22:44:32.240 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
22:44:32.335 INFO Mutect2 - ------------------------------------------------------------
22:44:32.337 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:32.338 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:32.338 INFO Mutect2 - Executing as ?@nf-f204d5822f8228d75eec1754a3a11650-089b7-6r6kb on Linux v6.12.88 amd64
22:44:32.338 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:32.338 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:32 PM GMT
22:44:32.338 INFO Mutect2 - ------------------------------------------------------------
22:44:32.338 INFO Mutect2 - ------------------------------------------------------------
22:44:32.339 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:32.339 INFO Mutect2 - Picard Version: 3.1.1
22:44:32.339 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:32.339 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:32.339 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:32.339 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:32.339 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:32.340 INFO Mutect2 - Deflater: IntelDeflater
22:44:32.340 INFO Mutect2 - Inflater: IntelInflater
22:44:32.340 INFO Mutect2 - GCS max retries/reopens: 20
22:44:32.340 INFO Mutect2 - Requester pays: disabled
22:44:32.340 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.ZkEnyIHeTV/LS0894_tumor.bam.bai is older than BAM /tmp/nxf.ZkEnyIHeTV/LS0894_tumor.bam
22:44:32.495 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.ZkEnyIHeTV/af-only-gnomad.hg38.vcf.gz
22:44:32.614 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.ZkEnyIHeTV/TST500C_manifest.bed
22:44:32.648 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:32.675 INFO Mutect2 - Done initializing engine
22:44:32.684 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
22:44:32.686 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
22:44:32.687 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:32.687 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:32.696 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
22:44:32.704 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:32.705 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:32.705 INFO IntelPairHmm - Available threads: 384
22:44:32.705 INFO IntelPairHmm - Requested threads: 4
22:44:32.705 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:32.743 INFO ProgressMeter - Starting traversal
22:44:32.744 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:42.804 INFO ProgressMeter - chr1:9724802 0.2 60 357.9
22:44:53.115 INFO ProgressMeter - chr1:11232434 0.3 130 382.9
22:45:03.405 INFO ProgressMeter - chr1:15929300 0.5 190 371.8
22:45:15.805 INFO ProgressMeter - chr1:15935815 0.7 240 334.4
22:45:28.609 INFO ProgressMeter - chr1:18746395 0.9 310 332.9
22:45:39.426 INFO ProgressMeter - chr1:26773344 1.1 370 332.9
22:45:50.222 INFO ProgressMeter - chr1:39892246 1.3 440 340.7
22:46:01.282 INFO ProgressMeter - chr1:43339962 1.5 510 345.6
22:46:11.930 INFO ProgressMeter - chr1:46260990 1.7 590 356.9
22:46:22.891 INFO ProgressMeter - chr1:64867090 1.8 670 365.0
22:46:33.473 INFO ProgressMeter - chr1:114711401 2.0 750 372.7
22:46:45.926 INFO ProgressMeter - chr1:119514498 2.2 820 369.4
