22:44:25.448 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
22:44:25.556 INFO Mutect2 - ------------------------------------------------------------
22:44:25.558 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:25.558 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:25.558 INFO Mutect2 - Executing as ?@nf-9747620e86f126683c4d7df399e6b172-204de-xfrtg on Linux v6.12.88 amd64
22:44:25.558 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:25.559 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:25 PM GMT
22:44:25.559 INFO Mutect2 - ------------------------------------------------------------
22:44:25.559 INFO Mutect2 - ------------------------------------------------------------
22:44:25.559 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:25.559 INFO Mutect2 - Picard Version: 3.1.1
22:44:25.559 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:25.560 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:25.560 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:25.560 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:25.560 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:25.560 INFO Mutect2 - Deflater: IntelDeflater
22:44:25.560 INFO Mutect2 - Inflater: IntelInflater
22:44:25.560 INFO Mutect2 - GCS max retries/reopens: 20
22:44:25.560 INFO Mutect2 - Requester pays: disabled
22:44:25.561 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.AGG35TGp6a/LS0913_tumor.bam.bai is older than BAM /tmp/nxf.AGG35TGp6a/LS0913_tumor.bam
22:44:25.818 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.AGG35TGp6a/af-only-gnomad.hg38.vcf.gz
22:44:25.931 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.AGG35TGp6a/TST500C_manifest.bed
22:44:25.967 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:26.001 INFO Mutect2 - Done initializing engine
22:44:26.014 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
22:44:26.016 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
22:44:26.017 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:26.017 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:26.030 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
22:44:26.039 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:26.039 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:26.039 INFO IntelPairHmm - Available threads: 384
22:44:26.040 INFO IntelPairHmm - Requested threads: 4
22:44:26.040 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:26.079 INFO ProgressMeter - Starting traversal
22:44:26.080 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:36.920 INFO ProgressMeter - chr1:9724274 0.2 60 332.1
22:44:47.126 INFO ProgressMeter - chr1:11216203 0.4 110 313.6
22:44:59.177 INFO ProgressMeter - chr1:15928306 0.6 160 290.1
22:45:09.239 INFO ProgressMeter - chr1:15932759 0.7 190 264.1
22:45:20.453 INFO ProgressMeter - chr1:17027747 0.9 230 253.8
22:45:33.538 INFO ProgressMeter - chr1:18747566 1.1 280 249.0
22:45:44.554 INFO ProgressMeter - chr1:26772810 1.3 340 260.0
22:45:55.002 INFO ProgressMeter - chr1:36467228 1.5 390 263.2
22:46:05.196 INFO ProgressMeter - chr1:39899094 1.7 450 272.4
22:46:16.259 INFO ProgressMeter - chr1:45331773 1.8 510 277.7
22:46:28.060 INFO ProgressMeter - chr1:54252500 2.0 580 285.3
22:46:38.430 INFO ProgressMeter - chr1:72282317 2.2 640 290.1
22:46:49.098 INFO ProgressMeter - chr1:114714938 2.4 730 306.3
22:47:00.139 INFO ProgressMeter - chr1:119916264 2.6 780 303.8
22:47:11.373 INFO ProgressMeter - chr1:150578970 2.8 850 308.5
22:47:25.299 INFO ProgressMeter - chr1:156874711 3.0 890 298.0
22:47:37.030 INFO ProgressMeter - chr1:158636639 3.2 930 292.2
