22:44:16.993 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
22:44:17.118 INFO Mutect2 - ------------------------------------------------------------
22:44:17.121 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:17.121 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:17.122 INFO Mutect2 - Executing as ?@nf-3930d6d6b42d2078a0eaffd1fa9c68be-64fdd-nr2zh on Linux v6.12.88 amd64
22:44:17.122 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:17.122 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:16 PM GMT
22:44:17.122 INFO Mutect2 - ------------------------------------------------------------
22:44:17.122 INFO Mutect2 - ------------------------------------------------------------
22:44:17.123 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:17.123 INFO Mutect2 - Picard Version: 3.1.1
22:44:17.123 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:17.123 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:17.123 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:17.123 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:17.124 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:17.124 INFO Mutect2 - Deflater: IntelDeflater
22:44:17.124 INFO Mutect2 - Inflater: IntelInflater
22:44:17.124 INFO Mutect2 - GCS max retries/reopens: 20
22:44:17.124 INFO Mutect2 - Requester pays: disabled
22:44:17.124 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.V5HjmjBmPJ/LS0911_tumor.bam.bai is older than BAM /tmp/nxf.V5HjmjBmPJ/LS0911_tumor.bam
22:44:17.332 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.V5HjmjBmPJ/af-only-gnomad.hg38.vcf.gz
22:44:17.435 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.V5HjmjBmPJ/TST500C_manifest.bed
22:44:17.478 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:17.512 INFO Mutect2 - Done initializing engine
22:44:17.524 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
22:44:17.526 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
22:44:17.527 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:17.527 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:17.539 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
22:44:17.548 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:17.548 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:17.549 INFO IntelPairHmm - Available threads: 384
22:44:17.549 INFO IntelPairHmm - Requested threads: 4
22:44:17.549 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:17.592 INFO ProgressMeter - Starting traversal
22:44:17.593 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:27.626 INFO ProgressMeter - chr1:11133078 0.2 80 478.5
22:44:39.070 INFO ProgressMeter - chr1:15931078 0.4 160 447.0
22:44:50.389 INFO ProgressMeter - chr1:18746752 0.5 230 420.8
22:45:00.972 INFO ProgressMeter - chr1:26780130 0.7 300 414.9
22:45:11.395 INFO ProgressMeter - chr1:39907046 0.9 390 434.9
