Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/f3/c4b392c1e10e86909d6f89a74dde97/.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/LS0900/LS0900_tumor.bam.bai
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/f3/c4b392c1e10e86909d6f89a74dde97/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0900/LS0900_tumor.bam
==> STAGING COMPLETE (10 inputs)
22:44:10.362 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
22:44:10.463 INFO Mutect2 - ------------------------------------------------------------
22:44:10.467 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:10.467 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:10.467 INFO Mutect2 - Executing as ?@nf-f3c4b392c1e10e86909d6f89a74dde97-cbf32-wfcrn on Linux v6.12.88 amd64
22:44:10.467 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:10.468 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:10 PM GMT
22:44:10.468 INFO Mutect2 - ------------------------------------------------------------
22:44:10.468 INFO Mutect2 - ------------------------------------------------------------
22:44:10.469 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:10.469 INFO Mutect2 - Picard Version: 3.1.1
22:44:10.469 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:10.469 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:10.469 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:10.469 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:10.469 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:10.469 INFO Mutect2 - Deflater: IntelDeflater
22:44:10.470 INFO Mutect2 - Inflater: IntelInflater
22:44:10.470 INFO Mutect2 - GCS max retries/reopens: 20
22:44:10.470 INFO Mutect2 - Requester pays: disabled
22:44:10.470 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.6KUqejLQ1q/LS0900_tumor.bam.bai is older than BAM /tmp/nxf.6KUqejLQ1q/LS0900_tumor.bam
22:44:10.647 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.6KUqejLQ1q/af-only-gnomad.hg38.vcf.gz
22:44:10.754 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.6KUqejLQ1q/TST500C_manifest.bed
22:44:10.787 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:10.813 INFO Mutect2 - Done initializing engine
22:44:10.821 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
22:44:10.822 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
22:44:10.823 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:10.823 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:10.833 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
22:44:10.842 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:10.842 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:10.842 INFO IntelPairHmm - Available threads: 384
22:44:10.842 INFO IntelPairHmm - Requested threads: 4
22:44:10.842 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:10.879 INFO ProgressMeter - Starting traversal
22:44:10.879 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:21.416 INFO ProgressMeter - chr1:11128853 0.2 80 455.7
22:44:32.862 INFO ProgressMeter - chr1:15928602 0.4 160 436.7
22:44:43.871 INFO ProgressMeter - chr1:18636235 0.5 230 418.3
22:44:53.881 INFO ProgressMeter - chr1:26731150 0.7 290 404.6
