22:44:22.080 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
22:44:22.213 INFO Mutect2 - ------------------------------------------------------------
22:44:22.215 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:22.215 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:22.215 INFO Mutect2 - Executing as ?@nf-a98aca5418416015f2a4b7723d545782-116b0-sd8l8 on Linux v6.12.88 amd64
22:44:22.215 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:22.215 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:22 PM GMT
22:44:22.215 INFO Mutect2 - ------------------------------------------------------------
22:44:22.215 INFO Mutect2 - ------------------------------------------------------------
22:44:22.217 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:22.217 INFO Mutect2 - Picard Version: 3.1.1
22:44:22.217 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:22.217 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:22.217 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:22.217 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:22.217 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:22.217 INFO Mutect2 - Deflater: IntelDeflater
22:44:22.218 INFO Mutect2 - Inflater: IntelInflater
22:44:22.218 INFO Mutect2 - GCS max retries/reopens: 20
22:44:22.218 INFO Mutect2 - Requester pays: disabled
22:44:22.218 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.GcHqM4xRyK/LS0903_tumor.bam.bai is older than BAM /tmp/nxf.GcHqM4xRyK/LS0903_tumor.bam
22:44:22.366 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.GcHqM4xRyK/af-only-gnomad.hg38.vcf.gz
22:44:22.511 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.GcHqM4xRyK/TST500C_manifest.bed
22:44:22.548 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:22.578 INFO Mutect2 - Done initializing engine
22:44:22.588 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
22:44:22.590 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
22:44:22.591 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:22.591 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:22.602 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
22:44:22.611 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:22.611 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:22.612 INFO IntelPairHmm - Available threads: 384
22:44:22.612 INFO IntelPairHmm - Requested threads: 4
22:44:22.612 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:22.650 INFO ProgressMeter - Starting traversal
22:44:22.651 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:33.047 INFO ProgressMeter - chr1:11210812 0.2 110 634.9
22:44:43.851 INFO ProgressMeter - chr1:15931436 0.4 190 537.7
22:44:55.175 INFO ProgressMeter - chr1:18747142 0.5 290 535.0
22:45:05.338 INFO ProgressMeter - chr1:36479431 0.7 400 562.2
22:45:15.717 INFO ProgressMeter - chr1:46077513 0.9 530 599.3
22:45:26.079 INFO ProgressMeter - chr1:77968163 1.1 670 633.8
22:45:36.544 INFO ProgressMeter - chr1:119919492 1.2 780 633.3
22:45:50.876 INFO ProgressMeter - chr1:156873807 1.5 880 598.5
22:46:01.760 INFO ProgressMeter - chr1:158643320 1.7 940 569.1
22:46:11.864 INFO ProgressMeter - chr1:162754766 1.8 1020 560.4
22:46:22.863 INFO ProgressMeter - chr1:179133310 2.0 1110 554.0
22:46:33.476 INFO ProgressMeter - chr1:206478941 2.2 1260 577.9
