Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/d4/8cbf81060ea639251a00f1787545d7/.command.sh
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Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/d4/8cbf81060ea639251a00f1787545d7/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:11.105 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
22:44:11.207 INFO Mutect2 - ------------------------------------------------------------
22:44:11.209 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:11.210 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:11.210 INFO Mutect2 - Executing as ?@nf-d48cbf81060ea639251a00f1787545d7-2944a-nwqqm on Linux v6.12.88 amd64
22:44:11.210 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:11.210 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:11 PM GMT
22:44:11.210 INFO Mutect2 - ------------------------------------------------------------
22:44:11.210 INFO Mutect2 - ------------------------------------------------------------
22:44:11.211 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:11.211 INFO Mutect2 - Picard Version: 3.1.1
22:44:11.211 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:11.211 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:11.212 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:11.212 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:11.212 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:11.212 INFO Mutect2 - Deflater: IntelDeflater
22:44:11.212 INFO Mutect2 - Inflater: IntelInflater
22:44:11.212 INFO Mutect2 - GCS max retries/reopens: 20
22:44:11.212 INFO Mutect2 - Requester pays: disabled
22:44:11.213 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.7lz5ajWxXJ/LS0896_tumor.bam.bai is older than BAM /tmp/nxf.7lz5ajWxXJ/LS0896_tumor.bam
22:44:11.453 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.7lz5ajWxXJ/af-only-gnomad.hg38.vcf.gz
22:44:11.558 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.7lz5ajWxXJ/TST500C_manifest.bed
22:44:11.593 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:11.622 INFO Mutect2 - Done initializing engine
22:44:11.633 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
22:44:11.635 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
22:44:11.636 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:11.636 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:11.648 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
22:44:11.657 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:11.657 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:11.657 INFO IntelPairHmm - Available threads: 384
22:44:11.657 INFO IntelPairHmm - Requested threads: 4
22:44:11.657 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:11.697 INFO ProgressMeter - Starting traversal
22:44:11.698 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:22.423 INFO ProgressMeter - chr1:11134349 0.2 90 503.5
22:44:32.807 INFO ProgressMeter - chr1:15928505 0.4 170 483.2
