22:44:14.911 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
22:44:15.019 INFO Mutect2 - ------------------------------------------------------------
22:44:15.022 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:15.022 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:15.022 INFO Mutect2 - Executing as ?@nf-fc489759ee5cf383fc5cdbde99a1d8b7-67b80-mzzsn on Linux v6.12.88 amd64
22:44:15.022 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:15.022 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:14 PM GMT
22:44:15.022 INFO Mutect2 - ------------------------------------------------------------
22:44:15.022 INFO Mutect2 - ------------------------------------------------------------
22:44:15.023 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:15.023 INFO Mutect2 - Picard Version: 3.1.1
22:44:15.023 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:15.023 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:15.023 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:15.023 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:15.024 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:15.024 INFO Mutect2 - Deflater: IntelDeflater
22:44:15.024 INFO Mutect2 - Inflater: IntelInflater
22:44:15.024 INFO Mutect2 - GCS max retries/reopens: 20
22:44:15.024 INFO Mutect2 - Requester pays: disabled
22:44:15.024 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.U0UleEWFyX/LS0925_tumor.bam.bai is older than BAM /tmp/nxf.U0UleEWFyX/LS0925_tumor.bam
22:44:15.215 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.U0UleEWFyX/af-only-gnomad.hg38.vcf.gz
22:44:15.418 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.U0UleEWFyX/TST500C_manifest.bed
22:44:15.455 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:15.483 INFO Mutect2 - Done initializing engine
22:44:15.492 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
22:44:15.493 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
22:44:15.494 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:15.494 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:15.504 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
22:44:15.512 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:15.513 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:15.513 INFO IntelPairHmm - Available threads: 384
22:44:15.513 INFO IntelPairHmm - Requested threads: 4
22:44:15.513 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:15.563 INFO ProgressMeter - Starting traversal
22:44:15.563 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:25.630 INFO ProgressMeter - chr1:9716957 0.2 30 178.8
22:44:37.023 INFO ProgressMeter - chr1:11157150 0.4 90 251.6
22:44:48.036 INFO ProgressMeter - chr1:15876500 0.5 140 258.7
22:45:01.064 INFO ProgressMeter - chr1:15935285 0.8 180 237.4
22:45:11.787 INFO ProgressMeter - chr1:18703213 0.9 220 234.8
22:45:23.091 INFO ProgressMeter - chr1:26696402 1.1 260 231.0
22:45:35.245 INFO ProgressMeter - chr1:26775575 1.3 300 225.9
22:45:46.373 INFO ProgressMeter - chr1:39890423 1.5 350 231.3
22:45:57.821 INFO ProgressMeter - chr1:39906953 1.7 400 234.7
22:46:09.581 INFO ProgressMeter - chr1:46260540 1.9 460 242.1
22:46:20.396 INFO ProgressMeter - chr1:64845511 2.1 510 245.1
22:46:30.469 INFO ProgressMeter - chr1:85280873 2.2 570 253.5
22:46:40.967 INFO ProgressMeter - chr1:119513909 2.4 630 260.0
22:46:52.812 INFO ProgressMeter - chr1:119966374 2.6 680 259.5
22:47:04.384 INFO ProgressMeter - chr1:156872788 2.8 730 259.4
22:47:15.428 INFO ProgressMeter - chr1:156879120 3.0 750 250.2