22:47:47.566 INFO ProgressMeter - chr1:162754622 3.4 990 294.8
22:47:57.613 INFO ProgressMeter - chr1:179108490 3.5 1050 297.8
22:48:08.711 INFO ProgressMeter - chr1:204449906 3.7 1130 304.5
22:48:20.401 INFO ProgressMeter - chr1:204549353 3.9 1200 307.3
22:48:30.822 INFO ProgressMeter - chr1:226379571 4.1 1270 311.3
22:48:44.009 INFO ProgressMeter - chr1:243502122 4.3 1340 311.7
22:48:55.659 INFO ProgressMeter - chr10:8069471 4.5 1390 309.4
22:49:06.432 INFO ProgressMeter - chr10:27060324 4.7 1450 310.3
22:49:17.776 INFO ProgressMeter - chr10:32035961 4.9 1510 310.6
22:49:29.785 INFO ProgressMeter - chr10:43114579 5.1 1570 310.2
22:49:40.131 INFO ProgressMeter - chr10:43119529 5.2 1610 307.6
22:49:51.933 INFO ProgressMeter - chr10:62092674 5.4 1660 305.7
22:50:03.270 INFO ProgressMeter - chr10:68667103 5.6 1700 302.5
22:50:14.067 INFO ProgressMeter - chr10:87941652 5.8 1770 305.2
22:50:25.195 INFO ProgressMeter - chr10:101775867 6.0 1830 305.8
22:50:35.353 INFO ProgressMeter - chr10:110599633 6.2 1900 308.7
22:50:46.002 INFO ProgressMeter - chr10:121480062 6.3 1950 308.0
22:50:56.459 INFO ProgressMeter - chr10:121500907 6.5 1990 305.9
22:51:07.478 INFO ProgressMeter - chr11:11074637 6.7 2060 307.9
22:51:17.871 INFO ProgressMeter - chr11:64371281 6.9 2130 310.4
22:51:29.584 INFO ProgressMeter - chr11:69648874 7.1 2200 311.7
22:51:42.663 INFO ProgressMeter - chr11:69701917 7.3 2260 310.6
22:51:53.236 INFO ProgressMeter - chr11:69777915 7.5 2320 311.3
22:52:04.975 INFO ProgressMeter - chr11:69813032 7.6 2350 307.3
22:52:15.081 INFO ProgressMeter - chr11:76472562 7.8 2390 305.8
22:52:25.607 INFO ProgressMeter - chr11:77358896 8.0 2440 305.3
22:52:36.409 INFO ProgressMeter - chr11:94456274 8.2 2510 307.1
22:52:51.777 INFO ProgressMeter - chr11:102325253 8.4 2570 304.9
22:53:02.069 INFO ProgressMeter - chr11:108312409 8.6 2640 307.0
22:53:12.328 INFO ProgressMeter - chr11:118472933 8.8 2700 307.8
22:53:24.588 INFO ProgressMeter - chr11:118504004 9.0 2760 307.5
22:53:35.442 INFO ProgressMeter - chr11:119278713 9.2 2810 306.9
22:53:46.089 INFO ProgressMeter - chr11:125644089 9.3 2850 305.4
22:54:01.177 INFO ProgressMeter - chr11:128460663 9.6 2890 301.5
22:54:12.838 INFO ProgressMeter - chr11:128811555 9.8 2940 300.6
22:54:24.120 INFO ProgressMeter - chr12:365932 10.0 2990 300.0
22:54:35.216 INFO ProgressMeter - chr12:4380050 10.2 3060 301.4
22:54:45.255 INFO ProgressMeter - chr12:4445306 10.3 3110 301.4
22:54:57.400 INFO ProgressMeter - chr12:6602374 10.5 3180 302.2
22:55:08.518 INFO ProgressMeter - chr12:11857103 10.7 3210 299.8
22:55:21.661 INFO ProgressMeter - chr12:11862028 10.9 3250 297.4
22:55:33.674 INFO ProgressMeter - chr12:11867941 11.1 3290 295.7
22:55:44.845 INFO ProgressMeter - chr12:18293899 11.3 3330 294.4
22:55:56.765 INFO ProgressMeter - chr12:25231544 11.5 3410 296.2
22:56:08.437 INFO ProgressMeter - chr12:45851288 11.7 3470 296.4
22:56:19.523 INFO ProgressMeter - chr12:49030891 11.9 3530 296.9
22:56:31.961 INFO ProgressMeter - chr12:49038219 12.1 3570 295.1
22:56:42.467 INFO ProgressMeter - chr12:49050320 12.3 3620 295.0
22:56:52.924 INFO ProgressMeter - chr12:51984038 12.4 3680 295.6
22:57:04.155 INFO ProgressMeter - chr12:56101827 12.6 3750 296.8
22:57:15.748 INFO ProgressMeter - chr12:57467468 12.8 3800 296.2
22:57:26.753 INFO ProgressMeter - chr12:57751868 13.0 3860 296.7
22:57:37.084 INFO ProgressMeter - chr12:68837017 13.2 3920 297.3
22:57:48.384 INFO ProgressMeter - chr12:112477855 13.4 3990 298.4
22:57:59.107 INFO ProgressMeter - chr12:132626115 13.6 4050 298.9
22:58:10.100 INFO ProgressMeter - chr12:132680176 13.7 4120 300.0