22:46:56.430 INFO ProgressMeter - chr1:119950739 2.4 870 363.3
22:47:09.616 INFO ProgressMeter - chr1:156873365 2.6 950 363.4
22:47:20.252 INFO ProgressMeter - chr1:158613848 2.8 980 351.0
22:47:30.456 INFO ProgressMeter - chr1:158671341 3.0 1050 354.5
22:47:40.863 INFO ProgressMeter - chr1:176162867 3.1 1130 360.4
22:47:50.922 INFO ProgressMeter - chr1:204433791 3.3 1210 366.3
22:48:01.974 INFO ProgressMeter - chr1:204544942 3.5 1290 369.9
22:48:13.219 INFO ProgressMeter - chr1:226379571 3.7 1370 372.8
22:48:25.584 INFO ProgressMeter - chr1:243501651 3.9 1440 371.1
22:48:36.257 INFO ProgressMeter - chr1:243563718 4.1 1480 364.7
22:48:46.896 INFO ProgressMeter - chr10:27046465 4.2 1550 365.9
22:48:57.174 INFO ProgressMeter - chr10:32022218 4.4 1610 365.3
22:49:08.228 INFO ProgressMeter - chr10:43113461 4.6 1680 365.9
22:49:20.235 INFO ProgressMeter - chr10:43119529 4.8 1730 361.1
22:49:32.724 INFO ProgressMeter - chr10:68573088 5.0 1790 358.0
22:49:43.238 INFO ProgressMeter - chr10:68691008 5.2 1840 355.6
22:49:53.498 INFO ProgressMeter - chr10:89003092 5.3 1920 359.2
22:50:04.661 INFO ProgressMeter - chr10:102593634 5.5 1990 359.7
22:50:15.878 INFO ProgressMeter - chr10:110604210 5.7 2060 360.2
22:50:27.763 INFO ProgressMeter - chr10:121482457 5.9 2120 358.3
22:50:38.574 INFO ProgressMeter - chr10:121560711 6.1 2180 357.5
22:50:49.690 INFO ProgressMeter - chr11:61437793 6.3 2270 361.3
22:51:00.178 INFO ProgressMeter - chr11:69647992 6.5 2370 367.0
22:51:11.727 INFO ProgressMeter - chr11:69701916 6.6 2430 365.4
22:51:23.025 INFO ProgressMeter - chr11:69808367 6.8 2510 367.1
22:51:33.422 INFO ProgressMeter - chr11:69817376 7.0 2550 363.7
22:51:44.011 INFO ProgressMeter - chr11:77349062 7.2 2620 364.5
22:51:54.248 INFO ProgressMeter - chr11:77442651 7.4 2680 364.2
22:52:04.730 INFO ProgressMeter - chr11:101127867 7.5 2760 366.4
22:52:16.060 INFO ProgressMeter - chr11:102331168 7.7 2800 362.6
22:52:26.325 INFO ProgressMeter - chr11:108316054 7.9 2880 364.9
22:52:37.533 INFO ProgressMeter - chr11:118481867 8.1 2960 366.3
22:52:50.250 INFO ProgressMeter - chr11:118506028 8.3 3020 364.2
22:53:00.890 INFO ProgressMeter - chr11:125620935 8.5 3070 362.5
22:53:11.439 INFO ProgressMeter - chr11:128458980 8.6 3130 362.1
22:53:22.328 INFO ProgressMeter - chr11:128461366 8.8 3150 356.9
22:53:34.163 INFO ProgressMeter - chr11:128812674 9.0 3210 355.7
22:53:44.502 INFO ProgressMeter - chr12:4299858 9.2 3290 357.8
22:53:54.675 INFO ProgressMeter - chr12:4433341 9.4 3360 358.8
22:54:05.134 INFO ProgressMeter - chr12:6587478 9.5 3430 359.5
22:54:17.063 INFO ProgressMeter - chr12:11855348 9.7 3500 359.4
22:54:28.743 INFO ProgressMeter - chr12:11860968 9.9 3550 357.4
22:54:41.335 INFO ProgressMeter - chr12:11867454 10.1 3600 354.9
22:54:51.346 INFO ProgressMeter - chr12:18282717 10.3 3650 354.0
22:55:01.558 INFO ProgressMeter - chr12:25240044 10.5 3740 356.9
22:55:12.562 INFO ProgressMeter - chr12:45851743 10.7 3800 356.4
22:55:25.271 INFO ProgressMeter - chr12:49033184 10.9 3870 355.8
22:55:36.611 INFO ProgressMeter - chr12:49045918 11.1 3930 355.2
22:55:47.774 INFO ProgressMeter - chr12:56082013 11.3 4010 356.4
22:55:58.522 INFO ProgressMeter - chr12:57091856 11.4 4090 357.8
22:56:08.654 INFO ProgressMeter - chr12:57471576 11.6 4150 357.8
