Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0902/LS0902_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/36/f6133db8ba2bc86c713e98a863cf4c/.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/LS0902/LS0902_tumor.bam
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.dict
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/36/f6133db8ba2bc86c713e98a863cf4c/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:21.633 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
22:44:21.740 INFO Mutect2 - ------------------------------------------------------------
22:44:21.744 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:21.744 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:21.744 INFO Mutect2 - Executing as ?@nf-36f6133db8ba2bc86c713e98a863cf4c-d8a0f-ffj9n on Linux v6.12.88 amd64
22:44:21.745 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:21.745 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:21 PM GMT
22:44:21.745 INFO Mutect2 - ------------------------------------------------------------
22:44:21.745 INFO Mutect2 - ------------------------------------------------------------
22:44:21.746 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:21.746 INFO Mutect2 - Picard Version: 3.1.1
22:44:21.746 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:21.747 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:21.747 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:21.747 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:21.747 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:21.747 INFO Mutect2 - Deflater: IntelDeflater
22:44:21.747 INFO Mutect2 - Inflater: IntelInflater
22:44:21.747 INFO Mutect2 - GCS max retries/reopens: 20
22:44:21.748 INFO Mutect2 - Requester pays: disabled
22:44:21.748 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.zjXYfS47AP/LS0902_tumor.bam.bai is older than BAM /tmp/nxf.zjXYfS47AP/LS0902_tumor.bam
22:44:21.983 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.zjXYfS47AP/af-only-gnomad.hg38.vcf.gz
22:44:22.109 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.zjXYfS47AP/TST500C_manifest.bed
22:44:22.150 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:22.184 INFO Mutect2 - Done initializing engine
22:44:22.198 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
22:44:22.199 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
22:44:22.200 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:22.200 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:22.213 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
22:44:22.222 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:22.222 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:22.222 INFO IntelPairHmm - Available threads: 384
22:44:22.222 INFO IntelPairHmm - Requested threads: 4
22:44:22.223 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:22.262 INFO ProgressMeter - Starting traversal
