Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/09/8a6f168e5dacab7bb7b4a8de17ea57/.command.sh
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0897/LS0897_tumor.bam
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://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0897/LS0897_tumor.bam.bai
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/09/8a6f168e5dacab7bb7b4a8de17ea57/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:29.490 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
22:44:29.595 INFO Mutect2 - ------------------------------------------------------------
22:44:29.597 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:29.597 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:29.597 INFO Mutect2 - Executing as ?@nf-098a6f168e5dacab7bb7b4a8de17ea57-420f6-zm4ll on Linux v6.12.88 amd64
22:44:29.598 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:29.598 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:29 PM GMT
22:44:29.598 INFO Mutect2 - ------------------------------------------------------------
22:44:29.598 INFO Mutect2 - ------------------------------------------------------------
22:44:29.599 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:29.599 INFO Mutect2 - Picard Version: 3.1.1
22:44:29.609 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:29.609 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:29.609 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:29.609 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:29.609 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:29.610 INFO Mutect2 - Deflater: IntelDeflater
22:44:29.610 INFO Mutect2 - Inflater: IntelInflater
22:44:29.610 INFO Mutect2 - GCS max retries/reopens: 20
22:44:29.610 INFO Mutect2 - Requester pays: disabled
22:44:29.610 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.V08ylHh8lW/LS0897_tumor.bam.bai is older than BAM /tmp/nxf.V08ylHh8lW/LS0897_tumor.bam
22:44:29.836 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.V08ylHh8lW/af-only-gnomad.hg38.vcf.gz
22:44:29.941 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.V08ylHh8lW/TST500C_manifest.bed
22:44:29.971 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:29.998 INFO Mutect2 - Done initializing engine
22:44:30.008 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
22:44:30.009 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
22:44:30.010 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:30.010 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:30.019 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
22:44:30.028 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:30.028 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:30.029 INFO IntelPairHmm - Available threads: 384
22:44:30.029 INFO IntelPairHmm - Requested threads: 4
22:44:30.029 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:30.065 INFO ProgressMeter - Starting traversal
22:44:30.066 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:40.807 INFO ProgressMeter - chr1:11109647 0.2 60 335.2
