22:44:10.991 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
22:44:11.102 INFO Mutect2 - ------------------------------------------------------------
22:44:11.104 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:11.105 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:11.105 INFO Mutect2 - Executing as ?@nf-43ed0a4ad18b82a55bf1218a4bdcaf0a-b7ce0-zmlmf on Linux v6.12.88 amd64
22:44:11.105 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:11.105 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:10 PM GMT
22:44:11.105 INFO Mutect2 - ------------------------------------------------------------
22:44:11.105 INFO Mutect2 - ------------------------------------------------------------
22:44:11.106 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:11.107 INFO Mutect2 - Picard Version: 3.1.1
22:44:11.107 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:11.107 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:11.107 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:11.107 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:11.107 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:11.107 INFO Mutect2 - Deflater: IntelDeflater
22:44:11.107 INFO Mutect2 - Inflater: IntelInflater
22:44:11.108 INFO Mutect2 - GCS max retries/reopens: 20
22:44:11.108 INFO Mutect2 - Requester pays: disabled
22:44:11.108 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.ZtM04aTHy9/LS0885_tumor.bam.bai is older than BAM /tmp/nxf.ZtM04aTHy9/LS0885_tumor.bam
22:44:11.285 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.ZtM04aTHy9/af-only-gnomad.hg38.vcf.gz
22:44:11.400 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.ZtM04aTHy9/TST500C_manifest.bed
22:44:11.435 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:11.464 INFO Mutect2 - Done initializing engine
22:44:11.474 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
22:44:11.475 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
22:44:11.476 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:11.476 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:11.486 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
22:44:11.494 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:11.494 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:11.495 INFO IntelPairHmm - Available threads: 384
22:44:11.495 INFO IntelPairHmm - Requested threads: 4
22:44:11.495 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:11.526 INFO ProgressMeter - Starting traversal
22:44:11.527 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:21.986 INFO ProgressMeter - chr1:11145039 0.2 80 459.0
22:44:33.406 INFO ProgressMeter - chr1:15929051 0.4 150 411.4
22:44:44.395 INFO ProgressMeter - chr1:18634301 0.5 210 383.4
22:44:54.792 INFO ProgressMeter - chr1:23557510 0.7 260 360.6
22:45:05.975 INFO ProgressMeter - chr1:36472515 0.9 350 385.7
22:45:16.485 INFO ProgressMeter - chr1:43352214 1.1 430 397.2
22:45:27.458 INFO ProgressMeter - chr1:64845623 1.3 530 418.8
22:45:38.584 INFO ProgressMeter - chr1:117156624 1.5 640 441.1
22:45:49.184 INFO ProgressMeter - chr1:119967582 1.6 710 436.2
22:45:59.442 INFO ProgressMeter - chr1:156873768 1.8 760 422.6
