Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/14/94c8d7435388eb97ef25efecc6775b/.command.sh
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0907/LS0907_tumor.bam.bai
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.fai
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Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/14/94c8d7435388eb97ef25efecc6775b/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:23.008 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
22:44:23.116 INFO Mutect2 - ------------------------------------------------------------
22:44:23.118 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:23.118 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:23.118 INFO Mutect2 - Executing as ?@nf-1494c8d7435388eb97ef25efecc6775b-4fa4a-c467l on Linux v6.12.88 amd64
22:44:23.118 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:23.119 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:22 PM GMT
22:44:23.119 INFO Mutect2 - ------------------------------------------------------------
22:44:23.119 INFO Mutect2 - ------------------------------------------------------------
22:44:23.119 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:23.120 INFO Mutect2 - Picard Version: 3.1.1
22:44:23.120 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:23.120 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:23.120 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:23.120 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:23.120 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:23.120 INFO Mutect2 - Deflater: IntelDeflater
22:44:23.120 INFO Mutect2 - Inflater: IntelInflater
22:44:23.120 INFO Mutect2 - GCS max retries/reopens: 20
22:44:23.120 INFO Mutect2 - Requester pays: disabled
22:44:23.121 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.XsPdLt3MU5/LS0907_tumor.bam.bai is older than BAM /tmp/nxf.XsPdLt3MU5/LS0907_tumor.bam
22:44:23.265 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.XsPdLt3MU5/af-only-gnomad.hg38.vcf.gz
22:44:23.379 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.XsPdLt3MU5/TST500C_manifest.bed
22:44:23.415 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:23.445 INFO Mutect2 - Done initializing engine
22:44:23.455 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
22:44:23.457 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
22:44:23.458 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:23.458 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:23.467 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
22:44:23.475 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:23.475 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:23.476 INFO IntelPairHmm - Available threads: 384
22:44:23.476 INFO IntelPairHmm - Requested threads: 4
22:44:23.476 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:23.508 INFO ProgressMeter - Starting traversal
22:44:23.509 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:34.301 INFO ProgressMeter - chr1:9720742 0.2 50 278.0
22:44:44.399 INFO ProgressMeter - chr1:11213440 0.3 130 373.4
22:44:55.897 INFO ProgressMeter - chr1:15929273 0.5 190 352.0
22:45:07.250 INFO ProgressMeter - chr1:15935748 0.7 240 329.2
22:45:20.046 INFO ProgressMeter - chr1:18747491 0.9 310 329.0
22:45:32.021 INFO ProgressMeter - chr1:26779688 1.1 380 332.8
22:45:43.024 INFO ProgressMeter - chr1:39898701 1.3 460 347.1
22:45:53.383 INFO ProgressMeter - chr1:45333411 1.5 530 353.8
22:46:04.521 INFO ProgressMeter - chr1:64838513 1.7 620 368.3
22:46:15.384 INFO ProgressMeter - chr1:85270616 1.9 700 375.4