22:44:43.137 INFO ProgressMeter - chr1:15937359 0.5 220 419.9
22:44:53.336 INFO ProgressMeter - chr1:18747851 0.7 290 417.9
22:45:03.818 INFO ProgressMeter - chr1:36344118 0.9 370 425.9
22:45:14.810 INFO ProgressMeter - chr1:43340118 1.1 470 446.8
22:45:25.176 INFO ProgressMeter - chr1:64839601 1.2 570 465.4
22:45:35.226 INFO ProgressMeter - chr1:114710360 1.4 670 481.3
22:45:45.296 INFO ProgressMeter - chr1:119915787 1.6 740 474.4
22:45:55.403 INFO ProgressMeter - chr1:156815828 1.7 820 474.4
22:46:05.998 INFO ProgressMeter - chr1:156881455 1.9 870 456.7
22:46:17.393 INFO ProgressMeter - chr1:158674327 2.1 950 453.5
22:46:27.981 INFO ProgressMeter - chr1:179109022 2.3 1040 457.9
22:46:38.416 INFO ProgressMeter - chr1:204542459 2.4 1160 474.4
22:46:49.096 INFO ProgressMeter - chr1:239718566 2.6 1270 484.1
22:47:00.382 INFO ProgressMeter - chr1:243512322 2.8 1330 473.1
22:47:10.428 INFO ProgressMeter - chr10:27046391 3.0 1400 470.0
22:47:21.110 INFO ProgressMeter - chr10:32055846 3.2 1480 468.8
22:47:31.338 INFO ProgressMeter - chr10:43115947 3.3 1540 462.8
22:47:43.082 INFO ProgressMeter - chr10:68572878 3.5 1610 457.0
22:47:53.312 INFO ProgressMeter - chr10:87866449 3.7 1680 454.8
22:48:03.431 INFO ProgressMeter - chr10:101775867 3.9 1770 458.3
22:48:13.870 INFO ProgressMeter - chr10:113165848 4.0 1880 465.8
22:48:24.653 INFO ProgressMeter - chr10:121521439 4.2 1950 462.5
22:48:35.426 INFO ProgressMeter - chr11:64805032 4.4 2070 470.9
22:48:46.277 INFO ProgressMeter - chr11:69699544 4.6 2170 474.2
22:48:56.480 INFO ProgressMeter - chr11:69774459 4.7 2230 469.8
22:49:07.104 INFO ProgressMeter - chr11:69811667 4.9 2270 461.1
22:49:17.668 INFO ProgressMeter - chr11:76523153 5.1 2330 456.9
22:49:28.466 INFO ProgressMeter - chr11:77437687 5.3 2410 456.5
22:49:42.843 INFO ProgressMeter - chr11:102324508 5.5 2510 454.8
22:49:53.458 INFO ProgressMeter - chr11:108307895 5.7 2580 452.9
22:50:03.716 INFO ProgressMeter - chr11:118482024 5.9 2660 453.4
22:50:14.480 INFO ProgressMeter - chr11:118519955 6.0 2730 451.5
22:50:25.033 INFO ProgressMeter - chr11:125654978 6.2 2800 450.0
22:50:36.062 INFO ProgressMeter - chr11:128748235 6.4 2860 446.5
22:50:46.529 INFO ProgressMeter - chr12:318404 6.6 2930 445.3
22:50:56.911 INFO ProgressMeter - chr12:4373398 6.8 3010 445.7
22:51:07.037 INFO ProgressMeter - chr12:4439592 6.9 3070 443.5
22:51:18.067 INFO ProgressMeter - chr12:6597892 7.1 3130 440.5
22:51:28.197 INFO ProgressMeter - chr12:11855696 7.3 3180 437.1
22:51:39.639 INFO ProgressMeter - chr12:11859830 7.5 3220 431.3
22:51:51.381 INFO ProgressMeter - chr12:11864236 7.7 3260 425.5
22:52:04.421 INFO ProgressMeter - chr12:11869281 7.9 3300 418.8
22:52:17.049 INFO ProgressMeter - chr12:25225612 8.1 3390 419.1
22:52:28.619 INFO ProgressMeter - chr12:45851161 8.3 3460 417.8
22:52:39.490 INFO ProgressMeter - chr12:49032742 8.5 3520 415.9
22:52:50.015 INFO ProgressMeter - chr12:49047963 8.6 3580 414.4