22:44:51.421 INFO ProgressMeter - chr1:11256931 0.4 130 365.3
22:45:02.358 INFO ProgressMeter - chr1:15934207 0.5 190 353.0
22:45:14.500 INFO ProgressMeter - chr1:18747491 0.7 250 337.6
22:45:25.228 INFO ProgressMeter - chr1:36341767 0.9 320 348.1
22:45:35.252 INFO ProgressMeter - chr1:39903053 1.1 400 368.2
22:45:46.229 INFO ProgressMeter - chr1:50974068 1.3 500 393.9
22:45:56.637 INFO ProgressMeter - chr1:114710360 1.4 610 422.8
22:46:08.021 INFO ProgressMeter - chr1:119937280 1.6 690 422.6
22:46:18.418 INFO ProgressMeter - chr1:156873459 1.8 760 420.9
22:46:28.720 INFO ProgressMeter - chr1:158647537 2.0 830 419.7
22:46:39.135 INFO ProgressMeter - chr1:176043708 2.2 920 427.7
22:46:49.533 INFO ProgressMeter - chr1:204469054 2.3 1020 438.8
22:47:00.204 INFO ProgressMeter - chr1:226361967 2.5 1120 447.6
22:47:12.406 INFO ProgressMeter - chr1:243503612 2.7 1200 443.5
22:47:22.875 INFO ProgressMeter - chr10:27048831 2.9 1270 440.9
22:47:32.953 INFO ProgressMeter - chr10:43109029 3.0 1360 446.2
22:47:45.004 INFO ProgressMeter - chr10:43117553 3.2 1410 434.0
22:47:56.394 INFO ProgressMeter - chr10:68573547 3.4 1480 430.4
22:48:07.335 INFO ProgressMeter - chr10:87965436 3.6 1570 433.6
22:48:17.681 INFO ProgressMeter - chr10:110577814 3.8 1650 434.9
22:48:29.955 INFO ProgressMeter - chr10:121481463 4.0 1730 432.7
22:48:40.624 INFO ProgressMeter - chr10:130900194 4.2 1790 428.6
22:48:50.742 INFO ProgressMeter - chr11:64805709 4.3 1890 435.0
22:49:01.985 INFO ProgressMeter - chr11:69701323 4.5 1990 439.1
22:49:12.594 INFO ProgressMeter - chr11:69777079 4.7 2050 435.4
22:49:23.607 INFO ProgressMeter - chr11:69817001 4.9 2090 427.2
22:49:33.723 INFO ProgressMeter - chr11:77355666 5.1 2160 426.8
22:49:43.808 INFO ProgressMeter - chr11:101049927 5.2 2250 430.3
22:49:54.316 INFO ProgressMeter - chr11:102336758 5.4 2300 425.6
22:50:05.803 INFO ProgressMeter - chr11:118473696 5.6 2410 430.7
22:50:16.084 INFO ProgressMeter - chr11:118510078 5.8 2480 430.0
22:50:26.498 INFO ProgressMeter - chr11:125652336 5.9 2550 429.3
22:50:37.972 INFO ProgressMeter - chr11:128810798 6.1 2620 427.3
22:50:48.655 INFO ProgressMeter - chr12:4299858 6.3 2710 429.5
22:50:59.682 INFO ProgressMeter - chr12:4443523 6.5 2790 429.7
22:51:11.029 INFO ProgressMeter - chr12:11854749 6.7 2870 429.5
22:51:23.506 INFO ProgressMeter - chr12:11861176 6.9 2930 425.2
22:51:33.720 INFO ProgressMeter - chr12:11868284 7.1 2980 422.0
22:51:44.130 INFO ProgressMeter - chr12:25206243 7.2 3050 421.6
22:51:55.511 INFO ProgressMeter - chr12:45850871 7.4 3140 422.9
22:52:06.202 INFO ProgressMeter - chr12:49033608 7.6 3200 420.9
22:52:17.871 INFO ProgressMeter - chr12:49051154 7.8 3270 419.4
22:52:28.541 INFO ProgressMeter - chr12:56094400 8.0 3370 422.6
22:52:40.136 INFO ProgressMeter - chr12:57470861 8.2 3450 422.4
22:52:50.591 INFO ProgressMeter - chr12:68837480 8.3 3550 425.6
22:53:01.691 INFO ProgressMeter - chr12:120979024 8.5 3650 428.0