22:46:09.632 INFO ProgressMeter - chr1:158626837 2.0 800 406.4
22:46:21.377 INFO ProgressMeter - chr1:158685106 2.2 860 397.4
22:46:34.491 INFO ProgressMeter - chr1:179108158 2.4 940 394.5
22:46:46.030 INFO ProgressMeter - chr1:204460602 2.6 1020 396.1
22:46:56.761 INFO ProgressMeter - chr1:204554071 2.8 1080 392.2
22:47:08.271 INFO ProgressMeter - chr1:226386324 2.9 1150 390.4
22:47:21.610 INFO ProgressMeter - chr1:243502261 3.2 1210 381.9
22:47:32.187 INFO ProgressMeter - chr10:17151286 3.3 1260 376.8
22:47:42.477 INFO ProgressMeter - chr10:27100516 3.5 1320 375.4
22:47:52.564 INFO ProgressMeter - chr10:43105128 3.7 1390 377.3
22:48:03.202 INFO ProgressMeter - chr10:43116190 3.9 1440 372.9
22:48:14.223 INFO ProgressMeter - chr10:62091160 4.0 1500 370.8
22:48:25.272 INFO ProgressMeter - chr10:68691106 4.2 1550 366.5
22:48:38.254 INFO ProgressMeter - chr10:101770136 4.4 1640 368.9
22:48:49.464 INFO ProgressMeter - chr10:110600512 4.6 1730 373.5
22:49:03.055 INFO ProgressMeter - chr10:121481907 4.9 1790 368.4
22:49:13.689 INFO ProgressMeter - chr10:121565465 5.0 1850 367.4
22:49:23.788 INFO ProgressMeter - chr11:64804332 5.2 1950 374.7
22:49:33.943 INFO ProgressMeter - chr11:69699036 5.4 2040 379.6
22:49:45.279 INFO ProgressMeter - chr11:69776415 5.6 2110 379.3
22:49:57.143 INFO ProgressMeter - chr11:69814682 5.8 2150 373.2
22:50:08.273 INFO ProgressMeter - chr11:77323272 5.9 2210 371.7
22:50:19.165 INFO ProgressMeter - chr11:77405739 6.1 2260 368.8
22:50:30.798 INFO ProgressMeter - chr11:102227467 6.3 2350 371.8
22:50:41.105 INFO ProgressMeter - chr11:108251835 6.5 2380 366.6
22:50:51.142 INFO ProgressMeter - chr11:108365080 6.7 2450 367.9
22:51:02.451 INFO ProgressMeter - chr11:118502696 6.8 2520 368.0
22:51:17.688 INFO ProgressMeter - chr11:125626226 7.1 2580 363.2
22:51:29.911 INFO ProgressMeter - chr11:128459081 7.3 2640 361.3
22:51:41.995 INFO ProgressMeter - chr11:128694042 7.5 2680 357.0
22:51:53.529 INFO ProgressMeter - chr12:323129 7.7 2740 355.8
22:52:03.799 INFO ProgressMeter - chr12:4374929 7.9 2810 357.0
22:52:14.995 INFO ProgressMeter - chr12:4448101 8.1 2870 356.2
22:52:25.065 INFO ProgressMeter - chr12:6602374 8.2 2930 356.2
22:52:36.913 INFO ProgressMeter - chr12:11859214 8.4 2980 353.8
22:52:49.755 INFO ProgressMeter - chr12:11862961 8.6 3010 348.5
22:52:59.947 INFO ProgressMeter - chr12:11868277 8.8 3050 346.3
22:53:09.959 INFO ProgressMeter - chr12:18503279 9.0 3110 346.6
22:53:22.114 INFO ProgressMeter - chr12:31804367 9.2 3180 346.5
22:53:32.354 INFO ProgressMeter - chr12:49031383 9.3 3250 347.7
22:53:42.653 INFO ProgressMeter - chr12:49043361 9.5 3310 347.7
22:53:52.680 INFO ProgressMeter - chr12:56084993 9.7 3400 351.0
22:54:04.366 INFO ProgressMeter - chr12:57094593 9.9 3480 352.2
22:54:14.938 INFO ProgressMeter - chr12:57754537 10.1 3560 354.0
22:54:25.649 INFO ProgressMeter - chr12:69574846 10.2 3640 355.6
22:54:37.063 INFO ProgressMeter - chr12:120999481 10.4 3730 357.8
22:54:47.119 INFO ProgressMeter - chr12:132681136 10.6 3800 358.7
22:54:57.526 INFO ProgressMeter - chr13:28004050 10.8 3890 361.3
22:55:12.714 INFO ProgressMeter - chr13:28387653 11.0 3960 359.4
22:55:23.758 INFO ProgressMeter - chr13:32338531 11.2 4030 359.7