22:45:22.107 INFO ProgressMeter - chr1:64834560 1.1 490 455.7
22:45:32.334 INFO ProgressMeter - chr1:114716048 1.2 610 489.7
22:45:43.071 INFO ProgressMeter - chr1:119941524 1.4 680 477.3
22:46:00.053 INFO ProgressMeter - chr1:156874983 1.7 750 439.2
22:46:11.029 INFO ProgressMeter - chr1:158649854 1.9 810 428.4
22:46:22.207 INFO ProgressMeter - chr1:175945151 2.1 880 423.7
22:46:32.243 INFO ProgressMeter - chr1:204425611 2.2 960 427.8
22:46:42.406 INFO ProgressMeter - chr1:204542549 2.4 1030 426.8
22:46:53.513 INFO ProgressMeter - chr1:226380157 2.6 1110 427.1
22:47:03.960 INFO ProgressMeter - chr1:243502301 2.8 1170 422.0
22:47:14.294 INFO ProgressMeter - chr10:27014473 2.9 1230 417.7
22:47:24.794 INFO ProgressMeter - chr10:32022138 3.1 1320 423.1
22:47:36.952 INFO ProgressMeter - chr10:43113599 3.3 1390 418.3
22:47:47.727 INFO ProgressMeter - chr10:43117847 3.5 1430 408.3
22:47:59.211 INFO ProgressMeter - chr10:68572861 3.7 1490 403.4
22:48:10.020 INFO ProgressMeter - chr10:89003027 3.9 1590 410.5
22:48:20.282 INFO ProgressMeter - chr10:110593052 4.0 1680 415.3
22:48:33.426 INFO ProgressMeter - chr10:121483150 4.3 1750 410.4
22:48:44.351 INFO ProgressMeter - chr11:32416488 4.4 1850 416.1
22:48:55.459 INFO ProgressMeter - chr11:69650612 4.6 1960 423.2
22:49:06.060 INFO ProgressMeter - chr11:69769828 4.8 2030 422.2
22:49:17.797 INFO ProgressMeter - chr11:69810867 5.0 2080 415.7
22:49:29.291 INFO ProgressMeter - chr11:77349171 5.2 2160 415.8
22:49:40.105 INFO ProgressMeter - chr11:101128913 5.4 2270 422.3
22:49:50.452 INFO ProgressMeter - chr11:108315821 5.5 2350 423.6
22:50:00.871 INFO ProgressMeter - chr11:118505475 5.7 2450 428.2
22:50:12.013 INFO ProgressMeter - chr11:128459746 5.9 2550 431.7
22:50:22.926 INFO ProgressMeter - chr12:328833 6.1 2640 433.6
22:50:33.534 INFO ProgressMeter - chr12:4437023 6.3 2740 437.3
22:50:43.628 INFO ProgressMeter - chr12:6602374 6.4 2820 438.3
22:50:55.185 INFO ProgressMeter - chr12:11860601 6.6 2880 434.6
22:51:05.411 INFO ProgressMeter - chr12:11868061 6.8 2930 431.1
22:51:16.388 INFO ProgressMeter - chr12:25221195 7.0 3020 432.7
22:51:26.853 INFO ProgressMeter - chr12:49026475 7.2 3100 433.3
22:51:37.628 INFO ProgressMeter - chr12:49040733 7.3 3160 430.9
22:51:48.400 INFO ProgressMeter - chr12:56084993 7.5 3260 433.9
22:51:58.879 INFO ProgressMeter - chr12:57465786 7.7 3350 435.7
22:52:09.478 INFO ProgressMeter - chr12:68836916 7.9 3450 438.7
22:52:19.921 INFO ProgressMeter - chr12:120099028 8.0 3550 441.6
22:52:30.165 INFO ProgressMeter - chr12:132668633 8.2 3630 442.2
22:52:40.902 INFO ProgressMeter - chr13:26401464 8.4 3730 444.7
22:52:52.336 INFO ProgressMeter - chr13:28388167 8.6 3810 444.1
22:53:02.810 INFO ProgressMeter - chr13:32338439 8.8 3870 442.1
22:53:13.183 INFO ProgressMeter - chr13:72763449 8.9 3970 444.7
22:53:23.270 INFO ProgressMeter - chr13:102875866 9.1 4060 446.4
