18:52:50.361 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
18:52:50.481 INFO Mutect2 - ------------------------------------------------------------
18:52:50.484 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
18:52:50.484 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
18:52:50.484 INFO Mutect2 - Executing as ?@nf-4e2c2da3ac01d520247f96d35e321f20-048af-jzv22 on Linux v6.12.83 amd64
18:52:50.485 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
18:52:50.485 INFO Mutect2 - Start Date/Time: May 29, 2026 at 6:52:50 PM GMT
18:52:50.485 INFO Mutect2 - ------------------------------------------------------------
18:52:50.485 INFO Mutect2 - ------------------------------------------------------------
18:52:50.486 INFO Mutect2 - HTSJDK Version: 4.1.0
18:52:50.486 INFO Mutect2 - Picard Version: 3.1.1
18:52:50.486 INFO Mutect2 - Built for Spark Version: 3.5.0
18:52:50.486 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:52:50.487 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:52:50.487 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:52:50.487 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:52:50.487 INFO Mutect2 - Deflater: IntelDeflater
18:52:50.487 INFO Mutect2 - Inflater: IntelInflater
18:52:50.487 INFO Mutect2 - GCS max retries/reopens: 20
18:52:50.488 INFO Mutect2 - Requester pays: disabled
18:52:50.488 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.FWySEdKLPw/LS0888.markdup.deduped.nosingletons.bam.bai is older than BAM /tmp/nxf.FWySEdKLPw/LS0888.markdup.deduped.nosingletons.bam
18:52:50.636 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.FWySEdKLPw/af-only-gnomad.hg38.vcf.gz
18:52:50.745 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.FWySEdKLPw/TST500C_manifest.bed
18:52:50.790 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
18:52:50.828 INFO Mutect2 - Done initializing engine
18:52:50.842 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
18:52:50.843 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
18:52:50.844 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
18:52:50.844 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
18:52:50.855 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
18:52:50.865 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
18:52:50.865 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
18:52:50.866 INFO IntelPairHmm - Available threads: 192
18:52:50.866 INFO IntelPairHmm - Requested threads: 4
18:52:50.866 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
18:52:50.897 INFO ProgressMeter - Starting traversal
18:52:50.898 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
18:53:02.517 INFO ProgressMeter - chr1:11130527 0.2 60 309.9
18:53:13.616 INFO ProgressMeter - chr1:15918924 0.4 110 290.5
18:53:24.661 INFO ProgressMeter - chr1:15934459 0.6 140 248.8
18:53:36.575 INFO ProgressMeter - chr1:18747970 0.8 190 249.6
18:53:47.293 INFO ProgressMeter - chr1:36467820 0.9 250 266.0
18:53:58.673 INFO ProgressMeter - chr1:45331180 1.1 320 283.3
18:54:10.527 INFO ProgressMeter - chr1:64844062 1.3 400 301.4
18:54:21.189 INFO ProgressMeter - chr1:114714110 1.5 480 319.0
18:54:33.955 INFO ProgressMeter - chr1:119928974 1.7 530 308.6
18:54:45.555 INFO ProgressMeter - chr1:156875281 1.9 590 308.7