22:58:20.919 INFO ProgressMeter - chr13:21672392 13.9 4160 299.0
22:58:30.986 INFO ProgressMeter - chr13:28023348 14.1 4230 300.4
22:58:43.146 INFO ProgressMeter - chr13:28386294 14.3 4290 300.3
22:58:54.551 INFO ProgressMeter - chr13:28388734 14.5 4310 297.8
22:59:05.101 INFO ProgressMeter - chr13:32332630 14.7 4360 297.6
22:59:17.549 INFO ProgressMeter - chr13:32346825 14.9 4400 296.1
22:59:28.472 INFO ProgressMeter - chr13:40560628 15.0 4450 295.9
22:59:39.176 INFO ProgressMeter - chr13:101726759 15.2 4530 297.7
22:59:50.067 INFO ProgressMeter - chr13:102862328 15.4 4590 298.1
23:00:01.381 INFO ProgressMeter - chr13:113302748 15.6 4650 298.3
23:00:14.187 INFO ProgressMeter - chr14:25381560 15.8 4700 297.4
23:00:24.837 INFO ProgressMeter - chr14:37591721 16.0 4760 297.9
23:00:35.736 INFO ProgressMeter - chr14:65102302 16.2 4820 298.3
23:00:47.977 INFO ProgressMeter - chr14:95103644 16.4 4880 298.2
23:00:58.022 INFO ProgressMeter - chr14:102084777 16.5 4940 298.8
23:01:09.484 INFO ProgressMeter - chr15:34347051 16.7 5000 299.0
23:01:19.508 INFO ProgressMeter - chr15:34357101 16.9 5030 297.8
23:01:29.586 INFO ProgressMeter - chr15:41713149 17.1 5080 297.8
23:01:42.108 INFO ProgressMeter - chr15:44711545 17.3 5130 297.1
23:01:52.198 INFO ProgressMeter - chr15:67164893 17.4 5200 298.2
23:02:04.698 INFO ProgressMeter - chr15:87979253 17.6 5260 298.1
23:02:15.490 INFO ProgressMeter - chr15:89306060 17.8 5330 299.0
23:02:26.115 INFO ProgressMeter - chr15:90803519 18.0 5390 299.4
23:02:36.788 INFO ProgressMeter - chr15:93002175 18.2 5450 299.8
23:02:47.021 INFO ProgressMeter - chr15:98957237 18.3 5510 300.3
23:02:57.836 INFO ProgressMeter - chr16:2076066 18.5 5570 300.6
23:03:08.653 INFO ProgressMeter - chr16:3583292 18.7 5660 302.5
23:03:21.899 INFO ProgressMeter - chr16:3728617 18.9 5710 301.6
23:03:32.248 INFO ProgressMeter - chr16:5556153 19.1 5770 302.0
23:03:42.650 INFO ProgressMeter - chr16:11255261 19.3 5820 301.9
23:03:52.692 INFO ProgressMeter - chr16:23630466 19.4 5870 301.9
23:04:03.097 INFO ProgressMeter - chr16:50796360 19.6 5930 302.3
23:04:15.057 INFO ProgressMeter - chr16:68819278 19.8 6000 302.8
23:04:25.922 INFO ProgressMeter - chr16:72794542 20.0 6040 302.0
23:04:38.208 INFO ProgressMeter - chr16:72889729 20.2 6080 301.0
23:04:49.842 INFO ProgressMeter - chr16:81910518 20.4 6130 300.5
23:05:00.553 INFO ProgressMeter - chr16:89282091 20.6 6180 300.4
23:05:10.958 INFO ProgressMeter - chr16:89290623 20.7 6210 299.3
23:05:21.631 INFO ProgressMeter - chr17:7313378 20.9 6290 300.6
23:05:34.017 INFO ProgressMeter - chr17:7675450 21.1 6330 299.5
23:05:44.346 INFO ProgressMeter - chr17:12069841 21.3 6400 300.4
23:05:54.601 INFO ProgressMeter - chr17:16101409 21.5 6460 300.8
23:06:05.004 INFO ProgressMeter - chr17:31200420 21.6 6530 301.6
23:06:16.165 INFO ProgressMeter - chr17:31338702 21.8 6590 301.8
23:06:27.999 INFO ProgressMeter - chr17:39471008 22.0 6660 302.3
23:06:38.600 INFO ProgressMeter - chr17:39716299 22.2 6720 302.6
23:06:50.169 INFO ProgressMeter - chr17:40404150 22.4 6790 303.1
23:07:00.998 INFO ProgressMeter - chr17:42309486 22.6 6870 304.2
23:07:11.857 INFO ProgressMeter - chr17:43074329 22.8 6930 304.4
23:07:22.863 INFO ProgressMeter - chr17:43094414 22.9 6970 303.8
23:07:34.977 INFO ProgressMeter - chr17:43531817 23.1 7020 303.3
23:07:46.386 INFO ProgressMeter - chr17:43539354 23.3 7070 302.9
23:07:57.670 INFO ProgressMeter - chr17:43545556 23.5 7110 302.2
23:08:09.114 INFO ProgressMeter - chr17:49618979 23.7 7170 302.3
23:08:19.601 INFO ProgressMeter - chr17:59900825 23.9 7230 302.6
23:08:29.929 INFO ProgressMeter - chr17:60648013 24.1 7290 302.9
