22:44:19.880 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
22:44:19.994 INFO Mutect2 - ------------------------------------------------------------
22:44:19.998 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:19.998 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:19.998 INFO Mutect2 - Executing as ?@nf-91f40eb6cdb1383e2a848da4f274d342-1425d-6nnqh on Linux v6.12.88 amd64
22:44:19.998 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:19.999 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:19 PM GMT
22:44:19.999 INFO Mutect2 - ------------------------------------------------------------
22:44:19.999 INFO Mutect2 - ------------------------------------------------------------
22:44:19.999 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:20.000 INFO Mutect2 - Picard Version: 3.1.1
22:44:20.000 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:20.000 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:20.000 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:20.000 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:20.000 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:20.000 INFO Mutect2 - Deflater: IntelDeflater
22:44:20.000 INFO Mutect2 - Inflater: IntelInflater
22:44:20.001 INFO Mutect2 - GCS max retries/reopens: 20
22:44:20.001 INFO Mutect2 - Requester pays: disabled
22:44:20.001 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.LEB9ssU9rM/LS0920_tumor.bam.bai is older than BAM /tmp/nxf.LEB9ssU9rM/LS0920_tumor.bam
22:44:20.254 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.LEB9ssU9rM/af-only-gnomad.hg38.vcf.gz
22:44:20.382 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.LEB9ssU9rM/TST500C_manifest.bed
22:44:20.418 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:20.449 INFO Mutect2 - Done initializing engine
22:44:20.460 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
22:44:20.461 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
22:44:20.462 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:20.462 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:20.473 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
22:44:20.481 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:20.481 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:20.481 INFO IntelPairHmm - Available threads: 384
22:44:20.481 INFO IntelPairHmm - Requested threads: 4
22:44:20.481 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:20.518 INFO ProgressMeter - Starting traversal
22:44:20.518 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:32.014 INFO ProgressMeter - chr1:9720740 0.2 40 208.8
22:44:43.478 INFO ProgressMeter - chr1:11209310 0.4 100 261.3
22:44:55.672 INFO ProgressMeter - chr1:15916126 0.6 150 256.0
22:45:07.999 INFO ProgressMeter - chr1:15932323 0.8 190 240.1
22:45:18.509 INFO ProgressMeter - chr1:15939396 1.0 220 227.6
22:45:29.533 INFO ProgressMeter - chr1:18746763 1.2 260 226.0
22:45:40.905 INFO ProgressMeter - chr1:26772498 1.3 310 231.4
22:45:51.346 INFO ProgressMeter - chr1:26780706 1.5 340 224.6
22:46:03.346 INFO ProgressMeter - chr1:39897724 1.7 400 233.4
22:46:13.567 INFO ProgressMeter - chr1:43340385 1.9 450 238.8
22:46:25.200 INFO ProgressMeter - chr1:46267457 2.1 510 245.4
22:46:36.529 INFO ProgressMeter - chr1:64847530 2.3 570 251.5
22:46:46.763 INFO ProgressMeter - chr1:85270785 2.4 630 258.5
22:46:59.224 INFO ProgressMeter - chr1:119513832 2.6 710 268.4
22:47:09.487 INFO ProgressMeter - chr1:119926600 2.8 750 266.3
22:47:21.427 INFO ProgressMeter - chr1:156860877 3.0 810 268.6
22:47:35.574 INFO ProgressMeter - chr1:156872825 3.3 830 255.3
22:47:48.074 INFO ProgressMeter - chr1:156876079 3.5 850 245.7
22:47:59.630 INFO ProgressMeter - chr1:158647537 3.7 900 246.4
22:48:10.248 INFO ProgressMeter - chr1:161362327 3.8 950 248.1
