Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0884/LS0884_tumor.bam
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/0b/548db5276f3cd7ae6e45b4cbf4328e/.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/0b/548db5276f3cd7ae6e45b4cbf4328e/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0884/LS0884_tumor.bam.bai
==> STAGING COMPLETE (10 inputs)
22:44:29.768 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
22:44:29.880 INFO Mutect2 - ------------------------------------------------------------
22:44:29.882 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:29.882 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:29.882 INFO Mutect2 - Executing as ?@nf-0b548db5276f3cd7ae6e45b4cbf4328e-7545f-lj264 on Linux v6.12.88 amd64
22:44:29.882 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:29.882 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:29 PM GMT
22:44:29.882 INFO Mutect2 - ------------------------------------------------------------
22:44:29.882 INFO Mutect2 - ------------------------------------------------------------
22:44:29.883 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:29.883 INFO Mutect2 - Picard Version: 3.1.1
22:44:29.883 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:29.883 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:29.883 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:29.883 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:29.883 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:29.883 INFO Mutect2 - Deflater: IntelDeflater
22:44:29.884 INFO Mutect2 - Inflater: IntelInflater
22:44:29.884 INFO Mutect2 - GCS max retries/reopens: 20
22:44:29.884 INFO Mutect2 - Requester pays: disabled
22:44:29.884 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.5zlgkwwrpu/LS0884_tumor.bam.bai is older than BAM /tmp/nxf.5zlgkwwrpu/LS0884_tumor.bam
22:44:30.029 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.5zlgkwwrpu/af-only-gnomad.hg38.vcf.gz
22:44:30.148 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.5zlgkwwrpu/TST500C_manifest.bed
22:44:30.181 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:30.209 INFO Mutect2 - Done initializing engine
22:44:30.221 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
22:44:30.222 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
22:44:30.223 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:30.223 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:30.232 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
22:44:30.240 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:30.240 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:30.241 INFO IntelPairHmm - Available threads: 384
22:44:30.241 INFO IntelPairHmm - Requested threads: 4
22:44:30.241 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:30.278 INFO ProgressMeter - Starting traversal
22:44:30.278 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:41.597 INFO ProgressMeter - chr1:9717615 0.2 50 265.1
22:44:52.792 INFO ProgressMeter - chr1:11199605 0.4 120 319.8
22:45:03.557 INFO ProgressMeter - chr1:15876481 0.6 170 306.5
22:45:15.366 INFO ProgressMeter - chr1:15932229 0.8 210 279.5
22:45:26.815 INFO ProgressMeter - chr1:17027747 0.9 250 265.3
22:45:38.188 INFO ProgressMeter - chr1:18746525 1.1 290 256.2
22:45:48.706 INFO ProgressMeter - chr1:26762259 1.3 340 260.1
22:46:00.077 INFO ProgressMeter - chr1:36361219 1.5 390 260.6
22:46:12.510 INFO ProgressMeter - chr1:39899814 1.7 450 264.1
22:46:23.100 INFO ProgressMeter - chr1:45332916 1.9 510 271.2
22:46:34.394 INFO ProgressMeter - chr1:50975629 2.1 570 275.5
22:46:45.602 INFO ProgressMeter - chr1:71698006 2.3 630 279.3
22:46:55.970 INFO ProgressMeter - chr1:114717661 2.4 710 292.4
22:47:09.354 INFO ProgressMeter - chr1:119915988 2.7 760 286.7