22:53:34.241 INFO ProgressMeter - chr14:28567526 9.3 4140 446.2
22:53:44.558 INFO ProgressMeter - chr14:37598403 9.4 4230 447.6
22:53:55.158 INFO ProgressMeter - chr14:95131507 9.6 4320 448.8
22:54:05.961 INFO ProgressMeter - chr15:34348559 9.8 4400 448.7
22:54:16.399 INFO ProgressMeter - chr15:41742992 10.0 4470 447.9
22:54:27.418 INFO ProgressMeter - chr15:67165251 10.2 4570 449.6
22:54:37.537 INFO ProgressMeter - chr15:89273375 10.3 4650 450.0
22:54:48.049 INFO ProgressMeter - chr15:92978232 10.5 4760 453.0
22:54:58.577 INFO ProgressMeter - chr16:2048633 10.7 4850 454.0
22:55:09.258 INFO ProgressMeter - chr16:3589939 10.9 4970 457.6
22:55:19.528 INFO ProgressMeter - chr16:3770568 11.0 5040 456.8
22:55:29.670 INFO ProgressMeter - chr16:13934250 11.2 5120 457.1
22:55:40.006 INFO ProgressMeter - chr16:56830526 11.4 5210 458.1
22:55:51.750 INFO ProgressMeter - chr16:72795030 11.6 5290 457.2
22:56:02.555 INFO ProgressMeter - chr16:72959992 11.7 5350 455.3
22:56:13.969 INFO ProgressMeter - chr16:89283195 11.9 5440 455.6
22:56:24.177 INFO ProgressMeter - chr17:7314957 12.1 5540 457.5
22:56:34.711 INFO ProgressMeter - chr17:16048894 12.3 5650 459.9
22:56:45.909 INFO ProgressMeter - chr17:18054125 12.5 5730 459.4
22:56:56.521 INFO ProgressMeter - chr17:31947615 12.6 5810 459.3
22:57:07.667 INFO ProgressMeter - chr17:39531205 12.8 5880 458.1
22:57:18.336 INFO ProgressMeter - chr17:40351978 13.0 5950 457.3
22:57:29.378 INFO ProgressMeter - chr17:42310573 13.2 6050 458.5
22:57:41.850 INFO ProgressMeter - chr17:43093258 13.4 6130 457.3
22:57:52.507 INFO ProgressMeter - chr17:43531980 13.6 6190 455.8
22:58:03.950 INFO ProgressMeter - chr17:43541576 13.8 6250 453.8
22:58:15.903 INFO ProgressMeter - chr17:45274121 14.0 6300 450.9
22:58:27.846 INFO ProgressMeter - chr17:58695229 14.2 6360 448.8
22:58:38.948 INFO ProgressMeter - chr17:60663035 14.4 6440 448.6
22:58:50.120 INFO ProgressMeter - chr17:65537727 14.5 6510 447.7
22:59:00.929 INFO ProgressMeter - chr17:80880461 14.7 6590 447.6
22:59:13.861 INFO ProgressMeter - chr18:44951393 14.9 6700 448.5
22:59:24.726 INFO ProgressMeter - chr19:1615402 15.1 6800 449.8
22:59:34.876 INFO ProgressMeter - chr19:5214359 15.3 6920 452.6
22:59:45.411 INFO ProgressMeter - chr19:10154291 15.5 7020 454.0
22:59:55.555 INFO ProgressMeter - chr19:14516112 15.6 7130 456.1
23:00:06.519 INFO ProgressMeter - chr19:15243081 15.8 7220 456.5
23:00:16.620 INFO ProgressMeter - chr19:27972467 16.0 7320 458.0
23:00:26.827 INFO ProgressMeter - chr19:35725721 16.2 7410 458.7
23:00:37.246 INFO ProgressMeter - chr19:41220634 16.3 7510 460.0
23:00:47.496 INFO ProgressMeter - chr19:42290993 16.5 7570 458.8
23:00:58.215 INFO ProgressMeter - chr19:45416592 16.7 7680 460.5
23:01:09.277 INFO ProgressMeter - chr2:15940559 16.9 7770 460.8
23:01:19.305 INFO ProgressMeter - chr2:25275498 17.0 7860 461.6
