22:44:29.017 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
22:44:29.116 INFO Mutect2 - ------------------------------------------------------------
22:44:29.118 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:29.118 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:29.118 INFO Mutect2 - Executing as ?@nf-514d4c643acffe0932eeebe5bd9031d4-26f07-lttvw on Linux v6.12.88 amd64
22:44:29.118 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:29.118 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:28 PM GMT
22:44:29.118 INFO Mutect2 - ------------------------------------------------------------
22:44:29.118 INFO Mutect2 - ------------------------------------------------------------
22:44:29.119 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:29.119 INFO Mutect2 - Picard Version: 3.1.1
22:44:29.119 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:29.119 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:29.119 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:29.120 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:29.120 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:29.120 INFO Mutect2 - Deflater: IntelDeflater
22:44:29.120 INFO Mutect2 - Inflater: IntelInflater
22:44:29.120 INFO Mutect2 - GCS max retries/reopens: 20
22:44:29.120 INFO Mutect2 - Requester pays: disabled
22:44:29.120 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.JG3e6ObpCZ/LS0882_tumor.bam.bai is older than BAM /tmp/nxf.JG3e6ObpCZ/LS0882_tumor.bam
22:44:29.260 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.JG3e6ObpCZ/af-only-gnomad.hg38.vcf.gz
22:44:29.383 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.JG3e6ObpCZ/TST500C_manifest.bed
22:44:29.418 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:29.448 INFO Mutect2 - Done initializing engine
22:44:29.458 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
22:44:29.460 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
22:44:29.460 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:29.460 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:29.469 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
22:44:29.478 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:29.478 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:29.478 INFO IntelPairHmm - Available threads: 384
22:44:29.478 INFO IntelPairHmm - Requested threads: 4
22:44:29.478 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:29.520 INFO ProgressMeter - Starting traversal
22:44:29.520 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:40.749 INFO ProgressMeter - chr1:9721976 0.2 50 267.2
22:44:52.073 INFO ProgressMeter - chr1:11228666 0.4 120 319.2
22:45:04.821 INFO ProgressMeter - chr1:15929187 0.6 180 305.9
22:45:15.041 INFO ProgressMeter - chr1:15937161 0.8 220 290.0
22:45:25.308 INFO ProgressMeter - chr1:18746161 0.9 270 290.4
22:45:36.718 INFO ProgressMeter - chr1:26772498 1.1 330 294.7
22:45:47.363 INFO ProgressMeter - chr1:39890723 1.3 390 300.6
22:45:57.760 INFO ProgressMeter - chr1:39901439 1.5 440 299.2
22:46:07.985 INFO ProgressMeter - chr1:46077513 1.6 510 310.8
22:46:18.069 INFO ProgressMeter - chr1:64866938 1.8 590 326.1
