Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0914/LS0914_tumor.bam
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/8a/097e0e1e4a71bf08919c968045a598/.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://fsdx-algo-644019535899-us-west-2-an/references/af-only-gnomad.hg38.vcf.gz
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0914/LS0914_tumor.bam.bai
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/8a/097e0e1e4a71bf08919c968045a598/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:33.809 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
22:44:33.909 INFO Mutect2 - ------------------------------------------------------------
22:44:33.911 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:33.911 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:33.911 INFO Mutect2 - Executing as ?@nf-8a097e0e1e4a71bf08919c968045a598-fa18b-ssznh on Linux v6.12.88 amd64
22:44:33.912 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:33.912 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:33 PM GMT
22:44:33.912 INFO Mutect2 - ------------------------------------------------------------
22:44:33.912 INFO Mutect2 - ------------------------------------------------------------
22:44:33.912 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:33.912 INFO Mutect2 - Picard Version: 3.1.1
22:44:33.912 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:33.913 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:33.913 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:33.913 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:33.913 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:33.913 INFO Mutect2 - Deflater: IntelDeflater
22:44:33.913 INFO Mutect2 - Inflater: IntelInflater
22:44:33.913 INFO Mutect2 - GCS max retries/reopens: 20
22:44:33.913 INFO Mutect2 - Requester pays: disabled
22:44:33.914 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.FCgmrvIv93/LS0914_tumor.bam.bai is older than BAM /tmp/nxf.FCgmrvIv93/LS0914_tumor.bam
22:44:34.069 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.FCgmrvIv93/af-only-gnomad.hg38.vcf.gz
22:44:34.189 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.FCgmrvIv93/TST500C_manifest.bed
22:44:34.224 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:34.251 INFO Mutect2 - Done initializing engine
22:44:34.261 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
22:44:34.262 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
22:44:34.263 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:34.263 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:34.272 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
22:44:34.280 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:34.280 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:34.280 INFO IntelPairHmm - Available threads: 384
22:44:34.280 INFO IntelPairHmm - Requested threads: 4
22:44:34.280 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:34.313 INFO ProgressMeter - Starting traversal