22:53:00.492 INFO ProgressMeter - chr12:56087793 8.8 3670 416.4
22:53:11.120 INFO ProgressMeter - chr12:57465611 9.0 3750 417.1
22:53:21.552 INFO ProgressMeter - chr12:68820323 9.2 3840 419.0
22:53:31.711 INFO ProgressMeter - chr12:111448020 9.3 3930 421.1
22:53:42.987 INFO ProgressMeter - chr12:132643468 9.5 4020 422.2
22:53:54.216 INFO ProgressMeter - chr13:21672445 9.7 4100 422.3
22:54:05.077 INFO ProgressMeter - chr13:28050120 9.9 4190 423.7
22:54:17.550 INFO ProgressMeter - chr13:28387871 10.1 4250 420.9
22:54:28.155 INFO ProgressMeter - chr13:32326497 10.3 4290 417.5
22:54:38.876 INFO ProgressMeter - chr13:32340093 10.5 4340 415.2
22:54:48.916 INFO ProgressMeter - chr13:48342597 10.6 4410 415.2
22:54:58.920 INFO ProgressMeter - chr13:102177277 10.8 4500 417.2
22:55:09.235 INFO ProgressMeter - chr13:109782877 11.0 4570 417.0
22:55:19.347 INFO ProgressMeter - chr14:23308066 11.1 4640 417.0
22:55:30.011 INFO ProgressMeter - chr14:67887019 11.3 4770 421.9
22:55:40.365 INFO ProgressMeter - chr14:98379232 11.5 4850 422.6
22:55:50.915 INFO ProgressMeter - chr15:34347226 11.7 4930 423.0
22:56:01.387 INFO ProgressMeter - chr15:41696179 11.8 4980 421.0
22:56:11.835 INFO ProgressMeter - chr15:41764884 12.0 5040 419.9
22:56:22.274 INFO ProgressMeter - chr15:73703657 12.2 5140 422.1
22:56:33.360 INFO ProgressMeter - chr15:89299798 12.4 5230 423.1
22:56:43.418 INFO ProgressMeter - chr15:92974877 12.5 5330 425.4
22:56:54.560 INFO ProgressMeter - chr16:346985 12.7 5420 426.3
22:57:04.630 INFO ProgressMeter - chr16:2565551 12.9 5510 427.7
22:57:15.530 INFO ProgressMeter - chr16:3727965 13.1 5580 427.1
22:57:26.139 INFO ProgressMeter - chr16:5818645 13.2 5640 426.0
22:57:37.165 INFO ProgressMeter - chr16:11256944 13.4 5700 424.6
22:57:48.178 INFO ProgressMeter - chr16:30123038 13.6 5770 424.0
22:57:59.329 INFO ProgressMeter - chr16:68821999 13.8 5870 425.6
22:58:10.452 INFO ProgressMeter - chr16:72797669 14.0 5920 423.5
22:58:21.319 INFO ProgressMeter - chr16:81936167 14.2 5990 423.0
22:58:31.447 INFO ProgressMeter - chr16:89285452 14.3 6050 422.2
22:58:42.100 INFO ProgressMeter - chr17:7671820 14.5 6150 423.9
22:58:52.138 INFO ProgressMeter - chr17:12113231 14.7 6240 425.2
22:59:03.160 INFO ProgressMeter - chr17:18039763 14.9 6340 426.7
22:59:13.473 INFO ProgressMeter - chr17:31229935 15.0 6390 425.2
22:59:25.379 INFO ProgressMeter - chr17:31338715 15.2 6440 422.9
22:59:36.208 INFO ProgressMeter - chr17:35107020 15.4 6490 421.2
22:59:49.018 INFO ProgressMeter - chr17:39519968 15.6 6530 418.0
23:00:01.337 INFO ProgressMeter - chr17:39704942 15.8 6560 414.5
23:00:11.883 INFO ProgressMeter - chr17:39717475 16.0 6590 411.8
23:00:23.386 INFO ProgressMeter - chr17:40342828 16.2 6630 409.4
23:00:34.191 INFO ProgressMeter - chr17:42324961 16.4 6750 412.2
23:00:46.106 INFO ProgressMeter - chr17:43094545 16.6 6840 412.7
23:00:56.218 INFO ProgressMeter - chr17:43535871 16.7 6910 412.7
