Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0895/LS0895_tumor.bam.bai Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/fc/180d98ec14d0149ee3b24b41ed8341/.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://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0895/LS0895_tumor.bam Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.dict Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/fc/180d98ec14d0149ee3b24b41ed8341/.command.run ==> STAGING COMPLETE (10 inputs) 22:44:12.971 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 22:44:13.074 INFO Mutect2 - ------------------------------------------------------------ 22:44:13.076 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0 22:44:13.076 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 22:44:13.077 INFO Mutect2 - Executing as ?@nf-fc180d98ec14d0149ee3b24b41ed8341-1c3f3-9v564 on Linux v6.12.88 amd64 22:44:13.077 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04 22:44:13.077 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:12 PM GMT 22:44:13.077 INFO Mutect2 - ------------------------------------------------------------ 22:44:13.077 INFO Mutect2 - ------------------------------------------------------------ 22:44:13.079 INFO Mutect2 - HTSJDK Version: 4.1.0 22:44:13.079 INFO Mutect2 - Picard Version: 3.1.1 22:44:13.079 INFO Mutect2 - Built for Spark Version: 3.5.0 22:44:13.079 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 22:44:13.079 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 22:44:13.079 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 22:44:13.080 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 22:44:13.080 INFO Mutect2 - Deflater: IntelDeflater 22:44:13.080 INFO Mutect2 - Inflater: IntelInflater 22:44:13.080 INFO Mutect2 - GCS max retries/reopens: 20 22:44:13.080 INFO Mutect2 - Requester pays: disabled 22:44:13.081 INFO Mutect2 - Initializing engine WARNING: BAM index file /tmp/nxf.faAXGBsntV/LS0895_tumor.bam.bai is older than BAM /tmp/nxf.faAXGBsntV/LS0895_tumor.bam 22:44:13.260 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.faAXGBsntV/af-only-gnomad.hg38.vcf.gz 22:44:13.375 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.faAXGBsntV/TST500C_manifest.bed 22:44:13.413 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals 22:44:13.443 INFO Mutect2 - Done initializing engine 22:44:13.455 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 22:44:13.456 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 22:44:13.457 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions 22:44:13.457 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation 22:44:13.468 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 22:44:13.477 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions 22:44:13.477 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 22:44:13.477 INFO IntelPairHmm - Available threads: 384 22:44:13.477 INFO IntelPairHmm - Requested threads: 4 22:44:13.477 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 22:44:13.519 INFO ProgressMeter - Starting traversal 22:44:13.519 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 22:44:24.675 INFO ProgressMeter - chr1:11234219 0.2 110 591.7 22:44:35.328 INFO ProgressMeter - chr1:15937161 0.4 190 522.8 22:44:45.511 INFO ProgressMeter - chr1:26729649 0.5 280 525.1 22:44:55.955 INFO ProgressMeter - chr1:39901452 0.7 390 551.4 22:45:06.391 INFO ProgressMeter - chr1:64857654 0.9 520 590.1 22:45:16.971 INFO ProgressMeter - chr1:119507475 1.1 640 605.2 22:45:27.611 INFO ProgressMeter - chr1:156864726 1.2 740 599.3 22:45:40.187 INFO ProgressMeter - chr1:156875602 1.4 770 533.1 22:45:50.682 INFO ProgressMeter - chr1:161328394 1.6 860 531.1 22:46:00.863 INFO ProgressMeter - chr1:193125205 1.8 950 531.0 22:46:11.293 INFO ProgressMeter - chr1:204548008 2.0 1060 540.0 22:46:21.329 INFO ProgressMeter - chr1:241500550 2.1 1160 544.6 22:46:31.836 INFO ProgressMeter - chr10:8069471 2.3 1240 537.9 22:46:42.823 INFO ProgressMeter - chr10:32010250 2.5 1320 530.5 22:46:53.623 INFO ProgressMeter - chr10:43114958 2.7 1410 528.4 22:47:04.484 INFO ProgressMeter - chr10:62092749 2.8 1490 522.9 22:47:14.986 INFO ProgressMeter - chr10:87922241 3.0 1570 519.1 22:47:25.347 INFO ProgressMeter - chr10:102593634 3.2 1670 522.3 22:47:36.554 INFO ProgressMeter - chr10:121481173 3.4 1770 523.1 22:47:47.105 INFO ProgressMeter - chr10:121594064 3.6 1840 516.9 22:47:57.831 INFO ProgressMeter - chr11:69651161 3.7 2000 535.0 22:48:07.868 INFO ProgressMeter - chr11:69777915 3.9 2100 537.7 22:48:18.477 INFO ProgressMeter - chr11:76516140 4.1 2170 531.5 22:48:29.658 INFO ProgressMeter - chr11:77361148 4.3 2230 522.4 22:48:40.214 INFO ProgressMeter - chr11:94447217 4.4 2300 517.4 22:48:51.625 INFO ProgressMeter - chr11:102325175 4.6 2360 509.2 22:49:01.697 INFO ProgressMeter - chr11:118472082 4.8 2470 514.3 22:49:12.416 INFO ProgressMeter - chr11:118509946 5.0 2540 509.9 22:49:24.955 INFO ProgressMeter - chr11:128459812 5.2 2630 506.7 22:49:35.408 INFO ProgressMeter - chr12:310883 5.4 2710 505.1 22:49:46.335 INFO ProgressMeter - chr12:4380591 5.5 2810 506.6 22:49:56.396 INFO ProgressMeter - chr12:6578027 5.7 2870 502.2 22:50:06.799 INFO ProgressMeter - chr12:11856019 5.9 2940 499.3 22:50:17.315 INFO ProgressMeter - chr12:11861482 6.1 2980 491.5 22:50:29.122 INFO ProgressMeter - chr12:11867672 6.3 3030 484.0 22:50:39.633 INFO ProgressMeter - chr12:25209793 6.4 3110 483.3 22:50:50.151 INFO ProgressMeter - chr12:45846854 6.6 3180 481.1 22:51:00.409 INFO ProgressMeter - chr12:49033194 6.8 3260 480.7 22:51:11.196 INFO ProgressMeter - chr12:49054654 7.0 3350 481.2 22:51:21.369 INFO ProgressMeter - chr12:57092827 7.1 3450 483.8 22:51:31.718 INFO ProgressMeter - chr12:68828769 7.3 3570 488.8 22:51:41.994 INFO ProgressMeter - chr12:120994162 7.5 3690 493.7 22:51:52.430 INFO ProgressMeter - chr13:20988656 7.6 3800 496.8 22:52:02.819 INFO ProgressMeter - chr13:28345443 7.8 3920 501.2 22:52:13.473 INFO ProgressMeter - chr13:28438219 8.0 3970 496.3 22:52:23.603 INFO ProgressMeter - chr13:32389276 8.2 4060 497.1 22:52:34.010 INFO ProgressMeter - chr13:102277277 8.3 4190 502.3 22:52:46.241 INFO ProgressMeter - chr14:23308814 8.5 4310 504.4 22:52:56.321 INFO ProgressMeter - chr14:81091067 8.7 4440 509.6 22:53:06.795 INFO ProgressMeter - chr15:32734505 8.9 4550 511.9 22:53:17.067 INFO ProgressMeter - chr15:41711138 9.1 4630 511.1 22:53:27.359 INFO ProgressMeter - chr15:49469984 9.2 4720 511.3 22:53:37.696 INFO ProgressMeter - chr15:88255904 9.4 4820 512.6 22:53:47.736 INFO ProgressMeter - chr15:92956457 9.6 4940 516.2 22:53:58.481 INFO ProgressMeter - chr16:2080163 9.7 5060 519.0 22:54:09.428 INFO ProgressMeter - chr16:3736730 9.9 5190 522.6 22:54:19.616 INFO ProgressMeter - chr16:11258844 10.1 5270 521.7 22:54:30.028 INFO ProgressMeter - chr16:55657899 10.3 5370 522.6 22:54:40.175 INFO ProgressMeter - chr16:72793822 10.4 5460 522.8 22:54:50.644 INFO ProgressMeter - chr16:81908414 10.6 5540 521.7 22:55:00.910 INFO ProgressMeter - chr16:89769953 10.8 5640 522.7 22:55:11.544 INFO ProgressMeter - chr17:8087294 11.0 