22:44:22.263 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:32.670 INFO ProgressMeter - chr1:11128853 0.2 70 403.6
22:44:44.003 INFO ProgressMeter - chr1:15928226 0.4 140 386.4
22:44:54.261 INFO ProgressMeter - chr1:17022606 0.5 200 375.0
22:45:04.802 INFO ProgressMeter - chr1:26760854 0.7 280 394.9
22:45:15.177 INFO ProgressMeter - chr1:39897451 0.9 370 419.6
22:45:25.798 INFO ProgressMeter - chr1:46260725 1.1 470 443.8
22:45:35.815 INFO ProgressMeter - chr1:77965067 1.2 570 465.0
22:45:46.411 INFO ProgressMeter - chr1:119917663 1.4 660 470.6
22:45:57.775 INFO ProgressMeter - chr1:156873119 1.6 750 471.1
22:46:08.138 INFO ProgressMeter - chr1:158676139 1.8 830 470.4
22:46:18.148 INFO ProgressMeter - chr1:179133310 1.9 920 476.3
22:46:28.771 INFO ProgressMeter - chr1:204542855 2.1 1020 483.8
22:46:39.871 INFO ProgressMeter - chr1:238275935 2.3 1120 488.3
22:46:52.296 INFO ProgressMeter - chr1:243545508 2.5 1180 471.9
22:47:03.761 INFO ProgressMeter - chr10:32017141 2.7 1270 471.8
22:47:14.319 INFO ProgressMeter - chr10:43114958 2.9 1350 470.8
22:47:25.138 INFO ProgressMeter - chr10:62091160 3.0 1410 462.6
22:47:35.144 INFO ProgressMeter - chr10:86912238 3.2 1470 457.3
22:47:45.997 INFO ProgressMeter - chr10:101773370 3.4 1560 459.4
22:47:56.341 INFO ProgressMeter - chr10:112964554 3.6 1650 462.4
22:48:06.581 INFO ProgressMeter - chr10:121487352 3.7 1710 457.4
22:48:17.010 INFO ProgressMeter - chr11:61433429 3.9 1810 462.6
22:48:27.013 INFO ProgressMeter - chr11:69696837 4.1 1920 470.7
22:48:37.058 INFO ProgressMeter - chr11:69774743 4.2 2000 471.0
22:48:48.520 INFO ProgressMeter - chr11:69818712 4.4 2050 462.0
22:48:59.228 INFO ProgressMeter - chr11:77404651 4.6 2130 461.4
22:49:09.400 INFO ProgressMeter - chr11:102229700 4.8 2220 463.9
22:49:19.531 INFO ProgressMeter - chr11:108292617 5.0 2270 458.2
22:49:30.650 INFO ProgressMeter - chr11:118502396 5.1 2370 461.1
22:49:42.894 INFO ProgressMeter - chr11:125620800 5.3 2430 454.7
22:49:53.646 INFO ProgressMeter - chr11:128460177 5.5 2490 450.8
22:50:05.122 INFO ProgressMeter - chr12:285573 5.7 2560 448.0
22:50:15.496 INFO ProgressMeter - chr12:4374696 5.9 2650 450.1
22:50:26.153 INFO ProgressMeter - chr12:6578844 6.1 2730 450.1
22:50:38.222 INFO ProgressMeter - chr12:11856978 6.3 2800 446.9
22:50:50.728 INFO ProgressMeter - chr12:11864253 6.5 2850 440.2
22:51:01.073 INFO ProgressMeter - chr12:18321032 6.6 2910 437.8
22:51:11.756 INFO ProgressMeter - chr12:40469175 6.8 3000 439.6
22:51:21.928 INFO ProgressMeter - chr12:49031360 7.0 3070 438.9
22:51:32.196 INFO ProgressMeter - chr12:49042739 7.2 3130 436.8
22:51:42.275 INFO ProgressMeter - chr12:56083749 7.3 3220 439.1
22:51:52.971 INFO ProgressMeter - chr12:57095205 7.5 3310 440.6
22:52:03.289 INFO ProgressMeter - chr12:68824361 7.7 3410 443.8
22:52:14.225 INFO ProgressMeter - chr12:114676311 7.9 3510 446.2