22:45:04.778 INFO ProgressMeter - chr1:39894023 0.9 380 423.0
22:45:15.523 INFO ProgressMeter - chr1:46061927 1.1 470 436.2
22:45:25.995 INFO ProgressMeter - chr1:77960182 1.3 570 455.3
22:45:37.669 INFO ProgressMeter - chr1:119915664 1.4 670 463.2
22:45:51.071 INFO ProgressMeter - chr1:156872899 1.7 760 455.1
22:46:01.254 INFO ProgressMeter - chr1:158666314 1.8 830 451.2
22:46:11.398 INFO ProgressMeter - chr1:179109390 2.0 920 458.0
22:46:22.814 INFO ProgressMeter - chr1:204530682 2.2 1030 468.4
22:46:32.884 INFO ProgressMeter - chr1:226383102 2.4 1120 473.2
22:46:43.058 INFO ProgressMeter - chr1:243503059 2.5 1180 465.2
22:46:53.290 INFO ProgressMeter - chr10:27039944 2.7 1250 461.8
22:47:03.346 INFO ProgressMeter - chr10:43096462 2.9 1330 462.7
22:47:14.936 INFO ProgressMeter - chr10:43117124 3.1 1390 453.1
22:47:26.178 INFO ProgressMeter - chr10:68644696 3.3 1460 448.5
22:47:36.312 INFO ProgressMeter - chr10:87938652 3.4 1540 449.8
22:47:46.597 INFO ProgressMeter - chr10:102627173 3.6 1630 453.4
22:47:58.500 INFO ProgressMeter - chr10:121481169 3.8 1720 453.4
22:48:09.415 INFO ProgressMeter - chr10:121560590 4.0 1780 447.7
22:48:19.504 INFO ProgressMeter - chr11:67429118 4.1 1900 458.5
22:48:30.186 INFO ProgressMeter - chr11:69701108 4.3 1980 458.1
22:48:40.923 INFO ProgressMeter - chr11:69775815 4.5 2040 453.3
22:48:52.313 INFO ProgressMeter - chr11:69816318 4.7 2080 443.4
22:49:03.111 INFO ProgressMeter - chr11:77358993 4.9 2160 443.5
22:49:14.594 INFO ProgressMeter - chr11:101128925 5.1 2260 446.5
22:49:26.538 INFO ProgressMeter - chr11:102336126 5.3 2290 435.3
22:49:37.634 INFO ProgressMeter - chr11:118473981 5.4 2390 438.9
22:49:48.391 INFO ProgressMeter - chr11:119278599 5.6 2470 439.1
22:49:59.215 INFO ProgressMeter - chr11:128458759 5.8 2540 437.5
22:50:10.276 INFO ProgressMeter - chr11:128812032 6.0 2600 434.1
22:50:20.712 INFO ProgressMeter - chr12:4370650 6.2 2680 434.8
22:50:31.968 INFO ProgressMeter - chr12:4448469 6.4 2760 434.5
22:50:42.539 INFO ProgressMeter - chr12:11854841 6.5 2830 433.5
22:50:53.435 INFO ProgressMeter - chr12:11861162 6.7 2880 429.3
22:51:05.290 INFO ProgressMeter - chr12:11868496 6.9 2930 424.2
22:51:15.900 INFO ProgressMeter - chr12:25231544 7.1 3030 427.7
22:51:26.991 INFO ProgressMeter - chr12:49027135 7.3 3110 427.9
22:51:37.509 INFO ProgressMeter - chr12:49040932 7.4 3170 425.9
22:51:47.683 INFO ProgressMeter - chr12:56080513 7.6 3260 428.2
22:51:58.879 INFO ProgressMeter - chr12:57095205 7.8 3350 429.5
22:52:09.260 INFO ProgressMeter - chr12:68821705 8.0 3440 431.5
22:52:20.667 INFO ProgressMeter - chr12:69574305 8.2 3490 427.5
22:52:31.067 INFO ProgressMeter - chr12:132624938 8.3 3590 430.6
22:52:41.348 INFO ProgressMeter - chr13:20983686 8.5 3670 431.4
22:52:51.888 INFO ProgressMeter - chr13:28035558 8.7 3760 433.0
22:53:06.831 INFO ProgressMeter - chr13:28388958 8.9 3830 428.8
22:53:17.217 INFO ProgressMeter - chr13:32339528 9.1 3900 428.3
22:53:27.537 INFO ProgressMeter - chr13:72761921 9.3 4000 431.1
22:53:38.431 INFO ProgressMeter - chr13:106285972 9.5 4100 433.4
22:53:49.390 INFO ProgressMeter - chr14:25381664 9.6 4190 434.6