22:46:28.307 INFO ProgressMeter - chr1:114715610 2.0 680 343.5
22:46:38.585 INFO ProgressMeter - chr1:119919557 2.2 730 339.4
22:46:49.886 INFO ProgressMeter - chr1:156860877 2.3 800 342.0
22:47:05.402 INFO ProgressMeter - chr1:156879997 2.6 840 323.3
22:47:16.617 INFO ProgressMeter - chr1:158676139 2.8 910 326.8
22:47:27.010 INFO ProgressMeter - chr1:179108145 3.0 980 331.3
22:47:37.297 INFO ProgressMeter - chr1:204457726 3.1 1060 338.7
22:47:47.781 INFO ProgressMeter - chr1:204556071 3.3 1130 342.0
22:47:58.443 INFO ProgressMeter - chr1:238275971 3.5 1210 347.5
22:48:10.965 INFO ProgressMeter - chr1:243503877 3.7 1260 341.4
22:48:21.884 INFO ProgressMeter - chr10:17151286 3.9 1300 335.7
22:48:33.164 INFO ProgressMeter - chr10:27092458 4.1 1360 334.9
22:48:44.274 INFO ProgressMeter - chr10:43092462 4.2 1430 336.8
22:48:54.398 INFO ProgressMeter - chr10:43114957 4.4 1470 333.0
22:49:04.507 INFO ProgressMeter - chr10:43126816 4.6 1510 329.5
22:49:16.152 INFO ProgressMeter - chr10:68646414 4.8 1560 326.6
22:49:26.614 INFO ProgressMeter - chr10:87952249 5.0 1640 331.2
22:49:36.830 INFO ProgressMeter - chr10:101780888 5.1 1710 333.9
22:49:46.855 INFO ProgressMeter - chr10:113126879 5.3 1770 334.7
22:49:58.869 INFO ProgressMeter - chr10:121498493 5.5 1830 333.4
22:50:10.204 INFO ProgressMeter - chr11:22625499 5.7 1920 338.1
22:50:20.341 INFO ProgressMeter - chr11:67434987 5.8 2010 343.8
22:50:32.811 INFO ProgressMeter - chr11:69702908 6.1 2090 345.2
22:50:47.952 INFO ProgressMeter - chr11:69809467 6.3 2160 342.5
22:50:59.470 INFO ProgressMeter - chr11:76546095 6.5 2230 343.1
22:51:10.022 INFO ProgressMeter - chr11:77406651 6.7 2290 343.1
22:51:21.153 INFO ProgressMeter - chr11:102223620 6.9 2380 346.9
22:51:31.699 INFO ProgressMeter - chr11:108257479 7.0 2420 343.9
22:51:42.082 INFO ProgressMeter - chr11:118472260 7.2 2500 346.8
22:51:54.425 INFO ProgressMeter - chr11:118504532 7.4 2560 345.2
22:52:08.787 INFO ProgressMeter - chr11:125629230 7.7 2620 342.3
22:52:24.377 INFO ProgressMeter - chr11:128460025 7.9 2680 338.6
22:52:35.855 INFO ProgressMeter - chr11:128811504 8.1 2740 338.0
22:52:46.768 INFO ProgressMeter - chr12:385895 8.3 2800 337.9
22:52:57.263 INFO ProgressMeter - chr12:4380014 8.5 2870 339.1
22:53:07.445 INFO ProgressMeter - chr12:4444466 8.6 2920 338.3
22:53:18.141 INFO ProgressMeter - chr12:6600924 8.8 2980 338.2
22:53:28.388 INFO ProgressMeter - chr12:11856732 9.0 3020 336.3
22:53:39.211 INFO ProgressMeter - chr12:11860529 9.2 3050 332.9
22:53:49.724 INFO ProgressMeter - chr12:11865503 9.3 3090 331.0
22:54:00.806 INFO ProgressMeter - chr12:11884424 9.5 3120 327.7
22:54:12.520 INFO ProgressMeter - chr12:25227585 9.7 3210 330.4
22:54:24.037 INFO ProgressMeter - chr12:45852297 9.9 3270 330.0
22:54:35.967 INFO ProgressMeter - chr12:49033053 10.1 3330 329.5
22:54:46.741 INFO ProgressMeter - chr12:49040932 10.3 3370 327.6
22:54:56.925 INFO ProgressMeter - chr12:50089882 10.5 3440 329.0
22:55:07.691 INFO ProgressMeter - chr12:56101170 10.6 3520 330.9
22:55:19.482 INFO ProgressMeter - chr12:57470613 10.8 3580 330.5
22:55:29.940 INFO ProgressMeter - chr12:68828769 11.0 3660 332.5