23:01:11.052 INFO ProgressMeter - chr17:43544305 17.0 6970 410.3
23:01:22.282 INFO ProgressMeter - chr17:58363273 17.2 7050 410.4
23:01:33.173 INFO ProgressMeter - chr17:60600814 17.4 7140 411.3
23:01:44.257 INFO ProgressMeter - chr17:65538170 17.5 7220 411.6
23:01:54.729 INFO ProgressMeter - chr17:80962499 17.7 7320 413.2
23:02:05.117 INFO ProgressMeter - chr18:44951784 17.9 7420 414.7
23:02:15.241 INFO ProgressMeter - chr19:1222983 18.1 7520 416.4
23:02:26.294 INFO ProgressMeter - chr19:4097290 18.2 7630 418.2
23:02:36.893 INFO ProgressMeter - chr19:7142814 18.4 7730 419.7
23:02:47.265 INFO ProgressMeter - chr19:10499393 18.6 7820 420.6
23:02:58.326 INFO ProgressMeter - chr19:15165516 18.8 7920 421.8
23:03:08.520 INFO ProgressMeter - chr19:15265607 18.9 8010 422.8
23:03:21.418 INFO ProgressMeter - chr19:29819201 19.2 8120 423.8
23:03:32.704 INFO ProgressMeter - chr19:35732083 19.4 8210 424.3
23:03:43.887 INFO ProgressMeter - chr19:41219404 19.5 8290 424.3
23:03:55.359 INFO ProgressMeter - chr19:41261157 19.7 8330 422.2
23:04:05.900 INFO ProgressMeter - chr19:45353889 19.9 8400 422.0
23:04:17.024 INFO ProgressMeter - chr19:45418828 20.1 8480 422.1
23:04:30.211 INFO ProgressMeter - chr2:15937790 20.3 8570 422.0
23:04:41.515 INFO ProgressMeter - chr2:25235705 20.5 8650 422.0
23:04:52.707 INFO ProgressMeter - chr2:25744167 20.7 8710 421.1
23:05:02.912 INFO ProgressMeter - chr2:29223666 20.9 8770 420.6
23:05:13.789 INFO ProgressMeter - chr2:29232302 21.0 8800 418.4
23:05:24.643 INFO ProgressMeter - chr2:42317425 21.2 8870 418.1
23:05:38.473 INFO ProgressMeter - chr2:47445618 21.4 8920 415.9
23:05:49.347 INFO ProgressMeter - chr2:58204143 21.6 8990 415.7
23:05:59.640 INFO ProgressMeter - chr2:96254836 21.8 9060 415.6
23:06:11.911 INFO ProgressMeter - chr2:108765772 22.0 9150 415.8
23:06:22.265 INFO ProgressMeter - chr2:111127537 22.2 9200 414.9
23:06:32.960 INFO ProgressMeter - chr2:113222972 22.4 9250 413.8
23:06:44.432 INFO ProgressMeter - chr2:113226069 22.5 9280 411.6
23:06:56.457 INFO ProgressMeter - chr2:113229771 22.7 9310 409.3
23:07:15.667 INFO ProgressMeter - chr2:113233990 23.1 9350 405.4
23:07:25.937 INFO ProgressMeter - chr2:140495645 23.2 9460 407.1
23:07:36.680 INFO ProgressMeter - chr2:189805650 23.4 9590 409.5
23:07:46.768 INFO ProgressMeter - chr2:201266459 23.6 9680 410.4
23:07:57.487 INFO ProgressMeter - chr2:222201379 23.8 9800 412.4
23:08:09.118 INFO ProgressMeter - chr2:222210912 24.0 9870 412.0
23:08:20.667 INFO ProgressMeter - chr2:222218323 24.1 9920 410.8
23:08:31.475 INFO ProgressMeter - chr20:4466874 24.3 10030 412.3
23:08:44.198 INFO ProgressMeter - chr20:32435992 24.5 10100 411.5
23:08:55.045 INFO ProgressMeter - chr20:41100173 24.7 10180 411.8
23:09:06.567 INFO ProgressMeter - chr20:47635889 24.9 10260 411.8
23:09:17.570 INFO ProgressMeter - chr20:56386255 25.1 10320 411.2
23:09:28.128 INFO ProgressMeter - chr21:35048840 25.3 10400 411.5
