18:52:47.248 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
18:52:47.366 INFO Mutect2 - ------------------------------------------------------------
18:52:47.369 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
18:52:47.369 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
18:52:47.369 INFO Mutect2 - Executing as ?@nf-2d2cc1865fdf0fc8c34cfe2f56af34d1-206e9-wmxxf on Linux v6.12.83 amd64
18:52:47.369 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
18:52:47.369 INFO Mutect2 - Start Date/Time: May 29, 2026 at 6:52:47 PM GMT
18:52:47.369 INFO Mutect2 - ------------------------------------------------------------
18:52:47.369 INFO Mutect2 - ------------------------------------------------------------
18:52:47.370 INFO Mutect2 - HTSJDK Version: 4.1.0
18:52:47.370 INFO Mutect2 - Picard Version: 3.1.1
18:52:47.371 INFO Mutect2 - Built for Spark Version: 3.5.0
18:52:47.371 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:52:47.371 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:52:47.371 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:52:47.371 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:52:47.371 INFO Mutect2 - Deflater: IntelDeflater
18:52:47.371 INFO Mutect2 - Inflater: IntelInflater
18:52:47.371 INFO Mutect2 - GCS max retries/reopens: 20
18:52:47.371 INFO Mutect2 - Requester pays: disabled
18:52:47.372 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.rTaLvvhOio/LS0890.markdup.deduped.nosingletons.bam.bai is older than BAM /tmp/nxf.rTaLvvhOio/LS0890.markdup.deduped.nosingletons.bam
18:52:47.530 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.rTaLvvhOio/af-only-gnomad.hg38.vcf.gz
18:52:47.656 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.rTaLvvhOio/TST500C_manifest.bed
18:52:47.690 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
18:52:47.725 INFO Mutect2 - Done initializing engine
18:52:47.740 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
18:52:47.742 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
18:52:47.743 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
18:52:47.743 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
18:52:47.755 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
18:52:47.768 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
18:52:47.769 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
18:52:47.769 INFO IntelPairHmm - Available threads: 192
18:52:47.770 INFO IntelPairHmm - Requested threads: 4
18:52:47.770 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
18:52:47.805 INFO ProgressMeter - Starting traversal
18:52:47.806 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
18:52:58.003 INFO ProgressMeter - chr1:9724802 0.2 40 235.4
18:53:10.473 INFO ProgressMeter - chr1:11253837 0.4 100 264.7
18:53:22.625 INFO ProgressMeter - chr1:15933656 0.6 140 241.2
18:53:33.692 INFO ProgressMeter - chr1:18745221 0.8 180 235.4
18:53:44.159 INFO ProgressMeter - chr1:26772498 0.9 220 234.2
18:53:54.579 INFO ProgressMeter - chr1:39890521 1.1 270 242.6