22:53:59.644 INFO ProgressMeter - chr14:37597503 9.8 4280 436.2
22:54:10.101 INFO ProgressMeter - chr14:95107878 10.0 4360 436.6
22:54:23.756 INFO ProgressMeter - chr15:34347980 10.2 4450 435.7
22:54:33.770 INFO ProgressMeter - chr15:41736179 10.4 4520 435.4
22:54:44.568 INFO ProgressMeter - chr15:49469984 10.6 4600 435.5
22:54:54.568 INFO ProgressMeter - chr15:88136465 10.7 4680 436.2
22:55:04.763 INFO ProgressMeter - chr15:90794226 10.9 4780 438.6
22:55:16.060 INFO ProgressMeter - chr16:288240 11.1 4880 440.2
22:55:26.238 INFO ProgressMeter - chr16:3582520 11.3 5000 444.2
22:55:36.945 INFO ProgressMeter - chr16:3810601 11.4 5090 445.1
22:55:48.187 INFO ProgressMeter - chr16:23629938 11.6 5170 444.9
22:55:59.010 INFO ProgressMeter - chr16:67620737 11.8 5270 446.5
22:56:09.420 INFO ProgressMeter - chr16:72796039 12.0 5330 445.1
22:56:19.700 INFO ProgressMeter - chr16:81859114 12.1 5390 443.7
22:56:30.656 INFO ProgressMeter - chr16:89284336 12.3 5470 443.6
22:56:40.659 INFO ProgressMeter - chr17:7669607 12.5 5570 445.7
22:56:51.148 INFO ProgressMeter - chr17:10232605 12.7 5670 447.5
22:57:01.489 INFO ProgressMeter - chr17:17226196 12.8 5770 449.3
22:57:12.040 INFO ProgressMeter - chr17:35103452 13.0 5880 451.6
22:57:22.127 INFO ProgressMeter - chr17:39718088 13.2 5960 451.9
22:57:32.664 INFO ProgressMeter - chr17:42289864 13.4 6070 454.2
22:57:43.974 INFO ProgressMeter - chr17:43093963 13.6 6170 455.3
22:57:54.917 INFO ProgressMeter - chr17:43537815 13.7 6250 455.1
22:58:05.035 INFO ProgressMeter - chr17:43544198 13.9 6290 452.4
22:58:15.955 INFO ProgressMeter - chr17:59894055 14.1 6380 453.0
22:58:26.604 INFO ProgressMeter - chr17:61801251 14.3 6470 453.7
22:58:37.202 INFO ProgressMeter - chr17:80846471 14.4 6570 455.0
22:58:47.358 INFO ProgressMeter - chr18:44869209 14.6 6670 456.6
22:58:57.455 INFO ProgressMeter - chr18:58709974 14.8 6740 456.1
22:59:07.995 INFO ProgressMeter - chr19:4048037 15.0 6870 459.5
22:59:18.297 INFO ProgressMeter - chr19:7172288 15.1 6980 461.5
22:59:29.056 INFO ProgressMeter - chr19:11023516 15.3 7090 463.3
22:59:39.561 INFO ProgressMeter - chr19:15181664 15.5 7190 464.5
22:59:51.491 INFO ProgressMeter - chr19:17843775 15.7 7290 465.0
23:00:02.208 INFO ProgressMeter - chr19:35722566 15.9 7400 466.7
23:00:12.213 INFO ProgressMeter - chr19:40281718 16.0 7500 468.1
23:00:22.935 INFO ProgressMeter - chr19:42294822 16.2 7580 467.9
23:00:33.283 INFO ProgressMeter - chr19:45418828 16.4 7680 469.1
23:00:44.030 INFO ProgressMeter - chr2:15941761 16.6 7770 469.4
23:00:54.692 INFO ProgressMeter - chr2:25247639 16.7 7850 469.2
23:01:05.326 INFO ProgressMeter - chr2:29222386 16.9 7920 468.4
23:01:16.171 INFO ProgressMeter - chr2:29318302 17.1 7970 466.4
23:01:27.152 INFO ProgressMeter - chr2:47379767 17.3 8050 466.1
23:01:38.060 INFO ProgressMeter - chr2:47806450 17.5 8110 464.7
23:01:48.947 INFO ProgressMeter - chr2:98539633 17.6 8190 464.4
23:01:59.181 INFO ProgressMeter - chr2:111125724 17.8 8280 465.0
23:02:10.291 INFO ProgressMeter - chr2:113221674 18.0 8320 462.5
23:02:22.703 INFO ProgressMeter - chr2:113227220 18.2 8370 460.0
23:02:34.441 INFO ProgressMeter - chr2:113233460 18.4 8420 457.8
