22:44:23.493 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
22:44:23.622 INFO Mutect2 - ------------------------------------------------------------
22:44:23.625 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:23.625 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:23.626 INFO Mutect2 - Executing as ?@nf-b0f4dbbab8cf6fdb6cb28fbf1ae677b3-07d49-8ldcp on Linux v6.12.88 amd64
22:44:23.626 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:23.626 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:23 PM GMT
22:44:23.626 INFO Mutect2 - ------------------------------------------------------------
22:44:23.626 INFO Mutect2 - ------------------------------------------------------------
22:44:23.627 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:23.627 INFO Mutect2 - Picard Version: 3.1.1
22:44:23.627 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:23.627 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:23.628 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:23.628 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:23.628 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:23.628 INFO Mutect2 - Deflater: IntelDeflater
22:44:23.628 INFO Mutect2 - Inflater: IntelInflater
22:44:23.628 INFO Mutect2 - GCS max retries/reopens: 20
22:44:23.628 INFO Mutect2 - Requester pays: disabled
22:44:23.629 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.A80rxBSe0V/LS0905_tumor.bam.bai is older than BAM /tmp/nxf.A80rxBSe0V/LS0905_tumor.bam
22:44:23.823 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.A80rxBSe0V/af-only-gnomad.hg38.vcf.gz
22:44:23.956 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.A80rxBSe0V/TST500C_manifest.bed
22:44:23.995 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:24.025 INFO Mutect2 - Done initializing engine
22:44:24.036 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
22:44:24.038 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
22:44:24.039 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:24.039 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:24.052 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
22:44:24.061 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:24.061 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:24.062 INFO IntelPairHmm - Available threads: 384
22:44:24.062 INFO IntelPairHmm - Requested threads: 4
22:44:24.062 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:24.114 INFO ProgressMeter - Starting traversal
22:44:24.115 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:35.285 INFO ProgressMeter - chr1:11121977 0.2 60 322.3
22:44:46.368 INFO ProgressMeter - chr1:11255990 0.4 120 323.6
22:44:57.124 INFO ProgressMeter - chr1:15933656 0.6 170 309.0
22:45:07.257 INFO ProgressMeter - chr1:18745811 0.7 230 319.9
22:45:18.184 INFO ProgressMeter - chr1:26775118 0.9 290 321.8
22:45:29.713 INFO ProgressMeter - chr1:39897420 1.1 360 329.3
22:45:39.854 INFO ProgressMeter - chr1:45332572 1.3 420 332.7
22:45:51.134 INFO ProgressMeter - chr1:64847596 1.5 510 351.6
22:46:01.682 INFO ProgressMeter - chr1:114713798 1.6 600 369.0