22:55:34.431 INFO ProgressMeter - chr13:48459686 11.4 4120 362.0
22:55:46.759 INFO ProgressMeter - chr13:102862897 11.6 4210 363.3
22:55:59.907 INFO ProgressMeter - chr14:23307775 11.8 4310 365.1
22:56:10.614 INFO ProgressMeter - chr14:37593442 12.0 4380 365.5
22:56:20.852 INFO ProgressMeter - chr14:80955679 12.2 4450 366.1
22:56:31.909 INFO ProgressMeter - chr14:102083791 12.3 4520 366.3
22:56:44.345 INFO ProgressMeter - chr15:34348055 12.5 4580 365.0
22:56:54.488 INFO ProgressMeter - chr15:41734520 12.7 4650 365.7
22:57:04.630 INFO ProgressMeter - chr15:49434048 12.9 4710 365.5
22:57:15.205 INFO ProgressMeter - chr15:87978087 13.1 4800 367.5
22:57:25.266 INFO ProgressMeter - chr15:89315334 13.2 4880 368.9
22:57:36.138 INFO ProgressMeter - chr15:92991474 13.4 4970 370.6
22:57:46.583 INFO ProgressMeter - chr16:346816 13.6 5050 371.8
22:57:56.940 INFO ProgressMeter - chr16:3590065 13.8 5170 375.8
22:58:07.805 INFO ProgressMeter - chr16:3810601 13.9 5250 376.7
22:58:18.895 INFO ProgressMeter - chr16:13947612 14.1 5320 376.7
22:58:29.498 INFO ProgressMeter - chr16:56798495 14.3 5400 377.6
22:58:41.275 INFO ProgressMeter - chr16:72793253 14.5 5480 378.0
22:58:52.850 INFO ProgressMeter - chr16:72958430 14.7 5530 376.5
22:59:03.074 INFO ProgressMeter - chr16:89280871 14.9 5610 377.5
22:59:13.617 INFO ProgressMeter - chr16:89783022 15.0 5680 377.8
22:59:24.380 INFO ProgressMeter - chr17:8079394 15.2 5780 379.9
22:59:34.438 INFO ProgressMeter - chr17:17219017 15.4 5880 382.3
22:59:45.193 INFO ProgressMeter - chr17:31334878 15.6 5960 383.0
22:59:56.304 INFO ProgressMeter - chr17:39525862 15.7 6050 384.2
23:00:06.754 INFO ProgressMeter - chr17:40399131 15.9 6150 386.3
23:00:17.365 INFO ProgressMeter - chr17:43051061 16.1 6260 388.9
23:00:28.818 INFO ProgressMeter - chr17:43095844 16.3 6320 388.0
23:00:39.673 INFO ProgressMeter - chr17:43535438 16.5 6380 387.4
23:00:54.157 INFO ProgressMeter - chr17:43544045 16.7 6440 385.4
23:01:05.170 INFO ProgressMeter - chr17:58363273 16.9 6520 385.9
23:01:15.872 INFO ProgressMeter - chr17:60623624 17.1 6600 386.6
23:01:26.320 INFO ProgressMeter - chr17:65549518 17.2 6670 386.7
23:01:37.584 INFO ProgressMeter - chr18:732886 17.4 6770 388.3
23:01:47.880 INFO ProgressMeter - chr18:44950510 17.6 6850 389.1
23:01:58.816 INFO ProgressMeter - chr18:58715933 17.8 6920 389.0
23:02:09.221 INFO ProgressMeter - chr19:2227737 18.0 7030 391.4
23:02:19.842 INFO ProgressMeter - chr19:7152696 18.1 7150 394.2
23:02:29.939 INFO ProgressMeter - chr19:10994826 18.3 7250 396.0
23:02:40.242 INFO ProgressMeter - chr19:15181088 18.5 7350 397.8
23:02:52.010 INFO ProgressMeter - chr19:17843808 18.7 7450 398.9
23:03:02.304 INFO ProgressMeter - chr19:29823653 18.8 7530 399.5
23:03:12.327 INFO ProgressMeter - chr19:40236014 19.0 7620 400.8
23:03:28.171 INFO ProgressMeter - chr19:41261119 19.3 7700 399.4
23:03:38.923 INFO ProgressMeter - chr19:45359343 19.5 7780 399.9
23:03:49.843 INFO ProgressMeter - chr19:45423268 19.6 7870 400.7
23:04:00.636 INFO ProgressMeter - chr2:15941561 19.8 7940 400.6
23:04:11.691 INFO ProgressMeter - chr2:25742027 20.0 8030 401.4
23:04:21.801 INFO ProgressMeter - chr2:29223079 20.2 8090 401.1