23:08:40.622 INFO ProgressMeter - chr17:65014389 24.2 7340 302.8
23:08:51.016 INFO ProgressMeter - chr17:72123691 24.4 7400 303.1
23:09:02.058 INFO ProgressMeter - chr18:1127945 24.6 7480 304.1
23:09:12.470 INFO ProgressMeter - chr18:44950368 24.8 7540 304.4
23:09:23.567 INFO ProgressMeter - chr18:51058123 25.0 7590 304.1
23:09:34.260 INFO ProgressMeter - chr19:1612205 25.1 7660 304.7
23:09:44.745 INFO ProgressMeter - chr19:3094650 25.3 7740 305.8
23:09:55.603 INFO ProgressMeter - chr19:5222121 25.5 7810 306.4
23:10:07.229 INFO ProgressMeter - chr19:7267390 25.7 7880 306.8
23:10:18.472 INFO ProgressMeter - chr19:10175538 25.9 7940 306.9
23:10:29.933 INFO ProgressMeter - chr19:11041296 26.1 8010 307.3
23:10:39.965 INFO ProgressMeter - chr19:15170084 26.2 8060 307.3
23:10:51.235 INFO ProgressMeter - chr19:15239164 26.4 8120 307.4
23:11:01.596 INFO ProgressMeter - chr19:17842392 26.6 8180 307.6
23:11:12.825 INFO ProgressMeter - chr19:29817135 26.8 8250 308.1
23:11:23.525 INFO ProgressMeter - chr19:35727696 27.0 8320 308.6
23:11:34.624 INFO ProgressMeter - chr19:40255156 27.1 8390 309.1
23:11:44.891 INFO ProgressMeter - chr19:41259898 27.3 8450 309.4
23:11:55.655 INFO ProgressMeter - chr19:42287628 27.5 8480 308.4
23:12:06.839 INFO ProgressMeter - chr19:45359343 27.7 8550 308.9
23:12:17.796 INFO ProgressMeter - chr19:45416819 27.9 8620 309.4
23:12:28.415 INFO ProgressMeter - chr19:52225715 28.0 8700 310.3
23:12:38.633 INFO ProgressMeter - chr2:15943786 28.2 8730 309.5
23:12:49.173 INFO ProgressMeter - chr2:25239128 28.4 8790 309.7
23:12:59.612 INFO ProgressMeter - chr2:25743073 28.6 8840 309.5
23:13:09.951 INFO ProgressMeter - chr2:29209784 28.7 8890 309.4
23:13:27.976 INFO ProgressMeter - chr2:29227572 29.0 8930 307.6
23:13:38.212 INFO ProgressMeter - chr2:42280848 29.2 8990 307.9
23:13:49.471 INFO ProgressMeter - chr2:47410180 29.4 9050 307.9
23:14:00.445 INFO ProgressMeter - chr2:47798932 29.6 9090 307.4
23:14:12.044 INFO ProgressMeter - chr2:61490640 29.8 9160 307.7
23:14:22.919 INFO ProgressMeter - chr2:98554269 29.9 9210 307.5
23:14:34.184 INFO ProgressMeter - chr2:108766114 30.1 9280 307.9
23:14:52.680 INFO ProgressMeter - chr2:111128565 30.4 9330 306.5
23:15:03.934 INFO ProgressMeter - chr2:113224334 30.6 9370 305.9
23:15:16.052 INFO ProgressMeter - chr2:113228021 30.8 9400 304.9
23:15:26.993 INFO ProgressMeter - chr2:113232788 31.0 9440 304.4
23:15:38.563 INFO ProgressMeter - chr2:113235521 31.2 9460 303.1
23:15:48.866 INFO ProgressMeter - chr2:136115827 31.4 9520 303.4
23:16:00.074 INFO ProgressMeter - chr2:140536579 31.6 9590 303.8
23:16:10.255 INFO ProgressMeter - chr2:141013694 31.7 9650 304.1
23:16:22.093 INFO ProgressMeter - chr2:177232390 31.9 9720 304.4
23:16:32.238 INFO ProgressMeter - chr2:197400713 32.1 9790 305.0
23:16:42.282 INFO ProgressMeter - chr2:208242015 32.3 9850 305.2
23:16:53.044 INFO ProgressMeter - chr2:219567279 32.4 9920 305.7
23:17:04.824 INFO ProgressMeter - chr2:222203107 32.6 9960 305.1
23:17:15.720 INFO ProgressMeter - chr2:222207379 32.8 9990 304.3
23:17:27.838 INFO ProgressMeter - chr2:222211913 33.0 10030 303.7
23:17:42.533 INFO ProgressMeter - chr2:222217271 33.3 10070 302.6
23:17:52.589 INFO ProgressMeter - chr2:222293967 33.4 10100 302.0
23:18:04.710 INFO ProgressMeter - chr2:226797128 33.6 10160 302.0
23:18:15.028 INFO ProgressMeter - chr20:15144220 33.8 10220 302.2
23:18:27.325 INFO ProgressMeter - chr20:32435918 34.0 10260 301.6
23:18:38.706 INFO ProgressMeter - chr20:41029066 34.2 10320 301.7
23:18:49.661 INFO ProgressMeter - chr20:42771536 34.4 10390 302.1
