22:44:26.569 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
22:44:26.696 INFO Mutect2 - ------------------------------------------------------------
22:44:26.699 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:26.699 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:26.699 INFO Mutect2 - Executing as ?@nf-47a1d6f66457cd963c84f5320bdb2a2f-bfe97-w6kcz on Linux v6.12.88 amd64
22:44:26.699 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:26.700 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:26 PM GMT
22:44:26.700 INFO Mutect2 - ------------------------------------------------------------
22:44:26.700 INFO Mutect2 - ------------------------------------------------------------
22:44:26.702 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:26.702 INFO Mutect2 - Picard Version: 3.1.1
22:44:26.702 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:26.702 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:26.702 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:26.702 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:26.703 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:26.703 INFO Mutect2 - Deflater: IntelDeflater
22:44:26.703 INFO Mutect2 - Inflater: IntelInflater
22:44:26.703 INFO Mutect2 - GCS max retries/reopens: 20
22:44:26.703 INFO Mutect2 - Requester pays: disabled
22:44:26.703 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.J2AarHYkD5/LS0912_tumor.bam.bai is older than BAM /tmp/nxf.J2AarHYkD5/LS0912_tumor.bam
22:44:26.936 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.J2AarHYkD5/af-only-gnomad.hg38.vcf.gz
22:44:27.044 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.J2AarHYkD5/TST500C_manifest.bed
22:44:27.084 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:27.123 INFO Mutect2 - Done initializing engine
22:44:27.136 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
22:44:27.138 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
22:44:27.139 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:27.139 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:27.152 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
22:44:27.160 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:27.160 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:27.161 INFO IntelPairHmm - Available threads: 384
22:44:27.161 INFO IntelPairHmm - Requested threads: 4
22:44:27.161 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:27.204 INFO ProgressMeter - Starting traversal
22:44:27.205 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:37.620 INFO ProgressMeter - chr1:9721185 0.2 40 230.5
22:44:48.320 INFO ProgressMeter - chr1:11144730 0.4 100 284.2
22:44:58.879 INFO ProgressMeter - chr1:15848066 0.5 150 284.1
22:45:10.886 INFO ProgressMeter - chr1:15932117 0.7 200 274.7
22:45:22.149 INFO ProgressMeter - chr1:15938786 0.9 250 273.0
22:45:34.721 INFO ProgressMeter - chr1:18747372 1.1 310 275.5
22:45:45.443 INFO ProgressMeter - chr1:26775593 1.3 370 283.7
22:45:55.947 INFO ProgressMeter - chr1:39891023 1.5 430 290.7
22:46:06.334 INFO ProgressMeter - chr1:39905214 1.7 490 296.6
22:46:17.304 INFO ProgressMeter - chr1:46077513 1.8 560 305.2
22:46:28.633 INFO ProgressMeter - chr1:64844844 2.0 640 316.2
22:46:38.839 INFO ProgressMeter - chr1:85274379 2.2 710 323.6
22:46:49.628 INFO ProgressMeter - chr1:119514132 2.4 780 328.6
22:47:00.291 INFO ProgressMeter - chr1:119937388 2.6 830 325.3