22:44:34.314 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:44.419 INFO ProgressMeter - chr1:11107483 0.2 60 356.3
22:44:55.928 INFO ProgressMeter - chr1:11258483 0.4 140 388.7
22:45:06.609 INFO ProgressMeter - chr1:15932837 0.5 190 353.0
22:45:18.824 INFO ProgressMeter - chr1:18745699 0.7 260 350.5
22:45:29.336 INFO ProgressMeter - chr1:26773800 0.9 320 349.0
22:45:39.406 INFO ProgressMeter - chr1:39891449 1.1 380 350.3
22:45:50.053 INFO ProgressMeter - chr1:39904253 1.3 430 340.6
22:46:01.266 INFO ProgressMeter - chr1:46277815 1.4 510 351.9
22:46:11.385 INFO ProgressMeter - chr1:77956679 1.6 590 364.7
22:46:22.640 INFO ProgressMeter - chr1:117627377 1.8 680 376.6
22:46:33.540 INFO ProgressMeter - chr1:119959390 2.0 740 372.4
22:46:47.938 INFO ProgressMeter - chr1:156875779 2.2 800 359.2
22:46:58.131 INFO ProgressMeter - chr1:158667856 2.4 870 363.0
22:47:10.028 INFO ProgressMeter - chr1:179108650 2.6 960 369.9
22:47:20.280 INFO ProgressMeter - chr1:204464448 2.8 1050 379.6
22:47:31.067 INFO ProgressMeter - chr1:206474991 2.9 1120 380.2
22:47:42.222 INFO ProgressMeter - chr1:241504191 3.1 1210 386.4
22:47:52.581 INFO ProgressMeter - chr1:243504304 3.3 1250 378.3
22:48:02.910 INFO ProgressMeter - chr10:27034775 3.5 1310 376.8
22:48:13.891 INFO ProgressMeter - chr10:32033843 3.7 1380 377.1
22:48:24.594 INFO ProgressMeter - chr10:43114968 3.8 1440 375.2
22:48:35.615 INFO ProgressMeter - chr10:62000156 4.0 1500 373.0
22:48:46.831 INFO ProgressMeter - chr10:68667043 4.2 1550 368.3
22:48:57.312 INFO ProgressMeter - chr10:87961076 4.4 1630 371.9
22:49:07.646 INFO ProgressMeter - chr10:102593634 4.6 1700 373.2
22:49:18.417 INFO ProgressMeter - chr10:113150981 4.7 1770 373.8
22:49:28.431 INFO ProgressMeter - chr10:121487352 4.9 1810 369.2
22:49:39.559 INFO ProgressMeter - chr11:22624986 5.1 1890 371.5
22:49:49.657 INFO ProgressMeter - chr11:67434375 5.3 1980 376.7
22:49:59.733 INFO ProgressMeter - chr11:69701108 5.4 2050 378.0
22:50:11.294 INFO ProgressMeter - chr11:69777335 5.6 2120 377.5
22:50:22.545 INFO ProgressMeter - chr11:69814632 5.8 2150 370.4
22:50:32.905 INFO ProgressMeter - chr11:76535893 6.0 2200 368.1
22:50:44.661 INFO ProgressMeter - chr11:77415689 6.2 2270 367.8
22:50:56.134 INFO ProgressMeter - chr11:102229876 6.4 2360 370.9
22:51:07.233 INFO ProgressMeter - chr11:108271249 6.5 2400 366.5
22:51:17.911 INFO ProgressMeter - chr11:118472608 6.7 2480 368.7
22:51:31.403 INFO ProgressMeter - chr11:118505475 7.0 2540 365.4
22:51:43.411 INFO ProgressMeter - chr11:125629389 7.2 2590 362.2
22:51:54.988 INFO ProgressMeter - chr11:128461263 7.3 2650 360.8
22:52:05.354 INFO ProgressMeter - chr12:295571 7.5 2710 360.5
22:52:16.664 INFO ProgressMeter - chr12:4371515 7.7 2790 362.1
22:52:27.848 INFO ProgressMeter - chr12:4442023 7.9 2850 361.1
22:52:40.137 INFO ProgressMeter - chr12:11752429 8.1 2920 360.6
22:52:50.578 INFO ProgressMeter - chr12:11858549 8.3 2960 357.9
22:53:02.406 INFO ProgressMeter - chr12:11861936 8.5 2990 353.1
22:53:12.493 INFO ProgressMeter - chr12:11867274 8.6 3030 350.8