22:47:20.409 INFO ProgressMeter - chr1:119965487 2.8 810 285.7
22:47:34.349 INFO ProgressMeter - chr1:156874574 3.1 870 283.6
22:47:44.423 INFO ProgressMeter - chr1:158614264 3.2 900 278.1
22:47:56.269 INFO ProgressMeter - chr1:158671341 3.4 960 279.6
22:48:06.981 INFO ProgressMeter - chr1:176184631 3.6 1030 285.2
22:48:18.694 INFO ProgressMeter - chr1:204434494 3.8 1100 288.9
22:48:29.935 INFO ProgressMeter - chr1:204542459 4.0 1170 292.9
22:48:40.066 INFO ProgressMeter - chr1:206484995 4.2 1220 293.0
22:48:50.254 INFO ProgressMeter - chr1:241497826 4.3 1290 297.7
22:49:01.745 INFO ProgressMeter - chr1:243503445 4.5 1330 294.0
22:49:12.824 INFO ProgressMeter - chr10:27012861 4.7 1380 293.0
22:49:24.312 INFO ProgressMeter - chr10:27077481 4.9 1430 291.8
22:49:34.555 INFO ProgressMeter - chr10:32039325 5.1 1480 291.8
22:49:45.727 INFO ProgressMeter - chr10:43113702 5.3 1530 291.0
22:49:57.570 INFO ProgressMeter - chr10:43117726 5.5 1570 287.8
22:50:08.614 INFO ProgressMeter - chr10:62092756 5.6 1620 287.3
22:50:20.614 INFO ProgressMeter - chr10:68690910 5.8 1660 284.3
22:50:31.145 INFO ProgressMeter - chr10:89008887 6.0 1730 287.6
22:50:41.520 INFO ProgressMeter - chr10:102593634 6.2 1790 289.3
22:50:52.801 INFO ProgressMeter - chr10:110602492 6.4 1840 288.6
22:51:05.372 INFO ProgressMeter - chr10:121482475 6.6 1900 288.5
22:51:16.868 INFO ProgressMeter - chr10:121593946 6.8 1950 287.8
22:51:27.697 INFO ProgressMeter - chr11:64359234 7.0 2020 290.4
22:51:39.298 INFO ProgressMeter - chr11:69650543 7.2 2100 293.7
22:51:49.876 INFO ProgressMeter - chr11:69706077 7.3 2160 294.8
22:52:06.198 INFO ProgressMeter - chr11:69809467 7.6 2220 292.2
22:52:16.671 INFO ProgressMeter - chr11:76528266 7.8 2280 293.3
22:52:27.157 INFO ProgressMeter - chr11:77375496 7.9 2330 293.2
22:52:38.371 INFO ProgressMeter - chr11:86268454 8.1 2380 292.6
22:52:49.975 INFO ProgressMeter - chr11:102162454 8.3 2440 293.0
22:53:02.095 INFO ProgressMeter - chr11:108235668 8.5 2470 289.6
22:53:13.342 INFO ProgressMeter - chr11:108329019 8.7 2530 290.2
22:53:26.904 INFO ProgressMeter - chr11:118476803 8.9 2590 289.6
22:53:38.901 INFO ProgressMeter - chr11:118503496 9.1 2640 288.7
22:53:49.493 INFO ProgressMeter - chr11:118511949 9.3 2670 286.5
22:54:05.107 INFO ProgressMeter - chr11:125620976 9.6 2710 282.9
22:54:18.834 INFO ProgressMeter - chr11:125666949 9.8 2760 281.4
22:54:30.421 INFO ProgressMeter - chr11:128460750 10.0 2780 277.9
22:54:43.020 INFO ProgressMeter - chr11:128758267 10.2 2820 276.1
22:54:53.232 INFO ProgressMeter - chr11:128812784 10.4 2850 274.5
22:55:04.434 INFO ProgressMeter - chr12:384029 10.6 2910 275.3
22:55:14.979 INFO ProgressMeter - chr12:4378798 10.7 2980 277.3
22:55:25.420 INFO ProgressMeter - chr12:4441023 10.9 3030 277.5
22:55:35.686 INFO ProgressMeter - chr12:6587744 11.1 3080 277.7
22:55:46.911 INFO ProgressMeter - chr12:11854824 11.3 3130 277.6
22:55:57.416 INFO ProgressMeter - chr12:11857312 11.5 3160 275.9
22:56:10.318 INFO ProgressMeter - chr12:11862050 11.7 3200 274.3
22:56:22.135 INFO ProgressMeter - chr12:11866776 11.9 3240 273.1
22:56:33.170 INFO ProgressMeter - chr12:11884424 12.0 3260 270.6
22:56:43.455 INFO ProgressMeter - chr12:25214043 12.2 3330 272.5
22:56:55.403 INFO ProgressMeter - chr12:45811416 12.4 3390 273.0
22:57:06.176 INFO ProgressMeter - chr12:49022041 12.6 3440 273.1
22:57:18.828 INFO ProgressMeter - chr12:49033422 12.8 3480 271.7
22:57:29.690 INFO ProgressMeter - chr12:49043074 13.0 3520 271.0
22:57:40.811 INFO ProgressMeter - chr12:50086262 13.2 3580 271.7
22:57:51.931 INFO ProgressMeter - chr12:56094987 13.4 3650 273.2
22:58:03.412 INFO ProgressMeter - chr12:57094069 13.6 3700 273.0
22:58:13.891 INFO ProgressMeter - chr12:57746326 13.7 3750 273.2