22:47:26.340 INFO ProgressMeter - chr1:158666393 3.2 810 254.7
22:47:36.373 INFO ProgressMeter - chr1:176081150 3.3 870 259.9
22:47:46.970 INFO ProgressMeter - chr1:204433825 3.5 940 266.8
22:47:57.609 INFO ProgressMeter - chr1:204536148 3.7 1000 270.2
22:48:08.653 INFO ProgressMeter - chr1:206490817 3.9 1050 270.3
22:48:19.116 INFO ProgressMeter - chr1:241502441 4.1 1110 273.5
22:48:31.765 INFO ProgressMeter - chr1:243504678 4.3 1150 269.3
22:48:42.179 INFO ProgressMeter - chr10:27034921 4.4 1210 272.3
22:48:52.683 INFO ProgressMeter - chr10:32011129 4.6 1260 272.8
22:49:04.782 INFO ProgressMeter - chr10:43111913 4.8 1320 273.8
22:49:16.804 INFO ProgressMeter - chr10:43116223 5.0 1360 270.9
22:49:26.967 INFO ProgressMeter - chr10:52682603 5.2 1400 269.7
22:49:38.928 INFO ProgressMeter - chr10:68645829 5.4 1440 267.2
22:49:49.413 INFO ProgressMeter - chr10:87925688 5.6 1500 269.6
22:50:00.336 INFO ProgressMeter - chr10:101772770 5.7 1550 269.7
22:50:11.329 INFO ProgressMeter - chr10:110589584 5.9 1610 271.5
22:50:25.184 INFO ProgressMeter - chr10:121481360 6.2 1670 271.1
22:50:36.455 INFO ProgressMeter - chr10:121530300 6.3 1710 269.4
22:50:46.908 INFO ProgressMeter - chr11:17719931 6.5 1760 269.8
22:50:58.441 INFO ProgressMeter - chr11:64370223 6.7 1810 269.6
22:51:08.442 INFO ProgressMeter - chr11:69643244 6.9 1860 270.3
22:51:18.738 INFO ProgressMeter - chr11:69698037 7.1 1900 269.4
22:51:31.383 INFO ProgressMeter - chr11:69701908 7.3 1920 264.3
22:51:43.238 INFO ProgressMeter - chr11:69774743 7.5 1970 264.0
22:51:59.584 INFO ProgressMeter - chr11:69810303 7.7 2000 258.6
22:52:10.078 INFO ProgressMeter - chr11:69819066 7.9 2040 257.9
22:52:23.491 INFO ProgressMeter - chr11:77349182 8.1 2100 258.2
22:52:34.730 INFO ProgressMeter - chr11:86278397 8.3 2170 260.8
22:52:51.515 INFO ProgressMeter - chr11:102324508 8.6 2230 259.3
22:53:02.821 INFO ProgressMeter - chr11:108327643 8.8 2300 261.7
22:53:14.856 INFO ProgressMeter - chr11:118491742 9.0 2360 262.6
22:53:26.349 INFO ProgressMeter - chr11:118511949 9.2 2400 261.4
22:53:36.378 INFO ProgressMeter - chr11:125620819 9.3 2430 260.0
22:53:47.408 INFO ProgressMeter - chr11:126418958 9.5 2480 260.2
22:53:57.952 INFO ProgressMeter - chr11:128460477 9.7 2490 256.5
22:54:08.720 INFO ProgressMeter - chr11:128758113 9.9 2520 254.9
22:54:20.201 INFO ProgressMeter - chr12:310924 10.1 2570 255.0
22:54:30.397 INFO ProgressMeter - chr12:4370444 10.2 2630 256.7
22:54:44.833 INFO ProgressMeter - chr12:4440523 10.5 2690 256.5
22:54:56.295 INFO ProgressMeter - chr12:6591914 10.7 2750 257.5
22:55:07.522 INFO ProgressMeter - chr12:11752429 10.9 2780 255.8
22:55:18.820 INFO ProgressMeter - chr12:11856705 11.1 2810 254.2
22:55:31.641 INFO ProgressMeter - chr12:11861014 11.3 2850 252.9
22:55:44.976 INFO ProgressMeter - chr12:11865378 11.5 2880 250.6
22:55:59.052 INFO ProgressMeter - chr12:11885905 11.7 2910 248.2
22:56:09.176 INFO ProgressMeter - chr12:25221202 11.9 2980 250.6
22:56:21.445 INFO ProgressMeter - chr12:45850287 12.1 3030 250.5
22:56:33.568 INFO ProgressMeter - chr12:49031473 12.3 3080 250.4
22:56:45.654 INFO ProgressMeter - chr12:49038092 12.5 3110 248.8
22:56:56.313 INFO ProgressMeter - chr12:49049103 12.7 3160 249.2
22:57:06.548 INFO ProgressMeter - chr12:51951742 12.8 3200 249.0
22:57:17.668 INFO ProgressMeter - chr12:56091699 13.0 3240 248.6
22:57:28.972 INFO ProgressMeter - chr12:57093269 13.2 3290 248.8
22:57:40.329 INFO ProgressMeter - chr12:57471863 13.4 3330 248.3