22:46:44.596 INFO ProgressMeter - chr1:243500975 2.4 1360 574.9
22:46:55.114 INFO ProgressMeter - chr1:243695625 2.5 1420 558.8
22:47:05.847 INFO ProgressMeter - chr10:27100306 2.7 1510 555.2
22:47:17.233 INFO ProgressMeter - chr10:43114262 2.9 1600 549.9
22:47:29.040 INFO ProgressMeter - chr10:68573296 3.1 1690 544.0
22:47:39.182 INFO ProgressMeter - chr10:89007722 3.3 1800 549.5
22:47:49.307 INFO ProgressMeter - chr10:110593052 3.4 1910 554.5
22:47:59.512 INFO ProgressMeter - chr10:121482138 3.6 1990 550.6
22:48:09.663 INFO ProgressMeter - chr11:22625286 3.8 2100 555.0
22:48:20.251 INFO ProgressMeter - chr11:69700046 4.0 2250 568.2
22:48:30.354 INFO ProgressMeter - chr11:69815701 4.1 2350 569.2
22:48:41.153 INFO ProgressMeter - chr11:77415651 4.3 2470 573.3
22:48:55.486 INFO ProgressMeter - chr11:102325045 4.5 2590 569.6
22:49:05.989 INFO ProgressMeter - chr11:108345741 4.7 2700 571.8
22:49:16.324 INFO ProgressMeter - chr11:118502396 4.9 2780 568.0
22:49:27.269 INFO ProgressMeter - chr11:119285339 5.1 2850 561.4
22:49:38.804 INFO ProgressMeter - chr11:125667041 5.3 2920 554.2
22:49:48.887 INFO ProgressMeter - chr11:128522189 5.4 2970 546.2
22:49:59.529 INFO ProgressMeter - chr12:309801 5.6 3030 539.7
22:50:09.874 INFO ProgressMeter - chr12:4374929 5.8 3130 540.9
22:50:20.103 INFO ProgressMeter - chr12:6570925 6.0 3210 538.8
22:50:31.743 INFO ProgressMeter - chr12:11855344 6.2 3290 534.8
22:50:42.394 INFO ProgressMeter - chr12:11860716 6.3 3340 527.7
22:50:53.099 INFO ProgressMeter - chr12:11866483 6.5 3390 520.9
22:51:04.049 INFO ProgressMeter - chr12:18491449 6.7 3460 517.2
22:51:15.064 INFO ProgressMeter - chr12:45817668 6.9 3560 517.9
22:51:26.055 INFO ProgressMeter - chr12:49031173 7.1 3640 515.8
22:51:36.279 INFO ProgressMeter - chr12:49040254 7.2 3690 510.6
22:51:46.332 INFO ProgressMeter - chr12:49054305 7.4 3770 509.8
22:51:57.365 INFO ProgressMeter - chr12:57089231 7.6 3880 512.0
22:52:08.295 INFO ProgressMeter - chr12:57743026 7.8 3950 509.0
22:52:18.719 INFO ProgressMeter - chr12:68824361 7.9 4030 507.9
22:52:31.078 INFO ProgressMeter - chr12:69574201 8.1 4080 501.2
22:52:41.658 INFO ProgressMeter - chr12:112450387 8.3 4140 497.8
22:52:52.270 INFO ProgressMeter - chr12:132664368 8.5 4260 501.6
22:53:02.516 INFO ProgressMeter - chr13:28015155 8.7 4390 506.7
22:53:15.713 INFO ProgressMeter - chr13:28388958 8.9 4480 504.3
22:53:26.798 INFO ProgressMeter - chr13:32339380 9.1 4550 501.7
22:53:37.239 INFO ProgressMeter - chr13:48368525 9.2 4640 502.0
22:53:47.518 INFO ProgressMeter - chr13:102865665 9.4 4770 506.7
22:53:57.923 INFO ProgressMeter - chr14:23183281 9.6 4870 507.9
22:54:09.085 INFO ProgressMeter - chr14:81143375 9.8 5020 513.6
22:54:19.717 INFO ProgressMeter - chr14:102085756 10.0 5110 513.5
22:54:30.398 INFO ProgressMeter - chr15:34354546 10.1 5180 511.4
22:54:41.434 INFO ProgressMeter - chr15:41749109 10.3 5270 511.0
22:54:51.556 INFO ProgressMeter - chr15:67190462 10.5 5390 514.2
22:55:02.493 INFO ProgressMeter - chr15:89293035 10.7 5490 514.8
22:55:12.577 INFO ProgressMeter - chr15:92984328 10.8 5600 517.0
22:55:22.693 INFO ProgressMeter - chr16:2061869 11.0 5710 519.1
22:55:33.100 INFO ProgressMeter - chr16:3600977 11.2 5850 523.5
22:55:43.789 INFO ProgressMeter - chr16:9834103 11.4 5950 524.1
22:55:53.901 INFO ProgressMeter - chr16:23635745 11.5 6030 523.4