22:53:22.821 INFO ProgressMeter - chr12:18399657 8.8 3080 349.7
22:53:33.580 INFO ProgressMeter - chr12:40469213 9.0 3160 351.6
22:53:44.612 INFO ProgressMeter - chr12:49029214 9.2 3230 352.2
22:53:54.842 INFO ProgressMeter - chr12:49038030 9.3 3270 350.0
22:54:05.563 INFO ProgressMeter - chr12:49053565 9.5 3340 350.8
22:54:16.491 INFO ProgressMeter - chr12:56099836 9.7 3420 352.5
22:54:27.777 INFO ProgressMeter - chr12:57471501 9.9 3480 351.8
22:54:39.163 INFO ProgressMeter - chr12:68838080 10.1 3580 355.1
22:54:49.588 INFO ProgressMeter - chr12:114674581 10.3 3660 356.9
22:54:59.869 INFO ProgressMeter - chr12:132643222 10.4 3730 357.8
22:55:09.920 INFO ProgressMeter - chr13:20988847 10.6 3800 358.7
22:55:21.098 INFO ProgressMeter - chr13:28035493 10.8 3880 359.9
22:55:32.443 INFO ProgressMeter - chr13:28387396 11.0 3940 359.2
22:55:42.746 INFO ProgressMeter - chr13:32329441 11.1 3990 358.2
22:55:53.561 INFO ProgressMeter - chr13:32354859 11.3 4040 356.9
22:56:03.790 INFO ProgressMeter - chr13:72760527 11.5 4120 358.5
22:56:14.255 INFO ProgressMeter - chr13:102852130 11.7 4200 360.0
22:56:25.330 INFO ProgressMeter - chr13:113305296 11.9 4280 361.2
22:56:36.353 INFO ProgressMeter - chr14:37584551 12.0 4340 360.6
22:56:48.358 INFO ProgressMeter - chr14:37598103 12.2 4410 360.5
22:56:59.237 INFO ProgressMeter - chr14:95096064 12.4 4480 360.8
22:57:10.411 INFO ProgressMeter - chr14:104772876 12.6 4550 361.1
22:57:21.781 INFO ProgressMeter - chr15:34355937 12.8 4610 360.4
22:57:32.984 INFO ProgressMeter - chr15:41739983 13.0 4670 359.8
22:57:43.233 INFO ProgressMeter - chr15:49430808 13.1 4730 359.7
22:57:54.080 INFO ProgressMeter - chr15:73709646 13.3 4810 360.9
22:58:04.562 INFO ProgressMeter - chr15:89261819 13.5 4870 360.6
22:58:16.082 INFO ProgressMeter - chr15:90769131 13.7 4950 361.4
22:58:26.386 INFO ProgressMeter - chr15:93024597 13.9 5020 362.0
22:58:36.782 INFO ProgressMeter - chr16:2056194 14.0 5090 362.5
22:58:48.732 INFO ProgressMeter - chr16:3590060 14.2 5200 365.2
22:58:58.798 INFO ProgressMeter - chr16:3740397 14.4 5250 364.4
22:59:09.843 INFO ProgressMeter - chr16:9938026 14.6 5320 364.6
22:59:20.191 INFO ProgressMeter - chr16:30123129 14.8 5390 365.1
22:59:30.455 INFO ProgressMeter - chr16:67628368 14.9 5470 366.2
22:59:41.299 INFO ProgressMeter - chr16:72794224 15.1 5520 365.2
22:59:53.860 INFO ProgressMeter - chr16:72959007 15.3 5570 363.4
23:00:04.418 INFO ProgressMeter - chr16:89280679 15.5 5650 364.5
23:00:15.055 INFO ProgressMeter - chr16:89773269 15.7 5710 364.2
23:00:25.844 INFO ProgressMeter - chr17:7676380 15.9 5790 365.1
23:00:37.426 INFO ProgressMeter - chr17:16070214 16.1 5890 366.9
23:00:48.113 INFO ProgressMeter - chr17:31206275 16.2 5980 368.5
23:00:59.234 INFO ProgressMeter - chr17:35118499 16.4 6070 369.8
23:01:09.235 INFO ProgressMeter - chr17:39715284 16.6 6140 370.3
23:01:19.872 INFO ProgressMeter - chr17:40411107 16.8 6220 371.1
23:01:31.563 INFO ProgressMeter - chr17:43064151 17.0 6320 372.8