23:19:00.181 INFO ProgressMeter - chr20:53575725 34.6 10440 302.0
23:19:11.138 INFO ProgressMeter - chr20:58853598 34.8 10480 301.6
23:19:22.862 INFO ProgressMeter - chr21:34880555 34.9 10550 301.9
23:19:32.862 INFO ProgressMeter - chr21:38400071 35.1 10590 301.6
23:19:43.788 INFO ProgressMeter - chr21:41465999 35.3 10630 301.2
23:19:59.011 INFO ProgressMeter - chr21:41491098 35.5 10670 300.2
23:20:11.330 INFO ProgressMeter - chr21:41498515 35.8 10700 299.3
23:20:23.030 INFO ProgressMeter - chr21:41502557 35.9 10740 298.8
23:20:34.763 INFO ProgressMeter - chr21:41508020 36.1 10780 298.2
23:20:45.752 INFO ProgressMeter - chr22:21788255 36.3 10850 298.7
23:20:57.187 INFO ProgressMeter - chr22:23291100 36.5 10900 298.5
23:21:08.333 INFO ProgressMeter - chr22:28711907 36.7 10960 298.6
23:21:22.242 INFO ProgressMeter - chr22:29285599 36.9 11030 298.6
23:21:33.216 INFO ProgressMeter - chr22:29681567 37.1 11080 298.5
23:21:44.629 INFO ProgressMeter - chr22:41176771 37.3 11150 298.9
23:21:55.471 INFO ProgressMeter - chr3:10072909 37.5 11200 298.7
23:22:08.477 INFO ProgressMeter - chr3:12355931 37.7 11260 298.6
23:22:19.954 INFO ProgressMeter - chr3:12360229 37.9 11290 297.9
23:22:30.954 INFO ProgressMeter - chr3:12364688 38.1 11320 297.3
23:22:42.968 INFO ProgressMeter - chr3:12370334 38.3 11360 296.7
23:22:54.182 INFO ProgressMeter - chr3:12376540 38.5 11400 296.3
23:23:04.656 INFO ProgressMeter - chr3:12604176 38.6 11450 296.3
23:23:14.755 INFO ProgressMeter - chr3:30688382 38.8 11490 296.0
23:23:27.218 INFO ProgressMeter - chr3:47067068 39.0 11570 296.5
23:23:37.377 INFO ProgressMeter - chr3:47122581 39.2 11610 296.3
23:23:48.490 INFO ProgressMeter - chr3:49895165 39.4 11670 296.4
23:23:59.791 INFO ProgressMeter - chr3:52576539 39.6 11740 296.8
23:24:09.907 INFO ProgressMeter - chr3:69965063 39.7 11800 297.0
23:24:20.445 INFO ProgressMeter - chr3:89340914 39.9 11860 297.2
23:24:32.394 INFO ProgressMeter - chr3:135192744 40.1 11930 297.5
23:24:42.797 INFO ProgressMeter - chr3:136604304 40.3 11990 297.7
23:24:53.461 INFO ProgressMeter - chr3:138946438 40.5 12060 298.1
23:25:04.182 INFO ProgressMeter - chr3:142558771 40.6 12130 298.5
23:25:14.287 INFO ProgressMeter - chr3:179204501 40.8 12200 299.0
23:25:24.922 INFO ProgressMeter - chr3:185285604 41.0 12270 299.4
23:25:35.853 INFO ProgressMeter - chr3:186048056 41.2 12310 299.1
23:25:47.053 INFO ProgressMeter - chr3:189868578 41.3 12380 299.4
23:25:57.698 INFO ProgressMeter - chr4:1795974 41.5 12450 299.8
23:26:08.542 INFO ProgressMeter - chr4:20567260 41.7 12530 300.4
23:26:20.055 INFO ProgressMeter - chr4:54258767 41.9 12600 300.7
23:26:30.495 INFO ProgressMeter - chr4:54683213 42.1 12650 300.7
23:26:43.255 INFO ProgressMeter - chr4:54737173 42.3 12690 300.1
23:26:53.418 INFO ProgressMeter - chr4:65367355 42.5 12750 300.3
23:27:04.216 INFO ProgressMeter - chr4:80286323 42.6 12810 300.5
23:27:16.721 INFO ProgressMeter - chr4:105237815 42.8 12870 300.4
23:27:27.220 INFO ProgressMeter - chr4:105275046 43.0 12910 300.1
23:27:37.325 INFO ProgressMeter - chr4:142112540 43.2 12980 300.6
23:27:47.696 INFO ProgressMeter - chr4:184408156 43.4 13040 300.7
23:28:00.183 INFO ProgressMeter - chr4:186618319 43.6 13100 300.7
23:28:10.897 INFO ProgressMeter - chr4:186708024 43.7 13140 300.4
23:28:21.321 INFO ProgressMeter - chr5:35873509 43.9 13200 300.5
23:28:32.196 INFO ProgressMeter - chr5:44311704 44.1 13270 300.9
23:28:42.495 INFO ProgressMeter - chr5:56881842 44.3 13340 301.3
23:28:53.232 INFO ProgressMeter - chr5:80672242 44.5 13410 301.7
23:29:03.656 INFO ProgressMeter - chr5:112835021 44.6 13500 302.5