23:04:31.916 INFO ProgressMeter - chr2:29226698 20.3 8120 399.2
23:04:43.088 INFO ProgressMeter - chr2:42330030 20.5 8200 399.5
23:04:53.359 INFO ProgressMeter - chr2:47476365 20.7 8240 398.1
23:05:04.282 INFO ProgressMeter - chr2:61498671 20.9 8330 399.0
23:05:14.460 INFO ProgressMeter - chr2:108753099 21.0 8400 399.1
23:05:28.497 INFO ProgressMeter - chr2:111127845 21.3 8460 397.5
23:05:39.242 INFO ProgressMeter - chr2:113223483 21.5 8500 396.1
23:05:50.774 INFO ProgressMeter - chr2:113227816 21.7 8530 393.9
23:06:02.196 INFO ProgressMeter - chr2:113233287 21.8 8570 392.3
23:06:13.038 INFO ProgressMeter - chr2:127289687 22.0 8620 391.4
23:06:24.189 INFO ProgressMeter - chr2:140601448 22.2 8710 392.1
23:06:34.355 INFO ProgressMeter - chr2:157766166 22.4 8780 392.3
23:06:45.087 INFO ProgressMeter - chr2:191058200 22.6 8860 392.7
23:06:55.223 INFO ProgressMeter - chr2:208243425 22.7 8940 393.3
23:07:05.360 INFO ProgressMeter - chr2:222200785 22.9 9020 393.9
23:07:17.257 INFO ProgressMeter - chr2:222208273 23.1 9070 392.7
23:07:27.438 INFO ProgressMeter - chr2:222214727 23.3 9110 391.6
23:07:38.954 INFO ProgressMeter - chr2:222293628 23.5 9150 390.1
23:07:49.071 INFO ProgressMeter - chr20:4466799 23.6 9230 390.7
23:07:59.402 INFO ProgressMeter - chr20:32436054 23.8 9290 390.4
23:08:10.195 INFO ProgressMeter - chr20:41121694 24.0 9370 390.8
23:08:21.083 INFO ProgressMeter - chr20:47636132 24.2 9440 390.7
23:08:31.576 INFO ProgressMeter - chr20:58840105 24.3 9490 390.0
23:08:42.413 INFO ProgressMeter - chr21:38380789 24.5 9570 390.4
23:08:53.040 INFO ProgressMeter - chr21:41465744 24.7 9630 390.0
23:09:07.061 INFO ProgressMeter - chr21:41492291 24.9 9670 388.0
23:09:17.486 INFO ProgressMeter - chr21:41502281 25.1 9710 386.9
23:09:28.294 INFO ProgressMeter - chr21:44235270 25.3 9770 386.5
23:09:38.685 INFO ProgressMeter - chr22:23291258 25.5 9860 387.4
23:09:50.095 INFO ProgressMeter - chr22:29283411 25.6 9970 388.8
23:10:00.683 INFO ProgressMeter - chr22:29658187 25.8 10020 388.1
23:10:10.946 INFO ProgressMeter - chr22:41178235 26.0 10110 389.0
23:10:21.620 INFO ProgressMeter - chr3:12352973 26.2 10190 389.4
23:10:31.886 INFO ProgressMeter - chr3:12359058 26.3 10230 388.4
23:10:43.700 INFO ProgressMeter - chr3:12365925 26.5 10280 387.4
23:10:53.947 INFO ProgressMeter - chr3:12372662 26.7 10320 386.4
23:11:04.425 INFO ProgressMeter - chr3:12379659 26.9 10370 385.8
23:11:15.349 INFO ProgressMeter - chr3:30650423 27.1 10440 385.8
23:11:25.969 INFO ProgressMeter - chr3:47113913 27.2 10540 386.9
23:11:36.884 INFO ProgressMeter - chr3:49896282 27.4 10620 387.3
23:11:46.982 INFO ProgressMeter - chr3:69959271 27.6 10720 388.5
23:11:57.579 INFO ProgressMeter - chr3:119905753 27.8 10810 389.3
23:12:08.688 INFO ProgressMeter - chr3:136500202 28.0 10890 389.6
23:12:18.710 INFO ProgressMeter - chr3:142470084 28.1 10970 390.1
23:12:28.873 INFO ProgressMeter - chr3:179173522 28.3 11060 391.0
23:12:40.051 INFO ProgressMeter - chr3:185428580 28.5 11140 391.2
23:12:50.157 INFO ProgressMeter - chr3:186786162 28.6 11200 391.0
23:13:00.658 INFO ProgressMeter - chr3:196069453 28.8 11290 391.8
23:13:11.353 INFO ProgressMeter - chr4:20542524 29.0 11390 392.8
23:13:22.324 INFO ProgressMeter - chr4:54267664 29.2 11470 393.1