23:09:38.820 INFO ProgressMeter - chr21:38471075 25.5 10440 410.2
23:09:51.909 INFO ProgressMeter - chr21:41490036 25.7 10490 408.6
23:10:04.716 INFO ProgressMeter - chr21:41493985 25.9 10520 406.4
23:10:15.618 INFO ProgressMeter - chr21:41502519 26.1 10560 405.1
23:10:26.050 INFO ProgressMeter - chr21:43095436 26.2 10610 404.4
23:10:36.095 INFO ProgressMeter - chr22:23290772 26.4 10710 405.6
23:10:46.518 INFO ProgressMeter - chr22:28715208 26.6 10780 405.6
23:10:57.509 INFO ProgressMeter - chr22:29286326 26.8 10850 405.4
23:11:07.830 INFO ProgressMeter - chr22:33163485 26.9 10910 405.0
23:11:18.001 INFO ProgressMeter - chr22:41178194 27.1 10980 405.1
23:11:28.376 INFO ProgressMeter - chr3:10093283 27.3 11040 404.7
23:11:40.461 INFO ProgressMeter - chr3:12354596 27.5 11080 403.2
23:11:51.453 INFO ProgressMeter - chr3:12358084 27.7 11110 401.6
23:12:04.540 INFO ProgressMeter - chr3:12361342 27.9 11140 399.6
23:12:17.743 INFO ProgressMeter - chr3:12366027 28.1 11180 397.9
23:12:28.129 INFO ProgressMeter - chr3:12368925 28.3 11210 396.5
23:12:38.817 INFO ProgressMeter - chr3:12373270 28.5 11240 395.1
23:12:50.094 INFO ProgressMeter - chr3:12377507 28.6 11270 393.5
23:13:02.776 INFO ProgressMeter - chr3:12598057 28.9 11320 392.4
23:13:13.071 INFO ProgressMeter - chr3:12661883 29.0 11360 391.4
23:13:24.324 INFO ProgressMeter - chr3:47086193 29.2 11460 392.3
23:13:34.631 INFO ProgressMeter - chr3:49887545 29.4 11540 392.8
23:13:45.217 INFO ProgressMeter - chr3:52641952 29.6 11640 393.8
23:13:56.325 INFO ProgressMeter - chr3:89408065 29.7 11740 394.7
23:14:06.747 INFO ProgressMeter - chr3:135241146 29.9 11810 394.8
23:14:17.979 INFO ProgressMeter - chr3:138684623 30.1 11890 395.0
23:14:29.197 INFO ProgressMeter - chr3:142512258 30.3 11980 395.5
23:14:40.061 INFO ProgressMeter - chr3:179165522 30.5 12060 395.8
23:14:50.237 INFO ProgressMeter - chr3:183494210 30.6 12130 395.9
23:15:01.754 INFO ProgressMeter - chr3:186048628 30.8 12190 395.3
23:15:12.676 INFO ProgressMeter - chr3:196054957 31.0 12280 395.9
23:15:23.591 INFO ProgressMeter - chr4:20491858 31.2 12390 397.1
23:15:34.761 INFO ProgressMeter - chr4:54263865 31.4 12490 398.0
23:15:49.761 INFO ProgressMeter - chr4:54732114 31.6 12580 397.7
23:16:00.236 INFO ProgressMeter - chr4:80265289 31.8 12670 398.3
23:16:10.430 INFO ProgressMeter - chr4:98901874 32.0 12750 398.7
23:16:22.485 INFO ProgressMeter - chr4:105259617 32.2 12810 398.1
23:16:32.773 INFO ProgressMeter - chr4:142237862 32.4 12910 399.1
23:16:43.960 INFO ProgressMeter - chr4:186617826 32.5 13000 399.5
23:16:54.602 INFO ProgressMeter - chr5:236564 32.7 13080 399.8
23:17:05.397 INFO ProgressMeter - chr5:38955593 32.9 13150 399.8
23:17:17.636 INFO ProgressMeter - chr5:44370019 33.1 13230 399.7
23:17:28.328 INFO ProgressMeter - chr5:80854200 33.3 13350 401.2
23:17:38.660 INFO ProgressMeter - chr5:112840591 33.4 13440 401.8
23:17:49.536 INFO ProgressMeter - chr5:122452923 33.6 13500 401.4