22:56:03.941 INFO ProgressMeter - chr16:67610831 11.7 6130 524.5
22:56:14.727 INFO ProgressMeter - chr16:72794557 11.9 6210 523.3
22:56:25.268 INFO ProgressMeter - chr16:72959571 12.0 6270 520.6
22:56:35.856 INFO ProgressMeter - chr16:89282557 12.2 6360 520.5
22:56:46.155 INFO ProgressMeter - chr16:89791401 12.4 6440 519.7
22:56:56.472 INFO ProgressMeter - chr17:12095694 12.6 6590 524.5
22:57:07.204 INFO ProgressMeter - chr17:31206238 12.7 6740 528.9
22:57:18.015 INFO ProgressMeter - chr17:39470877 12.9 6860 530.8
22:57:28.033 INFO ProgressMeter - chr17:40351978 13.1 6970 532.5
22:57:38.445 INFO ProgressMeter - chr17:42337761 13.3 7100 535.3
22:57:49.978 INFO ProgressMeter - chr17:43094344 13.5 7180 533.6
22:58:00.010 INFO ProgressMeter - chr17:43538145 13.6 7270 533.7
22:58:10.400 INFO ProgressMeter - chr17:45267090 13.8 7330 531.3
22:58:21.244 INFO ProgressMeter - chr17:59909059 14.0 7440 532.3
22:58:31.737 INFO ProgressMeter - chr17:61784268 14.2 7530 532.1
22:58:42.501 INFO ProgressMeter - chr17:80754008 14.3 7640 533.1
22:58:52.771 INFO ProgressMeter - chr18:41993268 14.5 7740 533.7
22:59:03.574 INFO ProgressMeter - chr18:51048684 14.7 7830 533.3
22:59:13.844 INFO ProgressMeter - chr19:4090596 14.9 8000 538.6
22:59:24.074 INFO ProgressMeter - chr19:10486792 15.0 8170 543.8
22:59:34.722 INFO ProgressMeter - chr19:15192375 15.2 8330 548.0
22:59:45.277 INFO ProgressMeter - chr19:29810084 15.4 8450 549.5
22:59:55.883 INFO ProgressMeter - chr19:35719812 15.6 8530 548.4
23:00:06.795 INFO ProgressMeter - chr19:40235939 15.7 8620 547.8
23:00:18.669 INFO ProgressMeter - chr19:41261194 15.9 8710 546.6
23:00:28.672 INFO ProgressMeter - chr19:45408200 16.1 8830 548.4
23:00:40.328 INFO ProgressMeter - chr2:15938592 16.3 8950 549.3
23:00:50.984 INFO ProgressMeter - chr2:25281739 16.5 9070 550.6
23:01:01.402 INFO ProgressMeter - chr2:29207209 16.6 9150 549.7
23:01:11.997 INFO ProgressMeter - chr2:29318302 16.8 9210 547.5
23:01:22.433 INFO ProgressMeter - chr2:42330728 17.0 9290 546.6
23:01:33.887 INFO ProgressMeter - chr2:47799348 17.2 9360 544.6
23:01:43.918 INFO ProgressMeter - chr2:95183454 17.4 9460 545.1
23:01:54.446 INFO ProgressMeter - chr2:108764490 17.5 9560 545.4
23:02:04.885 INFO ProgressMeter - chr2:113220664 17.7 9640 544.5
23:02:16.814 INFO ProgressMeter - chr2:113227165 17.9 9690 541.3
23:02:26.955 INFO ProgressMeter - chr2:113231509 18.1 9730 538.4
23:02:37.773 INFO ProgressMeter - chr2:127272863 18.3 9790 536.4
23:02:48.644 INFO ProgressMeter - chr2:140700474 18.4 9900 537.1
23:02:58.916 INFO ProgressMeter - chr2:168943744 18.6 10000 537.5
23:03:09.547 INFO ProgressMeter - chr2:197401740 18.8 10110 538.3
23:03:20.659 INFO ProgressMeter - chr2:211679127 19.0 10210 538.3
23:03:30.746 INFO ProgressMeter - chr2:222204944 19.1 10300 538.3
23:03:42.996 INFO ProgressMeter - chr2:222217028 19.3 10380 536.7
23:03:53.840 INFO ProgressMeter - chr20:9565891 19.5 10500 537.9
23:04:04.716 INFO ProgressMeter - chr20:32436780 19.7 10570 536.5
23:04:15.171 INFO ProgressMeter - chr20:42282487 19.9 10670 536.8
23:04:26.537 INFO ProgressMeter - chr20:53576993 20.1 10750 535.8
23:04:37.075 INFO ProgressMeter - chr21:34887035 20.2 10860 536.6
23:04:49.129 INFO ProgressMeter - chr21:41465756 20.4 10940 535.2