23:01:30.262 INFO ProgressMeter - chr2:29222571 17.2 7930 460.7
23:01:40.971 INFO ProgressMeter - chr2:29328348 17.4 7980 458.9
23:01:53.474 INFO ProgressMeter - chr2:47416294 17.6 8070 458.6
23:02:03.968 INFO ProgressMeter - chr2:61498863 17.8 8170 459.7
23:02:15.385 INFO ProgressMeter - chr2:108764462 18.0 8260 459.8
23:02:27.293 INFO ProgressMeter - chr2:111128565 18.2 8310 457.6
23:02:37.536 INFO ProgressMeter - chr2:113226502 18.3 8360 456.0
23:02:50.938 INFO ProgressMeter - chr2:113234233 18.6 8420 453.8
23:03:01.185 INFO ProgressMeter - chr2:140457461 18.7 8520 455.0
23:03:11.878 INFO ProgressMeter - chr2:157760945 18.9 8620 456.0
23:03:22.383 INFO ProgressMeter - chr2:197420376 19.1 8730 457.6
23:03:32.846 INFO ProgressMeter - chr2:219572373 19.3 8830 458.6
23:03:43.002 INFO ProgressMeter - chr2:222206732 19.4 8880 457.2
23:03:53.996 INFO ProgressMeter - chr2:222215796 19.6 8930 455.5
23:04:04.662 INFO ProgressMeter - chr2:224584942 19.8 8990 454.4
23:04:15.152 INFO ProgressMeter - chr20:32428126 20.0 9070 454.4
23:04:25.893 INFO ProgressMeter - chr20:41116276 20.1 9160 454.9
23:04:36.966 INFO ProgressMeter - chr20:53582139 20.3 9250 455.2
23:04:48.775 INFO ProgressMeter - chr21:38381849 20.5 9350 455.7
23:05:01.101 INFO ProgressMeter - chr21:41489292 20.7 9420 454.5
23:05:12.110 INFO ProgressMeter - chr21:41493435 20.9 9450 452.0
23:05:23.006 INFO ProgressMeter - chr21:41505008 21.1 9500 450.4
23:05:33.952 INFO ProgressMeter - chr22:20996694 21.3 9580 450.3
23:05:44.063 INFO ProgressMeter - chr22:23315440 21.4 9640 449.6
23:05:54.945 INFO ProgressMeter - chr22:29285666 21.6 9740 450.5
23:06:05.752 INFO ProgressMeter - chr22:41137651 21.8 9820 450.4
23:06:16.416 INFO ProgressMeter - chr3:10087132 22.0 9910 450.9
23:06:27.770 INFO ProgressMeter - chr3:12357540 22.2 9970 449.7
23:06:37.931 INFO ProgressMeter - chr3:12363514 22.3 10010 448.1
23:06:49.188 INFO ProgressMeter - chr3:12372478 22.5 10060 446.6
23:06:59.913 INFO ProgressMeter - chr3:12591706 22.7 10120 445.7
23:07:10.375 INFO ProgressMeter - chr3:37047517 22.9 10200 445.8
23:07:21.724 INFO ProgressMeter - chr3:47124274 23.1 10280 445.6
23:07:31.776 INFO ProgressMeter - chr3:52406251 23.2 10370 446.3
23:07:42.336 INFO ProgressMeter - chr3:72406850 23.4 10480 447.6
23:07:52.956 INFO ProgressMeter - chr3:135259010 23.6 10570 448.1
23:08:03.827 INFO ProgressMeter - chr3:142467932 23.8 10680 449.3
23:08:13.916 INFO ProgressMeter - chr3:179210696 23.9 10790 450.7
23:08:24.084 INFO ProgressMeter - chr3:186046712 24.1 10870 450.9
23:08:34.113 INFO ProgressMeter - chr3:196057867 24.3 10960 451.5
23:08:44.452 INFO ProgressMeter - chr4:20550825 24.4 11080 453.2
23:08:55.085 INFO ProgressMeter - chr4:54274596 24.6 11170 453.6
23:09:06.279 INFO ProgressMeter - chr4:54732108 24.8 11230 452.6
23:09:16.624 INFO ProgressMeter - chr4:80270811 25.0 11320 453.1