23:18:00.802 INFO ProgressMeter - chr5:142642550 33.8 13590 401.9
23:18:11.392 INFO ProgressMeter - chr5:150078110 34.0 13660 401.8
23:18:22.605 INFO ProgressMeter - chr5:150412623 34.2 13740 402.0
23:18:33.162 INFO ProgressMeter - chr5:177092319 34.4 13810 401.9
23:18:43.707 INFO ProgressMeter - chr5:177210329 34.5 13860 401.3
23:18:54.301 INFO ProgressMeter - chr5:180614066 34.7 13940 401.6
23:19:05.422 INFO ProgressMeter - chr6:20464963 34.9 14040 402.3
23:19:18.621 INFO ProgressMeter - chr6:29943266 35.1 14130 402.4
23:19:31.280 INFO ProgressMeter - chr6:30708156 35.3 14170 401.1
23:19:41.745 INFO ProgressMeter - chr6:32202454 35.5 14220 400.6
23:19:52.523 INFO ProgressMeter - chr6:33322860 35.7 14280 400.2
23:20:03.087 INFO ProgressMeter - chr6:93259352 35.9 14410 401.9
23:20:13.636 INFO ProgressMeter - chr6:117317232 36.0 14490 402.1
23:20:24.059 INFO ProgressMeter - chr6:117323088 36.2 14530 401.3
23:20:34.540 INFO ProgressMeter - chr6:117329818 36.4 14580 400.8
23:20:46.035 INFO ProgressMeter - chr6:117339594 36.6 14640 400.3
23:20:56.257 INFO ProgressMeter - chr6:135190125 36.7 14710 400.4
23:21:07.962 INFO ProgressMeter - chr6:135207696 36.9 14760 399.6
23:21:21.699 INFO ProgressMeter - chr6:135212323 37.2 14800 398.2
23:21:32.707 INFO ProgressMeter - chr6:137198029 37.4 14840 397.3
23:21:43.767 INFO ProgressMeter - chr6:151804389 37.5 14910 397.2
23:21:54.524 INFO ProgressMeter - chr6:157133140 37.7 14980 397.2
23:22:05.682 INFO ProgressMeter - chr6:161106643 37.9 15060 397.4
23:22:16.479 INFO ProgressMeter - chr7:2944533 38.1 15140 397.6
23:22:27.345 INFO ProgressMeter - chr7:13895401 38.3 15200 397.3
23:22:37.791 INFO ProgressMeter - chr7:13931558 38.4 15230 396.3
23:22:48.935 INFO ProgressMeter - chr7:13937631 38.6 15270 395.4
23:22:59.409 INFO ProgressMeter - chr7:13943782 38.8 15320 394.9
23:23:10.618 INFO ProgressMeter - chr7:13947838 39.0 15350 393.8
23:23:22.015 INFO ProgressMeter - chr7:13951405 39.2 15380 392.6
23:23:32.879 INFO ProgressMeter - chr7:13957236 39.4 15420 391.8
23:23:45.423 INFO ProgressMeter - chr7:13963180 39.6 15460 390.8
23:23:55.502 INFO ProgressMeter - chr7:13967748 39.7 15500 390.1
23:24:07.686 INFO ProgressMeter - chr7:13973940 39.9 15550 389.4
23:24:20.149 INFO ProgressMeter - chr7:13977883 40.1 15580 388.1
23:24:34.892 INFO ProgressMeter - chr7:13982703 40.4 15620 386.8
23:24:46.201 INFO ProgressMeter - chr7:13986526 40.6 15650 385.7
23:24:57.472 INFO ProgressMeter - chr7:50400107 40.8 15690 384.9
23:25:10.271 INFO ProgressMeter - chr7:55157661 41.0 15740 384.1
23:25:22.912 INFO ProgressMeter - chr7:55168513 41.2 15780 383.1
23:25:35.353 INFO ProgressMeter - chr7:55174844 41.4 15810 381.9
23:25:45.490 INFO ProgressMeter - chr7:55178097 41.6 15840 381.1
23:25:57.180 INFO ProgressMeter - chr7:55192764 41.8 15870 380.0
23:26:08.085 INFO ProgressMeter - chr7:78489759 41.9 15930 379.8
23:26:19.104 INFO ProgressMeter - chr7:92817732 42.1 16020 380.3