18:54:06.512 INFO ProgressMeter - chr1:45332389 1.3 330 251.6
18:54:17.693 INFO ProgressMeter - chr1:64844062 1.5 400 267.0
18:54:27.874 INFO ProgressMeter - chr1:114711860 1.7 470 281.8
18:54:40.505 INFO ProgressMeter - chr1:119919310 1.9 520 276.8
18:54:51.395 INFO ProgressMeter - chr1:156842079 2.1 570 276.7
18:55:02.640 INFO ProgressMeter - chr1:158634541 2.2 620 275.9
18:55:14.576 INFO ProgressMeter - chr1:162759794 2.4 680 278.0
18:55:25.667 INFO ProgressMeter - chr1:193138083 2.6 740 281.3
18:55:36.022 INFO ProgressMeter - chr1:204525517 2.8 800 285.3
18:55:47.257 INFO ProgressMeter - chr1:226368197 3.0 870 290.9
18:55:58.464 INFO ProgressMeter - chr10:27022537 3.2 960 302.1
18:56:09.965 INFO ProgressMeter - chr10:32019856 3.4 1010 299.8
18:56:20.894 INFO ProgressMeter - chr10:43113553 3.6 1060 298.5
18:56:33.021 INFO ProgressMeter - chr10:43126732 3.8 1100 293.1
18:56:44.925 INFO ProgressMeter - chr10:68646061 4.0 1140 288.5
18:56:56.477 INFO ProgressMeter - chr10:87965285 4.1 1210 292.0
18:57:07.457 INFO ProgressMeter - chr10:110583820 4.3 1280 295.8
18:57:17.482 INFO ProgressMeter - chr10:121480811 4.5 1330 295.9
18:57:27.892 INFO ProgressMeter - chr10:121562590 4.7 1380 295.6
18:57:38.660 INFO ProgressMeter - chr11:64361850 4.8 1450 299.1
18:57:49.174 INFO ProgressMeter - chr11:69652007 5.0 1520 302.6
18:57:59.763 INFO ProgressMeter - chr11:69775584 5.2 1590 305.8
18:58:10.834 INFO ProgressMeter - chr11:69818155 5.4 1640 304.6
18:58:22.482 INFO ProgressMeter - chr11:77361283 5.6 1700 304.8
18:58:34.336 INFO ProgressMeter - chr11:101127732 5.8 1780 308.2
18:58:45.505 INFO ProgressMeter - chr11:108297285 6.0 1840 308.6
18:58:56.924 INFO ProgressMeter - chr11:118480172 6.2 1900 308.8
18:59:07.969 INFO ProgressMeter - chr11:118509946 6.3 1940 306.2
18:59:21.057 INFO ProgressMeter - chr11:128460137 6.6 2010 306.7
18:59:32.186 INFO ProgressMeter - chr12:293057 6.7 2060 305.7
18:59:42.951 INFO ProgressMeter - chr12:4370721 6.9 2120 306.4
18:59:54.586 INFO ProgressMeter - chr12:4444868 7.1 2180 306.5
19:00:05.443 INFO ProgressMeter - chr12:11853406 7.3 2230 305.7
19:00:16.421 INFO ProgressMeter - chr12:11860601 7.5 2270 303.6
19:00:26.527 INFO ProgressMeter - chr12:11866046 7.6 2300 300.8
19:00:36.780 INFO ProgressMeter - chr12:18423943 7.8 2350 300.7
19:00:48.517 INFO ProgressMeter - chr12:45849578 8.0 2430 303.3
19:01:00.580 INFO ProgressMeter - chr12:49032373 8.2 2470 300.7
19:01:12.426 INFO ProgressMeter - chr12:49044401 8.4 2510 298.4
19:01:22.906 INFO ProgressMeter - chr12:51993983 8.6 2560 298.2
19:01:35.275 INFO ProgressMeter - chr12:57092588 8.8 2620 298.0
19:01:45.400 INFO ProgressMeter - chr12:57746926 9.0 2660 296.9
19:01:55.543 INFO ProgressMeter - chr12:69574045 9.1 2730 299.0
19:02:06.734 INFO ProgressMeter - chr12:120098809 9.3 2790 299.5
19:02:17.377 INFO ProgressMeter - chr12:132649675 9.5 2840 299.2
19:02:29.256 INFO ProgressMeter - chr13:21674090 9.7 2900 299.3
19:02:39.273 INFO ProgressMeter - chr13:28052543 9.9 2970 301.3
