Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0879/LS0879_tumor.bam
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/29/9e2ace16be94e966e13ee7116101a8/.command.sh
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.fai
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/TSO500/TST500C_manifest.bed
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/af-only-gnomad.hg38.vcf.gz
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/af-only-gnomad.hg38.vcf.gz.tbi
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.dict
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/29/9e2ace16be94e966e13ee7116101a8/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0879/LS0879_tumor.bam.bai
==> STAGING COMPLETE (10 inputs)
22:44:18.853 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
22:44:18.974 INFO Mutect2 - ------------------------------------------------------------
22:44:18.978 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:18.978 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:18.978 INFO Mutect2 - Executing as ?@nf-299e2ace16be94e966e13ee7116101a8-d0026-sfcjc on Linux v6.12.88 amd64
22:44:18.978 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:18.978 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:18 PM GMT
22:44:18.978 INFO Mutect2 - ------------------------------------------------------------
22:44:18.979 INFO Mutect2 - ------------------------------------------------------------
22:44:18.979 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:18.979 INFO Mutect2 - Picard Version: 3.1.1
22:44:18.980 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:18.980 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:18.980 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:18.980 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:18.980 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:18.980 INFO Mutect2 - Deflater: IntelDeflater
22:44:18.980 INFO Mutect2 - Inflater: IntelInflater
22:44:18.980 INFO Mutect2 - GCS max retries/reopens: 20
22:44:18.980 INFO Mutect2 - Requester pays: disabled
22:44:18.981 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.QfXX8pzALJ/LS0879_tumor.bam.bai is older than BAM /tmp/nxf.QfXX8pzALJ/LS0879_tumor.bam
22:44:19.173 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.QfXX8pzALJ/af-only-gnomad.hg38.vcf.gz
22:44:19.287 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.QfXX8pzALJ/TST500C_manifest.bed
22:44:19.320 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:19.348 INFO Mutect2 - Done initializing engine
22:44:19.359 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
22:44:19.361 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
22:44:19.361 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:19.361 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:19.370 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
22:44:19.379 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:19.379 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:19.380 INFO IntelPairHmm - Available threads: 384
22:44:19.380 INFO IntelPairHmm - Requested threads: 4
22:44:19.380 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:19.433 INFO ProgressMeter - Starting traversal
22:44:19.434 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:30.629 INFO ProgressMeter - chr1:9724284 0.2 50 268.0
22:44:41.108 INFO ProgressMeter - chr1:11233396 0.4 110 304.5
22:44:53.143 INFO ProgressMeter - chr1:15930831 0.6 160 284.8
22:45:03.204 INFO ProgressMeter - chr1:15939294 0.7 200 274.2
22:45:14.484 INFO ProgressMeter - chr1:18746708 0.9 250 272.5