22:47:11.195 INFO ProgressMeter - chr1:156872828 2.7 900 329.3
22:47:22.069 INFO ProgressMeter - chr1:158615272 2.9 930 319.1
22:47:32.993 INFO ProgressMeter - chr1:161323612 3.1 1010 326.2
22:47:44.908 INFO ProgressMeter - chr1:179114876 3.3 1090 330.8
22:47:55.355 INFO ProgressMeter - chr1:204468868 3.5 1170 337.3
22:48:06.449 INFO ProgressMeter - chr1:206474965 3.7 1240 339.3
22:48:17.633 INFO ProgressMeter - chr1:228425216 3.8 1320 343.7
22:48:30.679 INFO ProgressMeter - chr1:243503957 4.1 1380 340.1
22:48:42.045 INFO ProgressMeter - chr10:27034775 4.2 1450 341.4
22:48:52.157 INFO ProgressMeter - chr10:32009556 4.4 1510 341.9
22:49:03.401 INFO ProgressMeter - chr10:43111205 4.6 1580 343.2
22:49:13.525 INFO ProgressMeter - chr10:43114957 4.8 1620 339.5
22:49:24.890 INFO ProgressMeter - chr10:43123790 5.0 1670 336.6
22:49:36.468 INFO ProgressMeter - chr10:68572337 5.2 1720 333.7
22:49:47.285 INFO ProgressMeter - chr10:68646943 5.3 1760 329.9
22:49:58.333 INFO ProgressMeter - chr10:87936383 5.5 1840 333.4
22:50:08.589 INFO ProgressMeter - chr10:101773931 5.7 1900 333.9
22:50:18.842 INFO ProgressMeter - chr10:110596377 5.9 1980 337.8
22:50:29.279 INFO ProgressMeter - chr10:121480154 6.0 2030 336.4
22:50:40.008 INFO ProgressMeter - chr10:121487989 6.2 2060 331.5
22:50:50.821 INFO ProgressMeter - chr11:2133515 6.4 2130 333.1
22:51:01.635 INFO ProgressMeter - chr11:64368702 6.6 2210 336.2
22:51:12.933 INFO ProgressMeter - chr11:69650543 6.8 2290 338.7
22:51:23.507 INFO ProgressMeter - chr11:69702308 6.9 2340 337.3
22:51:37.284 INFO ProgressMeter - chr11:69778815 7.2 2410 336.2
22:51:47.987 INFO ProgressMeter - chr11:69816318 7.3 2440 332.1
22:51:58.716 INFO ProgressMeter - chr11:76542295 7.5 2490 330.9
22:52:08.767 INFO ProgressMeter - chr11:77392329 7.7 2540 330.2
22:52:18.867 INFO ProgressMeter - chr11:101062445 7.9 2620 333.3
22:52:32.760 INFO ProgressMeter - chr11:102325146 8.1 2660 328.7
22:52:43.714 INFO ProgressMeter - chr11:108335843 8.3 2750 332.3
22:52:54.410 INFO ProgressMeter - chr11:118484181 8.5 2810 332.4
22:53:04.943 INFO ProgressMeter - chr11:118505400 8.6 2860 331.4
22:53:16.708 INFO ProgressMeter - chr11:125620922 8.8 2910 329.7
22:53:27.577 INFO ProgressMeter - chr11:128459801 9.0 2980 330.9
22:53:40.303 INFO ProgressMeter - chr11:128758113 9.2 3020 327.6
22:53:50.381 INFO ProgressMeter - chr12:295771 9.4 3060 326.0
22:54:01.192 INFO ProgressMeter - chr12:4367139 9.6 3130 327.2
22:54:12.094 INFO ProgressMeter - chr12:4433475 9.7 3190 327.2
22:54:23.270 INFO ProgressMeter - chr12:6578027 9.9 3240 326.1
22:54:33.746 INFO ProgressMeter - chr12:6606272 10.1 3290 325.5
22:54:44.096 INFO ProgressMeter - chr12:11857383 10.3 3330 323.9
22:54:56.706 INFO ProgressMeter - chr12:11862887 10.5 3380 322.2
22:55:11.887 INFO ProgressMeter - chr12:11868562 10.7 3420 318.3
22:55:23.230 INFO ProgressMeter - chr12:18566947 10.9 3490 319.2
22:55:34.383 INFO ProgressMeter - chr12:40469213 11.1 3550 319.3
22:55:45.246 INFO ProgressMeter - chr12:49022714 11.3 3610 319.4
22:55:58.097 INFO ProgressMeter - chr12:49033531 11.5 3660 317.8
22:56:09.028 INFO ProgressMeter - chr12:49041159 11.7 3700 316.3
22:56:19.601 INFO ProgressMeter - chr12:49052562 11.9 3750 315.8
22:56:30.832 INFO ProgressMeter - chr12:56088868 12.1 3830 317.6
22:56:42.329 INFO ProgressMeter - chr12:57092902 12.3 3890 317.5
22:56:53.281 INFO ProgressMeter - chr12:57471719 12.4 3940 316.9