22:46:13.569 INFO ProgressMeter - chr1:119935217 1.8 670 367.3
22:46:28.441 INFO ProgressMeter - chr1:156873548 2.1 740 357.1
22:46:39.349 INFO ProgressMeter - chr1:158642409 2.3 790 350.5
22:46:49.863 INFO ProgressMeter - chr1:162772081 2.4 850 349.9
22:47:00.577 INFO ProgressMeter - chr1:193250674 2.6 920 352.8
22:47:11.476 INFO ProgressMeter - chr1:204544815 2.8 1000 358.5
22:47:21.508 INFO ProgressMeter - chr1:226392274 3.0 1080 365.3
22:47:31.626 INFO ProgressMeter - chr1:243503445 3.1 1130 361.6
22:47:41.737 INFO ProgressMeter - chr10:27035040 3.3 1190 361.3
22:47:52.157 INFO ProgressMeter - chr10:32035643 3.5 1260 363.4
22:48:03.191 INFO ProgressMeter - chr10:43117749 3.7 1320 361.5
22:48:15.286 INFO ProgressMeter - chr10:68646436 3.9 1380 358.2
22:48:28.111 INFO ProgressMeter - chr10:101770219 4.1 1470 361.5
22:48:40.256 INFO ProgressMeter - chr10:110602453 4.3 1560 365.4
22:48:50.791 INFO ProgressMeter - chr10:121485393 4.4 1620 364.5
22:49:01.370 INFO ProgressMeter - chr11:30156124 4.6 1700 367.9
22:49:11.696 INFO ProgressMeter - chr11:69651116 4.8 1810 377.6
22:49:22.287 INFO ProgressMeter - chr11:69768328 5.0 1870 376.3
22:49:36.313 INFO ProgressMeter - chr11:69811632 5.2 1930 370.9
22:49:48.037 INFO ProgressMeter - chr11:76546095 5.4 1990 368.6
22:49:58.117 INFO ProgressMeter - chr11:77466651 5.6 2060 370.1
22:50:11.560 INFO ProgressMeter - chr11:102322897 5.8 2130 367.8
22:50:22.067 INFO ProgressMeter - chr11:112093078 6.0 2220 372.1
22:50:34.030 INFO ProgressMeter - chr11:118506369 6.2 2290 371.4
22:50:44.190 INFO ProgressMeter - chr11:125632591 6.3 2340 369.4
22:50:54.773 INFO ProgressMeter - chr11:128460181 6.5 2390 367.1
22:51:04.903 INFO ProgressMeter - chr11:128812859 6.7 2450 366.8
22:51:14.998 INFO ProgressMeter - chr12:4369025 6.8 2520 368.0
22:51:25.163 INFO ProgressMeter - chr12:4436064 7.0 2580 367.7
22:51:36.043 INFO ProgressMeter - chr12:6592694 7.2 2640 366.7
22:51:47.101 INFO ProgressMeter - chr12:11856705 7.4 2690 364.3
22:52:01.076 INFO ProgressMeter - chr12:11862934 7.6 2730 358.5
22:52:15.977 INFO ProgressMeter - chr12:11869757 7.9 2770 352.2
22:52:27.251 INFO ProgressMeter - chr12:25226441 8.1 2850 353.9
22:52:38.691 INFO ProgressMeter - chr12:45892009 8.2 2920 354.2
22:52:50.504 INFO ProgressMeter - chr12:49037214 8.4 2980 353.1
22:53:01.196 INFO ProgressMeter - chr12:49051551 8.6 3040 352.7
22:53:12.333 INFO ProgressMeter - chr12:56098498 8.8 3130 355.5
22:53:24.013 INFO ProgressMeter - chr12:57472001 9.0 3200 355.6
22:53:34.250 INFO ProgressMeter - chr12:68837005 9.2 3290 358.8
22:53:45.353 INFO ProgressMeter - chr12:120988831 9.4 3380 361.3
22:53:55.817 INFO ProgressMeter - chr12:132672213 9.5 3450 362.1
22:54:06.017 INFO ProgressMeter - chr13:21688777 9.7 3520 362.9
22:54:16.531 INFO ProgressMeter - chr13:28317547 9.9 3600 364.6
22:54:32.505 INFO ProgressMeter - chr13:28389113 10.1 3640 359.0
22:54:43.604 INFO ProgressMeter - chr13:32340156 10.3 3700 358.4
22:54:53.966 INFO ProgressMeter - chr13:72759793 10.5 3780 360.1
22:55:04.968 INFO ProgressMeter - chr13:102862028 10.7 3860 361.4
