Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/ce/ec171720f0cbc4648d49a6fab6dac5/.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://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0899/LS0899_tumor.bam
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/ce/ec171720f0cbc4648d49a6fab6dac5/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0899/LS0899_tumor.bam.bai
==> STAGING COMPLETE (10 inputs)
22:44:26.972 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
22:44:27.099 INFO Mutect2 - ------------------------------------------------------------
22:44:27.103 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:27.103 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:27.103 INFO Mutect2 - Executing as ?@nf-ceec171720f0cbc4648d49a6fab6dac5-101ad-b5jd7 on Linux v6.12.88 amd64
22:44:27.103 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:27.104 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:26 PM GMT
22:44:27.104 INFO Mutect2 - ------------------------------------------------------------
22:44:27.104 INFO Mutect2 - ------------------------------------------------------------
22:44:27.105 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:27.105 INFO Mutect2 - Picard Version: 3.1.1
22:44:27.106 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:27.106 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:27.106 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:27.106 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:27.106 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:27.107 INFO Mutect2 - Deflater: IntelDeflater
22:44:27.107 INFO Mutect2 - Inflater: IntelInflater
22:44:27.107 INFO Mutect2 - GCS max retries/reopens: 20
22:44:27.107 INFO Mutect2 - Requester pays: disabled
22:44:27.108 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.eX1VE09kmX/LS0899_tumor.bam.bai is older than BAM /tmp/nxf.eX1VE09kmX/LS0899_tumor.bam
22:44:27.330 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.eX1VE09kmX/af-only-gnomad.hg38.vcf.gz
22:44:27.436 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.eX1VE09kmX/TST500C_manifest.bed
22:44:27.473 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:27.505 INFO Mutect2 - Done initializing engine
22:44:27.518 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
22:44:27.520 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
22:44:27.521 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:27.521 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:27.533 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
22:44:27.542 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:27.542 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:27.542 INFO IntelPairHmm - Available threads: 384
22:44:27.543 INFO IntelPairHmm - Requested threads: 4
22:44:27.543 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:27.584 INFO ProgressMeter - Starting traversal
22:44:27.584 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:38.245 INFO ProgressMeter - chr1:11130544 0.2 80 450.3