23:29:16.443 INFO ProgressMeter - chr5:112843281 44.8 13550 302.2
23:29:27.657 INFO ProgressMeter - chr5:132604804 45.0 13600 302.0
23:29:37.756 INFO ProgressMeter - chr5:142630759 45.2 13660 302.2
23:29:48.762 INFO ProgressMeter - chr5:149525083 45.4 13710 302.1
23:30:00.120 INFO ProgressMeter - chr5:150130537 45.6 13770 302.2
23:30:10.319 INFO ProgressMeter - chr5:150407209 45.7 13820 302.2
23:30:21.957 INFO ProgressMeter - chr5:177090423 45.9 13870 302.0
23:30:33.560 INFO ProgressMeter - chr5:177210508 46.1 13920 301.8
23:30:43.869 INFO ProgressMeter - chr5:177294675 46.3 13960 301.5
23:30:54.661 INFO ProgressMeter - chr5:180621793 46.5 14030 301.9
23:31:05.178 INFO ProgressMeter - chr6:20458089 46.7 14100 302.2
23:31:16.096 INFO ProgressMeter - chr6:26045739 46.8 14160 302.3
23:31:28.850 INFO ProgressMeter - chr6:29945449 47.0 14210 302.0
23:31:39.330 INFO ProgressMeter - chr6:30711983 47.2 14250 301.8
23:31:50.947 INFO ProgressMeter - chr6:32220403 47.4 14310 301.8
23:32:01.306 INFO ProgressMeter - chr6:37170771 47.6 14370 302.0
23:32:11.916 INFO ProgressMeter - chr6:43778887 47.8 14450 302.5
23:32:23.729 INFO ProgressMeter - chr6:106107089 48.0 14520 302.7
23:32:33.775 INFO ProgressMeter - chr6:117318486 48.1 14570 302.7
23:32:45.874 INFO ProgressMeter - chr6:117322857 48.3 14600 302.1
23:32:55.951 INFO ProgressMeter - chr6:117327495 48.5 14640 301.9
23:33:06.554 INFO ProgressMeter - chr6:117333905 48.7 14680 301.6
23:33:18.429 INFO ProgressMeter - chr6:117340851 48.9 14720 301.2
23:33:29.463 INFO ProgressMeter - chr6:135197111 49.1 14780 301.3
23:33:41.816 INFO ProgressMeter - chr6:135208026 49.3 14820 300.8
23:33:52.750 INFO ProgressMeter - chr6:135212323 49.4 14850 300.3
23:34:04.550 INFO ProgressMeter - chr6:135217947 49.6 14890 300.0
23:34:16.688 INFO ProgressMeter - chr6:149695072 49.8 14950 299.9
23:34:27.177 INFO ProgressMeter - chr6:152011654 50.0 15000 299.9
23:34:38.541 INFO ProgressMeter - chr6:157200785 50.2 15060 300.0
23:34:49.015 INFO ProgressMeter - chr6:161086582 50.4 15100 299.7
23:34:59.356 INFO ProgressMeter - chr7:2913285 50.6 15170 300.1
23:35:10.733 INFO ProgressMeter - chr7:13891622 50.7 15240 300.3
23:35:26.781 INFO ProgressMeter - chr7:13909201 51.0 15280 299.5
23:35:37.136 INFO ProgressMeter - chr7:13935649 51.2 15310 299.1
23:35:48.465 INFO ProgressMeter - chr7:13940972 51.4 15350 298.8
23:35:59.873 INFO ProgressMeter - chr7:13946153 51.6 15380 298.3
23:36:11.513 INFO ProgressMeter - chr7:13950455 51.8 15410 297.7
23:36:22.538 INFO ProgressMeter - chr7:13952798 51.9 15430 297.1
23:36:34.520 INFO ProgressMeter - chr7:13957378 52.1 15460 296.5
23:36:49.542 INFO ProgressMeter - chr7:13961674 52.4 15490 295.7
23:37:01.601 INFO ProgressMeter - chr7:13966567 52.6 15530 295.3
23:37:12.622 INFO ProgressMeter - chr7:13970085 52.8 15560 294.8
23:37:24.145 INFO ProgressMeter - chr7:13975245 53.0 15600 294.5
23:37:36.024 INFO ProgressMeter - chr7:13977863 53.2 15620 293.8
23:37:47.887 INFO ProgressMeter - chr7:13981756 53.4 15660 293.5
23:38:01.112 INFO ProgressMeter - chr7:13985887 53.6 15690 292.8
23:38:11.794 INFO ProgressMeter - chr7:13989993 53.8 15710 292.2
23:38:21.830 INFO ProgressMeter - chr7:55152545 53.9 15760 292.2
23:38:33.913 INFO ProgressMeter - chr7:55166354 54.1 15800 291.9
23:38:46.303 INFO ProgressMeter - chr7:55173075 54.3 15830 291.3
23:38:58.424 INFO ProgressMeter - chr7:55179071 54.5 15870 291.0
23:39:10.174 INFO ProgressMeter - chr7:55201565 54.7 15910 290.7
23:39:20.525 INFO ProgressMeter - chr7:81744998 54.9 15970 290.9
23:39:31.782 INFO ProgressMeter - chr7:92829963 55.1 16030 291.0