22:56:18.851 INFO ProgressMeter - chr12:68835563 11.8 4240 360.3
22:56:29.300 INFO ProgressMeter - chr12:111434900 11.9 4300 360.1
22:56:40.066 INFO ProgressMeter - chr12:120996268 12.1 4380 361.3
22:56:50.642 INFO ProgressMeter - chr12:132672213 12.3 4460 362.7
22:57:02.360 INFO ProgressMeter - chr13:21677690 12.5 4540 363.4
22:57:12.838 INFO ProgressMeter - chr13:28049382 12.7 4630 365.5
22:57:23.983 INFO ProgressMeter - chr13:28387144 12.9 4690 364.9
22:57:35.724 INFO ProgressMeter - chr13:28389836 13.0 4710 360.9
22:57:46.858 INFO ProgressMeter - chr13:32337277 13.2 4780 361.2
22:57:58.002 INFO ProgressMeter - chr13:32379748 13.4 4840 360.6
22:58:09.079 INFO ProgressMeter - chr13:72772157 13.6 4940 363.1
22:58:20.302 INFO ProgressMeter - chr13:102862559 13.8 5020 364.0
22:58:31.822 INFO ProgressMeter - chr13:113310707 14.0 5110 365.4
22:58:42.808 INFO ProgressMeter - chr14:37585751 14.2 5180 365.6
22:58:53.802 INFO ProgressMeter - chr14:37598103 14.4 5250 365.8
22:59:04.288 INFO ProgressMeter - chr14:95090621 14.5 5330 366.9
22:59:17.439 INFO ProgressMeter - chr14:102084429 14.7 5400 366.2
22:59:28.783 INFO ProgressMeter - chr15:34347770 14.9 5470 366.3
22:59:40.137 INFO ProgressMeter - chr15:41696373 15.1 5530 365.7
22:59:50.336 INFO ProgressMeter - chr15:41750165 15.3 5580 364.9
23:00:00.991 INFO ProgressMeter - chr15:49435984 15.5 5640 364.6
23:00:12.701 INFO ProgressMeter - chr15:87876755 15.7 5730 365.8
23:00:22.722 INFO ProgressMeter - chr15:88256295 15.8 5790 365.7
23:00:33.049 INFO ProgressMeter - chr15:90749781 16.0 5880 367.4
23:00:43.344 INFO ProgressMeter - chr15:92981363 16.2 5960 368.4
23:00:54.339 INFO ProgressMeter - chr16:293715 16.4 6040 369.2
23:01:05.032 INFO ProgressMeter - chr16:2088225 16.5 6120 370.1
23:01:15.529 INFO ProgressMeter - chr16:3600977 16.7 6220 372.2
23:01:26.669 INFO ProgressMeter - chr16:3850295 16.9 6290 372.2
23:01:37.819 INFO ProgressMeter - chr16:10179996 17.1 6340 371.1
23:01:49.089 INFO ProgressMeter - chr16:23636095 17.3 6420 371.7
23:02:00.171 INFO ProgressMeter - chr16:67036705 17.5 6510 372.9
23:02:11.180 INFO ProgressMeter - chr16:72788527 17.6 6580 373.0
23:02:22.588 INFO ProgressMeter - chr16:72798095 17.8 6630 371.8
23:02:32.753 INFO ProgressMeter - chr16:81854442 18.0 6680 371.1
23:02:44.895 INFO ProgressMeter - chr16:89282781 18.2 6760 371.4
23:02:55.272 INFO ProgressMeter - chr16:89771771 18.4 6830 371.7
23:03:09.574 INFO ProgressMeter - chr17:7676117 18.6 6920 371.8
23:03:20.561 INFO ProgressMeter - chr17:16048843 18.8 7020 373.5
23:03:31.580 INFO ProgressMeter - chr17:17213653 19.0 7100 374.1
23:03:42.665 INFO ProgressMeter - chr17:31258342 19.2 7190 375.2
23:03:53.010 INFO ProgressMeter - chr17:39462957 19.3 7280 376.5
23:04:03.923 INFO ProgressMeter - chr17:39719785 19.5 7360 377.1
23:04:13.950 INFO ProgressMeter - chr17:42201768 19.7 7450 378.4
23:04:24.579 INFO ProgressMeter - chr17:43063331 19.9 7550 380.1
23:04:35.619 INFO ProgressMeter - chr17:43093971 20.0 7610 379.6
23:04:46.273 INFO ProgressMeter - chr17:43532323 20.2 7670 379.2
23:04:57.341 INFO ProgressMeter - chr17:43540672 20.4 7730 378.7
23:05:08.412 INFO ProgressMeter - chr17:45266535 20.6 7780 377.8
23:05:18.524 INFO ProgressMeter - chr17:58370909 20.8 7850 378.1