18:54:55.759 INFO ProgressMeter - chr1:158669707 2.1 650 312.3
18:55:07.806 INFO ProgressMeter - chr1:179110803 2.3 720 315.5
18:55:17.947 INFO ProgressMeter - chr1:204517648 2.5 790 322.3
18:55:29.018 INFO ProgressMeter - chr1:226365952 2.6 870 330.1
18:55:40.018 INFO ProgressMeter - chr10:27029265 2.8 970 344.1
18:55:51.113 INFO ProgressMeter - chr10:32038161 3.0 1030 342.9
18:56:03.462 INFO ProgressMeter - chr10:43114970 3.2 1080 336.5
18:56:14.832 INFO ProgressMeter - chr10:43128398 3.4 1120 329.5
18:56:27.277 INFO ProgressMeter - chr10:68651844 3.6 1160 321.7
18:56:37.619 INFO ProgressMeter - chr10:87957851 3.8 1220 322.9
18:56:50.081 INFO ProgressMeter - chr10:110596377 4.0 1300 326.1
18:57:01.181 INFO ProgressMeter - chr10:121482550 4.2 1360 326.0
18:57:11.221 INFO ProgressMeter - chr11:8230337 4.3 1420 327.3
18:57:21.586 INFO ProgressMeter - chr11:67432598 4.5 1500 332.5
18:57:31.719 INFO ProgressMeter - chr11:69701708 4.7 1560 333.3
18:57:42.854 INFO ProgressMeter - chr11:69808267 4.9 1620 332.9
18:57:54.073 INFO ProgressMeter - chr11:76446937 5.1 1670 330.5
18:58:05.353 INFO ProgressMeter - chr11:77353534 5.2 1710 326.3
18:58:16.445 INFO ProgressMeter - chr11:94464111 5.4 1770 326.2
18:58:26.479 INFO ProgressMeter - chr11:108248931 5.6 1830 327.2
18:58:39.607 INFO ProgressMeter - chr11:118474026 5.8 1910 328.6
18:58:50.850 INFO ProgressMeter - chr11:118506075 6.0 1950 325.0
18:59:01.181 INFO ProgressMeter - chr11:125675449 6.2 2020 327.3
18:59:12.644 INFO ProgressMeter - chr11:128812930 6.4 2070 325.3
18:59:23.904 INFO ProgressMeter - chr12:4369025 6.6 2130 325.2
18:59:35.057 INFO ProgressMeter - chr12:4444131 6.7 2190 325.1
18:59:46.725 INFO ProgressMeter - chr12:11854306 6.9 2250 324.7
18:59:56.918 INFO ProgressMeter - chr12:11861014 7.1 2290 322.5
19:00:07.767 INFO ProgressMeter - chr12:11869061 7.3 2330 320.0
19:00:17.999 INFO ProgressMeter - chr12:25219692 7.5 2400 322.1
19:00:30.052 INFO ProgressMeter - chr12:49026180 7.7 2470 322.8
19:00:41.209 INFO ProgressMeter - chr12:49039722 7.8 2510 320.2
19:00:51.490 INFO ProgressMeter - chr12:51951742 8.0 2570 320.9
19:01:01.794 INFO ProgressMeter - chr12:57091123 8.2 2630 321.5
19:01:12.562 INFO ProgressMeter - chr12:57748977 8.4 2680 320.5
19:01:23.680 INFO ProgressMeter - chr12:105934439 8.5 2770 324.1
19:01:34.046 INFO ProgressMeter - chr12:120997472 8.7 2830 324.6
19:01:44.601 INFO ProgressMeter - chr12:132672213 8.9 2880 323.8
19:01:54.693 INFO ProgressMeter - chr13:21694277 9.1 2940 324.4
19:02:05.897 INFO ProgressMeter - chr13:28368276 9.2 3020 326.5
19:02:16.949 INFO ProgressMeter - chr13:32333230 9.4 3080 326.5
19:02:28.007 INFO ProgressMeter - chr13:40559521 9.6 3130 325.4
19:02:38.314 INFO ProgressMeter - chr13:102181777 9.8 3220 328.9
19:02:48.906 INFO ProgressMeter - chr13:113311298 10.0 3300 331.1
19:02:59.430 INFO ProgressMeter - chr14:37592842 10.1 3370 332.3
19:03:10.448 INFO ProgressMeter - chr14:81143494 10.3 3440 333.1
19:03:21.948 INFO ProgressMeter - chr14:102084979 10.5 3490 331.8
19:03:32.997 INFO ProgressMeter - chr15:34355486 10.7 3550 331.7
19:03:45.341 INFO ProgressMeter - chr15:41743144 10.9 3600 330.1
19:03:56.044 INFO ProgressMeter - chr15:49464246 11.1 3660 330.2