22:45:25.410 INFO ProgressMeter - chr1:26771117 1.1 300 272.8
22:45:36.851 INFO ProgressMeter - chr1:36467961 1.3 350 271.3
22:45:48.548 INFO ProgressMeter - chr1:39901320 1.5 410 276.1
22:45:58.673 INFO ProgressMeter - chr1:46061927 1.7 480 290.2
22:46:09.204 INFO ProgressMeter - chr1:64838007 1.8 540 295.2
22:46:19.347 INFO ProgressMeter - chr1:77964150 2.0 600 300.2
22:46:31.459 INFO ProgressMeter - chr1:117623032 2.2 680 309.0
22:46:41.568 INFO ProgressMeter - chr1:119925303 2.4 720 303.9
22:46:52.300 INFO ProgressMeter - chr1:156860877 2.5 780 306.2
22:47:05.077 INFO ProgressMeter - chr1:156875877 2.8 820 297.0
22:47:15.675 INFO ProgressMeter - chr1:158656562 2.9 880 299.6
22:47:26.079 INFO ProgressMeter - chr1:162778578 3.1 940 302.2
22:47:36.555 INFO ProgressMeter - chr1:193232991 3.3 1010 307.4
22:47:47.642 INFO ProgressMeter - chr1:204538207 3.5 1080 311.2
22:47:57.671 INFO ProgressMeter - chr1:206771354 3.6 1140 313.4
22:48:08.634 INFO ProgressMeter - chr1:241519589 3.8 1210 316.8
22:48:22.010 INFO ProgressMeter - chr1:243503877 4.0 1240 306.7
22:48:32.237 INFO ProgressMeter - chr10:27012994 4.2 1290 306.2
22:48:43.182 INFO ProgressMeter - chr10:27086518 4.4 1340 304.8
22:48:54.359 INFO ProgressMeter - chr10:43096505 4.6 1400 305.5
22:49:05.543 INFO ProgressMeter - chr10:43114958 4.8 1450 304.1
22:49:15.642 INFO ProgressMeter - chr10:43120148 4.9 1490 301.8
22:49:26.867 INFO ProgressMeter - chr10:68573887 5.1 1540 300.6
22:49:36.997 INFO ProgressMeter - chr10:87866180 5.3 1590 300.4
22:49:49.458 INFO ProgressMeter - chr10:101770327 5.5 1660 301.8
22:50:00.712 INFO ProgressMeter - chr10:110590970 5.7 1740 305.9
22:50:12.322 INFO ProgressMeter - chr10:121480523 5.9 1800 306.0
22:50:24.123 INFO ProgressMeter - chr10:121515224 6.1 1840 302.7
22:50:35.238 INFO ProgressMeter - chr11:17720296 6.3 1900 303.3
22:50:45.279 INFO ProgressMeter - chr11:64805032 6.4 1970 306.3
22:50:57.118 INFO ProgressMeter - chr11:69651268 6.6 2040 307.8
22:51:08.050 INFO ProgressMeter - chr11:69702351 6.8 2080 305.4
22:51:18.394 INFO ProgressMeter - chr11:69775515 7.0 2130 305.0
22:51:35.154 INFO ProgressMeter - chr11:69810871 7.3 2160 297.4
22:51:45.190 INFO ProgressMeter - chr11:69818355 7.4 2190 294.8
22:51:55.815 INFO ProgressMeter - chr11:77336197 7.6 2240 294.5
22:52:06.524 INFO ProgressMeter - chr11:77415756 7.8 2290 294.2
22:52:16.707 INFO ProgressMeter - chr11:101127867 8.0 2360 296.7
22:52:27.343 INFO ProgressMeter - chr11:102324912 8.1 2390 293.9
22:52:38.360 INFO ProgressMeter - chr11:108330212 8.3 2460 295.8
22:52:49.431 INFO ProgressMeter - chr11:118493055 8.5 2520 296.5
22:53:00.708 INFO ProgressMeter - chr11:118506204 8.7 2560 294.7
22:53:13.608 INFO ProgressMeter - chr11:125631639 8.9 2610 293.2
22:53:24.149 INFO ProgressMeter - chr11:128459813 9.1 2660 293.0
22:53:35.214 INFO ProgressMeter - chr11:128772780 9.3 2700 291.5
22:53:47.083 INFO ProgressMeter - chr12:322415 9.5 2750 290.7
22:53:58.152 INFO ProgressMeter - chr12:4373698 9.6 2820 292.4
22:54:09.616 INFO ProgressMeter - chr12:4442023 9.8 2880 292.8
22:54:19.981 INFO ProgressMeter - chr12:6594509 10.0 2930 292.7
22:54:30.029 INFO ProgressMeter - chr12:11854997 10.2 2970 291.8
22:54:40.516 INFO ProgressMeter - chr12:11858647 10.4 3000 289.8
22:54:50.741 INFO ProgressMeter - chr12:11862149 10.5 3030 288.0
22:55:02.538 INFO ProgressMeter - chr12:11866310 10.7 3060 285.5
22:55:13.905 INFO ProgressMeter - chr12:12718069 10.9 3090 283.3
22:55:24.948 INFO ProgressMeter - chr12:25221301 11.1 3160 284.9
22:55:36.262 INFO ProgressMeter - chr12:45850256 11.3 3220 285.4
22:55:47.402 INFO ProgressMeter - chr12:49030891 11.5 3270 285.2