22:53:12.377 INFO ProgressMeter - chr12:132679495 8.7 3730 428.5
22:53:22.755 INFO ProgressMeter - chr13:21697277 8.9 3800 428.0
22:53:33.788 INFO ProgressMeter - chr13:28385549 9.1 3900 430.4
22:53:44.416 INFO ProgressMeter - chr13:32325074 9.2 3960 428.6
22:53:55.655 INFO ProgressMeter - chr13:32396896 9.4 4040 428.6
22:54:06.515 INFO ProgressMeter - chr13:102295837 9.6 4160 433.0
22:54:17.547 INFO ProgressMeter - chr13:113312498 9.8 4260 435.1
22:54:28.007 INFO ProgressMeter - chr14:37590249 10.0 4330 434.5
22:54:39.718 INFO ProgressMeter - chr14:81143818 10.2 4420 435.0
22:54:50.040 INFO ProgressMeter - chr14:104773077 10.3 4500 435.5
22:55:00.871 INFO ProgressMeter - chr15:40709100 10.5 4570 434.7
22:55:11.818 INFO ProgressMeter - chr15:41766446 10.7 4640 433.8
22:55:22.587 INFO ProgressMeter - chr15:73703798 10.9 4740 435.8
22:55:33.275 INFO ProgressMeter - chr15:89281168 11.1 4820 436.1
22:55:44.059 INFO ProgressMeter - chr15:92948950 11.2 4920 438.0
22:55:54.740 INFO ProgressMeter - chr16:298185 11.4 5010 439.0
22:56:04.957 INFO ProgressMeter - chr16:2561478 11.6 5100 440.4
22:56:16.191 INFO ProgressMeter - chr16:3731774 11.8 5180 440.1
22:56:26.628 INFO ProgressMeter - chr16:11253417 11.9 5260 440.4
22:56:36.660 INFO ProgressMeter - chr16:50754459 12.1 5340 441.0
22:56:47.582 INFO ProgressMeter - chr16:68829652 12.3 5430 441.8
22:56:58.732 INFO ProgressMeter - chr16:72889729 12.5 5480 439.2
22:57:09.195 INFO ProgressMeter - chr16:81939967 12.7 5550 438.7
22:57:19.469 INFO ProgressMeter - chr16:89739476 12.8 5610 437.5
22:57:29.670 INFO ProgressMeter - chr17:7674271 13.0 5700 438.7
22:57:40.894 INFO ProgressMeter - chr17:16061637 13.2 5800 440.0
22:57:50.989 INFO ProgressMeter - chr17:31219003 13.3 5900 442.0
22:58:01.249 INFO ProgressMeter - chr17:39471294 13.5 6000 443.8
22:58:11.977 INFO ProgressMeter - chr17:40389963 13.7 6090 444.6
22:58:22.950 INFO ProgressMeter - chr17:43064082 13.9 6210 447.4
22:58:33.226 INFO ProgressMeter - chr17:43124227 14.1 6280 446.9
22:58:43.255 INFO ProgressMeter - chr17:43536273 14.2 6330 445.2
22:58:59.630 INFO ProgressMeter - chr17:43543970 14.5 6390 440.9
22:59:10.310 INFO ProgressMeter - chr17:58358706 14.7 6460 440.3
22:59:22.099 INFO ProgressMeter - chr17:61683598 14.9 6560 441.2
22:59:32.486 INFO ProgressMeter - chr17:72122757 15.0 6640 441.5
22:59:43.169 INFO ProgressMeter - chr18:22182755 15.2 6740 442.9
22:59:53.829 INFO ProgressMeter - chr18:47865057 15.4 6810 442.3
23:00:04.394 INFO ProgressMeter - chr19:2210619 15.6 6920 444.4
23:00:15.273 INFO ProgressMeter - chr19:5214649 15.8 7020 445.6
23:00:25.562 INFO ProgressMeter - chr19:10137117 15.9 7110 446.5
23:00:36.649 INFO ProgressMeter - chr19:11034994 16.1 7210 447.6
23:00:47.790 INFO ProgressMeter - chr19:15187879 16.3 7290 447.4
23:00:59.953 INFO ProgressMeter - chr19:17844232 16.5 7380 447.3
23:01:10.354 INFO ProgressMeter - chr19:29822444 16.7 7470 448.1
23:01:20.465 INFO ProgressMeter - chr19:40236255 16.8 7560 448.9
23:01:34.014 INFO ProgressMeter - chr19:41261010 17.1 7640 447.7