22:48:20.649 INFO ProgressMeter - chr1:176206570 4.0 1000 249.9
22:48:32.167 INFO ProgressMeter - chr1:193212063 4.2 1050 250.3
22:48:43.741 INFO ProgressMeter - chr1:204460322 4.4 1100 250.7
22:48:54.841 INFO ProgressMeter - chr1:204546795 4.6 1150 251.5
22:49:05.873 INFO ProgressMeter - chr1:226064350 4.8 1200 252.3
22:49:16.285 INFO ProgressMeter - chr1:228425033 4.9 1250 253.6
22:49:27.337 INFO ProgressMeter - chr1:243501518 5.1 1290 252.3
22:49:37.664 INFO ProgressMeter - chr1:243504688 5.3 1310 247.8
22:49:49.810 INFO ProgressMeter - chr10:27035205 5.5 1370 249.6
22:50:01.350 INFO ProgressMeter - chr10:32011429 5.7 1430 251.7
22:50:14.679 INFO ProgressMeter - chr10:43112651 5.9 1500 254.1
22:50:26.038 INFO ProgressMeter - chr10:43116380 6.1 1540 252.8
22:50:36.662 INFO ProgressMeter - chr10:43128482 6.3 1580 252.0
22:50:47.338 INFO ProgressMeter - chr10:68573700 6.4 1620 251.3
22:50:57.529 INFO ProgressMeter - chr10:68691317 6.6 1660 250.9
22:51:07.784 INFO ProgressMeter - chr10:89007698 6.8 1730 254.9
22:51:18.612 INFO ProgressMeter - chr10:101779801 7.0 1780 255.4
22:51:29.740 INFO ProgressMeter - chr10:110601148 7.2 1840 257.2
22:51:42.433 INFO ProgressMeter - chr10:121481522 7.4 1900 258.0
22:51:53.020 INFO ProgressMeter - chr10:121551288 7.5 1950 258.6
22:52:04.727 INFO ProgressMeter - chr11:32389056 7.7 2010 259.8
22:52:16.605 INFO ProgressMeter - chr11:64809960 7.9 2080 262.1
22:52:27.738 INFO ProgressMeter - chr11:69652778 8.1 2140 263.5
22:52:38.294 INFO ProgressMeter - chr11:69702508 8.3 2180 262.8
22:52:50.218 INFO ProgressMeter - chr11:69776847 8.5 2240 263.7
22:53:01.165 INFO ProgressMeter - chr11:69810504 8.7 2260 260.4
22:53:11.754 INFO ProgressMeter - chr11:76496357 8.9 2310 260.9
22:53:22.724 INFO ProgressMeter - chr11:77349081 9.0 2350 260.0
22:53:33.267 INFO ProgressMeter - chr11:77452785 9.2 2410 261.6
22:53:44.433 INFO ProgressMeter - chr11:102186016 9.4 2480 263.9
22:53:55.139 INFO ProgressMeter - chr11:102331174 9.6 2500 261.0
22:54:06.415 INFO ProgressMeter - chr11:108333884 9.8 2570 263.2
22:54:16.935 INFO ProgressMeter - chr11:118474144 9.9 2620 263.6
22:54:28.323 INFO ProgressMeter - chr11:118505018 10.1 2670 263.6
22:54:38.578 INFO ProgressMeter - chr11:119298356 10.3 2720 264.1
22:54:49.223 INFO ProgressMeter - chr11:125650774 10.5 2760 263.4
22:55:02.714 INFO ProgressMeter - chr11:128461596 10.7 2800 261.6
22:55:13.088 INFO ProgressMeter - chr11:128810663 10.9 2840 261.1
22:55:24.120 INFO ProgressMeter - chr12:318203 11.1 2880 260.4
22:55:34.726 INFO ProgressMeter - chr12:4369625 11.2 2940 261.6
22:55:46.633 INFO ProgressMeter - chr12:4434523 11.4 3000 262.3
22:55:56.827 INFO ProgressMeter - chr12:4450638 11.6 3040 262.0
22:56:08.327 INFO ProgressMeter - chr12:6600215 11.8 3090 261.9
22:56:21.792 INFO ProgressMeter - chr12:11855018 12.0 3120 259.5
22:56:32.776 INFO ProgressMeter - chr12:11859059 12.2 3150 258.1
22:56:43.856 INFO ProgressMeter - chr12:11861952 12.4 3170 255.9
22:56:55.908 INFO ProgressMeter - chr12:11866777 12.6 3200 254.2
22:57:06.994 INFO ProgressMeter - chr12:11884424 12.8 3220 252.1
22:57:17.977 INFO ProgressMeter - chr12:25209904 13.0 3280 253.1
22:57:31.290 INFO ProgressMeter - chr12:45729835 13.2 3340 253.4
22:57:41.311 INFO ProgressMeter - chr12:45852580 13.3 3380 253.2
22:57:53.559 INFO ProgressMeter - chr12:49032459 13.6 3430 253.1
22:58:07.008 INFO ProgressMeter - chr12:49038787 13.8 3460 251.2
22:58:19.566 INFO ProgressMeter - chr12:49050310 14.0 3510 251.0
22:58:30.975 INFO ProgressMeter - chr12:50090347 14.2 3550 250.5
22:58:41.107 INFO ProgressMeter - chr12:56093020 14.3 3600 251.0
22:58:52.798 INFO ProgressMeter - chr12:57093554 14.5 3650 251.1
22:59:04.484 INFO ProgressMeter - chr12:57471116 14.7 3690 250.5