22:58:26.025 INFO ProgressMeter - chr12:68837480 13.9 3830 275.0
22:58:36.451 INFO ProgressMeter - chr12:112455948 14.1 3890 275.8
22:58:47.596 INFO ProgressMeter - chr12:120997502 14.3 3950 276.4
22:58:58.455 INFO ProgressMeter - chr12:132673162 14.5 4010 277.1
22:59:10.761 INFO ProgressMeter - chr13:21676821 14.7 4070 277.3
22:59:21.568 INFO ProgressMeter - chr13:28034299 14.9 4140 278.7
22:59:31.697 INFO ProgressMeter - chr13:28385849 15.0 4190 278.9
22:59:43.480 INFO ProgressMeter - chr13:28389637 15.2 4220 277.3
22:59:54.545 INFO ProgressMeter - chr13:32338881 15.4 4280 277.8
23:00:05.218 INFO ProgressMeter - chr13:40665569 15.6 4340 278.5
23:00:15.273 INFO ProgressMeter - chr13:101875184 15.7 4420 280.6
23:00:26.548 INFO ProgressMeter - chr13:102865776 15.9 4480 281.1
23:00:37.812 INFO ProgressMeter - chr13:113306483 16.1 4550 282.2
23:00:48.832 INFO ProgressMeter - chr14:36514796 16.3 4600 282.0
23:00:59.249 INFO ProgressMeter - chr14:37594342 16.5 4660 282.7
23:01:10.013 INFO ProgressMeter - chr14:81091067 16.7 4730 283.9
23:01:21.498 INFO ProgressMeter - chr14:95111393 16.9 4780 283.6
23:01:32.934 INFO ProgressMeter - chr15:32730884 17.0 4850 284.6
23:01:44.660 INFO ProgressMeter - chr15:34356021 17.2 4890 283.6
23:01:55.708 INFO ProgressMeter - chr15:41713191 17.4 4940 283.5
23:02:07.725 INFO ProgressMeter - chr15:41766542 17.6 4990 283.1
23:02:18.355 INFO ProgressMeter - chr15:67184725 17.8 5070 284.8
23:02:29.596 INFO ProgressMeter - chr15:88135099 18.0 5120 284.6
23:02:40.347 INFO ProgressMeter - chr15:90090477 18.2 5200 286.2
23:02:50.383 INFO ProgressMeter - chr15:92943044 18.3 5260 286.9
23:03:02.092 INFO ProgressMeter - chr15:98948572 18.5 5330 287.6
23:03:12.576 INFO ProgressMeter - chr16:2079030 18.7 5390 288.2
23:03:23.232 INFO ProgressMeter - chr16:3589629 18.9 5480 290.2
23:03:34.176 INFO ProgressMeter - chr16:3728256 19.1 5520 289.5
23:03:45.487 INFO ProgressMeter - chr16:9764028 19.3 5580 289.8
23:03:56.487 INFO ProgressMeter - chr16:13948233 19.4 5640 290.2
23:04:07.622 INFO ProgressMeter - chr16:50786853 19.6 5710 291.0
23:04:19.079 INFO ProgressMeter - chr16:68801668 19.8 5780 291.7
23:04:29.333 INFO ProgressMeter - chr16:72788488 20.0 5810 290.7
23:04:40.625 INFO ProgressMeter - chr16:72796165 20.2 5840 289.5
23:04:53.045 INFO ProgressMeter - chr16:72889930 20.4 5870 288.0
23:05:03.265 INFO ProgressMeter - chr16:72959984 20.5 5900 287.1
23:05:14.528 INFO ProgressMeter - chr16:89281309 20.7 5970 287.9
23:05:25.693 INFO ProgressMeter - chr16:89749893 20.9 6020 287.7
23:05:36.252 INFO ProgressMeter - chr17:7671656 21.1 6090 288.6
23:05:47.164 INFO ProgressMeter - chr17:8077077 21.3 6150 289.0
23:05:57.223 INFO ProgressMeter - chr17:16080694 21.4 6220 290.0
23:06:08.082 INFO ProgressMeter - chr17:31222407 21.6 6300 291.3
23:06:19.613 INFO ProgressMeter - chr17:31996796 21.8 6370 291.9
23:06:31.118 INFO ProgressMeter - chr17:39530764 22.0 6420 291.6
23:06:42.966 INFO ProgressMeter - chr17:39726908 22.2 6480 291.7
23:06:53.846 INFO ProgressMeter - chr17:42207556 22.4 6550 292.5
23:07:04.544 INFO ProgressMeter - chr17:43045676 22.6 6620 293.3
23:07:18.145 INFO ProgressMeter - chr17:43093909 22.8 6680 293.0
23:07:30.533 INFO ProgressMeter - chr17:43532181 23.0 6730 292.6
23:07:43.961 INFO ProgressMeter - chr17:43539279 23.2 6780 291.9
23:07:58.563 INFO ProgressMeter - chr17:43543828 23.5 6810 290.1
23:08:10.631 INFO ProgressMeter - chr17:48727043 23.7 6860 289.8
23:08:21.900 INFO ProgressMeter - chr17:58696691 23.9 6910 289.6
23:08:32.379 INFO ProgressMeter - chr17:59936213 24.0 6970 290.0
23:08:43.377 INFO ProgressMeter - chr17:61693434 24.2 7010 289.5
23:08:54.813 INFO ProgressMeter - chr17:65538245 24.4 7060 289.2
