Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/71/a9471ed730e8f2c3a71777cb0a39d0/.command.sh Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.fai Downloading: s3://fsdx-algo-644019535899-us-west-2-an/TSO500/TST500C_manifest.bed Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0908/LS0908_tumor.bam.bai Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/af-only-gnomad.hg38.vcf.gz Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/af-only-gnomad.hg38.vcf.gz.tbi Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.dict Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/71/a9471ed730e8f2c3a71777cb0a39d0/.command.run Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0908/LS0908_tumor.bam ==> STAGING COMPLETE (10 inputs) 22:44:04.701 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 22:44:04.814 INFO Mutect2 - ------------------------------------------------------------ 22:44:04.816 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0 22:44:04.816 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 22:44:04.816 INFO Mutect2 - Executing as ?@nf-71a9471ed730e8f2c3a71777cb0a39d0-8ae9d-2v2mt on Linux v6.12.88 amd64 22:44:04.816 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04 22:44:04.816 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:04 PM GMT 22:44:04.816 INFO Mutect2 - ------------------------------------------------------------ 22:44:04.816 INFO Mutect2 - ------------------------------------------------------------ 22:44:04.817 INFO Mutect2 - HTSJDK Version: 4.1.0 22:44:04.817 INFO Mutect2 - Picard Version: 3.1.1 22:44:04.817 INFO Mutect2 - Built for Spark Version: 3.5.0 22:44:04.818 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 22:44:04.818 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 22:44:04.818 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 22:44:04.818 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 22:44:04.818 INFO Mutect2 - Deflater: IntelDeflater 22:44:04.818 INFO Mutect2 - Inflater: IntelInflater 22:44:04.818 INFO Mutect2 - GCS max retries/reopens: 20 22:44:04.818 INFO Mutect2 - Requester pays: disabled 22:44:04.819 INFO Mutect2 - Initializing engine WARNING: BAM index file /tmp/nxf.3plxTH3foa/LS0908_tumor.bam.bai is older than BAM /tmp/nxf.3plxTH3foa/LS0908_tumor.bam 22:44:05.014 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.3plxTH3foa/af-only-gnomad.hg38.vcf.gz 22:44:05.120 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.3plxTH3foa/TST500C_manifest.bed 22:44:05.154 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals 22:44:05.179 INFO Mutect2 - Done initializing engine 22:44:05.187 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 22:44:05.188 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 22:44:05.189 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions 22:44:05.189 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation 22:44:05.197 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 22:44:05.205 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions 22:44:05.205 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 22:44:05.205 INFO IntelPairHmm - Available threads: 384 22:44:05.206 INFO IntelPairHmm - Requested threads: 4 22:44:05.206 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 22:44:05.237 INFO ProgressMeter - Starting traversal 22:44:05.237 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 22:44:15.748 INFO ProgressMeter - chr1:11209310 0.2 90 513.8 22:44:26.852 INFO ProgressMeter - chr1:15931433 0.4 160 444.1 22:44:37.594 INFO ProgressMeter - chr1:18745296 0.5 230 426.5 22:44:47.907 INFO ProgressMeter - chr1:26775668 0.7 300 421.8 22:44:58.881 INFO ProgressMeter - chr1:39900082 0.9 380 425.0 22:45:09.402 INFO ProgressMeter - chr1:46278070 1.1 480 448.8 22:45:19.549 INFO ProgressMeter - chr1:85267772 1.2 580 468.3 22:45:30.371 INFO ProgressMeter - chr1:119920227 1.4 670 472.2 22:45:41.899 INFO ProgressMeter - chr1:156872391 1.6 750 465.5 22:45:53.039 INFO ProgressMeter - chr1:156875375 1.8 770 428.6 22:46:04.459 INFO ProgressMeter - chr1:158638213 2.0 810 407.6 22:46:15.865 INFO ProgressMeter - chr1:158685284 2.2 870 399.6 22:46:27.579 INFO ProgressMeter - chr1:179110280 2.4 940 396.2 22:46:38.306 INFO ProgressMeter - chr1:204457035 2.6 1010 395.9 22:46:48.648 INFO ProgressMeter - chr1:204549393 2.7 1070 392.9 22:47:00.033 INFO ProgressMeter - chr1:226386324 2.9 1140 391.3 22:47:12.421 INFO ProgressMeter - chr1:243502773 3.1 1200 384.6 22:47:22.455 INFO ProgressMeter - chr10:27005572 3.3 1250 380.3 22:47:33.867 INFO ProgressMeter - chr10:32011443 3.5 1320 379.6 22:47:45.906 INFO ProgressMeter - chr10:43114174 3.7 1400 380.7 22:47:56.330 INFO ProgressMeter - chr10:43127448 3.9 1450 376.5 22:48:07.327 INFO ProgressMeter - chr10:68681397 4.0 1510 374.2 22:48:19.034 INFO ProgressMeter - chr10:101770750 4.2 1600 378.3 22:48:29.277 INFO ProgressMeter - chr10:110593052 4.4 1670 379.5 22:48:39.805 INFO ProgressMeter - chr10:121480811 4.6 1720 375.9 22:48:51.134 INFO ProgressMeter - chr10:121530311 4.8 1770 371.5 22:49:01.816 INFO ProgressMeter - chr11:32430528 4.9 1850 374.3 22:49:12.211 INFO ProgressMeter - chr11:69650274 5.1 1950 381.1 22:49:22.736 INFO ProgressMeter - chr11:69769528 5.3 2030 383.6 22:49:34.856 INFO ProgressMeter - chr11:69811742 5.5 2080 378.6 22:49:45.225 INFO ProgressMeter - chr11:76546209 5.7 2140 377.7 22:49:55.303 INFO ProgressMeter - chr11:77429651 5.8 2210 378.8 22:50:10.037 INFO ProgressMeter - chr11:102328895 6.1 2300 378.3 22:50:21.226 INFO ProgressMeter - chr11:118472083 6.3 2400 383.0 22:50:32.067 INFO ProgressMeter - chr11:118505029 6.4 2460 381.6 22:50:42.798 INFO ProgressMeter - chr11:125620963 6.6 2510 378.8 22:50:53.100 INFO ProgressMeter - chr11:128460022 6.8 2570 378.1 22:51:05.382 INFO ProgressMeter - chr11:128812859 7.0 2630 375.6 22:51:15.433 INFO ProgressMeter - chr12:4370492 7.2 2710 378.0 22:51:25.777 INFO ProgressMeter - chr12:4444131 7.3 2780 378.6 22:51:36.703 INFO ProgressMeter - chr12:11853706 7.5 2850 378.8 22:51:47.081 INFO ProgressMeter - chr12:11859303 7.7 2890 375.5 22:51:57.862 INFO ProgressMeter - chr12:11865071 7.9 2930 372.0 22:52:08.232 INFO ProgressMeter - chr12:12717882 8.0 2970 368.9 22:52:19.488 INFO ProgressMeter - chr12:40469175 8.2 3070 372.7 22:52:29.875 INFO ProgressMeter - chr12:49031473 8.4 3140 373.3 22:52:40.725 INFO ProgressMeter - chr12:49040082 8.6 3180 370.1 22:52:50.983 INFO ProgressMeter - chr12:49054898 8.8 3240 369.8 22:53:01.752 INFO ProgressMeter - chr12:56101648 8.9 3330 372.4 22:53:11.865 INFO ProgressMeter - chr12:57471382 9.1 3390 372.1 22:53:22.106 INFO