23:09:26.979 INFO ProgressMeter - chr4:105238708 25.2 11410 453.6
23:09:37.217 INFO ProgressMeter - chr4:142082029 25.3 11490 453.7
23:09:47.686 INFO ProgressMeter - chr4:186611435 25.5 11580 454.1
23:09:58.193 INFO ProgressMeter - chr4:186708633 25.7 11640 453.3
23:10:08.403 INFO ProgressMeter - chr5:39003556 25.8 11740 454.2
23:10:18.664 INFO ProgressMeter - chr5:58454909 26.0 11830 454.7
23:10:29.627 INFO ProgressMeter - chr5:112828902 26.2 11960 456.5
23:10:40.124 INFO ProgressMeter - chr5:122451325 26.4 12020 455.7
23:10:50.272 INFO ProgressMeter - chr5:142672805 26.5 12110 456.2
23:11:00.293 INFO ProgressMeter - chr5:150121202 26.7 12180 456.0
23:11:10.936 INFO ProgressMeter - chr5:175351638 26.9 12270 456.3
23:11:24.312 INFO ProgressMeter - chr5:177191882 27.1 12330 454.8
23:11:35.025 INFO ProgressMeter - chr5:180614066 27.3 12410 454.7
23:11:45.716 INFO ProgressMeter - chr6:20455963 27.5 12500 455.1
23:11:57.095 INFO ProgressMeter - chr6:26171773 27.7 12580 454.8
23:12:07.181 INFO ProgressMeter - chr6:30704546 27.8 12630 453.9
23:12:20.030 INFO ProgressMeter - chr6:32204175 28.0 12690 452.6
23:12:30.523 INFO ProgressMeter - chr6:33322860 28.2 12740 451.5
23:12:41.625 INFO ProgressMeter - chr6:41976281 28.4 12810 451.0
23:12:51.761 INFO ProgressMeter - chr6:106105839 28.6 12890 451.2
23:13:03.072 INFO ProgressMeter - chr6:117321785 28.8 12950 450.3
23:13:13.333 INFO ProgressMeter - chr6:117332115 28.9 13000 449.4
23:13:24.346 INFO ProgressMeter - chr6:117383315 29.1 13070 448.9
23:13:35.803 INFO ProgressMeter - chr6:135209328 29.3 13150 448.8
23:13:46.149 INFO ProgressMeter - chr6:137200910 29.5 13200 447.8
23:13:57.081 INFO ProgressMeter - chr6:151843419 29.7 13280 447.8
23:14:07.743 INFO ProgressMeter - chr6:157201214 29.8 13350 447.4
23:14:18.198 INFO ProgressMeter - chr6:163415192 30.0 13430 447.5
23:14:29.217 INFO ProgressMeter - chr7:13895101 30.2 13520 447.8
23:14:39.336 INFO ProgressMeter - chr7:13934510 30.4 13560 446.6
23:14:52.442 INFO ProgressMeter - chr7:13943133 30.6 13620 445.4
23:15:04.094 INFO ProgressMeter - chr7:13950012 30.8 13670 444.2
23:15:14.925 INFO ProgressMeter - chr7:13956624 31.0 13710 442.9
23:15:26.005 INFO ProgressMeter - chr7:13964302 31.1 13760 441.9
23:15:38.435 INFO ProgressMeter - chr7:13973865 31.3 13820 440.9
23:15:49.115 INFO ProgressMeter - chr7:13979655 31.5 13860 439.6
23:16:00.202 INFO ProgressMeter - chr7:13989406 31.7 13910 438.7
23:16:11.692 INFO ProgressMeter - chr7:55156614 31.9 13980 438.2
23:16:22.383 INFO ProgressMeter - chr7:55170122 32.1 14020 437.0
23:16:34.562 INFO ProgressMeter - chr7:55179802 32.3 14070 435.8
23:16:45.110 INFO ProgressMeter - chr7:78489759 32.5 14140 435.6
23:16:55.707 INFO ProgressMeter - chr7:102115186 32.6 14240 436.3
23:17:06.050 INFO ProgressMeter - chr7:116699083 32.8 14320 436.5