23:01:45.119 INFO ProgressMeter - chr19:45364233 17.3 7730 448.1
23:01:55.207 INFO ProgressMeter - chr19:50406405 17.4 7820 448.9
23:02:05.346 INFO ProgressMeter - chr2:15943986 17.6 7890 448.6
23:02:16.186 INFO ProgressMeter - chr2:25742113 17.8 7970 448.5
23:02:27.622 INFO ProgressMeter - chr2:29223715 18.0 8040 447.7
23:02:38.316 INFO ProgressMeter - chr2:29694848 18.1 8090 446.0
23:02:48.809 INFO ProgressMeter - chr2:47379767 18.3 8160 445.6
23:02:59.506 INFO ProgressMeter - chr2:58161520 18.5 8220 444.5
23:03:10.345 INFO ProgressMeter - chr2:98520047 18.7 8290 444.0
23:03:21.178 INFO ProgressMeter - chr2:108768305 18.9 8380 444.5
23:03:31.977 INFO ProgressMeter - chr2:111150042 19.0 8420 442.4
23:03:42.642 INFO ProgressMeter - chr2:113224738 19.2 8470 440.9
23:03:52.972 INFO ProgressMeter - chr2:113230154 19.4 8510 439.1
23:04:03.390 INFO ProgressMeter - chr2:113234504 19.6 8540 436.7
23:04:13.745 INFO ProgressMeter - chr2:140350906 19.7 8620 436.9
23:04:25.061 INFO ProgressMeter - chr2:141188419 19.9 8720 437.8
23:04:35.835 INFO ProgressMeter - chr2:197400713 20.1 8830 439.4
23:04:46.154 INFO ProgressMeter - chr2:212124750 20.3 8930 440.6
23:04:56.365 INFO ProgressMeter - chr2:222204205 20.4 8990 439.9
23:05:07.814 INFO ProgressMeter - chr2:222212512 20.6 9050 438.7
23:05:19.052 INFO ProgressMeter - chr2:222220467 20.8 9100 437.2
23:05:29.461 INFO ProgressMeter - chr2:226797670 21.0 9170 436.9
23:05:41.388 INFO ProgressMeter - chr20:32436905 21.2 9250 436.6
23:05:52.031 INFO ProgressMeter - chr20:42282487 21.4 9350 437.6
23:06:03.139 INFO ProgressMeter - chr20:56370293 21.6 9430 437.6
23:06:13.384 INFO ProgressMeter - chr21:38380026 21.7 9520 438.3
23:06:24.572 INFO ProgressMeter - chr21:41465145 21.9 9580 437.3
23:06:38.097 INFO ProgressMeter - chr21:41491678 22.1 9620 434.6
23:06:50.219 INFO ProgressMeter - chr21:41504421 22.3 9670 432.9
23:07:00.802 INFO ProgressMeter - chr22:20994157 22.5 9740 432.7
23:07:11.895 INFO ProgressMeter - chr22:23292471 22.7 9800 431.8
23:07:23.091 INFO ProgressMeter - chr22:29284586 22.9 9900 432.6
23:07:36.422 INFO ProgressMeter - chr22:29654655 23.1 9940 430.2
23:07:47.854 INFO ProgressMeter - chr22:41178423 23.3 10030 430.5
23:08:01.714 INFO ProgressMeter - chr3:12354639 23.5 10120 430.1
23:08:14.495 INFO ProgressMeter - chr3:12361583 23.7 10160 428.0
23:08:26.900 INFO ProgressMeter - chr3:12369533 23.9 10210 426.4
23:08:38.509 INFO ProgressMeter - chr3:12376144 24.1 10250 424.6
23:08:50.419 INFO ProgressMeter - chr3:12653648 24.3 10320 424.0
23:09:01.377 INFO ProgressMeter - chr3:47116621 24.5 10420 424.9
23:09:11.573 INFO ProgressMeter - chr3:49891195 24.7 10490 424.8
23:09:22.335 INFO ProgressMeter - chr3:52644702 24.9 10580 425.4
23:09:33.091 INFO ProgressMeter - chr3:119866588 25.1 10680 426.3
23:09:43.566 INFO ProgressMeter - chr3:138681965 25.2 10770 427.0
23:09:54.559 INFO ProgressMeter - chr3:142558622 25.4 10880 428.2
23:10:04.588 INFO ProgressMeter - chr3:181714713 25.6 10980 429.3
