418.1 22:45:25.392 INFO ProgressMeter - chr1:45329318 1.1 460 433.6 22:45:36.443 INFO ProgressMeter - chr1:64845511 1.2 570 457.8 22:45:48.192 INFO ProgressMeter - chr1:117623656 1.4 690 478.9 22:45:58.663 INFO ProgressMeter - chr1:119966374 1.6 760 470.5 22:46:09.022 INFO ProgressMeter - chr1:156875084 1.8 820 458.6 22:46:20.380 INFO ProgressMeter - chr1:158672057 2.0 900 455.2 22:46:31.143 INFO ProgressMeter - chr1:193122199 2.2 1000 463.7 22:46:41.533 INFO ProgressMeter - chr1:204536244 2.3 1110 476.4 22:46:51.898 INFO ProgressMeter - chr1:226386324 2.5 1200 479.5 22:47:02.549 INFO ProgressMeter - chr1:243503358 2.7 1260 470.1 22:47:13.199 INFO ProgressMeter - chr10:27040054 2.9 1340 468.9 22:47:23.298 INFO ProgressMeter - chr10:43106374 3.0 1440 475.9 22:47:35.440 INFO ProgressMeter - chr10:43117731 3.2 1500 464.6 22:47:46.366 INFO ProgressMeter - chr10:68645959 3.4 1570 460.4 22:47:56.451 INFO ProgressMeter - chr10:87965431 3.6 1670 466.7 22:48:07.091 INFO ProgressMeter - chr10:110580883 3.8 1760 468.6 22:48:18.836 INFO ProgressMeter - chr10:121482243 4.0 1840 465.6 22:48:29.092 INFO ProgressMeter - chr11:8226973 4.1 1920 465.7 22:48:39.526 INFO ProgressMeter - chr11:67434580 4.3 2030 472.5 22:48:49.813 INFO ProgressMeter - chr11:69701515 4.5 2110 472.3 22:49:00.240 INFO ProgressMeter - chr11:69808267 4.6 2190 471.8 22:49:11.028 INFO ProgressMeter - chr11:76453312 4.8 2240 464.6 22:49:22.480 INFO ProgressMeter - chr11:77420651 5.0 2320 462.9 22:49:35.599 INFO ProgressMeter - chr11:102330997 5.2 2420 462.6 22:49:47.317 INFO ProgressMeter - chr11:118477965 5.4 2530 466.3 22:49:58.193 INFO ProgressMeter - chr11:119285187 5.6 2610 465.4 22:50:08.427 INFO ProgressMeter - chr11:125640797 5.8 2650 458.6 22:50:18.529 INFO ProgressMeter - chr11:128484931 5.9 2710 455.7 22:50:28.548 INFO ProgressMeter - chr12:354074 6.1 2790 456.4 22:50:39.971 INFO ProgressMeter - chr12:4441023 6.3 2890 458.5 22:50:51.311 INFO ProgressMeter - chr12:11854372 6.5 2980 459.0 22:51:01.689 INFO ProgressMeter - chr12:11860218 6.7 3030 454.6 22:51:12.150 INFO ProgressMeter - chr12:11866993 6.8 3080 450.3 22:51:22.879 INFO ProgressMeter - chr12:25225612 7.0 3180 453.1 22:51:34.011 INFO ProgressMeter - chr12:49024808 7.2 3260 452.5 22:51:45.565 INFO ProgressMeter - chr12:49038834 7.4 3320 448.8 22:51:55.566 INFO ProgressMeter - chr12:49054526 7.6 3390 448.2 22:52:06.011 INFO ProgressMeter - chr12:57091123 7.7 3490 451.0 22:52:16.529 INFO ProgressMeter - chr12:57746926 7.9 3560 449.9 22:52:26.949 INFO ProgressMeter - chr12:69574688 8.1 3660 452.6 22:52:38.283 INFO ProgressMeter - chr12:132632356 8.3 3760 454.3 22:52:48.865 INFO ProgressMeter - chr13:20988287 8.5 3840 454.3 22:52:59.602 INFO ProgressMeter - chr13:26396283 8.6 3910 453.0 22:53:09.624 INFO ProgressMeter - chr13:28368460 8.8 3980 452.4 22:53:20.196 INFO ProgressMeter - chr13:28430048 9.0 4020 447.9 22:53:30.539 INFO ProgressMeter - chr13:32340017 9.1 4080 446.1 22:53:41.638 INFO ProgressMeter - chr13:72771079 9.3 4180 447.9 22:53:52.411 INFO ProgressMeter - chr13:102862978 9.5 4260 447.9 22:54:02.619 INFO ProgressMeter - chr13:113310813 9.7 4330 447.3 22:54:12.875 INFO ProgressMeter - chr14:37590549 9.9 4410 447.6 22:54:22.947 INFO ProgressMeter - chr14:81087952 10.0 4500 449.1 22:54:33.326 INFO ProgressMeter - chr14:102085776 10.2 4580 