22:59:15.234 INFO ProgressMeter - chr12:68809924 14.9 3750 251.5
22:59:25.292 INFO ProgressMeter - chr12:69570329 15.1 3800 252.0
22:59:36.166 INFO ProgressMeter - chr12:112486643 15.3 3850 252.3
22:59:46.904 INFO ProgressMeter - chr12:120997556 15.4 3900 252.6
22:59:56.916 INFO ProgressMeter - chr12:132643835 15.6 3940 252.5
23:00:07.676 INFO ProgressMeter - chr13:20975310 15.8 3990 252.8
23:00:19.958 INFO ProgressMeter - chr13:21688777 16.0 4040 252.6
23:00:30.117 INFO ProgressMeter - chr13:28050120 16.2 4100 253.7
23:00:42.267 INFO ProgressMeter - chr13:28386797 16.4 4150 253.6
23:00:56.529 INFO ProgressMeter - chr13:28389643 16.6 4170 251.2
23:01:08.080 INFO ProgressMeter - chr13:32337745 16.8 4220 251.3
23:01:18.238 INFO ProgressMeter - chr13:32363664 17.0 4260 251.1
23:01:29.421 INFO ProgressMeter - chr13:48477353 17.1 4330 252.5
23:01:40.883 INFO ProgressMeter - chr13:102380277 17.3 4400 253.8
23:01:51.977 INFO ProgressMeter - chr13:109783376 17.5 4450 253.9
23:02:03.875 INFO ProgressMeter - chr13:113319467 17.7 4510 254.5
23:02:14.974 INFO ProgressMeter - chr14:37585151 17.9 4560 254.6
23:02:25.623 INFO ProgressMeter - chr14:37596003 18.1 4610 254.9
23:02:35.842 INFO ProgressMeter - chr14:81091067 18.3 4670 255.8
23:02:46.325 INFO ProgressMeter - chr14:95116451 18.4 4720 256.1
23:02:57.732 INFO ProgressMeter - chr15:32730688 18.6 4780 256.7
23:03:08.927 INFO ProgressMeter - chr15:34353734 18.8 4810 255.8
23:03:20.086 INFO ProgressMeter - chr15:41669908 19.0 4850 255.4
23:03:30.104 INFO ProgressMeter - chr15:41749477 19.2 4890 255.2
23:03:40.488 INFO ProgressMeter - chr15:49436058 19.3 4940 255.5
23:03:52.028 INFO ProgressMeter - chr15:87876755 19.5 5010 256.6
23:04:02.270 INFO ProgressMeter - chr15:88183416 19.7 5050 256.4
23:04:13.003 INFO ProgressMeter - chr15:90102388 19.9 5120 257.6
23:04:23.315 INFO ProgressMeter - chr15:92944413 20.0 5170 257.9
23:04:33.723 INFO ProgressMeter - chr15:98899475 20.2 5220 258.2
23:04:45.039 INFO ProgressMeter - chr16:2054294 20.4 5280 258.7
23:04:56.290 INFO ProgressMeter - chr16:2173786 20.6 5350 259.8
23:05:07.345 INFO ProgressMeter - chr16:3596392 20.8 5420 260.8
23:05:17.796 INFO ProgressMeter - chr16:3757286 21.0 5460 260.6
23:05:29.639 INFO ProgressMeter - chr16:9829421 21.2 5510 260.5
23:05:40.769 INFO ProgressMeter - chr16:23614002 21.3 5560 260.6
23:05:51.731 INFO ProgressMeter - chr16:50779833 21.5 5620 261.1
23:06:03.157 INFO ProgressMeter - chr16:68810195 21.7 5690 262.1
23:06:13.389 INFO ProgressMeter - chr16:72793412 21.9 5730 261.9
23:06:26.308 INFO ProgressMeter - chr16:72798574 22.1 5770 261.1
23:06:37.435 INFO ProgressMeter - chr16:81883267 22.3 5820 261.2
23:06:49.298 INFO ProgressMeter - chr16:89281859 22.5 5880 261.6
23:07:00.241 INFO ProgressMeter - chr16:89767139 22.7 5930 261.7
23:07:14.596 INFO ProgressMeter - chr17:7670422 22.9 5990 261.6
23:07:24.935 INFO ProgressMeter - chr17:7677844 23.1 6030 261.3
23:07:34.986 INFO ProgressMeter - chr17:8205214 23.2 6080 261.6
23:07:47.427 INFO ProgressMeter - chr17:16072143 23.4 6140 261.9
23:07:59.840 INFO ProgressMeter - chr17:17222499 23.7 6200 262.1
23:08:10.980 INFO ProgressMeter - chr17:31265227 23.8 6260 262.6
23:08:21.250 INFO ProgressMeter - chr17:35106431 24.0 6320 263.2
23:08:32.332 INFO ProgressMeter - chr17:39688737 24.2 6370 263.3
23:08:42.850 INFO ProgressMeter - chr17:39725325 24.4 6420 263.4
23:08:53.759 INFO ProgressMeter - chr17:40412757 24.6 6480 263.9
23:09:04.700 INFO ProgressMeter - chr17:42337433 24.7 6550 264.8
23:09:18.816 INFO ProgressMeter - chr17:43093633 25.0 6610 264.7
23:09:30.541 INFO ProgressMeter - chr17:43531757 25.2 6660 264.6
23:09:44.505 INFO ProgressMeter - chr17:43539126 25.4 6710 264.2
23:10:00.611 INFO ProgressMeter - chr17:43543348 25.7 6740 262.6