23:10:15.581 INFO ProgressMeter - chr3:186048628 25.8 11050 429.0
23:10:26.256 INFO ProgressMeter - chr3:196067516 25.9 11150 429.9
23:10:37.237 INFO ProgressMeter - chr4:20617036 26.1 11260 431.1
23:10:48.680 INFO ProgressMeter - chr4:54695510 26.3 11350 431.4
23:10:59.578 INFO ProgressMeter - chr4:55102479 26.5 11410 430.7
23:11:10.350 INFO ProgressMeter - chr4:83470320 26.7 11510 431.5
23:11:21.375 INFO ProgressMeter - chr4:105269608 26.9 11580 431.2
23:11:31.691 INFO ProgressMeter - chr4:152382379 27.0 11680 432.2
23:11:43.344 INFO ProgressMeter - chr4:186621052 27.2 11760 432.0
23:11:53.558 INFO ProgressMeter - chr5:1295197 27.4 11830 431.9
23:12:04.006 INFO ProgressMeter - chr5:44362662 27.6 11940 433.1
23:12:14.925 INFO ProgressMeter - chr5:68295418 27.7 12040 433.9
23:12:26.885 INFO ProgressMeter - chr5:112840411 27.9 12150 434.8
23:12:37.671 INFO ProgressMeter - chr5:132603298 28.1 12220 434.5
23:12:47.928 INFO ProgressMeter - chr5:142692614 28.3 12300 434.7
23:12:58.905 INFO ProgressMeter - chr5:150142178 28.5 12390 435.0
23:13:12.359 INFO ProgressMeter - chr5:177090423 28.7 12470 434.4
23:13:22.909 INFO ProgressMeter - chr5:177135347 28.9 12510 433.2
23:13:33.776 INFO ProgressMeter - chr5:177516704 29.1 12580 432.9
23:13:43.798 INFO ProgressMeter - chr6:20443963 29.2 12670 433.5
23:13:53.863 INFO ProgressMeter - chr6:29942755 29.4 12770 434.4
23:14:04.761 INFO ProgressMeter - chr6:30714013 29.6 12830 433.8
23:14:15.077 INFO ProgressMeter - chr6:33320734 29.8 12900 433.6
23:14:25.218 INFO ProgressMeter - chr6:43777512 29.9 13010 434.8
23:14:35.837 INFO ProgressMeter - chr6:112068203 30.1 13100 435.3
23:14:47.050 INFO ProgressMeter - chr6:117324147 30.3 13150 434.2
23:14:57.996 INFO ProgressMeter - chr6:117335730 30.5 13210 433.6
23:15:08.171 INFO ProgressMeter - chr6:117388019 30.6 13270 433.2
23:15:18.579 INFO ProgressMeter - chr6:135207896 30.8 13340 433.0
23:15:30.633 INFO ProgressMeter - chr6:135212323 31.0 13370 431.2
23:15:41.028 INFO ProgressMeter - chr6:137871269 31.2 13420 430.4
23:15:52.712 INFO ProgressMeter - chr6:151880653 31.4 13490 429.9
23:16:04.714 INFO ProgressMeter - chr6:157206628 31.6 13560 429.4
23:16:15.708 INFO ProgressMeter - chr7:2906636 31.8 13650 429.8
23:16:26.636 INFO ProgressMeter - chr7:13894514 31.9 13730 429.8
23:16:37.059 INFO ProgressMeter - chr7:13932518 32.1 13770 428.8
23:16:48.154 INFO ProgressMeter - chr7:13941909 32.3 13830 428.2
23:16:58.265 INFO ProgressMeter - chr7:13948861 32.5 13870 427.2
23:17:09.350 INFO ProgressMeter - chr7:13954905 32.7 13910 426.0
23:17:19.649 INFO ProgressMeter - chr7:13963152 32.8 13960 425.3
23:17:31.929 INFO ProgressMeter - chr7:13971038 33.0 14010 424.1
23:17:43.820 INFO ProgressMeter - chr7:13976252 33.2 14050 422.8
23:17:55.786 INFO ProgressMeter - chr7:13982935 33.4 14090 421.5
23:18:05.833 INFO ProgressMeter - chr7:13988444 33.6 14120 420.3
23:18:18.424 INFO ProgressMeter - chr7:55153470 33.8 14180 419.5
23:18:31.587 INFO ProgressMeter - chr7:55170348 34.0 14230 418.2