23:01:41.746 INFO ProgressMeter - chr17:43094688 17.1 6370 372.0
23:01:52.411 INFO ProgressMeter - chr17:43534792 17.3 6430 371.6
23:02:07.466 INFO ProgressMeter - chr17:43543221 17.6 6490 369.7
23:02:17.524 INFO ProgressMeter - chr17:49621944 17.7 6550 369.6
23:02:27.639 INFO ProgressMeter - chr17:59919705 17.9 6620 370.1
23:02:38.711 INFO ProgressMeter - chr17:61776505 18.1 6680 369.6
23:02:49.842 INFO ProgressMeter - chr17:75778593 18.3 6760 370.2
23:03:00.197 INFO ProgressMeter - chr18:41970325 18.4 6850 371.6
23:03:11.734 INFO ProgressMeter - chr18:45038464 18.6 6910 371.0
23:03:21.941 INFO ProgressMeter - chr19:1221286 18.8 6990 371.9
23:03:32.458 INFO ProgressMeter - chr19:3119311 19.0 7090 373.8
23:03:43.561 INFO ProgressMeter - chr19:7142814 19.2 7190 375.4
23:03:53.813 INFO ProgressMeter - chr19:10489190 19.3 7270 376.2
23:04:05.637 INFO ProgressMeter - chr19:14517226 19.5 7360 377.0
23:04:15.642 INFO ProgressMeter - chr19:15192071 19.7 7420 376.9
23:04:26.589 INFO ProgressMeter - chr19:17842500 19.9 7490 376.9
23:04:36.589 INFO ProgressMeter - chr19:29819287 20.0 7560 377.3
23:04:47.347 INFO ProgressMeter - chr19:35733761 20.2 7650 378.4
23:05:01.359 INFO ProgressMeter - chr19:41260378 20.5 7740 378.5
23:05:12.164 INFO ProgressMeter - chr19:45358763 20.6 7810 378.6
23:05:23.403 INFO ProgressMeter - chr19:50401997 20.8 7900 379.5
23:05:35.077 INFO ProgressMeter - chr2:15941761 21.0 7970 379.3
23:05:46.021 INFO ProgressMeter - chr2:17781548 21.2 8030 378.9
23:05:56.757 INFO ProgressMeter - chr2:25749994 21.4 8090 378.5
23:06:06.831 INFO ProgressMeter - chr2:29223994 21.5 8140 377.9
23:06:17.790 INFO ProgressMeter - chr2:29275400 21.7 8180 376.5
23:06:30.941 INFO ProgressMeter - chr2:42331075 21.9 8250 376.0
23:06:42.254 INFO ProgressMeter - chr2:47796014 22.1 8300 375.0
23:06:53.140 INFO ProgressMeter - chr2:61495453 22.3 8380 375.6
23:07:03.178 INFO ProgressMeter - chr2:108736102 22.5 8450 375.9
23:07:15.523 INFO ProgressMeter - chr2:111127056 22.7 8520 375.5
23:07:26.998 INFO ProgressMeter - chr2:113221111 22.9 8550 373.7
23:07:38.839 INFO ProgressMeter - chr2:113225899 23.1 8590 372.3
23:07:49.175 INFO ProgressMeter - chr2:113229244 23.2 8610 370.4
23:08:03.279 INFO ProgressMeter - chr2:113234676 23.5 8650 368.4
23:08:13.987 INFO ProgressMeter - chr2:140364659 23.7 8730 369.0
23:08:25.205 INFO ProgressMeter - chr2:141013554 23.8 8810 369.4
23:08:35.493 INFO ProgressMeter - chr2:181548549 24.0 8880 369.7
23:08:46.504 INFO ProgressMeter - chr2:201258310 24.2 8970 370.6
23:08:57.228 INFO ProgressMeter - chr2:214752445 24.4 9050 371.2
23:09:10.144 INFO ProgressMeter - chr2:222203670 24.6 9100 370.0
23:09:21.833 INFO ProgressMeter - chr2:222210512 24.8 9140 368.7
23:09:32.808 INFO ProgressMeter - chr2:222216351 25.0 9180 367.6
23:09:44.401 INFO ProgressMeter - chr2:222232283 25.2 9220 366.3
23:09:55.648 INFO ProgressMeter - chr2:226797789 25.4 9280 366.0
23:10:05.684 INFO ProgressMeter - chr20:32433854 25.5 9350 366.3