ProgressMeter - chr12:68836415 9.3 3480 375.0 22:53:33.299 INFO ProgressMeter - chr12:114672288 9.5 3560 376.0 22:53:44.574 INFO ProgressMeter - chr12:132657347 9.7 3640 377.0 22:53:56.470 INFO ProgressMeter - chr13:21672321 9.9 3710 376.5 22:54:06.650 INFO ProgressMeter - chr13:28034299 10.0 3790 378.1 22:54:17.775 INFO ProgressMeter - chr13:28387655 10.2 3850 377.1 22:54:28.039 INFO ProgressMeter - chr13:32332270 10.4 3900 375.7 22:54:39.391 INFO ProgressMeter - chr13:32363177 10.6 3950 373.7 22:54:50.110 INFO ProgressMeter - chr13:72772691 10.7 4030 375.0 22:55:01.637 INFO ProgressMeter - chr13:102862328 10.9 4100 374.8 22:55:12.327 INFO ProgressMeter - chr13:113300127 11.1 4160 374.2 22:55:22.331 INFO ProgressMeter - chr14:23183020 11.3 4200 372.2 22:55:32.423 INFO ProgressMeter - chr14:37596003 11.5 4280 373.7 22:55:43.456 INFO ProgressMeter - chr14:81143814 11.6 4350 373.8 22:55:53.466 INFO ProgressMeter - chr14:102085756 11.8 4420 374.5 22:56:05.003 INFO ProgressMeter - chr15:34346802 12.0 4470 372.6 22:56:16.327 INFO ProgressMeter - chr15:41669604 12.2 4520 371.0 22:56:27.706 INFO ProgressMeter - chr15:41767063 12.4 4580 370.1 22:56:37.914 INFO ProgressMeter - chr15:73703957 12.5 4670 372.3 22:56:48.843 INFO ProgressMeter - chr15:89276709 12.7 4740 372.4 22:56:58.891 INFO ProgressMeter - chr15:90784919 12.9 4820 373.8 22:57:09.027 INFO ProgressMeter - chr15:98891323 13.1 4900 375.1 22:57:20.028 INFO ProgressMeter - chr16:2050468 13.2 4960 374.4 22:57:31.649 INFO ProgressMeter - chr16:2173479 13.4 5020 373.5 22:57:42.531 INFO ProgressMeter - chr16:3597377 13.6 5090 373.7 22:57:55.250 INFO ProgressMeter - chr16:3728532 13.8 5110 369.4 22:58:06.037 INFO ProgressMeter - chr16:5556153 14.0 5170 368.9 22:58:16.828 INFO ProgressMeter - chr16:11258844 14.2 5220 367.8 22:58:27.016 INFO ProgressMeter - chr16:30116666 14.4 5280 367.6 22:58:37.211 INFO ProgressMeter - chr16:56834368 14.5 5350 368.1 22:58:48.508 INFO ProgressMeter - chr16:68833350 14.7 5410 367.5 22:58:58.877 INFO ProgressMeter - chr16:72795966 14.9 5440 365.2 22:59:10.014 INFO ProgressMeter - chr16:72958360 15.1 5480 363.4 22:59:20.487 INFO ProgressMeter - chr16:81937836 15.3 5540 363.2 22:59:31.284 INFO ProgressMeter - chr16:89284636 15.4 5590 362.2 22:59:41.839 INFO ProgressMeter - chr17:7672346 15.6 5690 364.5 22:59:52.779 INFO ProgressMeter - chr17:16032294 15.8 5790 366.6 23:00:03.801 INFO ProgressMeter - chr17:31200420 16.0 5890 368.7 23:00:14.051 INFO ProgressMeter - chr17:31937361 16.1 5960 369.1 23:00:24.601 INFO ProgressMeter - chr17:39509703 16.3 6020 368.8 23:00:35.108 INFO ProgressMeter - chr17:39710612 16.5 6060 367.3 23:00:46.118 INFO ProgressMeter - chr17:39727844 16.7 6100 365.7 23:00:56.981 INFO ProgressMeter - chr17:42211982 16.9 6170 365.9 23:01:08.952 INFO ProgressMeter - chr17:43081530 17.1 6260 366.9 23:01:19.753 INFO ProgressMeter - chr17:43104924 17.2 6300 365.4 23:01:29.956 INFO ProgressMeter - chr17:43536497 17.4 6360 365.3 23:01:42.911 INFO ProgressMeter - chr17:43544126 17.6 6410 363.6 23:01:53.594 INFO ProgressMeter - chr17:59893183 17.8 6500 365.0 23:02:03.993 INFO ProgressMeter - chr17:61693428 18.0 6580 366.0 23:02:14.645 INFO ProgressMeter - chr17:76737055 18.2 6670 367.4 23:02:24.925 INFO ProgressMeter - chr18:42057881 18.3 6780 369.9 23:02:35.134 