449.3 22:54:44.055 INFO ProgressMeter - chr15:34354526 10.4 4640 447.4 22:54:55.724 INFO ProgressMeter - chr15:41749474 10.6 4720 446.7 22:55:05.998 INFO ProgressMeter - chr15:67181260 10.7 4820 448.9 22:55:16.144 INFO ProgressMeter - chr15:89285132 10.9 4910 450.2 22:55:26.828 INFO ProgressMeter - chr15:92978232 11.1 5020 452.9 22:55:37.577 INFO ProgressMeter - chr16:2058792 11.3 5110 453.7 22:55:49.475 INFO ProgressMeter - chr16:3589817 11.5 5230 456.3 22:56:00.081 INFO ProgressMeter - chr16:3778698 11.6 5300 455.4 22:56:11.238 INFO ProgressMeter - chr16:23603457 11.8 5380 455.0 22:56:22.317 INFO ProgressMeter - chr16:56834126 12.0 5470 455.5 22:56:32.474 INFO ProgressMeter - chr16:72788679 12.2 5540 454.9 22:56:42.927 INFO ProgressMeter - chr16:72958346 12.4 5590 452.5 22:56:54.336 INFO ProgressMeter - chr16:89281823 12.5 5670 452.0 22:57:04.564 INFO ProgressMeter - chr16:89783005 12.7 5740 451.5 22:57:16.470 INFO ProgressMeter - chr17:7676697 12.9 5820 450.7 22:57:27.471 INFO ProgressMeter - chr17:16126080 13.1 5940 453.6 22:57:38.098 INFO ProgressMeter - chr17:31358478 13.3 6060 456.6 22:57:48.311 INFO ProgressMeter - chr17:39694469 13.4 6140 456.7 22:57:59.465 INFO ProgressMeter - chr17:40351978 13.6 6210 455.7 22:58:09.497 INFO ProgressMeter - chr17:42307591 13.8 6310 457.4 22:58:20.562 INFO ProgressMeter - chr17:43094491 14.0 6400 457.8 22:58:32.285 INFO ProgressMeter - chr17:43536808 14.2 6470 456.4 22:58:43.498 INFO ProgressMeter - chr17:43544945 14.4 6520 454.0 22:58:54.647 INFO ProgressMeter - chr17:58694929 14.5 6600 453.7 22:59:05.410 INFO ProgressMeter - chr17:61743011 14.7 6690 454.2 22:59:15.928 INFO ProgressMeter - chr17:76736159 14.9 6780 454.9 22:59:25.983 INFO ProgressMeter - chr18:42057881 15.1 6890 457.2 22:59:36.049 INFO ProgressMeter - chr18:57558508 15.2 6960 456.7 22:59:47.116 INFO ProgressMeter - chr19:2226181 15.4 7080 459.1 22:59:57.424 INFO ProgressMeter - chr19:5258015 15.6 7190 461.1 23:00:07.496 INFO ProgressMeter - chr19:10489646 15.8 7290 462.5 23:00:18.493 INFO ProgressMeter - chr19:15160998 15.9 7390 463.4 23:00:28.507 INFO ProgressMeter - chr19:15244758 16.1 7470 463.6 23:00:39.790 INFO ProgressMeter - chr19:29816213 16.3 7580 465.0 23:00:51.123 INFO ProgressMeter - chr19:35732680 16.5 7680 465.7 23:01:01.864 INFO ProgressMeter - chr19:41239692 16.7 7770 466.1 23:01:12.332 INFO ProgressMeter - chr19:42293933 16.8 7840 465.5 23:01:23.846 INFO ProgressMeter - chr19:45416598 17.0 7940 466.1 23:01:35.031 INFO ProgressMeter - chr2:15937660 17.2 8040 466.9 23:01:45.050 INFO ProgressMeter - chr2:25247111 17.4 8130 467.6 23:01:56.773 INFO ProgressMeter - chr2:29222970 17.6 8210 466.9 23:02:06.905 INFO ProgressMeter - chr2:29275400 17.8 8250 464.7 23:02:17.061 INFO ProgressMeter - chr2:42331248 17.9 8320 464.2 23:02:27.928 INFO ProgressMeter - chr2:47804908 18.1 8390 463.5 23:02:38.246 INFO ProgressMeter - chr2:98572813 18.3 8490 464.6 23:02:48.283 INFO ProgressMeter - chr2:111126799 18.4 8580 465.2 23:02:59.371 INFO ProgressMeter - chr2:113222198 18.6 8620 462.8 23:03:12.546 INFO ProgressMeter - chr2:113227430 18.8 8660 459.5 23:03:24.401 INFO ProgressMeter - chr2:113233289 19.0 8710 457.4 23:03:34.816 INFO ProgressMeter - chr2:136115314 19.2 8770 456.3 23:03:44.873 INFO ProgressMeter - chr2:140922963 19.4 8870 457.6 23:03:55.548 INFO