22:52:24.906 INFO ProgressMeter - chr12:132664368 8.0 3600 447.5
22:52:34.974 INFO ProgressMeter - chr13:21698277 8.2 3690 449.4
22:52:47.828 INFO ProgressMeter - chr13:28384883 8.4 3780 448.6
22:52:58.403 INFO ProgressMeter - chr13:32332693 8.6 3840 446.4
22:53:08.403 INFO ProgressMeter - chr13:32396940 8.8 3910 445.9
22:53:19.480 INFO ProgressMeter - chr13:102283296 9.0 4030 450.1
22:53:30.207 INFO ProgressMeter - chr13:113321597 9.1 4130 452.2
22:53:40.498 INFO ProgressMeter - chr14:37593538 9.3 4210 452.5
22:53:52.139 INFO ProgressMeter - chr14:95095770 9.5 4300 452.7
22:54:02.710 INFO ProgressMeter - chr15:32731012 9.7 4390 453.8
22:54:13.480 INFO ProgressMeter - chr15:41669165 9.9 4450 451.6
22:54:24.013 INFO ProgressMeter - chr15:41767040 10.0 4510 449.7
22:54:34.282 INFO ProgressMeter - chr15:73708339 10.2 4600 451.0
22:54:45.111 INFO ProgressMeter - chr15:89299798 10.4 4680 450.8
22:54:55.165 INFO ProgressMeter - chr15:92955421 10.5 4770 452.2
22:55:05.652 INFO ProgressMeter - chr16:346302 10.7 4860 453.2
22:55:16.717 INFO ProgressMeter - chr16:3589176 10.9 4980 456.6
22:55:26.842 INFO ProgressMeter - chr16:3773866 11.1 5050 455.9
22:55:36.938 INFO ProgressMeter - chr16:13935744 11.2 5120 455.3
22:55:47.347 INFO ProgressMeter - chr16:56823705 11.4 5200 455.4
22:55:58.505 INFO ProgressMeter - chr16:72788671 11.6 5280 455.0
22:56:09.539 INFO ProgressMeter - chr16:72957863 11.8 5330 452.2
22:56:19.595 INFO ProgressMeter - chr16:89281383 12.0 5410 452.5
22:56:30.149 INFO ProgressMeter - chr16:89792469 12.1 5490 452.5
22:56:40.583 INFO ProgressMeter - chr17:7676446 12.3 5560 451.8
22:56:51.298 INFO ProgressMeter - chr17:16073427 12.5 5670 454.2
22:57:01.800 INFO ProgressMeter - chr17:31232071 12.7 5770 455.8
22:57:11.873 INFO ProgressMeter - chr17:39494522 12.8 5860 456.9
22:57:22.397 INFO ProgressMeter - chr17:40391504 13.0 5950 457.6
22:57:33.725 INFO ProgressMeter - chr17:43063331 13.2 6070 460.2
22:57:45.515 INFO ProgressMeter - chr17:43124227 13.4 6140 458.6
22:57:56.149 INFO ProgressMeter - chr17:43537907 13.6 6200 457.1
22:58:08.916 INFO ProgressMeter - chr17:43543583 13.8 6240 452.9
22:58:19.543 INFO ProgressMeter - chr17:58358184 14.0 6310 452.2
22:58:30.528 INFO ProgressMeter - chr17:59947385 14.1 6390 452.0
22:58:41.946 INFO ProgressMeter - chr17:65541453 14.3 6470 451.6
22:58:52.929 INFO ProgressMeter - chr18:736806 14.5 6570 452.8
22:59:04.974 INFO ProgressMeter - chr18:44953203 14.7 6660 452.7
22:59:15.121 INFO ProgressMeter - chr19:1627357 14.9 6770 454.9
22:59:25.614 INFO ProgressMeter - chr19:5219380 15.1 6890 457.6
22:59:35.668 INFO ProgressMeter - chr19:10149851 15.2 6980 458.5
22:59:45.751 INFO ProgressMeter - chr19:11033382 15.4 7070 459.3
22:59:56.900 INFO ProgressMeter - chr19:15192071 15.6 7170 460.3
23:00:07.289 INFO ProgressMeter - chr19:19149387 15.8 7280 462.2
23:00:17.805 INFO ProgressMeter - chr19:35726234 15.9 7370 462.8