22:55:41.442 INFO ProgressMeter - chr12:112486473 11.2 3740 334.0
22:55:52.038 INFO ProgressMeter - chr12:132634184 11.4 3810 334.9
22:56:02.364 INFO ProgressMeter - chr13:20974933 11.5 3880 336.0
22:56:12.537 INFO ProgressMeter - chr13:21682277 11.7 3930 335.4
22:56:23.550 INFO ProgressMeter - chr13:28061985 11.9 4010 337.0
22:56:37.394 INFO ProgressMeter - chr13:28388167 12.1 4070 335.5
22:56:48.485 INFO ProgressMeter - chr13:32332555 12.3 4120 334.5
22:56:58.654 INFO ProgressMeter - chr13:32340831 12.5 4160 333.2
22:57:08.936 INFO ProgressMeter - chr13:48342597 12.7 4220 333.4
22:57:19.077 INFO ProgressMeter - chr13:101937656 12.8 4300 335.3
22:57:30.219 INFO ProgressMeter - chr13:106285972 13.0 4360 335.1
22:57:41.614 INFO ProgressMeter - chr13:113321641 13.2 4440 336.3
22:57:52.620 INFO ProgressMeter - chr14:37590849 13.4 4500 336.2
22:58:02.869 INFO ProgressMeter - chr14:67825462 13.6 4570 337.1
22:58:13.721 INFO ProgressMeter - chr14:95105676 13.7 4630 337.1
22:58:25.203 INFO ProgressMeter - chr15:32730874 13.9 4710 338.2
22:58:36.987 INFO ProgressMeter - chr15:34357269 14.1 4760 337.0
22:58:49.918 INFO ProgressMeter - chr15:41750152 14.3 4830 336.8
22:59:00.282 INFO ProgressMeter - chr15:53189298 14.5 4900 337.6
22:59:11.578 INFO ProgressMeter - chr15:87978932 14.7 4970 338.1
22:59:22.858 INFO ProgressMeter - chr15:90749917 14.9 5060 339.8
22:59:33.391 INFO ProgressMeter - chr15:92980813 15.1 5130 340.5
22:59:43.436 INFO ProgressMeter - chr15:98957099 15.2 5190 340.7
22:59:53.445 INFO ProgressMeter - chr16:2084226 15.4 5260 341.6
23:00:04.545 INFO ProgressMeter - chr16:3597795 15.6 5360 343.9
23:00:15.772 INFO ProgressMeter - chr16:3810601 15.8 5420 343.7
23:00:26.476 INFO ProgressMeter - chr16:13935309 15.9 5480 343.6
23:00:37.688 INFO ProgressMeter - chr16:50754459 16.1 5550 343.9
23:00:48.443 INFO ProgressMeter - chr16:67636688 16.3 5620 344.5
23:01:00.042 INFO ProgressMeter - chr16:72795039 16.5 5670 343.5
23:01:11.855 INFO ProgressMeter - chr16:72958171 16.7 5710 341.8
23:01:22.296 INFO ProgressMeter - chr16:81919482 16.9 5760 341.2
23:01:33.469 INFO ProgressMeter - chr16:89283668 17.1 5820 341.0
23:01:44.081 INFO ProgressMeter - chr16:89816535 17.2 5900 342.2
23:01:54.110 INFO ProgressMeter - chr17:7677113 17.4 5960 342.3
23:02:05.576 INFO ProgressMeter - chr17:16075532 17.6 6060 344.3
23:02:16.403 INFO ProgressMeter - chr17:31206359 17.8 6150 345.9
23:02:27.795 INFO ProgressMeter - chr17:35100951 18.0 6230 346.7
23:02:38.953 INFO ProgressMeter - chr17:39700037 18.2 6290 346.4
23:02:49.672 INFO ProgressMeter - chr17:39727687 18.3 6340 345.8
23:03:00.792 INFO ProgressMeter - chr17:42218721 18.5 6430 347.2
23:03:11.326 INFO ProgressMeter - chr17:43056248 18.7 6510 348.2
23:03:21.326 INFO ProgressMeter - chr17:43093924 18.9 6560 347.8
23:03:33.117 INFO ProgressMeter - chr17:43534992 19.1 6620 347.3
23:03:43.742 INFO ProgressMeter - chr17:43541714 19.2 6670 346.7
23:03:54.526 INFO ProgressMeter - chr17:45274538 19.4 6710 345.6
23:04:05.671 INFO ProgressMeter - chr17:58709857 19.6 6770 345.4
23:04:16.936 INFO ProgressMeter - chr17:60647890 19.8 6850 346.1
23:04:28.016 INFO ProgressMeter - chr17:65535624 20.0 6910 345.9