22:55:59.960 INFO ProgressMeter - chr12:49033684 11.7 3290 281.8
22:56:10.224 INFO ProgressMeter - chr12:49040654 11.8 3330 281.1
22:56:21.555 INFO ProgressMeter - chr12:49053976 12.0 3390 281.7
22:56:31.579 INFO ProgressMeter - chr12:56095255 12.2 3460 283.6
22:56:41.832 INFO ProgressMeter - chr12:57094069 12.4 3510 283.7
22:56:52.798 INFO ProgressMeter - chr12:57748977 12.6 3570 284.3
22:57:06.450 INFO ProgressMeter - chr12:68839572 12.8 3650 285.5
22:57:16.894 INFO ProgressMeter - chr12:112489022 13.0 3710 286.3
22:57:27.883 INFO ProgressMeter - chr12:132632719 13.1 3770 286.9
22:57:39.265 INFO ProgressMeter - chr12:132680605 13.3 3840 288.1
22:57:50.373 INFO ProgressMeter - chr13:21688777 13.5 3900 288.6
22:58:01.057 INFO ProgressMeter - chr13:28303266 13.7 3970 289.9
22:58:15.953 INFO ProgressMeter - chr13:28388583 13.9 4020 288.3
22:58:27.117 INFO ProgressMeter - chr13:32336263 14.1 4070 288.1
22:58:37.306 INFO ProgressMeter - chr13:32359060 14.3 4110 287.5
22:58:47.676 INFO ProgressMeter - chr13:48379592 14.5 4170 288.2
22:58:57.865 INFO ProgressMeter - chr13:102181777 14.6 4240 289.6
22:59:08.625 INFO ProgressMeter - chr13:106286100 14.8 4290 289.5
22:59:19.779 INFO ProgressMeter - chr13:113322334 15.0 4370 291.2
22:59:30.580 INFO ProgressMeter - chr14:37587851 15.2 4420 291.1
22:59:41.700 INFO ProgressMeter - chr14:37599003 15.4 4480 291.5
22:59:54.585 INFO ProgressMeter - chr14:95099778 15.6 4550 291.9
23:00:05.477 INFO ProgressMeter - chr14:104302924 15.8 4610 292.4
23:00:17.426 INFO ProgressMeter - chr15:34347579 16.0 4650 291.2
23:00:28.985 INFO ProgressMeter - chr15:41696073 16.2 4700 290.9
23:00:40.817 INFO ProgressMeter - chr15:41762127 16.4 4750 290.4
23:00:50.987 INFO ProgressMeter - chr15:49464755 16.5 4810 291.1
23:01:03.648 INFO ProgressMeter - chr15:87977962 16.7 4880 291.6
23:01:14.260 INFO ProgressMeter - chr15:89305113 16.9 4940 292.1
23:01:25.111 INFO ProgressMeter - chr15:92901236 17.1 5000 292.5
23:01:36.340 INFO ProgressMeter - chr15:98891623 17.3 5060 292.8
23:01:47.056 INFO ProgressMeter - chr16:2055495 17.5 5120 293.2
23:01:58.020 INFO ProgressMeter - chr16:2538111 17.6 5200 294.7
23:02:09.251 INFO ProgressMeter - chr16:3608428 17.8 5270 295.6
23:02:20.622 INFO ProgressMeter - chr16:3767766 18.0 5310 294.7
23:02:31.510 INFO ProgressMeter - chr16:9849772 18.2 5360 294.5
23:02:41.811 INFO ProgressMeter - chr16:23630360 18.4 5410 294.5
23:02:53.304 INFO ProgressMeter - chr16:56823815 18.6 5480 295.2
23:03:04.818 INFO ProgressMeter - chr16:68828172 18.8 5540 295.4
23:03:15.471 INFO ProgressMeter - chr16:72796369 18.9 5570 294.2
23:03:28.002 INFO ProgressMeter - chr16:72958797 19.1 5610 293.1
23:03:38.408 INFO ProgressMeter - chr16:81938799 19.3 5660 293.0
23:03:50.046 INFO ProgressMeter - chr16:89283668 19.5 5710 292.7
23:04:00.697 INFO ProgressMeter - chr16:89791925 19.7 5770 293.1
23:04:13.033 INFO ProgressMeter - chr17:7676115 19.9 5840 293.6
23:04:24.651 INFO ProgressMeter - chr17:16061427 20.1 5920 294.7
23:04:35.631 INFO ProgressMeter - chr17:17221464 20.3 5990 295.5
23:04:47.576 INFO ProgressMeter - chr17:31249014 20.5 6060 296.1
23:04:59.405 INFO ProgressMeter - chr17:35101288 20.7 6130 296.6
23:05:10.602 INFO ProgressMeter - chr17:39519954 20.9 6170 295.9
23:05:20.774 INFO ProgressMeter - chr17:39704947 21.0 6200 294.9
23:05:34.175 INFO ProgressMeter - chr17:39726813 21.2 6240 293.7
23:05:45.463 INFO ProgressMeter - chr17:42210169 21.4 6310 294.4
23:05:56.281 INFO ProgressMeter - chr17:43049119 21.6 6380 295.2
23:06:07.984 INFO ProgressMeter - chr17:43093472 21.8 6430 294.8
23:06:18.983 INFO ProgressMeter - chr17:43532495 22.0 6480 294.6
