22:44:34.969 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
22:44:35.086 INFO Mutect2 - ------------------------------------------------------------
22:44:35.089 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:35.089 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:35.090 INFO Mutect2 - Executing as ?@nf-ba803fe2855d2ba3f5f58dbe4dffecad-349dd-28rst on Linux v6.12.88 amd64
22:44:35.090 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:35.090 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:34 PM GMT
22:44:35.090 INFO Mutect2 - ------------------------------------------------------------
22:44:35.090 INFO Mutect2 - ------------------------------------------------------------
22:44:35.092 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:35.092 INFO Mutect2 - Picard Version: 3.1.1
22:44:35.092 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:35.092 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:35.092 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:35.092 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:35.093 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:35.093 INFO Mutect2 - Deflater: IntelDeflater
22:44:35.093 INFO Mutect2 - Inflater: IntelInflater
22:44:35.093 INFO Mutect2 - GCS max retries/reopens: 20
22:44:35.093 INFO Mutect2 - Requester pays: disabled
22:44:35.094 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.9hto0drC5P/LS0922_tumor.bam.bai is older than BAM /tmp/nxf.9hto0drC5P/LS0922_tumor.bam
22:44:35.254 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.9hto0drC5P/af-only-gnomad.hg38.vcf.gz
22:44:35.376 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.9hto0drC5P/TST500C_manifest.bed
22:44:35.420 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:35.460 INFO Mutect2 - Done initializing engine
22:44:35.474 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
22:44:35.476 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
22:44:35.477 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:35.477 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:35.490 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
22:44:35.502 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:35.502 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:35.503 INFO IntelPairHmm - Available threads: 384
22:44:35.503 INFO IntelPairHmm - Requested threads: 4
22:44:35.503 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:35.549 INFO ProgressMeter - Starting traversal
22:44:35.549 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:47.382 INFO ProgressMeter - chr1:9724274 0.2 50 253.5
22:44:58.655 INFO ProgressMeter - chr1:11237841 0.4 110 285.6
22:45:11.129 INFO ProgressMeter - chr1:15930860 0.6 160 269.8
22:45:22.270 INFO ProgressMeter - chr1:15937810 0.8 190 244.0
22:45:33.953 INFO ProgressMeter - chr1:18747242 1.0 230 236.3
22:45:45.836 INFO ProgressMeter - chr1:26773344 1.2 280 239.0
22:45:56.673 INFO ProgressMeter - chr1:36466655 1.4 320 236.7
22:46:08.432 INFO ProgressMeter - chr1:39900630 1.5 370 239.0
22:46:20.554 INFO ProgressMeter - chr1:43352232 1.8 410 234.3
22:46:31.730 INFO ProgressMeter - chr1:46278168 1.9 470 242.7
22:46:43.034 INFO ProgressMeter - chr1:71592907 2.1 530 249.4
22:46:53.953 INFO ProgressMeter - chr1:114718861 2.3 610 264.4
22:47:04.915 INFO ProgressMeter - chr1:119916404 2.5 650 261.1
22:47:15.087 INFO ProgressMeter - chr1:149841045 2.7 700 263.3
22:47:25.760 INFO ProgressMeter - chr1:156873419 2.8 740 260.9
22:47:37.349 INFO ProgressMeter - chr1:158611262 3.0 760 250.8