22:57:50.442 INFO ProgressMeter - chr12:57754237 13.6 3370 248.1
22:58:01.654 INFO ProgressMeter - chr12:69570451 13.8 3430 249.1
22:58:13.316 INFO ProgressMeter - chr12:112504693 14.0 3490 250.0
22:58:23.579 INFO ProgressMeter - chr12:132624695 14.1 3540 250.5
22:58:33.793 INFO ProgressMeter - chr12:132672213 14.3 3590 251.0
22:58:44.799 INFO ProgressMeter - chr13:21671488 14.5 3640 251.3
22:58:56.753 INFO ProgressMeter - chr13:28023348 14.7 3710 252.6
22:59:08.489 INFO ProgressMeter - chr13:28386149 14.9 3770 253.3
22:59:20.122 INFO ProgressMeter - chr13:28431134 15.1 3810 252.7
22:59:32.082 INFO ProgressMeter - chr13:32340697 15.3 3860 252.7
22:59:42.734 INFO ProgressMeter - chr13:48367492 15.5 3920 253.7
22:59:53.456 INFO ProgressMeter - chr13:102181777 15.6 3990 255.3
23:00:03.581 INFO ProgressMeter - chr13:109782040 15.8 4040 255.7
23:00:14.117 INFO ProgressMeter - chr13:113302896 16.0 4080 255.4
23:00:26.620 INFO ProgressMeter - chr14:23183020 16.2 4120 254.6
23:00:37.847 INFO ProgressMeter - chr14:37590549 16.4 4180 255.3
23:00:50.254 INFO ProgressMeter - chr14:52750043 16.6 4230 255.2
23:01:02.424 INFO ProgressMeter - chr14:95095770 16.8 4290 255.6
23:01:13.015 INFO ProgressMeter - chr14:102085756 17.0 4340 255.9
23:01:25.498 INFO ProgressMeter - chr15:34346573 17.2 4390 255.7
23:01:36.708 INFO ProgressMeter - chr15:40698755 17.4 4430 255.3
23:01:49.009 INFO ProgressMeter - chr15:41749409 17.6 4480 255.2
23:01:59.140 INFO ProgressMeter - chr15:49453215 17.7 4530 255.6
23:02:11.434 INFO ProgressMeter - chr15:87933055 17.9 4600 256.5
23:02:21.597 INFO ProgressMeter - chr15:89274281 18.1 4650 256.9
23:02:32.755 INFO ProgressMeter - chr15:90766908 18.3 4710 257.6
23:02:43.364 INFO ProgressMeter - chr15:92998497 18.5 4770 258.3
23:02:54.656 INFO ProgressMeter - chr16:297054 18.7 4820 258.4
23:03:06.774 INFO ProgressMeter - chr16:2086730 18.9 4880 258.8
23:03:17.537 INFO ProgressMeter - chr16:3590570 19.0 4950 260.1
23:03:35.671 INFO ProgressMeter - chr16:3729082 19.3 4980 257.6
23:03:48.620 INFO ProgressMeter - chr16:9764252 19.6 5040 257.8
23:03:58.873 INFO ProgressMeter - chr16:13935444 19.7 5080 257.6
23:04:10.558 INFO ProgressMeter - chr16:31132680 19.9 5130 257.6
23:04:22.643 INFO ProgressMeter - chr16:67637686 20.1 5200 258.5
23:04:32.913 INFO ProgressMeter - chr16:72788044 20.3 5230 257.8
23:04:44.217 INFO ProgressMeter - chr16:72797171 20.5 5260 256.9
23:04:57.431 INFO ProgressMeter - chr16:72959831 20.7 5290 255.6
23:05:10.088 INFO ProgressMeter - chr16:89281547 20.9 5360 256.4
23:05:20.656 INFO ProgressMeter - chr16:89288526 21.1 5390 255.6
23:05:30.783 INFO ProgressMeter - chr17:4066820 21.3 5450 256.4
23:05:44.924 INFO ProgressMeter - chr17:7675992 21.5 5500 255.9
23:05:55.743 INFO ProgressMeter - chr17:12110373 21.7 5560 256.6
23:06:06.578 INFO ProgressMeter - chr17:16143604 21.9 5620 257.2
23:06:16.874 INFO ProgressMeter - chr17:31222550 22.0 5680 257.9
23:06:28.223 INFO ProgressMeter - chr17:35103289 22.2 5750 258.9
23:06:39.643 INFO ProgressMeter - chr17:39699558 22.4 5800 258.9
23:06:51.516 INFO ProgressMeter - chr17:39727987 22.6 5850 258.9
23:07:02.524 INFO ProgressMeter - chr17:42218721 22.8 5920 259.8
23:07:13.154 INFO ProgressMeter - chr17:43056248 23.0 5990 260.9
23:07:23.320 INFO ProgressMeter - chr17:43112664 23.1 6040 261.1
23:07:37.456 INFO ProgressMeter - chr17:43532515 23.4 6080 260.2
23:07:50.507 INFO ProgressMeter - chr17:43539743 23.6 6120 259.5
23:08:05.139 INFO ProgressMeter - chr17:43543739 23.8 6150 258.1