23:02:45.159 INFO ProgressMeter - chr2:136115347 18.6 8490 457.2
23:02:55.399 INFO ProgressMeter - chr2:140950233 18.7 8580 457.8
23:03:05.533 INFO ProgressMeter - chr2:189854875 18.9 8660 457.9
23:03:16.105 INFO ProgressMeter - chr2:203872706 19.1 8760 458.9
23:03:29.603 INFO ProgressMeter - chr2:222201864 19.3 8850 458.3
23:03:40.971 INFO ProgressMeter - chr2:222211628 19.5 8900 456.4
23:03:52.499 INFO ProgressMeter - chr2:222219150 19.7 8940 454.0
23:04:02.640 INFO ProgressMeter - chr2:226796365 19.9 9000 453.1
23:04:13.789 INFO ProgressMeter - chr20:32435206 20.0 9080 452.9
23:04:24.032 INFO ProgressMeter - chr20:42081890 20.2 9170 453.5
23:04:34.058 INFO ProgressMeter - chr20:52679586 20.4 9250 453.7
23:04:45.006 INFO ProgressMeter - chr21:34859332 20.6 9340 454.1
23:04:57.035 INFO ProgressMeter - chr21:41465547 20.8 9410 453.1
23:05:10.921 INFO ProgressMeter - chr21:41492051 21.0 9450 450.0
23:05:22.733 INFO ProgressMeter - chr21:41503115 21.2 9500 448.2
23:05:33.675 INFO ProgressMeter - chr22:20985891 21.4 9570 447.6
23:05:44.170 INFO ProgressMeter - chr22:23291090 21.6 9640 447.2
23:05:54.377 INFO ProgressMeter - chr22:28731804 21.7 9730 447.9
23:06:05.445 INFO ProgressMeter - chr22:29286949 21.9 9790 446.8
23:06:16.467 INFO ProgressMeter - chr22:41157268 22.1 9880 447.2
23:06:27.215 INFO ProgressMeter - chr3:10141846 22.3 9970 447.6
23:06:38.867 INFO ProgressMeter - chr3:12358885 22.5 10020 446.0
23:06:51.121 INFO ProgressMeter - chr3:12365625 22.7 10070 444.2
23:07:03.680 INFO ProgressMeter - chr3:12375147 22.9 10120 442.3
23:07:13.692 INFO ProgressMeter - chr3:12600150 23.0 10180 441.7
23:07:24.726 INFO ProgressMeter - chr3:41235722 23.2 10280 442.5
23:07:34.787 INFO ProgressMeter - chr3:49684026 23.4 10350 442.3
23:07:45.846 INFO ProgressMeter - chr3:52563281 23.6 10440 442.7
23:07:56.778 INFO ProgressMeter - chr3:89127207 23.8 10540 443.5
23:08:07.182 INFO ProgressMeter - chr3:136421072 23.9 10630 444.1
23:08:17.457 INFO ProgressMeter - chr3:142503360 24.1 10730 445.1
23:08:27.682 INFO ProgressMeter - chr3:179224803 24.3 10830 446.0
23:08:38.464 INFO ProgressMeter - chr3:186047312 24.5 10910 446.0
23:08:48.877 INFO ProgressMeter - chr3:196057532 24.6 11010 447.0
23:08:59.129 INFO ProgressMeter - chr4:20528947 24.8 11120 448.3
23:09:10.420 INFO ProgressMeter - chr4:54274839 25.0 11210 448.5
23:09:23.511 INFO ProgressMeter - chr4:54736719 25.2 11280 447.4
23:09:33.966 INFO ProgressMeter - chr4:80278644 25.4 11370 447.9
23:09:44.593 INFO ProgressMeter - chr4:105240305 25.6 11450 447.9
23:09:55.461 INFO ProgressMeter - chr4:122896525 25.7 11530 447.9
23:10:06.077 INFO ProgressMeter - chr4:186613107 25.9 11620 448.3
23:10:17.176 INFO ProgressMeter - chr4:186709179 26.1 11680 447.4
23:10:27.357 INFO ProgressMeter - chr5:38964790 26.3 11770 448.0
23:10:38.035 INFO ProgressMeter - chr5:56882322 26.5 11870 448.7
23:10:48.307 INFO ProgressMeter - chr5:112738351 26.6 11990 450.3
23:10:59.654 INFO ProgressMeter - chr5:122440627 26.8 12060 449.8
23:11:09.817 INFO ProgressMeter - chr5:142650259 27.0 12150 450.3
23:11:20.624 INFO ProgressMeter - chr5:150119465 27.2 12230 450.3
23:11:30.656 INFO ProgressMeter - chr5:171392708 27.3 12310 450.4