23:09:06.567 INFO ProgressMeter - chr17:80846471 24.6 7120 289.4
23:09:17.731 INFO ProgressMeter - chr18:22171262 24.8 7180 289.6
23:09:28.373 INFO ProgressMeter - chr18:44950678 25.0 7240 290.0
23:09:38.431 INFO ProgressMeter - chr18:47869241 25.1 7280 289.6
23:09:49.306 INFO ProgressMeter - chr19:1219322 25.3 7340 289.9
23:10:00.016 INFO ProgressMeter - chr19:2228204 25.5 7430 291.4
23:10:10.778 INFO ProgressMeter - chr19:5238917 25.7 7510 292.5
23:10:20.863 INFO ProgressMeter - chr19:7267746 25.8 7570 292.9
23:10:32.453 INFO ProgressMeter - chr19:10985340 26.0 7650 293.8
23:10:44.666 INFO ProgressMeter - chr19:14517312 26.2 7730 294.6
23:10:54.935 INFO ProgressMeter - chr19:15191526 26.4 7790 295.0
23:11:05.621 INFO ProgressMeter - chr19:17834569 26.6 7860 295.6
23:11:15.909 INFO ProgressMeter - chr19:19147696 26.8 7920 296.0
23:11:25.910 INFO ProgressMeter - chr19:29821298 26.9 7960 295.6
23:11:36.257 INFO ProgressMeter - chr19:35724635 27.1 8020 295.9
23:11:46.941 INFO ProgressMeter - chr19:40246839 27.3 8090 296.6
23:12:02.654 INFO ProgressMeter - chr19:41260378 27.5 8160 296.3
23:12:14.172 INFO ProgressMeter - chr19:42293974 27.7 8220 296.4
23:12:24.944 INFO ProgressMeter - chr19:45407331 27.9 8290 297.0
23:12:35.789 INFO ProgressMeter - chr19:50406405 28.1 8360 297.6
23:12:47.562 INFO ProgressMeter - chr2:15941161 28.3 8420 297.7
23:12:59.099 INFO ProgressMeter - chr2:17765014 28.5 8470 297.4
23:13:12.078 INFO ProgressMeter - chr2:25282694 28.7 8530 297.2
23:13:22.368 INFO ProgressMeter - chr2:25771438 28.9 8570 296.9
23:13:32.398 INFO ProgressMeter - chr2:29223140 29.0 8610 296.5
23:13:46.781 INFO ProgressMeter - chr2:29228978 29.3 8640 295.1
23:13:58.395 INFO ProgressMeter - chr2:42245563 29.5 8690 294.9
23:14:09.942 INFO ProgressMeter - chr2:47373806 29.7 8740 294.7
23:14:22.072 INFO ProgressMeter - chr2:47476556 29.9 8780 294.0
23:14:32.563 INFO ProgressMeter - chr2:58204128 30.0 8830 294.0
23:14:47.672 INFO ProgressMeter - chr2:96254916 30.3 8900 293.8
23:14:59.048 INFO ProgressMeter - chr2:108764258 30.5 8970 294.3
23:15:09.382 INFO ProgressMeter - chr2:111126068 30.7 9020 294.3
23:15:25.142 INFO ProgressMeter - chr2:111128661 30.9 9040 292.4
23:15:35.511 INFO ProgressMeter - chr2:113223260 31.1 9070 291.8
23:15:49.650 INFO ProgressMeter - chr2:113225607 31.3 9090 290.2
23:16:02.584 INFO ProgressMeter - chr2:113227631 31.5 9110 288.9
23:16:14.378 INFO ProgressMeter - chr2:113231653 31.7 9140 288.0
23:16:27.757 INFO ProgressMeter - chr2:113234643 32.0 9170 286.9
23:16:38.220 INFO ProgressMeter - chr2:127290222 32.1 9220 286.9
23:16:49.374 INFO ProgressMeter - chr2:140502961 32.3 9290 287.5
23:17:00.484 INFO ProgressMeter - chr2:140989586 32.5 9350 287.7
23:17:12.189 INFO ProgressMeter - chr2:177231383 32.7 9410 287.8
23:17:22.805 INFO ProgressMeter - chr2:191076284 32.9 9470 288.1
23:17:33.580 INFO ProgressMeter - chr2:201285165 33.1 9530 288.3
23:17:44.590 INFO ProgressMeter - chr2:214781158 33.2 9600 288.8
23:17:57.717 INFO ProgressMeter - chr2:222203883 33.5 9640 288.1
23:18:09.221 INFO ProgressMeter - chr2:222209790 33.6 9680 287.7
23:18:21.165 INFO ProgressMeter - chr2:222214507 33.8 9720 287.2
23:18:32.087 INFO ProgressMeter - chr2:222218204 34.0 9750 286.5
23:18:42.515 INFO ProgressMeter - chr2:224482057 34.2 9800 286.5
23:18:54.286 INFO ProgressMeter - chr2:241852286 34.4 9860 286.6
23:19:04.935 INFO ProgressMeter - chr20:32372162 34.6 9910 286.6
23:19:15.692 INFO ProgressMeter - chr20:32436779 34.8 9940 286.0
23:19:25.713 INFO ProgressMeter - chr20:41081227 34.9 10000 286.3
23:19:36.400 INFO ProgressMeter - chr20:42350626 35.1 10060 286.6
23:19:46.509 INFO ProgressMeter - chr20:47647243 35.3 10110 286.6
23:19:57.103 INFO ProgressMeter - chr20:53576284 35.4 10130 285.8