22:44:50.171 INFO ProgressMeter - chr1:15929187 0.4 160 425.0
22:45:00.820 INFO ProgressMeter - chr1:17033058 0.6 220 397.2
22:45:11.611 INFO ProgressMeter - chr1:23559125 0.7 280 381.6
22:45:22.528 INFO ProgressMeter - chr1:36467228 0.9 370 404.0
22:45:33.367 INFO ProgressMeter - chr1:43346790 1.1 460 419.6
22:45:44.125 INFO ProgressMeter - chr1:64837930 1.3 560 439.0
22:45:54.760 INFO ProgressMeter - chr1:114712729 1.5 660 454.3
22:46:05.377 INFO ProgressMeter - chr1:119925687 1.6 730 447.9
22:46:17.827 INFO ProgressMeter - chr1:156873856 1.8 820 446.3
22:46:28.096 INFO ProgressMeter - chr1:158653296 2.0 890 443.1
22:46:38.310 INFO ProgressMeter - chr1:176184631 2.2 980 449.8
22:46:48.490 INFO ProgressMeter - chr1:204460322 2.3 1070 455.6
22:46:58.497 INFO ProgressMeter - chr1:206479868 2.5 1150 457.2
22:47:08.682 INFO ProgressMeter - chr1:243500493 2.7 1240 461.8
22:47:19.031 INFO ProgressMeter - chr10:2364318 2.9 1290 451.5
22:47:30.148 INFO ProgressMeter - chr10:32009422 3.0 1370 450.3
22:47:41.313 INFO ProgressMeter - chr10:43114286 3.2 1450 449.1
22:47:52.727 INFO ProgressMeter - chr10:43126883 3.4 1510 441.6
22:48:04.905 INFO ProgressMeter - chr10:68646521 3.6 1570 433.5
22:48:17.880 INFO ProgressMeter - chr10:101770750 3.8 1670 435.1
22:48:29.985 INFO ProgressMeter - chr10:110601945 4.0 1760 435.6
22:48:40.392 INFO ProgressMeter - chr10:121482550 4.2 1820 431.9
22:48:50.878 INFO ProgressMeter - chr11:17712454 4.4 1900 433.0
22:49:02.332 INFO ProgressMeter - chr11:69649774 4.6 2030 443.3
22:49:12.380 INFO ProgressMeter - chr11:69702046 4.7 2080 438.2
22:49:30.674 INFO ProgressMeter - chr11:69810065 5.1 2160 427.6
22:49:42.051 INFO ProgressMeter - chr11:77323272 5.2 2230 425.5
22:49:52.834 INFO ProgressMeter - chr11:77460651 5.4 2300 424.3
22:50:04.446 INFO ProgressMeter - chr11:102324508 5.6 2370 422.1
22:50:15.586 INFO ProgressMeter - chr11:108365193 5.8 2470 425.9
22:50:26.463 INFO ProgressMeter - chr11:118503898 6.0 2540 424.7
22:50:37.903 INFO ProgressMeter - chr11:125626767 6.2 2600 421.3
22:50:49.296 INFO ProgressMeter - chr11:128460800 6.4 2660 418.1
22:50:59.825 INFO ProgressMeter - chr11:134797609 6.5 2720 416.1
22:51:10.570 INFO ProgressMeter - chr12:4373398 6.7 2810 418.4
22:51:20.779 INFO ProgressMeter - chr12:4450501 6.9 2880 418.2
22:51:31.830 INFO ProgressMeter - chr12:11854193 7.1 2950 417.2
22:51:44.411 INFO ProgressMeter - chr12:11861244 7.3 3000 412.1
22:51:57.757 INFO ProgressMeter - chr12:11868621 7.5 3050 406.5
22:52:09.099 INFO ProgressMeter - chr12:25225612 7.7 3140 408.2
22:52:20.176 INFO ProgressMeter - chr12:45893418 7.9 3210 407.5
22:52:30.786 INFO ProgressMeter - chr12:49037571 8.1 3270 406.0
22:52:41.523 INFO ProgressMeter - chr12:50090239 8.2 3360 408.1
22:52:52.104 INFO ProgressMeter - chr12:57092053 8.4 3450 410.3
22:53:03.054 INFO ProgressMeter - chr12:57750524 8.6 3530 410.9
22:53:13.737 INFO ProgressMeter - chr12:102417816 8.8 3620 412.8
22:53:23.978 INFO ProgressMeter - chr12:130277079 8.9 3710 415.0