INFO ProgressMeter - chr18:51049293 18.5 6830 369.2 23:02:45.291 INFO ProgressMeter - chr19:2213944 18.7 6940 371.8 23:02:55.297 INFO ProgressMeter - chr19:5231308 18.8 7040 373.8 23:03:06.008 INFO ProgressMeter - chr19:10160382 19.0 7130 375.0 23:03:17.078 INFO ProgressMeter - chr19:14517310 19.2 7230 376.6 23:03:27.586 INFO ProgressMeter - chr19:15253557 19.4 7320 377.9 23:03:38.460 INFO ProgressMeter - chr19:29816038 19.6 7430 380.0 23:03:49.542 INFO ProgressMeter - chr19:35733353 19.7 7530 381.5 23:04:01.014 INFO ProgressMeter - chr19:41260822 19.9 7630 382.8 23:04:11.057 INFO ProgressMeter - chr19:45362973 20.1 7710 383.6 23:04:21.577 INFO ProgressMeter - chr19:50407325 20.3 7810 385.3 23:04:32.372 INFO ProgressMeter - chr2:15945491 20.5 7880 385.3 23:04:42.577 INFO ProgressMeter - chr2:25282085 20.6 7950 385.5 23:04:54.243 INFO ProgressMeter - chr2:29222482 20.8 8010 384.8 23:05:05.482 INFO ProgressMeter - chr2:29251103 21.0 8050 383.3 23:05:17.625 INFO ProgressMeter - chr2:42331816 21.2 8120 382.9 23:05:27.713 INFO ProgressMeter - chr2:47799528 21.4 8170 382.2 23:05:40.805 INFO ProgressMeter - chr2:96253997 21.6 8260 382.5 23:05:51.162 INFO ProgressMeter - chr2:108765562 21.8 8340 383.2 23:06:03.435 INFO ProgressMeter - chr2:111128440 22.0 8390 381.9 23:06:16.552 INFO ProgressMeter - chr2:113225697 22.2 8440 380.4 23:06:28.920 INFO ProgressMeter - chr2:113231059 22.4 8470 378.2 23:06:41.232 INFO ProgressMeter - chr2:113234835 22.6 8500 376.1 23:06:51.527 INFO ProgressMeter - chr2:140335740 22.8 8570 376.3 23:07:01.773 INFO ProgressMeter - chr2:141013554 22.9 8650 377.0 23:07:12.985 INFO ProgressMeter - chr2:189854837 23.1 8730 377.4 23:07:23.426 INFO ProgressMeter - chr2:201285114 23.3 8820 378.5 23:07:35.111 INFO ProgressMeter - chr2:219575426 23.5 8910 379.2 23:07:45.536 INFO ProgressMeter - chr2:222205544 23.7 8950 378.1 23:07:56.343 INFO ProgressMeter - chr2:222212183 23.9 8990 376.9 23:08:06.845 INFO ProgressMeter - chr2:222217575 24.0 9020 375.4 23:08:17.075 INFO ProgressMeter - chr2:224513522 24.2 9080 375.2 23:08:28.172 INFO ProgressMeter - chr20:9644123 24.4 9150 375.3 23:08:39.464 INFO ProgressMeter - chr20:32780316 24.6 9200 374.4 23:08:50.226 INFO ProgressMeter - chr20:41116276 24.7 9270 374.5 23:09:00.818 INFO ProgressMeter - chr20:47627676 24.9 9330 374.3 23:09:12.495 INFO ProgressMeter - chr20:53582744 25.1 9380 373.4 23:09:23.139 INFO ProgressMeter - chr20:63701828 25.3 9440 373.1 23:09:35.243 INFO ProgressMeter - chr21:38445516 25.5 9510 372.9 23:09:48.848 INFO ProgressMeter - chr21:41491047 25.7 9570 372.0 23:09:59.290 INFO ProgressMeter - chr21:41498566 25.9 9600 370.6 23:10:11.396 INFO ProgressMeter - chr21:41506821 26.1 9650 369.7 23:10:21.431 INFO ProgressMeter - chr22:23268406 26.3 9740 370.8 23:10:32.080 INFO ProgressMeter - chr22:28694030 26.4 9800 370.5 23:10:42.846 INFO ProgressMeter - chr22:29286552 26.6 9890 371.4 23:10:53.369 INFO ProgressMeter - chr22:41151831 26.8 9970 372.0 23:11:05.167 INFO ProgressMeter - chr3:12353944 27.0 10070 373.0 23:11:16.043 INFO ProgressMeter - chr3:12360936 27.2 10110 372.0 23:11:27.332 INFO ProgressMeter - chr3:12369672 27.4 10170 371.6 23:11:37.539 INFO ProgressMeter - chr3:12378115 27.5 10220 371.1 23:11:48.072 INFO ProgressMeter - chr3:36993642 27.7 10300 371.7 