19:02:50.252 INFO ProgressMeter - chr13:28389603 10.0 3020 300.8
19:03:01.849 INFO ProgressMeter - chr13:32354028 10.2 3080 301.0
19:03:12.468 INFO ProgressMeter - chr13:72763449 10.4 3150 302.6
19:03:24.682 INFO ProgressMeter - chr13:102862328 10.6 3220 303.4
19:03:35.752 INFO ProgressMeter - chr13:113320343 10.8 3280 303.7
19:03:46.590 INFO ProgressMeter - chr14:37592842 11.0 3350 305.1
19:03:59.716 INFO ProgressMeter - chr14:95093886 11.2 3430 306.3
19:04:09.809 INFO ProgressMeter - chr14:102139331 11.4 3480 306.2
19:04:21.647 INFO ProgressMeter - chr15:40701062 11.6 3540 306.1
19:04:31.839 INFO ProgressMeter - chr15:41749109 11.7 3580 305.1
19:04:41.920 INFO ProgressMeter - chr15:54918467 11.9 3640 305.8
19:04:52.463 INFO ProgressMeter - chr15:87978563 12.1 3690 305.5
19:05:03.568 INFO ProgressMeter - chr15:90084999 12.3 3760 306.6
19:05:14.207 INFO ProgressMeter - chr15:92981363 12.4 3820 307.1
19:05:24.662 INFO ProgressMeter - chr16:291188 12.6 3870 306.8
19:05:35.051 INFO ProgressMeter - chr16:2084526 12.8 3920 306.6
19:05:45.777 INFO ProgressMeter - chr16:3590976 13.0 3990 307.7
19:05:56.040 INFO ProgressMeter - chr16:3770868 13.1 4030 306.8
19:06:06.332 INFO ProgressMeter - chr16:9937957 13.3 4070 305.8
19:06:17.652 INFO ProgressMeter - chr16:30116835 13.5 4120 305.2
19:06:28.115 INFO ProgressMeter - chr16:67036637 13.7 4180 305.7
19:06:41.893 INFO ProgressMeter - chr16:72795997 13.9 4230 304.3
19:06:53.138 INFO ProgressMeter - chr16:81859114 14.1 4270 303.1
19:07:07.674 INFO ProgressMeter - chr16:89283307 14.3 4330 302.1
19:07:18.178 INFO ProgressMeter - chr16:89810705 14.5 4390 302.6
19:07:28.682 INFO ProgressMeter - chr17:7687308 14.7 4460 303.8
19:07:39.524 INFO ProgressMeter - chr17:16072143 14.9 4520 304.1
19:07:51.401 INFO ProgressMeter - chr17:31222148 15.1 4590 304.8
19:08:03.353 INFO ProgressMeter - chr17:35118499 15.3 4660 305.4
19:08:13.950 INFO ProgressMeter - chr17:39709316 15.4 4700 304.5
19:08:24.363 INFO ProgressMeter - chr17:40398556 15.6 4750 304.3
19:08:34.897 INFO ProgressMeter - chr17:42323571 15.8 4820 305.4
19:08:48.244 INFO ProgressMeter - chr17:43092756 16.0 4880 304.9
19:08:59.720 INFO ProgressMeter - chr17:43533185 16.2 4930 304.3
19:09:12.204 INFO ProgressMeter - chr17:43543942 16.4 4970 302.9
19:09:23.455 INFO ProgressMeter - chr17:58360147 16.6 5020 302.5
19:09:35.877 INFO ProgressMeter - chr17:60600713 16.8 5090 303.0
19:09:47.723 INFO ProgressMeter - chr17:65538117 17.0 5140 302.4
19:09:59.901 INFO ProgressMeter - chr17:80892727 17.2 5200 302.3
19:10:11.486 INFO ProgressMeter - chr18:42037690 17.4 5260 302.4
19:10:21.579 INFO ProgressMeter - chr18:44953203 17.6 5290 301.2
19:10:31.929 INFO ProgressMeter - chr18:63318609 17.7 5350 301.7
19:10:42.327 INFO ProgressMeter - chr19:2228337 17.9 5420 302.6
19:10:52.794 INFO ProgressMeter - chr19:5222121 18.1 5480 303.0
19:11:04.637 INFO ProgressMeter - chr19:10140779 18.3 5540 303.1
19:11:15.529 INFO ProgressMeter - chr19:11010379 18.5 5600 303.3