23:10:11.701 INFO ProgressMeter - chr17:45286718 25.9 6780 262.3
23:10:22.785 INFO ProgressMeter - chr17:58370909 26.0 6830 262.3
23:10:35.298 INFO ProgressMeter - chr17:59946924 26.2 6900 262.9
23:10:46.021 INFO ProgressMeter - chr17:63929249 26.4 6950 263.0
23:10:57.201 INFO ProgressMeter - chr17:68522754 26.6 7000 263.0
23:11:08.454 INFO ProgressMeter - chr17:80908860 26.8 7070 263.8
23:11:18.992 INFO ProgressMeter - chr18:41957568 27.0 7130 264.3
23:11:29.226 INFO ProgressMeter - chr18:44951709 27.1 7180 264.5
23:11:39.947 INFO ProgressMeter - chr18:51067144 27.3 7230 264.6
23:11:50.870 INFO ProgressMeter - chr19:1615798 27.5 7300 265.4
23:12:02.810 INFO ProgressMeter - chr19:2226625 27.7 7370 266.0
23:12:13.508 INFO ProgressMeter - chr19:5174060 27.9 7430 266.5
23:12:24.053 INFO ProgressMeter - chr19:5262962 28.1 7480 266.6
23:12:34.373 INFO ProgressMeter - chr19:10133665 28.2 7530 266.7
23:12:44.632 INFO ProgressMeter - chr19:10175538 28.4 7580 266.9
23:12:54.839 INFO ProgressMeter - chr19:11021498 28.6 7630 267.0
23:13:06.640 INFO ProgressMeter - chr19:14517347 28.8 7690 267.3
23:13:17.119 INFO ProgressMeter - chr19:15187879 28.9 7740 267.4
23:13:27.482 INFO ProgressMeter - chr19:15265385 29.1 7790 267.5
23:13:37.681 INFO ProgressMeter - chr19:18161277 29.3 7840 267.7
23:13:50.290 INFO ProgressMeter - chr19:29817135 29.5 7900 267.8
23:14:01.732 INFO ProgressMeter - chr19:35721723 29.7 7960 268.1
23:14:12.922 INFO ProgressMeter - chr19:35738455 29.9 8020 268.5
23:14:23.114 INFO ProgressMeter - chr19:40281899 30.0 8080 268.9
23:14:37.856 INFO ProgressMeter - chr19:41260896 30.3 8130 268.4
23:14:49.369 INFO ProgressMeter - chr19:42294171 30.5 8180 268.4
23:15:00.950 INFO ProgressMeter - chr19:45406532 30.7 8250 269.0
23:15:12.551 INFO ProgressMeter - chr19:50398850 30.9 8310 269.2
23:15:26.873 INFO ProgressMeter - chr2:15937660 31.1 8370 269.1
23:15:37.056 INFO ProgressMeter - chr2:15950395 31.3 8420 269.2
23:15:49.483 INFO ProgressMeter - chr2:25282678 31.5 8480 269.4
23:16:02.297 INFO ProgressMeter - chr2:29213982 31.7 8530 269.1
23:16:14.327 INFO ProgressMeter - chr2:29226167 31.9 8560 268.4
23:16:25.546 INFO ProgressMeter - chr2:29510990 32.1 8600 268.0
23:16:38.046 INFO ProgressMeter - chr2:42330094 32.3 8660 268.2
23:16:52.068 INFO ProgressMeter - chr2:47414526 32.5 8700 267.5
23:17:02.910 INFO ProgressMeter - chr2:47803544 32.7 8740 267.2
23:17:13.200 INFO ProgressMeter - chr2:95183454 32.9 8820 268.3
23:17:24.374 INFO ProgressMeter - chr2:108735530 33.1 8870 268.3
23:17:34.685 INFO ProgressMeter - chr2:108772866 33.2 8920 268.4
23:17:46.427 INFO ProgressMeter - chr2:111127777 33.4 8950 267.7
23:18:00.160 INFO ProgressMeter - chr2:113222997 33.7 8990 267.1
23:18:10.588 INFO ProgressMeter - chr2:113225863 33.8 9010 266.3
23:18:24.171 INFO ProgressMeter - chr2:113229319 34.1 9040 265.4
23:18:36.762 INFO ProgressMeter - chr2:113232967 34.3 9070 264.7
23:18:48.182 INFO ProgressMeter - chr2:113234508 34.5 9080 263.5
23:18:59.701 INFO ProgressMeter - chr2:136115025 34.7 9130 263.5
23:19:10.411 INFO ProgressMeter - chr2:140526235 34.8 9200 264.1
23:19:21.431 INFO ProgressMeter - chr2:141058881 35.0 9260 264.5
23:19:31.895 INFO ProgressMeter - chr2:177231512 35.2 9310 264.6
23:19:43.604 INFO ProgressMeter - chr2:197400765 35.4 9380 265.1
23:19:54.657 INFO ProgressMeter - chr2:211383613 35.6 9440 265.4
23:20:05.747 INFO ProgressMeter - chr2:219575353 35.8 9500 265.7
23:20:17.926 INFO ProgressMeter - chr2:222203446 36.0 9530 265.0
23:20:30.193 INFO ProgressMeter - chr2:222209571 36.2 9570 264.6
23:20:40.293 INFO ProgressMeter - chr2:222213733 36.3 9600 264.2
23:20:52.030 INFO ProgressMeter - chr2:222218706 36.5 9630 263.7
23:21:03.718 INFO ProgressMeter - chr2:224506856 36.7 9680 263.6