ProgressMeter - chr2:189863741 19.6 8960 458.0 23:04:05.590 INFO ProgressMeter - chr2:208237077 19.7 9060 459.2 23:04:15.983 INFO ProgressMeter - chr2:222200176 19.9 9150 459.7 23:04:26.296 INFO ProgressMeter - chr2:222207628 20.1 9200 458.3 23:04:36.680 INFO ProgressMeter - chr2:222215065 20.2 9250 456.8 23:04:46.866 INFO ProgressMeter - chr2:222294117 20.4 9290 455.0 23:04:57.806 INFO ProgressMeter - chr20:9565891 20.6 9370 454.8 23:05:08.451 INFO ProgressMeter - chr20:32792624 20.8 9440 454.3 23:05:19.683 INFO ProgressMeter - chr20:42472564 21.0 9550 455.5 23:05:29.689 INFO ProgressMeter - chr20:56370483 21.1 9620 455.2 23:05:40.130 INFO ProgressMeter - chr21:34886948 21.3 9710 455.7 23:05:51.044 INFO ProgressMeter - chr21:41043940 21.5 9770 454.7 23:06:07.470 INFO ProgressMeter - chr21:41491875 21.8 9820 451.2 23:06:17.609 INFO ProgressMeter - chr21:41503124 21.9 9870 450.0 23:06:28.286 INFO ProgressMeter - chr22:20934077 22.1 9940 449.6 23:06:41.992 INFO ProgressMeter - chr22:23291954 22.3 10030 449.0 23:06:52.845 INFO ProgressMeter - chr22:29283738 22.5 10140 450.3 23:07:03.345 INFO ProgressMeter - chr22:29603997 22.7 10190 449.0 23:07:13.848 INFO ProgressMeter - chr22:41177519 22.9 10280 449.5 23:07:24.387 INFO ProgressMeter - chr3:12352376 23.0 10370 450.0 23:07:34.635 INFO ProgressMeter - chr3:12359185 23.2 10420 448.8 23:07:46.251 INFO ProgressMeter - chr3:12365625 23.4 10460 446.8 23:07:57.454 INFO ProgressMeter - chr3:12374130 23.6 10520 445.9 23:08:09.400 INFO ProgressMeter - chr3:12606199 23.8 10590 445.1 23:08:20.303 INFO ProgressMeter - chr3:41225658 24.0 10680 445.4 23:08:30.815 INFO ProgressMeter - chr3:47126646 24.2 10760 445.5 23:08:41.354 INFO ProgressMeter - chr3:52403136 24.3 10850 446.0 23:08:52.465 INFO ProgressMeter - chr3:71198254 24.5 10960 447.1 23:09:03.135 INFO ProgressMeter - chr3:135166940 24.7 11060 448.0 23:09:13.363 INFO ProgressMeter - chr3:138733359 24.9 11160 448.9 23:09:23.401 INFO ProgressMeter - chr3:170263377 25.0 11260 449.9 23:09:33.805 INFO ProgressMeter - chr3:183555359 25.2 11360 450.8 23:09:44.400 INFO ProgressMeter - chr3:186786500 25.4 11430 450.4 23:09:56.156 INFO ProgressMeter - chr3:196069699 25.6 11520 450.5 23:10:06.763 INFO ProgressMeter - chr4:20610011 25.8 11630 451.6 23:10:17.112 INFO ProgressMeter - chr4:54285369 25.9 11720 452.1 23:10:27.246 INFO ProgressMeter - chr4:54738436 26.1 11780 451.5 23:10:37.586 INFO ProgressMeter - chr4:80274176 26.3 11880 452.3 23:10:47.610 INFO ProgressMeter - chr4:105238525 26.4 11960 452.5 23:10:57.645 INFO ProgressMeter - chr4:122881056 26.6 12040 452.7 23:11:07.850 INFO ProgressMeter - chr4:186599896 26.8 12140 453.5 23:11:18.937 INFO ProgressMeter - chr4:186707939 27.0 12210 453.0 23:11:29.879 INFO ProgressMeter - chr5:38957650 27.1 12300 453.3 23:11:40.795 INFO ProgressMeter - chr5:56884662 27.3 12410 454.3 23:11:51.333 INFO ProgressMeter - chr5:112818964 27.5 12540 456.1 23:12:02.455 INFO ProgressMeter - chr5:122423630 27.7 12600 455.2 23:12:13.141 INFO ProgressMeter - chr5:142620759 27.9 12690 455.5 23:12:24.162 INFO ProgressMeter - chr5:150070051 28.0 12760 455.1 23:12:35.556 INFO ProgressMeter - chr5:150403910 28.2 12840 454.8 23:12:46.995 INFO ProgressMeter - chr5:177092644 28.4 12910 454.2 23:12:57.410 INFO ProgressMeter - chr5:177211455 28.6 12950 452.9 23:13:07.801 