23:05:00.400 INFO ProgressMeter - chr21:41493158 20.6 10990 532.7
23:05:11.594 INFO ProgressMeter - chr21:41506138 20.8 11060 531.3
23:05:21.672 INFO ProgressMeter - chr22:23181485 21.0 11160 531.8
23:05:31.861 INFO ProgressMeter - chr22:23291795 21.2 11200 529.5
23:05:42.284 INFO ProgressMeter - chr22:29272378 21.3 11300 529.8
23:05:53.355 INFO ProgressMeter - chr22:29286857 21.5 11340 527.2
23:06:03.842 INFO ProgressMeter - chr22:41155020 21.7 11430 527.1
23:06:16.160 INFO ProgressMeter - chr3:12352547 21.9 11540 527.1
23:06:28.143 INFO ProgressMeter - chr3:12355214 22.1 11560 523.3
23:06:38.199 INFO ProgressMeter - chr3:12359293 22.3 11590 520.7
23:06:50.917 INFO ProgressMeter - chr3:12361612 22.5 11610 516.7
23:07:02.953 INFO ProgressMeter - chr3:12365916 22.7 11650 513.9
23:07:13.996 INFO ProgressMeter - chr3:12369550 22.9 11680 511.0
23:07:27.781 INFO ProgressMeter - chr3:12374156 23.1 11720 507.7
23:07:39.936 INFO ProgressMeter - chr3:12378317 23.3 11760 505.0
23:07:52.338 INFO ProgressMeter - chr3:12604248 23.5 11810 502.7
23:08:02.810 INFO ProgressMeter - chr3:30672105 23.7 11860 501.1
23:08:14.337 INFO ProgressMeter - chr3:47057252 23.9 11950 500.8
23:08:27.450 INFO ProgressMeter - chr3:47122461 24.1 12000 498.3
23:08:38.260 INFO ProgressMeter - chr3:49898865 24.3 12090 498.3
23:08:48.467 INFO ProgressMeter - chr3:71112534 24.4 12220 500.2
23:08:59.291 INFO ProgressMeter - chr3:135154150 24.6 12330 501.0
23:09:10.247 INFO ProgressMeter - chr3:138700301 24.8 12420 500.9
23:09:20.319 INFO ProgressMeter - chr3:142553638 25.0 12520 501.6
23:09:31.019 INFO ProgressMeter - chr3:179220984 25.1 12630 502.4
23:09:41.716 INFO ProgressMeter - chr3:186046315 25.3 12720 502.4
23:09:52.114 INFO ProgressMeter - chr3:189631514 25.5 12800 502.1
23:10:02.535 INFO ProgressMeter - chr4:1797774 25.7 12900 502.6
23:10:13.361 INFO ProgressMeter - chr4:54262543 25.8 13040 504.5
23:10:26.360 INFO ProgressMeter - chr4:54736719 26.1 13120 503.4
23:10:36.830 INFO ProgressMeter - chr4:80281207 26.2 13230 504.3
23:10:47.826 INFO ProgressMeter - chr4:105241025 26.4 13320 504.2
23:10:58.150 INFO ProgressMeter - chr4:142160356 26.6 13410 504.3
23:11:08.500 INFO ProgressMeter - chr4:186609799 26.8 13510 504.8
23:11:19.399 INFO ProgressMeter - chr4:186708748 26.9 13590 504.3
23:11:29.570 INFO ProgressMeter - chr5:38950010 27.1 13670 504.1
23:11:39.813 INFO ProgressMeter - chr5:44362662 27.3 13760 504.3
23:11:50.098 INFO ProgressMeter - chr5:80768010 27.5 13880 505.5
23:12:00.610 INFO ProgressMeter - chr5:112841691 27.6 13990 506.3
23:12:10.765 INFO ProgressMeter - chr5:138933800 27.8 14100 507.2
23:12:21.159 INFO ProgressMeter - chr5:150124248 28.0 14220 508.3
23:12:33.183 INFO ProgressMeter - chr5:177090759 28.2 14340 509.0
23:12:44.143 INFO ProgressMeter - chr5:177294478 28.4 14440 509.2
23:12:54.975 INFO ProgressMeter - chr6:20455963 28.5 14580 510.9
23:13:09.173 INFO ProgressMeter - chr6:29945449 28.8 14690 510.5
23:13:19.602 INFO ProgressMeter - chr6:32204135 28.9 14760 509.9
23:13:30.769 INFO ProgressMeter - chr6:41975380 29.1 14890 511.1
23:13:40.849 INFO ProgressMeter - chr6:111694691 29.3 15000 511.9
23:13:50.875 INFO ProgressMeter - chr6:117324625 29.5 15070 511.4
23:14:01.155 INFO ProgressMeter - chr6:117337012 29.6 15150 511.1
23:14:11.704 INFO ProgressMeter - chr6:135200083 29.8 15250 511.4