22:57:03.484 INFO ProgressMeter - chr12:68820201 12.6 4020 318.9
22:57:14.777 INFO ProgressMeter - chr12:102475641 12.8 4090 319.7
22:57:26.145 INFO ProgressMeter - chr12:120988831 13.0 4170 321.2
22:57:37.451 INFO ProgressMeter - chr12:132649729 13.2 4230 321.2
22:57:50.713 INFO ProgressMeter - chr13:20991270 13.4 4290 320.3
22:58:01.008 INFO ProgressMeter - chr13:26254640 13.6 4350 320.7
22:58:12.645 INFO ProgressMeter - chr13:28322788 13.8 4420 321.3
22:58:27.123 INFO ProgressMeter - chr13:28388415 14.0 4460 318.6
22:58:37.571 INFO ProgressMeter - chr13:32330978 14.2 4510 318.2
22:58:50.204 INFO ProgressMeter - chr13:32340598 14.4 4560 317.0
22:59:01.252 INFO ProgressMeter - chr13:40587864 14.6 4620 317.1
22:59:13.175 INFO ProgressMeter - chr13:101937546 14.8 4700 318.3
22:59:25.026 INFO ProgressMeter - chr13:102875305 15.0 4770 318.8
22:59:36.658 INFO ProgressMeter - chr13:113308537 15.2 4830 318.7
22:59:48.174 INFO ProgressMeter - chr14:37584851 15.3 4890 318.6
23:00:00.118 INFO ProgressMeter - chr14:37598103 15.5 4960 319.0
23:00:10.489 INFO ProgressMeter - chr14:95093886 15.7 5030 319.9
23:00:21.645 INFO ProgressMeter - chr14:102139391 15.9 5100 320.6
23:00:32.587 INFO ProgressMeter - chr15:34347741 16.1 5140 319.5
23:00:43.530 INFO ProgressMeter - chr15:41669193 16.3 5190 319.0
23:00:54.810 INFO ProgressMeter - chr15:41749889 16.5 5240 318.3
23:01:05.452 INFO ProgressMeter - chr15:49464215 16.6 5310 319.2
23:01:16.119 INFO ProgressMeter - chr15:87977666 16.8 5380 319.9
23:01:26.162 INFO ProgressMeter - chr15:89281168 17.0 5440 320.3
23:01:36.320 INFO ProgressMeter - chr15:90769187 17.2 5510 321.2
23:01:48.050 INFO ProgressMeter - chr15:93014744 17.3 5590 322.2
23:01:58.810 INFO ProgressMeter - chr16:304403 17.5 5650 322.4
23:02:09.847 INFO ProgressMeter - chr16:2084263 17.7 5710 322.4
23:02:21.531 INFO ProgressMeter - chr16:3589902 17.9 5790 323.4
23:02:34.359 INFO ProgressMeter - chr16:3729264 18.1 5840 322.3
23:02:46.851 INFO ProgressMeter - chr16:9764356 18.3 5910 322.5
23:02:58.235 INFO ProgressMeter - chr16:13935144 18.5 5970 322.4
23:03:09.443 INFO ProgressMeter - chr16:30117152 18.7 6020 321.9
23:03:19.878 INFO ProgressMeter - chr16:56830526 18.9 6090 322.6
23:03:29.941 INFO ProgressMeter - chr16:68812133 19.0 6150 322.9
23:03:39.959 INFO ProgressMeter - chr16:72793897 19.2 6190 322.2
23:03:51.912 INFO ProgressMeter - chr16:72798014 19.4 6230 320.9
23:04:03.113 INFO ProgressMeter - chr16:81786084 19.6 6270 319.9
23:04:15.158 INFO ProgressMeter - chr16:89280796 19.8 6340 320.2
23:04:27.065 INFO ProgressMeter - chr16:89288526 20.0 6380 319.0
23:04:37.391 INFO ProgressMeter - chr17:4066820 20.2 6460 320.3
23:04:49.229 INFO ProgressMeter - chr17:7677113 20.4 6520 320.1
23:05:00.223 INFO ProgressMeter - chr17:16058469 20.6 6610 321.7
23:05:11.447 INFO ProgressMeter - chr17:17219017 20.7 6680 322.1
23:05:23.020 INFO ProgressMeter - chr17:31327800 20.9 6760 323.0
23:05:34.895 INFO ProgressMeter - chr17:39471166 21.1 6850 324.2
23:05:46.806 INFO ProgressMeter - chr17:39723910 21.3 6920 324.5
23:05:57.524 INFO ProgressMeter - chr17:40413193 21.5 7000 325.5
23:06:07.988 INFO ProgressMeter - chr17:42345557 21.7 7080 326.6
23:06:18.591 INFO ProgressMeter - chr17:43093145 21.9 7140 326.7
23:06:29.928 INFO ProgressMeter - chr17:43531483 22.0 7190 326.1
23:06:42.694 INFO ProgressMeter - chr17:43539729 22.3 7250 325.7
23:06:53.995 INFO ProgressMeter - chr17:43543683 22.4 7280 324.3