23:08:15.804 INFO ProgressMeter - chr17:45284862 24.0 6190 257.9
23:08:27.394 INFO ProgressMeter - chr17:58692642 24.2 6240 257.9
23:08:39.567 INFO ProgressMeter - chr17:59946756 24.4 6310 258.6
23:08:50.049 INFO ProgressMeter - chr17:63931333 24.6 6360 258.8
23:09:01.352 INFO ProgressMeter - chr17:72121390 24.8 6410 258.9
23:09:13.007 INFO ProgressMeter - chr17:80957622 25.0 6470 259.2
23:09:23.912 INFO ProgressMeter - chr18:44701619 25.1 6540 260.2
23:09:34.688 INFO ProgressMeter - chr18:45063654 25.3 6570 259.5
23:09:45.905 INFO ProgressMeter - chr18:63318574 25.5 6630 259.9
23:09:56.636 INFO ProgressMeter - chr19:2211097 25.7 6690 260.5
23:10:08.236 INFO ProgressMeter - chr19:4054504 25.9 6740 260.5
23:10:18.544 INFO ProgressMeter - chr19:5225725 26.0 6800 261.0
23:10:29.245 INFO ProgressMeter - chr19:10133665 26.2 6860 261.6
23:10:39.688 INFO ProgressMeter - chr19:10180776 26.4 6910 261.7
23:10:49.992 INFO ProgressMeter - chr19:11027782 26.6 6960 261.9
23:11:00.129 INFO ProgressMeter - chr19:14517480 26.7 7000 261.8
23:11:12.153 INFO ProgressMeter - chr19:15184293 26.9 7050 261.7
23:11:23.758 INFO ProgressMeter - chr19:15255411 27.1 7100 261.6
23:11:38.193 INFO ProgressMeter - chr19:18156081 27.4 7150 261.2
23:11:51.190 INFO ProgressMeter - chr19:29817404 27.6 7200 260.9
23:12:02.874 INFO ProgressMeter - chr19:35721011 27.8 7250 260.9
23:12:13.218 INFO ProgressMeter - chr19:35732752 28.0 7300 261.1
23:12:23.612 INFO ProgressMeter - chr19:40260196 28.1 7350 261.2
23:12:34.058 INFO ProgressMeter - chr19:41259551 28.3 7400 261.4
23:12:44.126 INFO ProgressMeter - chr19:42284703 28.5 7420 260.6
23:12:55.565 INFO ProgressMeter - chr19:45352304 28.7 7470 260.6
23:13:07.115 INFO ProgressMeter - chr19:45411426 28.9 7540 261.3
23:13:19.212 INFO ProgressMeter - chr19:50402272 29.1 7590 261.2
23:13:34.028 INFO ProgressMeter - chr2:15940559 29.3 7650 261.0
23:13:45.527 INFO ProgressMeter - chr2:15950395 29.5 7690 260.7
23:13:58.261 INFO ProgressMeter - chr2:25742383 29.7 7750 260.8
23:14:09.353 INFO ProgressMeter - chr2:29207169 29.9 7800 260.9
23:14:23.064 INFO ProgressMeter - chr2:29226595 30.1 7830 259.9
23:14:36.152 INFO ProgressMeter - chr2:42256538 30.3 7880 259.7
23:14:46.444 INFO ProgressMeter - chr2:47410092 30.5 7930 259.9
23:14:57.595 INFO ProgressMeter - chr2:47798942 30.7 7960 259.3
23:15:07.845 INFO ProgressMeter - chr2:61488163 30.9 8020 259.8
23:15:18.484 INFO ProgressMeter - chr2:96265136 31.0 8050 259.3
23:15:31.095 INFO ProgressMeter - chr2:108766322 31.3 8120 259.8
23:15:48.084 INFO ProgressMeter - chr2:111128562 31.5 8160 258.7
23:15:59.008 INFO ProgressMeter - chr2:113223860 31.7 8200 258.5
23:16:13.401 INFO ProgressMeter - chr2:113227097 32.0 8220 257.2
23:16:23.733 INFO ProgressMeter - chr2:113231860 32.1 8250 256.7
23:16:35.060 INFO ProgressMeter - chr2:113236209 32.3 8280 256.1
23:16:45.574 INFO ProgressMeter - chr2:140323891 32.5 8340 256.6
23:16:58.011 INFO ProgressMeter - chr2:140907875 32.7 8410 257.1
23:17:09.868 INFO ProgressMeter - chr2:177231279 32.9 8470 257.4
23:17:20.669 INFO ProgressMeter - chr2:197401983 33.1 8540 258.1
23:17:31.235 INFO ProgressMeter - chr2:211424153 33.3 8600 258.6
23:17:41.691 INFO ProgressMeter - chr2:219576879 33.4 8660 259.0
23:17:53.631 INFO ProgressMeter - chr2:222205298 33.6 8690 258.4
23:18:03.989 INFO ProgressMeter - chr2:222210837 33.8 8720 257.9
23:18:14.383 INFO ProgressMeter - chr2:222216101 34.0 8750 257.5
23:18:27.091 INFO ProgressMeter - chr2:222294273 34.2 8790 257.1