22:47:48.483 INFO ProgressMeter - chr1:158672057 3.2 820 255.0
22:48:00.137 INFO ProgressMeter - chr1:179108158 3.4 890 261.0
22:48:11.739 INFO ProgressMeter - chr1:204457726 3.6 960 266.4
22:48:23.032 INFO ProgressMeter - chr1:204549411 3.8 1020 269.0
22:48:33.584 INFO ProgressMeter - chr1:226370432 4.0 1080 272.2
22:48:46.274 INFO ProgressMeter - chr1:243501645 4.2 1140 272.8
22:48:57.696 INFO ProgressMeter - chr10:27012861 4.4 1190 272.4
22:49:10.229 INFO ProgressMeter - chr10:32010220 4.6 1250 273.0
22:49:21.670 INFO ProgressMeter - chr10:43106374 4.8 1310 274.7
22:49:33.147 INFO ProgressMeter - chr10:43115901 5.0 1340 270.2
22:49:44.420 INFO ProgressMeter - chr10:43128398 5.1 1380 268.1
22:49:55.678 INFO ProgressMeter - chr10:68645364 5.3 1420 266.1
22:50:05.747 INFO ProgressMeter - chr10:87890684 5.5 1470 267.1
22:50:18.269 INFO ProgressMeter - chr10:101772501 5.7 1530 267.9
22:50:29.191 INFO ProgressMeter - chr10:110578697 5.9 1590 269.8
22:50:40.112 INFO ProgressMeter - chr10:113159918 6.1 1640 269.9
22:50:53.784 INFO ProgressMeter - chr10:121482243 6.3 1670 264.9
22:51:05.618 INFO ProgressMeter - chr10:121577912 6.5 1720 264.6
22:51:15.758 INFO ProgressMeter - chr11:32389056 6.7 1770 265.4
22:51:26.158 INFO ProgressMeter - chr11:64804715 6.8 1820 265.9
22:51:36.163 INFO ProgressMeter - chr11:69646123 7.0 1870 266.8
22:51:47.435 INFO ProgressMeter - chr11:69700708 7.2 1920 266.7
22:51:57.626 INFO ProgressMeter - chr11:69703259 7.4 1940 263.3
22:52:09.359 INFO ProgressMeter - chr11:69776715 7.6 1990 263.1
22:52:23.447 INFO ProgressMeter - chr11:69810065 7.8 2010 257.7
22:52:39.228 INFO ProgressMeter - chr11:69819332 8.1 2050 254.3
22:52:50.470 INFO ProgressMeter - chr11:77344159 8.2 2100 254.6
22:53:01.081 INFO ProgressMeter - chr11:77423651 8.4 2140 254.0
22:53:12.832 INFO ProgressMeter - chr11:101128738 8.6 2210 256.3
22:53:24.834 INFO ProgressMeter - chr11:102325509 8.8 2230 252.8
22:53:35.706 INFO ProgressMeter - chr11:108331877 9.0 2300 255.5
22:53:45.929 INFO ProgressMeter - chr11:118474026 9.2 2340 255.1
22:53:58.548 INFO ProgressMeter - chr11:118519616 9.4 2390 254.7
22:54:09.259 INFO ProgressMeter - chr11:125620819 9.6 2420 253.1
22:54:31.020 INFO ProgressMeter - chr11:128460024 9.9 2480 249.9
22:54:43.497 INFO ProgressMeter - chr11:128764649 10.1 2510 247.7
22:54:53.675 INFO ProgressMeter - chr12:297089 10.3 2550 247.5
22:55:04.697 INFO ProgressMeter - chr12:4368324 10.5 2610 248.9
22:55:17.043 INFO ProgressMeter - chr12:4435023 10.7 2660 248.8
22:55:27.916 INFO ProgressMeter - chr12:6581289 10.9 2710 249.2
22:55:40.303 INFO ProgressMeter - chr12:6836718 11.1 2750 248.2
22:55:52.867 INFO ProgressMeter - chr12:11856903 11.3 2780 246.3
22:56:03.707 INFO ProgressMeter - chr12:11860716 11.5 2810 245.0
22:56:13.864 INFO ProgressMeter - chr12:11863887 11.6 2830 243.2
22:56:26.448 INFO ProgressMeter - chr12:11868686 11.8 2860 241.4
22:56:36.555 INFO ProgressMeter - chr12:18313960 12.0 2890 240.5
22:56:46.964 INFO ProgressMeter - chr12:25240313 12.2 2960 242.8
22:56:58.682 INFO ProgressMeter - chr12:45852578 12.4 3010 243.0
22:57:13.318 INFO ProgressMeter - chr12:49033339 12.6 3060 242.3
22:57:23.767 INFO ProgressMeter - chr12:49040289 12.8 3090 241.3
22:57:36.269 INFO ProgressMeter - chr12:49051510 13.0 3130 240.5
22:57:46.712 INFO ProgressMeter - chr12:56080299 13.2 3180 241.2
22:57:58.434 INFO ProgressMeter - chr12:56103471 13.4 3240 242.1
22:58:08.561 INFO ProgressMeter - chr12:57094473 13.6 3270 241.3
22:58:20.033 INFO ProgressMeter - chr12:57747226 13.7 3320 241.6