23:07:04.829 INFO ProgressMeter - chr17:48723639 22.6 7330 323.9
23:07:14.960 INFO ProgressMeter - chr17:58695231 22.8 7390 324.2
23:07:26.423 INFO ProgressMeter - chr17:60633962 23.0 7470 325.0
23:07:36.787 INFO ProgressMeter - chr17:65056394 23.2 7530 325.1
23:07:47.026 INFO ProgressMeter - chr17:76736159 23.3 7590 325.3
23:07:57.170 INFO ProgressMeter - chr18:745768 23.5 7660 326.0
23:08:09.527 INFO ProgressMeter - chr18:44950839 23.7 7740 326.5
23:08:19.883 INFO ProgressMeter - chr18:58681168 23.9 7800 326.7
23:08:30.523 INFO ProgressMeter - chr19:1620966 24.1 7870 327.2
23:08:40.812 INFO ProgressMeter - chr19:4053950 24.2 7950 328.1
23:08:51.601 INFO ProgressMeter - chr19:5244305 24.4 8030 329.0
23:09:02.109 INFO ProgressMeter - chr19:10140155 24.6 8100 329.5
23:09:12.328 INFO ProgressMeter - chr19:10499902 24.8 8160 329.7
23:09:22.662 INFO ProgressMeter - chr19:12940794 24.9 8230 330.2
23:09:34.434 INFO ProgressMeter - chr19:15181089 25.1 8290 330.0
23:09:45.074 INFO ProgressMeter - chr19:15244425 25.3 8350 330.1
23:09:55.632 INFO ProgressMeter - chr19:17843775 25.5 8410 330.1
23:10:06.896 INFO ProgressMeter - chr19:29822002 25.7 8500 331.2
23:10:17.087 INFO ProgressMeter - chr19:35728772 25.8 8570 331.8
23:10:28.020 INFO ProgressMeter - chr19:40260196 26.0 8640 332.1
23:10:42.668 INFO ProgressMeter - chr19:41261111 26.3 8710 331.7
23:10:52.943 INFO ProgressMeter - chr19:45350055 26.4 8770 331.8
23:11:03.964 INFO ProgressMeter - chr19:45408831 26.6 8850 332.5
23:11:14.535 INFO ProgressMeter - chr19:50403161 26.8 8920 333.0
23:11:26.240 INFO ProgressMeter - chr2:15941161 27.0 8980 332.8
23:11:37.370 INFO ProgressMeter - chr2:25235705 27.2 9040 332.7
23:11:48.647 INFO ProgressMeter - chr2:25742817 27.4 9090 332.3
23:11:59.136 INFO ProgressMeter - chr2:29209824 27.5 9150 332.3
23:12:14.923 INFO ProgressMeter - chr2:29227029 27.8 9190 330.6
23:12:25.518 INFO ProgressMeter - chr2:42169620 28.0 9250 330.7
23:12:40.394 INFO ProgressMeter - chr2:47429740 28.2 9320 330.3
23:12:50.928 INFO ProgressMeter - chr2:47806202 28.4 9370 330.0
23:13:06.370 INFO ProgressMeter - chr2:96254831 28.7 9460 330.2
23:13:16.391 INFO ProgressMeter - chr2:108755174 28.8 9540 331.0
23:13:26.515 INFO ProgressMeter - chr2:111125659 29.0 9590 330.8
23:13:39.604 INFO ProgressMeter - chr2:111128793 29.2 9620 329.4
23:13:50.969 INFO ProgressMeter - chr2:113224174 29.4 9670 329.0
23:14:04.460 INFO ProgressMeter - chr2:113227528 29.6 9700 327.5
23:14:16.617 INFO ProgressMeter - chr2:113231616 29.8 9740 326.6
23:14:28.060 INFO ProgressMeter - chr2:113235064 30.0 9770 325.5
23:14:39.215 INFO ProgressMeter - chr2:136114867 30.2 9830 325.5
23:14:49.807 INFO ProgressMeter - chr2:140509926 30.4 9910 326.2
23:15:00.245 INFO ProgressMeter - chr2:141049138 30.6 9980 326.7
23:15:11.262 INFO ProgressMeter - chr2:177234163 30.7 10050 327.0
23:15:22.189 INFO ProgressMeter - chr2:197407996 30.9 10130 327.7
23:15:32.288 INFO ProgressMeter - chr2:211430980 31.1 10200 328.1
23:15:43.215 INFO ProgressMeter - chr2:222200495 31.3 10270 328.5
23:15:55.793 INFO ProgressMeter - chr2:222205290 31.5 10310 327.5
23:16:08.530 INFO ProgressMeter - chr2:222210912 31.7 10350 326.6
23:16:19.978 INFO ProgressMeter - chr2:222216111 31.9 10390 325.9
23:16:31.513 INFO ProgressMeter - chr2:222220775 32.1 10420 324.9
23:16:41.515 INFO ProgressMeter - chr2:226795382 32.2 10480 325.1
23:16:51.894 INFO ProgressMeter - chr20:9542584 32.4 10530 324.9