23:05:29.650 INFO ProgressMeter - chr17:59947109 20.9 7940 379.0
23:05:40.611 INFO ProgressMeter - chr17:63929432 21.1 8010 379.1
23:05:51.240 INFO ProgressMeter - chr17:75779095 21.3 8090 379.7
23:06:01.388 INFO ProgressMeter - chr18:22171143 21.5 8180 380.9
23:06:13.263 INFO ProgressMeter - chr18:44952477 21.7 8260 381.1
23:06:24.224 INFO ProgressMeter - chr18:58747746 21.9 8340 381.6
23:06:35.445 INFO ProgressMeter - chr19:2226181 22.0 8450 383.3
23:06:46.445 INFO ProgressMeter - chr19:5225829 22.2 8550 384.6
23:06:57.285 INFO ProgressMeter - chr19:10140779 22.4 8640 385.6
23:07:07.375 INFO ProgressMeter - chr19:10986542 22.6 8710 385.8
23:07:18.041 INFO ProgressMeter - chr19:14517780 22.8 8790 386.3
23:07:28.139 INFO ProgressMeter - chr19:15191553 22.9 8860 386.5
23:07:38.440 INFO ProgressMeter - chr19:17841387 23.1 8950 387.5
23:07:48.738 INFO ProgressMeter - chr19:29820240 23.3 9030 388.1
23:07:59.328 INFO ProgressMeter - chr19:35733135 23.4 9120 389.0
23:08:10.403 INFO ProgressMeter - chr19:41239692 23.6 9210 389.8
23:08:21.803 INFO ProgressMeter - chr19:42290866 23.8 9270 389.2
23:08:32.027 INFO ProgressMeter - chr19:45369994 24.0 9360 390.2
23:08:42.328 INFO ProgressMeter - chr19:50409133 24.2 9450 391.1
23:08:53.547 INFO ProgressMeter - chr2:15943489 24.3 9520 391.0
23:09:04.122 INFO ProgressMeter - chr2:25244567 24.5 9590 391.1
23:09:14.615 INFO ProgressMeter - chr2:25799383 24.7 9650 390.7
23:09:26.763 INFO ProgressMeter - chr2:29224650 24.9 9700 389.6
23:09:37.871 INFO ProgressMeter - chr2:29694875 25.1 9760 389.1
23:09:49.057 INFO ProgressMeter - chr2:42331772 25.3 9820 388.6
23:09:59.263 INFO ProgressMeter - chr2:47482885 25.4 9870 387.9
23:10:09.663 INFO ProgressMeter - chr2:61478818 25.6 9950 388.4
23:10:19.908 INFO ProgressMeter - chr2:98538889 25.8 10010 388.2
23:10:30.421 INFO ProgressMeter - chr2:108766448 26.0 10090 388.7
23:10:43.010 INFO ProgressMeter - chr2:111127738 26.2 10140 387.5
23:10:54.760 INFO ProgressMeter - chr2:113223420 26.4 10190 386.5
23:11:05.881 INFO ProgressMeter - chr2:113228500 26.6 10230 385.3
23:11:17.478 INFO ProgressMeter - chr2:113232973 26.7 10270 384.0
23:11:28.038 INFO ProgressMeter - chr2:127280602 26.9 10330 383.7
23:11:39.228 INFO ProgressMeter - chr2:140501685 27.1 10420 384.4
23:11:49.804 INFO ProgressMeter - chr2:140994021 27.3 10500 384.8
23:11:59.935 INFO ProgressMeter - chr2:157780595 27.5 10550 384.3
23:12:10.063 INFO ProgressMeter - chr2:191062760 27.6 10630 384.8
23:12:20.268 INFO ProgressMeter - chr2:203871376 27.8 10710 385.4
23:12:30.790 INFO ProgressMeter - chr2:214781435 28.0 10790 385.8
23:12:42.569 INFO ProgressMeter - chr2:222203361 28.2 10840 384.9
23:12:53.144 INFO ProgressMeter - chr2:222208967 28.3 10880 383.9
23:13:04.219 INFO ProgressMeter - chr2:222214201 28.5 10930 383.2
23:13:17.539 INFO ProgressMeter - chr2:222217845 28.7 10960 381.3
23:13:27.585 INFO ProgressMeter - chr2:224481892 28.9 11010 380.8
23:13:38.119 INFO ProgressMeter - chr2:238654902 29.1 11070 380.5
23:13:49.701 INFO ProgressMeter - chr20:32434843 29.3 11150 380.8
23:14:00.467 INFO ProgressMeter - chr20:37402590 29.5 11220 380.8
23:14:11.535 INFO ProgressMeter - chr20:42756460 29.6 11300 381.2
23:14:23.031 INFO ProgressMeter - chr20:53581534 29.8 11370 381.1