22:55:17.339 INFO ProgressMeter - chr13:113310824 10.9 3940 361.9
22:55:28.587 INFO ProgressMeter - chr14:37589359 11.1 4010 362.1
22:55:39.786 INFO ProgressMeter - chr14:68497122 11.3 4090 363.2
22:55:50.005 INFO ProgressMeter - chr14:95117701 11.4 4150 363.0
22:56:03.245 INFO ProgressMeter - chr15:34347483 11.7 4230 363.0
22:56:13.397 INFO ProgressMeter - chr15:41699080 11.8 4290 362.9
22:56:23.841 INFO ProgressMeter - chr15:41766968 12.0 4340 361.8
22:56:34.700 INFO ProgressMeter - chr15:73703657 12.2 4430 363.8
22:56:45.069 INFO ProgressMeter - chr15:89274166 12.3 4500 364.4
22:56:56.346 INFO ProgressMeter - chr15:92924319 12.5 4580 365.3
22:57:06.460 INFO ProgressMeter - chr15:98916777 12.7 4650 366.0
22:57:17.733 INFO ProgressMeter - chr16:2084526 12.9 4730 366.8
22:57:28.942 INFO ProgressMeter - chr16:3727888 13.1 4830 369.3
22:57:39.148 INFO ProgressMeter - chr16:9764047 13.3 4890 369.0
22:57:49.952 INFO ProgressMeter - chr16:23630005 13.4 4960 369.3
22:58:00.424 INFO ProgressMeter - chr16:67029725 13.6 5040 370.4
22:58:13.521 INFO ProgressMeter - chr16:72794542 13.8 5100 368.9
22:58:25.596 INFO ProgressMeter - chr16:72959999 14.0 5150 367.2
22:58:35.992 INFO ProgressMeter - chr16:89281762 14.2 5220 367.7
22:58:46.236 INFO ProgressMeter - chr16:89799056 14.4 5290 368.2
22:58:57.187 INFO ProgressMeter - chr17:7676665 14.6 5360 368.4
22:59:07.547 INFO ProgressMeter - chr17:16071563 14.7 5450 370.1
22:59:18.619 INFO ProgressMeter - chr17:31230258 14.9 5540 371.6
22:59:29.860 INFO ProgressMeter - chr17:39471477 15.1 5630 373.0
22:59:40.908 INFO ProgressMeter - chr17:40352329 15.3 5710 373.7
22:59:51.239 INFO ProgressMeter - chr17:42309045 15.5 5800 375.4
23:00:03.495 INFO ProgressMeter - chr17:43092957 15.7 5880 375.6
23:00:13.709 INFO ProgressMeter - chr17:43531757 15.8 5930 374.7
23:00:25.505 INFO ProgressMeter - chr17:43541236 16.0 5990 373.8
23:00:35.586 INFO ProgressMeter - chr17:43546183 16.2 6020 371.8
23:00:46.074 INFO ProgressMeter - chr17:58696691 16.4 6090 372.1
23:00:57.562 INFO ProgressMeter - chr17:60663403 16.6 6170 372.6
23:01:07.897 INFO ProgressMeter - chr17:65549518 16.7 6240 373.0
23:01:18.506 INFO ProgressMeter - chr17:80960076 16.9 6330 374.4
23:01:28.852 INFO ProgressMeter - chr18:44949917 17.1 6410 375.3
23:01:39.569 INFO ProgressMeter - chr18:58710919 17.3 6470 374.9
23:01:50.282 INFO ProgressMeter - chr19:2220106 17.4 6570 376.8
23:02:01.382 INFO ProgressMeter - chr19:5245774 17.6 6670 378.5
23:02:11.886 INFO ProgressMeter - chr19:10160016 17.8 6750 379.3
23:02:22.529 INFO ProgressMeter - chr19:12940051 18.0 6840 380.6
23:02:32.726 INFO ProgressMeter - chr19:15188233 18.1 6910 380.9
23:02:44.917 INFO ProgressMeter - chr19:17843775 18.3 6990 381.0
23:02:55.192 INFO ProgressMeter - chr19:33301699 18.5 7080 382.3
23:03:06.557 INFO ProgressMeter - chr19:40236255 18.7 7170 383.3
23:03:18.106 INFO ProgressMeter - chr19:41261048 18.9 7250 383.6
23:03:29.036 INFO ProgressMeter - chr19:45364233 19.1 7330 384.1
23:03:39.540 INFO ProgressMeter - chr19:50407325 19.3 7420 385.3
23:03:50.338 INFO ProgressMeter - chr2:15945186 19.4 7490 385.3