INFO ProgressMeter - chr5:180619533 28.8 13030 452.9 23:13:18.343 INFO ProgressMeter - chr6:20466963 28.9 13120 453.3 23:13:35.699 INFO ProgressMeter - chr6:29945232 29.2 13220 452.2 23:13:46.517 INFO ProgressMeter - chr6:32198647 29.4 13290 451.8 23:13:57.467 INFO ProgressMeter - chr6:35457914 29.6 13370 451.8 23:14:08.162 INFO ProgressMeter - chr6:93246790 29.8 13490 453.1 23:14:19.443 INFO ProgressMeter - chr6:117310231 30.0 13580 453.2 23:14:29.721 INFO ProgressMeter - chr6:117324369 30.1 13620 452.0 23:14:44.312 INFO ProgressMeter - chr6:117333842 30.4 13680 450.4 23:14:55.658 INFO ProgressMeter - chr6:117344106 30.6 13730 449.2 23:15:07.903 INFO ProgressMeter - chr6:135205668 30.8 13820 449.1 23:15:24.476 INFO ProgressMeter - chr6:135212634 31.0 13880 447.1 23:15:34.743 INFO ProgressMeter - chr6:137206961 31.2 13930 446.2 23:15:44.759 INFO ProgressMeter - chr6:151841765 31.4 14000 446.1 23:15:54.842 INFO ProgressMeter - chr6:157174006 31.6 14070 445.9 23:16:05.394 INFO ProgressMeter - chr6:161569353 31.7 14150 446.0 23:16:16.197 INFO ProgressMeter - chr7:13892633 31.9 14250 446.6 23:16:27.203 INFO ProgressMeter - chr7:13933625 32.1 14300 445.6 23:16:37.965 INFO ProgressMeter - chr7:13943213 32.3 14360 445.0 23:16:49.859 INFO ProgressMeter - chr7:13950311 32.5 14410 443.8 23:17:00.351 INFO ProgressMeter - chr7:13956086 32.6 14450 442.7 23:17:13.951 INFO ProgressMeter - chr7:13964792 32.9 14500 441.1 23:17:24.103 INFO ProgressMeter - chr7:13971329 33.0 14550 440.4 23:17:35.576 INFO ProgressMeter - chr7:13976642 33.2 14590 439.1 23:17:45.800 INFO ProgressMeter - chr7:13983098 33.4 14640 438.3 23:17:57.864 INFO ProgressMeter - chr7:13990619 33.6 14680 436.9 23:18:08.249 INFO ProgressMeter - chr7:55163731 33.8 14750 436.7 23:18:19.576 INFO ProgressMeter - chr7:55176169 34.0 14800 435.8 23:18:31.076 INFO ProgressMeter - chr7:55201635 34.2 14860 435.1 23:18:41.097 INFO ProgressMeter - chr7:86850368 34.3 14950 435.6 23:18:51.621 INFO ProgressMeter - chr7:102277928 34.5 15050 436.3 23:19:02.452 INFO ProgressMeter - chr7:116777387 34.7 15130 436.3 23:19:14.455 INFO ProgressMeter - chr7:140791343 34.9 15210 436.1 23:19:24.767 INFO ProgressMeter - chr7:142960926 35.1 15300 436.5 23:19:35.853 INFO ProgressMeter - chr7:152177165 35.2 15390 436.8 23:19:45.936 INFO ProgressMeter - chr7:152273816 35.4 15450 436.4 23:19:57.378 INFO ProgressMeter - chr8:32648297 35.6 15560 437.2 23:20:08.239 INFO ProgressMeter - chr8:38420866 35.8 15650 437.5 23:20:19.350 INFO ProgressMeter - chr8:47778726 36.0 15740 437.7 23:20:29.772 INFO ProgressMeter - chr8:47953805 36.1 15840 438.4 23:20:40.275 INFO ProgressMeter - chr8:73962766 36.3 15940 439.0 23:20:51.727 INFO ProgressMeter - chr8:127732335 36.5 16020 438.9 23:21:02.802 INFO ProgressMeter - chr8:144516191 36.7 16100 438.9 23:21:13.014 INFO ProgressMeter - chr9:8485760 36.9 16210 439.8 23:21:23.855 INFO ProgressMeter - chr9:35076558 37.0 16300 440.1 23:21:38.870 INFO ProgressMeter - chr9:84743992 37.3 16390 439.6 23:21:50.478 INFO ProgressMeter - chr9:84863402 37.5 16440 438.6 23:22:02.894 INFO ProgressMeter - chr9:84875810 37.7 16490 437.6 23:22:16.460 INFO ProgressMeter - chr9:85026658 37.9 16550 436.5 23:22:27.363 INFO ProgressMeter - chr9:99132599 38.1 16650 437.1 23:22:37.508 INFO ProgressMeter - chr9:130886073 38.3 16730 437.2 