23:11:46.152 INFO ProgressMeter - chr5:177209634 27.6 12380 448.7
23:11:56.773 INFO ProgressMeter - chr5:177516312 27.8 12450 448.4
23:12:07.034 INFO ProgressMeter - chr6:20447021 27.9 12550 449.2
23:12:22.001 INFO ProgressMeter - chr6:29945449 28.2 12650 448.8
23:12:33.104 INFO ProgressMeter - chr6:32213686 28.4 12730 448.7
23:12:43.701 INFO ProgressMeter - chr6:41941451 28.5 12820 449.1
23:12:55.191 INFO ProgressMeter - chr6:106107102 28.7 12930 449.9
23:13:08.502 INFO ProgressMeter - chr6:117323034 29.0 12990 448.5
23:13:19.211 INFO ProgressMeter - chr6:117332355 29.1 13040 447.5
23:13:29.428 INFO ProgressMeter - chr6:117357802 29.3 13090 446.6
23:13:39.496 INFO ProgressMeter - chr6:135205668 29.5 13150 446.1
23:13:55.299 INFO ProgressMeter - chr6:135213757 29.7 13200 443.8
23:14:07.140 INFO ProgressMeter - chr6:137878624 29.9 13250 442.6
23:14:17.909 INFO ProgressMeter - chr6:151944171 30.1 13320 442.3
23:14:30.024 INFO ProgressMeter - chr6:157207181 30.3 13400 442.0
23:14:40.619 INFO ProgressMeter - chr7:2913285 30.5 13490 442.4
23:14:51.275 INFO ProgressMeter - chr7:13895606 30.7 13570 442.4
23:15:03.568 INFO ProgressMeter - chr7:13933920 30.9 13610 440.8
23:15:14.903 INFO ProgressMeter - chr7:13941909 31.1 13660 439.7
23:15:26.462 INFO ProgressMeter - chr7:13948849 31.3 13700 438.3
23:15:38.847 INFO ProgressMeter - chr7:13955135 31.5 13740 436.7
23:15:49.963 INFO ProgressMeter - chr7:13962158 31.7 13780 435.4
23:16:01.322 INFO ProgressMeter - chr7:13970842 31.8 13830 434.3
23:16:14.979 INFO ProgressMeter - chr7:13976851 32.1 13870 432.5
23:16:26.432 INFO ProgressMeter - chr7:13983230 32.3 13920 431.5
23:16:38.818 INFO ProgressMeter - chr7:13989934 32.5 13960 430.0
23:16:49.960 INFO ProgressMeter - chr7:55161525 32.7 14030 429.7
23:17:00.292 INFO ProgressMeter - chr7:55170809 32.8 14070 428.7
23:17:11.412 INFO ProgressMeter - chr7:55180864 33.0 14120 427.8
23:17:21.588 INFO ProgressMeter - chr7:81710145 33.2 14190 427.7
23:17:32.301 INFO ProgressMeter - chr7:102197213 33.4 14290 428.4
23:17:44.173 INFO ProgressMeter - chr7:116739948 33.6 14370 428.3
23:17:54.341 INFO ProgressMeter - chr7:129208757 33.7 14420 427.6
23:18:06.520 INFO ProgressMeter - chr7:140793868 33.9 14490 427.1
23:18:17.307 INFO ProgressMeter - chr7:151471392 34.1 14590 427.8
23:18:29.169 INFO ProgressMeter - chr7:152187260 34.3 14660 427.3
23:18:39.481 INFO ProgressMeter - chr8:26293214 34.5 14750 427.8
23:18:49.562 INFO ProgressMeter - chr8:32742688 34.6 14820 427.8
23:19:00.785 INFO ProgressMeter - chr8:38430079 34.8 14910 428.1
23:19:11.101 INFO ProgressMeter - chr8:41981886 35.0 14980 428.0
23:19:22.056 INFO ProgressMeter - chr8:47929851 35.2 15070 428.3
23:19:32.118 INFO ProgressMeter - chr8:68191720 35.4 15160 428.8
23:19:44.525 INFO ProgressMeter - chr8:127732335 35.6 15240 428.6
23:19:55.038 INFO ProgressMeter - chr8:144517093 35.7 15320 428.7
23:20:05.538 INFO ProgressMeter - chr9:8504282 35.9 15430 429.7
23:20:15.945 INFO ProgressMeter - chr9:78031098 36.1 15520 430.1
23:20:27.326 INFO ProgressMeter - chr9:84744498 36.3 15580 429.5
23:20:41.510 INFO ProgressMeter - chr9:84862237 36.5 15620 427.8