5770 526.1 22:55:21.908 INFO ProgressMeter - chr17:18054125 11.1 5890 528.7 22:55:32.771 INFO ProgressMeter - chr17:39490555 11.3 6010 530.9 22:55:43.288 INFO ProgressMeter - chr17:40411107 11.5 6130 533.2 22:55:53.626 INFO ProgressMeter - chr17:43079332 11.7 6250 535.6 22:56:05.382 INFO ProgressMeter - chr17:43531659 11.9 6330 533.5 22:56:17.393 INFO ProgressMeter - chr17:43544045 12.1 6400 530.5 22:56:27.732 INFO ProgressMeter - chr17:58696691 12.2 6490 530.4 22:56:38.759 INFO ProgressMeter - chr17:61776399 12.4 6590 530.6 22:56:48.913 INFO ProgressMeter - chr17:80883417 12.6 6710 533.0 22:57:00.462 INFO ProgressMeter - chr18:44952691 12.8 6830 534.3 22:57:10.898 INFO ProgressMeter - chr19:2211749 13.0 6970 538.0 22:57:21.463 INFO ProgressMeter - chr19:7267643 13.1 7130 542.9 22:57:31.559 INFO ProgressMeter - chr19:14516832 13.3 7260 545.8 22:57:43.349 INFO ProgressMeter - chr19:17843378 13.5 7390 547.5 22:57:53.379 INFO ProgressMeter - chr19:35728096 13.7 7520 550.3 22:58:03.496 INFO ProgressMeter - chr19:41257491 13.8 7630 551.6 22:58:13.996 INFO ProgressMeter - chr19:45355663 14.0 7710 550.4 22:58:26.511 INFO ProgressMeter - chr2:15936270 14.2 7860 552.9 22:58:38.388 INFO ProgressMeter - chr2:25743151 14.4 7970 552.9 22:58:49.941 INFO ProgressMeter - chr2:29226109 14.6 8050 551.1 22:59:01.206 INFO ProgressMeter - chr2:42330450 14.8 8140 550.2 22:59:12.266 INFO ProgressMeter - chr2:47799951 15.0 8210 548.1 22:59:23.073 INFO ProgressMeter - chr2:98555551 15.2 8310 548.2 22:59:33.373 INFO ProgressMeter - chr2:111126377 15.3 8410 548.6 22:59:43.834 INFO ProgressMeter - chr2:111161417 15.5 8440 544.3 22:59:58.057 INFO ProgressMeter - chr2:113227722 15.7 8500 539.9 23:00:08.304 INFO ProgressMeter - chr2:113234212 15.9 8550 537.3 23:00:18.769 INFO ProgressMeter - chr2:140502961 16.1 8660 538.3 23:00:29.294 INFO ProgressMeter - chr2:172564976 16.3 8760 538.6 23:00:39.543 INFO ProgressMeter - chr2:201266759 16.4 8870 539.7 23:00:50.320 INFO ProgressMeter - chr2:219576879 16.6 8980 540.5 23:01:00.681 INFO ProgressMeter - chr2:222206868 16.8 9030 537.9 23:01:12.322 INFO ProgressMeter - chr2:222215325 17.0 9090 535.3 23:01:22.809 INFO ProgressMeter - chr2:222293973 17.2 9140 532.8 23:01:33.483 INFO ProgressMeter - chr20:32358774 17.3 9250 533.7 23:01:44.282 INFO ProgressMeter - chr20:41116276 17.5 9360 534.5 23:01:54.933 INFO ProgressMeter - chr20:53582359 17.7 9460 534.8 23:02:05.197 INFO ProgressMeter - chr21:38381826 17.9 9560 535.2 23:02:17.556 INFO ProgressMeter - chr21:41490556 18.1 9640 533.6 23:02:28.264 INFO ProgressMeter - chr21:41499331 18.2 9680 530.5 23:02:38.558 INFO ProgressMeter - chr21:42186824 18.4 9740 528.9 23:02:50.124 INFO ProgressMeter - chr22:23291559 18.6 9850 529.3 23:03:02.130 INFO ProgressMeter - chr22:29285666 18.8 9970 530.0 23:03:12.612 INFO ProgressMeter - chr22:41168719 19.0 10080 530.9 23:03:23.277 INFO ProgressMeter - chr3:12354075 19.2 10180 531.2 23:03:35.910 INFO ProgressMeter - chr3:12361583 19.4 10230 528.0 23:03:47.377 INFO ProgressMeter - chr3:12370431 19.6 10290 526.0 23:03:58.591 INFO ProgressMeter - chr3:12417002 19.8 10360 524.5 23:04:09.352 INFO ProgressMeter - chr3:41094711 19.9 10470 525.3 23:04:19.365 INFO ProgressMeter - chr3:49368426 20.1 10560 525.4 23:04:29.918 INFO ProgressMeter - chr3:52678498 20.3 10690 527.3 23:04:40.318 INFO ProgressMeter - chr3:128486016 20.4 10810 528.7 23:04:50.626 INFO ProgressMeter - chr3:138694784 20.6 10910 529.1 23:05:00.888 INFO ProgressMeter - chr3:142561383 20.8 11010 529.6 23:05:12.009 INFO ProgressMeter - chr3:185449898 21.0 11130 530.6 23:05:22.656 INFO ProgressMeter - chr3:189789799 21.2 11220 530.4 23:05:33.369 INFO ProgressMeter - chr4:1806049 21.3 11330 531.2 23:05:43.543 INFO ProgressMeter - chr4:54267550 21.5 11440 532.1 23:05:56.807 INFO ProgressMeter - chr4:54736719 21.7 11510 529.9 23:06:07.436 INFO ProgressMeter - chr4:80278756 21.9 11610 530.2 23:06:17.968 INFO ProgressMeter - chr4:105272562 22.1 11710 530.5 23:06:28.301 INFO ProgressMeter - chr4:184419467 22.2 11830 531.8 23:06:38.946 INFO ProgressMeter - chr4:186663597 22.4 11910 531.1 23:06:49.335 INFO ProgressMeter - chr5:38962913 22.6 12010 531.5 23:06:59.379 INFO ProgressMeter - chr5:58456490 22.8 12120 532.4 23:07:11.140 INFO ProgressMeter - chr5:112838731 23.0 12260 534.0 23:07:21.904 INFO ProgressMeter - chr5:132594867 23.1 12340 533.3 23:07:33.003 INFO ProgressMeter - chr5:149496836 23.3 12440 533.3 23:07:43.394 INFO ProgressMeter - chr5:150406879 23.5 12540 533.7 23:07:57.848 INFO ProgressMeter - chr5:177135462 23.7 12630 532.0 23:08:08.149 INFO ProgressMeter - chr5:180619103 23.9 12730 532.4 23:08:18.238 INFO ProgressMeter - chr6:20486982 24.1 12840 533.3 23:08:29.627 INFO ProgressMeter - chr6:30711665 24.3 12950 533.6 23:08:40.249 INFO ProgressMeter - chr6:36682724 24.4 13060 534.3 23:08:50.837 INFO ProgressMeter - chr6:106104898 24.6 13190 535.7 23:09:02.514 INFO ProgressMeter - chr6:117321909 24.8 13260 534.3 23:09:13.003 INFO ProgressMeter - chr6:117332512 25.0 13320 533.0 23:09:23.138 INFO ProgressMeter - chr6:117366074 25.2 13380 531.8 23:09:33.648 INFO ProgressMeter - chr6:135207796 25.3 13460 531.3 23:09:46.545 INFO ProgressMeter - chr6:135213153 25.6 13500 528.4 23:09:57.479 INFO ProgressMeter - chr6:149676553 25.7 13570 527.3 23:10:07.904 INFO ProgressMeter - chr6:156779358 25.9 13660 527.3 23:10:18.857 INFO ProgressMeter - chr6:161111834 26.1 13760 527.4 23:10:29.907 INFO ProgressMeter - chr7:13893783 26.3 13880 528.3 23:10:40.794 INFO ProgressMeter - chr7:13933735 26.5 13930 526.6 23:10:51.557 INFO ProgressMeter - chr7:13941063 26.6 13980 524.9 23:11:02.577 INFO ProgressMeter - chr7:13948111 26.8 14030 523.2 23:11:13.452 INFO ProgressMeter - chr7:13955619 27.0 14080 521.5 23:11:23.674 INFO ProgressMeter - chr7:13964195 27.2 14130 520.1 23:11:34.397 INFO ProgressMeter - chr7:13973557 27.3 14190 518.9 23:11:45.772 INFO ProgressMeter - chr7:13978698 27.5 14230 516.7 23:11:56.455 INFO ProgressMeter - chr7:13984438 27.7 14270 514.9 23:12:06.954 INFO ProgressMeter - chr7:50319060 27.9 14320 513.4 23:12:16.975 INFO ProgressMeter - chr7:55166527 28.1 14390 512.9 23:12:28.132 INFO ProgressMeter - chr7:55177544 28.2 14440 511.3 23:12:38.338 INFO ProgressMeter - chr7:78127370 28.4 14510 510.7 23:12:48.767 INFO ProgressMeter - chr7:92827732 28.6 14620 511.4 23:12:58.810 INFO ProgressMeter - chr7:116758457 28.8 14730 512.3 23:13:10.447 INFO ProgressMeter - chr7:140791166 28.9 14820 511.9 23:13:21.212 INFO ProgressMeter - chr7:148846468 29.1 14930 512.6 23:13:31.549 INFO ProgressMeter - chr7:152238705 29.3 15030 513.0 23:13:42.545 INFO ProgressMeter - chr8:32646870 29.5 15140 513.5 23:13:53.015 INFO ProgressMeter - chr8:38417304 29.7 15230 513.5 23:14:03.238 INFO ProgressMeter - chr8:41943746 29.8 15300 512.9 23:14:14.332 INFO ProgressMeter - chr8:47890432 30.0 15400 513.1 23:14:24.398 INFO ProgressMeter - chr8:68191720 30.2 15510 513.9 23:14:34.998 INFO ProgressMeter - chr8:127739351 30.4 15610 514.2 23:14:45.526 INFO ProgressMeter - chr9:8375934 30.5 15740 515.5 23:14:55.623 INFO ProgressMeter - chr9:83970932 30.7 15860 516.6 23:15:06.906 INFO ProgressMeter - chr9:84811983 30.9 15930 515.7 23:15:19.063 INFO ProgressMeter - chr9:84865545 31.1 15980 514.0 23:15:29.092 INFO ProgressMeter - chr9:85023001 31.3 16040 513.1 23:15:39.302 INFO ProgressMeter - chr9:95449187 31.4 16110 512.6 23:15:50.447 INFO ProgressMeter - chr9:132896235 31.6 16230 513.4 23:16:01.102 INFO ProgressMeter - chrX:40063044 31.8 16380 515.2 23:16:11.179 INFO ProgressMeter - chrX:48793791 32.0 16500 516.3 23:16:21.795 INFO ProgressMeter - chrX:53196984 32.1 16580 515.9 23:16:31.852 INFO ProgressMeter - chrX:64192987 32.3 16670 516.0 23:16:41.952 INFO ProgressMeter - chrX:71136579 32.5 16780 516.7 23:16:52.752 INFO ProgressMeter - chrX:77683908 32.7 16890 517.2 23:17:04.142 INFO ProgressMeter - chrX:130015893 32.8 17030 518.5 23:17:06.705 INFO Mutect2 - 484341 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 89 read(s) filtered by: GoodCigarReadFilter 0 read(s) filtered by: WellformedReadFilter 484432 total reads filtered out of 60501148 reads processed 23:17:06.706 INFO ProgressMeter - chrY:20960482 32.9 17101 520.0 23:17:06.706 INFO ProgressMeter - Traversal complete. Processed 17101 total regions in 32.9 minutes. 23:17:06.720 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 4.063908842 23:17:06.721 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 176.761959493 23:17:06.721 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 6.61 sec 23:17:06.721 INFO Mutect2 - Shutting down engine [June 8, 2026 at 11:17:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 32.90 minutes. Runtime.totalMemory()=2004877312 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 LS0895_tumor.bam --tumor-sample LS0895 -L TST500C_manifest.bed -O LS0895.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz 23:17:07.988 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 23:17:08.096 INFO FilterMutectCalls - ------------------------------------------------------------ 23:17:08.098 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0 23:17:08.098 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/ 23:17:08.098 INFO FilterMutectCalls - Executing as ?@nf-fc180d98ec14d0149ee3b24b41ed8341-1c3f3-9v564 on Linux v6.12.88 amd64 23:17:08.099 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04 23:17:08.099 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:17:07 PM GMT 23:17:08.099 INFO FilterMutectCalls - ------------------------------------------------------------ 23:17:08.099 INFO FilterMutectCalls - ------------------------------------------------------------ 23:17:08.100 INFO FilterMutectCalls - HTSJDK Version: 4.1.0 23:17:08.100 INFO FilterMutectCalls - Picard Version: 3.1.1 23:17:08.100 INFO FilterMutectCalls - Built for Spark Version: 3.5.0 23:17:08.100 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2 23:17:08.100 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 23:17:08.100 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 23:17:08.100 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 23:17:08.100 INFO FilterMutectCalls - Deflater: IntelDeflater 23:17:08.100 INFO FilterMutectCalls - Inflater: IntelInflater 23:17:08.100 INFO FilterMutectCalls - GCS max retries/reopens: 20 23:17:08.100 INFO FilterMutectCalls - Requester pays: disabled 23:17:08.101 INFO FilterMutectCalls - Initializing engine 23:17:08.272 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.faAXGBsntV/LS0895.mutect2.raw.vcf.gz 23:17:08.379 INFO FilterMutectCalls - Done initializing engine 23:17:08.435 INFO ProgressMeter - Starting traversal 23:17:08.436 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 23:17:08.436 INFO FilterMutectCalls - Starting pass 0 through the variants 23:17:09.442 INFO FilterMutectCalls - Finished pass 0 through the variants 23:17:11.994 INFO FilterMutectCalls - Starting pass 1 through the variants 23:17:12.973 INFO FilterMutectCalls - Finished pass 1 through the variants 23:17:13.391 INFO FilterMutectCalls - Starting pass 2 through the variants 23:17:14.322 INFO FilterMutectCalls - Finished pass 2 through the variants 23:17:14.323 INFO FilterMutectCalls - Starting pass 3 through the variants 23:17:15.194 INFO FilterMutectCalls - Finished pass 3 through the variants 23:17:15.203 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter 23:17:15.203 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter 23:17:15.204 INFO ProgressMeter - chr9:130885614 0.1 9080 80508.3 23:17:15.204 INFO ProgressMeter - Traversal complete. Processed 9080 total variants in 0.1 minutes. 23:17:15.216 INFO FilterMutectCalls - Shutting down engine [June 8, 2026 at 11:17:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=520093696 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 LS0895.mutect2.raw.vcf.gz --stats LS0895.mutect2.raw.vcf.gz.stats -O LS0895.mutect2.filtered.vcf.gz 23:17:16.637 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 23:17:16.755 INFO SelectVariants - ------------------------------------------------------------ 23:17:16.757 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0 23:17:16.757 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 23:17:16.757 INFO SelectVariants - Executing as ?@nf-fc180d98ec14d0149ee3b24b41ed8341-1c3f3-9v564 on Linux v6.12.88 amd64 23:17:16.757 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04 23:17:16.758 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:17:16 PM GMT 23:17:16.758 INFO SelectVariants - ------------------------------------------------------------ 23:17:16.758 INFO SelectVariants - ------------------------------------------------------------ 23:17:16.758 INFO SelectVariants - HTSJDK Version: 4.1.0 23:17:16.758 INFO SelectVariants - Picard Version: 3.1.1 23:17:16.758 INFO SelectVariants - Built for Spark Version: 3.5.0 23:17:16.758 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 23:17:16.759 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 23:17:16.759 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 23:17:16.759 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 23:17:16.759 INFO SelectVariants - Deflater: IntelDeflater 23:17:16.759 INFO SelectVariants - Inflater: IntelInflater 23:17:16.759 INFO SelectVariants - GCS max retries/reopens: 20 23:17:16.759 INFO SelectVariants - Requester pays: disabled 23:17:16.759 INFO SelectVariants - Initializing engine 23:17:16.925 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.faAXGBsntV/LS0895.mutect2.filtered.vcf.gz 23:17:17.030 INFO SelectVariants - Done initializing engine 23:17:17.067 INFO ProgressMeter - Starting traversal 23:17:17.068 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 23:17:17.139 INFO ProgressMeter - chr7:78627209 0.0 2270 1973913.0 23:17:17.139 INFO ProgressMeter - Traversal complete. Processed 2270 total variants in 0.0 minutes. 23:17:17.150 INFO SelectVariants - Shutting down engine [June 8, 2026 at 11:17:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=301989888 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 LS0895.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0895.mutect2.pass.vcf.gz