23:21:14.719 INFO ProgressMeter - chr2:226798401 36.9 9720 263.4
23:21:26.549 INFO ProgressMeter - chr20:32113582 37.1 9770 263.3
23:21:38.708 INFO ProgressMeter - chr20:32436525 37.3 9810 263.0
23:21:50.421 INFO ProgressMeter - chr20:40858427 37.5 9870 263.2
23:22:03.044 INFO ProgressMeter - chr20:42472448 37.7 9930 263.3
23:22:14.416 INFO ProgressMeter - chr20:47651096 37.9 9970 263.1
23:22:25.805 INFO ProgressMeter - chr20:58840105 38.1 10010 262.8
23:22:36.810 INFO ProgressMeter - chr21:27235771 38.3 10060 262.9
23:22:48.499 INFO ProgressMeter - chr21:38400589 38.5 10110 262.8
23:22:58.782 INFO ProgressMeter - chr21:41470726 38.6 10150 262.7
23:23:10.900 INFO ProgressMeter - chr21:41491047 38.8 10180 262.1
23:23:21.534 INFO ProgressMeter - chr21:41493158 39.0 10200 261.4
23:23:34.286 INFO ProgressMeter - chr21:41502341 39.2 10240 261.0
23:23:46.358 INFO ProgressMeter - chr21:41507617 39.4 10280 260.7
23:23:56.569 INFO ProgressMeter - chr22:20994102 39.6 10340 261.1
23:24:11.672 INFO ProgressMeter - chr22:23291173 39.9 10400 261.0
23:24:22.252 INFO ProgressMeter - chr22:28710190 40.0 10460 261.3
23:24:33.165 INFO ProgressMeter - chr22:29284972 40.2 10520 261.6
23:24:43.931 INFO ProgressMeter - chr22:29299232 40.4 10550 261.2
23:24:54.596 INFO ProgressMeter - chr22:41125862 40.6 10600 261.3
23:25:07.111 INFO ProgressMeter - chr22:41178082 40.8 10650 261.2
23:25:18.130 INFO ProgressMeter - chr3:10096324 41.0 10710 261.5
23:25:29.890 INFO ProgressMeter - chr3:12354409 41.2 10750 261.2
23:25:42.234 INFO ProgressMeter - chr3:12355794 41.4 10760 260.1
23:26:01.486 INFO ProgressMeter - chr3:12360936 41.7 10790 258.9
23:26:12.334 INFO ProgressMeter - chr3:12365329 41.9 10820 258.5
23:26:24.848 INFO ProgressMeter - chr3:12369979 42.1 10850 257.9
23:26:36.659 INFO ProgressMeter - chr3:12374135 42.3 10880 257.4
23:26:48.274 INFO ProgressMeter - chr3:12379432 42.5 10920 257.2
23:27:01.699 INFO ProgressMeter - chr3:12624852 42.7 10970 257.0
23:27:12.182 INFO ProgressMeter - chr3:38140386 42.9 11030 257.3
23:27:23.239 INFO ProgressMeter - chr3:47097953 43.0 11080 257.4
23:27:34.284 INFO ProgressMeter - chr3:47123885 43.2 11120 257.2
23:27:45.137 INFO ProgressMeter - chr3:49895959 43.4 11180 257.5
23:27:55.981 INFO ProgressMeter - chr3:52407302 43.6 11220 257.4
23:28:07.277 INFO ProgressMeter - chr3:52678498 43.8 11270 257.4
23:28:19.307 INFO ProgressMeter - chr3:72446494 44.0 11330 257.6
23:28:31.515 INFO ProgressMeter - chr3:128485950 44.2 11390 257.8
23:28:42.250 INFO ProgressMeter - chr3:136369087 44.4 11440 257.9
23:28:52.461 INFO ProgressMeter - chr3:138707549 44.5 11500 258.2
23:29:03.050 INFO ProgressMeter - chr3:142538480 44.7 11570 258.8
23:29:14.116 INFO ProgressMeter - chr3:179173522 44.9 11640 259.3
23:29:24.871 INFO ProgressMeter - chr3:182963990 45.1 11700 259.6
23:29:38.131 INFO ProgressMeter - chr3:186047749 45.3 11750 259.4
23:29:48.787 INFO ProgressMeter - chr3:189738640 45.5 11810 259.7
23:30:00.279 INFO ProgressMeter - chr3:196076208 45.7 11880 260.2
23:30:12.252 INFO ProgressMeter - chr4:1806827 45.9 11940 260.3
23:30:23.129 INFO ProgressMeter - chr4:24532995 46.0 12000 260.6
23:30:34.026 INFO ProgressMeter - chr4:54267597 46.2 12050 260.7
23:30:44.474 INFO ProgressMeter - chr4:54695510 46.4 12100 260.8
23:30:56.472 INFO ProgressMeter - chr4:54733068 46.6 12130 260.3
23:31:08.337 INFO ProgressMeter - chr4:65365988 46.8 12190 260.5
23:31:18.632 INFO ProgressMeter - chr4:80279513 47.0 12240 260.6
23:31:30.133 INFO ProgressMeter - chr4:105235402 47.2 12300 260.8
23:31:44.358 INFO ProgressMeter - chr4:105242852 47.4 12340 260.4
23:31:54.677 INFO ProgressMeter - chr4:142123290 47.6 12410 260.9
23:32:06.032 INFO ProgressMeter - chr4:186596953 47.8 12480 261.3