19:04:08.818 INFO ProgressMeter - chr15:88032992 11.3 3730 330.1
19:04:20.230 INFO ProgressMeter - chr15:90765294 11.5 3810 331.6
19:04:31.741 INFO ProgressMeter - chr15:98891623 11.7 3880 332.2
19:04:42.209 INFO ProgressMeter - chr16:2076489 11.9 3940 332.3
19:04:52.457 INFO ProgressMeter - chr16:3589939 12.0 4020 334.3
19:05:04.029 INFO ProgressMeter - chr16:3770868 12.2 4070 333.1
19:05:15.401 INFO ProgressMeter - chr16:13937764 12.4 4130 332.8
19:05:25.502 INFO ProgressMeter - chr16:50781244 12.6 4180 332.4
19:05:35.604 INFO ProgressMeter - chr16:68813311 12.7 4240 332.7
19:05:48.973 INFO ProgressMeter - chr16:72798574 13.0 4280 330.0
19:05:59.263 INFO ProgressMeter - chr16:81912595 13.1 4330 329.5
19:06:10.588 INFO ProgressMeter - chr16:89286037 13.3 4380 328.6
19:06:21.309 INFO ProgressMeter - chr17:7675482 13.5 4470 330.9
19:06:33.136 INFO ProgressMeter - chr17:16070463 13.7 4550 332.0
19:06:43.664 INFO ProgressMeter - chr17:31221848 13.9 4620 332.9
19:06:55.011 INFO ProgressMeter - chr17:39470877 14.1 4700 334.1
19:07:05.857 INFO ProgressMeter - chr17:40355261 14.2 4770 334.8
19:07:15.994 INFO ProgressMeter - chr17:42337433 14.4 4860 337.1
19:07:28.122 INFO ProgressMeter - chr17:43094687 14.6 4920 336.5
19:07:40.786 INFO ProgressMeter - chr17:43540914 14.8 4990 336.4
19:07:51.506 INFO ProgressMeter - chr17:49607872 15.0 5040 335.8
19:08:02.709 INFO ProgressMeter - chr17:59945404 15.2 5120 336.9
19:08:14.338 INFO ProgressMeter - chr17:65535624 15.4 5180 336.6
19:08:24.802 INFO ProgressMeter - chr17:80923488 15.6 5250 337.3
19:08:38.301 INFO ProgressMeter - chr18:44951960 15.8 5330 337.6
19:08:49.024 INFO ProgressMeter - chr19:1219322 16.0 5400 338.2
19:08:59.211 INFO ProgressMeter - chr19:4101102 16.1 5490 340.2
19:09:09.542 INFO ProgressMeter - chr19:7163030 16.3 5560 340.9
19:09:19.821 INFO ProgressMeter - chr19:10987664 16.5 5630 341.6
19:09:30.692 INFO ProgressMeter - chr19:15174066 16.7 5700 342.1
19:09:41.786 INFO ProgressMeter - chr19:17837127 16.8 5770 342.5
19:09:53.111 INFO ProgressMeter - chr19:35723732 17.0 5870 344.5
19:10:03.287 INFO ProgressMeter - chr19:40280168 17.2 5940 345.2
19:10:13.695 INFO ProgressMeter - chr19:42291556 17.4 6000 345.2
19:10:24.660 INFO ProgressMeter - chr19:45418828 17.6 6080 346.2
19:10:35.595 INFO ProgressMeter - chr2:15942846 17.7 6160 347.1
19:10:47.056 INFO ProgressMeter - chr2:25247049 17.9 6220 346.8
19:10:57.267 INFO ProgressMeter - chr2:26794131 18.1 6260 345.7
19:11:09.530 INFO ProgressMeter - chr2:29232364 18.3 6300 344.1
19:11:22.206 INFO ProgressMeter - chr2:42332181 18.5 6370 343.9
19:11:32.890 INFO ProgressMeter - chr2:47806450 18.7 6420 343.3
19:11:43.436 INFO ProgressMeter - chr2:98555551 18.9 6500 344.4
19:11:54.132 INFO ProgressMeter - chr2:108767674 19.1 6550 343.8
19:12:04.526 INFO ProgressMeter - chr2:113221036 19.2 6600 343.3
19:12:18.128 INFO ProgressMeter - chr2:113227947 19.5 6640 341.3
19:12:29.511 INFO ProgressMeter - chr2:113235569 19.6 6680 340.1
19:12:40.671 INFO ProgressMeter - chr2:140442502 19.8 6750 340.4
19:12:51.382 INFO ProgressMeter - chr2:141005333 20.0 6810 340.4
19:13:02.832 INFO ProgressMeter - chr2:189873494 20.2 6880 340.6
19:13:13.714 INFO ProgressMeter - chr2:208248367 20.4 6960 341.5