23:06:31.860 INFO ProgressMeter - chr17:43539796 22.2 6530 294.1
23:06:42.162 INFO ProgressMeter - chr17:43545556 22.4 6560 293.1
23:06:53.190 INFO ProgressMeter - chr17:49619232 22.6 6620 293.4
23:07:03.835 INFO ProgressMeter - chr17:59914633 22.7 6690 294.2
23:07:14.285 INFO ProgressMeter - chr17:61683294 22.9 6740 294.1
23:07:24.911 INFO ProgressMeter - chr17:65537560 23.1 6800 294.5
23:07:35.251 INFO ProgressMeter - chr17:80823077 23.3 6860 294.9
23:07:45.751 INFO ProgressMeter - chr18:22200654 23.4 6930 295.7
23:07:56.202 INFO ProgressMeter - chr18:44951282 23.6 6980 295.6
23:08:06.304 INFO ProgressMeter - chr18:51058123 23.8 7020 295.2
23:08:16.691 INFO ProgressMeter - chr19:1223032 24.0 7090 296.0
23:08:27.299 INFO ProgressMeter - chr19:4047926 24.1 7180 297.5
23:08:38.112 INFO ProgressMeter - chr19:5262962 24.3 7260 298.6
23:08:50.260 INFO ProgressMeter - chr19:10156439 24.5 7330 299.0
23:09:00.305 INFO ProgressMeter - chr19:11033288 24.7 7400 299.8
23:09:11.479 INFO ProgressMeter - chr19:15165961 24.9 7460 300.0
23:09:23.102 INFO ProgressMeter - chr19:15254150 25.1 7530 300.5
23:09:34.193 INFO ProgressMeter - chr19:18156178 25.2 7580 300.2
23:09:44.895 INFO ProgressMeter - chr19:29821642 25.4 7650 300.9
23:09:55.969 INFO ProgressMeter - chr19:35729002 25.6 7720 301.5
23:10:06.296 INFO ProgressMeter - chr19:40265413 25.8 7790 302.2
23:10:21.131 INFO ProgressMeter - chr19:41261585 26.0 7850 301.6
23:10:31.264 INFO ProgressMeter - chr19:45352504 26.2 7910 301.9
23:10:42.163 INFO ProgressMeter - chr19:45416592 26.4 7990 302.9
23:10:52.655 INFO ProgressMeter - chr19:52205961 26.6 8060 303.5
23:11:03.221 INFO ProgressMeter - chr2:15943448 26.7 8100 303.0
23:11:13.321 INFO ProgressMeter - chr2:25235705 26.9 8150 303.0
23:11:25.341 INFO ProgressMeter - chr2:25744377 27.1 8200 302.6
23:11:35.674 INFO ProgressMeter - chr2:29222895 27.3 8250 302.5
23:11:47.052 INFO ProgressMeter - chr2:29226811 27.5 8280 301.5
23:11:58.138 INFO ProgressMeter - chr2:42282841 27.6 8340 301.7
23:12:09.152 INFO ProgressMeter - chr2:47412412 27.8 8390 301.5
23:12:19.945 INFO ProgressMeter - chr2:47799535 28.0 8420 300.6
23:12:30.331 INFO ProgressMeter - chr2:61533770 28.2 8490 301.3
23:12:41.067 INFO ProgressMeter - chr2:98565638 28.4 8530 300.8
23:12:51.546 INFO ProgressMeter - chr2:108773045 28.5 8590 301.0
23:13:04.029 INFO ProgressMeter - chr2:111128434 28.7 8620 299.9
23:13:14.775 INFO ProgressMeter - chr2:113222738 28.9 8650 299.1
23:13:26.204 INFO ProgressMeter - chr2:113226020 29.1 8680 298.2
23:13:38.646 INFO ProgressMeter - chr2:113229619 29.3 8700 296.7
23:13:53.067 INFO ProgressMeter - chr2:113233757 29.6 8730 295.3
23:14:03.965 INFO ProgressMeter - chr2:127290222 29.7 8780 295.2
23:14:15.417 INFO ProgressMeter - chr2:140501685 29.9 8850 295.7
23:14:27.093 INFO ProgressMeter - chr2:141058881 30.1 8910 295.7
23:14:37.888 INFO ProgressMeter - chr2:177231683 30.3 8960 295.6
23:14:49.487 INFO ProgressMeter - chr2:197401983 30.5 9040 296.4
23:15:00.100 INFO ProgressMeter - chr2:211561901 30.7 9110 297.0
23:15:12.202 INFO ProgressMeter - chr2:222201002 30.9 9170 297.0
23:15:25.904 INFO ProgressMeter - chr2:222207256 31.1 9210 296.1
23:15:38.504 INFO ProgressMeter - chr2:222213549 31.3 9250 295.4
23:15:52.519 INFO ProgressMeter - chr2:222218323 31.6 9280 294.1
23:16:02.815 INFO ProgressMeter - chr2:226733283 31.7 9330 294.1
23:16:14.014 INFO ProgressMeter - chr20:9557606 31.9 9380 294.0
23:16:26.281 INFO ProgressMeter - chr20:32436035 32.1 9440 294.0
23:16:37.145 INFO ProgressMeter - chr20:41100054 32.3 9510 294.5