23:04:02.573 INFO ProgressMeter - chr2:25743336 19.6 7570 385.4
23:04:14.190 INFO ProgressMeter - chr2:29224350 19.8 7630 384.7
23:04:24.748 INFO ProgressMeter - chr2:29920591 20.0 7680 383.8
23:04:35.702 INFO ProgressMeter - chr2:47385164 20.2 7740 383.3
23:04:45.961 INFO ProgressMeter - chr2:58160106 20.4 7790 382.5
23:04:56.473 INFO ProgressMeter - chr2:98520047 20.5 7860 382.7
23:05:06.913 INFO ProgressMeter - chr2:108775730 20.7 7940 383.3
23:05:17.807 INFO ProgressMeter - chr2:113220090 20.9 7980 381.9
23:05:29.360 INFO ProgressMeter - chr2:113226697 21.1 8020 380.3
23:05:42.287 INFO ProgressMeter - chr2:113235363 21.3 8070 378.8
23:05:53.279 INFO ProgressMeter - chr2:140485341 21.5 8160 379.8
23:06:04.116 INFO ProgressMeter - chr2:142130646 21.7 8240 380.3
23:06:15.175 INFO ProgressMeter - chr2:197398459 21.9 8330 381.2
23:06:25.186 INFO ProgressMeter - chr2:211630460 22.0 8410 382.0
23:06:35.243 INFO ProgressMeter - chr2:222202326 22.2 8470 381.8
23:06:45.308 INFO ProgressMeter - chr2:222209354 22.4 8510 380.7
23:06:57.688 INFO ProgressMeter - chr2:222216673 22.6 8550 379.0
23:07:07.806 INFO ProgressMeter - chr2:224503650 22.7 8600 378.4
23:07:17.856 INFO ProgressMeter - chr20:9542584 22.9 8660 378.2
23:07:29.232 INFO ProgressMeter - chr20:32780114 23.1 8720 377.7
23:07:39.675 INFO ProgressMeter - chr20:42161350 23.3 8810 378.8
23:07:50.451 INFO ProgressMeter - chr20:56370156 23.4 8880 378.9
23:08:00.518 INFO ProgressMeter - chr21:38380071 23.6 8960 379.6
23:08:10.727 INFO ProgressMeter - chr21:41464607 23.8 9010 378.9
23:08:26.792 INFO ProgressMeter - chr21:41492067 24.0 9050 376.4
23:08:37.909 INFO ProgressMeter - chr21:41502128 24.2 9090 375.2
23:08:48.422 INFO ProgressMeter - chr21:43101364 24.4 9140 374.5
23:08:59.265 INFO ProgressMeter - chr22:23289577 24.6 9220 375.0
23:09:10.314 INFO ProgressMeter - chr22:25354830 24.8 9260 373.8
23:09:21.503 INFO ProgressMeter - chr22:29284993 25.0 9350 374.7
23:09:31.904 INFO ProgressMeter - chr22:29654655 25.1 9390 373.7
23:09:42.604 INFO ProgressMeter - chr22:41178231 25.3 9470 374.2
23:09:53.782 INFO ProgressMeter - chr3:12354559 25.5 9550 374.6
23:10:05.545 INFO ProgressMeter - chr3:12360523 25.7 9580 372.9
23:10:17.947 INFO ProgressMeter - chr3:12367563 25.9 9620 371.5
23:10:29.326 INFO ProgressMeter - chr3:12375299 26.1 9660 370.3
23:10:39.768 INFO ProgressMeter - chr3:12609231 26.3 9720 370.1
23:10:50.987 INFO ProgressMeter - chr3:41233527 26.4 9800 370.5
23:11:01.643 INFO ProgressMeter - chr3:47123731 26.6 9860 370.3
23:11:12.240 INFO ProgressMeter - chr3:52403236 26.8 9940 370.9
23:11:22.851 INFO ProgressMeter - chr3:70958269 27.0 10020 371.4
23:11:33.668 INFO ProgressMeter - chr3:119912702 27.2 10100 371.9
23:11:44.264 INFO ProgressMeter - chr3:136422832 27.3 10170 372.0
23:11:54.585 INFO ProgressMeter - chr3:142453126 27.5 10250 372.6
23:12:04.685 INFO ProgressMeter - chr3:170293381 27.7 10330 373.2
23:12:15.762 INFO ProgressMeter - chr3:183494201 27.9 10410 373.6
23:12:26.148 INFO ProgressMeter - chr3:186048619 28.0 10460 373.1