23:04:38.108 INFO ProgressMeter - chr17:80545635 20.1 6970 346.0
23:04:48.232 INFO ProgressMeter - chr18:22181491 20.3 7050 347.1
23:04:59.325 INFO ProgressMeter - chr18:44952591 20.5 7110 346.9
23:05:09.830 INFO ProgressMeter - chr18:58747587 20.7 7180 347.3
23:05:20.645 INFO ProgressMeter - chr19:2226181 20.9 7270 348.6
23:05:31.450 INFO ProgressMeter - chr19:5229489 21.0 7360 349.9
23:05:42.380 INFO ProgressMeter - chr19:10140044 21.2 7440 350.7
23:05:52.419 INFO ProgressMeter - chr19:10984150 21.4 7500 350.8
23:06:04.330 INFO ProgressMeter - chr19:14516824 21.6 7580 351.2
23:06:15.006 INFO ProgressMeter - chr19:15186876 21.8 7650 351.6
23:06:25.172 INFO ProgressMeter - chr19:15272813 21.9 7720 352.1
23:06:35.681 INFO ProgressMeter - chr19:29813169 22.1 7800 352.9
23:06:47.083 INFO ProgressMeter - chr19:35720639 22.3 7870 353.0
23:06:57.891 INFO ProgressMeter - chr19:40236628 22.5 7950 353.8
23:07:12.262 INFO ProgressMeter - chr19:41261491 22.7 8030 353.6
23:07:22.906 INFO ProgressMeter - chr19:45357628 22.9 8110 354.3
23:07:34.287 INFO ProgressMeter - chr19:50398875 23.1 8200 355.3
23:07:45.518 INFO ProgressMeter - chr2:15942015 23.3 8270 355.4
23:07:55.900 INFO ProgressMeter - chr2:25244538 23.4 8340 355.8
23:08:06.694 INFO ProgressMeter - chr2:25799383 23.6 8400 355.6
23:08:18.165 INFO ProgressMeter - chr2:29225375 23.8 8450 354.9
23:08:30.355 INFO ProgressMeter - chr2:42169620 24.0 8500 354.0
23:08:44.591 INFO ProgressMeter - chr2:47470963 24.3 8570 353.4
23:08:55.368 INFO ProgressMeter - chr2:60920572 24.4 8640 353.7
23:09:05.512 INFO ProgressMeter - chr2:98543875 24.6 8700 353.7
23:09:15.716 INFO ProgressMeter - chr2:108767130 24.8 8770 354.1
23:09:27.750 INFO ProgressMeter - chr2:111128359 25.0 8810 352.8
23:09:42.690 INFO ProgressMeter - chr2:113224916 25.2 8860 351.3
23:09:54.364 INFO ProgressMeter - chr2:113229762 25.4 8890 349.8
23:10:06.318 INFO ProgressMeter - chr2:113235377 25.6 8930 348.6
23:10:16.622 INFO ProgressMeter - chr2:140371177 25.8 9010 349.4
23:10:27.330 INFO ProgressMeter - chr2:140994125 26.0 9090 350.1
23:10:39.236 INFO ProgressMeter - chr2:177234003 26.2 9160 350.1
23:10:49.530 INFO ProgressMeter - chr2:197416908 26.3 9240 350.9
23:11:00.372 INFO ProgressMeter - chr2:214780558 26.5 9330 351.9
23:11:11.676 INFO ProgressMeter - chr2:222204025 26.7 9380 351.3
23:11:23.862 INFO ProgressMeter - chr2:222211299 26.9 9430 350.5
23:11:36.633 INFO ProgressMeter - chr2:222217674 27.1 9470 349.2
23:11:48.157 INFO ProgressMeter - chr2:226795382 27.3 9530 348.9
23:11:59.035 INFO ProgressMeter - chr20:9580742 27.5 9590 348.8
23:12:10.022 INFO ProgressMeter - chr20:32784841 27.7 9650 348.7
23:12:20.894 INFO ProgressMeter - chr20:42098419 27.9 9730 349.3
23:12:31.094 INFO ProgressMeter - chr20:47639923 28.0 9790 349.3
23:12:42.666 INFO ProgressMeter - chr20:58854182 28.2 9850 349.1
23:12:54.166 INFO ProgressMeter - chr21:38382587 28.4 9930 349.5
23:13:04.792 INFO ProgressMeter - chr21:41473323 28.6 9980 349.1
23:13:16.594 INFO ProgressMeter - chr21:41491289 28.8 10010 347.8
23:13:29.182 INFO ProgressMeter - chr21:41500933 29.0 10050 346.6