23:14:23.160 INFO ProgressMeter - chr6:135210966 30.0 15320 510.5
23:14:34.293 INFO ProgressMeter - chr6:135215217 30.2 15350 508.4
23:14:44.296 INFO ProgressMeter - chr6:149680363 30.4 15430 508.2
23:14:54.504 INFO ProgressMeter - chr6:156778640 30.5 15520 508.3
23:15:05.098 INFO ProgressMeter - chr6:161109753 30.7 15620 508.7
23:15:15.470 INFO ProgressMeter - chr7:13891609 30.9 15740 509.7
23:15:29.023 INFO ProgressMeter - chr7:13909437 31.1 15800 507.9
23:15:39.815 INFO ProgressMeter - chr7:13937171 31.3 15860 506.9
23:15:50.353 INFO ProgressMeter - chr7:13944188 31.5 15920 506.0
23:16:00.701 INFO ProgressMeter - chr7:13949505 31.6 15960 504.5
23:16:11.556 INFO ProgressMeter - chr7:13955683 31.8 16010 503.2
23:16:22.292 INFO ProgressMeter - chr7:13962571 32.0 16060 502.0
23:16:33.456 INFO ProgressMeter - chr7:13969946 32.2 16120 500.9
23:16:48.011 INFO ProgressMeter - chr7:13976822 32.4 16170 498.7
23:16:59.802 INFO ProgressMeter - chr7:13984804 32.6 16230 497.6
23:17:10.542 INFO ProgressMeter - chr7:50400020 32.8 16290 496.7
23:17:21.059 INFO ProgressMeter - chr7:55167310 33.0 16360 496.2
23:17:31.350 INFO ProgressMeter - chr7:55177083 33.1 16420 495.4
23:17:41.567 INFO ProgressMeter - chr7:78079034 33.3 16490 495.0
23:17:51.634 INFO ProgressMeter - chr7:92822963 33.5 16610 496.1
23:18:02.493 INFO ProgressMeter - chr7:116739948 33.7 16730 497.0
23:18:13.345 INFO ProgressMeter - chr7:140788280 33.8 16820 497.0
23:18:23.800 INFO ProgressMeter - chr7:140919113 34.0 16910 497.1
23:18:34.302 INFO ProgressMeter - chr7:152174129 34.2 17020 497.7
23:18:44.943 INFO ProgressMeter - chr7:152311796 34.4 17100 497.5
23:18:55.073 INFO ProgressMeter - chr8:37797267 34.5 17240 499.1
23:19:05.433 INFO ProgressMeter - chr8:47782163 34.7 17390 501.0
23:19:15.891 INFO ProgressMeter - chr8:54459850 34.9 17520 502.2
23:19:26.434 INFO ProgressMeter - chr8:89970362 35.1 17630 502.8
23:19:36.530 INFO ProgressMeter - chr8:127732268 35.2 17700 502.4
23:19:47.037 INFO ProgressMeter - chr9:5089672 35.4 17840 503.9
23:19:57.489 INFO ProgressMeter - chr9:83971651 35.6 18010 506.2
23:20:08.528 INFO ProgressMeter - chr9:84811367 35.8 18080 505.5
23:20:19.689 INFO ProgressMeter - chr9:84862026 36.0 18130 504.3
23:20:31.461 INFO ProgressMeter - chr9:84872627 36.1 18180 502.9
23:20:43.041 INFO ProgressMeter - chr9:85022508 36.3 18240 501.9
23:20:53.137 INFO ProgressMeter - chr9:90888571 36.5 18290 501.0
23:21:03.986 INFO ProgressMeter - chr9:125189708 36.7 18410 501.8
23:21:14.726 INFO ProgressMeter - chr9:132921361 36.9 18500 501.8
23:21:24.940 INFO ProgressMeter - chrX:40072329 37.0 18650 503.5
23:21:36.206 INFO ProgressMeter - chrX:49036262 37.2 18810 505.3
23:21:47.121 INFO ProgressMeter - chrX:64192988 37.4 18950 506.6
23:21:57.265 INFO ProgressMeter - chrX:77633564 37.6 19150 509.6
23:22:07.497 INFO ProgressMeter - chrY:2945039 37.7 19350 512.6
23:22:12.733 INFO Mutect2 - 482036 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
2 read(s) filtered by: ReadLengthReadFilter
83 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
482121 total reads filtered out of 60479993 reads processed
23:22:12.733 INFO ProgressMeter - chrY:20398623 37.8 19415 513.2
23:22:12.733 INFO ProgressMeter - Traversal complete. Processed 19415 total regions in 37.8 minutes.