23:18:39.110 INFO ProgressMeter - chr2:226797433 34.4 8840 257.0
23:18:49.556 INFO ProgressMeter - chr20:31721653 34.6 8890 257.2
23:18:59.900 INFO ProgressMeter - chr20:32781351 34.7 8930 257.1
23:19:10.106 INFO ProgressMeter - chr20:41113968 34.9 8990 257.5
23:19:21.163 INFO ProgressMeter - chr20:47636189 35.1 9050 257.9
23:19:31.596 INFO ProgressMeter - chr20:52679538 35.3 9070 257.2
23:19:42.737 INFO ProgressMeter - chr20:58854009 35.5 9110 257.0
23:19:53.275 INFO ProgressMeter - chr21:34859364 35.6 9170 257.4
23:20:04.220 INFO ProgressMeter - chr21:38445402 35.8 9210 257.2
23:20:19.294 INFO ProgressMeter - chr21:41489743 36.1 9260 256.8
23:20:31.364 INFO ProgressMeter - chr21:41491323 36.3 9270 255.6
23:20:42.089 INFO ProgressMeter - chr21:41494299 36.4 9290 254.9
23:20:59.232 INFO ProgressMeter - chr21:41503040 36.7 9320 253.8
23:21:10.136 INFO ProgressMeter - chr21:41507945 36.9 9350 253.3
23:21:20.595 INFO ProgressMeter - chr22:20994102 37.1 9400 253.5
23:21:33.000 INFO ProgressMeter - chr22:23290412 37.3 9450 253.4
23:21:45.246 INFO ProgressMeter - chr22:23291618 37.5 9460 252.3
23:21:56.529 INFO ProgressMeter - chr22:28712279 37.7 9520 252.6
23:22:12.378 INFO ProgressMeter - chr22:29285076 37.9 9580 252.5
23:22:22.667 INFO ProgressMeter - chr22:29603997 38.1 9610 252.1
23:22:34.094 INFO ProgressMeter - chr22:41152204 38.3 9670 252.4
23:22:46.614 INFO ProgressMeter - chr3:10063790 38.5 9730 252.6
23:23:01.418 INFO ProgressMeter - chr3:12355096 38.8 9790 252.6
23:23:13.323 INFO ProgressMeter - chr3:12360237 39.0 9820 252.0
23:23:26.679 INFO ProgressMeter - chr3:12365531 39.2 9850 251.4
23:23:36.849 INFO ProgressMeter - chr3:12370579 39.4 9880 251.0
23:23:50.191 INFO ProgressMeter - chr3:12377151 39.6 9920 250.6
23:24:00.792 INFO ProgressMeter - chr3:12615193 39.8 9970 250.8
23:24:11.088 INFO ProgressMeter - chr3:36993871 39.9 10010 250.7
23:24:21.253 INFO ProgressMeter - chr3:47046485 40.1 10070 251.2
23:24:32.202 INFO ProgressMeter - chr3:47123342 40.3 10110 251.0
23:24:43.274 INFO ProgressMeter - chr3:49896538 40.5 10170 251.3
23:24:53.470 INFO ProgressMeter - chr3:52586498 40.6 10220 251.5
23:25:03.556 INFO ProgressMeter - chr3:70987992 40.8 10280 252.0
23:25:14.049 INFO ProgressMeter - chr3:89479395 41.0 10340 252.4
23:25:25.488 INFO ProgressMeter - chr3:136366990 41.2 10400 252.6
23:25:35.573 INFO ProgressMeter - chr3:138732850 41.3 10460 253.1
23:25:47.999 INFO ProgressMeter - chr3:142562230 41.5 10530 253.5
23:26:00.392 INFO ProgressMeter - chr3:179204501 41.7 10590 253.7
23:26:11.484 INFO ProgressMeter - chr3:185285604 41.9 10650 254.0
23:26:21.812 INFO ProgressMeter - chr3:186057421 42.1 10690 253.9
23:26:32.760 INFO ProgressMeter - chr3:196049881 42.3 10750 254.2
23:26:43.357 INFO ProgressMeter - chr4:1799745 42.5 10820 254.8
23:26:53.804 INFO ProgressMeter - chr4:20542492 42.6 10880 255.2
23:27:04.574 INFO ProgressMeter - chr4:41746161 42.8 10930 255.3
23:27:16.363 INFO ProgressMeter - chr4:54693213 43.0 10990 255.5
23:27:27.411 INFO ProgressMeter - chr4:54733193 43.2 11020 255.1
23:27:38.923 INFO ProgressMeter - chr4:65643361 43.4 11090 255.6
23:27:49.461 INFO ProgressMeter - chr4:83476641 43.6 11150 255.9
23:28:01.023 INFO ProgressMeter - chr4:105241096 43.8 11200 256.0
23:28:12.137 INFO ProgressMeter - chr4:122876319 43.9 11250 256.0
23:28:23.572 INFO ProgressMeter - chr4:184408156 44.1 11320 256.5
23:28:36.215 INFO ProgressMeter - chr4:186618689 44.3 11370 256.4
23:28:48.609 INFO ProgressMeter - chr4:186708976 44.6 11410 256.1