22:46:26.812 INFO ProgressMeter - chr1:119514454 2.1 780 379.6
22:46:38.353 INFO ProgressMeter - chr1:119967487 2.2 840 373.8
22:46:53.780 INFO ProgressMeter - chr1:156873119 2.5 890 355.4
22:47:05.324 INFO ProgressMeter - chr1:158611262 2.7 920 341.1
22:47:17.436 INFO ProgressMeter - chr1:158656605 2.9 980 338.1
22:47:28.371 INFO ProgressMeter - chr1:162767229 3.1 1040 337.5
22:47:39.617 INFO ProgressMeter - chr1:179110280 3.3 1100 336.5
22:47:49.889 INFO ProgressMeter - chr1:204443415 3.4 1170 340.1
22:47:59.942 INFO ProgressMeter - chr1:204525193 3.6 1220 338.2
22:48:10.933 INFO ProgressMeter - chr1:206474407 3.8 1270 335.1
22:48:22.751 INFO ProgressMeter - chr1:226390542 4.0 1340 336.1
22:48:34.510 INFO ProgressMeter - chr1:243501303 4.2 1390 332.3
22:48:47.803 INFO ProgressMeter - chr1:243545508 4.4 1420 322.4
22:48:59.909 INFO ProgressMeter - chr10:27039944 4.6 1490 323.4
22:49:10.443 INFO ProgressMeter - chr10:32017166 4.8 1550 324.1
22:49:21.469 INFO ProgressMeter - chr10:43112817 5.0 1620 326.2
22:49:33.106 INFO ProgressMeter - chr10:43117948 5.2 1660 321.7
22:49:44.736 INFO ProgressMeter - chr10:68572759 5.4 1720 321.3
22:49:55.363 INFO ProgressMeter - chr10:86912309 5.5 1770 320.0
22:50:07.380 INFO ProgressMeter - chr10:101770750 5.7 1850 322.8
22:50:18.405 INFO ProgressMeter - chr10:110598118 5.9 1940 328.0
22:50:30.563 INFO ProgressMeter - chr10:121481456 6.1 2010 328.6
22:50:41.713 INFO ProgressMeter - chr10:121562590 6.3 2070 328.4
22:50:51.728 INFO ProgressMeter - chr11:32435012 6.5 2150 332.3
22:51:02.475 INFO ProgressMeter - chr11:69648273 6.6 2250 338.4
22:51:14.119 INFO ProgressMeter - chr11:69701918 6.8 2310 337.5
22:51:24.649 INFO ProgressMeter - chr11:69777060 7.0 2380 339.1
22:51:36.523 INFO ProgressMeter - chr11:69814432 7.2 2410 333.9
22:51:46.612 INFO ProgressMeter - chr11:76537793 7.4 2470 334.5
22:51:57.539 INFO ProgressMeter - chr11:77358898 7.6 2520 333.0
22:52:07.613 INFO ProgressMeter - chr11:77452710 7.7 2570 332.3
22:52:17.624 INFO ProgressMeter - chr11:101127806 7.9 2640 334.1
22:52:27.825 INFO ProgressMeter - chr11:102331174 8.1 2680 332.0
22:52:38.322 INFO ProgressMeter - chr11:108325330 8.2 2750 333.5
22:52:49.896 INFO ProgressMeter - chr11:118474026 8.4 2810 332.9
22:53:00.285 INFO ProgressMeter - chr11:118504379 8.6 2860 332.1
22:53:11.124 INFO ProgressMeter - chr11:119285246 8.8 2910 330.9
22:53:21.245 INFO ProgressMeter - chr11:125644089 9.0 2950 329.2
22:53:38.405 INFO ProgressMeter - chr11:128460805 9.2 3000 324.4
22:53:49.070 INFO ProgressMeter - chr11:128768116 9.4 3040 322.5
22:54:00.480 INFO ProgressMeter - chr12:313054 9.6 3090 321.3
22:54:10.812 INFO ProgressMeter - chr12:4370915 9.8 3160 322.8
22:54:20.892 INFO ProgressMeter - chr12:4436116 10.0 3210 322.4
22:54:31.136 INFO ProgressMeter - chr12:6577850 10.1 3250 320.9
22:54:42.745 INFO ProgressMeter - chr12:6606272 10.3 3310 320.7
22:54:55.611 INFO ProgressMeter - chr12:11857457 10.5 3350 318.0
22:55:08.257 INFO ProgressMeter - chr12:11861272 10.7 3380 314.5
22:55:21.598 INFO ProgressMeter - chr12:11867574 11.0 3420 311.8
22:55:31.857 INFO ProgressMeter - chr12:18391120 11.1 3470 311.5
22:55:43.089 INFO ProgressMeter - chr12:25236915 11.3 3530 311.7
22:55:54.834 INFO ProgressMeter - chr12:45850610 11.5 3590 311.6
22:56:06.337 INFO ProgressMeter - chr12:49028826 11.7 3640 310.7
22:56:17.471 INFO ProgressMeter - chr12:49033811 11.9 3680 309.3
22:56:27.597 INFO ProgressMeter - chr12:49043361 12.1 3730 309.1
22:56:37.919 INFO ProgressMeter - chr12:50086754 12.2 3790 309.6
22:56:48.740 INFO ProgressMeter - chr12:56093501 12.4 3860 310.8
22:56:59.648 INFO ProgressMeter - chr12:57093901 12.6 3920 311.1