22:53:34.569 INFO ProgressMeter - chr13:20983748 9.1 3790 415.7
22:53:45.602 INFO ProgressMeter - chr13:28028176 9.3 3880 417.2
22:53:58.106 INFO ProgressMeter - chr13:28387867 9.5 3950 415.4
22:54:09.496 INFO ProgressMeter - chr13:32338125 9.7 4020 414.5
22:54:19.804 INFO ProgressMeter - chr13:40587903 9.9 4080 413.4
22:54:30.310 INFO ProgressMeter - chr13:102353777 10.0 4190 417.1
22:54:41.385 INFO ProgressMeter - chr13:113312498 10.2 4280 418.4
22:54:52.156 INFO ProgressMeter - chr14:37590549 10.4 4350 417.9
22:55:02.636 INFO ProgressMeter - chr14:81108547 10.6 4440 419.5
22:55:13.620 INFO ProgressMeter - chr14:102085851 10.8 4510 418.9
22:55:25.342 INFO ProgressMeter - chr15:34355498 11.0 4580 417.8
22:55:35.676 INFO ProgressMeter - chr15:41739904 11.1 4640 416.7
22:55:46.346 INFO ProgressMeter - chr15:49454215 11.3 4710 416.3
22:55:58.223 INFO ProgressMeter - chr15:88032855 11.5 4800 417.0
22:56:09.518 INFO ProgressMeter - chr15:90761010 11.7 4900 418.8
22:56:19.610 INFO ProgressMeter - chr15:93020010 11.9 4980 419.6
22:56:29.702 INFO ProgressMeter - chr16:2071782 12.0 5060 420.4
22:56:40.542 INFO ProgressMeter - chr16:3597377 12.2 5180 424.0
22:56:50.640 INFO ProgressMeter - chr16:3850595 12.4 5250 423.9
22:57:01.393 INFO ProgressMeter - chr16:23603457 12.6 5320 423.4
22:57:12.597 INFO ProgressMeter - chr16:56834368 12.8 5410 424.3
22:57:23.356 INFO ProgressMeter - chr16:72793689 12.9 5480 423.8
22:57:34.327 INFO ProgressMeter - chr16:72957948 13.1 5530 421.7
22:57:45.289 INFO ProgressMeter - chr16:89280051 13.3 5610 422.0
22:57:55.858 INFO ProgressMeter - chr16:89748657 13.5 5670 420.9
22:58:08.071 INFO ProgressMeter - chr17:7675992 13.7 5770 421.9
22:58:18.777 INFO ProgressMeter - chr17:16067892 13.9 5870 423.7
22:58:29.556 INFO ProgressMeter - chr17:31230840 14.0 5970 425.4
22:58:40.675 INFO ProgressMeter - chr17:39471106 14.2 6070 426.9
22:58:50.730 INFO ProgressMeter - chr17:40351978 14.4 6160 428.2
22:59:01.323 INFO ProgressMeter - chr17:42333889 14.6 6280 431.3
22:59:11.732 INFO ProgressMeter - chr17:43093787 14.7 6350 430.9
22:59:22.796 INFO ProgressMeter - chr17:43534653 14.9 6410 429.6
22:59:34.871 INFO ProgressMeter - chr17:43544315 15.1 6470 427.9
22:59:45.305 INFO ProgressMeter - chr17:58415324 15.3 6550 428.2
22:59:55.548 INFO ProgressMeter - chr17:60647890 15.5 6630 428.7
23:00:06.822 INFO ProgressMeter - chr17:65558185 15.7 6710 428.6
23:00:16.854 INFO ProgressMeter - chr18:22171845 15.8 6820 431.1
23:00:27.999 INFO ProgressMeter - chr18:47845661 16.0 6900 431.1
23:00:38.011 INFO ProgressMeter - chr19:1612299 16.2 6980 431.6
23:00:48.096 INFO ProgressMeter - chr19:5218418 16.3 7110 435.1
23:00:59.038 INFO ProgressMeter - chr19:10156389 16.5 7210 436.3
23:01:10.390 INFO ProgressMeter - chr19:14517388 16.7 7320 438.0
23:01:20.469 INFO ProgressMeter - chr19:15243198 16.9 7410 438.9
23:01:33.608 INFO ProgressMeter - chr19:29816438 17.1 7530 440.3
23:01:44.218 INFO ProgressMeter - chr19:35732537 17.3 7620 441.0