23:13:32.944 INFO ProgressMeter - chr4:54731890 29.4 11540 393.1
23:13:43.118 INFO ProgressMeter - chr4:55113429 29.5 11580 392.2
23:13:53.697 INFO ProgressMeter - chr4:83467452 29.7 11660 392.6
23:14:04.184 INFO ProgressMeter - chr4:105241325 29.9 11720 392.3
23:14:14.256 INFO ProgressMeter - chr4:142028780 30.0 11790 392.4
23:14:25.240 INFO ProgressMeter - chr4:186604375 30.2 11880 393.0
23:14:35.926 INFO ProgressMeter - chr4:186707843 30.4 11940 392.7
23:14:45.931 INFO ProgressMeter - chr5:38949429 30.6 12010 392.8
23:14:57.248 INFO ProgressMeter - chr5:44357005 30.8 12100 393.3
23:15:07.256 INFO ProgressMeter - chr5:58459839 30.9 12170 393.5
23:15:17.492 INFO ProgressMeter - chr5:112738420 31.1 12270 394.5
23:15:28.936 INFO ProgressMeter - chr5:122403791 31.3 12330 394.1
23:15:40.132 INFO ProgressMeter - chr5:138933800 31.5 12410 394.3
23:15:50.166 INFO ProgressMeter - chr5:149517773 31.6 12470 394.1
23:16:01.039 INFO ProgressMeter - chr5:150401635 31.8 12550 394.3
23:16:15.907 INFO ProgressMeter - chr5:177090936 32.1 12630 393.8
23:16:28.238 INFO ProgressMeter - chr5:177210277 32.3 12670 392.5
23:16:38.673 INFO ProgressMeter - chr5:177515664 32.5 12730 392.3
23:16:49.060 INFO ProgressMeter - chr6:20402231 32.6 12800 392.3
23:17:00.146 INFO ProgressMeter - chr6:26020488 32.8 12880 392.6
23:17:10.488 INFO ProgressMeter - chr6:30703102 33.0 12940 392.3
23:17:21.091 INFO ProgressMeter - chr6:32196923 33.2 12990 391.7
23:17:31.980 INFO ProgressMeter - chr6:35457554 33.3 13060 391.7
23:17:42.363 INFO ProgressMeter - chr6:43784539 33.5 13160 392.7
23:17:52.821 INFO ProgressMeter - chr6:112069382 33.7 13240 393.0
23:18:03.944 INFO ProgressMeter - chr6:117322006 33.9 13280 392.0
23:18:15.213 INFO ProgressMeter - chr6:117332812 34.1 13330 391.4
23:18:27.108 INFO ProgressMeter - chr6:117340439 34.3 13370 390.3
23:18:38.399 INFO ProgressMeter - chr6:135204703 34.4 13450 390.4
23:18:53.040 INFO ProgressMeter - chr6:135213291 34.7 13500 389.1
23:19:03.053 INFO ProgressMeter - chr6:137878817 34.9 13550 388.7
23:19:14.401 INFO ProgressMeter - chr6:151989140 35.0 13620 388.6
23:19:25.826 INFO ProgressMeter - chr6:161049133 35.2 13700 388.8
23:19:36.233 INFO ProgressMeter - chr7:2944250 35.4 13800 389.7
23:19:50.434 INFO ProgressMeter - chr7:13909057 35.6 13870 389.1
23:20:00.714 INFO ProgressMeter - chr7:13938603 35.8 13920 388.6
23:20:14.985 INFO ProgressMeter - chr7:13947810 36.1 13970 387.4
23:20:25.405 INFO ProgressMeter - chr7:13953559 36.2 14010 386.7
23:20:36.166 INFO ProgressMeter - chr7:13960541 36.4 14050 385.9
23:20:47.135 INFO ProgressMeter - chr7:13966149 36.6 14090 385.0
23:20:58.723 INFO ProgressMeter - chr7:13973865 36.8 14150 384.7
23:21:10.581 INFO ProgressMeter - chr7:13978220 37.0 14180 383.4
23:21:22.652 INFO ProgressMeter - chr7:13983719 37.2 14220 382.4
23:21:33.740 INFO ProgressMeter - chr7:13988752 37.4 14250 381.3
23:21:44.406 INFO ProgressMeter - chr7:55156060 37.5 14320 381.4
23:21:54.538 INFO ProgressMeter - chr7:55169628 37.7 14360 380.7
23:22:06.411 INFO ProgressMeter - chr7:55180501 37.9 14420 380.3
23:22:16.822 INFO ProgressMeter - chr7:78369154 38.1 14480 380.2