22:57:11.116 INFO ProgressMeter - chr12:57748262 12.8 3980 311.1
22:57:21.725 INFO ProgressMeter - chr12:68836415 13.0 4050 312.3
22:57:32.328 INFO ProgressMeter - chr12:105934409 13.1 4100 311.9
22:57:43.013 INFO ProgressMeter - chr12:120116597 13.3 4170 312.9
22:57:53.656 INFO ProgressMeter - chr12:132649675 13.5 4230 313.3
22:58:04.010 INFO ProgressMeter - chr13:20983405 13.7 4290 313.7
22:58:15.104 INFO ProgressMeter - chr13:26349070 13.9 4360 314.6
22:58:26.024 INFO ProgressMeter - chr13:28339166 14.0 4430 315.5
22:58:37.779 INFO ProgressMeter - chr13:28389188 14.2 4470 314.0
22:58:49.631 INFO ProgressMeter - chr13:32337789 14.4 4530 313.8
22:59:00.071 INFO ProgressMeter - chr13:32379488 14.6 4580 313.5
22:59:10.309 INFO ProgressMeter - chr13:72761921 14.8 4660 315.3
22:59:21.442 INFO ProgressMeter - chr13:102401469 15.0 4740 316.7
22:59:31.494 INFO ProgressMeter - chr13:109783998 15.1 4800 317.2
22:59:44.505 INFO ProgressMeter - chr14:28567526 15.3 4870 317.3
22:59:56.092 INFO ProgressMeter - chr14:37591363 15.5 4930 317.2
23:00:06.559 INFO ProgressMeter - chr14:65076602 15.7 4990 317.5
23:00:16.853 INFO ProgressMeter - chr14:95095770 15.9 5050 317.8
23:00:27.327 INFO ProgressMeter - chr14:102085354 16.1 5110 318.1
23:00:40.780 INFO ProgressMeter - chr15:34347730 16.3 5170 317.4
23:00:53.546 INFO ProgressMeter - chr15:41696073 16.5 5230 317.0
23:01:05.078 INFO ProgressMeter - chr15:41750123 16.7 5280 316.3
23:01:15.661 INFO ProgressMeter - chr15:49453215 16.9 5340 316.6
23:01:26.587 INFO ProgressMeter - chr15:87977363 17.1 5420 317.9
23:01:37.404 INFO ProgressMeter - chr15:89292686 17.2 5480 318.0
23:01:48.076 INFO ProgressMeter - chr15:90762964 17.4 5540 318.2
23:01:59.186 INFO ProgressMeter - chr15:92985496 17.6 5610 318.8
23:02:10.496 INFO ProgressMeter - chr15:98923874 17.8 5670 318.8
23:02:20.960 INFO ProgressMeter - chr16:2048614 18.0 5720 318.5
23:02:30.994 INFO ProgressMeter - chr16:2173970 18.1 5800 320.0
23:02:41.168 INFO ProgressMeter - chr16:3597585 18.3 5870 320.9
23:02:52.049 INFO ProgressMeter - chr16:3758852 18.5 5920 320.4
23:03:02.560 INFO ProgressMeter - chr16:9764416 18.7 5970 320.1
23:03:12.857 INFO ProgressMeter - chr16:13935442 18.8 6020 319.8
23:03:23.320 INFO ProgressMeter - chr16:23641108 19.0 6060 319.0
23:03:33.588 INFO ProgressMeter - chr16:56833213 19.2 6130 319.8
23:03:44.705 INFO ProgressMeter - chr16:72787277 19.4 6200 320.4
23:03:55.429 INFO ProgressMeter - chr16:72796678 19.5 6240 319.5
23:04:08.122 INFO ProgressMeter - chr16:72959453 19.7 6290 318.6
23:04:18.666 INFO ProgressMeter - chr16:89280438 19.9 6360 319.3
23:04:30.950 INFO ProgressMeter - chr16:89284929 20.1 6400 318.0
23:04:41.326 INFO ProgressMeter - chr16:89814518 20.3 6480 319.3
23:04:51.745 INFO ProgressMeter - chr17:7674917 20.5 6530 319.0
23:05:02.738 INFO ProgressMeter - chr17:8207335 20.7 6590 319.1
23:05:14.641 INFO ProgressMeter - chr17:16101248 20.9 6660 319.4
23:05:25.825 INFO ProgressMeter - chr17:18054125 21.0 6730 319.9
23:05:36.878 INFO ProgressMeter - chr17:31330294 21.2 6790 319.9
23:05:47.408 INFO ProgressMeter - chr17:39462312 21.4 6860 320.6
23:05:57.944 INFO ProgressMeter - chr17:39701942 21.6 6910 320.3
23:06:08.950 INFO ProgressMeter - chr17:40352419 21.8 6970 320.4
23:06:19.130 INFO ProgressMeter - chr17:42210490 21.9 7040 321.1
23:06:29.691 INFO ProgressMeter - chr17:43049325 22.1 7120 322.1
23:06:41.521 INFO ProgressMeter - chr17:43092797 22.3 7170 321.5
23:06:52.333 INFO ProgressMeter - chr17:43530105 22.5 7220 321.2
23:07:05.439 INFO ProgressMeter - chr17:43536808 22.7 7270 320.3