23:39:42.397 INFO ProgressMeter - chr7:102280015 55.3 16090 291.1
23:39:54.348 INFO ProgressMeter - chr7:116740085 55.5 16140 291.0
23:40:05.006 INFO ProgressMeter - chr7:129206564 55.6 16190 290.9
23:40:16.425 INFO ProgressMeter - chr7:140790250 55.8 16250 291.0
23:40:27.139 INFO ProgressMeter - chr7:140850109 56.0 16290 290.8
23:40:37.902 INFO ProgressMeter - chr7:148817950 56.2 16360 291.1
23:40:52.046 INFO ProgressMeter - chr7:152163081 56.4 16420 291.0
23:41:08.160 INFO ProgressMeter - chr7:152181159 56.7 16450 290.1
23:41:18.780 INFO ProgressMeter - chr7:152435677 56.9 16510 290.3
23:41:29.825 INFO ProgressMeter - chr8:32262262 57.1 16590 290.7
23:41:41.885 INFO ProgressMeter - chr8:32760498 57.3 16640 290.6
23:41:52.449 INFO ProgressMeter - chr8:38415868 57.4 16710 290.9
23:42:03.621 INFO ProgressMeter - chr8:41932770 57.6 16770 291.0
23:42:15.232 INFO ProgressMeter - chr8:47774171 57.8 16820 290.9
23:42:25.544 INFO ProgressMeter - chr8:47862371 58.0 16890 291.3
23:42:36.691 INFO ProgressMeter - chr8:55966713 58.2 16970 291.7
23:42:47.007 INFO ProgressMeter - chr8:89943251 58.3 17040 292.0
23:42:58.032 INFO ProgressMeter - chr8:116856711 58.5 17100 292.1
23:43:08.050 INFO ProgressMeter - chr8:127739282 58.7 17150 292.2
23:43:19.196 INFO ProgressMeter - chr8:144515384 58.9 17210 292.3
23:43:29.594 INFO ProgressMeter - chr9:5126331 59.1 17280 292.6
23:43:40.804 INFO ProgressMeter - chr9:20346441 59.2 17350 292.8
23:43:51.664 INFO ProgressMeter - chr9:35078235 59.4 17410 293.0
23:44:02.709 INFO ProgressMeter - chr9:84670718 59.6 17480 293.2
23:44:14.843 INFO ProgressMeter - chr9:84744576 59.8 17510 292.7
23:44:28.086 INFO ProgressMeter - chr9:84814820 60.0 17550 292.3
23:44:40.466 INFO ProgressMeter - chr9:84864306 60.2 17580 291.8
23:44:52.229 INFO ProgressMeter - chr9:84872643 60.4 17610 291.4
23:45:03.447 INFO ProgressMeter - chr9:84877860 60.6 17650 291.1
23:45:16.791 INFO ProgressMeter - chr9:85025626 60.8 17690 290.7
23:45:26.998 INFO ProgressMeter - chr9:95149921 61.0 17730 290.6
23:45:38.159 INFO ProgressMeter - chr9:99137857 61.2 17790 290.7
23:45:50.578 INFO ProgressMeter - chr9:130884680 61.4 17860 290.8
23:46:00.942 INFO ProgressMeter - chr9:132912280 61.6 17910 290.8
23:46:11.402 INFO ProgressMeter - chr9:136511150 61.8 17970 291.0
23:46:21.692 INFO ProgressMeter - chrX:15809198 61.9 18050 291.5
23:46:31.842 INFO ProgressMeter - chrX:40074150 62.1 18100 291.5
23:46:42.913 INFO ProgressMeter - chrX:47181964 62.3 18170 291.7
23:46:54.524 INFO ProgressMeter - chrX:49034294 62.5 18230 291.8
23:47:07.037 INFO ProgressMeter - chrX:49038847 62.7 18270 291.5
23:47:18.920 INFO ProgressMeter - chrX:53217794 62.9 18320 291.3
23:47:31.752 INFO ProgressMeter - chrX:53413404 63.1 18370 291.2
23:47:46.120 INFO ProgressMeter - chrX:67545276 63.3 18410 290.7
23:47:57.563 INFO ProgressMeter - chrX:67711400 63.5 18460 290.6
23:48:08.380 INFO ProgressMeter - chrX:71136365 63.7 18520 290.7
23:48:19.421 INFO ProgressMeter - chrX:71398610 63.9 18570 290.7
23:48:29.742 INFO ProgressMeter - chrX:77664753 64.1 18630 290.8
23:48:40.311 INFO ProgressMeter - chrX:101362559 64.2 18680 290.8
23:48:50.374 INFO ProgressMeter - chrX:124056126 64.4 18740 291.0
23:49:02.758 INFO ProgressMeter - chrX:130020983 64.6 18800 291.0
23:49:10.060 INFO Mutect2 - 764142 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
128 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
764272 total reads filtered out of 107876125 reads processed
23:49:10.061 INFO ProgressMeter - chrY:21207343 64.7 18870 291.5
23:49:10.061 INFO ProgressMeter - Traversal complete. Processed 18870 total regions in 64.7 minutes.