23:14:33.736 INFO ProgressMeter - chr21:15313317 30.0 11450 381.5
23:14:45.096 INFO ProgressMeter - chr21:38445449 30.2 11520 381.4
23:14:55.914 INFO ProgressMeter - chr21:41488829 30.4 11570 380.8
23:15:08.538 INFO ProgressMeter - chr21:41491289 30.6 11600 379.1
23:15:19.785 INFO ProgressMeter - chr21:41498924 30.8 11640 378.1
23:15:32.197 INFO ProgressMeter - chr21:41503558 31.0 11680 376.9
23:15:43.148 INFO ProgressMeter - chr21:43101364 31.2 11730 376.3
23:15:53.291 INFO ProgressMeter - chr22:21867353 31.3 11810 376.8
23:16:04.271 INFO ProgressMeter - chr22:23291795 31.5 11860 376.2
23:16:14.272 INFO ProgressMeter - chr22:28727505 31.7 11940 376.7
23:16:25.145 INFO ProgressMeter - chr22:29285867 31.9 12000 376.5
23:16:35.369 INFO ProgressMeter - chr22:29300309 32.0 12030 375.4
23:16:47.057 INFO ProgressMeter - chr22:41177036 32.2 12120 375.9
23:16:58.511 INFO ProgressMeter - chr3:10096324 32.4 12200 376.2
23:17:09.036 INFO ProgressMeter - chr3:12355346 32.6 12250 375.7
23:17:22.160 INFO ProgressMeter - chr3:12360860 32.8 12290 374.4
23:17:33.183 INFO ProgressMeter - chr3:12366474 33.0 12340 373.9
23:17:45.005 INFO ProgressMeter - chr3:12372173 33.2 12380 372.8
23:17:55.333 INFO ProgressMeter - chr3:12377224 33.4 12420 372.1
23:18:06.207 INFO ProgressMeter - chr3:12604237 33.6 12480 371.9
23:18:17.062 INFO ProgressMeter - chr3:38139862 33.7 12560 372.3
23:18:27.081 INFO ProgressMeter - chr3:47120245 33.9 12630 372.5
23:18:37.507 INFO ProgressMeter - chr3:49687147 34.1 12690 372.4
23:18:48.256 INFO ProgressMeter - chr3:52409712 34.3 12770 372.8
23:18:59.466 INFO ProgressMeter - chr3:70958265 34.4 12860 373.3
23:19:10.520 INFO ProgressMeter - chr3:89408065 34.6 12940 373.7
23:19:21.603 INFO ProgressMeter - chr3:136341420 34.8 13020 374.0
23:19:32.995 INFO ProgressMeter - chr3:138714704 35.0 13110 374.5
23:19:43.467 INFO ProgressMeter - chr3:142549520 35.2 13200 375.2
23:19:54.571 INFO ProgressMeter - chr3:179198966 35.4 13280 375.5
23:20:05.261 INFO ProgressMeter - chr3:183527891 35.5 13360 375.9
23:20:16.193 INFO ProgressMeter - chr3:186048175 35.7 13410 375.4
23:20:26.222 INFO ProgressMeter - chr3:189869322 35.9 13490 375.9
23:20:36.640 INFO ProgressMeter - chr4:1800243 36.1 13580 376.5
23:20:47.559 INFO ProgressMeter - chr4:20596413 36.2 13670 377.1
23:20:59.064 INFO ProgressMeter - chr4:54264917 36.4 13750 377.3
23:21:10.168 INFO ProgressMeter - chr4:54725864 36.6 13820 377.4
23:21:21.533 INFO ProgressMeter - chr4:55098695 36.8 13870 376.8
23:21:32.208 INFO ProgressMeter - chr4:80268505 37.0 13940 376.8
23:21:43.808 INFO ProgressMeter - chr4:105234280 37.2 14020 377.0
23:21:54.750 INFO ProgressMeter - chr4:105238905 37.4 14060 376.3
23:22:05.087 INFO ProgressMeter - chr4:105276276 37.5 14110 375.9
23:22:15.753 INFO ProgressMeter - chr4:152324182 37.7 14200 376.5
23:22:26.244 INFO ProgressMeter - chr4:186602901 37.9 14270 376.6
23:22:36.267 INFO ProgressMeter - chr4:186620407 38.1 14320 376.3
23:22:47.598 INFO ProgressMeter - chr4:186709449 38.2 14370 375.7
23:22:57.812 INFO ProgressMeter - chr5:38950010 38.4 14440 375.9
23:23:08.366 INFO ProgressMeter - chr5:44369931 38.6 14530 376.5
23:23:18.411 INFO ProgressMeter - chr5:58458723 38.8 14600 376.7
23:23:29.054 INFO ProgressMeter - chr5:112754871 38.9 14710 377.8