19:13:26.572 INFO ProgressMeter - chr2:222201775 20.6 7030 341.4
19:13:39.269 INFO ProgressMeter - chr2:222212258 20.8 7080 340.3
19:13:53.044 INFO ProgressMeter - chr2:222221199 21.0 7120 338.5
19:14:04.649 INFO ProgressMeter - chr20:9580443 21.2 7190 338.7
19:14:15.226 INFO ProgressMeter - chr20:32795648 21.4 7240 338.2
19:14:25.475 INFO ProgressMeter - chr20:42248685 21.6 7310 338.8
19:14:36.279 INFO ProgressMeter - chr20:53576925 21.8 7360 338.3
19:14:47.344 INFO ProgressMeter - chr21:34834562 21.9 7430 338.6
19:14:57.897 INFO ProgressMeter - chr21:38498361 22.1 7470 337.8
19:15:09.470 INFO ProgressMeter - chr21:41493360 22.3 7520 337.1
19:15:20.618 INFO ProgressMeter - chr21:41503754 22.5 7550 335.6
19:15:31.104 INFO ProgressMeter - chr22:20995961 22.7 7620 336.1
19:15:41.567 INFO ProgressMeter - chr22:23315431 22.8 7680 336.2
19:15:51.646 INFO ProgressMeter - chr22:29286646 23.0 7770 337.6
19:16:01.859 INFO ProgressMeter - chr22:41160640 23.2 7840 338.2
19:16:12.837 INFO ProgressMeter - chr3:10096348 23.4 7910 338.5
19:16:24.487 INFO ProgressMeter - chr3:12360537 23.6 7960 337.9
19:16:35.477 INFO ProgressMeter - chr3:12370087 23.7 8010 337.4
19:16:45.700 INFO ProgressMeter - chr3:12379039 23.9 8050 336.6
19:16:56.174 INFO ProgressMeter - chr3:37025635 24.1 8130 337.5
19:17:06.372 INFO ProgressMeter - chr3:47121380 24.3 8190 337.6
19:17:18.443 INFO ProgressMeter - chr3:52402286 24.5 8260 337.7
19:17:28.513 INFO ProgressMeter - chr3:70958265 24.6 8330 338.2
19:17:39.209 INFO ProgressMeter - chr3:120093345 24.8 8400 338.6
19:17:49.997 INFO ProgressMeter - chr3:136542098 25.0 8460 338.6
19:18:01.338 INFO ProgressMeter - chr3:142536106 25.2 8540 339.2
19:18:12.493 INFO ProgressMeter - chr3:179229270 25.4 8620 339.9
19:18:24.567 INFO ProgressMeter - chr3:186047612 25.6 8680 339.6
19:18:35.743 INFO ProgressMeter - chr3:196054889 25.7 8750 339.8
19:18:46.889 INFO ProgressMeter - chr4:20539439 25.9 8840 340.9
19:18:58.832 INFO ProgressMeter - chr4:54270879 26.1 8900 340.6
19:19:10.109 INFO ProgressMeter - chr4:54727414 26.3 8950 340.0
19:19:20.182 INFO ProgressMeter - chr4:55114872 26.5 8990 339.4
19:19:30.563 INFO ProgressMeter - chr4:80286623 26.7 9060 339.8
19:19:41.517 INFO ProgressMeter - chr4:105242291 26.8 9120 339.7
19:19:51.622 INFO ProgressMeter - chr4:142314710 27.0 9190 340.2
19:20:03.396 INFO ProgressMeter - chr4:186614189 27.2 9250 340.0
19:20:16.606 INFO ProgressMeter - chr4:186709224 27.4 9290 338.7
19:20:26.793 INFO ProgressMeter - chr5:38953459 27.6 9350 338.8
19:20:36.827 INFO ProgressMeter - chr5:56872639 27.8 9430 339.6
19:20:47.899 INFO ProgressMeter - chr5:80725451 28.0 9510 340.3
19:21:00.227 INFO ProgressMeter - chr5:112840591 28.2 9590 340.6
19:21:11.400 INFO ProgressMeter - chr5:132604804 28.3 9640 340.1
19:21:21.852 INFO ProgressMeter - chr5:149513049 28.5 9710 340.5
19:21:33.783 INFO ProgressMeter - chr5:150402235 28.7 9780 340.6
19:21:44.751 INFO ProgressMeter - chr5:177095328 28.9 9860 341.2
19:21:55.337 INFO ProgressMeter - chr5:177512075 29.1 9910 340.9
19:22:05.846 INFO ProgressMeter - chr6:20428963 29.2 9990 341.5
19:22:16.427 INFO ProgressMeter - chr6:29943266 29.4 10090 342.9
19:22:27.657 INFO ProgressMeter - chr6:93357015 29.6 10280 347.1