22:58:30.311 INFO ProgressMeter - chr12:68809015 13.9 3360 241.5
22:58:41.359 INFO ProgressMeter - chr12:102419507 14.1 3420 242.6
22:58:51.677 INFO ProgressMeter - chr12:114674677 14.3 3470 243.2
22:59:01.860 INFO ProgressMeter - chr12:132635890 14.4 3520 243.8
22:59:12.109 INFO ProgressMeter - chr12:132681136 14.6 3570 244.4
22:59:23.033 INFO ProgressMeter - chr13:21672392 14.8 3610 244.1
22:59:33.427 INFO ProgressMeter - chr13:28049382 15.0 3680 245.9
22:59:44.129 INFO ProgressMeter - chr13:28386494 15.1 3730 246.3
22:59:55.125 INFO ProgressMeter - chr13:32317658 15.3 3770 246.0
23:00:06.549 INFO ProgressMeter - chr13:32340831 15.5 3810 245.5
23:00:17.074 INFO ProgressMeter - chr13:48342597 15.7 3860 246.0
23:00:28.643 INFO ProgressMeter - chr13:102239568 15.9 3940 248.0
23:00:41.605 INFO ProgressMeter - chr13:109783444 16.1 4000 248.4
23:00:52.355 INFO ProgressMeter - chr13:113307937 16.3 4040 248.2
23:01:02.436 INFO ProgressMeter - chr14:23307948 16.4 4070 247.4
23:01:12.915 INFO ProgressMeter - chr14:37589051 16.6 4120 247.9
23:01:23.052 INFO ProgressMeter - chr14:37597803 16.8 4160 247.7
23:01:34.961 INFO ProgressMeter - chr14:81144277 17.0 4220 248.4
23:01:45.709 INFO ProgressMeter - chr14:102084504 17.2 4270 248.7
23:01:57.154 INFO ProgressMeter - chr15:34345855 17.4 4320 248.8
23:02:07.288 INFO ProgressMeter - chr15:34355693 17.5 4350 248.2
23:02:19.866 INFO ProgressMeter - chr15:41729162 17.7 4400 248.0
23:02:30.365 INFO ProgressMeter - chr15:49425215 17.9 4440 247.9
23:02:40.822 INFO ProgressMeter - chr15:67190411 18.1 4510 249.3
23:02:51.768 INFO ProgressMeter - chr15:88032855 18.3 4550 249.0
23:03:01.989 INFO ProgressMeter - chr15:90084814 18.4 4620 250.5
23:03:12.695 INFO ProgressMeter - chr15:90811313 18.6 4670 250.8
23:03:22.774 INFO ProgressMeter - chr15:93020072 18.8 4720 251.2
23:03:34.464 INFO ProgressMeter - chr16:309971 19.0 4770 251.3
23:03:45.132 INFO ProgressMeter - chr16:2083693 19.2 4820 251.6
23:03:58.015 INFO ProgressMeter - chr16:3589419 19.4 4900 252.9
23:04:09.922 INFO ProgressMeter - chr16:3728724 19.6 4930 251.9
23:04:20.847 INFO ProgressMeter - chr16:9763147 19.8 4980 252.1
23:04:30.898 INFO ProgressMeter - chr16:13920164 19.9 5020 252.0
23:04:41.036 INFO ProgressMeter - chr16:23635949 20.1 5060 251.8
23:04:52.586 INFO ProgressMeter - chr16:56832293 20.3 5130 252.9
23:05:04.158 INFO ProgressMeter - chr16:68823501 20.5 5190 253.5
23:05:16.988 INFO ProgressMeter - chr16:72795134 20.7 5220 252.3
23:05:27.841 INFO ProgressMeter - chr16:72950807 20.9 5250 251.5
23:05:38.813 INFO ProgressMeter - chr16:81907752 21.1 5290 251.3
23:05:50.383 INFO ProgressMeter - chr16:89281859 21.2 5340 251.3
23:06:00.547 INFO ProgressMeter - chr16:89288607 21.4 5370 250.7
23:06:11.617 INFO ProgressMeter - chr17:7313378 21.6 5440 251.8
23:06:23.549 INFO ProgressMeter - chr17:7677113 21.8 5490 251.8
23:06:34.875 INFO ProgressMeter - chr17:16046899 22.0 5560 252.9
23:06:45.511 INFO ProgressMeter - chr17:17214983 22.2 5620 253.5
23:06:56.661 INFO ProgressMeter - chr17:31252936 22.4 5680 254.1
23:07:06.844 INFO ProgressMeter - chr17:35118499 22.5 5740 254.9
23:07:19.281 INFO ProgressMeter - chr17:39704942 22.7 5790 254.7
23:07:29.591 INFO ProgressMeter - chr17:39727293 22.9 5830 254.6
23:07:39.606 INFO ProgressMeter - chr17:40412757 23.1 5890 255.3
23:07:50.870 INFO ProgressMeter - chr17:42329552 23.3 5960 256.3
23:08:03.351 INFO ProgressMeter - chr17:43094237 23.5 6020 256.6
23:08:13.667 INFO ProgressMeter - chr17:43532006 23.6 6060 256.4