23:23:40.878 INFO ProgressMeter - chr5:112841981 39.1 14770 377.4
23:23:51.665 INFO ProgressMeter - chr5:132591875 39.3 14830 377.2
23:24:02.756 INFO ProgressMeter - chr5:142627759 39.5 14920 377.7
23:24:13.297 INFO ProgressMeter - chr5:150054320 39.7 14980 377.6
23:24:23.395 INFO ProgressMeter - chr5:150130793 39.8 15050 377.7
23:24:33.684 INFO ProgressMeter - chr5:161689070 40.0 15120 377.9
23:24:45.339 INFO ProgressMeter - chr5:177092661 40.2 15180 377.5
23:24:55.486 INFO ProgressMeter - chr5:177210352 40.4 15230 377.2
23:25:05.880 INFO ProgressMeter - chr5:177513474 40.6 15300 377.3
23:25:16.111 INFO ProgressMeter - chr6:394819 40.7 15380 377.7
23:25:26.162 INFO ProgressMeter - chr6:20481556 40.9 15460 378.1
23:25:38.518 INFO ProgressMeter - chr6:29944498 41.1 15550 378.4
23:25:48.563 INFO ProgressMeter - chr6:30713694 41.3 15610 378.3
23:25:59.230 INFO ProgressMeter - chr6:33319154 41.4 15690 378.6
23:26:09.843 INFO ProgressMeter - chr6:42021281 41.6 15790 379.4
23:26:20.057 INFO ProgressMeter - chr6:93827465 41.8 15870 379.8
23:26:31.311 INFO ProgressMeter - chr6:117317141 42.0 15940 379.7
23:26:44.058 INFO ProgressMeter - chr6:117322913 42.2 15980 378.8
23:26:55.166 INFO ProgressMeter - chr6:117329575 42.4 16030 378.3
23:27:06.069 INFO ProgressMeter - chr6:117338064 42.6 16090 378.1
23:27:17.462 INFO ProgressMeter - chr6:117394160 42.7 16150 377.8
23:27:28.883 INFO ProgressMeter - chr6:135206139 42.9 16210 377.5
23:27:46.631 INFO ProgressMeter - chr6:135213303 43.2 16260 376.1
23:27:57.094 INFO ProgressMeter - chr6:137198209 43.4 16300 375.5
23:28:08.826 INFO ProgressMeter - chr6:151365686 43.6 16370 375.4
23:28:19.516 INFO ProgressMeter - chr6:152065321 43.8 16440 375.5
23:28:30.090 INFO ProgressMeter - chr6:157206509 44.0 16500 375.4
23:28:40.158 INFO ProgressMeter - chr6:161108768 44.1 16560 375.3
23:28:51.173 INFO ProgressMeter - chr7:2945839 44.3 16650 375.8
23:29:02.872 INFO ProgressMeter - chr7:13895026 44.5 16730 375.9
23:29:14.240 INFO ProgressMeter - chr7:13909574 44.7 16770 375.2
23:29:25.711 INFO ProgressMeter - chr7:13936890 44.9 16820 374.8
23:29:37.341 INFO ProgressMeter - chr7:13943669 45.1 16870 374.3
23:29:48.512 INFO ProgressMeter - chr7:13947655 45.3 16910 373.6
23:29:58.889 INFO ProgressMeter - chr7:13951641 45.4 16940 372.8
23:30:09.515 INFO ProgressMeter - chr7:13957460 45.6 16980 372.3
23:30:20.796 INFO ProgressMeter - chr7:13962922 45.8 17020 371.6
23:30:30.830 INFO ProgressMeter - chr7:13967868 46.0 17060 371.1
23:30:41.269 INFO ProgressMeter - chr7:13973790 46.1 17110 370.8
23:30:52.889 INFO ProgressMeter - chr7:13977467 46.3 17140 369.9
23:31:03.203 INFO ProgressMeter - chr7:13981587 46.5 17180 369.4
23:31:13.659 INFO ProgressMeter - chr7:13985380 46.7 17210 368.7
23:31:25.322 INFO ProgressMeter - chr7:41690317 46.9 17240 367.8
23:31:36.980 INFO ProgressMeter - chr7:55161497 47.1 17310 367.7
23:31:49.652 INFO ProgressMeter - chr7:55170122 47.3 17360 367.2
23:32:01.236 INFO ProgressMeter - chr7:55179282 47.5 17410 366.7
23:32:11.486 INFO ProgressMeter - chr7:78019593 47.6 17460 366.5
23:32:22.478 INFO ProgressMeter - chr7:86786259 47.8 17550 366.9
23:32:32.637 INFO ProgressMeter - chr7:92823317 48.0 17620 367.1
23:32:43.009 INFO ProgressMeter - chr7:106867560 48.2 17700 367.4