23:16:49.217 INFO ProgressMeter - chr20:47637646 32.5 9580 294.8
23:16:59.285 INFO ProgressMeter - chr20:56381431 32.7 9620 294.5
23:17:09.746 INFO ProgressMeter - chr21:34792263 32.8 9690 295.1
23:17:21.417 INFO ProgressMeter - chr21:38400549 33.0 9740 294.9
23:17:33.009 INFO ProgressMeter - chr21:41489342 33.2 9790 294.6
23:17:46.086 INFO ProgressMeter - chr21:41492508 33.4 9810 293.3
23:18:00.171 INFO ProgressMeter - chr21:41501484 33.7 9850 292.5
23:18:10.287 INFO ProgressMeter - chr21:41506853 33.8 9880 291.9
23:18:20.590 INFO ProgressMeter - chr22:21788255 34.0 9950 292.5
23:18:30.730 INFO ProgressMeter - chr22:23292385 34.2 10000 292.5
23:18:41.275 INFO ProgressMeter - chr22:29268307 34.4 10090 293.6
23:18:53.691 INFO ProgressMeter - chr22:29290411 34.6 10130 293.0
23:19:04.866 INFO ProgressMeter - chr22:41117619 34.8 10190 293.2
23:19:16.018 INFO ProgressMeter - chr3:10034693 34.9 10250 293.3
23:19:28.310 INFO ProgressMeter - chr3:12352053 35.1 10310 293.3
23:19:38.461 INFO ProgressMeter - chr3:12356942 35.3 10340 292.8
23:19:51.676 INFO ProgressMeter - chr3:12360938 35.5 10360 291.5
23:20:03.673 INFO ProgressMeter - chr3:12367582 35.7 10400 291.0
23:20:14.776 INFO ProgressMeter - chr3:12371434 35.9 10430 290.3
23:20:27.134 INFO ProgressMeter - chr3:12377402 36.1 10470 289.8
23:20:38.576 INFO ProgressMeter - chr3:12618513 36.3 10520 289.7
23:20:49.682 INFO ProgressMeter - chr3:38138660 36.5 10580 289.8
23:21:01.859 INFO ProgressMeter - chr3:47120884 36.7 10640 289.9
23:21:12.183 INFO ProgressMeter - chr3:49687769 36.9 10690 289.9
23:21:23.469 INFO ProgressMeter - chr3:52406251 37.1 10750 290.0
23:21:34.678 INFO ProgressMeter - chr3:69949157 37.3 10820 290.4
23:21:45.356 INFO ProgressMeter - chr3:89341914 37.4 10880 290.7
23:21:56.232 INFO ProgressMeter - chr3:135249429 37.6 10940 290.9
23:22:06.981 INFO ProgressMeter - chr3:138679334 37.8 11000 291.1
23:22:18.318 INFO ProgressMeter - chr3:142465095 38.0 11070 291.5
23:22:29.111 INFO ProgressMeter - chr3:170281164 38.2 11140 291.9
23:22:40.110 INFO ProgressMeter - chr3:181713239 38.3 11210 292.3
23:22:50.182 INFO ProgressMeter - chr3:185477324 38.5 11260 292.4
23:23:00.572 INFO ProgressMeter - chr3:186786162 38.7 11310 292.4
23:23:11.182 INFO ProgressMeter - chr3:196057532 38.9 11370 292.6
23:23:22.129 INFO ProgressMeter - chr4:1805557 39.0 11450 293.3
23:23:33.262 INFO ProgressMeter - chr4:24540161 39.2 11520 293.6
23:23:45.507 INFO ProgressMeter - chr4:54277192 39.4 11580 293.7
23:23:55.648 INFO ProgressMeter - chr4:54727216 39.6 11630 293.7
23:24:05.747 INFO ProgressMeter - chr4:55082534 39.8 11650 292.9
23:24:15.880 INFO ProgressMeter - chr4:65669586 39.9 11710 293.2
23:24:26.140 INFO ProgressMeter - chr4:83482152 40.1 11770 293.4
23:24:38.136 INFO ProgressMeter - chr4:105240945 40.3 11820 293.2
23:24:50.979 INFO ProgressMeter - chr4:105275924 40.5 11850 292.4
23:25:02.016 INFO ProgressMeter - chr4:142429171 40.7 11930 293.1
23:25:13.097 INFO ProgressMeter - chr4:186597008 40.9 11980 292.9
23:25:25.418 INFO ProgressMeter - chr4:186618855 41.1 12030 292.7
23:25:37.404 INFO ProgressMeter - chr4:186707098 41.3 12070 292.3
23:25:48.700 INFO ProgressMeter - chr5:35871054 41.5 12120 292.1
23:25:58.979 INFO ProgressMeter - chr5:44313162 41.7 12190 292.6
23:26:10.725 INFO ProgressMeter - chr5:56882022 41.9 12250 292.7
23:26:22.020 INFO ProgressMeter - chr5:80675058 42.0 12320 293.0
23:26:32.875 INFO ProgressMeter - chr5:112837841 42.2 12400 293.7
23:26:44.673 INFO ProgressMeter - chr5:122423076 42.4 12440 293.3
23:26:55.277 INFO ProgressMeter - chr5:138783192 42.6 12500 293.4
23:27:06.798 INFO ProgressMeter - chr5:142685259 42.8 12560 293.5