19:22:39.710 INFO ProgressMeter - chr6:117318802 29.8 10340 346.8
19:22:50.360 INFO ProgressMeter - chr6:117325647 30.0 10380 346.1
19:23:00.622 INFO ProgressMeter - chr6:117334770 30.2 10430 345.8
19:23:11.898 INFO ProgressMeter - chr6:117394614 30.4 10480 345.3
19:23:22.261 INFO ProgressMeter - chr6:135210464 30.5 10550 345.6
19:23:33.401 INFO ProgressMeter - chr6:137206134 30.7 10600 345.2
19:23:44.069 INFO ProgressMeter - chr6:151804272 30.9 10650 344.8
19:23:54.568 INFO ProgressMeter - chr6:157201189 31.1 10720 345.1
19:24:04.901 INFO ProgressMeter - chr6:162571200 31.2 10780 345.1
19:24:16.274 INFO ProgressMeter - chr7:13891595 31.4 10850 345.3
19:24:28.631 INFO ProgressMeter - chr7:13932085 31.6 10890 344.3
19:24:40.951 INFO ProgressMeter - chr7:13939644 31.8 10930 343.3
19:24:52.201 INFO ProgressMeter - chr7:13947642 32.0 10970 342.6
19:25:02.389 INFO ProgressMeter - chr7:13953074 32.2 11000 341.7
19:25:15.292 INFO ProgressMeter - chr7:13964166 32.4 11040 340.7
19:25:26.471 INFO ProgressMeter - chr7:13972514 32.6 11080 340.0
19:25:38.528 INFO ProgressMeter - chr7:13980553 32.8 11130 339.4
19:25:50.635 INFO ProgressMeter - chr7:41689948 33.0 11190 339.1
19:26:02.931 INFO ProgressMeter - chr7:55166642 33.2 11240 338.5
19:26:13.255 INFO ProgressMeter - chr7:55176520 33.4 11270 337.7
19:26:24.202 INFO ProgressMeter - chr7:55200914 33.6 11300 336.8
19:26:36.404 INFO ProgressMeter - chr7:86839137 33.8 11370 336.8
19:26:46.748 INFO ProgressMeter - chr7:102234031 33.9 11440 337.2
19:26:57.043 INFO ProgressMeter - chr7:116765399 34.1 11500 337.2
19:27:08.459 INFO ProgressMeter - chr7:140791945 34.3 11570 337.4
19:27:19.196 INFO ProgressMeter - chr7:152154008 34.5 11670 338.5
19:27:29.311 INFO ProgressMeter - chr7:152229921 34.6 11720 338.3
19:27:40.406 INFO ProgressMeter - chr8:32083130 34.8 11800 338.8
19:27:51.755 INFO ProgressMeter - chr8:37833686 35.0 11860 338.7
19:28:02.446 INFO ProgressMeter - chr8:38468663 35.2 11910 338.4
19:28:12.890 INFO ProgressMeter - chr8:47817448 35.4 11960 338.2
19:28:23.321 INFO ProgressMeter - chr8:47959971 35.5 12030 338.5
19:28:34.613 INFO ProgressMeter - chr8:89955281 35.7 12110 338.9
19:28:45.275 INFO ProgressMeter - chr8:144511679 35.9 12190 339.5
19:28:55.358 INFO ProgressMeter - chr9:5557710 36.1 12270 340.1
19:29:05.970 INFO ProgressMeter - chr9:35075277 36.3 12350 340.7
19:29:17.173 INFO ProgressMeter - chr9:84751984 36.4 12430 341.1
19:29:27.321 INFO ProgressMeter - chr9:84864681 36.6 12470 340.6
19:29:38.322 INFO ProgressMeter - chr9:85021662 36.8 12510 340.0
19:29:49.598 INFO ProgressMeter - chr9:95449067 37.0 12570 339.9
19:30:01.006 INFO ProgressMeter - chr9:130884267 37.2 12650 340.3
19:30:12.494 INFO ProgressMeter - chr9:136506525 37.4 12710 340.2
19:30:24.400 INFO ProgressMeter - chrX:40074124 37.6 12800 340.8
19:30:36.040 INFO ProgressMeter - chrX:49030229 37.8 12890 341.4
19:30:47.958 INFO ProgressMeter - chrX:53403545 38.0 12970 341.8
19:30:59.252 INFO ProgressMeter - chrX:67546615 38.1 13010 341.1
19:31:09.704 INFO ProgressMeter - chrX:71134711 38.3 13080 341.4
19:31:20.414 INFO ProgressMeter - chrX:77652112 38.5 13150 341.6
19:31:31.543 INFO ProgressMeter - chrX:123891236 38.7 13220 341.8
19:31:42.953 INFO ProgressMeter - chrX:134393888 38.9 13290 341.9