23:13:40.457 INFO ProgressMeter - chr21:41505973 29.2 10090 345.8
23:13:50.777 INFO ProgressMeter - chr22:20995961 29.4 10160 346.1
23:14:00.906 INFO ProgressMeter - chr22:23290908 29.5 10210 345.8
23:14:11.061 INFO ProgressMeter - chr22:28704698 29.7 10260 345.5
23:14:24.933 INFO ProgressMeter - chr22:29286028 29.9 10340 345.5
23:14:36.300 INFO ProgressMeter - chr22:37973796 30.1 10400 345.4
23:14:47.634 INFO ProgressMeter - chr22:41178025 30.3 10470 345.5
23:14:57.905 INFO ProgressMeter - chr3:10098887 30.5 10540 345.9
23:15:07.906 INFO ProgressMeter - chr3:12355820 30.6 10580 345.3
23:15:18.302 INFO ProgressMeter - chr3:12360075 30.8 10610 344.3
23:15:30.410 INFO ProgressMeter - chr3:12364103 31.0 10640 343.1
23:15:44.483 INFO ProgressMeter - chr3:12371227 31.2 10680 341.8
23:15:55.901 INFO ProgressMeter - chr3:12377452 31.4 10720 341.0
23:16:06.391 INFO ProgressMeter - chr3:12608764 31.6 10770 340.7
23:16:16.634 INFO ProgressMeter - chr3:36996617 31.8 10820 340.4
23:16:26.639 INFO ProgressMeter - chr3:47057460 32.0 10890 340.8
23:16:37.037 INFO ProgressMeter - chr3:49375432 32.1 10940 340.5
23:16:48.217 INFO ProgressMeter - chr3:52402600 32.3 11010 340.7
23:16:58.616 INFO ProgressMeter - chr3:52648342 32.5 11080 341.1
23:17:08.662 INFO ProgressMeter - chr3:89127207 32.7 11150 341.5
23:17:18.733 INFO ProgressMeter - chr3:135165966 32.8 11220 341.9
23:17:29.111 INFO ProgressMeter - chr3:138679334 33.0 11290 342.2
23:17:40.206 INFO ProgressMeter - chr3:142547783 33.2 11380 343.0
23:17:51.685 INFO ProgressMeter - chr3:179210696 33.4 11460 343.4
23:18:02.571 INFO ProgressMeter - chr3:185437586 33.6 11530 343.7
23:18:12.597 INFO ProgressMeter - chr3:186108938 33.7 11580 343.4
23:18:23.791 INFO ProgressMeter - chr3:196054889 33.9 11650 343.6
23:18:35.310 INFO ProgressMeter - chr4:1807127 34.1 11740 344.3
23:18:46.423 INFO ProgressMeter - chr4:41744982 34.3 11820 344.8
23:18:56.559 INFO ProgressMeter - chr4:54683250 34.5 11890 345.1
23:19:09.002 INFO ProgressMeter - chr4:54732185 34.7 11930 344.2
23:19:20.060 INFO ProgressMeter - chr4:65490375 34.8 12000 344.4
23:19:31.567 INFO ProgressMeter - chr4:83463492 35.0 12070 344.5
23:19:42.940 INFO ProgressMeter - chr4:105241038 35.2 12130 344.4
23:19:53.355 INFO ProgressMeter - chr4:122838998 35.4 12170 343.8
23:20:03.691 INFO ProgressMeter - chr4:152411284 35.6 12250 344.4
23:20:16.168 INFO ProgressMeter - chr4:186619514 35.8 12320 344.4
23:20:28.180 INFO ProgressMeter - chr4:186709155 36.0 12370 343.8
23:20:39.243 INFO ProgressMeter - chr5:38959193 36.2 12450 344.3
23:20:49.736 INFO ProgressMeter - chr5:56872639 36.3 12540 345.1
23:21:00.437 INFO ProgressMeter - chr5:68293099 36.5 12600 345.1
23:21:10.849 INFO ProgressMeter - chr5:112775627 36.7 12690 345.9
23:21:22.691 INFO ProgressMeter - chr5:112842985 36.9 12740 345.4
23:21:33.837 INFO ProgressMeter - chr5:138781921 37.1 12810 345.5
23:21:44.154 INFO ProgressMeter - chr5:142671759 37.2 12880 345.8
23:21:54.428 INFO ProgressMeter - chr5:150086377 37.4 12940 345.8
23:22:05.743 INFO ProgressMeter - chr5:150403451 37.6 13010 346.0
23:22:19.065 INFO ProgressMeter - chr5:177091487 37.8 13080 345.8