23:01:59.152 INFO ProgressMeter - chr19:41260791 17.5 7720 440.5
23:02:10.027 INFO ProgressMeter - chr19:45365089 17.7 7820 441.6
23:02:20.101 INFO ProgressMeter - chr19:52215777 17.9 7930 443.6
23:02:30.262 INFO ProgressMeter - chr2:17759942 18.0 7990 442.8
23:02:41.445 INFO ProgressMeter - chr2:25744182 18.2 8070 442.7
23:02:52.494 INFO ProgressMeter - chr2:29225401 18.4 8130 441.5
23:03:03.136 INFO ProgressMeter - chr2:42282821 18.6 8200 441.0
23:03:15.720 INFO ProgressMeter - chr2:47416294 18.8 8260 439.3
23:03:26.625 INFO ProgressMeter - chr2:61483994 19.0 8350 439.8
23:03:36.791 INFO ProgressMeter - chr2:108751426 19.2 8430 440.1
23:03:48.133 INFO ProgressMeter - chr2:111127352 19.3 8500 439.4
23:03:58.762 INFO ProgressMeter - chr2:113220730 19.5 8530 437.0
23:04:09.066 INFO ProgressMeter - chr2:113227897 19.7 8570 435.2
23:04:20.811 INFO ProgressMeter - chr2:113234847 19.9 8620 433.4
23:04:30.967 INFO ProgressMeter - chr2:140475136 20.1 8720 434.8
23:04:41.626 INFO ProgressMeter - chr2:141254520 20.2 8800 434.9
23:04:51.887 INFO ProgressMeter - chr2:191036162 20.4 8880 435.2
23:05:02.150 INFO ProgressMeter - chr2:208248420 20.6 8970 435.9
23:05:15.536 INFO ProgressMeter - chr2:222202192 20.8 9060 435.6
23:05:27.289 INFO ProgressMeter - chr2:222210270 21.0 9110 433.9
23:05:42.474 INFO ProgressMeter - chr2:222217770 21.2 9160 431.1
23:05:52.880 INFO ProgressMeter - chr2:226795895 21.4 9230 430.9
23:06:03.427 INFO ProgressMeter - chr20:32429899 21.6 9310 431.1
23:06:14.355 INFO ProgressMeter - chr20:37403272 21.8 9390 431.1
23:06:25.466 INFO ProgressMeter - chr20:47635889 22.0 9480 431.6
23:06:35.626 INFO ProgressMeter - chr20:56386523 22.1 9540 431.0
23:06:45.736 INFO ProgressMeter - chr21:38381143 22.3 9630 431.8
23:06:56.545 INFO ProgressMeter - chr21:41476575 22.5 9690 431.0
23:07:11.648 INFO ProgressMeter - chr21:41492071 22.7 9720 427.5
23:07:21.699 INFO ProgressMeter - chr21:41501564 22.9 9760 426.2
23:07:31.753 INFO ProgressMeter - chr21:41508078 23.1 9810 425.2
23:07:42.786 INFO ProgressMeter - chr22:23290516 23.3 9910 426.2
23:07:52.814 INFO ProgressMeter - chr22:28719440 23.4 9980 426.1
23:08:04.066 INFO ProgressMeter - chr22:29291560 23.6 10050 425.7
23:08:14.385 INFO ProgressMeter - chr22:41158410 23.8 10130 426.0
23:08:24.480 INFO ProgressMeter - chr3:10088826 23.9 10210 426.3
23:08:36.367 INFO ProgressMeter - chr3:12355494 24.1 10270 425.3
23:08:48.106 INFO ProgressMeter - chr3:12360527 24.3 10300 423.1
23:08:58.125 INFO ProgressMeter - chr3:12366599 24.5 10340 421.9
23:09:09.339 INFO ProgressMeter - chr3:12372807 24.7 10380 420.3
23:09:20.471 INFO ProgressMeter - chr3:12434111 24.9 10430 419.2
23:09:30.757 INFO ProgressMeter - chr3:30674103 25.1 10490 418.7
23:09:42.741 INFO ProgressMeter - chr3:47121746 25.3 10590 419.4
23:09:52.888 INFO ProgressMeter - chr3:49898632 25.4 10670 419.7
23:10:03.343 INFO ProgressMeter - chr3:69941234 25.6 10760 420.4
23:10:13.588 INFO ProgressMeter - chr3:119843253 25.8 10850 421.1
23:10:23.716 INFO ProgressMeter - chr3:136398743 25.9 10930 421.4