23:20:07.793 INFO ProgressMeter - chr20:58840690 35.6 10170 285.5
23:20:17.972 INFO ProgressMeter - chr21:34834418 35.8 10230 285.8
23:20:29.633 INFO ProgressMeter - chr21:38403549 36.0 10280 285.6
23:20:42.528 INFO ProgressMeter - chr21:41489368 36.2 10330 285.3
23:20:55.312 INFO ProgressMeter - chr21:41492049 36.4 10350 284.2
23:21:05.512 INFO ProgressMeter - chr21:41499766 36.6 10380 283.7
23:21:17.965 INFO ProgressMeter - chr21:41504771 36.8 10420 283.2
23:21:29.519 INFO ProgressMeter - chr21:44235270 37.0 10470 283.1
23:21:39.696 INFO ProgressMeter - chr22:23283975 37.2 10550 283.9
23:21:50.847 INFO ProgressMeter - chr22:23309422 37.3 10580 283.3
23:22:01.128 INFO ProgressMeter - chr22:29268007 37.5 10660 284.2
23:22:11.193 INFO ProgressMeter - chr22:29291560 37.7 10700 284.0
23:22:22.725 INFO ProgressMeter - chr22:41127485 37.9 10750 283.8
23:22:34.273 INFO ProgressMeter - chr3:920014 38.1 10810 284.0
23:22:45.804 INFO ProgressMeter - chr3:12312378 38.3 10880 284.4
23:22:57.870 INFO ProgressMeter - chr3:12356094 38.5 10910 283.7
23:23:08.218 INFO ProgressMeter - chr3:12359427 38.6 10940 283.2
23:23:19.450 INFO ProgressMeter - chr3:12360819 38.8 10950 282.1
23:23:31.624 INFO ProgressMeter - chr3:12365925 39.0 10990 281.6
23:23:47.735 INFO ProgressMeter - chr3:12371418 39.3 11030 280.7
23:23:57.866 INFO ProgressMeter - chr3:12374608 39.5 11050 280.0
23:24:08.174 INFO ProgressMeter - chr3:12379114 39.6 11080 279.6
23:24:21.258 INFO ProgressMeter - chr3:12647702 39.8 11140 279.6
23:24:31.844 INFO ProgressMeter - chr3:41233339 40.0 11210 280.1
23:24:44.752 INFO ProgressMeter - chr3:47122965 40.2 11270 280.1
23:24:54.754 INFO ProgressMeter - chr3:49895165 40.4 11330 280.4
23:25:06.459 INFO ProgressMeter - chr3:52561765 40.6 11390 280.5
23:25:17.581 INFO ProgressMeter - chr3:70987992 40.8 11460 281.0
23:25:29.085 INFO ProgressMeter - chr3:89408065 41.0 11520 281.1
23:25:41.180 INFO ProgressMeter - chr3:135162016 41.2 11580 281.2
23:25:53.046 INFO ProgressMeter - chr3:136623125 41.4 11640 281.3
23:26:03.158 INFO ProgressMeter - chr3:138945728 41.5 11700 281.6
23:26:13.772 INFO ProgressMeter - chr3:142558657 41.7 11760 281.8
23:26:25.390 INFO ProgressMeter - chr3:179198824 41.9 11830 282.2
23:26:36.976 INFO ProgressMeter - chr3:183555359 42.1 11890 282.3
23:26:49.585 INFO ProgressMeter - chr3:186048144 42.3 11930 281.9
23:27:00.799 INFO ProgressMeter - chr3:189872857 42.5 12000 282.3
23:27:11.891 INFO ProgressMeter - chr4:1792811 42.7 12070 282.7
23:27:22.523 INFO ProgressMeter - chr4:20541605 42.9 12150 283.4
23:27:32.557 INFO ProgressMeter - chr4:41748503 43.0 12210 283.7
23:27:43.232 INFO ProgressMeter - chr4:54290346 43.2 12270 283.9
23:27:57.911 INFO ProgressMeter - chr4:54733075 43.5 12320 283.5
23:28:08.401 INFO ProgressMeter - chr4:65336045 43.6 12380 283.7
23:28:18.985 INFO ProgressMeter - chr4:80283144 43.8 12440 283.9
23:28:30.737 INFO ProgressMeter - chr4:105235540 44.0 12500 284.0
23:28:43.351 INFO ProgressMeter - chr4:105242128 44.2 12540 283.6
23:28:54.005 INFO ProgressMeter - chr4:122884325 44.4 12600 283.8
23:29:05.329 INFO ProgressMeter - chr4:184388862 44.6 12670 284.2
23:29:17.750 INFO ProgressMeter - chr4:186618173 44.8 12730 284.2
23:29:29.645 INFO ProgressMeter - chr4:186707664 45.0 12780 284.1
23:29:41.014 INFO ProgressMeter - chr5:35871126 45.2 12840 284.2
23:29:51.456 INFO ProgressMeter - chr5:39021037 45.4 12900 284.4
23:30:03.267 INFO ProgressMeter - chr5:56881888 45.5 12970 284.7
23:30:13.588 INFO ProgressMeter - chr5:68293831 45.7 13030 285.0
23:30:23.860 INFO ProgressMeter - chr5:112792444 45.9 13120 285.9
23:30:34.311 INFO ProgressMeter - chr5:112841448 46.1 13160 285.7
23:30:46.074 INFO ProgressMeter - chr5:122451337 46.3 13200 285.3