23:11:58.716 INFO ProgressMeter - chr3:47122409 27.9 10390 372.5 23:12:09.493 INFO ProgressMeter - chr3:52402600 28.1 10480 373.3 23:12:20.218 INFO ProgressMeter - chr3:70965888 28.2 10570 374.2 23:12:31.628 INFO ProgressMeter - chr3:128486299 28.4 10660 374.8 23:12:41.951 INFO ProgressMeter - chr3:138657688 28.6 10730 375.0 23:12:52.982 INFO ProgressMeter - chr3:142547723 28.8 10820 375.7 23:13:03.968 INFO ProgressMeter - chr3:179224079 29.0 10910 376.5 23:13:14.684 INFO ProgressMeter - chr3:185482353 29.2 10980 376.6 23:13:24.721 INFO ProgressMeter - chr3:187728461 29.3 11040 376.5 23:13:35.035 INFO ProgressMeter - chr3:196077062 29.5 11120 377.0 23:13:46.354 INFO ProgressMeter - chr4:24556369 29.7 11240 378.6 23:13:56.568 INFO ProgressMeter - chr4:54707096 29.9 11330 379.5 23:14:07.400 INFO ProgressMeter - chr4:55101895 30.0 11380 378.9 23:14:18.080 INFO ProgressMeter - chr4:80287801 30.2 11480 380.0 23:14:28.631 INFO ProgressMeter - chr4:105241025 30.4 11550 380.1 23:14:39.354 INFO ProgressMeter - chr4:152322919 30.6 11650 381.1 23:14:50.339 INFO ProgressMeter - chr4:186618772 30.8 11730 381.4 23:15:01.176 INFO ProgressMeter - chr5:233582 30.9 11800 381.5 23:15:11.964 INFO ProgressMeter - chr5:44331940 31.1 11900 382.5 23:15:22.767 INFO ProgressMeter - chr5:58458397 31.3 11980 382.8 23:15:33.191 INFO ProgressMeter - chr5:112821894 31.5 12090 384.2 23:15:43.423 INFO ProgressMeter - chr5:122403791 31.6 12140 383.7 23:15:53.436 INFO ProgressMeter - chr5:138904347 31.8 12210 383.9 23:16:05.155 INFO ProgressMeter - chr5:149496841 32.0 12270 383.5 23:16:15.273 INFO ProgressMeter - chr5:150123040 32.2 12330 383.3 23:16:25.357 INFO ProgressMeter - chr5:150404480 32.3 12380 382.9 23:16:36.043 INFO ProgressMeter - chr5:177090743 32.5 12440 382.6 23:16:47.472 INFO ProgressMeter - chr5:177135237 32.7 12480 381.6 23:16:58.393 INFO ProgressMeter - chr5:177294300 32.9 12530 381.0 23:17:09.715 INFO ProgressMeter - chr5:180629941 33.1 12600 381.0 23:17:20.306 INFO ProgressMeter - chr6:20488041 33.3 12690 381.6 23:17:31.169 INFO ProgressMeter - chr6:29945057 33.4 12760 381.7 23:17:41.804 INFO ProgressMeter - chr6:32196035 33.6 12820 381.4 23:17:52.365 INFO ProgressMeter - chr6:33321099 33.8 12880 381.2 23:18:02.527 INFO ProgressMeter - chr6:43777555 34.0 12980 382.3 23:18:13.571 INFO ProgressMeter - chr6:111700102 34.1 13060 382.6 23:18:26.550 INFO ProgressMeter - chr6:117322487 34.4 13110 381.6 23:18:36.945 INFO ProgressMeter - chr6:117330749 34.5 13150 380.8 23:18:49.001 INFO ProgressMeter - chr6:117340426 34.7 13210 380.4 23:18:59.315 INFO ProgressMeter - chr6:135200405 34.9 13280 380.5 23:19:10.303 INFO ProgressMeter - chr6:135208317 35.1 13320 379.7 23:19:25.391 INFO ProgressMeter - chr6:135212911 35.3 13350 377.8 23:19:36.874 INFO ProgressMeter - chr6:137198029 35.5 13390 376.9 23:19:48.993 INFO ProgressMeter - chr6:151366393 35.7 13450 376.4 23:20:00.331 INFO ProgressMeter - chr6:156778343 35.9 13510 376.1 23:20:10.482 INFO ProgressMeter - chr6:157207689 36.1 13560 375.8 23:20:20.663 INFO ProgressMeter - chr6:163455277 36.3 13630 375.9 23:20:32.847 INFO ProgressMeter - chr7:13892248 36.5 13710 376.0 23:20:43.246 INFO ProgressMeter - chr7:13908517 36.6 13750 375.3 23:20:53.839 INFO ProgressMeter - chr7:13935575 36.8 13780 374.4 23:21:05.886 INFO