23:22:12.750 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 4.497084887000001
23:22:12.750 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 177.501819915
23:22:12.751 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 6.99 sec
23:22:12.751 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:22:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 37.85 minutes.
Runtime.totalMemory()=7272923136
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 LS0903_tumor.bam --tumor-sample LS0903 -L TST500C_manifest.bed -O LS0903.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:22:14.565 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
23:22:14.690 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:14.692 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:22:14.692 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:22:14.693 INFO FilterMutectCalls - Executing as ?@nf-a98aca5418416015f2a4b7723d545782-116b0-sd8l8 on Linux v6.12.88 amd64
23:22:14.693 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:22:14.693 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:22:14 PM GMT
23:22:14.693 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:14.693 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:14.694 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:22:14.694 INFO FilterMutectCalls - Picard Version: 3.1.1
23:22:14.694 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:22:14.694 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:22:14.694 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:22:14.694 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:22:14.695 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:22:14.695 INFO FilterMutectCalls - Deflater: IntelDeflater
23:22:14.695 INFO FilterMutectCalls - Inflater: IntelInflater
23:22:14.695 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:22:14.695 INFO FilterMutectCalls - Requester pays: disabled
23:22:14.695 INFO FilterMutectCalls - Initializing engine
23:22:14.856 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.GcHqM4xRyK/LS0903.mutect2.raw.vcf.gz
23:22:14.978 INFO FilterMutectCalls - Done initializing engine
23:22:15.035 INFO ProgressMeter - Starting traversal
23:22:15.036 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:22:15.037 INFO FilterMutectCalls - Starting pass 0 through the variants
23:22:15.976 INFO FilterMutectCalls - Finished pass 0 through the variants
23:22:17.467 INFO FilterMutectCalls - Starting pass 1 through the variants
23:22:18.315 INFO FilterMutectCalls - Finished pass 1 through the variants
23:22:18.715 INFO FilterMutectCalls - Starting pass 2 through the variants
23:22:19.507 INFO FilterMutectCalls - Finished pass 2 through the variants
23:22:19.508 INFO FilterMutectCalls - Starting pass 3 through the variants
23:22:20.267 INFO FilterMutectCalls - Finished pass 3 through the variants
23:22:20.275 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:22:20.276 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:22:20.276 INFO ProgressMeter - chr9:5003338 0.1 10172 116495.5
23:22:20.276 INFO ProgressMeter - Traversal complete. Processed 10172 total variants in 0.1 minutes.
23:22:20.288 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:22:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.10 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 LS0903.mutect2.raw.vcf.gz --stats LS0903.mutect2.raw.vcf.gz.stats -O LS0903.mutect2.filtered.vcf.gz
23:22:21.680 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
23:22:21.807 INFO SelectVariants - ------------------------------------------------------------
23:22:21.810 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:22:21.810 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:22:21.811 INFO SelectVariants - Executing as ?@nf-a98aca5418416015f2a4b7723d545782-116b0-sd8l8 on Linux v6.12.88 amd64
23:22:21.811 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:22:21.811 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:22:21 PM GMT
23:22:21.812 INFO SelectVariants - ------------------------------------------------------------
23:22:21.812 INFO SelectVariants - ------------------------------------------------------------
23:22:21.813 INFO SelectVariants - HTSJDK Version: 4.1.0
23:22:21.813 INFO SelectVariants - Picard Version: 3.1.1
23:22:21.813 INFO SelectVariants - Built for Spark Version: 3.5.0
23:22:21.813 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:22:21.813 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:22:21.813 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:22:21.813 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:22:21.814 INFO SelectVariants - Deflater: IntelDeflater
23:22:21.814 INFO SelectVariants - Inflater: IntelInflater
23:22:21.814 INFO SelectVariants - GCS max retries/reopens: 20
23:22:21.815 INFO SelectVariants - Requester pays: disabled
23:22:21.816 INFO SelectVariants - Initializing engine
23:22:21.974 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.GcHqM4xRyK/LS0903.mutect2.filtered.vcf.gz
23:22:22.092 INFO SelectVariants - Done initializing engine
23:22:22.131 INFO ProgressMeter - Starting traversal
23:22:22.131 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:22:22.218 INFO ProgressMeter - chr6:135212224 0.0 2543 1838313.3
23:22:22.218 INFO ProgressMeter - Traversal complete. Processed 2543 total variants in 0.0 minutes.
23:22:22.232 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:22:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=377487360
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 LS0903.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0903.mutect2.pass.vcf.gz