23:30:56.499 INFO ProgressMeter - chr5:142595288 46.4 13270 285.8
23:31:07.406 INFO ProgressMeter - chr5:149511773 46.6 13320 285.7
23:31:17.584 INFO ProgressMeter - chr5:150120980 46.8 13380 286.0
23:31:28.469 INFO ProgressMeter - chr5:150404652 47.0 13430 285.9
23:31:39.872 INFO ProgressMeter - chr5:177090388 47.2 13490 286.0
23:31:54.809 INFO ProgressMeter - chr5:177204118 47.4 13540 285.6
23:32:07.180 INFO ProgressMeter - chr5:177294258 47.6 13590 285.4
23:32:17.745 INFO ProgressMeter - chr5:180616942 47.8 13650 285.6
23:32:28.355 INFO ProgressMeter - chr6:20427963 48.0 13710 285.8
23:32:39.769 INFO ProgressMeter - chr6:26031648 48.2 13780 286.1
23:32:53.489 INFO ProgressMeter - chr6:29945232 48.4 13830 285.8
23:33:03.850 INFO ProgressMeter - chr6:30708249 48.6 13870 285.6
23:33:15.687 INFO ProgressMeter - chr6:32210876 48.8 13920 285.5
23:33:26.314 INFO ProgressMeter - chr6:35455745 48.9 13970 285.5
23:33:36.966 INFO ProgressMeter - chr6:41983281 49.1 14040 285.9
23:33:47.624 INFO ProgressMeter - chr6:93414701 49.3 14110 286.3
23:33:58.427 INFO ProgressMeter - chr6:112064753 49.5 14160 286.2
23:34:08.427 INFO ProgressMeter - chr6:117320612 49.6 14200 286.1
23:34:18.443 INFO ProgressMeter - chr6:117323644 49.8 14220 285.5
23:34:30.578 INFO ProgressMeter - chr6:117329917 50.0 14260 285.2
23:34:43.432 INFO ProgressMeter - chr6:117337901 50.2 14300 284.8
23:34:53.516 INFO ProgressMeter - chr6:117366074 50.4 14340 284.6
23:35:06.263 INFO ProgressMeter - chr6:135204485 50.6 14400 284.6
23:35:17.958 INFO ProgressMeter - chr6:135208986 50.8 14440 284.3
23:35:31.587 INFO ProgressMeter - chr6:135212323 51.0 14460 283.4
23:35:43.681 INFO ProgressMeter - chr6:135217334 51.2 14500 283.1
23:35:54.085 INFO ProgressMeter - chr6:149679873 51.4 14550 283.1
23:36:05.187 INFO ProgressMeter - chr6:151842595 51.6 14600 283.0
23:36:16.655 INFO ProgressMeter - chr6:156778802 51.8 14640 282.8
23:36:29.164 INFO ProgressMeter - chr6:161034257 52.0 14700 282.8
23:36:39.326 INFO ProgressMeter - chr6:161548901 52.2 14750 282.8
23:36:50.192 INFO ProgressMeter - chr7:2938677 52.3 14820 283.2
23:37:02.903 INFO ProgressMeter - chr7:13894590 52.5 14880 283.2
23:37:15.417 INFO ProgressMeter - chr7:13909195 52.8 14910 282.6
23:37:28.632 INFO ProgressMeter - chr7:13934921 53.0 14940 282.0
23:37:39.099 INFO ProgressMeter - chr7:13941363 53.1 14980 281.9
23:37:49.341 INFO ProgressMeter - chr7:13946062 53.3 15010 281.5
23:37:59.749 INFO ProgressMeter - chr7:13950087 53.5 15040 281.2
23:38:12.241 INFO ProgressMeter - chr7:13952266 53.7 15060 280.5
23:38:24.705 INFO ProgressMeter - chr7:13955862 53.9 15090 279.9
23:38:38.135 INFO ProgressMeter - chr7:13961588 54.1 15130 279.5
23:38:49.949 INFO ProgressMeter - chr7:13965230 54.3 15160 279.0
23:39:03.635 INFO ProgressMeter - chr7:13970580 54.6 15200 278.6
23:39:19.202 INFO ProgressMeter - chr7:13975746 54.8 15240 278.0
23:39:29.420 INFO ProgressMeter - chr7:13978773 55.0 15260 277.5
23:39:40.513 INFO ProgressMeter - chr7:13982628 55.2 15290 277.1
23:39:50.667 INFO ProgressMeter - chr7:13985205 55.3 15310 276.7
23:40:01.360 INFO ProgressMeter - chr7:13988812 55.5 15330 276.1
23:40:12.282 INFO ProgressMeter - chr7:55142284 55.7 15380 276.1
23:40:23.725 INFO ProgressMeter - chr7:55161497 55.9 15410 275.7
23:40:37.016 INFO ProgressMeter - chr7:55167022 56.1 15430 275.0
23:40:49.434 INFO ProgressMeter - chr7:55169859 56.3 15450 274.3
23:41:01.590 INFO ProgressMeter - chr7:55177331 56.5 15480 273.9
23:41:14.770 INFO ProgressMeter - chr7:55180501 56.7 15510 273.3
23:41:29.399 INFO ProgressMeter - chr7:55202515 57.0 15550 272.9
23:41:39.579 INFO ProgressMeter - chr7:81702579 57.2 15600 272.9
23:41:50.308 INFO ProgressMeter - chr7:92707499 57.3 15670 273.3