23:00:27.977 INFO ProgressMeter - chr19:40280168 16.1 7470 464.1
23:00:38.162 INFO ProgressMeter - chr19:41880865 16.3 7520 462.3
23:00:48.843 INFO ProgressMeter - chr19:45409331 16.4 7630 464.0
23:00:58.896 INFO ProgressMeter - chr19:52222097 16.6 7730 465.4
23:01:10.160 INFO ProgressMeter - chr2:17780619 16.8 7800 464.3
23:01:20.334 INFO ProgressMeter - chr2:25878164 17.0 7870 463.8
23:01:30.796 INFO ProgressMeter - chr2:29225076 17.1 7920 462.0
23:01:41.961 INFO ProgressMeter - chr2:42169447 17.3 7980 460.5
23:01:53.131 INFO ProgressMeter - chr2:47470963 17.5 8050 459.6
23:02:03.511 INFO ProgressMeter - chr2:61498671 17.7 8140 460.2
23:02:14.320 INFO ProgressMeter - chr2:108765160 17.9 8230 460.6
23:02:28.923 INFO ProgressMeter - chr2:111128293 18.1 8280 457.2
23:02:39.724 INFO ProgressMeter - chr2:113224973 18.3 8330 455.4
23:02:50.675 INFO ProgressMeter - chr2:113231811 18.5 8380 453.6
23:03:00.737 INFO ProgressMeter - chr2:113236621 18.6 8420 451.7
23:03:11.677 INFO ProgressMeter - chr2:140598720 18.8 8520 452.6
23:03:22.246 INFO ProgressMeter - chr2:177230783 19.0 8610 453.2
23:03:32.587 INFO ProgressMeter - chr2:197434970 19.2 8710 454.3
23:03:43.825 INFO ProgressMeter - chr2:219575142 19.4 8810 455.1
23:03:55.594 INFO ProgressMeter - chr2:222207955 19.6 8860 453.1
23:04:07.993 INFO ProgressMeter - chr2:222216982 19.8 8910 450.9
23:04:18.783 INFO ProgressMeter - chr2:226795288 19.9 8980 450.3
23:04:29.361 INFO ProgressMeter - chr20:32372162 20.1 9060 450.3
23:04:39.404 INFO ProgressMeter - chr20:37393969 20.3 9130 450.1
23:04:50.062 INFO ProgressMeter - chr20:47627559 20.5 9220 450.6
23:05:00.870 INFO ProgressMeter - chr20:58853431 20.6 9280 449.5
23:05:11.898 INFO ProgressMeter - chr21:38383386 20.8 9370 449.9
23:05:25.587 INFO ProgressMeter - chr21:41490939 21.1 9440 448.3
23:05:36.837 INFO ProgressMeter - chr21:41499631 21.2 9470 445.8
23:05:48.969 INFO ProgressMeter - chr21:41507712 21.4 9520 443.9
23:06:00.537 INFO ProgressMeter - chr22:23289735 21.6 9620 444.6
23:06:10.687 INFO ProgressMeter - chr22:23791754 21.8 9660 443.0
23:06:20.900 INFO ProgressMeter - chr22:29283788 22.0 9740 443.2
23:06:30.986 INFO ProgressMeter - chr22:37977865 22.1 9810 443.0
23:06:42.311 INFO ProgressMeter - chr3:10060292 22.3 9890 442.8
23:06:52.373 INFO ProgressMeter - chr3:12355419 22.5 9950 442.2
23:07:05.384 INFO ProgressMeter - chr3:12360935 22.7 9980 439.3
23:07:16.347 INFO ProgressMeter - chr3:12367572 22.9 10030 438.0
23:07:26.808 INFO ProgressMeter - chr3:12375208 23.1 10080 436.8
23:07:39.492 INFO ProgressMeter - chr3:12624852 23.3 10150 435.9
23:07:49.722 INFO ProgressMeter - chr3:47083985 23.5 10250 437.0
23:08:00.214 INFO ProgressMeter - chr3:49891195 23.6 10330 437.1
23:08:11.273 INFO ProgressMeter - chr3:52628892 23.8 10420 437.5
23:08:21.599 INFO ProgressMeter - chr3:89340971 24.0 10510 438.1
23:08:32.880 INFO ProgressMeter - chr3:136369087 24.2 10600 438.4