23:17:04.581 INFO ProgressMeter - chr20:32435375 32.6 10590 324.6
23:17:16.273 INFO ProgressMeter - chr20:37402434 32.8 10650 324.5
23:17:26.686 INFO ProgressMeter - chr20:42248697 33.0 10720 324.9
23:17:37.153 INFO ProgressMeter - chr20:47647071 33.2 10780 325.0
23:17:48.001 INFO ProgressMeter - chr20:56381431 33.3 10830 324.8
23:17:58.291 INFO ProgressMeter - chr20:63707013 33.5 10890 324.9
23:18:08.350 INFO ProgressMeter - chr21:38382653 33.7 10940 324.8
23:18:19.690 INFO ProgressMeter - chr21:41465784 33.9 10990 324.4
23:18:35.443 INFO ProgressMeter - chr21:41491693 34.1 11030 323.1
23:18:46.680 INFO ProgressMeter - chr21:41499841 34.3 11070 322.5
23:18:59.557 INFO ProgressMeter - chr21:41504421 34.5 11110 321.7
23:19:11.387 INFO ProgressMeter - chr21:44231278 34.7 11160 321.3
23:19:24.008 INFO ProgressMeter - chr22:23289775 34.9 11240 321.6
23:19:34.486 INFO ProgressMeter - chr22:23311695 35.1 11270 320.9
23:19:44.822 INFO ProgressMeter - chr22:28736852 35.3 11350 321.6
23:19:56.514 INFO ProgressMeter - chr22:29286395 35.5 11390 320.9
23:20:07.847 INFO ProgressMeter - chr22:37978032 35.7 11450 320.9
23:20:20.471 INFO ProgressMeter - chr22:41178604 35.9 11520 321.0
23:20:30.507 INFO ProgressMeter - chr3:12352024 36.1 11590 321.5
23:20:44.009 INFO ProgressMeter - chr3:12357673 36.3 11630 320.6
23:20:56.900 INFO ProgressMeter - chr3:12361581 36.5 11660 319.5
23:21:07.707 INFO ProgressMeter - chr3:12367316 36.7 11700 319.0
23:21:20.036 INFO ProgressMeter - chr3:12372568 36.9 11740 318.3
23:21:30.753 INFO ProgressMeter - chr3:12379039 37.1 11780 317.9
23:21:43.021 INFO ProgressMeter - chr3:12647648 37.3 11840 317.7
23:21:54.037 INFO ProgressMeter - chr3:41234137 37.4 11920 318.3
23:22:04.049 INFO ProgressMeter - chr3:47121134 37.6 11970 318.2
23:22:15.028 INFO ProgressMeter - chr3:49687554 37.8 12030 318.3
23:22:25.702 INFO ProgressMeter - chr3:52405228 38.0 12090 318.4
23:22:36.407 INFO ProgressMeter - chr3:69951810 38.2 12170 319.0
23:22:46.552 INFO ProgressMeter - chr3:72832465 38.3 12240 319.4
23:22:56.563 INFO ProgressMeter - chr3:128486174 38.5 12310 319.8
23:23:07.772 INFO ProgressMeter - chr3:136422747 38.7 12380 320.1
23:23:18.753 INFO ProgressMeter - chr3:138734997 38.9 12450 320.4
23:23:29.044 INFO ProgressMeter - chr3:142555941 39.0 12530 321.0
23:23:39.530 INFO ProgressMeter - chr3:179199843 39.2 12610 321.6
23:23:51.885 INFO ProgressMeter - chr3:183508312 39.4 12680 321.7
23:24:02.160 INFO ProgressMeter - chr3:186047485 39.6 12730 321.6
23:24:13.605 INFO ProgressMeter - chr3:187733531 39.8 12790 321.6
23:24:24.359 INFO ProgressMeter - chr3:196075157 40.0 12860 321.9
23:24:34.924 INFO ProgressMeter - chr4:20486198 40.1 12930 322.2
23:24:45.052 INFO ProgressMeter - chr4:24570633 40.3 13000 322.6
23:24:55.209 INFO ProgressMeter - chr4:54277186 40.5 13060 322.7
23:25:05.802 INFO ProgressMeter - chr4:54727869 40.6 13120 322.8
23:25:17.268 INFO ProgressMeter - chr4:55107794 40.8 13160 322.3
23:25:28.546 INFO ProgressMeter - chr4:80284013 41.0 13240 322.8
23:25:41.858 INFO ProgressMeter - chr4:105236712 41.2 13300 322.5
23:25:52.654 INFO ProgressMeter - chr4:105259710 41.4 13340 322.0
23:26:03.625 INFO ProgressMeter - chr4:122894525 41.6 13410 322.3
23:26:14.438 INFO ProgressMeter - chr4:184418530 41.8 13480 322.6
23:26:25.134 INFO ProgressMeter - chr4:186618187 42.0 13530 322.4
23:26:37.755 INFO ProgressMeter - chr4:186707949 42.2 13580 322.0