23:42:01.494 INFO ProgressMeter - chr7:102201956 57.5 15740 273.6
23:42:13.368 INFO ProgressMeter - chr7:106886133 57.7 15800 273.7
23:42:23.506 INFO ProgressMeter - chr7:116771757 57.9 15840 273.6
23:42:36.089 INFO ProgressMeter - chr7:140739810 58.1 15890 273.5
23:42:47.151 INFO ProgressMeter - chr7:140792202 58.3 15940 273.5
23:42:57.804 INFO ProgressMeter - chr7:140920344 58.5 16000 273.7
23:43:10.166 INFO ProgressMeter - chr7:152149118 58.7 16080 274.1
23:43:24.136 INFO ProgressMeter - chr7:152177546 58.9 16130 273.9
23:43:35.037 INFO ProgressMeter - chr7:152235902 59.1 16180 273.9
23:43:45.817 INFO ProgressMeter - chr8:23691051 59.3 16240 274.1
23:43:57.653 INFO ProgressMeter - chr8:32727947 59.5 16310 274.3
23:44:08.870 INFO ProgressMeter - chr8:38415922 59.6 16390 274.8
23:44:20.283 INFO ProgressMeter - chr8:41934448 59.8 16450 274.9
23:44:31.379 INFO ProgressMeter - chr8:47800791 60.0 16510 275.1
23:44:42.350 INFO ProgressMeter - chr8:47890255 60.2 16570 275.2
23:44:52.535 INFO ProgressMeter - chr8:54462441 60.4 16630 275.5
23:45:02.776 INFO ProgressMeter - chr8:68108299 60.5 16680 275.5
23:45:13.119 INFO ProgressMeter - chr8:91960475 60.7 16740 275.7
23:45:25.013 INFO ProgressMeter - chr8:127732334 60.9 16790 275.6
23:45:35.933 INFO ProgressMeter - chr8:127740394 61.1 16830 275.5
23:45:46.631 INFO ProgressMeter - chr8:144516549 61.3 16880 275.5
23:45:56.812 INFO ProgressMeter - chr9:5081723 61.4 16930 275.5
23:46:07.899 INFO ProgressMeter - chr9:8376007 61.6 16970 275.4
23:46:18.455 INFO ProgressMeter - chr9:20365667 61.8 17020 275.4
23:46:30.314 INFO ProgressMeter - chr9:35075277 62.0 17060 275.2
23:46:40.425 INFO ProgressMeter - chr9:83972032 62.2 17110 275.2
23:46:55.402 INFO ProgressMeter - chr9:84743551 62.4 17160 274.9
23:47:06.776 INFO ProgressMeter - chr9:84813475 62.6 17190 274.6
23:47:18.737 INFO ProgressMeter - chr9:84862013 62.8 17210 274.0
23:47:30.289 INFO ProgressMeter - chr9:84865075 63.0 17230 273.5
23:47:42.078 INFO ProgressMeter - chr9:84874141 63.2 17260 273.1
23:47:52.169 INFO ProgressMeter - chr9:84877421 63.4 17290 272.9
23:48:05.525 INFO ProgressMeter - chr9:85025684 63.6 17330 272.5
23:48:15.858 INFO ProgressMeter - chr9:95149921 63.8 17370 272.4
23:48:26.911 INFO ProgressMeter - chr9:95516739 63.9 17430 272.6
23:48:39.675 INFO ProgressMeter - chr9:130884151 64.2 17500 272.8
23:48:50.367 INFO ProgressMeter - chr9:132905660 64.3 17540 272.6
23:49:00.922 INFO ProgressMeter - chr9:136506525 64.5 17590 272.7
23:49:12.389 INFO ProgressMeter - chr9:136925767 64.7 17660 272.9
23:49:23.277 INFO ProgressMeter - chrX:40074278 64.9 17720 273.1
23:49:34.831 INFO ProgressMeter - chrX:47176498 65.1 17780 273.2
23:49:44.973 INFO ProgressMeter - chrX:49029393 65.2 17840 273.4
23:49:57.962 INFO ProgressMeter - chrX:49038662 65.5 17890 273.3
23:50:09.086 INFO ProgressMeter - chrX:53380997 65.6 17950 273.4
23:50:20.786 INFO ProgressMeter - chrX:64190193 65.8 18000 273.4
23:50:34.281 INFO ProgressMeter - chrX:67545872 66.1 18040 273.1
23:50:44.316 INFO ProgressMeter - chrX:71119371 66.2 18100 273.3
23:50:58.181 INFO ProgressMeter - chrX:71140693 66.5 18170 273.4
23:51:09.201 INFO ProgressMeter - chrX:71459670 66.6 18230 273.5
23:51:22.737 INFO ProgressMeter - chrX:77683690 66.9 18290 273.5
23:51:33.330 INFO ProgressMeter - chrX:124047352 67.1 18370 274.0
23:51:43.360 INFO ProgressMeter - chrX:130014306 67.2 18420 274.0
23:51:51.040 INFO Mutect2 - 717676 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
112 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
717790 total reads filtered out of 122127110 reads processed
23:51:51.040 INFO ProgressMeter - chrY:20557826 67.3 18503 274.7
23:51:51.040 INFO ProgressMeter - Traversal complete. Processed 18503 total regions in 67.3 minutes.