23:12:36.192 INFO ProgressMeter - chr3:196055078 28.2 10540 373.7
23:12:46.942 INFO ProgressMeter - chr4:20491759 28.4 10640 374.9
23:12:57.205 INFO ProgressMeter - chr4:54258096 28.6 10710 375.1
23:13:08.254 INFO ProgressMeter - chr4:54714701 28.7 10780 375.1
23:13:19.628 INFO ProgressMeter - chr4:55118602 28.9 10830 374.4
23:13:30.584 INFO ProgressMeter - chr4:105234047 29.1 10920 375.2
23:13:42.580 INFO ProgressMeter - chr4:105261757 29.3 10970 374.3
23:13:53.347 INFO ProgressMeter - chr4:152324380 29.5 11060 375.1
23:14:04.000 INFO ProgressMeter - chr4:186617751 29.7 11130 375.2
23:14:15.833 INFO ProgressMeter - chr4:186708579 29.9 11180 374.4
23:14:26.544 INFO ProgressMeter - chr5:38950637 30.0 11250 374.5
23:14:36.614 INFO ProgressMeter - chr5:56815962 30.2 11340 375.4
23:14:46.912 INFO ProgressMeter - chr5:68288672 30.4 11410 375.6
23:14:57.045 INFO ProgressMeter - chr5:112828854 30.5 11510 376.8
23:15:08.181 INFO ProgressMeter - chr5:122423152 30.7 11560 376.1
23:15:19.648 INFO ProgressMeter - chr5:142600700 30.9 11640 376.4
23:15:30.562 INFO ProgressMeter - chr5:150057565 31.1 11710 376.4
23:15:41.479 INFO ProgressMeter - chr5:150144178 31.3 11790 376.8
23:15:56.055 INFO ProgressMeter - chr5:177090936 31.5 11870 376.4
23:16:06.113 INFO ProgressMeter - chr5:177211627 31.7 11920 376.0
23:16:16.846 INFO ProgressMeter - chr5:180620874 31.9 12000 376.4
23:16:27.706 INFO ProgressMeter - chr6:20479844 32.1 12080 376.8
23:16:39.349 INFO ProgressMeter - chr6:29944520 32.3 12170 377.3
23:16:49.554 INFO ProgressMeter - chr6:30713646 32.4 12220 376.9
23:16:59.692 INFO ProgressMeter - chr6:32223854 32.6 12280 376.8
23:17:10.690 INFO ProgressMeter - chr6:42032781 32.8 12370 377.4
23:17:20.911 INFO ProgressMeter - chr6:106107094 32.9 12450 377.9
23:17:34.741 INFO ProgressMeter - chr6:117322002 33.2 12510 377.1
23:17:46.693 INFO ProgressMeter - chr6:117331851 33.4 12560 376.3
23:17:57.987 INFO ProgressMeter - chr6:117344058 33.6 12610 375.7
23:18:09.001 INFO ProgressMeter - chr6:135204432 33.7 12680 375.7
23:18:22.953 INFO ProgressMeter - chr6:135213723 34.0 12730 374.6
23:18:33.889 INFO ProgressMeter - chr6:137881142 34.2 12780 374.1
23:18:44.690 INFO ProgressMeter - chr6:151908902 34.3 12840 373.9
23:18:56.104 INFO ProgressMeter - chr6:161034257 34.5 12910 373.8
23:19:06.715 INFO ProgressMeter - chr7:2917334 34.7 12990 374.2
23:19:19.236 INFO ProgressMeter - chr7:13894201 34.9 13070 374.3
23:19:32.656 INFO ProgressMeter - chr7:13933346 35.1 13110 373.1
23:19:44.186 INFO ProgressMeter - chr7:13940493 35.3 13150 372.2
23:19:56.872 INFO ProgressMeter - chr7:13947342 35.5 13190 371.1
23:20:07.909 INFO ProgressMeter - chr7:13951634 35.7 13220 370.0
23:20:19.287 INFO ProgressMeter - chr7:13957147 35.9 13250 368.9
23:20:32.941 INFO ProgressMeter - chr7:13962845 36.1 13290 367.7
23:20:43.203 INFO ProgressMeter - chr7:13966970 36.3 13320 366.8
23:20:55.881 INFO ProgressMeter - chr7:13974017 36.5 13370 366.0
23:21:06.176 INFO ProgressMeter - chr7:13977553 36.7 13390 364.8
23:21:17.282 INFO ProgressMeter - chr7:13983800 36.9 13430 364.1