23:22:30.036 INFO ProgressMeter - chr5:177204118 38.0 13120 345.2
23:22:41.558 INFO ProgressMeter - chr5:177295165 38.2 13170 344.8
23:22:51.764 INFO ProgressMeter - chr5:180629941 38.4 13250 345.3
23:23:02.758 INFO ProgressMeter - chr6:20481204 38.6 13330 345.7
23:23:13.614 INFO ProgressMeter - chr6:29943015 38.7 13410 346.2
23:23:24.604 INFO ProgressMeter - chr6:30708173 38.9 13450 345.6
23:23:36.200 INFO ProgressMeter - chr6:32222509 39.1 13520 345.7
23:23:46.738 INFO ProgressMeter - chr6:41940571 39.3 13590 345.9
23:23:57.480 INFO ProgressMeter - chr6:93269509 39.5 13680 346.6
23:24:08.622 INFO ProgressMeter - chr6:117310079 39.7 13750 346.8
23:24:21.147 INFO ProgressMeter - chr6:117324113 39.9 13790 346.0
23:24:32.538 INFO ProgressMeter - chr6:117333049 40.1 13840 345.6
23:24:42.634 INFO ProgressMeter - chr6:117357830 40.2 13890 345.4
23:24:54.261 INFO ProgressMeter - chr6:135204628 40.4 13960 345.4
23:25:05.163 INFO ProgressMeter - chr6:135211999 40.6 14010 345.1
23:25:15.446 INFO ProgressMeter - chr6:135213471 40.8 14020 343.9
23:25:26.686 INFO ProgressMeter - chr6:137203497 41.0 14060 343.3
23:25:39.154 INFO ProgressMeter - chr6:151366765 41.2 14120 343.0
23:25:50.204 INFO ProgressMeter - chr6:152376495 41.3 14180 343.0
23:26:02.363 INFO ProgressMeter - chr6:157207013 41.5 14240 342.7
23:26:12.835 INFO ProgressMeter - chr6:161716075 41.7 14300 342.7
23:26:23.010 INFO ProgressMeter - chr7:6003970 41.9 14380 343.3
23:26:34.705 INFO ProgressMeter - chr7:13908331 42.1 14430 342.9
23:26:46.572 INFO ProgressMeter - chr7:13934446 42.3 14460 342.0
23:26:58.162 INFO ProgressMeter - chr7:13941091 42.5 14510 341.6
23:27:11.882 INFO ProgressMeter - chr7:13947769 42.7 14560 340.9
23:27:22.469 INFO ProgressMeter - chr7:13951802 42.9 14590 340.2
23:27:33.030 INFO ProgressMeter - chr7:13956221 43.1 14620 339.5
23:27:43.948 INFO ProgressMeter - chr7:13962160 43.2 14660 339.0
23:27:55.113 INFO ProgressMeter - chr7:13966670 43.4 14690 338.3
23:28:06.189 INFO ProgressMeter - chr7:13973419 43.6 14730 337.8
23:28:18.009 INFO ProgressMeter - chr7:13976771 43.8 14760 336.9
23:28:30.333 INFO ProgressMeter - chr7:13982345 44.0 14810 336.5
23:28:42.796 INFO ProgressMeter - chr7:13988488 44.2 14850 335.8
23:28:54.398 INFO ProgressMeter - chr7:50400016 44.4 14890 335.2
23:29:05.073 INFO ProgressMeter - chr7:55165634 44.6 14940 335.0
23:29:15.868 INFO ProgressMeter - chr7:55171213 44.8 14980 334.6
23:29:28.707 INFO ProgressMeter - chr7:55180758 45.0 15030 334.1
23:29:39.216 INFO ProgressMeter - chr7:78201160 45.2 15090 334.1
23:29:50.283 INFO ProgressMeter - chr7:92613919 45.3 15160 334.3
23:30:00.652 INFO ProgressMeter - chr7:102198781 45.5 15230 334.6
23:30:11.188 INFO ProgressMeter - chr7:106884207 45.7 15290 334.6
23:30:22.687 INFO ProgressMeter - chr7:116795931 45.9 15350 334.5
23:30:34.477 INFO ProgressMeter - chr7:140791512 46.1 15410 334.4
23:30:44.514 INFO ProgressMeter - chr7:142942988 46.2 15480 334.7
23:30:56.800 INFO ProgressMeter - chr7:152162115 46.5 15560 335.0
23:31:07.629 INFO ProgressMeter - chr7:152181342 46.6 15600 334.5
23:31:18.747 INFO ProgressMeter - chr7:152676039 46.8 15670 334.7