23:51:51.056 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 8.130339492000001
23:51:51.056 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 375.28516185300003
23:51:51.056 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 13.41 sec
23:51:51.057 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:51:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 67.36 minutes.
Runtime.totalMemory()=3120562176
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 LS0884_tumor.bam --tumor-sample LS0884 -L TST500C_manifest.bed -O LS0884.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:51:52.632 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
23:51:52.731 INFO FilterMutectCalls - ------------------------------------------------------------
23:51:52.738 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:51:52.738 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:51:52.738 INFO FilterMutectCalls - Executing as ?@nf-0b548db5276f3cd7ae6e45b4cbf4328e-7545f-lj264 on Linux v6.12.88 amd64
23:51:52.738 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:51:52.738 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:51:52 PM GMT
23:51:52.739 INFO FilterMutectCalls - ------------------------------------------------------------
23:51:52.739 INFO FilterMutectCalls - ------------------------------------------------------------
23:51:52.739 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:51:52.739 INFO FilterMutectCalls - Picard Version: 3.1.1
23:51:52.739 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:51:52.740 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:51:52.740 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:51:52.740 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:51:52.740 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:51:52.740 INFO FilterMutectCalls - Deflater: IntelDeflater
23:51:52.740 INFO FilterMutectCalls - Inflater: IntelInflater
23:51:52.740 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:51:52.740 INFO FilterMutectCalls - Requester pays: disabled
23:51:52.741 INFO FilterMutectCalls - Initializing engine
23:51:52.943 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.5zlgkwwrpu/LS0884.mutect2.raw.vcf.gz
23:51:53.036 INFO FilterMutectCalls - Done initializing engine
23:51:53.093 INFO ProgressMeter - Starting traversal
23:51:53.093 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:51:53.094 INFO FilterMutectCalls - Starting pass 0 through the variants
23:51:54.805 INFO FilterMutectCalls - Finished pass 0 through the variants
23:51:57.668 INFO FilterMutectCalls - Starting pass 1 through the variants
23:51:59.190 INFO FilterMutectCalls - Finished pass 1 through the variants
23:51:59.942 INFO FilterMutectCalls - Starting pass 2 through the variants
23:52:01.454 INFO FilterMutectCalls - Finished pass 2 through the variants
23:52:01.458 INFO FilterMutectCalls - Starting pass 3 through the variants
23:52:02.754 INFO FilterMutectCalls - Finished pass 3 through the variants
23:52:02.761 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:52:02.762 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:52:02.762 INFO ProgressMeter - chr7:2932581 0.2 11680 72479.1
23:52:02.762 INFO ProgressMeter - Traversal complete. Processed 11680 total variants in 0.2 minutes.
23:52:02.773 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:52:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.17 minutes.
Runtime.totalMemory()=411041792
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 LS0884.mutect2.raw.vcf.gz --stats LS0884.mutect2.raw.vcf.gz.stats -O LS0884.mutect2.filtered.vcf.gz
23:52:03.935 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
23:52:04.019 INFO SelectVariants - ------------------------------------------------------------
23:52:04.021 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:52:04.021 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:52:04.021 INFO SelectVariants - Executing as ?@nf-0b548db5276f3cd7ae6e45b4cbf4328e-7545f-lj264 on Linux v6.12.88 amd64
23:52:04.021 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:52:04.022 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:52:03 PM GMT
23:52:04.022 INFO SelectVariants - ------------------------------------------------------------
23:52:04.022 INFO SelectVariants - ------------------------------------------------------------
23:52:04.022 INFO SelectVariants - HTSJDK Version: 4.1.0
23:52:04.022 INFO SelectVariants - Picard Version: 3.1.1
23:52:04.022 INFO SelectVariants - Built for Spark Version: 3.5.0
23:52:04.022 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:52:04.022 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:52:04.022 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:52:04.023 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:52:04.023 INFO SelectVariants - Deflater: IntelDeflater
23:52:04.023 INFO SelectVariants - Inflater: IntelInflater
23:52:04.023 INFO SelectVariants - GCS max retries/reopens: 20
23:52:04.023 INFO SelectVariants - Requester pays: disabled
23:52:04.023 INFO SelectVariants - Initializing engine
23:52:04.132 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.5zlgkwwrpu/LS0884.mutect2.filtered.vcf.gz
23:52:04.226 INFO SelectVariants - Done initializing engine
23:52:04.260 INFO ProgressMeter - Starting traversal
23:52:04.260 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:52:04.336 INFO ProgressMeter - chr6:29942922 0.0 2920 2367567.6
23:52:04.336 INFO ProgressMeter - Traversal complete. Processed 2920 total variants in 0.0 minutes.
23:52:04.347 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:52:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=503316480
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 LS0884.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0884.mutect2.pass.vcf.gz