23:18:43.337 INFO ProgressMeter - chr7:55181143 34.2 14290 417.6
23:18:53.671 INFO ProgressMeter - chr7:81752159 34.4 14370 417.8
23:19:04.130 INFO ProgressMeter - chr7:102201339 34.6 14460 418.3
23:19:14.870 INFO ProgressMeter - chr7:116712415 34.7 14530 418.2
23:19:25.545 INFO ProgressMeter - chr7:140788075 34.9 14610 418.3
23:19:35.653 INFO ProgressMeter - chr7:142943781 35.1 14690 418.6
23:19:46.081 INFO ProgressMeter - chr7:152169184 35.3 14780 419.1
23:19:57.027 INFO ProgressMeter - chr7:152273703 35.4 14850 418.9
23:20:09.360 INFO ProgressMeter - chr8:32634041 35.7 14950 419.3
23:20:20.850 INFO ProgressMeter - chr8:37842336 35.8 15030 419.3
23:20:32.068 INFO ProgressMeter - chr8:41941045 36.0 15100 419.1
23:20:42.631 INFO ProgressMeter - chr8:47877722 36.2 15190 419.5
23:20:52.676 INFO ProgressMeter - chr8:68080441 36.4 15290 420.3
23:21:03.999 INFO ProgressMeter - chr8:118935543 36.6 15390 420.9
23:21:13.999 INFO ProgressMeter - chr8:144512713 36.7 15460 420.9
23:21:24.552 INFO ProgressMeter - chr9:8470993 36.9 15570 421.9
23:21:35.508 INFO ProgressMeter - chr9:35079439 37.1 15660 422.2
23:21:49.278 INFO ProgressMeter - chr9:84743787 37.3 15740 421.8
23:22:00.984 INFO ProgressMeter - chr9:84862817 37.5 15790 420.9
23:22:12.734 INFO ProgressMeter - chr9:84873698 37.7 15830 419.8
23:22:24.479 INFO ProgressMeter - chr9:85023971 37.9 15880 418.9
23:22:34.516 INFO ProgressMeter - chr9:95171077 38.1 15930 418.4
23:22:44.718 INFO ProgressMeter - chr9:125149671 38.2 16010 418.6
23:22:55.085 INFO ProgressMeter - chr9:132927211 38.4 16080 418.6
23:23:05.963 INFO ProgressMeter - chr9:136921046 38.6 16170 418.9
23:23:16.171 INFO ProgressMeter - chrX:40075037 38.8 16240 418.9
23:23:27.192 INFO ProgressMeter - chrX:47569891 39.0 16330 419.2
23:23:39.014 INFO ProgressMeter - chrX:49037401 39.1 16390 418.7
23:23:49.047 INFO ProgressMeter - chrX:53210674 39.3 16440 418.1
23:23:59.532 INFO ProgressMeter - chrX:64190646 39.5 16510 418.1
23:24:10.360 INFO ProgressMeter - chrX:67650544 39.7 16570 417.7
23:24:20.784 INFO ProgressMeter - chrX:71375165 39.8 16650 417.9
23:24:32.084 INFO ProgressMeter - chrX:77682809 40.0 16740 418.1
23:24:42.652 INFO ProgressMeter - chrX:124365759 40.2 16850 419.1
23:24:50.231 INFO Mutect2 - 565166 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
95 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
565263 total reads filtered out of 72955703 reads processed
23:24:50.231 INFO ProgressMeter - chrY:19742699 40.3 16937 419.9
23:24:50.231 INFO ProgressMeter - Traversal complete. Processed 16937 total regions in 40.3 minutes.
23:24:50.248 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 4.908072145
23:24:50.248 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 224.871568564
23:24:50.248 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 8.04 sec
23:24:50.248 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:24:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 40.35 minutes.