23:08:42.951 INFO ProgressMeter - chr3:142461938 24.3 10690 439.1
23:08:52.962 INFO ProgressMeter - chr3:179153613 24.5 10780 439.8
23:09:04.171 INFO ProgressMeter - chr3:185285604 24.7 10860 439.7
23:09:14.351 INFO ProgressMeter - chr3:187729048 24.9 10930 439.5
23:09:24.673 INFO ProgressMeter - chr4:1801365 25.0 11030 440.5
23:09:35.125 INFO ProgressMeter - chr4:41745805 25.2 11130 441.4
23:09:45.612 INFO ProgressMeter - chr4:54707447 25.4 11210 441.5
23:09:56.886 INFO ProgressMeter - chr4:55106685 25.6 11260 440.2
23:10:07.954 INFO ProgressMeter - chr4:83470201 25.8 11350 440.6
23:10:19.532 INFO ProgressMeter - chr4:105275946 26.0 11420 440.0
23:10:30.729 INFO ProgressMeter - chr4:186596838 26.1 11530 441.1
23:10:42.149 INFO ProgressMeter - chr4:186706733 26.3 11600 440.5
23:10:53.372 INFO ProgressMeter - chr5:38952262 26.5 11680 440.4
23:11:05.676 INFO ProgressMeter - chr5:56882428 26.7 11790 441.2
23:11:16.445 INFO ProgressMeter - chr5:87383711 26.9 11910 442.7
23:11:27.443 INFO ProgressMeter - chr5:122422958 27.1 11980 442.3
23:11:38.390 INFO ProgressMeter - chr5:142620759 27.3 12070 442.6
23:11:48.659 INFO ProgressMeter - chr5:150080765 27.4 12140 442.4
23:11:59.465 INFO ProgressMeter - chr5:161701718 27.6 12230 442.8
23:12:14.513 INFO ProgressMeter - chr5:177204118 27.9 12300 441.3
23:12:24.690 INFO ProgressMeter - chr5:180608279 28.0 12380 441.5
23:12:35.429 INFO ProgressMeter - chr6:20485051 28.2 12490 442.6
23:12:46.838 INFO ProgressMeter - chr6:29944120 28.4 12570 442.5
23:12:57.754 INFO ProgressMeter - chr6:32214108 28.6 12650 442.4
23:13:08.091 INFO ProgressMeter - chr6:36684449 28.8 12720 442.2
23:13:18.404 INFO ProgressMeter - chr6:93246846 28.9 12820 443.1
23:13:28.991 INFO ProgressMeter - chr6:117310117 29.1 12900 443.1
23:13:39.870 INFO ProgressMeter - chr6:117322821 29.3 12940 441.7
23:13:51.445 INFO ProgressMeter - chr6:117330542 29.5 12990 440.5
23:14:03.199 INFO ProgressMeter - chr6:117339452 29.7 13050 439.7
23:14:13.242 INFO ProgressMeter - chr6:135203321 29.8 13120 439.5
23:14:27.943 INFO ProgressMeter - chr6:135212568 30.1 13170 437.6
23:14:39.359 INFO ProgressMeter - chr6:137879192 30.3 13230 436.9
23:14:50.340 INFO ProgressMeter - chr6:151908902 30.5 13300 436.5
23:15:02.086 INFO ProgressMeter - chr6:161034257 30.7 13380 436.3
23:15:12.735 INFO ProgressMeter - chr7:2926737 30.8 13470 436.8
23:15:23.378 INFO ProgressMeter - chr7:13900736 31.0 13550 436.8
23:15:34.947 INFO ProgressMeter - chr7:13908976 31.2 13570 434.8
23:15:46.464 INFO ProgressMeter - chr7:13941728 31.4 13630 434.0
23:15:58.035 INFO ProgressMeter - chr7:13948660 31.6 13670 432.6
23:16:10.521 INFO ProgressMeter - chr7:13954413 31.8 13710 431.1
23:16:21.952 INFO ProgressMeter - chr7:13963222 32.0 13760 430.1
23:16:33.624 INFO ProgressMeter - chr7:13972514 32.2 13810 429.0
23:16:44.585 INFO ProgressMeter - chr7:13977163 32.4 13840 427.5