23:07:16.195 INFO ProgressMeter - chr17:43542269 22.9 7310 319.5
23:07:26.560 INFO ProgressMeter - chr17:43544546 23.1 7330 318.0
23:07:36.683 INFO ProgressMeter - chr17:49611278 23.2 7390 318.3
23:07:48.065 INFO ProgressMeter - chr17:59896137 23.4 7450 318.3
23:08:01.261 INFO ProgressMeter - chr17:59947148 23.6 7510 317.8
23:08:11.976 INFO ProgressMeter - chr17:61776534 23.8 7560 317.5
23:08:23.913 INFO ProgressMeter - chr17:68515398 24.0 7620 317.4
23:08:34.334 INFO ProgressMeter - chr17:80892727 24.2 7690 318.0
23:08:44.621 INFO ProgressMeter - chr18:22200725 24.4 7760 318.7
23:08:55.333 INFO ProgressMeter - chr18:44951717 24.5 7820 318.8
23:09:06.010 INFO ProgressMeter - chr18:58735200 24.7 7890 319.3
23:09:16.840 INFO ProgressMeter - chr19:2202698 24.9 7970 320.2
23:09:27.510 INFO ProgressMeter - chr19:4097290 25.1 8050 321.1
23:09:37.605 INFO ProgressMeter - chr19:5245902 25.2 8120 321.8
23:09:47.654 INFO ProgressMeter - chr19:7267671 25.4 8180 322.0
23:09:58.955 INFO ProgressMeter - chr19:10491983 25.6 8250 322.4
23:10:09.834 INFO ProgressMeter - chr19:11060043 25.8 8320 322.8
23:10:20.147 INFO ProgressMeter - chr19:15177537 25.9 8370 322.6
23:10:30.951 INFO ProgressMeter - chr19:15239657 26.1 8430 322.7
23:10:44.533 INFO ProgressMeter - chr19:18156158 26.4 8500 322.6
23:10:56.227 INFO ProgressMeter - chr19:29816477 26.5 8560 322.5
23:11:07.761 INFO ProgressMeter - chr19:35721560 26.7 8620 322.4
23:11:18.939 INFO ProgressMeter - chr19:35736688 26.9 8690 322.8
23:11:30.131 INFO ProgressMeter - chr19:41226909 27.1 8760 323.1
23:11:40.876 INFO ProgressMeter - chr19:41261623 27.3 8800 322.5
23:11:51.336 INFO ProgressMeter - chr19:45353240 27.5 8870 323.0
23:12:02.488 INFO ProgressMeter - chr19:45416700 27.6 8950 323.7
23:12:16.368 INFO ProgressMeter - chr2:15936270 27.9 9040 324.2
23:12:27.421 INFO ProgressMeter - chr2:17772723 28.1 9100 324.2
23:12:39.252 INFO ProgressMeter - chr2:25282195 28.3 9160 324.1
23:12:49.307 INFO ProgressMeter - chr2:26786206 28.4 9210 324.0
23:13:02.659 INFO ProgressMeter - chr2:29224673 28.7 9260 323.2
23:13:13.350 INFO ProgressMeter - chr2:29251103 28.8 9290 322.2
23:13:23.637 INFO ProgressMeter - chr2:42280848 29.0 9340 322.0
23:13:35.019 INFO ProgressMeter - chr2:47412412 29.2 9400 322.0
23:13:47.745 INFO ProgressMeter - chr2:47799606 29.4 9440 321.0
23:13:58.092 INFO ProgressMeter - chr2:61478818 29.6 9500 321.2
23:14:09.078 INFO ProgressMeter - chr2:98520047 29.8 9540 320.6
23:14:19.675 INFO ProgressMeter - chr2:108763235 29.9 9610 321.0
23:14:30.258 INFO ProgressMeter - chr2:108782576 30.1 9660 320.8
23:14:46.241 INFO ProgressMeter - chr2:111128517 30.4 9690 319.0
23:14:59.889 INFO ProgressMeter - chr2:113223598 30.6 9730 317.9
23:15:13.306 INFO ProgressMeter - chr2:113227387 30.8 9760 316.6
23:15:24.819 INFO ProgressMeter - chr2:113231109 31.0 9790 315.6
23:15:39.923 INFO ProgressMeter - chr2:113234587 31.3 9820 314.0
23:15:51.207 INFO ProgressMeter - chr2:136117025 31.5 9890 314.4
23:16:02.829 INFO ProgressMeter - chr2:140700473 31.7 9970 315.0
23:16:13.347 INFO ProgressMeter - chr2:141810277 31.8 10040 315.4
23:16:24.229 INFO ProgressMeter - chr2:189877270 32.0 10110 315.8
23:16:34.557 INFO ProgressMeter - chr2:201272636 32.2 10190 316.6
23:16:45.906 INFO ProgressMeter - chr2:214728731 32.4 10270 317.2
23:16:56.273 INFO ProgressMeter - chr2:222201277 32.5 10320 317.1
23:17:07.383 INFO ProgressMeter - chr2:222206632 32.7 10360 316.5
23:17:19.399 INFO ProgressMeter - chr2:222212574 32.9 10400 315.8
23:17:32.003 INFO ProgressMeter - chr2:222217229 33.1 10440 315.0
23:17:42.366 INFO ProgressMeter - chr2:222294290 33.3 10480 314.6