19:31:43.953 INFO Mutect2 - 939609 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
153 read(s) filtered by: ReadLengthReadFilter
0 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
939762 total reads filtered out of 76877767 reads processed
19:31:43.954 INFO ProgressMeter - chrY:20398623 38.9 13335 342.9
19:31:43.954 INFO ProgressMeter - Traversal complete. Processed 13335 total regions in 38.9 minutes.
19:31:43.965 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 2.926537674
19:31:43.965 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 18.410883405
19:31:43.965 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 0.73 sec
19:31:43.966 INFO Mutect2 - Shutting down engine
[May 29, 2026 at 7:31:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 38.89 minutes.
Runtime.totalMemory()=1115684864
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar Mutect2 -R hg38.fa -I LS0888.markdup.deduped.nosingletons.bam --tumor-sample LS0888 -L TST500C_manifest.bed -O LS0888.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 20 --germline-resource af-only-gnomad.hg38.vcf.gz
19:31:45.143 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
19:31:45.219 INFO FilterMutectCalls - ------------------------------------------------------------
19:31:45.221 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
19:31:45.221 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
19:31:45.221 INFO FilterMutectCalls - Executing as ?@nf-4e2c2da3ac01d520247f96d35e321f20-048af-jzv22 on Linux v6.12.83 amd64
19:31:45.221 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
19:31:45.221 INFO FilterMutectCalls - Start Date/Time: May 29, 2026 at 7:31:45 PM GMT
19:31:45.221 INFO FilterMutectCalls - ------------------------------------------------------------
19:31:45.221 INFO FilterMutectCalls - ------------------------------------------------------------
19:31:45.222 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
19:31:45.222 INFO FilterMutectCalls - Picard Version: 3.1.1
19:31:45.222 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
19:31:45.222 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:31:45.222 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:31:45.222 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:31:45.222 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:31:45.222 INFO FilterMutectCalls - Deflater: IntelDeflater
19:31:45.222 INFO FilterMutectCalls - Inflater: IntelInflater
19:31:45.222 INFO FilterMutectCalls - GCS max retries/reopens: 20
19:31:45.223 INFO FilterMutectCalls - Requester pays: disabled
19:31:45.223 INFO FilterMutectCalls - Initializing engine
19:31:45.305 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.FWySEdKLPw/LS0888.mutect2.raw.vcf.gz
19:31:45.347 INFO FilterMutectCalls - Done initializing engine
19:31:45.379 INFO ProgressMeter - Starting traversal
19:31:45.379 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:31:45.380 INFO FilterMutectCalls - Starting pass 0 through the variants
19:31:46.354 INFO FilterMutectCalls - Finished pass 0 through the variants
19:31:52.238 INFO FilterMutectCalls - Starting pass 1 through the variants
19:31:53.507 INFO FilterMutectCalls - Finished pass 1 through the variants