23:21:28.821 INFO ProgressMeter - chr7:13989266 37.1 13460 363.0
23:21:39.657 INFO ProgressMeter - chr7:55154092 37.3 13520 362.9
23:21:51.858 INFO ProgressMeter - chr7:55169783 37.5 13560 362.0
23:22:03.185 INFO ProgressMeter - chr7:55180139 37.7 13610 361.5
23:22:13.874 INFO ProgressMeter - chr7:78256283 37.8 13670 361.4
23:22:23.961 INFO ProgressMeter - chr7:92697167 38.0 13740 361.6
23:22:34.311 INFO ProgressMeter - chr7:106867560 38.2 13820 362.1
23:22:45.112 INFO ProgressMeter - chr7:116771796 38.3 13880 361.9
23:22:55.992 INFO ProgressMeter - chr7:140790370 38.5 13950 362.0
23:23:06.651 INFO ProgressMeter - chr7:142944387 38.7 14020 362.2
23:23:17.950 INFO ProgressMeter - chr7:152167144 38.9 14100 362.5
23:23:28.905 INFO ProgressMeter - chr7:152247900 39.1 14160 362.3
23:23:40.004 INFO ProgressMeter - chr8:32262230 39.3 14250 362.9
23:23:51.177 INFO ProgressMeter - chr8:37697398 39.5 14310 362.7
23:24:01.237 INFO ProgressMeter - chr8:38432079 39.6 14380 363.0
23:24:11.470 INFO ProgressMeter - chr8:47774171 39.8 14440 362.9
23:24:22.305 INFO ProgressMeter - chr8:47912408 40.0 14520 363.3
23:24:32.981 INFO ProgressMeter - chr8:68118600 40.1 14610 363.9
23:24:44.031 INFO ProgressMeter - chr8:116866584 40.3 14690 364.2
23:24:56.053 INFO ProgressMeter - chr8:144511909 40.5 14750 363.9
23:25:06.670 INFO ProgressMeter - chr9:5534743 40.7 14840 364.5
23:25:17.500 INFO ProgressMeter - chr9:20621969 40.9 14920 364.9
23:25:27.783 INFO ProgressMeter - chr9:83974496 41.1 15000 365.3
23:25:38.246 INFO ProgressMeter - chr9:84744087 41.2 15040 364.7
23:25:52.025 INFO ProgressMeter - chr9:84861338 41.5 15080 363.7
23:26:02.448 INFO ProgressMeter - chr9:84867355 41.6 15110 362.9
23:26:15.218 INFO ProgressMeter - chr9:85023001 41.9 15160 362.2
23:26:25.437 INFO ProgressMeter - chr9:90874696 42.0 15200 361.7
23:26:36.218 INFO ProgressMeter - chr9:99147652 42.2 15280 362.1
23:26:46.456 INFO ProgressMeter - chr9:130886568 42.4 15350 362.3
23:26:57.295 INFO ProgressMeter - chr9:136502342 42.6 15410 362.1
23:27:07.670 INFO ProgressMeter - chrX:40074124 42.7 15530 363.5
23:27:18.087 INFO ProgressMeter - chrX:53195343 42.9 15700 366.0
23:27:28.112 INFO ProgressMeter - chrX:67689292 43.1 15820 367.3
23:27:38.394 INFO ProgressMeter - chrX:77682434 43.2 15970 369.4
23:27:48.600 INFO ProgressMeter - chrY:7811001 43.4 16130 371.6
23:27:51.149 INFO Mutect2 - 566581 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
102 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
566685 total reads filtered out of 79624609 reads processed
23:27:51.150 INFO ProgressMeter - chrY:19773323 43.5 16178 372.3
23:27:51.150 INFO ProgressMeter - Traversal complete. Processed 16178 total regions in 43.5 minutes.
23:27:51.166 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 5.556611113000001
23:27:51.167 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 226.24779259000002
23:27:51.167 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 8.43 sec
23:27:51.167 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:27:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 43.46 minutes.