23:17:52.608 INFO ProgressMeter - chr2:226798055 33.5 10540 314.8
23:18:03.277 INFO ProgressMeter - chr20:32429992 33.7 10600 314.9
23:18:14.421 INFO ProgressMeter - chr20:32436929 33.8 10640 314.3
23:18:25.329 INFO ProgressMeter - chr20:41112898 34.0 10720 315.0
23:18:36.453 INFO ProgressMeter - chr20:47635369 34.2 10790 315.4
23:18:47.789 INFO ProgressMeter - chr20:53571742 34.4 10820 314.5
23:18:58.287 INFO ProgressMeter - chr20:58853894 34.6 10870 314.3
23:19:10.899 INFO ProgressMeter - chr21:38382094 34.8 10950 314.7
23:19:22.855 INFO ProgressMeter - chr21:41465360 35.0 11000 314.4
23:19:36.082 INFO ProgressMeter - chr21:41490935 35.2 11040 313.6
23:19:47.916 INFO ProgressMeter - chr21:41494445 35.4 11070 312.7
23:20:00.573 INFO ProgressMeter - chr21:41503172 35.6 11110 311.9
23:20:12.388 INFO ProgressMeter - chr21:41507291 35.8 11150 311.3
23:20:23.339 INFO ProgressMeter - chr22:20996913 36.0 11230 312.0
23:20:36.497 INFO ProgressMeter - chr22:23291494 36.2 11290 311.7
23:20:46.528 INFO ProgressMeter - chr22:28718148 36.4 11360 312.2
23:20:57.004 INFO ProgressMeter - chr22:29286023 36.6 11430 312.7
23:21:08.045 INFO ProgressMeter - chr22:37973732 36.7 11490 312.7
23:21:18.908 INFO ProgressMeter - chr22:41177234 36.9 11560 313.1
23:21:29.538 INFO ProgressMeter - chr3:10093283 37.1 11630 313.5
23:21:41.677 INFO ProgressMeter - chr3:12356308 37.3 11680 313.1
23:21:54.581 INFO ProgressMeter - chr3:12360530 37.5 11710 312.1
23:22:06.706 INFO ProgressMeter - chr3:12366817 37.7 11760 311.8
23:22:18.784 INFO ProgressMeter - chr3:12373238 37.9 11800 311.2
23:22:31.082 INFO ProgressMeter - chr3:12379585 38.1 11850 310.8
23:22:43.268 INFO ProgressMeter - chr3:12649729 38.3 11910 310.7
23:22:54.155 INFO ProgressMeter - chr3:41236586 38.5 11990 311.3
23:23:05.098 INFO ProgressMeter - chr3:47122220 38.7 12050 311.4
23:23:16.263 INFO ProgressMeter - chr3:49895713 38.9 12120 311.7
23:23:28.176 INFO ProgressMeter - chr3:52603653 39.1 12200 312.2
23:23:38.360 INFO ProgressMeter - chr3:71198200 39.2 12280 312.9
23:23:49.176 INFO ProgressMeter - chr3:119947266 39.4 12350 313.2
23:24:00.669 INFO ProgressMeter - chr3:136340470 39.6 12410 313.2
23:24:12.332 INFO ProgressMeter - chr3:138684734 39.8 12470 313.2
23:24:23.281 INFO ProgressMeter - chr3:142457699 40.0 12530 313.3
23:24:33.882 INFO ProgressMeter - chr3:142558622 40.2 12580 313.1
23:24:44.589 INFO ProgressMeter - chr3:179185529 40.4 12640 313.2
23:24:55.425 INFO ProgressMeter - chr3:181712689 40.5 12690 313.1
23:25:06.150 INFO ProgressMeter - chr3:185466844 40.7 12740 312.9
23:25:17.549 INFO ProgressMeter - chr3:186047519 40.9 12770 312.2
23:25:27.851 INFO ProgressMeter - chr3:187726729 41.1 12820 312.1
23:25:37.942 INFO ProgressMeter - chr3:196051144 41.2 12870 312.1
23:25:49.641 INFO ProgressMeter - chr3:196076111 41.4 12920 311.8
23:25:59.907 INFO ProgressMeter - chr4:20541451 41.6 13010 312.7
23:26:10.617 INFO ProgressMeter - chr4:54243096 41.8 13080 313.0
23:26:23.020 INFO ProgressMeter - chr4:54295123 42.0 13130 312.7
23:26:40.457 INFO ProgressMeter - chr4:54733068 42.3 13180 311.7
23:26:51.719 INFO ProgressMeter - chr4:65353040 42.5 13240 311.7
23:27:01.893 INFO ProgressMeter - chr4:80283144 42.6 13300 311.9
23:27:13.203 INFO ProgressMeter - chr4:105236639 42.8 13360 311.9
23:27:24.129 INFO ProgressMeter - chr4:105275046 43.0 13410 311.8
23:27:35.185 INFO ProgressMeter - chr4:142237909 43.2 13490 312.3
23:27:46.100 INFO ProgressMeter - chr4:186597970 43.4 13560 312.6
23:27:56.685 INFO ProgressMeter - chr4:186619307 43.6 13610 312.5
23:28:09.759 INFO ProgressMeter - chr4:186708831 43.8 13660 312.1