23:26:47.964 INFO ProgressMeter - chr5:35873553 42.3 13640 322.1
23:26:58.780 INFO ProgressMeter - chr5:44320046 42.5 13720 322.6
23:27:09.957 INFO ProgressMeter - chr5:56881879 42.7 13780 322.6
23:27:19.994 INFO ProgressMeter - chr5:68295146 42.9 13850 323.0
23:27:31.133 INFO ProgressMeter - chr5:112821894 43.1 13950 323.9
23:27:41.177 INFO ProgressMeter - chr5:112841807 43.2 13990 323.6
23:27:52.331 INFO ProgressMeter - chr5:132594867 43.4 14050 323.6
23:28:02.560 INFO ProgressMeter - chr5:142613957 43.6 14120 323.9
23:28:12.811 INFO ProgressMeter - chr5:149511773 43.8 14170 323.8
23:28:23.602 INFO ProgressMeter - chr5:150121878 43.9 14230 323.9
23:28:33.657 INFO ProgressMeter - chr5:150404185 44.1 14280 323.8
23:28:46.428 INFO ProgressMeter - chr5:177090759 44.3 14340 323.6
23:29:00.051 INFO ProgressMeter - chr5:177136027 44.5 14390 323.0
23:29:12.374 INFO ProgressMeter - chr5:177294948 44.8 14450 322.9
23:29:23.748 INFO ProgressMeter - chr5:180621104 44.9 14520 323.1
23:29:33.889 INFO ProgressMeter - chr6:20446963 45.1 14590 323.4
23:29:44.001 INFO ProgressMeter - chr6:26031648 45.3 14660 323.8
23:29:57.363 INFO ProgressMeter - chr6:29944120 45.5 14730 323.7
23:30:07.423 INFO ProgressMeter - chr6:30711665 45.7 14770 323.4
23:30:18.447 INFO ProgressMeter - chr6:32217225 45.9 14840 323.6
23:30:28.594 INFO ProgressMeter - chr6:36680524 46.0 14900 323.8
23:30:39.027 INFO ProgressMeter - chr6:43784605 46.2 14990 324.5
23:30:49.963 INFO ProgressMeter - chr6:111696354 46.4 15060 324.7
23:31:00.807 INFO ProgressMeter - chr6:117319804 46.6 15110 324.5
23:31:13.507 INFO ProgressMeter - chr6:117324577 46.8 15150 323.9
23:31:25.387 INFO ProgressMeter - chr6:117330468 47.0 15200 323.6
23:31:38.755 INFO ProgressMeter - chr6:117338953 47.2 15270 323.6
23:31:50.214 INFO ProgressMeter - chr6:117396913 47.4 15330 323.5
23:32:02.354 INFO ProgressMeter - chr6:135206399 47.6 15390 323.4
23:32:13.589 INFO ProgressMeter - chr6:135211524 47.8 15430 323.0
23:32:27.449 INFO ProgressMeter - chr6:135214568 48.0 15450 321.8
23:32:37.506 INFO ProgressMeter - chr6:137203585 48.2 15490 321.6
23:32:48.706 INFO ProgressMeter - chr6:149684361 48.4 15540 321.4
23:32:58.918 INFO ProgressMeter - chr6:151944350 48.5 15590 321.3
23:33:10.434 INFO ProgressMeter - chr6:157184229 48.7 15650 321.2
23:33:20.774 INFO ProgressMeter - chr6:161049838 48.9 15700 321.1
23:33:32.899 INFO ProgressMeter - chr7:2922632 49.1 15780 321.4
23:33:44.629 INFO ProgressMeter - chr7:13893389 49.3 15850 321.6
23:33:54.970 INFO ProgressMeter - chr7:13908781 49.5 15890 321.3
23:34:05.140 INFO ProgressMeter - chr7:13933344 49.6 15920 320.8
23:34:15.471 INFO ProgressMeter - chr7:13939411 49.8 15970 320.7
23:34:25.520 INFO ProgressMeter - chr7:13945879 50.0 16010 320.4
23:34:39.570 INFO ProgressMeter - chr7:13951261 50.2 16050 319.7
23:34:50.798 INFO ProgressMeter - chr7:13956361 50.4 16090 319.3
23:35:02.138 INFO ProgressMeter - chr7:13962616 50.6 16130 318.9
23:35:12.232 INFO ProgressMeter - chr7:13967827 50.8 16170 318.6
23:35:22.732 INFO ProgressMeter - chr7:13974151 50.9 16220 318.5
23:35:34.622 INFO ProgressMeter - chr7:13978163 51.1 16250 317.9
23:35:44.994 INFO ProgressMeter - chr7:13982935 51.3 16290 317.6
23:35:56.607 INFO ProgressMeter - chr7:13986648 51.5 16320 317.0
23:36:06.695 INFO ProgressMeter - chr7:41695513 51.7 16350 316.5
23:36:18.390 INFO ProgressMeter - chr7:55156314 51.9 16400 316.3