19:11:25.599 INFO ProgressMeter - chr19:15161598 18.6 5650 303.3
19:11:37.505 INFO ProgressMeter - chr19:15192377 18.8 5690 302.2
19:11:47.962 INFO ProgressMeter - chr19:17837930 19.0 5730 301.5
19:11:58.384 INFO ProgressMeter - chr19:29818572 19.2 5790 301.9
19:12:08.791 INFO ProgressMeter - chr19:35728772 19.3 5840 301.8
19:12:19.448 INFO ProgressMeter - chr19:40278899 19.5 5900 302.1
19:12:30.713 INFO ProgressMeter - chr19:42289179 19.7 5950 301.8
19:12:41.162 INFO ProgressMeter - chr19:45364039 19.9 6000 301.7
19:12:52.433 INFO ProgressMeter - chr19:50407325 20.1 6080 302.8
19:13:02.659 INFO ProgressMeter - chr2:15946224 20.2 6140 303.2
19:13:14.898 INFO ProgressMeter - chr2:25313921 20.5 6200 303.2
19:13:25.310 INFO ProgressMeter - chr2:29204807 20.6 6240 302.5
19:13:36.102 INFO ProgressMeter - chr2:29226218 20.8 6270 301.4
19:13:46.883 INFO ProgressMeter - chr2:42295379 21.0 6330 301.6
19:13:57.200 INFO ProgressMeter - chr2:47480694 21.2 6380 301.6
19:14:08.828 INFO ProgressMeter - chr2:61496877 21.4 6450 302.1
19:14:20.422 INFO ProgressMeter - chr2:108764759 21.5 6520 302.6
19:14:30.796 INFO ProgressMeter - chr2:111144486 21.7 6570 302.5
19:14:42.074 INFO ProgressMeter - chr2:113225178 21.9 6610 301.8
19:14:53.821 INFO ProgressMeter - chr2:113230953 22.1 6640 300.4
19:15:04.418 INFO ProgressMeter - chr2:113244425 22.3 6680 299.9
19:15:16.199 INFO ProgressMeter - chr2:140503062 22.5 6750 300.4
19:15:26.854 INFO ProgressMeter - chr2:141480394 22.7 6810 300.7
19:15:37.710 INFO ProgressMeter - chr2:191033909 22.8 6870 300.9
19:15:48.562 INFO ProgressMeter - chr2:203868029 23.0 6940 301.6
19:15:58.838 INFO ProgressMeter - chr2:219567279 23.2 7000 301.9
19:16:11.228 INFO ProgressMeter - chr2:222206789 23.4 7040 301.0
19:16:24.150 INFO ProgressMeter - chr2:222216145 23.6 7080 299.9
19:16:34.923 INFO ProgressMeter - chr2:224497799 23.8 7120 299.3
19:16:46.427 INFO ProgressMeter - chr20:25297810 24.0 7180 299.5
19:16:57.121 INFO ProgressMeter - chr20:32798606 24.2 7230 299.3
19:17:08.215 INFO ProgressMeter - chr20:42472264 24.3 7300 299.9
19:17:19.841 INFO ProgressMeter - chr20:53582359 24.5 7350 299.6
19:17:29.938 INFO ProgressMeter - chr21:34859332 24.7 7410 300.0
19:17:40.499 INFO ProgressMeter - chr21:38498361 24.9 7450 299.5
19:17:52.004 INFO ProgressMeter - chr21:41491759 25.1 7500 299.2
19:18:02.406 INFO ProgressMeter - chr21:41501608 25.2 7530 298.3
19:18:12.411 INFO ProgressMeter - chr21:42186850 25.4 7560 297.5
19:18:23.951 INFO ProgressMeter - chr22:23290184 25.6 7640 298.4
19:18:34.785 INFO ProgressMeter - chr22:28734852 25.8 7720 299.4
19:18:45.554 INFO ProgressMeter - chr22:37973493 26.0 7790 300.0
19:18:56.058 INFO ProgressMeter - chr22:47440629 26.1 7840 300.0
19:19:06.126 INFO ProgressMeter - chr3:12354512 26.3 7910 300.7
19:19:18.668 INFO ProgressMeter - chr3:12364069 26.5 7960 300.2
19:19:30.993 INFO ProgressMeter - chr3:12373259 26.7 8000 299.4
19:19:41.482 INFO ProgressMeter - chr3:12597923 26.9 8050 299.3
19:19:52.665 INFO ProgressMeter - chr3:41233527 27.1 8130 300.2