23:08:24.726 INFO ProgressMeter - chr17:43538757 23.8 6100 256.1
23:08:40.707 INFO ProgressMeter - chr17:43543347 24.1 6130 254.5
23:08:53.264 INFO ProgressMeter - chr17:45289234 24.3 6170 254.0
23:09:03.537 INFO ProgressMeter - chr17:58358704 24.5 6200 253.4
23:09:15.238 INFO ProgressMeter - chr17:59934432 24.7 6270 254.2
23:09:26.205 INFO ProgressMeter - chr17:61743011 24.8 6310 254.0
23:09:37.959 INFO ProgressMeter - chr17:65558436 25.0 6360 254.0
23:09:48.968 INFO ProgressMeter - chr17:80880413 25.2 6420 254.5
23:09:59.846 INFO ProgressMeter - chr18:22176953 25.4 6480 255.1
23:10:10.055 INFO ProgressMeter - chr18:44950986 25.6 6530 255.3
23:10:21.417 INFO ProgressMeter - chr18:58709376 25.8 6580 255.4
23:10:32.090 INFO ProgressMeter - chr19:1619109 25.9 6630 255.6
23:10:43.394 INFO ProgressMeter - chr19:2226927 26.1 6690 256.0
23:10:53.665 INFO ProgressMeter - chr19:5206772 26.3 6740 256.3
23:11:05.801 INFO ProgressMeter - chr19:7122877 26.5 6800 256.6
23:11:16.802 INFO ProgressMeter - chr19:10155851 26.7 6850 256.7
23:11:27.226 INFO ProgressMeter - chr19:11007900 26.9 6900 256.9
23:11:38.710 INFO ProgressMeter - chr19:14516582 27.1 6950 256.9
23:11:50.322 INFO ProgressMeter - chr19:15174155 27.2 6990 256.5
23:12:03.674 INFO ProgressMeter - chr19:15243214 27.5 7040 256.3
23:12:14.412 INFO ProgressMeter - chr19:17843431 27.6 7090 256.4
23:12:30.680 INFO ProgressMeter - chr19:29818572 27.9 7150 256.1
23:12:41.177 INFO ProgressMeter - chr19:35720488 28.1 7200 256.3
23:12:53.028 INFO ProgressMeter - chr19:35733059 28.3 7250 256.3
23:13:03.960 INFO ProgressMeter - chr19:40266398 28.5 7300 256.4
23:13:19.283 INFO ProgressMeter - chr19:41261464 28.7 7350 255.8
23:13:29.528 INFO ProgressMeter - chr19:42292695 28.9 7390 255.7
23:13:40.166 INFO ProgressMeter - chr19:45363741 29.1 7440 255.9
23:13:52.129 INFO ProgressMeter - chr19:45416600 29.3 7500 256.2
23:14:03.274 INFO ProgressMeter - chr19:50417047 29.5 7560 256.6
23:14:13.821 INFO ProgressMeter - chr2:15940807 29.6 7590 256.1
23:14:24.005 INFO ProgressMeter - chr2:15950395 29.8 7630 256.0
23:14:34.197 INFO ProgressMeter - chr2:25282195 30.0 7680 256.2
23:14:45.913 INFO ProgressMeter - chr2:29209784 30.2 7730 256.2
23:14:59.378 INFO ProgressMeter - chr2:29226595 30.4 7760 255.3
23:15:11.947 INFO ProgressMeter - chr2:42280848 30.6 7810 255.2
23:15:25.452 INFO ProgressMeter - chr2:47463029 30.8 7860 254.9
23:15:36.545 INFO ProgressMeter - chr2:47806202 31.0 7900 254.7
23:15:48.604 INFO ProgressMeter - chr2:95183454 31.2 7960 255.0
23:15:59.958 INFO ProgressMeter - chr2:108763235 31.4 8030 255.7
23:16:12.054 INFO ProgressMeter - chr2:111127248 31.6 8080 255.6
23:16:22.965 INFO ProgressMeter - chr2:113220248 31.8 8100 254.8
23:16:38.895 INFO ProgressMeter - chr2:113225563 32.1 8130 253.6
23:16:52.298 INFO ProgressMeter - chr2:113230887 32.3 8160 252.8
23:17:03.997 INFO ProgressMeter - chr2:113233986 32.5 8180 251.9
23:17:15.317 INFO ProgressMeter - chr2:136115034 32.7 8230 252.0
23:17:26.068 INFO ProgressMeter - chr2:140702268 32.8 8300 252.7
23:17:38.090 INFO ProgressMeter - chr2:157780509 33.0 8360 253.0
23:17:48.751 INFO ProgressMeter - chr2:197393034 33.2 8430 253.8
23:17:58.847 INFO ProgressMeter - chr2:208239069 33.4 8490 254.3
23:18:10.491 INFO ProgressMeter - chr2:214809463 33.6 8560 254.9
23:18:20.981 INFO ProgressMeter - chr2:222202945 33.8 8590 254.5
23:18:34.028 INFO ProgressMeter - chr2:222209788 34.0 8630 254.0
23:18:47.349 INFO ProgressMeter - chr2:222213292 34.2 8650 252.9