23:32:53.188 INFO ProgressMeter - chr7:116758457 48.3 17760 367.4
23:33:06.072 INFO ProgressMeter - chr7:140749285 48.6 17830 367.2
23:33:17.643 INFO ProgressMeter - chr7:140792865 48.7 17890 367.0
23:33:29.143 INFO ProgressMeter - chr7:142958302 48.9 17970 367.2
23:33:39.633 INFO ProgressMeter - chr7:152162449 49.1 18050 367.5
23:33:51.345 INFO ProgressMeter - chr7:152182296 49.3 18100 367.1
23:34:02.292 INFO ProgressMeter - chr8:11748975 49.5 18190 367.5
23:34:15.101 INFO ProgressMeter - chr8:32647749 49.7 18280 367.8
23:34:25.640 INFO ProgressMeter - chr8:37697717 49.9 18330 367.5
23:34:37.129 INFO ProgressMeter - chr8:38429680 50.1 18420 367.9
23:34:48.030 INFO ProgressMeter - chr8:41941001 50.3 18480 367.7
23:34:58.711 INFO ProgressMeter - chr8:47828166 50.4 18550 367.8
23:35:08.981 INFO ProgressMeter - chr8:47953639 50.6 18640 368.4
23:35:20.248 INFO ProgressMeter - chr8:68134212 50.8 18730 368.8
23:35:32.199 INFO ProgressMeter - chr8:116857265 51.0 18820 369.1
23:35:44.793 INFO ProgressMeter - chr8:127740582 51.2 18880 368.7
23:35:55.784 INFO ProgressMeter - chr9:5024344 51.4 18960 369.0
23:36:06.518 INFO ProgressMeter - chr9:8376661 51.6 19040 369.3
23:36:18.010 INFO ProgressMeter - chr9:20456702 51.8 19110 369.2
23:36:28.988 INFO ProgressMeter - chr9:83969332 51.9 19190 369.5
23:36:43.312 INFO ProgressMeter - chr9:84742933 52.2 19250 368.9
23:36:55.117 INFO ProgressMeter - chr9:84813529 52.4 19300 368.5
23:37:06.498 INFO ProgressMeter - chr9:84862587 52.6 19330 367.8
23:37:18.159 INFO ProgressMeter - chr9:84866356 52.8 19360 367.0
23:37:28.406 INFO ProgressMeter - chr9:84875482 52.9 19400 366.5
23:37:38.532 INFO ProgressMeter - chr9:85021658 53.1 19440 366.1
23:37:49.430 INFO ProgressMeter - chr9:85026277 53.3 19470 365.4
23:38:00.729 INFO ProgressMeter - chr9:95461854 53.5 19540 365.5
23:38:10.754 INFO ProgressMeter - chr9:124119132 53.6 19610 365.6
23:38:20.960 INFO ProgressMeter - chr9:130885910 53.8 19670 365.6
23:38:32.082 INFO ProgressMeter - chr9:136496830 54.0 19730 365.4
23:38:42.852 INFO ProgressMeter - chr9:136517923 54.2 19790 365.3
23:38:53.631 INFO ProgressMeter - chrX:40063906 54.3 19900 366.2
23:39:03.691 INFO ProgressMeter - chrX:49029141 54.5 20030 367.4
23:39:13.932 INFO ProgressMeter - chrX:53405224 54.7 20150 368.5
23:39:24.623 INFO ProgressMeter - chrX:67720355 54.9 20260 369.3
23:39:35.016 INFO ProgressMeter - chrX:77599409 55.0 20410 370.8
23:39:45.504 INFO ProgressMeter - chrX:124094016 55.2 20560 372.4
23:39:55.028 INFO Mutect2 - 584044 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
4 read(s) filtered by: ReadLengthReadFilter
120 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
584168 total reads filtered out of 82352751 reads processed
23:39:55.029 INFO ProgressMeter - chrY:19773357 55.4 20676 373.4
23:39:55.029 INFO ProgressMeter - Traversal complete. Processed 20676 total regions in 55.4 minutes.
23:39:55.044 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 6.979354107000001
23:39:55.044 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 278.364860959
23:39:55.044 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 10.69 sec
23:39:55.045 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:39:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 55.38 minutes.