19:20:03.999 INFO ProgressMeter - chr3:47163852 27.3 8180 300.0
19:20:15.579 INFO ProgressMeter - chr3:52403136 27.5 8240 300.0
19:20:26.691 INFO ProgressMeter - chr3:70976939 27.6 8310 300.6
19:20:37.250 INFO ProgressMeter - chr3:119912702 27.8 8370 300.8
19:20:48.948 INFO ProgressMeter - chr3:136472392 28.0 8430 300.9
19:20:59.433 INFO ProgressMeter - chr3:142496359 28.2 8500 301.5
19:21:10.750 INFO ProgressMeter - chr3:179204501 28.4 8580 302.3
19:21:21.404 INFO ProgressMeter - chr3:185472973 28.6 8640 302.5
19:21:31.926 INFO ProgressMeter - chr3:189808270 28.7 8700 302.8
19:21:43.235 INFO ProgressMeter - chr4:1803690 28.9 8780 303.6
19:21:53.774 INFO ProgressMeter - chr4:24554704 29.1 8840 303.8
19:22:04.480 INFO ProgressMeter - chr4:54692213 29.3 8900 304.0
19:22:15.146 INFO ProgressMeter - chr4:65324112 29.5 8960 304.2
19:22:25.798 INFO ProgressMeter - chr4:83472220 29.6 9030 304.7
19:22:38.554 INFO ProgressMeter - chr4:105276132 29.8 9090 304.6
19:22:50.047 INFO ProgressMeter - chr4:168742391 30.0 9170 305.3
19:23:03.400 INFO ProgressMeter - chr4:186619001 30.3 9230 305.0
19:23:15.631 INFO ProgressMeter - chr4:186708579 30.5 9270 304.3
19:23:26.531 INFO ProgressMeter - chr5:38960396 30.6 9340 304.8
19:23:36.886 INFO ProgressMeter - chr5:56881879 30.8 9420 305.7
19:23:48.054 INFO ProgressMeter - chr5:80873156 31.0 9500 306.4
19:23:59.925 INFO ProgressMeter - chr5:112841397 31.2 9570 306.7
19:24:10.751 INFO ProgressMeter - chr5:132638079 31.4 9620 306.5
19:24:21.124 INFO ProgressMeter - chr5:149496835 31.6 9680 306.8
19:24:32.891 INFO ProgressMeter - chr5:150135553 31.8 9740 306.8
19:24:43.431 INFO ProgressMeter - chr5:171660943 31.9 9800 306.9
19:24:55.452 INFO ProgressMeter - chr5:177211734 32.1 9860 306.9
19:25:06.279 INFO ProgressMeter - chr5:180619019 32.3 9920 307.0
19:25:16.284 INFO ProgressMeter - chr6:20466963 32.5 9990 307.6
19:25:26.296 INFO ProgressMeter - chr6:29945057 32.6 10070 308.5
19:25:37.465 INFO ProgressMeter - chr6:89085532 32.8 10240 311.9
19:25:48.760 INFO ProgressMeter - chr6:112064753 33.0 10300 312.0
19:26:00.136 INFO ProgressMeter - chr6:117325960 33.2 10340 311.4
19:26:10.294 INFO ProgressMeter - chr6:117337230 33.4 10380 311.0
19:26:20.897 INFO ProgressMeter - chr6:135187832 33.6 10430 310.9
19:26:31.896 INFO ProgressMeter - chr6:135212968 33.7 10480 310.7
19:26:43.952 INFO ProgressMeter - chr6:149680173 33.9 10530 310.3
19:26:54.337 INFO ProgressMeter - chr6:152041926 34.1 10580 310.2
19:27:04.421 INFO ProgressMeter - chr6:157207065 34.3 10630 310.1
19:27:15.225 INFO ProgressMeter - chr7:2912170 34.5 10700 310.5
19:27:27.287 INFO ProgressMeter - chr7:13895107 34.7 10770 310.8
19:27:39.361 INFO ProgressMeter - chr7:13936374 34.9 10810 310.1
19:27:50.178 INFO ProgressMeter - chr7:13946844 35.0 10860 309.9
19:28:01.491 INFO ProgressMeter - chr7:13954632 35.2 10900 309.4
19:28:11.517 INFO ProgressMeter - chr7:13964156 35.4 10940 309.1
19:28:22.629 INFO ProgressMeter - chr7:13972889 35.6 10990 308.9