23:26:30.821 INFO ProgressMeter - chr7:106868494 42.3 16110 380.7
23:26:41.834 INFO ProgressMeter - chr7:129189230 42.5 16190 380.9
23:26:53.853 INFO ProgressMeter - chr7:140789902 42.7 16250 380.5
23:27:04.394 INFO ProgressMeter - chr7:140793777 42.9 16280 379.7
23:27:15.168 INFO ProgressMeter - chr7:142952507 43.1 16350 379.7
23:27:26.355 INFO ProgressMeter - chr7:152167244 43.2 16440 380.2
23:27:37.461 INFO ProgressMeter - chr7:152250851 43.4 16510 380.2
23:27:49.364 INFO ProgressMeter - chr8:32647188 43.6 16620 381.0
23:27:59.744 INFO ProgressMeter - chr8:38426120 43.8 16730 382.0
23:28:09.842 INFO ProgressMeter - chr8:41946589 44.0 16790 381.9
23:28:20.384 INFO ProgressMeter - chr8:47855220 44.1 16870 382.2
23:28:30.927 INFO ProgressMeter - chr8:68022034 44.3 16970 382.9
23:28:41.377 INFO ProgressMeter - chr8:89981373 44.5 17050 383.2
23:28:55.337 INFO ProgressMeter - chr8:127734426 44.7 17110 382.5
23:29:05.661 INFO ProgressMeter - chr8:144512142 44.9 17170 382.4
23:29:16.812 INFO ProgressMeter - chr9:5457345 45.1 17260 382.8
23:29:28.133 INFO ProgressMeter - chr9:20620652 45.3 17350 383.2
23:29:38.291 INFO ProgressMeter - chr9:83971954 45.4 17440 383.8
23:29:49.690 INFO ProgressMeter - chr9:84810690 45.6 17500 383.5
23:29:59.767 INFO ProgressMeter - chr9:84815283 45.8 17540 383.0
23:30:09.862 INFO ProgressMeter - chr9:84864385 46.0 17570 382.2
23:30:22.017 INFO ProgressMeter - chr9:84873761 46.2 17610 381.4
23:30:33.737 INFO ProgressMeter - chr9:85023030 46.4 17660 380.9
23:30:45.171 INFO ProgressMeter - chr9:90874670 46.6 17700 380.2
23:30:55.528 INFO ProgressMeter - chr9:99132495 46.7 17780 380.5
23:31:07.526 INFO ProgressMeter - chr9:130886723 46.9 17860 380.6
23:31:18.242 INFO ProgressMeter - chr9:136504671 47.1 17930 380.6
23:31:28.292 INFO ProgressMeter - chrX:15790932 47.3 18020 381.2
23:31:39.187 INFO ProgressMeter - chrX:48794094 47.5 18170 382.9
23:31:49.378 INFO ProgressMeter - chrX:53217141 47.6 18270 383.6
23:31:59.973 INFO ProgressMeter - chrX:67546681 47.8 18360 384.1
23:32:10.048 INFO ProgressMeter - chrX:71388235 48.0 18490 385.4
23:32:20.186 INFO ProgressMeter - chrX:124076330 48.1 18670 387.8
23:32:28.987 INFO Mutect2 - 673427 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
212 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
673641 total reads filtered out of 84342538 reads processed
23:32:28.987 INFO ProgressMeter - chrY:20960482 48.3 18781 388.9
23:32:28.987 INFO ProgressMeter - Traversal complete. Processed 18781 total regions in 48.3 minutes.
23:32:29.003 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 5.795047879
23:32:29.003 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 255.38753223700002
23:32:29.003 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 9.38 sec
23:32:29.004 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:32:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 48.30 minutes.