23:28:19.776 INFO ProgressMeter - chr5:38945489 43.9 13720 312.3
23:28:30.991 INFO ProgressMeter - chr5:44352931 44.1 13800 312.8
23:28:42.044 INFO ProgressMeter - chr5:58456142 44.3 13870 313.0
23:28:52.333 INFO ProgressMeter - chr5:87337972 44.5 13960 313.8
23:29:04.728 INFO ProgressMeter - chr5:112841097 44.7 14030 314.0
23:29:16.365 INFO ProgressMeter - chr5:122451405 44.9 14080 313.7
23:29:27.243 INFO ProgressMeter - chr5:142600700 45.1 14160 314.2
23:29:38.382 INFO ProgressMeter - chr5:150054320 45.2 14220 314.3
23:29:48.548 INFO ProgressMeter - chr5:150133879 45.4 14290 314.6
23:29:59.370 INFO ProgressMeter - chr5:161692103 45.6 14350 314.7
23:30:10.626 INFO ProgressMeter - chr5:177093136 45.8 14410 314.7
23:30:22.868 INFO ProgressMeter - chr5:177210460 46.0 14460 314.4
23:30:32.960 INFO ProgressMeter - chr5:177295368 46.2 14510 314.4
23:30:43.547 INFO ProgressMeter - chr6:393270 46.3 14600 315.1
23:30:54.203 INFO ProgressMeter - chr6:20486934 46.5 14680 315.6
23:31:07.956 INFO ProgressMeter - chr6:30702551 46.7 14760 315.8
23:31:19.174 INFO ProgressMeter - chr6:32198419 46.9 14820 315.8
23:31:29.273 INFO ProgressMeter - chr6:33320457 47.1 14880 315.9
23:31:40.724 INFO ProgressMeter - chr6:41955850 47.3 14960 316.4
23:31:52.588 INFO ProgressMeter - chr6:89080893 47.5 15020 316.3
23:32:03.062 INFO ProgressMeter - chr6:106106993 47.7 15090 316.6
23:32:14.618 INFO ProgressMeter - chr6:117320383 47.9 15150 316.6
23:32:25.329 INFO ProgressMeter - chr6:117324147 48.0 15180 316.1
23:32:36.007 INFO ProgressMeter - chr6:117329600 48.2 15220 315.7
23:32:48.909 INFO ProgressMeter - chr6:117338504 48.4 15280 315.6
23:33:00.131 INFO ProgressMeter - chr6:117394614 48.6 15340 315.6
23:33:11.306 INFO ProgressMeter - chr6:135206061 48.8 15400 315.6
23:33:21.332 INFO ProgressMeter - chr6:135210625 49.0 15440 315.3
23:33:31.523 INFO ProgressMeter - chr6:135212044 49.1 15450 314.4
23:33:42.920 INFO ProgressMeter - chr6:135214676 49.3 15470 313.6
23:33:53.090 INFO ProgressMeter - chr6:137877074 49.5 15510 313.4
23:34:03.967 INFO ProgressMeter - chr6:151366885 49.7 15560 313.2
23:34:14.187 INFO ProgressMeter - chr6:156778127 49.8 15620 313.4
23:34:26.900 INFO ProgressMeter - chr6:161049905 50.1 15690 313.4
23:34:36.935 INFO ProgressMeter - chr7:2912199 50.2 15770 314.0
23:34:48.441 INFO ProgressMeter - chr7:13891636 50.4 15840 314.2
23:34:59.425 INFO ProgressMeter - chr7:13906597 50.6 15880 313.8
23:35:16.613 INFO ProgressMeter - chr7:13909510 50.9 15910 312.7
23:35:26.867 INFO ProgressMeter - chr7:13933949 51.1 15940 312.2
23:35:38.203 INFO ProgressMeter - chr7:13939793 51.2 15980 311.8
23:35:49.728 INFO ProgressMeter - chr7:13944213 51.4 16020 311.4
23:36:01.392 INFO ProgressMeter - chr7:13947810 51.6 16050 310.9
23:36:15.312 INFO ProgressMeter - chr7:13951559 51.9 16080 310.0
23:36:27.193 INFO ProgressMeter - chr7:13956265 52.1 16110 309.4
23:36:39.506 INFO ProgressMeter - chr7:13960536 52.3 16140 308.8
23:36:52.647 INFO ProgressMeter - chr7:13965123 52.5 16170 308.1
23:37:04.585 INFO ProgressMeter - chr7:13971059 52.7 16210 307.7
23:37:22.570 INFO ProgressMeter - chr7:13976245 53.0 16250 306.7
23:37:33.996 INFO ProgressMeter - chr7:13981129 53.2 16290 306.3
23:37:45.600 INFO ProgressMeter - chr7:13984809 53.4 16320 305.8
23:37:57.560 INFO ProgressMeter - chr7:13988523 53.6 16340 305.0
23:38:08.489 INFO ProgressMeter - chr7:55143306 53.7 16400 305.1
23:38:19.688 INFO ProgressMeter - chr7:55163731 53.9 16440 304.8
23:38:32.419 INFO ProgressMeter - chr7:55169702 54.1 16470 304.2
23:38:43.151 INFO ProgressMeter - chr7:55176993 54.3 16510 303.9