23:18:58.590 INFO ProgressMeter - chr2:222218398 34.4 8680 252.4
23:19:08.981 INFO ProgressMeter - chr2:224502963 34.6 8720 252.3
23:19:19.391 INFO ProgressMeter - chr2:226797872 34.7 8760 252.2
23:19:30.240 INFO ProgressMeter - chr20:32429336 34.9 8820 252.6
23:19:40.538 INFO ProgressMeter - chr20:32798458 35.1 8860 252.5
23:19:51.107 INFO ProgressMeter - chr20:42085726 35.3 8920 253.0
23:20:02.952 INFO ProgressMeter - chr20:47639923 35.5 8980 253.3
23:20:13.355 INFO ProgressMeter - chr20:56370156 35.6 9010 252.9
23:20:24.253 INFO ProgressMeter - chr20:58909949 35.8 9060 253.0
23:20:34.440 INFO ProgressMeter - chr21:38380843 36.0 9110 253.2
23:20:45.187 INFO ProgressMeter - chr21:41464549 36.2 9150 253.0
23:20:56.364 INFO ProgressMeter - chr21:41489443 36.3 9180 252.6
23:21:19.696 INFO ProgressMeter - chr21:41492278 36.7 9200 250.4
23:21:30.982 INFO ProgressMeter - chr21:41501025 36.9 9230 250.0
23:21:42.679 INFO ProgressMeter - chr21:41505188 37.1 9260 249.5
23:21:54.680 INFO ProgressMeter - chr21:44231278 37.3 9300 249.2
23:22:05.962 INFO ProgressMeter - chr22:23181920 37.5 9360 249.6
23:22:24.774 INFO ProgressMeter - chr22:23292471 37.8 9400 248.5
23:22:35.403 INFO ProgressMeter - chr22:28728768 38.0 9470 249.2
23:22:48.127 INFO ProgressMeter - chr22:29284577 38.2 9510 248.9
23:22:58.489 INFO ProgressMeter - chr22:29286168 38.4 9520 248.0
23:23:09.639 INFO ProgressMeter - chr22:29674834 38.6 9560 247.9
23:23:21.010 INFO ProgressMeter - chr22:41173621 38.8 9620 248.2
23:23:31.700 INFO ProgressMeter - chr3:10074528 38.9 9670 248.4
23:23:47.713 INFO ProgressMeter - chr3:12355461 39.2 9720 247.9
23:24:00.080 INFO ProgressMeter - chr3:12361013 39.4 9750 247.4
23:24:12.064 INFO ProgressMeter - chr3:12367563 39.6 9790 247.2
23:24:24.632 INFO ProgressMeter - chr3:12374225 39.8 9830 246.9
23:24:35.444 INFO ProgressMeter - chr3:12379531 40.0 9860 246.5
23:24:47.021 INFO ProgressMeter - chr3:12630777 40.2 9910 246.6
23:24:58.992 INFO ProgressMeter - chr3:41233527 40.4 9980 247.1
23:25:11.325 INFO ProgressMeter - chr3:47123187 40.6 10030 247.1
23:25:22.522 INFO ProgressMeter - chr3:49895165 40.8 10090 247.4
23:25:33.397 INFO ProgressMeter - chr3:52558249 41.0 10140 247.5
23:25:43.717 INFO ProgressMeter - chr3:70965888 41.1 10200 248.0
23:25:54.382 INFO ProgressMeter - chr3:89431148 41.3 10260 248.3
23:26:04.440 INFO ProgressMeter - chr3:135248314 41.5 10310 248.5
23:26:16.079 INFO ProgressMeter - chr3:138704441 41.7 10380 249.1
23:26:26.176 INFO ProgressMeter - chr3:142522726 41.8 10440 249.5
23:26:37.213 INFO ProgressMeter - chr3:179199124 42.0 10510 250.1
23:26:49.546 INFO ProgressMeter - chr3:185428580 42.2 10580 250.5
23:27:00.538 INFO ProgressMeter - chr3:186048791 42.4 10620 250.4
23:27:11.365 INFO ProgressMeter - chr3:189894204 42.6 10680 250.7
23:27:22.101 INFO ProgressMeter - chr4:1797835 42.8 10750 251.3
23:27:32.491 INFO ProgressMeter - chr4:20546029 42.9 10810 251.7
23:27:42.795 INFO ProgressMeter - chr4:54258102 43.1 10860 251.9
23:27:52.852 INFO ProgressMeter - chr4:54684279 43.3 10910 252.0
23:28:03.752 INFO ProgressMeter - chr4:54733068 43.5 10940 251.7
23:28:13.977 INFO ProgressMeter - chr4:65404372 43.6 11000 252.1
23:28:24.736 INFO ProgressMeter - chr4:80287876 43.8 11060 252.4
23:28:34.996 INFO ProgressMeter - chr4:105239475 44.0 11110 252.6
23:28:45.249 INFO ProgressMeter - chr4:105275046 44.2 11140 252.3
23:28:55.695 INFO ProgressMeter - chr4:142405204 44.3 11210 252.8
23:29:05.910 INFO ProgressMeter - chr4:186598015 44.5 11260 253.0
23:29:19.253 INFO ProgressMeter - chr4:186621459 44.7 11310 252.9