23:28:58.752 INFO ProgressMeter - chr5:35874447 44.7 11460 256.3
23:29:10.157 INFO ProgressMeter - chr5:44355299 44.9 11540 257.0
23:29:20.288 INFO ProgressMeter - chr5:56883525 45.1 11590 257.1
23:29:32.067 INFO ProgressMeter - chr5:80678925 45.3 11650 257.3
23:29:44.331 INFO ProgressMeter - chr5:112838579 45.5 11730 257.9
23:29:56.023 INFO ProgressMeter - chr5:122449843 45.7 11770 257.7
23:30:06.626 INFO ProgressMeter - chr5:138917740 45.9 11830 258.0
23:30:18.802 INFO ProgressMeter - chr5:142697259 46.1 11880 258.0
23:30:28.912 INFO ProgressMeter - chr5:150113836 46.2 11930 258.1
23:30:40.180 INFO ProgressMeter - chr5:150402027 46.4 11980 258.1
23:30:51.899 INFO ProgressMeter - chr5:177088864 46.6 12040 258.3
23:31:02.647 INFO ProgressMeter - chr5:177095328 46.8 12070 258.0
23:31:13.208 INFO ProgressMeter - chr5:177251728 47.0 12110 257.9
23:31:23.243 INFO ProgressMeter - chr5:177516704 47.1 12150 257.8
23:31:33.604 INFO ProgressMeter - chr6:393151 47.3 12200 257.9
23:31:44.693 INFO ProgressMeter - chr6:20467035 47.5 12260 258.2
23:31:56.221 INFO ProgressMeter - chr6:26158168 47.7 12320 258.4
23:32:10.781 INFO ProgressMeter - chr6:30700463 47.9 12350 257.7
23:32:22.628 INFO ProgressMeter - chr6:30712780 48.1 12390 257.5
23:32:33.309 INFO ProgressMeter - chr6:32216966 48.3 12440 257.6
23:32:44.739 INFO ProgressMeter - chr6:35455923 48.5 12480 257.4
23:32:55.669 INFO ProgressMeter - chr6:41975380 48.7 12540 257.7
23:33:05.984 INFO ProgressMeter - chr6:93258097 48.8 12600 258.0
23:33:17.478 INFO ProgressMeter - chr6:112068274 49.0 12660 258.2
23:33:30.944 INFO ProgressMeter - chr6:117323687 49.3 12700 257.8
23:33:42.360 INFO ProgressMeter - chr6:117331813 49.4 12740 257.7
23:33:54.258 INFO ProgressMeter - chr6:117339049 49.6 12780 257.4
23:34:04.369 INFO ProgressMeter - chr6:135181512 49.8 12830 257.6
23:34:17.233 INFO ProgressMeter - chr6:135206267 50.0 12870 257.3
23:34:27.474 INFO ProgressMeter - chr6:135211643 50.2 12900 257.0
23:34:38.030 INFO ProgressMeter - chr6:135213573 50.4 12910 256.3
23:34:54.847 INFO ProgressMeter - chr6:137200879 50.7 12940 255.5
23:35:05.740 INFO ProgressMeter - chr6:149701777 50.8 12990 255.5
23:35:16.992 INFO ProgressMeter - chr6:152041926 51.0 13040 255.6
23:35:32.811 INFO ProgressMeter - chr6:156935464 51.3 13070 254.8
23:35:43.156 INFO ProgressMeter - chr6:160992077 51.5 13110 254.8
23:35:54.141 INFO ProgressMeter - chr6:163415192 51.6 13170 255.0
23:36:05.201 INFO ProgressMeter - chr7:2958498 51.8 13220 255.1
23:36:16.400 INFO ProgressMeter - chr7:13900736 52.0 13270 255.1
23:36:32.232 INFO ProgressMeter - chr7:13932412 52.3 13310 254.6
23:36:43.611 INFO ProgressMeter - chr7:13941363 52.5 13360 254.6
23:36:57.284 INFO ProgressMeter - chr7:13946062 52.7 13390 254.1
23:37:08.750 INFO ProgressMeter - chr7:13951536 52.9 13420 253.8
23:37:19.146 INFO ProgressMeter - chr7:13957176 53.1 13450 253.5
23:37:29.395 INFO ProgressMeter - chr7:13962553 53.2 13480 253.2
23:37:43.515 INFO ProgressMeter - chr7:13970674 53.5 13520 252.9
23:37:59.907 INFO ProgressMeter - chr7:13975526 53.7 13560 252.3
23:38:11.649 INFO ProgressMeter - chr7:13981346 53.9 13600 252.2
23:38:23.329 INFO ProgressMeter - chr7:13985580 54.1 13630 251.8
23:38:34.550 INFO ProgressMeter - chr7:13989806 54.3 13650 251.3
23:38:46.988 INFO ProgressMeter - chr7:55156154 54.5 13700 251.3
23:39:04.721 INFO ProgressMeter - chr7:55169628 54.8 13740 250.6
23:39:16.871 INFO ProgressMeter - chr7:55177777 55.0 13780 250.4
23:39:27.510 INFO ProgressMeter - chr7:55183653 55.2 13810 250.2