23:16:57.184 INFO ProgressMeter - chr7:13983875 32.6 13890 426.3
23:17:09.266 INFO ProgressMeter - chr7:13988904 32.8 13920 424.6
23:17:20.505 INFO ProgressMeter - chr7:55156762 33.0 13990 424.3
23:17:32.465 INFO ProgressMeter - chr7:55173039 33.2 14040 423.3
23:17:43.793 INFO ProgressMeter - chr7:55181057 33.4 14090 422.4
23:17:54.389 INFO ProgressMeter - chr7:81729603 33.5 14170 422.5
23:18:05.751 INFO ProgressMeter - chr7:102201975 33.7 14270 423.1
23:18:15.890 INFO ProgressMeter - chr7:116765399 33.9 14350 423.4
23:18:27.613 INFO ProgressMeter - chr7:140792077 34.1 14430 423.3
23:18:38.230 INFO ProgressMeter - chr7:148846468 34.3 14530 424.0
23:18:49.024 INFO ProgressMeter - chr7:152177974 34.4 14600 423.9
23:18:59.831 INFO ProgressMeter - chr8:11756933 34.6 14690 424.2
23:19:10.068 INFO ProgressMeter - chr8:32648186 34.8 14770 424.5
23:19:21.200 INFO ProgressMeter - chr8:38427919 35.0 14860 424.8
23:19:31.505 INFO ProgressMeter - chr8:47778477 35.2 14930 424.7
23:19:42.156 INFO ProgressMeter - chr8:47954336 35.3 15020 425.1
23:19:53.432 INFO ProgressMeter - chr8:91991637 35.5 15130 426.0
23:20:04.406 INFO ProgressMeter - chr8:127741989 35.7 15200 425.7
23:20:14.679 INFO ProgressMeter - chr9:5126682 35.9 15300 426.5
23:20:26.670 INFO ProgressMeter - chr9:20620652 36.1 15390 426.6
23:20:37.028 INFO ProgressMeter - chr9:84668539 36.2 15490 427.4
23:20:48.106 INFO ProgressMeter - chr9:84811229 36.4 15530 426.3
23:20:59.178 INFO ProgressMeter - chr9:84861960 36.6 15560 425.0
23:21:10.627 INFO ProgressMeter - chr9:84867255 36.8 15600 423.8
23:21:21.642 INFO ProgressMeter - chr9:85022230 37.0 15650 423.1
23:21:31.994 INFO ProgressMeter - chr9:90888571 37.2 15700 422.5
23:21:42.702 INFO ProgressMeter - chr9:107487957 37.3 15790 422.9
23:21:52.996 INFO ProgressMeter - chr9:132897182 37.5 15860 422.8
23:22:03.502 INFO ProgressMeter - chr9:136670254 37.7 15960 423.5
23:22:13.518 INFO ProgressMeter - chrX:49035180 37.9 16150 426.6
23:22:23.929 INFO ProgressMeter - chrX:67546151 38.0 16290 428.4
23:22:34.112 INFO ProgressMeter - chrX:101354628 38.2 16490 431.7
23:22:44.203 INFO ProgressMeter - chrY:19564390 38.4 16660 434.2
23:22:44.601 INFO Mutect2 - 514724 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
71 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
514795 total reads filtered out of 68800311 reads processed
23:22:44.602 INFO ProgressMeter - chrY:20960482 38.4 16673 434.5
23:22:44.602 INFO ProgressMeter - Traversal complete. Processed 16673 total regions in 38.4 minutes.
23:22:44.619 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 4.933928204
23:22:44.619 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 214.68524157000002
23:22:44.619 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 7.85 sec
23:22:44.620 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:22:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 38.38 minutes.