Runtime.totalMemory()=2994733056
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 LS0905_tumor.bam --tumor-sample LS0905 -L TST500C_manifest.bed -O LS0905.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:27:52.498 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
23:27:52.611 INFO FilterMutectCalls - ------------------------------------------------------------
23:27:52.613 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:27:52.613 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:27:52.613 INFO FilterMutectCalls - Executing as ?@nf-b0f4dbbab8cf6fdb6cb28fbf1ae677b3-07d49-8ldcp on Linux v6.12.88 amd64
23:27:52.613 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:27:52.614 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:27:52 PM GMT
23:27:52.614 INFO FilterMutectCalls - ------------------------------------------------------------
23:27:52.614 INFO FilterMutectCalls - ------------------------------------------------------------
23:27:52.614 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:27:52.615 INFO FilterMutectCalls - Picard Version: 3.1.1
23:27:52.615 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:27:52.615 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:27:52.615 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:27:52.615 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:27:52.615 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:27:52.615 INFO FilterMutectCalls - Deflater: IntelDeflater
23:27:52.615 INFO FilterMutectCalls - Inflater: IntelInflater
23:27:52.615 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:27:52.615 INFO FilterMutectCalls - Requester pays: disabled
23:27:52.616 INFO FilterMutectCalls - Initializing engine
23:27:52.786 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.A80rxBSe0V/LS0905.mutect2.raw.vcf.gz
23:27:52.880 INFO FilterMutectCalls - Done initializing engine
23:27:52.930 INFO ProgressMeter - Starting traversal
23:27:52.930 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:27:52.931 INFO FilterMutectCalls - Starting pass 0 through the variants
23:27:54.361 INFO FilterMutectCalls - Finished pass 0 through the variants
23:27:56.403 INFO FilterMutectCalls - Starting pass 1 through the variants
23:27:57.975 INFO FilterMutectCalls - Finished pass 1 through the variants
23:27:58.433 INFO FilterMutectCalls - Starting pass 2 through the variants
23:27:59.974 INFO FilterMutectCalls - Finished pass 2 through the variants
23:27:59.977 INFO FilterMutectCalls - Starting pass 3 through the variants
23:28:01.318 INFO FilterMutectCalls - Finished pass 3 through the variants
23:28:01.326 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:28:01.326 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:28:01.326 INFO ProgressMeter - chr7:2924306 0.1 9540 68175.3
23:28:01.327 INFO ProgressMeter - Traversal complete. Processed 9540 total variants in 0.1 minutes.
23:28:01.336 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:28:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.15 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 FilterMutectCalls -R hg38.fa -V LS0905.mutect2.raw.vcf.gz --stats LS0905.mutect2.raw.vcf.gz.stats -O LS0905.mutect2.filtered.vcf.gz
23:28:02.662 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
23:28:02.786 INFO SelectVariants - ------------------------------------------------------------
23:28:02.789 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:28:02.789 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:28:02.789 INFO SelectVariants - Executing as ?@nf-b0f4dbbab8cf6fdb6cb28fbf1ae677b3-07d49-8ldcp on Linux v6.12.88 amd64
23:28:02.790 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:28:02.790 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:28:02 PM GMT
23:28:02.790 INFO SelectVariants - ------------------------------------------------------------
23:28:02.790 INFO SelectVariants - ------------------------------------------------------------
23:28:02.791 INFO SelectVariants - HTSJDK Version: 4.1.0
23:28:02.791 INFO SelectVariants - Picard Version: 3.1.1
23:28:02.791 INFO SelectVariants - Built for Spark Version: 3.5.0
23:28:02.791 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:28:02.791 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:28:02.791 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:28:02.791 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:28:02.791 INFO SelectVariants - Deflater: IntelDeflater
23:28:02.791 INFO SelectVariants - Inflater: IntelInflater
23:28:02.792 INFO SelectVariants - GCS max retries/reopens: 20
23:28:02.792 INFO SelectVariants - Requester pays: disabled
23:28:02.792 INFO SelectVariants - Initializing engine
23:28:02.964 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.A80rxBSe0V/LS0905.mutect2.filtered.vcf.gz
23:28:03.087 INFO SelectVariants - Done initializing engine
23:28:03.127 INFO ProgressMeter - Starting traversal
23:28:03.128 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:28:03.196 INFO ProgressMeter - chr7:13975625 0.0 2385 2168181.8
23:28:03.196 INFO ProgressMeter - Traversal complete. Processed 2385 total variants in 0.0 minutes.
23:28:03.208 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:28:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=335544320
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 LS0905.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0905.mutect2.pass.vcf.gz