23:10:16.739 INFO ProgressMeter - chr20:37403360 25.7 9420 366.4
23:10:27.109 INFO ProgressMeter - chr20:47622246 25.9 9500 367.1
23:10:37.984 INFO ProgressMeter - chr20:56381431 26.1 9560 366.8
23:10:48.491 INFO ProgressMeter - chr21:34892923 26.2 9640 367.4
23:10:58.873 INFO ProgressMeter - chr21:38471863 26.4 9690 366.9
23:11:10.101 INFO ProgressMeter - chr21:41490115 26.6 9730 365.8
23:11:20.165 INFO ProgressMeter - chr21:41493308 26.8 9750 364.3
23:11:32.878 INFO ProgressMeter - chr21:41502557 27.0 9790 362.9
23:11:43.966 INFO ProgressMeter - chr21:44230003 27.2 9840 362.3
23:11:54.065 INFO ProgressMeter - chr22:23290186 27.3 9920 363.0
23:12:05.304 INFO ProgressMeter - chr22:28704761 27.5 9980 362.7
23:12:17.780 INFO ProgressMeter - chr22:29285182 27.7 10060 362.9
23:12:28.308 INFO ProgressMeter - chr22:37973557 27.9 10120 362.7
23:12:39.336 INFO ProgressMeter - chr3:920014 28.1 10190 362.8
23:12:49.984 INFO ProgressMeter - chr3:12352673 28.3 10260 363.0
23:13:00.029 INFO ProgressMeter - chr3:12357206 28.4 10290 362.0
23:13:11.356 INFO ProgressMeter - chr3:12361833 28.6 10320 360.6
23:13:27.154 INFO ProgressMeter - chr3:12368528 28.9 10360 358.7
23:13:37.240 INFO ProgressMeter - chr3:12374465 29.0 10400 358.0
23:13:47.784 INFO ProgressMeter - chr3:12416702 29.2 10440 357.2
23:13:58.632 INFO ProgressMeter - chr3:30671768 29.4 10500 357.1
23:14:09.531 INFO ProgressMeter - chr3:47084233 29.6 10580 357.6
23:14:20.171 INFO ProgressMeter - chr3:49685858 29.8 10640 357.5
23:14:30.936 INFO ProgressMeter - chr3:52407172 29.9 10710 357.7
23:14:40.944 INFO ProgressMeter - chr3:70972534 30.1 10780 358.0
23:14:51.952 INFO ProgressMeter - chr3:119905753 30.3 10860 358.5
23:15:02.972 INFO ProgressMeter - chr3:136443266 30.5 10930 358.6
23:15:13.069 INFO ProgressMeter - chr3:138945810 30.6 11000 358.9
23:15:23.391 INFO ProgressMeter - chr3:142563108 30.8 11070 359.2
23:15:34.060 INFO ProgressMeter - chr3:181712635 31.0 11150 359.7
23:15:45.875 INFO ProgressMeter - chr3:186047094 31.2 11220 359.7
23:15:56.851 INFO ProgressMeter - chr3:189866680 31.4 11290 359.8
23:16:07.034 INFO ProgressMeter - chr4:1796052 31.5 11370 360.4
23:16:18.740 INFO ProgressMeter - chr4:24527906 31.7 11460 361.1
23:16:30.105 INFO ProgressMeter - chr4:54277203 31.9 11530 361.1
23:16:42.685 INFO ProgressMeter - chr4:54732108 32.1 11590 360.6
23:16:53.511 INFO ProgressMeter - chr4:65669692 32.3 11670 361.1
23:17:04.605 INFO ProgressMeter - chr4:105234085 32.5 11750 361.5
23:17:17.359 INFO ProgressMeter - chr4:105242228 32.7 11800 360.7
23:17:28.615 INFO ProgressMeter - chr4:142173630 32.9 11890 361.3
23:17:38.840 INFO ProgressMeter - chr4:186603563 33.1 11960 361.6
23:17:49.346 INFO ProgressMeter - chr4:186628672 33.3 12010 361.2
23:18:00.870 INFO ProgressMeter - chr5:1295049 33.4 12070 360.9
23:18:11.952 INFO ProgressMeter - chr5:44313239 33.6 12160 361.6
23:18:23.420 INFO ProgressMeter - chr5:58455579 33.8 12240 361.9
23:18:34.455 INFO ProgressMeter - chr5:87331491 34.0 12330 362.6