23:49:10.079 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 7.696290240000001
23:49:10.079 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 326.228966683
23:49:10.079 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 11.62 sec
23:49:10.080 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:49:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 64.74 minutes.
Runtime.totalMemory()=6341787648
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 LS0913_tumor.bam --tumor-sample LS0913 -L TST500C_manifest.bed -O LS0913.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:49:11.665 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
23:49:11.755 INFO FilterMutectCalls - ------------------------------------------------------------
23:49:11.764 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:49:11.764 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:49:11.764 INFO FilterMutectCalls - Executing as ?@nf-9747620e86f126683c4d7df399e6b172-204de-xfrtg on Linux v6.12.88 amd64
23:49:11.765 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:49:11.765 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:49:11 PM GMT
23:49:11.765 INFO FilterMutectCalls - ------------------------------------------------------------
23:49:11.765 INFO FilterMutectCalls - ------------------------------------------------------------
23:49:11.766 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:49:11.766 INFO FilterMutectCalls - Picard Version: 3.1.1
23:49:11.766 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:49:11.767 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:49:11.767 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:49:11.767 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:49:11.767 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:49:11.767 INFO FilterMutectCalls - Deflater: IntelDeflater
23:49:11.767 INFO FilterMutectCalls - Inflater: IntelInflater
23:49:11.767 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:49:11.767 INFO FilterMutectCalls - Requester pays: disabled
23:49:11.768 INFO FilterMutectCalls - Initializing engine
23:49:11.946 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.AGG35TGp6a/LS0913.mutect2.raw.vcf.gz
23:49:12.045 INFO FilterMutectCalls - Done initializing engine
23:49:12.095 INFO ProgressMeter - Starting traversal
23:49:12.096 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:49:12.097 INFO FilterMutectCalls - Starting pass 0 through the variants
23:49:13.581 INFO FilterMutectCalls - Finished pass 0 through the variants
23:49:14.250 INFO FilterMutectCalls - Starting pass 1 through the variants
23:49:15.486 INFO FilterMutectCalls - Finished pass 1 through the variants
23:49:15.789 INFO FilterMutectCalls - Starting pass 2 through the variants
23:49:16.999 INFO FilterMutectCalls - Finished pass 2 through the variants
23:49:17.001 INFO FilterMutectCalls - Starting pass 3 through the variants
23:49:17.969 INFO FilterMutectCalls - Finished pass 3 through the variants
23:49:17.976 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:49:17.977 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:49:17.977 INFO ProgressMeter - chr5:138930857 0.1 10860 110797.5
23:49:17.977 INFO ProgressMeter - Traversal complete. Processed 10860 total variants in 0.1 minutes.
23:49:17.987 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:49:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=494927872
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 LS0913.mutect2.raw.vcf.gz --stats LS0913.mutect2.raw.vcf.gz.stats -O LS0913.mutect2.filtered.vcf.gz
23:49:19.099 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
23:49:19.199 INFO SelectVariants - ------------------------------------------------------------
23:49:19.201 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:49:19.201 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:49:19.201 INFO SelectVariants - Executing as ?@nf-9747620e86f126683c4d7df399e6b172-204de-xfrtg on Linux v6.12.88 amd64
23:49:19.201 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:49:19.201 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:49:19 PM GMT
23:49:19.201 INFO SelectVariants - ------------------------------------------------------------
23:49:19.201 INFO SelectVariants - ------------------------------------------------------------
23:49:19.202 INFO SelectVariants - HTSJDK Version: 4.1.0
23:49:19.202 INFO SelectVariants - Picard Version: 3.1.1
23:49:19.202 INFO SelectVariants - Built for Spark Version: 3.5.0
23:49:19.202 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:49:19.203 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:49:19.203 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:49:19.203 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:49:19.203 INFO SelectVariants - Deflater: IntelDeflater
23:49:19.203 INFO SelectVariants - Inflater: IntelInflater
23:49:19.203 INFO SelectVariants - GCS max retries/reopens: 20
23:49:19.203 INFO SelectVariants - Requester pays: disabled
23:49:19.203 INFO SelectVariants - Initializing engine
23:49:19.378 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.AGG35TGp6a/LS0913.mutect2.filtered.vcf.gz
23:49:19.490 INFO SelectVariants - Done initializing engine
23:49:19.526 INFO ProgressMeter - Starting traversal
23:49:19.527 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:49:19.600 INFO ProgressMeter - chr6:32201386 0.0 2715 2294366.2
23:49:19.600 INFO ProgressMeter - Traversal complete. Processed 2715 total variants in 0.0 minutes.
23:49:19.615 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:49:19 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 LS0913.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0913.mutect2.pass.vcf.gz