23:36:29.939 INFO ProgressMeter - chr7:55169331 52.0 16440 315.9
23:36:40.912 INFO ProgressMeter - chr7:55177008 52.2 16480 315.5
23:36:52.160 INFO ProgressMeter - chr7:55181271 52.4 16520 315.2
23:37:02.338 INFO ProgressMeter - chr7:78167976 52.6 16570 315.1
23:37:13.363 INFO ProgressMeter - chr7:86839373 52.8 16640 315.3
23:37:24.678 INFO ProgressMeter - chr7:102195486 53.0 16710 315.5
23:37:37.787 INFO ProgressMeter - chr7:106868582 53.2 16780 315.6
23:37:49.699 INFO ProgressMeter - chr7:116775030 53.4 16840 315.5
23:38:00.983 INFO ProgressMeter - chr7:140739022 53.6 16890 315.3
23:38:11.618 INFO ProgressMeter - chr7:140792177 53.7 16940 315.2
23:38:22.595 INFO ProgressMeter - chr7:142944641 53.9 17020 315.6
23:38:34.072 INFO ProgressMeter - chr7:152155908 54.1 17100 316.0
23:38:47.079 INFO ProgressMeter - chr7:152181485 54.3 17150 315.7
23:38:58.312 INFO ProgressMeter - chr7:152435676 54.5 17220 315.9
23:39:08.657 INFO ProgressMeter - chr8:32327204 54.7 17300 316.3
23:39:19.387 INFO ProgressMeter - chr8:32743086 54.9 17350 316.2
23:39:30.662 INFO ProgressMeter - chr8:37840758 55.1 17420 316.4
23:39:42.611 INFO ProgressMeter - chr8:41932811 55.3 17490 316.5
23:39:53.766 INFO ProgressMeter - chr8:42048915 55.4 17540 316.4
23:40:04.573 INFO ProgressMeter - chr8:47881414 55.6 17610 316.6
23:40:15.857 INFO ProgressMeter - chr8:55999436 55.8 17690 317.0
23:40:26.763 INFO ProgressMeter - chr8:89955446 56.0 17770 317.4
23:40:39.098 INFO ProgressMeter - chr8:127733768 56.2 17840 317.4
23:40:49.962 INFO ProgressMeter - chr8:144512845 56.4 17900 317.5
23:40:59.971 INFO ProgressMeter - chr9:5089705 56.5 17970 317.8
23:41:11.321 INFO ProgressMeter - chr9:8528589 56.7 18050 318.1
23:41:22.456 INFO ProgressMeter - chr9:35075609 56.9 18110 318.2
23:41:33.986 INFO ProgressMeter - chr9:84670863 57.1 18190 318.5
23:41:44.813 INFO ProgressMeter - chr9:84810940 57.3 18230 318.2
23:41:56.977 INFO ProgressMeter - chr9:84861649 57.5 18270 317.8
23:42:10.817 INFO ProgressMeter - chr9:84865787 57.7 18310 317.2
23:42:21.426 INFO ProgressMeter - chr9:84874771 57.9 18350 316.9
23:42:32.428 INFO ProgressMeter - chr9:85021607 58.1 18390 316.6
23:42:45.412 INFO ProgressMeter - chr9:85026618 58.3 18430 316.1
23:42:56.250 INFO ProgressMeter - chr9:95467114 58.5 18500 316.3
23:43:07.689 INFO ProgressMeter - chr9:125158239 58.7 18570 316.5
23:43:18.332 INFO ProgressMeter - chr9:130886556 58.9 18620 316.4
23:43:29.775 INFO ProgressMeter - chr9:136497135 59.0 18680 316.4
23:43:40.524 INFO ProgressMeter - chr9:136544022 59.2 18740 316.4
23:43:51.307 INFO ProgressMeter - chrX:44961282 59.4 18840 317.2
23:44:01.908 INFO ProgressMeter - chrX:49036288 59.6 18960 318.2
23:44:12.722 INFO ProgressMeter - chrX:53405224 59.8 19060 318.9
23:44:23.405 INFO ProgressMeter - chrX:67557163 59.9 19130 319.2
23:44:33.607 INFO ProgressMeter - chrX:71382989 60.1 19250 320.3
23:44:43.607 INFO ProgressMeter - chrX:77683649 60.3 19350 321.0
23:44:54.432 INFO ProgressMeter - chrX:130014536 60.5 19480 322.2
23:45:02.439 INFO Mutect2 - 678329 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
5 read(s) filtered by: ReadLengthReadFilter
100 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
678434 total reads filtered out of 98819438 reads processed
23:45:02.439 INFO ProgressMeter - chrY:20819373 60.6 19574 323.1
23:45:02.439 INFO ProgressMeter - Traversal complete. Processed 19574 total regions in 60.6 minutes.