23:27:18.496 INFO ProgressMeter - chr5:150086377 43.0 12610 293.4
23:27:29.341 INFO ProgressMeter - chr5:150401635 43.2 12670 293.5
23:27:39.349 INFO ProgressMeter - chr5:177087619 43.3 12730 293.8
23:27:49.392 INFO ProgressMeter - chr5:177093385 43.5 12760 293.3
23:28:00.779 INFO ProgressMeter - chr5:177209919 43.7 12790 292.8
23:28:12.453 INFO ProgressMeter - chr5:177295367 43.9 12840 292.6
23:28:23.995 INFO ProgressMeter - chr6:393151 44.1 12910 292.9
23:28:34.925 INFO ProgressMeter - chr6:20483110 44.3 12980 293.3
23:28:44.936 INFO ProgressMeter - chr6:27890681 44.4 13050 293.8
23:28:55.140 INFO ProgressMeter - chr6:30705593 44.6 13080 293.3
23:29:06.573 INFO ProgressMeter - chr6:32216891 44.8 13150 293.6
23:29:17.999 INFO ProgressMeter - chr6:41936660 45.0 13220 293.9
23:29:28.395 INFO ProgressMeter - chr6:43782045 45.1 13290 294.4
23:29:38.870 INFO ProgressMeter - chr6:111661896 45.3 13350 294.5
23:29:51.575 INFO ProgressMeter - chr6:117319942 45.5 13400 294.3
23:30:02.200 INFO ProgressMeter - chr6:117322854 45.7 13420 293.6
23:30:15.173 INFO ProgressMeter - chr6:117328788 45.9 13460 293.1
23:30:25.914 INFO ProgressMeter - chr6:117335470 46.1 13510 293.0
23:30:36.633 INFO ProgressMeter - chr6:117338497 46.3 13530 292.3
23:30:47.345 INFO ProgressMeter - chr6:117389348 46.5 13570 292.0
23:30:57.744 INFO ProgressMeter - chr6:135204357 46.6 13620 292.0
23:31:09.000 INFO ProgressMeter - chr6:135208384 46.8 13650 291.5
23:31:21.400 INFO ProgressMeter - chr6:135212459 47.0 13680 290.9
23:31:34.194 INFO ProgressMeter - chr6:135216510 47.2 13710 290.2
23:31:44.493 INFO ProgressMeter - chr6:137880187 47.4 13750 290.0
23:31:55.553 INFO ProgressMeter - chr6:151700495 47.6 13790 289.7
23:32:07.525 INFO ProgressMeter - chr6:152098730 47.8 13840 289.5
23:32:18.811 INFO ProgressMeter - chr6:157189640 48.0 13880 289.2
23:32:29.595 INFO ProgressMeter - chr6:161086377 48.2 13920 289.0
23:32:39.674 INFO ProgressMeter - chr6:163534980 48.3 13980 289.2
23:32:50.752 INFO ProgressMeter - chr7:5997324 48.5 14040 289.4
23:33:00.944 INFO ProgressMeter - chr7:13900827 48.7 14080 289.2
23:33:15.073 INFO ProgressMeter - chr7:13911237 48.9 14110 288.4
23:33:26.830 INFO ProgressMeter - chr7:13938240 49.1 14140 287.8
23:33:39.533 INFO ProgressMeter - chr7:13945293 49.3 14180 287.4
23:33:53.115 INFO ProgressMeter - chr7:13949094 49.6 14210 286.7
23:34:05.845 INFO ProgressMeter - chr7:13952524 49.8 14230 285.9
23:34:18.666 INFO ProgressMeter - chr7:13959582 50.0 14270 285.5
23:34:31.814 INFO ProgressMeter - chr7:13964305 50.2 14300 284.8
23:34:43.025 INFO ProgressMeter - chr7:13970363 50.4 14340 284.6
23:34:59.582 INFO ProgressMeter - chr7:13976050 50.7 14380 283.8
23:35:09.639 INFO ProgressMeter - chr7:13979861 50.8 14410 283.5
23:35:22.557 INFO ProgressMeter - chr7:13984145 51.1 14440 282.8
23:35:35.725 INFO ProgressMeter - chr7:13991326 51.3 14470 282.2
23:35:45.929 INFO ProgressMeter - chr7:55153197 51.4 14520 282.3
23:35:58.780 INFO ProgressMeter - chr7:55167324 51.7 14560 281.9
23:36:08.790 INFO ProgressMeter - chr7:55173962 51.8 14590 281.5
23:36:20.908 INFO ProgressMeter - chr7:55178917 52.0 14620 281.0
23:36:31.457 INFO ProgressMeter - chr7:55201070 52.2 14650 280.6
23:36:41.744 INFO ProgressMeter - chr7:81702579 52.4 14700 280.7
23:36:52.467 INFO ProgressMeter - chr7:92685667 52.6 14750 280.7
23:37:03.873 INFO ProgressMeter - chr7:102201570 52.7 14810 280.8
23:37:14.146 INFO ProgressMeter - chr7:106883031 52.9 14860 280.8
23:37:24.686 INFO ProgressMeter - chr7:116769755 53.1 14900 280.7
23:37:36.818 INFO ProgressMeter - chr7:140747077 53.3 14950 280.5