23:29:29.799 INFO ProgressMeter - chr5:225942 44.9 11350 252.8
23:29:40.468 INFO ProgressMeter - chr5:38958441 45.1 11410 253.1
23:29:51.500 INFO ProgressMeter - chr5:56865923 45.3 11490 253.8
23:30:02.654 INFO ProgressMeter - chr5:68293707 45.5 11550 254.1
23:30:12.754 INFO ProgressMeter - chr5:87383711 45.6 11620 254.7
23:30:23.645 INFO ProgressMeter - chr5:112841097 45.8 11670 254.8
23:30:34.991 INFO ProgressMeter - chr5:132595571 46.0 11720 254.8
23:30:46.266 INFO ProgressMeter - chr5:142636259 46.2 11780 255.1
23:30:57.339 INFO ProgressMeter - chr5:150057289 46.4 11830 255.2
23:31:09.413 INFO ProgressMeter - chr5:150133879 46.6 11890 255.3
23:31:20.291 INFO ProgressMeter - chr5:161691939 46.7 11940 255.4
23:31:31.227 INFO ProgressMeter - chr5:177090511 46.9 11980 255.3
23:31:43.915 INFO ProgressMeter - chr5:177211513 47.1 12030 255.2
23:31:55.960 INFO ProgressMeter - chr5:177516267 47.3 12080 255.2
23:32:07.513 INFO ProgressMeter - chr6:20402231 47.5 12140 255.4
23:32:17.950 INFO ProgressMeter - chr6:20467035 47.7 12180 255.3
23:32:29.904 INFO ProgressMeter - chr6:26127573 47.9 12240 255.5
23:32:40.325 INFO ProgressMeter - chr6:29942755 48.1 12270 255.2
23:32:53.349 INFO ProgressMeter - chr6:30705718 48.3 12300 254.7
23:33:05.236 INFO ProgressMeter - chr6:32202074 48.5 12340 254.5
23:33:16.842 INFO ProgressMeter - chr6:33319009 48.7 12390 254.5
23:33:28.327 INFO ProgressMeter - chr6:37170979 48.9 12440 254.5
23:33:38.919 INFO ProgressMeter - chr6:43774339 49.1 12500 254.8
23:33:51.315 INFO ProgressMeter - chr6:106107209 49.3 12570 255.2
23:34:02.622 INFO ProgressMeter - chr6:117320910 49.5 12620 255.2
23:34:14.167 INFO ProgressMeter - chr6:117326153 49.6 12650 254.8
23:34:27.630 INFO ProgressMeter - chr6:117333502 49.9 12690 254.5
23:34:39.194 INFO ProgressMeter - chr6:117341151 50.1 12730 254.3
23:34:51.959 INFO ProgressMeter - chr6:135203756 50.3 12790 254.4
23:35:02.088 INFO ProgressMeter - chr6:135207696 50.4 12820 254.2
23:35:20.955 INFO ProgressMeter - chr6:135212911 50.8 12850 253.2
23:35:31.301 INFO ProgressMeter - chr6:135214947 50.9 12860 252.5
23:35:41.952 INFO ProgressMeter - chr6:137878817 51.1 12900 252.4
23:35:52.005 INFO ProgressMeter - chr6:151366718 51.3 12940 252.4
23:36:06.769 INFO ProgressMeter - chr6:156778662 51.5 13000 252.3
23:36:17.629 INFO ProgressMeter - chr6:157190036 51.7 13030 252.0
23:36:28.011 INFO ProgressMeter - chr6:161092008 51.9 13070 252.0
23:36:39.514 INFO ProgressMeter - chr7:2923130 52.1 13140 252.4
23:36:51.008 INFO ProgressMeter - chr7:13893614 52.3 13200 252.6
23:37:05.041 INFO ProgressMeter - chr7:13909189 52.5 13240 252.2
23:37:15.602 INFO ProgressMeter - chr7:13937087 52.7 13270 252.0
23:37:27.104 INFO ProgressMeter - chr7:13944057 52.9 13320 252.0
23:37:39.714 INFO ProgressMeter - chr7:13949455 53.1 13350 251.6
23:37:52.982 INFO ProgressMeter - chr7:13955821 53.3 13380 251.1
23:38:04.520 INFO ProgressMeter - chr7:13962041 53.5 13410 250.7
23:38:14.541 INFO ProgressMeter - chr7:13968003 53.6 13440 250.5
23:38:24.742 INFO ProgressMeter - chr7:13973557 53.8 13480 250.5
23:38:35.552 INFO ProgressMeter - chr7:13975746 54.0 13500 250.0
23:38:48.123 INFO ProgressMeter - chr7:13982024 54.2 13540 249.8
23:38:59.340 INFO ProgressMeter - chr7:13986479 54.4 13570 249.5
23:39:11.238 INFO ProgressMeter - chr7:41699985 54.6 13600 249.1
23:39:21.348 INFO ProgressMeter - chr7:55157661 54.8 13640 249.1
23:39:32.651 INFO ProgressMeter - chr7:55167199 55.0 13660 248.6