23:18:46.906 INFO ProgressMeter - chr5:112841242 34.2 12410 362.8
23:18:57.682 INFO ProgressMeter - chr5:132591222 34.4 12470 362.6
23:19:08.009 INFO ProgressMeter - chr5:142654528 34.6 12540 362.8
23:19:18.220 INFO ProgressMeter - chr5:150061721 34.7 12590 362.5
23:19:29.153 INFO ProgressMeter - chr5:150401900 34.9 12660 362.6
23:19:42.049 INFO ProgressMeter - chr5:177090483 35.1 12730 362.4
23:19:52.389 INFO ProgressMeter - chr5:177210023 35.3 12770 361.7
23:20:03.236 INFO ProgressMeter - chr5:177516704 35.5 12840 361.9
23:20:13.784 INFO ProgressMeter - chr6:20442963 35.7 12930 362.6
23:20:24.701 INFO ProgressMeter - chr6:26065773 35.8 13010 363.0
23:20:36.117 INFO ProgressMeter - chr6:30704603 36.0 13060 362.5
23:20:46.704 INFO ProgressMeter - chr6:32204326 36.2 13120 362.4
23:20:57.162 INFO ProgressMeter - chr6:35457554 36.4 13180 362.3
23:21:07.736 INFO ProgressMeter - chr6:43778458 36.6 13270 363.0
23:21:18.842 INFO ProgressMeter - chr6:106106909 36.7 13340 363.1
23:21:29.186 INFO ProgressMeter - chr6:117319402 36.9 13390 362.7
23:21:39.519 INFO ProgressMeter - chr6:117324072 37.1 13420 361.9
23:21:49.697 INFO ProgressMeter - chr6:117331212 37.3 13460 361.3
23:22:01.262 INFO ProgressMeter - chr6:117339737 37.4 13510 360.8
23:22:12.126 INFO ProgressMeter - chr6:135195746 37.6 13570 360.6
23:22:24.163 INFO ProgressMeter - chr6:135209684 37.8 13620 360.0
23:22:36.784 INFO ProgressMeter - chr6:135213212 38.0 13640 358.6
23:22:47.247 INFO ProgressMeter - chr6:137875686 38.2 13690 358.2
23:22:58.167 INFO ProgressMeter - chr6:151700495 38.4 13740 357.8
23:23:09.227 INFO ProgressMeter - chr6:156779159 38.6 13800 357.7
23:23:20.614 INFO ProgressMeter - chr6:161089320 38.8 13860 357.5
23:23:30.642 INFO ProgressMeter - chr7:2934609 38.9 13940 358.0
23:23:41.584 INFO ProgressMeter - chr7:13894771 39.1 14000 357.9
23:23:54.754 INFO ProgressMeter - chr7:13931998 39.3 14040 356.9
23:24:06.456 INFO ProgressMeter - chr7:13939147 39.5 14090 356.4
23:24:16.647 INFO ProgressMeter - chr7:13945201 39.7 14130 355.9
23:24:26.795 INFO ProgressMeter - chr7:13949501 39.9 14160 355.1
23:24:38.430 INFO ProgressMeter - chr7:13953721 40.1 14190 354.1
23:24:49.353 INFO ProgressMeter - chr7:13960192 40.3 14230 353.5
23:25:00.153 INFO ProgressMeter - chr7:13967197 40.4 14270 353.0
23:25:12.212 INFO ProgressMeter - chr7:13973618 40.6 14310 352.2
23:25:24.171 INFO ProgressMeter - chr7:13978464 40.8 14340 351.2
23:25:36.742 INFO ProgressMeter - chr7:13984819 41.0 14380 350.4
23:25:47.089 INFO ProgressMeter - chr7:41689905 41.2 14410 349.6
23:25:58.607 INFO ProgressMeter - chr7:55161762 41.4 14470 349.5
23:26:10.800 INFO ProgressMeter - chr7:55169928 41.6 14500 348.5
23:26:22.084 INFO ProgressMeter - chr7:55178456 41.8 14550 348.1
23:26:33.546 INFO ProgressMeter - chr7:55202515 42.0 14600 347.7
23:26:44.991 INFO ProgressMeter - chr7:86839437 42.2 14680 348.0
23:26:55.899 INFO ProgressMeter - chr7:102201906 42.4 14750 348.2
23:27:07.237 INFO ProgressMeter - chr7:116728415 42.5 14820 348.3