Runtime.totalMemory()=5343543296
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 LS0894_tumor.bam --tumor-sample LS0894 -L TST500C_manifest.bed -O LS0894.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:39:56.708 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
23:39:56.824 INFO FilterMutectCalls - ------------------------------------------------------------
23:39:56.826 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:39:56.826 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:39:56.826 INFO FilterMutectCalls - Executing as ?@nf-f204d5822f8228d75eec1754a3a11650-089b7-6r6kb on Linux v6.12.88 amd64
23:39:56.827 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:39:56.827 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:39:56 PM GMT
23:39:56.827 INFO FilterMutectCalls - ------------------------------------------------------------
23:39:56.827 INFO FilterMutectCalls - ------------------------------------------------------------
23:39:56.827 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:39:56.828 INFO FilterMutectCalls - Picard Version: 3.1.1
23:39:56.828 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:39:56.828 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:39:56.828 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:39:56.828 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:39:56.828 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:39:56.828 INFO FilterMutectCalls - Deflater: IntelDeflater
23:39:56.828 INFO FilterMutectCalls - Inflater: IntelInflater
23:39:56.828 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:39:56.828 INFO FilterMutectCalls - Requester pays: disabled
23:39:56.829 INFO FilterMutectCalls - Initializing engine
23:39:57.014 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.ZkEnyIHeTV/LS0894.mutect2.raw.vcf.gz
23:39:57.114 INFO FilterMutectCalls - Done initializing engine
23:39:57.169 INFO ProgressMeter - Starting traversal
23:39:57.169 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:39:57.171 INFO FilterMutectCalls - Starting pass 0 through the variants
23:39:58.501 INFO FilterMutectCalls - Finished pass 0 through the variants
23:39:59.555 INFO FilterMutectCalls - Starting pass 1 through the variants
23:40:00.988 INFO FilterMutectCalls - Finished pass 1 through the variants
23:40:01.223 INFO FilterMutectCalls - Starting pass 2 through the variants
23:40:02.623 INFO FilterMutectCalls - Finished pass 2 through the variants
23:40:02.624 INFO FilterMutectCalls - Starting pass 3 through the variants
23:40:03.825 INFO FilterMutectCalls - Finished pass 3 through the variants
23:40:03.832 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:40:03.833 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:40:03.833 INFO ProgressMeter - chr9:20414240 0.1 11184 100696.3
23:40:03.833 INFO ProgressMeter - Traversal complete. Processed 11184 total variants in 0.1 minutes.
23:40:03.843 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:40:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.12 minutes.
Runtime.totalMemory()=310378496
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 LS0894.mutect2.raw.vcf.gz --stats LS0894.mutect2.raw.vcf.gz.stats -O LS0894.mutect2.filtered.vcf.gz
23:40:05.041 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
23:40:05.138 INFO SelectVariants - ------------------------------------------------------------
23:40:05.140 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:40:05.140 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:40:05.140 INFO SelectVariants - Executing as ?@nf-f204d5822f8228d75eec1754a3a11650-089b7-6r6kb on Linux v6.12.88 amd64
23:40:05.140 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:40:05.141 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:40:05 PM GMT
23:40:05.141 INFO SelectVariants - ------------------------------------------------------------
23:40:05.141 INFO SelectVariants - ------------------------------------------------------------
23:40:05.141 INFO SelectVariants - HTSJDK Version: 4.1.0
23:40:05.142 INFO SelectVariants - Picard Version: 3.1.1
23:40:05.142 INFO SelectVariants - Built for Spark Version: 3.5.0
23:40:05.142 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:40:05.142 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:40:05.142 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:40:05.142 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:40:05.142 INFO SelectVariants - Deflater: IntelDeflater
23:40:05.142 INFO SelectVariants - Inflater: IntelInflater
23:40:05.142 INFO SelectVariants - GCS max retries/reopens: 20
23:40:05.142 INFO SelectVariants - Requester pays: disabled
23:40:05.142 INFO SelectVariants - Initializing engine
23:40:05.258 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.ZkEnyIHeTV/LS0894.mutect2.filtered.vcf.gz
23:40:05.362 INFO SelectVariants - Done initializing engine
23:40:05.396 INFO ProgressMeter - Starting traversal
23:40:05.396 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:40:05.467 INFO ProgressMeter - chr6:29944310 0.0 2796 2431304.3
23:40:05.468 INFO ProgressMeter - Traversal complete. Processed 2796 total variants in 0.0 minutes.
23:40:05.478 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:40:05 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 LS0894.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0894.mutect2.pass.vcf.gz