23:22:47.987 INFO ProgressMeter - chr9:136507332 38.4 16810 437.3 23:22:58.343 INFO ProgressMeter - chrX:45069577 38.6 16950 439.0 23:23:08.532 INFO ProgressMeter - chrX:53216072 38.8 17120 441.5 23:23:18.643 INFO ProgressMeter - chrX:71132843 38.9 17270 443.4 23:23:29.518 INFO ProgressMeter - chrX:130014273 39.1 17500 447.2 23:23:33.958 INFO Mutect2 - 555438 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 150 read(s) filtered by: GoodCigarReadFilter 0 read(s) filtered by: WellformedReadFilter 555588 total reads filtered out of 68294732 reads processed 23:23:33.958 INFO ProgressMeter - chrY:19773435 39.2 17587 448.6 23:23:33.958 INFO ProgressMeter - Traversal complete. Processed 17587 total regions in 39.2 minutes. 23:23:33.974 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 5.320350229000001 23:23:33.974 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 218.054654636 23:23:33.974 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 7.86 sec 23:23:33.975 INFO Mutect2 - Shutting down engine [June 8, 2026 at 11:23:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 39.21 minutes. Runtime.totalMemory()=3355443200 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 LS0909_tumor.bam --tumor-sample LS0909 -L TST500C_manifest.bed -O LS0909.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz 23:23:35.545 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 23:23:35.656 INFO FilterMutectCalls - ------------------------------------------------------------ 23:23:35.658 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0 23:23:35.658 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/ 23:23:35.658 INFO FilterMutectCalls - Executing as ?@nf-2ec2b10517a2ec509a1cb61374f4eb49-a65b7-ssrz2 on Linux v6.12.88 amd64 23:23:35.658 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04 23:23:35.658 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:23:35 PM GMT 23:23:35.659 INFO FilterMutectCalls - ------------------------------------------------------------ 23:23:35.659 INFO FilterMutectCalls - ------------------------------------------------------------ 23:23:35.659 INFO FilterMutectCalls - HTSJDK Version: 4.1.0 23:23:35.659 INFO FilterMutectCalls - Picard Version: 3.1.1 23:23:35.659 INFO FilterMutectCalls - Built for Spark Version: 3.5.0 23:23:35.659 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2 23:23:35.660 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 23:23:35.660 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 23:23:35.660 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 23:23:35.660 INFO FilterMutectCalls - Deflater: IntelDeflater 23:23:35.660 INFO FilterMutectCalls - Inflater: IntelInflater 23:23:35.660 INFO FilterMutectCalls - GCS max retries/reopens: 20 23:23:35.660 INFO FilterMutectCalls - Requester pays: disabled 23:23:35.660 INFO FilterMutectCalls - Initializing engine 23:23:35.820 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.RicrL5aqwA/LS0909.mutect2.raw.vcf.gz 23:23:35.932 INFO FilterMutectCalls - Done initializing engine 23:23:36.000 INFO ProgressMeter - Starting traversal 23:23:36.001 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 23:23:36.002 INFO FilterMutectCalls - Starting pass 0 through the variants 23:23:37.414 INFO FilterMutectCalls - Finished pass 0 through the variants 23:23:38.084 INFO