Runtime.totalMemory()=7759462400
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 LS0897_tumor.bam --tumor-sample LS0897 -L TST500C_manifest.bed -O LS0897.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:24:52.139 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
23:24:52.233 INFO FilterMutectCalls - ------------------------------------------------------------
23:24:52.236 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:24:52.236 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:24:52.236 INFO FilterMutectCalls - Executing as ?@nf-098a6f168e5dacab7bb7b4a8de17ea57-420f6-zm4ll on Linux v6.12.88 amd64
23:24:52.236 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:24:52.236 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:24:52 PM GMT
23:24:52.236 INFO FilterMutectCalls - ------------------------------------------------------------
23:24:52.237 INFO FilterMutectCalls - ------------------------------------------------------------
23:24:52.237 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:24:52.237 INFO FilterMutectCalls - Picard Version: 3.1.1
23:24:52.237 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:24:52.237 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:24:52.238 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:24:52.238 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:24:52.238 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:24:52.238 INFO FilterMutectCalls - Deflater: IntelDeflater
23:24:52.238 INFO FilterMutectCalls - Inflater: IntelInflater
23:24:52.238 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:24:52.238 INFO FilterMutectCalls - Requester pays: disabled
23:24:52.238 INFO FilterMutectCalls - Initializing engine
23:24:52.382 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.V08ylHh8lW/LS0897.mutect2.raw.vcf.gz
23:24:52.490 INFO FilterMutectCalls - Done initializing engine
23:24:52.545 INFO ProgressMeter - Starting traversal
23:24:52.545 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:24:52.546 INFO FilterMutectCalls - Starting pass 0 through the variants
23:24:53.849 INFO FilterMutectCalls - Finished pass 0 through the variants
23:24:54.361 INFO FilterMutectCalls - Starting pass 1 through the variants
23:24:55.591 INFO FilterMutectCalls - Finished pass 1 through the variants
23:24:55.729 INFO FilterMutectCalls - Starting pass 2 through the variants
23:24:56.934 INFO FilterMutectCalls - Finished pass 2 through the variants
23:24:56.936 INFO FilterMutectCalls - Starting pass 3 through the variants
23:24:57.942 INFO FilterMutectCalls - Finished pass 3 through the variants
23:24:57.951 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:24:57.951 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:24:57.951 INFO ProgressMeter - chr5:142638344 0.1 9740 108102.1
23:24:57.951 INFO ProgressMeter - Traversal complete. Processed 9740 total variants in 0.1 minutes.
23:24:57.962 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:24:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=494927872
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 LS0897.mutect2.raw.vcf.gz --stats LS0897.mutect2.raw.vcf.gz.stats -O LS0897.mutect2.filtered.vcf.gz
23:24:59.180 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
23:24:59.310 INFO SelectVariants - ------------------------------------------------------------
23:24:59.312 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:24:59.313 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:24:59.313 INFO SelectVariants - Executing as ?@nf-098a6f168e5dacab7bb7b4a8de17ea57-420f6-zm4ll on Linux v6.12.88 amd64
23:24:59.313 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:24:59.313 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:24:59 PM GMT
23:24:59.313 INFO SelectVariants - ------------------------------------------------------------
23:24:59.314 INFO SelectVariants - ------------------------------------------------------------
23:24:59.315 INFO SelectVariants - HTSJDK Version: 4.1.0
23:24:59.315 INFO SelectVariants - Picard Version: 3.1.1
23:24:59.315 INFO SelectVariants - Built for Spark Version: 3.5.0
23:24:59.315 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:24:59.315 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:24:59.315 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:24:59.315 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:24:59.315 INFO SelectVariants - Deflater: IntelDeflater
23:24:59.316 INFO SelectVariants - Inflater: IntelInflater
23:24:59.316 INFO SelectVariants - GCS max retries/reopens: 20
23:24:59.316 INFO SelectVariants - Requester pays: disabled
23:24:59.316 INFO SelectVariants - Initializing engine
23:24:59.528 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.V08ylHh8lW/LS0897.mutect2.filtered.vcf.gz
23:24:59.630 INFO SelectVariants - Done initializing engine
23:24:59.665 INFO ProgressMeter - Starting traversal
23:24:59.665 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:24:59.731 INFO ProgressMeter - chr7:13951596 0.0 2435 2282812.5
23:24:59.731 INFO ProgressMeter - Traversal complete. Processed 2435 total variants in 0.0 minutes.
23:24:59.743 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:24:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=436207616
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 LS0897.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0897.mutect2.pass.vcf.gz