23:17:17.143 INFO ProgressMeter - chr7:140747077 33.0 14400 436.5
23:17:27.932 INFO ProgressMeter - chr7:142944641 33.2 14500 437.1
23:17:39.216 INFO ProgressMeter - chr7:152177113 33.4 14590 437.3
23:17:49.517 INFO ProgressMeter - chr8:11708311 33.5 14680 437.8
23:17:59.601 INFO ProgressMeter - chr8:32634016 33.7 14760 438.0
23:18:10.664 INFO ProgressMeter - chr8:37697972 33.9 14800 436.8
23:18:20.683 INFO ProgressMeter - chr8:38427919 34.1 14870 436.7
23:18:31.473 INFO ProgressMeter - chr8:41940971 34.2 14920 435.9
23:18:42.364 INFO ProgressMeter - chr8:47849377 34.4 14990 435.6
23:18:52.857 INFO ProgressMeter - chr8:55946446 34.6 15070 435.7
23:19:03.656 INFO ProgressMeter - chr8:89947822 34.8 15150 435.7
23:19:14.445 INFO ProgressMeter - chr8:116857265 34.9 15200 434.9
23:19:26.974 INFO ProgressMeter - chr8:127740151 35.2 15250 433.8
23:19:38.780 INFO ProgressMeter - chr8:144517048 35.4 15310 433.1
23:19:49.810 INFO ProgressMeter - chr9:8518106 35.5 15420 433.9
23:20:00.824 INFO ProgressMeter - chr9:83972823 35.7 15520 434.5
23:20:12.069 INFO ProgressMeter - chr9:84813886 35.9 15580 433.9
23:20:25.327 INFO ProgressMeter - chr9:84866255 36.1 15620 432.3
23:20:35.394 INFO ProgressMeter - chr9:85021925 36.3 15670 431.7
23:20:45.585 INFO ProgressMeter - chr9:95135344 36.5 15730 431.4
23:20:55.734 INFO ProgressMeter - chr9:130835380 36.6 15830 432.1
23:21:05.947 INFO ProgressMeter - chr9:136496096 36.8 15900 432.0
23:21:16.416 INFO ProgressMeter - chrX:15804109 37.0 16000 432.7
23:21:26.831 INFO ProgressMeter - chrX:45085863 37.2 16090 433.1
23:21:37.315 INFO ProgressMeter - chrX:49034294 37.3 16170 433.2
23:21:49.253 INFO ProgressMeter - chrX:49038730 37.5 16200 431.7
23:21:59.535 INFO ProgressMeter - chrX:53405472 37.7 16280 431.8
23:22:09.940 INFO ProgressMeter - chrX:67546467 37.9 16330 431.2
23:22:20.740 INFO ProgressMeter - chrX:71137556 38.1 16430 431.8
23:22:31.154 INFO ProgressMeter - chrX:77681518 38.2 16520 432.2
23:22:41.371 INFO ProgressMeter - chrX:124056126 38.4 16620 432.9
23:22:51.502 INFO ProgressMeter - chrX:134425180 38.6 16690 432.8
23:22:51.722 INFO Mutect2 - 554872 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
34 read(s) filtered by: ReadLengthReadFilter
134 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
555040 total reads filtered out of 71033650 reads processed
23:22:51.722 INFO ProgressMeter - chrY:20819373 38.6 16732 433.8
23:22:51.722 INFO ProgressMeter - Traversal complete. Processed 16732 total regions in 38.6 minutes.
23:22:51.739 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 4.931294227
23:22:51.739 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 192.18812628100002
23:22:51.740 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 7.94 sec
23:22:51.740 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:22:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 38.58 minutes.