23:37:48.710 INFO ProgressMeter - chr7:140793586 53.5 15000 280.4
23:37:59.893 INFO ProgressMeter - chr7:148809069 53.7 15070 280.8
23:38:11.589 INFO ProgressMeter - chr7:152162572 53.9 15140 281.1
23:38:22.793 INFO ProgressMeter - chr7:152187713 54.1 15180 280.8
23:38:33.284 INFO ProgressMeter - chr8:11750109 54.2 15250 281.2
23:38:46.095 INFO ProgressMeter - chr8:32647030 54.4 15330 281.6
23:38:56.352 INFO ProgressMeter - chr8:37698030 54.6 15380 281.6
23:39:07.297 INFO ProgressMeter - chr8:38424072 54.8 15440 281.8
23:39:17.335 INFO ProgressMeter - chr8:41932618 55.0 15480 281.6
23:39:28.420 INFO ProgressMeter - chr8:41955294 55.1 15510 281.2
23:39:39.814 INFO ProgressMeter - chr8:47828208 55.3 15560 281.2
23:39:50.473 INFO ProgressMeter - chr8:47929090 55.5 15610 281.2
23:40:01.014 INFO ProgressMeter - chr8:68053176 55.7 15670 281.4
23:40:11.234 INFO ProgressMeter - chr8:68231331 55.9 15710 281.2
23:40:24.672 INFO ProgressMeter - chr8:118935543 56.1 15770 281.2
23:40:34.982 INFO ProgressMeter - chr8:127733768 56.3 15780 280.5
23:40:49.611 INFO ProgressMeter - chr8:127739751 56.5 15810 279.8
23:40:59.681 INFO ProgressMeter - chr8:144512291 56.7 15840 279.5
23:41:10.076 INFO ProgressMeter - chr9:5071269 56.8 15900 279.7
23:41:20.097 INFO ProgressMeter - chr9:8375934 57.0 15950 279.8
23:41:32.162 INFO ProgressMeter - chr9:20621807 57.2 16000 279.7
23:41:42.823 INFO ProgressMeter - chr9:68699486 57.4 16060 279.8
23:41:53.093 INFO ProgressMeter - chr9:84724222 57.6 16110 279.9
23:42:05.108 INFO ProgressMeter - chr9:84811096 57.8 16130 279.3
23:42:21.860 INFO ProgressMeter - chr9:84861480 58.0 16160 278.4
23:42:33.130 INFO ProgressMeter - chr9:84865470 58.2 16180 277.9
23:42:43.339 INFO ProgressMeter - chr9:84873773 58.4 16210 277.6
23:42:54.287 INFO ProgressMeter - chr9:84955328 58.6 16240 277.2
23:43:05.273 INFO ProgressMeter - chr9:85025822 58.8 16270 276.9
23:43:17.138 INFO ProgressMeter - chr9:95458144 59.0 16330 277.0
23:43:27.743 INFO ProgressMeter - chr9:107487268 59.1 16390 277.1
23:43:39.987 INFO ProgressMeter - chr9:130885952 59.3 16450 277.2
23:43:52.231 INFO ProgressMeter - chr9:134525507 59.5 16500 277.1
23:44:03.740 INFO ProgressMeter - chr9:136518629 59.7 16560 277.2
23:44:15.795 INFO ProgressMeter - chrX:40064402 59.9 16640 277.6
23:44:26.730 INFO ProgressMeter - chrX:45069577 60.1 16690 277.6
23:44:36.969 INFO ProgressMeter - chrX:47566637 60.3 16750 277.8
23:44:47.808 INFO ProgressMeter - chrX:49034912 60.5 16800 277.8
23:44:57.904 INFO ProgressMeter - chrX:49038643 60.6 16830 277.5
23:45:07.961 INFO ProgressMeter - chrX:53380085 60.8 16880 277.6
23:45:19.035 INFO ProgressMeter - chrX:64185119 61.0 16920 277.4
23:45:32.190 INFO ProgressMeter - chrX:67549894 61.2 16960 277.1
23:45:44.472 INFO ProgressMeter - chrX:71123592 61.4 17020 277.1
23:45:55.267 INFO ProgressMeter - chrX:71141228 61.6 17060 277.0
23:46:07.216 INFO ProgressMeter - chrX:77523355 61.8 17120 277.0
23:46:18.120 INFO ProgressMeter - chrX:77682765 62.0 17160 276.9
23:46:28.934 INFO ProgressMeter - chrX:111144858 62.2 17210 276.9
23:46:40.386 INFO ProgressMeter - chrX:124066173 62.3 17260 276.8
23:46:50.734 INFO ProgressMeter - chrX:130050715 62.5 17310 276.9
23:46:54.543 INFO Mutect2 - 714815 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
14 read(s) filtered by: ReadLengthReadFilter
139 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
714968 total reads filtered out of 119618566 reads processed
23:46:54.543 INFO ProgressMeter - chrY:19564390 62.6 17369 277.5
23:46:54.543 INFO ProgressMeter - Traversal complete. Processed 17369 total regions in 62.6 minutes.