23:32:16.321 INFO ProgressMeter - chr4:186618101 47.9 12530 261.4
23:32:26.515 INFO ProgressMeter - chr4:186639720 48.1 12570 261.3
23:32:37.831 INFO ProgressMeter - chr5:236461 48.3 12620 261.3
23:32:48.363 INFO ProgressMeter - chr5:38950637 48.5 12670 261.4
23:32:59.269 INFO ProgressMeter - chr5:44356931 48.6 12740 261.9
23:33:10.589 INFO ProgressMeter - chr5:58456943 48.8 12800 262.1
23:33:21.171 INFO ProgressMeter - chr5:87332505 49.0 12880 262.8
23:33:31.247 INFO ProgressMeter - chr5:112839533 49.2 12940 263.1
23:33:41.980 INFO ProgressMeter - chr5:122444561 49.4 12980 263.0
23:33:53.294 INFO ProgressMeter - chr5:138924566 49.5 13050 263.4
23:34:04.323 INFO ProgressMeter - chr5:149496836 49.7 13110 263.6
23:34:15.547 INFO ProgressMeter - chr5:150121878 49.9 13170 263.8
23:34:26.076 INFO ProgressMeter - chr5:150404367 50.1 13220 263.9
23:34:41.326 INFO ProgressMeter - chr5:177091026 50.3 13290 264.0
23:34:54.553 INFO ProgressMeter - chr5:177209948 50.6 13330 263.6
23:35:06.909 INFO ProgressMeter - chr5:177511773 50.8 13380 263.5
23:35:18.513 INFO ProgressMeter - chr6:397106 51.0 13450 263.9
23:35:29.797 INFO ProgressMeter - chr6:20478087 51.2 13510 264.1
23:35:41.397 INFO ProgressMeter - chr6:26171773 51.3 13570 264.3
23:35:55.051 INFO ProgressMeter - chr6:30702551 51.6 13600 263.7
23:36:06.477 INFO ProgressMeter - chr6:30707864 51.8 13630 263.3
23:36:16.578 INFO ProgressMeter - chr6:30714123 51.9 13650 262.8
23:36:27.251 INFO ProgressMeter - chr6:32219590 52.1 13700 262.9
23:36:38.331 INFO ProgressMeter - chr6:35457914 52.3 13740 262.7
23:36:49.927 INFO ProgressMeter - chr6:41975305 52.5 13800 262.9
23:37:00.336 INFO ProgressMeter - chr6:93245296 52.7 13860 263.2
23:37:11.461 INFO ProgressMeter - chr6:106107465 52.8 13920 263.4
23:37:23.182 INFO ProgressMeter - chr6:117321162 53.0 13970 263.4
23:37:34.660 INFO ProgressMeter - chr6:117325454 53.2 14000 263.0
23:37:46.075 INFO ProgressMeter - chr6:117332344 53.4 14040 262.8
23:37:56.354 INFO ProgressMeter - chr6:117338344 53.6 14080 262.7
23:38:07.672 INFO ProgressMeter - chr6:117394212 53.8 14130 262.7
23:38:17.747 INFO ProgressMeter - chr6:135205520 54.0 14180 262.8
23:38:36.028 INFO ProgressMeter - chr6:135212044 54.3 14220 262.1
23:38:47.779 INFO ProgressMeter - chr6:135214373 54.5 14240 261.5
23:38:58.505 INFO ProgressMeter - chr6:137206206 54.6 14280 261.4
23:39:09.306 INFO ProgressMeter - chr6:151365764 54.8 14330 261.4
23:39:19.543 INFO ProgressMeter - chr6:152065256 55.0 14380 261.5
23:39:31.147 INFO ProgressMeter - chr6:157148622 55.2 14410 261.2
23:39:41.905 INFO ProgressMeter - chr6:161073464 55.4 14450 261.0
23:39:53.904 INFO ProgressMeter - chr7:2919370 55.6 14530 261.5
23:40:04.442 INFO ProgressMeter - chr7:13892411 55.7 14590 261.8
23:40:16.260 INFO ProgressMeter - chr7:13908517 55.9 14630 261.6
23:40:26.662 INFO ProgressMeter - chr7:13933241 56.1 14650 261.1
23:40:37.617 INFO ProgressMeter - chr7:13939461 56.3 14690 261.0
23:40:47.720 INFO ProgressMeter - chr7:13944321 56.5 14720 260.7
23:41:01.174 INFO ProgressMeter - chr7:13949919 56.7 14750 260.2
23:41:12.554 INFO ProgressMeter - chr7:13952398 56.9 14770 259.7
23:41:22.814 INFO ProgressMeter - chr7:13954966 57.0 14790 259.3
23:41:36.598 INFO ProgressMeter - chr7:13960175 57.3 14830 259.0
23:41:51.439 INFO ProgressMeter - chr7:13965500 57.5 14860 258.4
23:42:03.321 INFO ProgressMeter - chr7:13970972 57.7 14900 258.2
23:42:21.393 INFO ProgressMeter - chr7:13976792 58.0 14940 257.5
23:42:35.700 INFO ProgressMeter - chr7:13981662 58.3 14980 257.2
23:42:49.178 INFO ProgressMeter - chr7:13985941 58.5 15010 256.7
23:43:00.249 INFO ProgressMeter - chr7:41686403 58.7 15030 256.2
23:43:12.054 INFO ProgressMeter - chr7:55153361 58.9 15080 256.2
23:43:25.423 INFO ProgressMeter - chr7:55168290 59.1 15120 255.9