23:31:32.230 INFO ProgressMeter - chr8:32647862 47.0 15760 335.0
23:31:43.322 INFO ProgressMeter - chr8:37833965 47.2 15830 335.2
23:31:56.269 INFO ProgressMeter - chr8:41933918 47.4 15910 335.3
23:32:07.123 INFO ProgressMeter - chr8:47820717 47.6 15980 335.5
23:32:17.661 INFO ProgressMeter - chr8:47936351 47.8 16060 336.0
23:32:28.313 INFO ProgressMeter - chr8:68120919 48.0 16140 336.4
23:32:40.686 INFO ProgressMeter - chr8:116863128 48.2 16220 336.6
23:32:51.652 INFO ProgressMeter - chr8:127740717 48.4 16270 336.4
23:33:02.128 INFO ProgressMeter - chr9:5054675 48.5 16340 336.6
23:33:13.669 INFO ProgressMeter - chr9:8518264 48.7 16430 337.1
23:33:24.249 INFO ProgressMeter - chr9:35079149 48.9 16500 337.3
23:33:38.315 INFO ProgressMeter - chr9:84744387 49.1 16580 337.4
23:33:50.957 INFO ProgressMeter - chr9:84815672 49.4 16620 336.7
23:34:03.326 INFO ProgressMeter - chr9:84866041 49.6 16660 336.1
23:34:14.919 INFO ProgressMeter - chr9:84955281 49.8 16710 335.8
23:34:25.588 INFO ProgressMeter - chr9:90844197 49.9 16750 335.4
23:34:36.280 INFO ProgressMeter - chr9:96235610 50.1 16830 335.8
23:34:47.634 INFO ProgressMeter - chr9:130885652 50.3 16910 336.2
23:34:58.862 INFO ProgressMeter - chr9:136501746 50.5 16980 336.3
23:35:09.449 INFO ProgressMeter - chrX:15818585 50.7 17070 336.9
23:35:19.807 INFO ProgressMeter - chrX:40077842 50.8 17130 337.0
23:35:30.015 INFO ProgressMeter - chrX:47181747 51.0 17190 337.0
23:35:40.712 INFO ProgressMeter - chrX:49034383 51.2 17250 337.0
23:35:51.397 INFO ProgressMeter - chrX:49038656 51.4 17280 336.4
23:36:01.826 INFO ProgressMeter - chrX:53396206 51.5 17340 336.4
23:36:13.761 INFO ProgressMeter - chrX:64191388 51.7 17390 336.1
23:36:24.204 INFO ProgressMeter - chrX:67595923 51.9 17430 335.8
23:36:35.447 INFO ProgressMeter - chrX:71137556 52.1 17510 336.1
23:36:46.548 INFO ProgressMeter - chrX:77521401 52.3 17570 336.1
23:36:57.026 INFO ProgressMeter - chrX:77688816 52.5 17630 336.1
23:37:07.955 INFO ProgressMeter - chrX:124086545 52.6 17720 336.6
23:37:18.933 INFO ProgressMeter - chrX:134413574 52.8 17780 336.6
23:37:19.654 INFO Mutect2 - 624881 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappingQualityNotZeroReadFilter
0 read(s) filtered by: MappedReadFilter
0 read(s) filtered by: NotSecondaryAlignmentReadFilter
0 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
0 read(s) filtered by: NonChimericOriginalAlignmentReadFilter
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
1 read(s) filtered by: ReadLengthReadFilter
114 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
624996 total reads filtered out of 96190414 reads processed
23:37:19.654 INFO ProgressMeter - chrY:20398623 52.8 17825 337.4
23:37:19.654 INFO ProgressMeter - Traversal complete. Processed 17825 total regions in 52.8 minutes.
23:37:19.669 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 6.356802068
23:37:19.669 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 266.421669931
23:37:19.669 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 10.44 sec
23:37:19.669 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:37:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 52.84 minutes.