23:39:45.409 INFO ProgressMeter - chr7:55175727 55.2 13700 248.3
23:39:57.766 INFO ProgressMeter - chr7:55180833 55.4 13740 248.1
23:40:08.378 INFO ProgressMeter - chr7:78132892 55.5 13780 248.1
23:40:20.008 INFO ProgressMeter - chr7:92615418 55.7 13840 248.3
23:40:30.509 INFO ProgressMeter - chr7:102198864 55.9 13900 248.6
23:40:40.576 INFO ProgressMeter - chr7:106868125 56.1 13940 248.6
23:40:51.301 INFO ProgressMeter - chr7:116765399 56.3 13980 248.5
23:41:02.082 INFO ProgressMeter - chr7:129212175 56.4 14020 248.4
23:41:12.401 INFO ProgressMeter - chr7:140788876 56.6 14050 248.2
23:41:26.985 INFO ProgressMeter - chr7:140794598 56.9 14090 247.8
23:41:37.088 INFO ProgressMeter - chr7:142958302 57.0 14150 248.1
23:41:49.555 INFO ProgressMeter - chr7:152163568 57.2 14220 248.5
23:42:00.775 INFO ProgressMeter - chr7:152238705 57.4 14270 248.5
23:42:11.227 INFO ProgressMeter - chr8:23682602 57.6 14330 248.8
23:42:23.278 INFO ProgressMeter - chr8:32646730 57.8 14390 249.0
23:42:33.536 INFO ProgressMeter - chr8:37697143 58.0 14430 248.9
23:42:44.363 INFO ProgressMeter - chr8:38413626 58.1 14480 249.0
23:42:56.442 INFO ProgressMeter - chr8:41932669 58.3 14530 249.0
23:43:06.913 INFO ProgressMeter - chr8:47778457 58.5 14570 249.0
23:43:18.076 INFO ProgressMeter - chr8:47912408 58.7 14640 249.4
23:43:28.264 INFO ProgressMeter - chr8:68027220 58.9 14710 249.8
23:43:39.305 INFO ProgressMeter - chr8:91975903 59.1 14790 250.4
23:43:49.943 INFO ProgressMeter - chr8:127732868 59.2 14830 250.3
23:44:02.240 INFO ProgressMeter - chr8:127740394 59.4 14860 250.0
23:44:12.949 INFO ProgressMeter - chr8:144517093 59.6 14910 250.1
23:44:22.992 INFO ProgressMeter - chr9:8340341 59.8 14980 250.5
23:44:36.404 INFO ProgressMeter - chr9:21968573 60.0 15050 250.8
23:44:46.993 INFO ProgressMeter - chr9:37033984 60.2 15100 250.9
23:45:02.109 INFO ProgressMeter - chr9:84743712 60.4 15160 250.8
23:45:12.430 INFO ProgressMeter - chr9:84813806 60.6 15190 250.6
23:45:23.898 INFO ProgressMeter - chr9:84862697 60.8 15210 250.1
23:45:35.987 INFO ProgressMeter - chr9:84872248 61.0 15240 249.8
23:45:48.613 INFO ProgressMeter - chr9:85021462 61.2 15280 249.6
23:46:00.989 INFO ProgressMeter - chr9:85026341 61.4 15310 249.3
23:46:11.110 INFO ProgressMeter - chr9:95456274 61.6 15360 249.4
23:46:23.383 INFO ProgressMeter - chr9:107487963 61.8 15420 249.5
23:46:34.208 INFO ProgressMeter - chr9:130885938 62.0 15470 249.6
23:46:46.355 INFO ProgressMeter - chr9:136500624 62.2 15520 249.6
23:46:57.474 INFO ProgressMeter - chr9:136523715 62.4 15570 249.7
23:47:08.856 INFO ProgressMeter - chrX:40072929 62.6 15650 250.2
23:47:19.793 INFO ProgressMeter - chrX:47186256 62.7 15730 250.7
23:47:31.039 INFO ProgressMeter - chrX:49037206 62.9 15810 251.3
23:47:41.221 INFO ProgressMeter - chrX:53380085 63.1 15870 251.5
23:47:51.804 INFO ProgressMeter - chrX:64199621 63.3 15930 251.8
23:48:02.107 INFO ProgressMeter - chrX:71122198 63.4 15990 252.0
23:48:13.331 INFO ProgressMeter - chrX:71383960 63.6 16050 252.2
23:48:23.862 INFO ProgressMeter - chrX:101377857 63.8 16160 253.3
23:48:35.106 INFO ProgressMeter - chrX:130055852 64.0 16260 254.1
23:48:40.995 INFO Mutect2 - 1011048 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
207 read(s) filtered by: ReadLengthReadFilter
128 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
1011383 total reads filtered out of 138004245 reads processed
23:48:40.995 INFO ProgressMeter - chrY:20398623 64.1 16325 254.7
23:48:40.995 INFO ProgressMeter - Traversal complete. Processed 16325 total regions in 64.1 minutes.