23:45:02.454 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 7.416386741
23:45:02.455 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 283.168580055
23:45:02.455 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 12.48 sec
23:45:02.455 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:45:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 60.60 minutes.
Runtime.totalMemory()=7415529472
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 LS0912_tumor.bam --tumor-sample LS0912 -L TST500C_manifest.bed -O LS0912.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:45:04.069 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
23:45:04.169 INFO FilterMutectCalls - ------------------------------------------------------------
23:45:04.171 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:45:04.171 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:45:04.171 INFO FilterMutectCalls - Executing as ?@nf-47a1d6f66457cd963c84f5320bdb2a2f-bfe97-w6kcz on Linux v6.12.88 amd64
23:45:04.172 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:45:04.172 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:45:04 PM GMT
23:45:04.172 INFO FilterMutectCalls - ------------------------------------------------------------
23:45:04.172 INFO FilterMutectCalls - ------------------------------------------------------------
23:45:04.173 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:45:04.173 INFO FilterMutectCalls - Picard Version: 3.1.1
23:45:04.173 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:45:04.173 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:45:04.173 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:45:04.173 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:45:04.173 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:45:04.173 INFO FilterMutectCalls - Deflater: IntelDeflater
23:45:04.174 INFO FilterMutectCalls - Inflater: IntelInflater
23:45:04.174 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:45:04.174 INFO FilterMutectCalls - Requester pays: disabled
23:45:04.174 INFO FilterMutectCalls - Initializing engine
23:45:04.345 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.J2AarHYkD5/LS0912.mutect2.raw.vcf.gz
23:45:04.451 INFO FilterMutectCalls - Done initializing engine
23:45:04.505 INFO ProgressMeter - Starting traversal
23:45:04.505 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:45:04.506 INFO FilterMutectCalls - Starting pass 0 through the variants
23:45:05.929 INFO FilterMutectCalls - Finished pass 0 through the variants
23:45:06.589 INFO FilterMutectCalls - Starting pass 1 through the variants
23:45:07.791 INFO FilterMutectCalls - Finished pass 1 through the variants
23:45:08.080 INFO FilterMutectCalls - Starting pass 2 through the variants
23:45:09.236 INFO FilterMutectCalls - Finished pass 2 through the variants
23:45:09.238 INFO FilterMutectCalls - Starting pass 3 through the variants
23:45:10.166 INFO FilterMutectCalls - Finished pass 3 through the variants
23:45:10.174 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:45:10.174 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:45:10.175 INFO ProgressMeter - chr5:177294197 0.1 10840 114729.2
23:45:10.175 INFO ProgressMeter - Traversal complete. Processed 10840 total variants in 0.1 minutes.
23:45:10.185 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:45:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.10 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 LS0912.mutect2.raw.vcf.gz --stats LS0912.mutect2.raw.vcf.gz.stats -O LS0912.mutect2.filtered.vcf.gz
23:45:11.326 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
23:45:11.445 INFO SelectVariants - ------------------------------------------------------------
23:45:11.448 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:45:11.448 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:45:11.448 INFO SelectVariants - Executing as ?@nf-47a1d6f66457cd963c84f5320bdb2a2f-bfe97-w6kcz on Linux v6.12.88 amd64
23:45:11.448 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:45:11.449 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:45:11 PM GMT
23:45:11.449 INFO SelectVariants - ------------------------------------------------------------
23:45:11.449 INFO SelectVariants - ------------------------------------------------------------
23:45:11.449 INFO SelectVariants - HTSJDK Version: 4.1.0
23:45:11.450 INFO SelectVariants - Picard Version: 3.1.1
23:45:11.450 INFO SelectVariants - Built for Spark Version: 3.5.0
23:45:11.450 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:45:11.450 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:45:11.450 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:45:11.450 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:45:11.453 INFO SelectVariants - Deflater: IntelDeflater
23:45:11.453 INFO SelectVariants - Inflater: IntelInflater
23:45:11.453 INFO SelectVariants - GCS max retries/reopens: 20
23:45:11.453 INFO SelectVariants - Requester pays: disabled
23:45:11.454 INFO SelectVariants - Initializing engine
23:45:11.662 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.J2AarHYkD5/LS0912.mutect2.filtered.vcf.gz
23:45:11.777 INFO SelectVariants - Done initializing engine
23:45:11.816 INFO ProgressMeter - Starting traversal
23:45:11.817 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:45:11.900 INFO ProgressMeter - chr6:117327318 0.0 2710 2007407.4
23:45:11.901 INFO ProgressMeter - Traversal complete. Processed 2710 total variants in 0.0 minutes.
23:45:11.915 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:45:11 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=503316480
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 LS0912.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0912.mutect2.pass.vcf.gz