19:28:33.080 INFO ProgressMeter - chr7:13981099 35.8 11040 308.8
19:28:43.643 INFO ProgressMeter - chr7:41699985 35.9 11100 308.9
19:28:54.825 INFO ProgressMeter - chr7:55166007 36.1 11150 308.7
19:29:06.445 INFO ProgressMeter - chr7:55175427 36.3 11190 308.2
19:29:18.310 INFO ProgressMeter - chr7:55181408 36.5 11230 307.6
19:29:28.882 INFO ProgressMeter - chr7:81729603 36.7 11290 307.8
19:29:40.392 INFO ProgressMeter - chr7:102193832 36.9 11360 308.1
19:29:50.664 INFO ProgressMeter - chr7:106883031 37.0 11410 308.0
19:30:00.982 INFO ProgressMeter - chr7:129206462 37.2 11460 307.9
19:30:11.170 INFO ProgressMeter - chr7:140833126 37.4 11520 308.1
19:30:22.630 INFO ProgressMeter - chr7:152163015 37.6 11610 308.9
19:30:33.426 INFO ProgressMeter - chr7:152248157 37.8 11660 308.8
19:30:44.777 INFO ProgressMeter - chr8:32605560 37.9 11740 309.4
19:30:55.289 INFO ProgressMeter - chr8:37835552 38.1 11790 309.2
19:31:08.335 INFO ProgressMeter - chr8:41937254 38.3 11850 309.1
19:31:19.458 INFO ProgressMeter - chr8:47858847 38.5 11910 309.1
19:31:29.956 INFO ProgressMeter - chr8:67952393 38.7 11980 309.5
19:31:40.650 INFO ProgressMeter - chr8:91975903 38.9 12050 309.9
19:31:50.755 INFO ProgressMeter - chr8:127744465 39.0 12110 310.1
19:32:01.892 INFO ProgressMeter - chr9:5089672 39.2 12180 310.4
19:32:12.220 INFO ProgressMeter - chr9:8526625 39.4 12240 310.6
19:32:23.151 INFO ProgressMeter - chr9:78031098 39.6 12310 310.9
19:32:35.468 INFO ProgressMeter - chr9:84812896 39.8 12370 310.8
19:32:47.327 INFO ProgressMeter - chr9:84871787 40.0 12410 310.3
19:32:59.527 INFO ProgressMeter - chr9:85024229 40.2 12450 309.7
19:33:11.196 INFO ProgressMeter - chr9:95469811 40.4 12510 309.7
19:33:22.545 INFO ProgressMeter - chr9:130874866 40.6 12580 310.0
19:33:34.636 INFO ProgressMeter - chr9:136496969 40.8 12630 309.7
19:33:44.920 INFO ProgressMeter - chrX:15815675 41.0 12700 310.1
19:33:55.655 INFO ProgressMeter - chrX:47570876 41.1 12810 311.4
19:34:06.778 INFO ProgressMeter - chrX:53411740 41.3 12910 312.5
19:34:17.721 INFO ProgressMeter - chrX:71129314 41.5 13000 313.3
19:34:28.072 INFO ProgressMeter - chrX:77688816 41.7 13100 314.4
19:34:39.058 INFO ProgressMeter - chrX:134413467 41.9 13220 315.9
19:34:42.775 INFO Mutect2 - 1098312 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
215 read(s) filtered by: ReadLengthReadFilter
0 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
1098527 total reads filtered out of 83798753 reads processed
19:34:42.776 INFO ProgressMeter - chrY:20398623 41.9 13269 316.6
19:34:42.776 INFO ProgressMeter - Traversal complete. Processed 13269 total regions in 41.9 minutes.
19:34:42.789 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 3.007378349
19:34:42.789 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 17.734219523
19:34:42.789 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 0.71 sec
19:34:42.789 INFO Mutect2 - Shutting down engine
[May 29, 2026 at 7:34:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 41.93 minutes.