23:27:17.268 INFO ProgressMeter - chr7:129210481 42.7 14880 348.3
23:27:29.412 INFO ProgressMeter - chr7:140792752 42.9 14940 348.1
23:27:40.240 INFO ProgressMeter - chr7:148816682 43.1 15020 348.5
23:27:51.670 INFO ProgressMeter - chr7:152176785 43.3 15090 348.6
23:28:02.400 INFO ProgressMeter - chr7:152263081 43.5 15150 348.5
23:28:13.344 INFO ProgressMeter - chr8:32327239 43.7 15240 349.1
23:28:24.273 INFO ProgressMeter - chr8:37695978 43.8 15290 348.8
23:28:35.071 INFO ProgressMeter - chr8:38429680 44.0 15370 349.2
23:28:46.310 INFO ProgressMeter - chr8:41987453 44.2 15430 349.1
23:28:56.647 INFO ProgressMeter - chr8:47889153 44.4 15510 349.5
23:29:06.923 INFO ProgressMeter - chr8:68087722 44.5 15600 350.2
23:29:17.808 INFO ProgressMeter - chr8:116848944 44.7 15690 350.8
23:29:28.427 INFO ProgressMeter - chr8:127736592 44.9 15720 350.1
23:29:38.452 INFO ProgressMeter - chr8:127744735 45.1 15760 349.7
23:29:49.128 INFO ProgressMeter - chr9:5077542 45.2 15840 350.1
23:29:59.287 INFO ProgressMeter - chr9:8486232 45.4 15910 350.3
23:30:09.757 INFO ProgressMeter - chr9:22012002 45.6 15970 350.3
23:30:20.566 INFO ProgressMeter - chr9:84707909 45.8 16050 350.7
23:30:34.898 INFO ProgressMeter - chr9:84811858 46.0 16090 349.7
23:30:46.094 INFO ProgressMeter - chr9:84862322 46.2 16120 348.9
23:30:56.299 INFO ProgressMeter - chr9:84867275 46.4 16150 348.3
23:31:07.308 INFO ProgressMeter - chr9:85020204 46.5 16190 347.8
23:31:21.763 INFO ProgressMeter - chr9:90844065 46.8 16230 346.9
23:31:33.407 INFO ProgressMeter - chr9:95461962 47.0 16280 346.5
23:31:43.444 INFO ProgressMeter - chr9:107488103 47.2 16340 346.5
23:31:55.388 INFO ProgressMeter - chr9:130886454 47.4 16400 346.3
23:32:06.221 INFO ProgressMeter - chr9:136498897 47.5 16450 346.1
23:32:16.624 INFO ProgressMeter - chr9:136900435 47.7 16520 346.3
23:32:26.807 INFO ProgressMeter - chrX:45078398 47.9 16620 347.2
23:32:37.092 INFO ProgressMeter - chrX:49037491 48.0 16730 348.2
23:32:48.498 INFO ProgressMeter - chrX:64191544 48.2 16840 349.1
23:32:59.831 INFO ProgressMeter - chrX:71141228 48.4 16960 350.2
23:33:09.966 INFO ProgressMeter - chrX:101358308 48.6 17080 351.5
23:33:20.021 INFO ProgressMeter - chrX:134413802 48.8 17210 352.9
23:33:23.680 INFO Mutect2 - 624885 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
0 read(s) filtered by: ReadLengthReadFilter
139 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
625024 total reads filtered out of 88572143 reads processed
23:33:23.680 INFO ProgressMeter - chrY:20398685 48.8 17269 353.7
23:33:23.680 INFO ProgressMeter - Traversal complete. Processed 17269 total regions in 48.8 minutes.
23:33:23.696 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 6.265804094000001
23:33:23.696 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 254.52415820200002
23:33:23.696 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 9.97 sec
23:33:23.696 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:33:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 48.83 minutes.