23:10:33.913 INFO ProgressMeter - chr3:142453126 26.1 11020 422.1
23:10:44.438 INFO ProgressMeter - chr3:170297302 26.3 11110 422.7
23:10:55.463 INFO ProgressMeter - chr3:183555359 26.5 11200 423.2
23:11:05.574 INFO ProgressMeter - chr3:186048628 26.6 11250 422.4
23:11:16.047 INFO ProgressMeter - chr3:196062580 26.8 11340 423.0
23:11:26.929 INFO ProgressMeter - chr4:20553803 27.0 11450 424.2
23:11:37.407 INFO ProgressMeter - chr4:54270631 27.2 11530 424.5
23:11:53.242 INFO ProgressMeter - chr4:54733068 27.4 11610 423.3
23:12:04.470 INFO ProgressMeter - chr4:80269311 27.6 11700 423.7
23:12:16.366 INFO ProgressMeter - chr4:105237026 27.8 11780 423.5
23:12:26.584 INFO ProgressMeter - chr4:105275757 28.0 11830 422.8
23:12:38.437 INFO ProgressMeter - chr4:168742502 28.2 11930 423.3
23:12:50.010 INFO ProgressMeter - chr4:186621346 28.4 12000 422.9
23:13:00.188 INFO ProgressMeter - chr5:251636 28.5 12060 422.5
23:13:10.188 INFO ProgressMeter - chr5:44311760 28.7 12150 423.2
23:13:21.034 INFO ProgressMeter - chr5:58454909 28.9 12230 423.3
23:13:31.679 INFO ProgressMeter - chr5:87385299 29.1 12340 424.5
23:13:42.871 INFO ProgressMeter - chr5:112843542 29.3 12400 423.9
23:13:53.803 INFO ProgressMeter - chr5:138824528 29.4 12480 424.0
23:14:04.298 INFO ProgressMeter - chr5:142692542 29.6 12540 423.5
23:14:15.346 INFO ProgressMeter - chr5:150401635 29.8 12630 423.9
23:14:26.463 INFO ProgressMeter - chr5:177090759 30.0 12700 423.6
23:14:36.686 INFO ProgressMeter - chr5:177282463 30.2 12770 423.5
23:14:46.822 INFO ProgressMeter - chr6:401810 30.3 12860 424.1
23:14:57.399 INFO ProgressMeter - chr6:26045739 30.5 12960 425.0
23:15:07.903 INFO ProgressMeter - chr6:30704035 30.7 13020 424.5
23:15:18.355 INFO ProgressMeter - chr6:32217993 30.8 13100 424.7
23:15:28.761 INFO ProgressMeter - chr6:41999550 31.0 13200 425.5
23:15:39.966 INFO ProgressMeter - chr6:111674497 31.2 13300 426.2
23:15:52.860 INFO ProgressMeter - chr6:117323493 31.4 13360 425.2
23:16:03.731 INFO ProgressMeter - chr6:117332125 31.6 13410 424.3
23:16:14.785 INFO ProgressMeter - chr6:117344058 31.8 13470 423.8
23:16:26.325 INFO ProgressMeter - chr6:135205668 32.0 13550 423.7
23:16:44.643 INFO ProgressMeter - chr6:135213562 32.3 13610 421.6
23:16:55.078 INFO ProgressMeter - chr6:137878892 32.5 13670 421.2
23:17:05.988 INFO ProgressMeter - chr6:151944194 32.6 13740 421.0
23:17:16.645 INFO ProgressMeter - chr6:157207104 32.8 13820 421.1
23:17:27.408 INFO ProgressMeter - chr6:164624222 33.0 13910 421.6
23:17:38.620 INFO ProgressMeter - chr7:13894292 33.2 13990 421.6
23:17:48.798 INFO ProgressMeter - chr7:13932253 33.4 14030 420.6
23:18:00.074 INFO ProgressMeter - chr7:13942087 33.5 14090 420.1
23:18:10.324 INFO ProgressMeter - chr7:13947343 33.7 14120 418.8
23:18:21.194 INFO ProgressMeter - chr7:13952873 33.9 14160 417.8
23:18:34.127 INFO ProgressMeter - chr7:13960992 34.1 14210 416.6
23:18:45.564 INFO ProgressMeter - chr7:13970004 34.3 14260 415.7