23:38:55.065 INFO ProgressMeter - chr7:55181196 54.5 16550 303.5
23:39:05.391 INFO ProgressMeter - chr7:78135117 54.7 16600 303.5
23:39:17.653 INFO ProgressMeter - chr7:86839137 54.9 16670 303.6
23:39:28.228 INFO ProgressMeter - chr7:92829963 55.1 16720 303.6
23:39:39.767 INFO ProgressMeter - chr7:102248793 55.3 16770 303.4
23:39:50.323 INFO ProgressMeter - chr7:106905198 55.4 16820 303.4
23:40:00.447 INFO ProgressMeter - chr7:116774988 55.6 16870 303.3
23:40:11.260 INFO ProgressMeter - chr7:140776910 55.8 16930 303.4
23:40:21.329 INFO ProgressMeter - chr7:140793048 56.0 16980 303.4
23:40:31.610 INFO ProgressMeter - chr7:142944321 56.1 17050 303.7
23:40:42.177 INFO ProgressMeter - chr7:152148833 56.3 17120 304.0
23:40:54.941 INFO ProgressMeter - chr7:152177938 56.5 17170 303.8
23:41:06.185 INFO ProgressMeter - chr7:152248338 56.7 17230 303.8
23:41:16.582 INFO ProgressMeter - chr8:31639983 56.9 17310 304.3
23:41:28.059 INFO ProgressMeter - chr8:32727947 57.1 17370 304.3
23:41:38.818 INFO ProgressMeter - chr8:37841470 57.3 17450 304.8
23:41:49.484 INFO ProgressMeter - chr8:41933320 57.4 17520 305.1
23:42:00.110 INFO ProgressMeter - chr8:47778726 57.6 17580 305.2
23:42:10.577 INFO ProgressMeter - chr8:47879543 57.8 17650 305.4
23:42:20.914 INFO ProgressMeter - chr8:55946446 58.0 17720 305.7
23:42:31.618 INFO ProgressMeter - chr8:68138413 58.1 17790 306.0
23:42:42.463 INFO ProgressMeter - chr8:116854243 58.3 17870 306.4
23:42:53.241 INFO ProgressMeter - chr8:127738983 58.5 17920 306.3
23:43:03.608 INFO ProgressMeter - chr8:144516627 58.7 17990 306.6
23:43:14.131 INFO ProgressMeter - chr9:5467838 58.8 18060 306.9
23:43:25.552 INFO ProgressMeter - chr9:8518214 59.0 18120 306.9
23:43:36.156 INFO ProgressMeter - chr9:22012092 59.2 18180 307.0
23:43:46.469 INFO ProgressMeter - chr9:83971861 59.4 18240 307.2
23:43:58.648 INFO ProgressMeter - chr9:84742875 59.6 18280 306.8
23:44:11.532 INFO ProgressMeter - chr9:84812728 59.8 18320 306.4
23:44:22.663 INFO ProgressMeter - chr9:84861038 60.0 18340 305.7
23:44:35.634 INFO ProgressMeter - chr9:84864681 60.2 18370 305.1
23:44:47.162 INFO ProgressMeter - chr9:84873766 60.4 18400 304.7
23:44:57.730 INFO ProgressMeter - chr9:84877458 60.6 18430 304.3
23:45:08.103 INFO ProgressMeter - chr9:85023629 60.7 18460 303.9
23:45:20.017 INFO ProgressMeter - chr9:90845528 60.9 18490 303.4
23:45:31.325 INFO ProgressMeter - chr9:95468780 61.1 18550 303.5
23:45:42.862 INFO ProgressMeter - chr9:125153531 61.3 18620 303.6
23:45:55.244 INFO ProgressMeter - chr9:130887235 61.5 18680 303.6
23:46:05.818 INFO ProgressMeter - chr9:136497134 61.7 18730 303.5
23:46:16.111 INFO ProgressMeter - chr9:136519441 61.9 18800 303.8
23:46:28.087 INFO ProgressMeter - chrX:40074506 62.1 18900 304.5
23:46:38.397 INFO ProgressMeter - chrX:49029066 62.2 19020 305.6
23:46:48.706 INFO ProgressMeter - chrX:53198516 62.4 19100 306.0
23:47:00.976 INFO ProgressMeter - chrX:64191002 62.6 19180 306.3
23:47:12.092 INFO ProgressMeter - chrX:67723730 62.8 19260 306.6
23:47:22.398 INFO ProgressMeter - chrX:71383960 63.0 19340 307.1
23:47:33.065 INFO ProgressMeter - chrX:101356050 63.2 19440 307.8
23:47:44.039 INFO ProgressMeter - chrX:130015539 63.3 19550 308.6
23:47:52.136 INFO Mutect2 - 721961 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
0 read(s) filtered by: ReadLengthReadFilter
90 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
722051 total reads filtered out of 103542076 reads processed
23:47:52.137 INFO ProgressMeter - chrY:20960482 63.5 19641 309.4
23:47:52.137 INFO ProgressMeter - Traversal complete. Processed 19641 total regions in 63.5 minutes.