Runtime.totalMemory()=3095396352
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 LS0882_tumor.bam --tumor-sample LS0882 -L TST500C_manifest.bed -O LS0882.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:37:20.997 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
23:37:21.115 INFO FilterMutectCalls - ------------------------------------------------------------
23:37:21.118 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:37:21.118 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:37:21.118 INFO FilterMutectCalls - Executing as ?@nf-514d4c643acffe0932eeebe5bd9031d4-26f07-lttvw on Linux v6.12.88 amd64
23:37:21.118 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:37:21.119 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:37:20 PM GMT
23:37:21.119 INFO FilterMutectCalls - ------------------------------------------------------------
23:37:21.119 INFO FilterMutectCalls - ------------------------------------------------------------
23:37:21.120 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:37:21.120 INFO FilterMutectCalls - Picard Version: 3.1.1
23:37:21.120 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:37:21.120 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:37:21.120 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:37:21.120 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:37:21.120 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:37:21.120 INFO FilterMutectCalls - Deflater: IntelDeflater
23:37:21.120 INFO FilterMutectCalls - Inflater: IntelInflater
23:37:21.121 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:37:21.121 INFO FilterMutectCalls - Requester pays: disabled
23:37:21.121 INFO FilterMutectCalls - Initializing engine
23:37:21.331 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.JG3e6ObpCZ/LS0882.mutect2.raw.vcf.gz
23:37:21.437 INFO FilterMutectCalls - Done initializing engine
23:37:21.492 INFO ProgressMeter - Starting traversal
23:37:21.493 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:37:21.493 INFO FilterMutectCalls - Starting pass 0 through the variants
23:37:22.910 INFO FilterMutectCalls - Finished pass 0 through the variants
23:37:26.783 INFO FilterMutectCalls - Starting pass 1 through the variants
23:37:28.621 INFO FilterMutectCalls - Finished pass 1 through the variants
23:37:29.401 INFO FilterMutectCalls - Starting pass 2 through the variants
23:37:31.217 INFO FilterMutectCalls - Finished pass 2 through the variants
23:37:31.218 INFO FilterMutectCalls - Starting pass 3 through the variants
23:37:31.730 INFO ProgressMeter - chr16:77983148 0.2 8000 46902.5
23:37:32.809 INFO FilterMutectCalls - Finished pass 3 through the variants
23:37:32.816 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:37:32.817 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:37:32.817 INFO ProgressMeter - chr6:42045311 0.2 9664 51204.5
23:37:32.817 INFO ProgressMeter - Traversal complete. Processed 9664 total variants in 0.2 minutes.
23:37:32.829 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:37:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.20 minutes.
Runtime.totalMemory()=226492416
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 LS0882.mutect2.raw.vcf.gz --stats LS0882.mutect2.raw.vcf.gz.stats -O LS0882.mutect2.filtered.vcf.gz
23:37:34.091 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
23:37:34.207 INFO SelectVariants - ------------------------------------------------------------
23:37:34.209 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:37:34.210 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:37:34.210 INFO SelectVariants - Executing as ?@nf-514d4c643acffe0932eeebe5bd9031d4-26f07-lttvw on Linux v6.12.88 amd64
23:37:34.210 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:37:34.210 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:37:34 PM GMT
23:37:34.210 INFO SelectVariants - ------------------------------------------------------------
23:37:34.210 INFO SelectVariants - ------------------------------------------------------------
23:37:34.211 INFO SelectVariants - HTSJDK Version: 4.1.0
23:37:34.211 INFO SelectVariants - Picard Version: 3.1.1
23:37:34.211 INFO SelectVariants - Built for Spark Version: 3.5.0
23:37:34.211 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:37:34.211 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:37:34.212 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:37:34.212 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:37:34.212 INFO SelectVariants - Deflater: IntelDeflater
23:37:34.212 INFO SelectVariants - Inflater: IntelInflater
23:37:34.212 INFO SelectVariants - GCS max retries/reopens: 20
23:37:34.212 INFO SelectVariants - Requester pays: disabled
23:37:34.213 INFO SelectVariants - Initializing engine
23:37:34.399 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.JG3e6ObpCZ/LS0882.mutect2.filtered.vcf.gz
23:37:34.503 INFO SelectVariants - Done initializing engine
23:37:34.541 INFO ProgressMeter - Starting traversal
23:37:34.542 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:37:34.621 INFO ProgressMeter - chr7:13975662 0.0 2416 1882597.4
23:37:34.621 INFO ProgressMeter - Traversal complete. Processed 2416 total variants in 0.0 minutes.
23:37:34.632 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:37:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=327155712
Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar SelectVariants -R hg38.fa -V LS0882.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0882.mutect2.pass.vcf.gz