23:46:54.561 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 7.617617256000001
23:46:54.561 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 328.044810202
23:46:54.561 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 11.79 sec
23:46:54.562 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:46:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 62.60 minutes.
Runtime.totalMemory()=6501171200
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 LS0879_tumor.bam --tumor-sample LS0879 -L TST500C_manifest.bed -O LS0879.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:46:56.261 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
23:46:56.361 INFO FilterMutectCalls - ------------------------------------------------------------
23:46:56.363 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:46:56.363 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:46:56.363 INFO FilterMutectCalls - Executing as ?@nf-299e2ace16be94e966e13ee7116101a8-d0026-sfcjc on Linux v6.12.88 amd64
23:46:56.363 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:46:56.363 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:46:56 PM GMT
23:46:56.363 INFO FilterMutectCalls - ------------------------------------------------------------
23:46:56.364 INFO FilterMutectCalls - ------------------------------------------------------------
23:46:56.364 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:46:56.364 INFO FilterMutectCalls - Picard Version: 3.1.1
23:46:56.365 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:46:56.366 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:46:56.367 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:46:56.367 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:46:56.367 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:46:56.367 INFO FilterMutectCalls - Deflater: IntelDeflater
23:46:56.367 INFO FilterMutectCalls - Inflater: IntelInflater
23:46:56.367 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:46:56.367 INFO FilterMutectCalls - Requester pays: disabled
23:46:56.367 INFO FilterMutectCalls - Initializing engine
23:46:56.477 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.QfXX8pzALJ/LS0879.mutect2.raw.vcf.gz
23:46:56.577 INFO FilterMutectCalls - Done initializing engine
23:46:56.627 INFO ProgressMeter - Starting traversal
23:46:56.627 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:46:56.628 INFO FilterMutectCalls - Starting pass 0 through the variants
23:46:57.980 INFO FilterMutectCalls - Finished pass 0 through the variants
23:46:58.706 INFO FilterMutectCalls - Starting pass 1 through the variants
23:46:59.881 INFO FilterMutectCalls - Finished pass 1 through the variants
23:47:00.219 INFO FilterMutectCalls - Starting pass 2 through the variants
23:47:01.380 INFO FilterMutectCalls - Finished pass 2 through the variants
23:47:01.382 INFO FilterMutectCalls - Starting pass 3 through the variants
23:47:02.310 INFO FilterMutectCalls - Finished pass 3 through the variants
23:47:02.316 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:47:02.317 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:47:02.317 INFO ProgressMeter - chr7:55169590 0.1 10368 109328.6
23:47:02.317 INFO ProgressMeter - Traversal complete. Processed 10368 total variants in 0.1 minutes.
23:47:02.328 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:47:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.10 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 LS0879.mutect2.raw.vcf.gz --stats LS0879.mutect2.raw.vcf.gz.stats -O LS0879.mutect2.filtered.vcf.gz
23:47:03.553 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
23:47:03.672 INFO SelectVariants - ------------------------------------------------------------
23:47:03.674 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:47:03.674 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:47:03.674 INFO SelectVariants - Executing as ?@nf-299e2ace16be94e966e13ee7116101a8-d0026-sfcjc on Linux v6.12.88 amd64
23:47:03.674 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:47:03.675 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:47:03 PM GMT
23:47:03.675 INFO SelectVariants - ------------------------------------------------------------
23:47:03.675 INFO SelectVariants - ------------------------------------------------------------
23:47:03.675 INFO SelectVariants - HTSJDK Version: 4.1.0
23:47:03.676 INFO SelectVariants - Picard Version: 3.1.1
23:47:03.676 INFO SelectVariants - Built for Spark Version: 3.5.0
23:47:03.676 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:47:03.676 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:47:03.676 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:47:03.676 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:47:03.676 INFO SelectVariants - Deflater: IntelDeflater
23:47:03.676 INFO SelectVariants - Inflater: IntelInflater
23:47:03.676 INFO SelectVariants - GCS max retries/reopens: 20
23:47:03.676 INFO SelectVariants - Requester pays: disabled
23:47:03.677 INFO SelectVariants - Initializing engine
23:47:03.867 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.QfXX8pzALJ/LS0879.mutect2.filtered.vcf.gz
23:47:03.966 INFO SelectVariants - Done initializing engine
23:47:04.002 INFO ProgressMeter - Starting traversal
23:47:04.003 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:47:04.075 INFO ProgressMeter - chr6:156778268 0.0 2592 2221714.3
23:47:04.075 INFO ProgressMeter - Traversal complete. Processed 2592 total variants in 0.0 minutes.
23:47:04.085 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:47:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=310378496
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 LS0879.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0879.mutect2.pass.vcf.gz