23:18:58.032 INFO ProgressMeter - chr7:13975517 34.5 14300 414.4
23:19:09.461 INFO ProgressMeter - chr7:13982380 34.7 14350 413.6
23:19:23.964 INFO ProgressMeter - chr7:13988812 34.9 14390 411.9
23:19:35.117 INFO ProgressMeter - chr7:55156060 35.1 14460 411.7
23:19:47.056 INFO ProgressMeter - chr7:55170964 35.3 14510 410.8
23:19:58.891 INFO ProgressMeter - chr7:55180204 35.5 14560 409.9
23:20:09.921 INFO ProgressMeter - chr7:78521428 35.7 14630 409.7
23:20:20.287 INFO ProgressMeter - chr7:102028090 35.9 14720 410.3
23:20:30.669 INFO ProgressMeter - chr7:106886133 36.1 14800 410.5
23:20:41.808 INFO ProgressMeter - chr7:129211634 36.2 14870 410.4
23:20:52.257 INFO ProgressMeter - chr7:140794175 36.4 14940 410.3
23:21:02.474 INFO ProgressMeter - chr7:151484735 36.6 15040 411.1
23:21:13.405 INFO ProgressMeter - chr7:152182286 36.8 15100 410.7
23:21:23.477 INFO ProgressMeter - chr8:23681263 36.9 15190 411.3
23:21:35.014 INFO ProgressMeter - chr8:32742973 37.1 15270 411.3
23:21:46.106 INFO ProgressMeter - chr8:38431079 37.3 15360 411.7
23:21:56.806 INFO ProgressMeter - chr8:47778457 37.5 15430 411.6
23:22:07.541 INFO ProgressMeter - chr8:47943207 37.7 15520 412.0
23:22:18.273 INFO ProgressMeter - chr8:73962766 37.8 15620 412.7
23:22:31.244 INFO ProgressMeter - chr8:127736592 38.1 15700 412.5
23:22:42.228 INFO ProgressMeter - chr9:5064881 38.2 15800 413.1
23:22:53.177 INFO ProgressMeter - chr9:8527343 38.4 15900 413.8
23:23:03.482 INFO ProgressMeter - chr9:83971861 38.6 15990 414.3
23:23:13.827 INFO ProgressMeter - chr9:84751984 38.8 16040 413.7
23:23:26.585 INFO ProgressMeter - chr9:84861458 39.0 16080 412.5
23:23:38.488 INFO ProgressMeter - chr9:84872568 39.2 16120 411.4
23:23:51.182 INFO ProgressMeter - chr9:85022300 39.4 16180 410.7
23:24:01.627 INFO ProgressMeter - chr9:90864587 39.6 16220 409.9
23:24:12.845 INFO ProgressMeter - chr9:99146483 39.8 16310 410.3
23:24:23.025 INFO ProgressMeter - chr9:130886240 39.9 16390 410.5
23:24:33.652 INFO ProgressMeter - chr9:136515522 40.1 16480 411.0
23:24:43.656 INFO ProgressMeter - chrX:47563262 40.3 16650 413.5
23:24:53.801 INFO ProgressMeter - chrX:53413146 40.4 16800 415.5
23:25:04.108 INFO ProgressMeter - chrX:71392887 40.6 16960 417.6
23:25:14.572 INFO ProgressMeter - chrX:130020983 40.8 17150 420.5
23:25:18.398 INFO Mutect2 - 553116 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
91 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
553207 total reads filtered out of 74151197 reads processed
23:25:18.398 INFO ProgressMeter - chrY:20557826 40.8 17223 421.6
23:25:18.398 INFO ProgressMeter - Traversal complete. Processed 17223 total regions in 40.8 minutes.
23:25:18.413 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 5.046455083000001
23:25:18.413 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 209.172310801
23:25:18.413 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 8.29 sec
23:25:18.414 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:25:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 40.86 minutes.