23:39:39.434 INFO ProgressMeter - chr7:78369154 55.4 13860 250.2
23:39:51.325 INFO ProgressMeter - chr7:92686936 55.6 13920 250.4
23:40:02.183 INFO ProgressMeter - chr7:102201965 55.8 13970 250.5
23:40:13.043 INFO ProgressMeter - chr7:106879517 56.0 14020 250.5
23:40:25.338 INFO ProgressMeter - chr7:116771946 56.2 14060 250.3
23:40:37.939 INFO ProgressMeter - chr7:140747077 56.4 14100 250.1
23:40:48.599 INFO ProgressMeter - chr7:140791601 56.6 14140 250.0
23:40:58.851 INFO ProgressMeter - chr7:140876954 56.7 14180 250.0
23:41:10.099 INFO ProgressMeter - chr7:148832632 56.9 14250 250.4
23:41:22.052 INFO ProgressMeter - chr7:152176189 57.1 14310 250.6
23:41:33.646 INFO ProgressMeter - chr7:152247900 57.3 14360 250.6
23:41:44.241 INFO ProgressMeter - chr8:26338888 57.5 14420 250.9
23:41:57.425 INFO ProgressMeter - chr8:32647610 57.7 14480 251.0
23:42:09.078 INFO ProgressMeter - chr8:37829849 57.9 14530 251.0
23:42:21.471 INFO ProgressMeter - chr8:38429680 58.1 14580 251.0
23:42:33.320 INFO ProgressMeter - chr8:41943746 58.3 14620 250.8
23:42:44.064 INFO ProgressMeter - chr8:47831812 58.5 14670 250.9
23:42:54.806 INFO ProgressMeter - chr8:47957353 58.7 14740 251.3
23:43:05.536 INFO ProgressMeter - chr8:68115751 58.8 14800 251.6
23:43:16.961 INFO ProgressMeter - chr8:116852649 59.0 14880 252.1
23:43:28.196 INFO ProgressMeter - chr8:127733768 59.2 14900 251.6
23:43:38.709 INFO ProgressMeter - chr8:127739751 59.4 14930 251.4
23:43:50.125 INFO ProgressMeter - chr8:144516197 59.6 14980 251.4
23:44:00.248 INFO ProgressMeter - chr9:5457390 59.7 15040 251.7
23:44:10.725 INFO ProgressMeter - chr9:8733778 59.9 15110 252.2
23:44:20.816 INFO ProgressMeter - chr9:22003650 60.1 15140 252.0
23:44:31.929 INFO ProgressMeter - chr9:83974542 60.3 15200 252.2
23:44:44.865 INFO ProgressMeter - chr9:84742877 60.5 15230 251.8
23:44:57.772 INFO ProgressMeter - chr9:84813556 60.7 15260 251.4
23:45:08.713 INFO ProgressMeter - chr9:84862308 60.9 15280 251.0
23:45:18.789 INFO ProgressMeter - chr9:84865606 61.1 15300 250.6
23:45:31.656 INFO ProgressMeter - chr9:84877635 61.3 15340 250.4
23:45:42.276 INFO ProgressMeter - chr9:85025247 61.4 15370 250.1
23:45:52.831 INFO ProgressMeter - chr9:95149921 61.6 15420 250.2
23:46:03.693 INFO ProgressMeter - chr9:99105204 61.8 15470 250.3
23:46:14.605 INFO ProgressMeter - chr9:130880066 62.0 15530 250.5
23:46:26.220 INFO ProgressMeter - chr9:132906729 62.2 15570 250.4
23:46:37.765 INFO ProgressMeter - chr9:136507953 62.4 15620 250.4
23:46:49.031 INFO ProgressMeter - chr9:136925681 62.6 15680 250.6
23:46:59.643 INFO ProgressMeter - chrX:45060607 62.7 15760 251.2
23:47:10.025 INFO ProgressMeter - chrX:48794091 62.9 15830 251.6
23:47:20.878 INFO ProgressMeter - chrX:49043109 63.1 15890 251.9
23:47:31.618 INFO ProgressMeter - chrX:53412879 63.3 15960 252.3
23:47:42.249 INFO ProgressMeter - chrX:67545753 63.4 15990 252.0
23:47:56.236 INFO ProgressMeter - chrX:71141369 63.7 16090 252.7
23:48:06.929 INFO ProgressMeter - chrX:77698572 63.9 16190 253.5
23:48:17.306 INFO ProgressMeter - chrX:130020983 64.0 16300 254.6
23:48:25.459 INFO Mutect2 - 1052280 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
180 read(s) filtered by: ReadLengthReadFilter
153 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
1052613 total reads filtered out of 140442208 reads processed
23:48:25.460 INFO ProgressMeter - chrY:19773375 64.2 16377 255.2
23:48:25.460 INFO ProgressMeter - Traversal complete. Processed 16377 total regions in 64.2 minutes.