23:22:27.554 INFO ProgressMeter - chr7:92675666 38.3 14550 380.2
23:22:37.603 INFO ProgressMeter - chr7:102277928 38.4 14630 380.6
23:22:47.611 INFO ProgressMeter - chr7:116767399 38.6 14690 380.6
23:22:58.769 INFO ProgressMeter - chr7:140788446 38.8 14760 380.5
23:23:08.834 INFO ProgressMeter - chr7:140808902 39.0 14810 380.2
23:23:19.219 INFO ProgressMeter - chr7:151490941 39.1 14900 380.8
23:23:30.778 INFO ProgressMeter - chr7:152180090 39.3 14960 380.5
23:23:41.666 INFO ProgressMeter - chr7:152330599 39.5 15030 380.5
23:23:52.190 INFO ProgressMeter - chr8:32605560 39.7 15120 381.1
23:24:02.248 INFO ProgressMeter - chr8:37697443 39.8 15170 380.7
23:24:13.006 INFO ProgressMeter - chr8:38458665 40.0 15260 381.3
23:24:24.736 INFO ProgressMeter - chr8:47778726 40.2 15330 381.2
23:24:35.482 INFO ProgressMeter - chr8:47889012 40.4 15390 380.9
23:24:46.003 INFO ProgressMeter - chr8:68030495 40.6 15470 381.3
23:24:57.538 INFO ProgressMeter - chr8:89978218 40.8 15540 381.2
23:25:10.760 INFO ProgressMeter - chr8:127732868 41.0 15600 380.6
23:25:21.085 INFO ProgressMeter - chr8:144515324 41.2 15680 381.0
23:25:31.605 INFO ProgressMeter - chr9:8449723 41.3 15780 381.8
23:25:42.463 INFO ProgressMeter - chr9:36882002 41.5 15870 382.3
23:25:53.675 INFO ProgressMeter - chr9:84742935 41.7 15940 382.2
23:26:05.399 INFO ProgressMeter - chr9:84813989 41.9 15980 381.4
23:26:20.339 INFO ProgressMeter - chr9:84864648 42.1 16010 379.9
23:26:30.914 INFO ProgressMeter - chr9:84875830 42.3 16050 379.2
23:26:42.647 INFO ProgressMeter - chr9:85024520 42.5 16090 378.4
23:26:52.833 INFO ProgressMeter - chr9:95101705 42.7 16130 377.9
23:27:03.762 INFO ProgressMeter - chr9:125153531 42.9 16220 378.3
23:27:14.167 INFO ProgressMeter - chr9:132902603 43.0 16280 378.2
23:27:24.945 INFO ProgressMeter - chr9:136900537 43.2 16380 379.0
23:27:35.365 INFO ProgressMeter - chrX:45069577 43.4 16480 379.7
23:27:46.259 INFO ProgressMeter - chrX:49030356 43.6 16570 380.2
23:27:56.367 INFO ProgressMeter - chrX:53193573 43.7 16630 380.1
23:28:07.847 INFO ProgressMeter - chrX:64190268 43.9 16710 380.3
23:28:18.702 INFO ProgressMeter - chrX:67689292 44.1 16780 380.3
23:28:28.840 INFO ProgressMeter - chrX:71368052 44.3 16860 380.7
23:28:40.194 INFO ProgressMeter - chrX:77681819 44.5 16950 381.1
23:28:50.556 INFO ProgressMeter - chrX:124037525 44.7 17040 381.6
23:29:01.523 INFO ProgressMeter - chrX:134378007 44.8 17120 381.9
23:29:02.908 INFO Mutect2 - 611285 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
3 read(s) filtered by: ReadLengthReadFilter
123 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
611411 total reads filtered out of 83426446 reads processed
23:29:02.908 INFO ProgressMeter - chrY:19564390 44.9 17169 382.8
23:29:02.908 INFO ProgressMeter - Traversal complete. Processed 17169 total regions in 44.9 minutes.
23:29:02.927 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 5.5706962650000005
23:29:02.928 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 261.264658251
23:29:02.928 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 9.10 sec
23:29:02.929 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:29:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 44.87 minutes.