ProgressMeter - chr7:13944859 37.0 13830 373.7 23:21:16.183 INFO ProgressMeter - chr7:13949043 37.2 13860 372.8 23:21:28.216 INFO ProgressMeter - chr7:13952873 37.4 13890 371.6 23:21:40.657 INFO ProgressMeter - chr7:13959158 37.6 13930 370.6 23:21:50.963 INFO ProgressMeter - chr7:13963179 37.8 13960 369.7 23:22:01.647 INFO ProgressMeter - chr7:13968078 37.9 13990 368.7 23:22:11.736 INFO ProgressMeter - chr7:13971083 38.1 14010 367.6 23:22:27.163 INFO ProgressMeter - chr7:13977277 38.4 14050 366.2 23:22:39.987 INFO ProgressMeter - chr7:13983704 38.6 14100 365.5 23:22:55.468 INFO ProgressMeter - chr7:13989266 38.8 14130 363.8 23:23:06.069 INFO ProgressMeter - chr7:55153449 39.0 14190 363.7 23:23:16.285 INFO ProgressMeter - chr7:55167932 39.2 14230 363.2 23:23:27.714 INFO ProgressMeter - chr7:55176454 39.4 14260 362.2 23:23:38.746 INFO ProgressMeter - chr7:55180501 39.6 14300 361.5 23:23:49.135 INFO ProgressMeter - chr7:78160274 39.7 14350 361.2 23:24:00.320 INFO ProgressMeter - chr7:92615418 39.9 14420 361.2 23:24:10.882 INFO ProgressMeter - chr7:102201350 40.1 14490 361.4 23:24:21.241 INFO ProgressMeter - chr7:106883031 40.3 14550 361.3 23:24:32.211 INFO ProgressMeter - chr7:116795653 40.4 14610 361.2 23:24:42.445 INFO ProgressMeter - chr7:140787546 40.6 14660 360.9 23:24:53.403 INFO ProgressMeter - chr7:140808890 40.8 14710 360.5 23:25:04.593 INFO ProgressMeter - chr7:148832632 41.0 14790 360.8 23:25:16.616 INFO ProgressMeter - chr7:152177020 41.2 14850 360.5 23:25:27.611 INFO ProgressMeter - chr7:152273703 41.4 14910 360.4 23:25:39.618 INFO ProgressMeter - chr8:32647945 41.6 15010 361.1 23:25:50.068 INFO ProgressMeter - chr8:37842324 41.7 15090 361.5 23:26:01.948 INFO ProgressMeter - chr8:41937379 41.9 15160 361.4 23:26:12.437 INFO ProgressMeter - chr8:47826776 42.1 15220 361.3 23:26:22.823 INFO ProgressMeter - chr8:47955872 42.3 15300 361.8 23:26:33.155 INFO ProgressMeter - chr8:68146261 42.5 15370 361.9 23:26:43.786 INFO ProgressMeter - chr8:116856253 42.6 15440 362.1 23:26:55.163 INFO ProgressMeter - chr8:144511429 42.8 15510 362.1 23:27:06.282 INFO ProgressMeter - chr9:5549333 43.0 15600 362.6 23:27:16.763 INFO ProgressMeter - chr9:21974702 43.2 15680 363.0 23:27:27.140 INFO ProgressMeter - chr9:84710635 43.4 15780 363.9 23:27:38.659 INFO ProgressMeter - chr9:84812613 43.6 15820 363.2 23:27:49.576 INFO ProgressMeter - chr9:84862873 43.7 15850 362.4 23:28:01.633 INFO ProgressMeter - chr9:84873379 43.9 15890 361.6 23:28:14.448 INFO ProgressMeter - chr9:85024520 44.2 15940 361.0 23:28:24.734 INFO ProgressMeter - chr9:95117313 44.3 15990 360.7 23:28:35.096 INFO ProgressMeter - chr9:125149671 44.5 16080 361.4 23:28:45.712 INFO ProgressMeter - chr9:132905879 44.7 16150 361.5 23:28:56.086 INFO ProgressMeter - chr9:136518186 44.8 16230 361.9 23:29:06.976 INFO ProgressMeter - chrX:44873550 45.0 16330 362.7 23:29:17.307 INFO ProgressMeter - chrX:49029004 45.2 16430 363.5 23:29:29.020 INFO ProgressMeter - chrX:49038705 45.4 16490 363.2 23:29:39.144 INFO ProgressMeter - chrX:53411740 45.6 16570 363.7 23:29:51.039 INFO ProgressMeter - chrX:67546022 45.8 16620 363.2 23:30:02.209 INFO ProgressMeter - chrX:71125661 45.9 16700 363.4 23:30:12.794 INFO ProgressMeter - chrX:71383107 46.1 16760 363.4 23:30:24.256 INFO ProgressMeter - chrX:77681943 46.3 16840 