23:48:41.011 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 8.014087618000001
23:48:41.011 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 428.70912952400005
23:48:41.011 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 13.95 sec
23:48:41.012 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:48:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 64.10 minutes.
Runtime.totalMemory()=3305111552
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 LS0922_tumor.bam --tumor-sample LS0922 -L TST500C_manifest.bed -O LS0922.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:48:42.360 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
23:48:42.447 INFO FilterMutectCalls - ------------------------------------------------------------
23:48:42.449 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:48:42.449 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:48:42.449 INFO FilterMutectCalls - Executing as ?@nf-ba803fe2855d2ba3f5f58dbe4dffecad-349dd-28rst on Linux v6.12.88 amd64
23:48:42.449 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:48:42.449 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:48:42 PM GMT
23:48:42.449 INFO FilterMutectCalls - ------------------------------------------------------------
23:48:42.450 INFO FilterMutectCalls - ------------------------------------------------------------
23:48:42.450 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:48:42.451 INFO FilterMutectCalls - Picard Version: 3.1.1
23:48:42.451 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:48:42.451 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:48:42.451 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:48:42.451 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:48:42.451 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:48:42.451 INFO FilterMutectCalls - Deflater: IntelDeflater
23:48:42.451 INFO FilterMutectCalls - Inflater: IntelInflater
23:48:42.451 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:48:42.451 INFO FilterMutectCalls - Requester pays: disabled
23:48:42.452 INFO FilterMutectCalls - Initializing engine
23:48:42.617 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.9hto0drC5P/LS0922.mutect2.raw.vcf.gz
23:48:42.723 INFO FilterMutectCalls - Done initializing engine
23:48:42.777 INFO ProgressMeter - Starting traversal
23:48:42.777 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:48:42.778 INFO FilterMutectCalls - Starting pass 0 through the variants
23:48:44.232 INFO FilterMutectCalls - Finished pass 0 through the variants
23:48:45.017 INFO FilterMutectCalls - Starting pass 1 through the variants
23:48:46.324 INFO FilterMutectCalls - Finished pass 1 through the variants
23:48:46.689 INFO FilterMutectCalls - Starting pass 2 through the variants
23:48:47.944 INFO FilterMutectCalls - Finished pass 2 through the variants
23:48:47.946 INFO FilterMutectCalls - Starting pass 3 through the variants
23:48:48.963 INFO FilterMutectCalls - Finished pass 3 through the variants
23:48:48.973 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:48:48.973 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:48:48.973 INFO ProgressMeter - chr6:156778737 0.1 11672 113027.8
23:48:48.974 INFO ProgressMeter - Traversal complete. Processed 11672 total variants in 0.1 minutes.
23:48:48.985 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:48:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.11 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 LS0922.mutect2.raw.vcf.gz --stats LS0922.mutect2.raw.vcf.gz.stats -O LS0922.mutect2.filtered.vcf.gz
23:48:50.211 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
23:48:50.313 INFO SelectVariants - ------------------------------------------------------------
23:48:50.315 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:48:50.315 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:48:50.315 INFO SelectVariants - Executing as ?@nf-ba803fe2855d2ba3f5f58dbe4dffecad-349dd-28rst on Linux v6.12.88 amd64
23:48:50.315 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:48:50.316 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:48:50 PM GMT
23:48:50.316 INFO SelectVariants - ------------------------------------------------------------
23:48:50.316 INFO SelectVariants - ------------------------------------------------------------
23:48:50.316 INFO SelectVariants - HTSJDK Version: 4.1.0
23:48:50.316 INFO SelectVariants - Picard Version: 3.1.1
23:48:50.317 INFO SelectVariants - Built for Spark Version: 3.5.0
23:48:50.317 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:48:50.317 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:48:50.317 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:48:50.317 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:48:50.317 INFO SelectVariants - Deflater: IntelDeflater
23:48:50.317 INFO SelectVariants - Inflater: IntelInflater
23:48:50.317 INFO SelectVariants - GCS max retries/reopens: 20
23:48:50.317 INFO SelectVariants - Requester pays: disabled
23:48:50.318 INFO SelectVariants - Initializing engine
23:48:50.451 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.9hto0drC5P/LS0922.mutect2.filtered.vcf.gz
23:48:50.564 INFO SelectVariants - Done initializing engine
23:48:50.601 INFO ProgressMeter - Starting traversal
23:48:50.601 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:48:50.678 INFO ProgressMeter - chr6:20461034 0.0 2918 2334400.0
23:48:50.678 INFO ProgressMeter - Traversal complete. Processed 2918 total variants in 0.0 minutes.
23:48:50.691 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:48:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=318767104
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 LS0922.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0922.mutect2.pass.vcf.gz