23:47:52.152 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 7.714521820000001
23:47:52.153 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 331.02150924100005
23:47:52.153 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 11.38 sec
23:47:52.153 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:47:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 63.49 minutes.
Runtime.totalMemory()=5007998976
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 LS0907_tumor.bam --tumor-sample LS0907 -L TST500C_manifest.bed -O LS0907.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:47:53.618 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
23:47:53.734 INFO FilterMutectCalls - ------------------------------------------------------------
23:47:53.737 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:47:53.737 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:47:53.737 INFO FilterMutectCalls - Executing as ?@nf-1494c8d7435388eb97ef25efecc6775b-4fa4a-c467l on Linux v6.12.88 amd64
23:47:53.737 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:47:53.738 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:47:53 PM GMT
23:47:53.738 INFO FilterMutectCalls - ------------------------------------------------------------
23:47:53.738 INFO FilterMutectCalls - ------------------------------------------------------------
23:47:53.739 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:47:53.739 INFO FilterMutectCalls - Picard Version: 3.1.1
23:47:53.739 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:47:53.739 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:47:53.739 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:47:53.739 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:47:53.740 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:47:53.740 INFO FilterMutectCalls - Deflater: IntelDeflater
23:47:53.740 INFO FilterMutectCalls - Inflater: IntelInflater
23:47:53.740 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:47:53.740 INFO FilterMutectCalls - Requester pays: disabled
23:47:53.740 INFO FilterMutectCalls - Initializing engine
23:47:53.941 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.XsPdLt3MU5/LS0907.mutect2.raw.vcf.gz
23:47:54.055 INFO FilterMutectCalls - Done initializing engine
23:47:54.110 INFO ProgressMeter - Starting traversal
23:47:54.111 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:47:54.112 INFO FilterMutectCalls - Starting pass 0 through the variants
23:47:55.536 INFO FilterMutectCalls - Finished pass 0 through the variants
23:47:57.801 INFO FilterMutectCalls - Starting pass 1 through the variants
23:47:59.137 INFO FilterMutectCalls - Finished pass 1 through the variants
23:47:59.838 INFO FilterMutectCalls - Starting pass 2 through the variants
23:48:01.139 INFO FilterMutectCalls - Finished pass 2 through the variants
23:48:01.141 INFO FilterMutectCalls - Starting pass 3 through the variants
23:48:02.225 INFO FilterMutectCalls - Finished pass 3 through the variants
23:48:02.234 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:48:02.234 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:48:02.235 INFO ProgressMeter - chr9:20414279 0.1 11200 82717.9
23:48:02.235 INFO ProgressMeter - Traversal complete. Processed 11200 total variants in 0.1 minutes.
23:48:02.245 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:48:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=226492416
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 LS0907.mutect2.raw.vcf.gz --stats LS0907.mutect2.raw.vcf.gz.stats -O LS0907.mutect2.filtered.vcf.gz
23:48:03.392 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
23:48:03.500 INFO SelectVariants - ------------------------------------------------------------
23:48:03.502 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:48:03.502 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:48:03.502 INFO SelectVariants - Executing as ?@nf-1494c8d7435388eb97ef25efecc6775b-4fa4a-c467l on Linux v6.12.88 amd64
23:48:03.503 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:48:03.503 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:48:03 PM GMT
23:48:03.503 INFO SelectVariants - ------------------------------------------------------------
23:48:03.503 INFO SelectVariants - ------------------------------------------------------------
23:48:03.504 INFO SelectVariants - HTSJDK Version: 4.1.0
23:48:03.504 INFO SelectVariants - Picard Version: 3.1.1
23:48:03.504 INFO SelectVariants - Built for Spark Version: 3.5.0
23:48:03.504 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:48:03.504 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:48:03.504 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:48:03.504 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:48:03.505 INFO SelectVariants - Deflater: IntelDeflater
23:48:03.505 INFO SelectVariants - Inflater: IntelInflater
23:48:03.505 INFO SelectVariants - GCS max retries/reopens: 20
23:48:03.505 INFO SelectVariants - Requester pays: disabled
23:48:03.505 INFO SelectVariants - Initializing engine
23:48:03.678 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.XsPdLt3MU5/LS0907.mutect2.filtered.vcf.gz
23:48:03.796 INFO SelectVariants - Done initializing engine
23:48:03.836 INFO ProgressMeter - Starting traversal
23:48:03.837 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:48:03.920 INFO ProgressMeter - chr6:29943542 0.0 2800 2074074.1
23:48:03.920 INFO ProgressMeter - Traversal complete. Processed 2800 total variants in 0.0 minutes.
23:48:03.932 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:48:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 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 SelectVariants -R hg38.fa -V LS0907.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0907.mutect2.pass.vcf.gz