363.6 23:30:35.318 INFO ProgressMeter - chrX:124037525 46.5 16920 363.9 23:30:46.368 INFO ProgressMeter - chrX:130021027 46.7 16990 363.9 23:30:50.243 INFO Mutect2 - 775812 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 1 read(s) filtered by: ReadLengthReadFilter 71 read(s) filtered by: GoodCigarReadFilter 0 read(s) filtered by: WellformedReadFilter 775884 total reads filtered out of 89367480 reads processed 23:30:50.243 INFO ProgressMeter - chrY:19742699 46.8 17057 364.9 23:30:50.243 INFO ProgressMeter - Traversal complete. Processed 17057 total regions in 46.8 minutes. 23:30:50.259 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 5.680769698000001 23:30:50.259 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 257.748803448 23:30:50.259 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 8.86 sec 23:30:50.260 INFO Mutect2 - Shutting down engine [June 8, 2026 at 11:30:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 46.76 minutes. Runtime.totalMemory()=3590324224 Tool returned: SUCCESS 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 LS0908_tumor.bam --tumor-sample LS0908 -L TST500C_manifest.bed -O LS0908.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz 23:30:51.698 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 23:30:51.815 INFO FilterMutectCalls - ------------------------------------------------------------ 23:30:51.818 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0 23:30:51.818 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/ 23:30:51.818 INFO FilterMutectCalls - Executing as ?@nf-71a9471ed730e8f2c3a71777cb0a39d0-8ae9d-2v2mt on Linux v6.12.88 amd64 23:30:51.818 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04 23:30:51.818 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:30:51 PM GMT 23:30:51.819 INFO FilterMutectCalls - ------------------------------------------------------------ 23:30:51.819 INFO FilterMutectCalls - ------------------------------------------------------------ 23:30:51.819 INFO FilterMutectCalls - HTSJDK Version: 4.1.0 23:30:51.819 INFO FilterMutectCalls - Picard Version: 3.1.1 23:30:51.819 INFO FilterMutectCalls - Built for Spark Version: 3.5.0 23:30:51.819 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2 23:30:51.819 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 23:30:51.820 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 23:30:51.820 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 23:30:51.820 INFO FilterMutectCalls - Deflater: IntelDeflater 23:30:51.820 INFO FilterMutectCalls - Inflater: IntelInflater 23:30:51.820 INFO FilterMutectCalls - GCS max retries/reopens: 20 23:30:51.820 INFO FilterMutectCalls - Requester pays: disabled 23:30:51.820 INFO FilterMutectCalls - Initializing engine 23:30:51.980 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.3plxTH3foa/LS0908.mutect2.raw.vcf.gz 23:30:52.090 INFO FilterMutectCalls - Done initializing engine 23:30:52.146 INFO ProgressMeter - Starting traversal 23:30:52.146 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 23:30:52.148 INFO FilterMutectCalls - Starting pass 0 through the variants 23:30:53.163 INFO FilterMutectCalls - Finished pass 0 through the variants 23:30:58.088 INFO FilterMutectCalls - Starting pass 1 through the variants 23:30:59.404 INFO FilterMutectCalls - Finished pass 1 through the variants 23:31:00.251 INFO FilterMutectCalls - Starting pass 2 through the variants 23:31:01.558 INFO FilterMutectCalls - Finished pass 2 through the variants 23:31:01.560 INFO FilterMutectCalls - Starting pass 3 through the variants 23:31:02.313 INFO ProgressMeter - chr4:186617788 0.2 9000 53133.9 23:31:02.709 INFO FilterMutectCalls - Finished pass 3 through the variants 23:31:02.715 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter 23:31:02.715 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter 23:31:02.715 INFO ProgressMeter - chr4:186617788 0.2 9888 56139.3 23:31:02.715 INFO ProgressMeter - Traversal complete. Processed 9888 total variants in 0.2 minutes. 23:31:02.727 INFO FilterMutectCalls - Shutting down engine [June 8, 2026 at 11:31:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.18 minutes. Runtime.totalMemory()=301989888 Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R hg38.fa -V LS0908.mutect2.raw.vcf.gz --stats LS0908.mutect2.raw.vcf.gz.stats -O LS0908.mutect2.filtered.vcf.gz 23:31:03.991 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 23:31:04.095 INFO SelectVariants - ------------------------------------------------------------ 23:31:04.101 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0 23:31:04.101 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 23:31:04.101 INFO SelectVariants - Executing as ?@nf-71a9471ed730e8f2c3a71777cb0a39d0-8ae9d-2v2mt on Linux v6.12.88 amd64 23:31:04.101 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04 23:31:04.101 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:31:03 PM GMT 23:31:04.101 INFO SelectVariants - ------------------------------------------------------------ 23:31:04.101 INFO SelectVariants - ------------------------------------------------------------ 23:31:04.102 INFO SelectVariants - HTSJDK Version: 4.1.0 23:31:04.102 INFO SelectVariants - Picard Version: 3.1.1 23:31:04.102 INFO SelectVariants - Built for Spark Version: 3.5.0 23:31:04.102 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 23:31:04.102 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 23:31:04.103 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 23:31:04.103 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 23:31:04.103 INFO SelectVariants - Deflater: IntelDeflater 23:31:04.103 INFO SelectVariants - Inflater: IntelInflater 23:31:04.103 INFO SelectVariants - GCS max retries/reopens: 20 23:31:04.103 INFO SelectVariants - Requester pays: disabled 23:31:04.103 INFO SelectVariants - Initializing engine 23:31:04.273 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.3plxTH3foa/LS0908.mutect2.filtered.vcf.gz 23:31:04.390 INFO SelectVariants - Done initializing engine 23:31:04.427 INFO ProgressMeter - Starting traversal 23:31:04.427 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 23:31:04.519 INFO ProgressMeter - chr7:13944217 0.0 2472 1648000.0 23:31:04.519 INFO ProgressMeter - Traversal complete. Processed 2472 total variants in 0.0 minutes. 23:31:04.531 INFO SelectVariants - Shutting down engine [June 8, 2026 at 11:31:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=327155712 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 LS0908.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0908.mutect2.pass.vcf.gz