Runtime.totalMemory()=6517948416
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 LS0885_tumor.bam --tumor-sample LS0885 -L TST500C_manifest.bed -O LS0885.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:29:04.476 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
23:29:04.596 INFO FilterMutectCalls - ------------------------------------------------------------
23:29:04.599 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:29:04.599 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:29:04.599 INFO FilterMutectCalls - Executing as ?@nf-43ed0a4ad18b82a55bf1218a4bdcaf0a-b7ce0-zmlmf on Linux v6.12.88 amd64
23:29:04.599 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:29:04.599 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:29:04 PM GMT
23:29:04.599 INFO FilterMutectCalls - ------------------------------------------------------------
23:29:04.600 INFO FilterMutectCalls - ------------------------------------------------------------
23:29:04.600 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:29:04.600 INFO FilterMutectCalls - Picard Version: 3.1.1
23:29:04.600 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:29:04.601 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:29:04.601 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:29:04.601 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:29:04.601 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:29:04.601 INFO FilterMutectCalls - Deflater: IntelDeflater
23:29:04.601 INFO FilterMutectCalls - Inflater: IntelInflater
23:29:04.601 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:29:04.601 INFO FilterMutectCalls - Requester pays: disabled
23:29:04.602 INFO FilterMutectCalls - Initializing engine
23:29:04.814 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.ZtM04aTHy9/LS0885.mutect2.raw.vcf.gz
23:29:04.915 INFO FilterMutectCalls - Done initializing engine
23:29:04.971 INFO ProgressMeter - Starting traversal
23:29:04.972 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:29:04.972 INFO FilterMutectCalls - Starting pass 0 through the variants
23:29:06.024 INFO FilterMutectCalls - Finished pass 0 through the variants
23:29:10.167 INFO FilterMutectCalls - Starting pass 1 through the variants
23:29:11.322 INFO FilterMutectCalls - Finished pass 1 through the variants
23:29:12.019 INFO FilterMutectCalls - Starting pass 2 through the variants
23:29:13.167 INFO FilterMutectCalls - Finished pass 2 through the variants
23:29:13.168 INFO FilterMutectCalls - Starting pass 3 through the variants
23:29:14.202 INFO FilterMutectCalls - Finished pass 3 through the variants
23:29:14.211 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:29:14.211 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:29:14.212 INFO ProgressMeter - chr3:12375245 0.2 9988 64864.2
23:29:14.212 INFO ProgressMeter - Traversal complete. Processed 9988 total variants in 0.2 minutes.
23:29:14.223 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:29:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=301989888
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 LS0885.mutect2.raw.vcf.gz --stats LS0885.mutect2.raw.vcf.gz.stats -O LS0885.mutect2.filtered.vcf.gz
23:29:15.465 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
23:29:15.578 INFO SelectVariants - ------------------------------------------------------------
23:29:15.580 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:29:15.580 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:29:15.580 INFO SelectVariants - Executing as ?@nf-43ed0a4ad18b82a55bf1218a4bdcaf0a-b7ce0-zmlmf on Linux v6.12.88 amd64
23:29:15.580 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:29:15.581 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:29:15 PM GMT
23:29:15.581 INFO SelectVariants - ------------------------------------------------------------
23:29:15.581 INFO SelectVariants - ------------------------------------------------------------
23:29:15.581 INFO SelectVariants - HTSJDK Version: 4.1.0
23:29:15.581 INFO SelectVariants - Picard Version: 3.1.1
23:29:15.582 INFO SelectVariants - Built for Spark Version: 3.5.0
23:29:15.582 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:29:15.582 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:29:15.582 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:29:15.582 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:29:15.582 INFO SelectVariants - Deflater: IntelDeflater
23:29:15.582 INFO SelectVariants - Inflater: IntelInflater
23:29:15.582 INFO SelectVariants - GCS max retries/reopens: 20
23:29:15.583 INFO SelectVariants - Requester pays: disabled
23:29:15.583 INFO SelectVariants - Initializing engine
23:29:15.758 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.ZtM04aTHy9/LS0885.mutect2.filtered.vcf.gz
23:29:15.865 INFO SelectVariants - Done initializing engine
23:29:15.900 INFO ProgressMeter - Starting traversal
23:29:15.901 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:29:15.975 INFO ProgressMeter - chr7:13891573 0.0 2497 2080833.3
23:29:15.975 INFO ProgressMeter - Traversal complete. Processed 2497 total variants in 0.0 minutes.
23:29:15.985 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:29:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=301989888
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 LS0885.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0885.mutect2.pass.vcf.gz