23:43:35.570 INFO ProgressMeter - chr7:55174954 59.3 15150 255.7
23:43:49.180 INFO ProgressMeter - chr7:55179399 59.5 15190 255.4
23:44:01.031 INFO ProgressMeter - chr7:55204878 59.7 15230 255.2
23:44:12.942 INFO ProgressMeter - chr7:86786675 59.9 15300 255.5
23:44:22.958 INFO ProgressMeter - chr7:102097343 60.0 15360 255.8
23:44:33.800 INFO ProgressMeter - chr7:102277928 60.2 15410 255.9
23:44:44.440 INFO ProgressMeter - chr7:116731758 60.4 15460 256.0
23:44:56.095 INFO ProgressMeter - chr7:129210415 60.6 15520 256.1
23:45:08.727 INFO ProgressMeter - chr7:140792568 60.8 15580 256.2
23:45:19.281 INFO ProgressMeter - chr7:140919114 61.0 15630 256.3
23:45:31.632 INFO ProgressMeter - chr7:152148331 61.2 15700 256.6
23:45:44.600 INFO ProgressMeter - chr7:152177874 61.4 15750 256.5
23:45:55.444 INFO ProgressMeter - chr7:152249874 61.6 15800 256.6
23:46:06.478 INFO ProgressMeter - chr8:31640632 61.8 15880 257.1
23:46:18.656 INFO ProgressMeter - chr8:32763972 62.0 15950 257.4
23:46:30.681 INFO ProgressMeter - chr8:37842036 62.2 16010 257.5
23:46:43.887 INFO ProgressMeter - chr8:41933174 62.4 16070 257.6
23:46:55.022 INFO ProgressMeter - chr8:47783740 62.6 16120 257.6
23:47:05.786 INFO ProgressMeter - chr8:47888516 62.8 16190 258.0
23:47:16.408 INFO ProgressMeter - chr8:55966841 62.9 16260 258.4
23:47:27.114 INFO ProgressMeter - chr8:89937024 63.1 16330 258.8
23:47:39.516 INFO ProgressMeter - chr8:116856253 63.3 16380 258.7
23:47:51.209 INFO ProgressMeter - chr8:127738451 63.5 16420 258.5
23:48:01.485 INFO ProgressMeter - chr8:144513709 63.7 16470 258.6
23:48:12.588 INFO ProgressMeter - chr9:5077465 63.9 16530 258.8
23:48:23.676 INFO ProgressMeter - chr9:8470993 64.1 16590 259.0
23:48:34.083 INFO ProgressMeter - chr9:21971127 64.2 16640 259.1
23:48:46.389 INFO ProgressMeter - chr9:83970716 64.4 16700 259.2
23:49:01.339 INFO ProgressMeter - chr9:84743005 64.7 16750 259.0
23:49:13.388 INFO ProgressMeter - chr9:84813667 64.9 16780 258.6
23:49:23.879 INFO ProgressMeter - chr9:84861631 65.1 16800 258.2
23:49:38.489 INFO ProgressMeter - chr9:84865978 65.3 16830 257.7
23:49:50.545 INFO ProgressMeter - chr9:84876301 65.5 16860 257.4
23:50:02.048 INFO ProgressMeter - chr9:85023929 65.7 16890 257.1
23:50:13.774 INFO ProgressMeter - chr9:90865046 65.9 16920 256.8
23:50:24.354 INFO ProgressMeter - chr9:95468883 66.1 16970 256.9
23:50:34.991 INFO ProgressMeter - chr9:107487798 66.2 17020 256.9
23:50:47.509 INFO ProgressMeter - chr9:130885577 66.4 17070 256.9
23:50:58.188 INFO ProgressMeter - chr9:132911451 66.6 17110 256.8
23:51:08.666 INFO ProgressMeter - chr9:136505619 66.8 17150 256.7
23:51:19.325 INFO ProgressMeter - chr9:136909918 67.0 17210 256.9
23:51:30.018 INFO ProgressMeter - chrX:40074473 67.2 17280 257.3
23:51:41.371 INFO ProgressMeter - chrX:47565024 67.3 17360 257.8
23:51:52.364 INFO ProgressMeter - chrX:49036580 67.5 17420 258.0
23:52:03.275 INFO ProgressMeter - chrX:53217141 67.7 17480 258.1
23:52:14.783 INFO ProgressMeter - chrX:64191765 67.9 17540 258.3
23:52:25.322 INFO ProgressMeter - chrX:67658808 68.1 17590 258.4
23:52:37.409 INFO ProgressMeter - chrX:71375165 68.3 17670 258.8
23:52:48.042 INFO ProgressMeter - chrX:77676224 68.5 17750 259.3
23:52:58.648 INFO ProgressMeter - chrX:123907064 68.6 17840 259.9
23:53:10.094 INFO ProgressMeter - chrX:130039135 68.8 17910 260.2
23:53:15.571 INFO Mutect2 - 911086 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
6 read(s) filtered by: ReadLengthReadFilter
254 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
911346 total reads filtered out of 125185851 reads processed
23:53:15.571 INFO ProgressMeter - chrY:19742699 68.9 17978 260.9
23:53:15.571 INFO ProgressMeter - Traversal complete. Processed 17978 total regions in 68.9 minutes.