Runtime.totalMemory()=3296722944
Tool returned:
SUCCESS
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 LS0896_tumor.bam --tumor-sample LS0896 -L TST500C_manifest.bed -O LS0896.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:32:30.325 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
23:32:30.435 INFO FilterMutectCalls - ------------------------------------------------------------
23:32:30.444 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:32:30.444 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:32:30.444 INFO FilterMutectCalls - Executing as ?@nf-d48cbf81060ea639251a00f1787545d7-2944a-nwqqm on Linux v6.12.88 amd64
23:32:30.444 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:32:30.444 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:32:30 PM GMT
23:32:30.445 INFO FilterMutectCalls - ------------------------------------------------------------
23:32:30.445 INFO FilterMutectCalls - ------------------------------------------------------------
23:32:30.445 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:32:30.445 INFO FilterMutectCalls - Picard Version: 3.1.1
23:32:30.445 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:32:30.446 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:32:30.446 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:32:30.446 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:32:30.446 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:32:30.446 INFO FilterMutectCalls - Deflater: IntelDeflater
23:32:30.446 INFO FilterMutectCalls - Inflater: IntelInflater
23:32:30.446 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:32:30.446 INFO FilterMutectCalls - Requester pays: disabled
23:32:30.447 INFO FilterMutectCalls - Initializing engine
23:32:30.651 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.7lz5ajWxXJ/LS0896.mutect2.raw.vcf.gz
23:32:30.763 INFO FilterMutectCalls - Done initializing engine
23:32:30.829 INFO ProgressMeter - Starting traversal
23:32:30.830 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:32:30.831 INFO FilterMutectCalls - Starting pass 0 through the variants
23:32:31.923 INFO FilterMutectCalls - Finished pass 0 through the variants
23:32:34.181 INFO FilterMutectCalls - Starting pass 1 through the variants
23:32:35.279 INFO FilterMutectCalls - Finished pass 1 through the variants
23:32:35.752 INFO FilterMutectCalls - Starting pass 2 through the variants
23:32:36.809 INFO FilterMutectCalls - Finished pass 2 through the variants
23:32:36.812 INFO FilterMutectCalls - Starting pass 3 through the variants
23:32:37.729 INFO FilterMutectCalls - Finished pass 3 through the variants
23:32:37.739 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:32:37.740 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:32:37.740 INFO ProgressMeter - chrX:67545400 0.1 10028 87073.8
23:32:37.740 INFO ProgressMeter - Traversal complete. Processed 10028 total variants in 0.1 minutes.
23:32:37.752 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:32:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.12 minutes.
Runtime.totalMemory()=234881024
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 LS0896.mutect2.raw.vcf.gz --stats LS0896.mutect2.raw.vcf.gz.stats -O LS0896.mutect2.filtered.vcf.gz
23:32:38.992 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
23:32:39.096 INFO SelectVariants - ------------------------------------------------------------
23:32:39.099 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:32:39.100 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:32:39.100 INFO SelectVariants - Executing as ?@nf-d48cbf81060ea639251a00f1787545d7-2944a-nwqqm on Linux v6.12.88 amd64
23:32:39.100 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:32:39.100 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:32:38 PM GMT
23:32:39.100 INFO SelectVariants - ------------------------------------------------------------
23:32:39.100 INFO SelectVariants - ------------------------------------------------------------
23:32:39.101 INFO SelectVariants - HTSJDK Version: 4.1.0
23:32:39.101 INFO SelectVariants - Picard Version: 3.1.1
23:32:39.101 INFO SelectVariants - Built for Spark Version: 3.5.0
23:32:39.101 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:32:39.102 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:32:39.102 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:32:39.102 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:32:39.102 INFO SelectVariants - Deflater: IntelDeflater
23:32:39.102 INFO SelectVariants - Inflater: IntelInflater
23:32:39.102 INFO SelectVariants - GCS max retries/reopens: 20
23:32:39.102 INFO SelectVariants - Requester pays: disabled
23:32:39.103 INFO SelectVariants - Initializing engine
23:32:39.294 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.7lz5ajWxXJ/LS0896.mutect2.filtered.vcf.gz
23:32:39.398 INFO SelectVariants - Done initializing engine
23:32:39.434 INFO ProgressMeter - Starting traversal
23:32:39.434 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:32:39.510 INFO ProgressMeter - chr7:5997349 0.0 2507 2032702.7
23:32:39.511 INFO ProgressMeter - Traversal complete. Processed 2507 total variants in 0.0 minutes.
23:32:39.521 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:32:39 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 LS0896.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0896.mutect2.pass.vcf.gz