Runtime.totalMemory()=6702497792
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 LS0902_tumor.bam --tumor-sample LS0902 -L TST500C_manifest.bed -O LS0902.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:22:46.155 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
23:22:46.265 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:46.266 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:22:46.267 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:22:46.267 INFO FilterMutectCalls - Executing as ?@nf-36f6133db8ba2bc86c713e98a863cf4c-d8a0f-ffj9n on Linux v6.12.88 amd64
23:22:46.267 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:22:46.267 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:22:46 PM GMT
23:22:46.267 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:46.268 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:46.268 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:22:46.269 INFO FilterMutectCalls - Picard Version: 3.1.1
23:22:46.269 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:22:46.269 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:22:46.269 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:22:46.269 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:22:46.269 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:22:46.269 INFO FilterMutectCalls - Deflater: IntelDeflater
23:22:46.269 INFO FilterMutectCalls - Inflater: IntelInflater
23:22:46.269 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:22:46.269 INFO FilterMutectCalls - Requester pays: disabled
23:22:46.270 INFO FilterMutectCalls - Initializing engine
23:22:46.385 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.zjXYfS47AP/LS0902.mutect2.raw.vcf.gz
23:22:46.502 INFO FilterMutectCalls - Done initializing engine
23:22:46.564 INFO ProgressMeter - Starting traversal
23:22:46.565 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:22:46.566 INFO FilterMutectCalls - Starting pass 0 through the variants
23:22:47.712 INFO FilterMutectCalls - Finished pass 0 through the variants
23:22:49.155 INFO FilterMutectCalls - Starting pass 1 through the variants
23:22:50.403 INFO FilterMutectCalls - Finished pass 1 through the variants
23:22:50.733 INFO FilterMutectCalls - Starting pass 2 through the variants
23:22:51.970 INFO FilterMutectCalls - Finished pass 2 through the variants
23:22:51.973 INFO FilterMutectCalls - Starting pass 3 through the variants
23:22:53.019 INFO FilterMutectCalls - Finished pass 3 through the variants
23:22:53.026 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:22:53.027 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:22:53.027 INFO ProgressMeter - chr9:84874870 0.1 10100 93779.0
23:22:53.027 INFO ProgressMeter - Traversal complete. Processed 10100 total variants in 0.1 minutes.
23:22:53.038 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:22:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.12 minutes.
Runtime.totalMemory()=226492416
Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R hg38.fa -V LS0902.mutect2.raw.vcf.gz --stats LS0902.mutect2.raw.vcf.gz.stats -O LS0902.mutect2.filtered.vcf.gz
23:22:54.377 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
23:22:54.493 INFO SelectVariants - ------------------------------------------------------------
23:22:54.496 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:22:54.496 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:22:54.496 INFO SelectVariants - Executing as ?@nf-36f6133db8ba2bc86c713e98a863cf4c-d8a0f-ffj9n on Linux v6.12.88 amd64
23:22:54.496 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:22:54.496 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:22:54 PM GMT
23:22:54.496 INFO SelectVariants - ------------------------------------------------------------
23:22:54.496 INFO SelectVariants - ------------------------------------------------------------
23:22:54.497 INFO SelectVariants - HTSJDK Version: 4.1.0
23:22:54.497 INFO SelectVariants - Picard Version: 3.1.1
23:22:54.497 INFO SelectVariants - Built for Spark Version: 3.5.0
23:22:54.497 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:22:54.497 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:22:54.497 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:22:54.498 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:22:54.498 INFO SelectVariants - Deflater: IntelDeflater
23:22:54.498 INFO SelectVariants - Inflater: IntelInflater
23:22:54.498 INFO SelectVariants - GCS max retries/reopens: 20
23:22:54.498 INFO SelectVariants - Requester pays: disabled
23:22:54.498 INFO SelectVariants - Initializing engine
23:22:54.649 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.zjXYfS47AP/LS0902.mutect2.filtered.vcf.gz
23:22:54.804 INFO SelectVariants - Done initializing engine
23:22:54.862 INFO ProgressMeter - Starting traversal
23:22:54.863 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:22:54.980 INFO ProgressMeter - chr6:152042056 0.0 2525 1317391.3
23:22:54.981 INFO ProgressMeter - Traversal complete. Processed 2525 total variants in 0.0 minutes.
23:22:54.993 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:22:54 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 LS0902.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0902.mutect2.pass.vcf.gz