Runtime.totalMemory()=6677331968
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 LS0911_tumor.bam --tumor-sample LS0911 -L TST500C_manifest.bed -O LS0911.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:22:53.255 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
23:22:53.361 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:53.364 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:22:53.364 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:22:53.364 INFO FilterMutectCalls - Executing as ?@nf-3930d6d6b42d2078a0eaffd1fa9c68be-64fdd-nr2zh on Linux v6.12.88 amd64
23:22:53.364 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:22:53.364 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:22:53 PM GMT
23:22:53.364 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:53.364 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:53.365 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:22:53.365 INFO FilterMutectCalls - Picard Version: 3.1.1
23:22:53.365 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:22:53.365 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:22:53.365 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:22:53.365 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:22:53.366 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:22:53.366 INFO FilterMutectCalls - Deflater: IntelDeflater
23:22:53.366 INFO FilterMutectCalls - Inflater: IntelInflater
23:22:53.366 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:22:53.366 INFO FilterMutectCalls - Requester pays: disabled
23:22:53.366 INFO FilterMutectCalls - Initializing engine
23:22:53.482 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.V5HjmjBmPJ/LS0911.mutect2.raw.vcf.gz
23:22:53.576 INFO FilterMutectCalls - Done initializing engine
23:22:53.632 INFO ProgressMeter - Starting traversal
23:22:53.632 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:22:53.633 INFO FilterMutectCalls - Starting pass 0 through the variants
23:22:54.696 INFO FilterMutectCalls - Finished pass 0 through the variants
23:22:55.348 INFO FilterMutectCalls - Starting pass 1 through the variants
23:22:56.199 INFO FilterMutectCalls - Finished pass 1 through the variants
23:22:56.387 INFO FilterMutectCalls - Starting pass 2 through the variants
23:22:57.214 INFO FilterMutectCalls - Finished pass 2 through the variants
23:22:57.216 INFO FilterMutectCalls - Starting pass 3 through the variants
23:22:57.930 INFO FilterMutectCalls - Finished pass 3 through the variants
23:22:57.937 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:22:57.937 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:22:57.938 INFO ProgressMeter - chr7:13892976 0.1 9524 132769.5
23:22:57.938 INFO ProgressMeter - Traversal complete. Processed 9524 total variants in 0.1 minutes.
23:22:57.950 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:22:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=478150656
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 LS0911.mutect2.raw.vcf.gz --stats LS0911.mutect2.raw.vcf.gz.stats -O LS0911.mutect2.filtered.vcf.gz
23:22:59.193 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
23:22:59.318 INFO SelectVariants - ------------------------------------------------------------
23:22:59.324 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:22:59.324 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:22:59.324 INFO SelectVariants - Executing as ?@nf-3930d6d6b42d2078a0eaffd1fa9c68be-64fdd-nr2zh on Linux v6.12.88 amd64
23:22:59.324 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:22:59.325 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:22:59 PM GMT
23:22:59.325 INFO SelectVariants - ------------------------------------------------------------
23:22:59.325 INFO SelectVariants - ------------------------------------------------------------
23:22:59.327 INFO SelectVariants - HTSJDK Version: 4.1.0
23:22:59.327 INFO SelectVariants - Picard Version: 3.1.1
23:22:59.327 INFO SelectVariants - Built for Spark Version: 3.5.0
23:22:59.328 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:22:59.328 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:22:59.328 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:22:59.328 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:22:59.328 INFO SelectVariants - Deflater: IntelDeflater
23:22:59.328 INFO SelectVariants - Inflater: IntelInflater
23:22:59.328 INFO SelectVariants - GCS max retries/reopens: 20
23:22:59.328 INFO SelectVariants - Requester pays: disabled
23:22:59.329 INFO SelectVariants - Initializing engine
23:22:59.549 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.V5HjmjBmPJ/LS0911.mutect2.filtered.vcf.gz
23:22:59.673 INFO SelectVariants - Done initializing engine
23:22:59.713 INFO ProgressMeter - Starting traversal
23:22:59.714 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:22:59.789 INFO ProgressMeter - chr7:13979276 0.0 2381 1984166.7
23:22:59.789 INFO ProgressMeter - Traversal complete. Processed 2381 total variants in 0.0 minutes.
23:22:59.801 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:22:59 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 LS0911.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0911.mutect2.pass.vcf.gz