23:48:25.476 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 8.203076719
23:48:25.476 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 437.543838838
23:48:25.476 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 13.46 sec
23:48:25.476 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:48:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 64.18 minutes.
Runtime.totalMemory()=3036676096
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 LS0925_tumor.bam --tumor-sample LS0925 -L TST500C_manifest.bed -O LS0925.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:48:26.867 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
23:48:26.987 INFO FilterMutectCalls - ------------------------------------------------------------
23:48:26.990 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:48:26.990 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:48:26.990 INFO FilterMutectCalls - Executing as ?@nf-fc489759ee5cf383fc5cdbde99a1d8b7-67b80-mzzsn on Linux v6.12.88 amd64
23:48:26.990 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:48:26.991 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:48:26 PM GMT
23:48:26.991 INFO FilterMutectCalls - ------------------------------------------------------------
23:48:26.991 INFO FilterMutectCalls - ------------------------------------------------------------
23:48:26.991 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:48:26.991 INFO FilterMutectCalls - Picard Version: 3.1.1
23:48:26.991 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:48:26.992 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:48:26.992 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:48:26.992 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:48:26.992 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:48:26.992 INFO FilterMutectCalls - Deflater: IntelDeflater
23:48:26.992 INFO FilterMutectCalls - Inflater: IntelInflater
23:48:26.992 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:48:26.992 INFO FilterMutectCalls - Requester pays: disabled
23:48:26.992 INFO FilterMutectCalls - Initializing engine
23:48:27.177 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.U0UleEWFyX/LS0925.mutect2.raw.vcf.gz
23:48:27.291 INFO FilterMutectCalls - Done initializing engine
23:48:27.343 INFO ProgressMeter - Starting traversal
23:48:27.343 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:48:27.344 INFO FilterMutectCalls - Starting pass 0 through the variants
23:48:28.814 INFO FilterMutectCalls - Finished pass 0 through the variants
23:48:31.551 INFO FilterMutectCalls - Starting pass 1 through the variants
23:48:33.129 INFO FilterMutectCalls - Finished pass 1 through the variants
23:48:33.638 INFO FilterMutectCalls - Starting pass 2 through the variants
23:48:35.217 INFO FilterMutectCalls - Finished pass 2 through the variants
23:48:35.219 INFO FilterMutectCalls - Starting pass 3 through the variants
23:48:36.595 INFO FilterMutectCalls - Finished pass 3 through the variants
23:48:36.603 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:48:36.603 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:48:36.603 INFO ProgressMeter - chr7:13981496 0.2 11484 74418.4
23:48:36.603 INFO ProgressMeter - Traversal complete. Processed 11484 total variants in 0.2 minutes.
23:48:36.614 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:48:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=637534208
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 LS0925.mutect2.raw.vcf.gz --stats LS0925.mutect2.raw.vcf.gz.stats -O LS0925.mutect2.filtered.vcf.gz
23:48:37.920 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
23:48:38.024 INFO SelectVariants - ------------------------------------------------------------
23:48:38.026 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:48:38.026 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:48:38.026 INFO SelectVariants - Executing as ?@nf-fc489759ee5cf383fc5cdbde99a1d8b7-67b80-mzzsn on Linux v6.12.88 amd64
23:48:38.027 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:48:38.027 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:48:37 PM GMT
23:48:38.027 INFO SelectVariants - ------------------------------------------------------------
23:48:38.027 INFO SelectVariants - ------------------------------------------------------------
23:48:38.028 INFO SelectVariants - HTSJDK Version: 4.1.0
23:48:38.028 INFO SelectVariants - Picard Version: 3.1.1
23:48:38.028 INFO SelectVariants - Built for Spark Version: 3.5.0
23:48:38.028 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:48:38.028 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:48:38.028 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:48:38.028 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:48:38.028 INFO SelectVariants - Deflater: IntelDeflater
23:48:38.028 INFO SelectVariants - Inflater: IntelInflater
23:48:38.028 INFO SelectVariants - GCS max retries/reopens: 20
23:48:38.029 INFO SelectVariants - Requester pays: disabled
23:48:38.029 INFO SelectVariants - Initializing engine
23:48:38.200 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.U0UleEWFyX/LS0925.mutect2.filtered.vcf.gz
23:48:38.300 INFO SelectVariants - Done initializing engine
23:48:38.335 INFO ProgressMeter - Starting traversal
23:48:38.335 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:48:38.410 INFO ProgressMeter - chr6:29943286 0.0 2871 2359726.0
23:48:38.410 INFO ProgressMeter - Traversal complete. Processed 2871 total variants in 0.0 minutes.
23:48:38.421 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:48:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=360710144
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 LS0925.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0925.mutect2.pass.vcf.gz