23:53:15.586 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 8.09094192
23:53:15.587 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 377.48663424
23:53:15.587 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 13.74 sec
23:53:15.587 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:53:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 68.93 minutes.
Runtime.totalMemory()=6006243328
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 LS0920_tumor.bam --tumor-sample LS0920 -L TST500C_manifest.bed -O LS0920.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:53:17.182 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
23:53:17.269 INFO FilterMutectCalls - ------------------------------------------------------------
23:53:17.270 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:53:17.270 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:53:17.270 INFO FilterMutectCalls - Executing as ?@nf-91f40eb6cdb1383e2a848da4f274d342-1425d-6nnqh on Linux v6.12.88 amd64
23:53:17.270 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:53:17.270 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:53:17 PM GMT
23:53:17.271 INFO FilterMutectCalls - ------------------------------------------------------------
23:53:17.271 INFO FilterMutectCalls - ------------------------------------------------------------
23:53:17.271 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:53:17.271 INFO FilterMutectCalls - Picard Version: 3.1.1
23:53:17.271 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:53:17.271 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:53:17.272 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:53:17.272 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:53:17.272 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:53:17.272 INFO FilterMutectCalls - Deflater: IntelDeflater
23:53:17.272 INFO FilterMutectCalls - Inflater: IntelInflater
23:53:17.272 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:53:17.272 INFO FilterMutectCalls - Requester pays: disabled
23:53:17.272 INFO FilterMutectCalls - Initializing engine
23:53:17.382 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.LEB9ssU9rM/LS0920.mutect2.raw.vcf.gz
23:53:17.469 INFO FilterMutectCalls - Done initializing engine
23:53:17.516 INFO ProgressMeter - Starting traversal
23:53:17.516 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:53:17.517 INFO FilterMutectCalls - Starting pass 0 through the variants
23:53:19.062 INFO FilterMutectCalls - Finished pass 0 through the variants
23:53:20.806 INFO FilterMutectCalls - Starting pass 1 through the variants
23:53:22.187 INFO FilterMutectCalls - Finished pass 1 through the variants
23:53:22.903 INFO FilterMutectCalls - Starting pass 2 through the variants
23:53:24.282 INFO FilterMutectCalls - Finished pass 2 through the variants
23:53:24.284 INFO FilterMutectCalls - Starting pass 3 through the variants
23:53:25.340 INFO FilterMutectCalls - Finished pass 3 through the variants
23:53:25.345 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:53:25.346 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:53:25.346 INFO ProgressMeter - chr6:161115143 0.1 10584 81103.4
23:53:25.346 INFO ProgressMeter - Traversal complete. Processed 10584 total variants in 0.1 minutes.
23:53:25.355 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:53:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=503316480
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 LS0920.mutect2.raw.vcf.gz --stats LS0920.mutect2.raw.vcf.gz.stats -O LS0920.mutect2.filtered.vcf.gz
23:53:26.584 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
23:53:26.685 INFO SelectVariants - ------------------------------------------------------------
23:53:26.687 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:53:26.688 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:53:26.688 INFO SelectVariants - Executing as ?@nf-91f40eb6cdb1383e2a848da4f274d342-1425d-6nnqh on Linux v6.12.88 amd64
23:53:26.688 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:53:26.688 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:53:26 PM GMT
23:53:26.688 INFO SelectVariants - ------------------------------------------------------------
23:53:26.688 INFO SelectVariants - ------------------------------------------------------------
23:53:26.689 INFO SelectVariants - HTSJDK Version: 4.1.0
23:53:26.689 INFO SelectVariants - Picard Version: 3.1.1
23:53:26.689 INFO SelectVariants - Built for Spark Version: 3.5.0
23:53:26.689 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:53:26.689 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:53:26.689 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:53:26.689 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:53:26.689 INFO SelectVariants - Deflater: IntelDeflater
23:53:26.689 INFO SelectVariants - Inflater: IntelInflater
23:53:26.689 INFO SelectVariants - GCS max retries/reopens: 20
23:53:26.689 INFO SelectVariants - Requester pays: disabled
23:53:26.690 INFO SelectVariants - Initializing engine
23:53:26.817 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.LEB9ssU9rM/LS0920.mutect2.filtered.vcf.gz
23:53:26.914 INFO SelectVariants - Done initializing engine
23:53:26.948 INFO ProgressMeter - Starting traversal
23:53:26.948 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:53:27.019 INFO ProgressMeter - chr6:135208081 0.0 2646 2334705.9
23:53:27.019 INFO ProgressMeter - Traversal complete. Processed 2646 total variants in 0.0 minutes.
23:53:27.028 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:53:27 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 LS0920.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0920.mutect2.pass.vcf.gz