FilterMutectCalls - Starting pass 1 through the variants 23:23:39.429 INFO FilterMutectCalls - Finished pass 1 through the variants 23:23:39.652 INFO FilterMutectCalls - Starting pass 2 through the variants 23:23:40.965 INFO FilterMutectCalls - Finished pass 2 through the variants 23:23:40.967 INFO FilterMutectCalls - Starting pass 3 through the variants 23:23:42.106 INFO FilterMutectCalls - Finished pass 3 through the variants 23:23:42.118 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter 23:23:42.119 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter 23:23:42.119 INFO ProgressMeter - chr9:96235628 0.1 11076 108623.7 23:23:42.119 INFO ProgressMeter - Traversal complete. Processed 11076 total variants in 0.1 minutes. 23:23:42.135 INFO FilterMutectCalls - Shutting down engine [June 8, 2026 at 11:23:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.11 minutes. Runtime.totalMemory()=352321536 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 LS0909.mutect2.raw.vcf.gz --stats LS0909.mutect2.raw.vcf.gz.stats -O LS0909.mutect2.filtered.vcf.gz 23:23:43.337 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 23:23:43.454 INFO SelectVariants - ------------------------------------------------------------ 23:23:43.457 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0 23:23:43.457 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 23:23:43.457 INFO SelectVariants - Executing as ?@nf-2ec2b10517a2ec509a1cb61374f4eb49-a65b7-ssrz2 on Linux v6.12.88 amd64 23:23:43.457 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04 23:23:43.458 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:23:43 PM GMT 23:23:43.458 INFO SelectVariants - ------------------------------------------------------------ 23:23:43.458 INFO SelectVariants - ------------------------------------------------------------ 23:23:43.459 INFO SelectVariants - HTSJDK Version: 4.1.0 23:23:43.459 INFO SelectVariants - Picard Version: 3.1.1 23:23:43.459 INFO SelectVariants - Built for Spark Version: 3.5.0 23:23:43.459 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 23:23:43.460 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 23:23:43.460 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 23:23:43.460 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 23:23:43.460 INFO SelectVariants - Deflater: IntelDeflater 23:23:43.460 INFO SelectVariants - Inflater: IntelInflater 23:23:43.460 INFO SelectVariants - GCS max retries/reopens: 20 23:23:43.460 INFO SelectVariants - Requester pays: disabled 23:23:43.460 INFO SelectVariants - Initializing engine 23:23:43.665 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.RicrL5aqwA/LS0909.mutect2.filtered.vcf.gz 23:23:43.780 INFO SelectVariants - Done initializing engine 23:23:43.818 INFO ProgressMeter - Starting traversal 23:23:43.819 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 23:23:43.902 INFO ProgressMeter - chr6:29943377 0.0 2769 2076750.0 23:23:43.902 INFO ProgressMeter - Traversal complete. Processed 2769 total variants in 0.0 minutes. 23:23:43.913 INFO SelectVariants - Shutting down engine [June 8, 2026 at 11:23:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 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 SelectVariants -R hg38.fa -V LS0909.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0909.mutect2.pass.vcf.gz