Runtime.totalMemory()=910163968
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar Mutect2 -R hg38.fa -I LS0890.markdup.deduped.nosingletons.bam --tumor-sample LS0890 -L TST500C_manifest.bed -O LS0890.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 20 --germline-resource af-only-gnomad.hg38.vcf.gz
19:34:43.901 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
19:34:43.973 INFO FilterMutectCalls - ------------------------------------------------------------
19:34:43.975 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
19:34:43.975 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
19:34:43.975 INFO FilterMutectCalls - Executing as ?@nf-2d2cc1865fdf0fc8c34cfe2f56af34d1-206e9-wmxxf on Linux v6.12.83 amd64
19:34:43.975 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
19:34:43.975 INFO FilterMutectCalls - Start Date/Time: May 29, 2026 at 7:34:43 PM GMT
19:34:43.976 INFO FilterMutectCalls - ------------------------------------------------------------
19:34:43.976 INFO FilterMutectCalls - ------------------------------------------------------------
19:34:43.976 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
19:34:43.976 INFO FilterMutectCalls - Picard Version: 3.1.1
19:34:43.976 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
19:34:43.976 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:34:43.977 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:34:43.977 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:34:43.977 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:34:43.977 INFO FilterMutectCalls - Deflater: IntelDeflater
19:34:43.977 INFO FilterMutectCalls - Inflater: IntelInflater
19:34:43.977 INFO FilterMutectCalls - GCS max retries/reopens: 20
19:34:43.977 INFO FilterMutectCalls - Requester pays: disabled
19:34:43.977 INFO FilterMutectCalls - Initializing engine
19:34:44.059 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.rTaLvvhOio/LS0890.mutect2.raw.vcf.gz
19:34:44.102 INFO FilterMutectCalls - Done initializing engine
19:34:44.139 INFO ProgressMeter - Starting traversal
19:34:44.140 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:34:44.140 INFO FilterMutectCalls - Starting pass 0 through the variants
19:34:45.133 INFO FilterMutectCalls - Finished pass 0 through the variants
19:34:50.183 INFO FilterMutectCalls - Starting pass 1 through the variants
19:34:51.333 INFO FilterMutectCalls - Finished pass 1 through the variants
19:34:52.331 INFO FilterMutectCalls - Starting pass 2 through the variants
19:34:53.407 INFO FilterMutectCalls - Finished pass 2 through the variants
19:34:53.410 INFO FilterMutectCalls - Starting pass 3 through the variants
19:34:54.335 INFO FilterMutectCalls - Finished pass 3 through the variants
19:34:54.340 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
19:34:54.340 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
19:34:54.341 INFO ProgressMeter - chr14:37588151 0.2 4932 29008.9
19:34:54.341 INFO ProgressMeter - Traversal complete. Processed 4932 total variants in 0.2 minutes.
19:34:54.351 INFO FilterMutectCalls - Shutting down engine
[May 29, 2026 at 7:34:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.17 minutes.
Runtime.totalMemory()=806354944
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R hg38.fa -V LS0890.mutect2.raw.vcf.gz --stats LS0890.mutect2.raw.vcf.gz.stats -O LS0890.mutect2.filtered.vcf.gz
19:34:55.389 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
19:34:55.459 INFO SelectVariants - ------------------------------------------------------------
19:34:55.460 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
19:34:55.461 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
19:34:55.461 INFO SelectVariants - Executing as ?@nf-2d2cc1865fdf0fc8c34cfe2f56af34d1-206e9-wmxxf on Linux v6.12.83 amd64
19:34:55.461 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
19:34:55.461 INFO SelectVariants - Start Date/Time: May 29, 2026 at 7:34:55 PM GMT
19:34:55.461 INFO SelectVariants - ------------------------------------------------------------
19:34:55.461 INFO SelectVariants - ------------------------------------------------------------
19:34:55.461 INFO SelectVariants - HTSJDK Version: 4.1.0
19:34:55.461 INFO SelectVariants - Picard Version: 3.1.1
19:34:55.461 INFO SelectVariants - Built for Spark Version: 3.5.0
19:34:55.461 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:34:55.462 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:34:55.462 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:34:55.462 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:34:55.462 INFO SelectVariants - Deflater: IntelDeflater
19:34:55.462 INFO SelectVariants - Inflater: IntelInflater
19:34:55.462 INFO SelectVariants - GCS max retries/reopens: 20
19:34:55.462 INFO SelectVariants - Requester pays: disabled
19:34:55.462 INFO SelectVariants - Initializing engine
19:34:55.534 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.rTaLvvhOio/LS0890.mutect2.filtered.vcf.gz
19:34:55.572 INFO SelectVariants - Done initializing engine
19:34:55.598 INFO ProgressMeter - Starting traversal
19:34:55.598 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:34:55.650 INFO ProgressMeter - chr7:13945841 0.0 1233 1450588.2
19:34:55.650 INFO ProgressMeter - Traversal complete. Processed 1233 total variants in 0.0 minutes.
19:34:55.660 INFO SelectVariants - Shutting down engine
[May 29, 2026 at 7:34:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=567803904
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar SelectVariants -R hg38.fa -V LS0890.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0890.mutect2.pass.vcf.gz