19:31:54.583 INFO FilterMutectCalls - Starting pass 2 through the variants
19:31:55.764 INFO FilterMutectCalls - Finished pass 2 through the variants
19:31:55.766 INFO FilterMutectCalls - Starting pass 3 through the variants
19:31:55.788 INFO ProgressMeter - chr1:15934421 0.2 4000 23059.2
19:31:56.809 INFO FilterMutectCalls - Finished pass 3 through the variants
19:31:56.814 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
19:31:56.815 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
19:31:56.815 INFO ProgressMeter - chr6:117334464 0.2 5324 27932.8
19:31:56.815 INFO ProgressMeter - Traversal complete. Processed 5324 total variants in 0.2 minutes.
19:31:56.826 INFO FilterMutectCalls - Shutting down engine
[May 29, 2026 at 7:31:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.20 minutes.
Runtime.totalMemory()=806354944
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R hg38.fa -V LS0888.mutect2.raw.vcf.gz --stats LS0888.mutect2.raw.vcf.gz.stats -O LS0888.mutect2.filtered.vcf.gz
19:31:57.895 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
19:31:57.968 INFO SelectVariants - ------------------------------------------------------------
19:31:57.969 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
19:31:57.969 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
19:31:57.969 INFO SelectVariants - Executing as ?@nf-4e2c2da3ac01d520247f96d35e321f20-048af-jzv22 on Linux v6.12.83 amd64
19:31:57.969 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
19:31:57.969 INFO SelectVariants - Start Date/Time: May 29, 2026 at 7:31:57 PM GMT
19:31:57.970 INFO SelectVariants - ------------------------------------------------------------
19:31:57.970 INFO SelectVariants - ------------------------------------------------------------
19:31:57.970 INFO SelectVariants - HTSJDK Version: 4.1.0
19:31:57.970 INFO SelectVariants - Picard Version: 3.1.1
19:31:57.970 INFO SelectVariants - Built for Spark Version: 3.5.0
19:31:57.970 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:31:57.970 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:31:57.970 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:31:57.970 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:31:57.971 INFO SelectVariants - Deflater: IntelDeflater
19:31:57.971 INFO SelectVariants - Inflater: IntelInflater
19:31:57.971 INFO SelectVariants - GCS max retries/reopens: 20
19:31:57.971 INFO SelectVariants - Requester pays: disabled
19:31:57.971 INFO SelectVariants - Initializing engine
19:31:58.047 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.FWySEdKLPw/LS0888.mutect2.filtered.vcf.gz
19:31:58.089 INFO SelectVariants - Done initializing engine
19:31:58.116 INFO ProgressMeter - Starting traversal
19:31:58.117 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:31:58.171 INFO ProgressMeter - chr6:117330763 0.0 1331 1535769.2
19:31:58.171 INFO ProgressMeter - Traversal complete. Processed 1331 total variants in 0.0 minutes.
19:31:58.181 INFO SelectVariants - Shutting down engine
[May 29, 2026 at 7:31:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=567803904
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar SelectVariants -R hg38.fa -V LS0888.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0888.mutect2.pass.vcf.gz