Runtime.totalMemory()=6761218048
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 LS0914_tumor.bam --tumor-sample LS0914 -L TST500C_manifest.bed -O LS0914.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:33:25.589 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
23:33:25.703 INFO FilterMutectCalls - ------------------------------------------------------------
23:33:25.706 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:33:25.706 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:33:25.706 INFO FilterMutectCalls - Executing as ?@nf-8a097e0e1e4a71bf08919c968045a598-fa18b-ssznh on Linux v6.12.88 amd64
23:33:25.706 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:33:25.707 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:33:25 PM GMT
23:33:25.707 INFO FilterMutectCalls - ------------------------------------------------------------
23:33:25.707 INFO FilterMutectCalls - ------------------------------------------------------------
23:33:25.707 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:33:25.707 INFO FilterMutectCalls - Picard Version: 3.1.1
23:33:25.708 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:33:25.708 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:33:25.708 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:33:25.708 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:33:25.708 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:33:25.708 INFO FilterMutectCalls - Deflater: IntelDeflater
23:33:25.708 INFO FilterMutectCalls - Inflater: IntelInflater
23:33:25.708 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:33:25.708 INFO FilterMutectCalls - Requester pays: disabled
23:33:25.709 INFO FilterMutectCalls - Initializing engine
23:33:25.934 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.FCgmrvIv93/LS0914.mutect2.raw.vcf.gz
23:33:26.036 INFO FilterMutectCalls - Done initializing engine
23:33:26.100 INFO ProgressMeter - Starting traversal
23:33:26.101 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:33:26.102 INFO FilterMutectCalls - Starting pass 0 through the variants
23:33:27.521 INFO FilterMutectCalls - Finished pass 0 through the variants
23:33:28.070 INFO FilterMutectCalls - Starting pass 1 through the variants
23:33:29.270 INFO FilterMutectCalls - Finished pass 1 through the variants
23:33:29.447 INFO FilterMutectCalls - Starting pass 2 through the variants
23:33:30.628 INFO FilterMutectCalls - Finished pass 2 through the variants
23:33:30.630 INFO FilterMutectCalls - Starting pass 3 through the variants
23:33:31.602 INFO FilterMutectCalls - Finished pass 3 through the variants
23:33:31.614 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:33:31.615 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:33:31.615 INFO ProgressMeter - chr4:186707925 0.1 9864 107334.1
23:33:31.615 INFO ProgressMeter - Traversal complete. Processed 9864 total variants in 0.1 minutes.
23:33:31.630 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:33:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=486539264
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 LS0914.mutect2.raw.vcf.gz --stats LS0914.mutect2.raw.vcf.gz.stats -O LS0914.mutect2.filtered.vcf.gz
23:33:32.820 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
23:33:32.944 INFO SelectVariants - ------------------------------------------------------------
23:33:32.946 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:33:32.947 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:33:32.947 INFO SelectVariants - Executing as ?@nf-8a097e0e1e4a71bf08919c968045a598-fa18b-ssznh on Linux v6.12.88 amd64
23:33:32.947 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:33:32.947 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:33:32 PM GMT
23:33:32.947 INFO SelectVariants - ------------------------------------------------------------
23:33:32.948 INFO SelectVariants - ------------------------------------------------------------
23:33:32.949 INFO SelectVariants - HTSJDK Version: 4.1.0
23:33:32.949 INFO SelectVariants - Picard Version: 3.1.1
23:33:32.949 INFO SelectVariants - Built for Spark Version: 3.5.0
23:33:32.949 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:33:32.949 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:33:32.949 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:33:32.949 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:33:32.950 INFO SelectVariants - Deflater: IntelDeflater
23:33:32.950 INFO SelectVariants - Inflater: IntelInflater
23:33:32.950 INFO SelectVariants - GCS max retries/reopens: 20
23:33:32.950 INFO SelectVariants - Requester pays: disabled
23:33:32.950 INFO SelectVariants - Initializing engine
23:33:33.069 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.FCgmrvIv93/LS0914.mutect2.filtered.vcf.gz
23:33:33.171 INFO SelectVariants - Done initializing engine
23:33:33.205 INFO ProgressMeter - Starting traversal
23:33:33.206 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:33:33.273 INFO ProgressMeter - chr7:13937208 0.0 2466 2311875.0
23:33:33.273 INFO ProgressMeter - Traversal complete. Processed 2466 total variants in 0.0 minutes.
23:33:33.286 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:33:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=478150656
Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar SelectVariants -R hg38.fa -V LS0914.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0914.mutect2.pass.vcf.gz