Runtime.totalMemory()=3179282432
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 LS0899_tumor.bam --tumor-sample LS0899 -L TST500C_manifest.bed -O LS0899.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:25:19.887 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
23:25:19.994 INFO FilterMutectCalls - ------------------------------------------------------------
23:25:20.000 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:25:20.000 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:25:20.000 INFO FilterMutectCalls - Executing as ?@nf-ceec171720f0cbc4648d49a6fab6dac5-101ad-b5jd7 on Linux v6.12.88 amd64
23:25:20.000 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:25:20.000 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:25:19 PM GMT
23:25:20.000 INFO FilterMutectCalls - ------------------------------------------------------------
23:25:20.001 INFO FilterMutectCalls - ------------------------------------------------------------
23:25:20.001 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:25:20.001 INFO FilterMutectCalls - Picard Version: 3.1.1
23:25:20.002 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:25:20.002 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:25:20.002 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:25:20.002 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:25:20.002 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:25:20.002 INFO FilterMutectCalls - Deflater: IntelDeflater
23:25:20.002 INFO FilterMutectCalls - Inflater: IntelInflater
23:25:20.002 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:25:20.002 INFO FilterMutectCalls - Requester pays: disabled
23:25:20.003 INFO FilterMutectCalls - Initializing engine
23:25:20.162 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.eX1VE09kmX/LS0899.mutect2.raw.vcf.gz
23:25:20.269 INFO FilterMutectCalls - Done initializing engine
23:25:20.322 INFO ProgressMeter - Starting traversal
23:25:20.323 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:25:20.323 INFO FilterMutectCalls - Starting pass 0 through the variants
23:25:21.408 INFO FilterMutectCalls - Finished pass 0 through the variants
23:25:22.281 INFO FilterMutectCalls - Starting pass 1 through the variants
23:25:23.507 INFO FilterMutectCalls - Finished pass 1 through the variants
23:25:23.724 INFO FilterMutectCalls - Starting pass 2 through the variants
23:25:24.871 INFO FilterMutectCalls - Finished pass 2 through the variants
23:25:24.873 INFO FilterMutectCalls - Starting pass 3 through the variants
23:25:25.789 INFO FilterMutectCalls - Finished pass 3 through the variants
23:25:25.796 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:25:25.797 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:25:25.797 INFO ProgressMeter - chr9:8389364 0.1 9128 100051.2
23:25:25.797 INFO ProgressMeter - Traversal complete. Processed 9128 total variants in 0.1 minutes.
23:25:25.808 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:25:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=318767104
Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R hg38.fa -V LS0899.mutect2.raw.vcf.gz --stats LS0899.mutect2.raw.vcf.gz.stats -O LS0899.mutect2.filtered.vcf.gz
23:25:27.145 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
23:25:27.274 INFO SelectVariants - ------------------------------------------------------------
23:25:27.277 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:25:27.277 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:25:27.277 INFO SelectVariants - Executing as ?@nf-ceec171720f0cbc4648d49a6fab6dac5-101ad-b5jd7 on Linux v6.12.88 amd64
23:25:27.277 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:25:27.278 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:25:27 PM GMT
23:25:27.278 INFO SelectVariants - ------------------------------------------------------------
23:25:27.278 INFO SelectVariants - ------------------------------------------------------------
23:25:27.278 INFO SelectVariants - HTSJDK Version: 4.1.0
23:25:27.278 INFO SelectVariants - Picard Version: 3.1.1
23:25:27.279 INFO SelectVariants - Built for Spark Version: 3.5.0
23:25:27.279 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:25:27.279 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:25:27.279 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:25:27.279 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:25:27.279 INFO SelectVariants - Deflater: IntelDeflater
23:25:27.279 INFO SelectVariants - Inflater: IntelInflater
23:25:27.279 INFO SelectVariants - GCS max retries/reopens: 20
23:25:27.279 INFO SelectVariants - Requester pays: disabled
23:25:27.280 INFO SelectVariants - Initializing engine
23:25:27.443 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.eX1VE09kmX/LS0899.mutect2.filtered.vcf.gz
23:25:27.547 INFO SelectVariants - Done initializing engine
23:25:27.582 INFO ProgressMeter - Starting traversal
23:25:27.583 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:25:27.660 INFO ProgressMeter - chr7:55179736 0.0 2282 1850270.3
23:25:27.660 INFO ProgressMeter - Traversal complete. Processed 2282 total variants in 0.0 minutes.
23:25:27.673 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:25:27 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 LS0899.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0899.mutect2.pass.vcf.gz