23:20:53.209 INFO ProgressMeter - chr9:84873763 36.7 15660 426.6
23:21:04.844 INFO ProgressMeter - chr9:85024194 36.9 15710 425.8
23:21:15.668 INFO ProgressMeter - chr9:95456323 37.1 15780 425.6
23:21:25.779 INFO ProgressMeter - chr9:130880498 37.2 15870 426.1
23:21:36.502 INFO ProgressMeter - chr9:134525497 37.4 15930 425.6
23:21:46.825 INFO ProgressMeter - chrX:15820206 37.6 16040 426.6
23:21:57.691 INFO ProgressMeter - chrX:49036500 37.8 16220 429.3
23:22:08.063 INFO ProgressMeter - chrX:67616923 38.0 16370 431.3
23:22:18.191 INFO ProgressMeter - chrX:101353868 38.1 16560 434.4
23:22:26.669 INFO Mutect2 - 533278 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
148 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
533426 total reads filtered out of 70350357 reads processed
23:22:26.669 INFO ProgressMeter - chrY:20398623 38.3 16745 437.6
23:22:26.669 INFO ProgressMeter - Traversal complete. Processed 16745 total regions in 38.3 minutes.
23:22:26.686 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 5.096136937000001
23:22:26.686 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 203.11358300400002
23:22:26.686 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 7.83 sec
23:22:26.687 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:22:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 38.27 minutes.
Runtime.totalMemory()=7390363648
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 LS0900_tumor.bam --tumor-sample LS0900 -L TST500C_manifest.bed -O LS0900.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:22:28.433 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
23:22:28.542 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:28.545 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:22:28.545 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:22:28.545 INFO FilterMutectCalls - Executing as ?@nf-f3c4b392c1e10e86909d6f89a74dde97-cbf32-wfcrn on Linux v6.12.88 amd64
23:22:28.545 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:22:28.545 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:22:28 PM GMT
23:22:28.545 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:28.545 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:28.546 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:22:28.546 INFO FilterMutectCalls - Picard Version: 3.1.1
23:22:28.546 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:22:28.546 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:22:28.546 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:22:28.546 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:22:28.546 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:22:28.546 INFO FilterMutectCalls - Deflater: IntelDeflater
23:22:28.546 INFO FilterMutectCalls - Inflater: IntelInflater
23:22:28.547 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:22:28.547 INFO FilterMutectCalls - Requester pays: disabled
23:22:28.547 INFO FilterMutectCalls - Initializing engine
23:22:28.747 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.6KUqejLQ1q/LS0900.mutect2.raw.vcf.gz
23:22:28.858 INFO FilterMutectCalls - Done initializing engine
23:22:28.924 INFO ProgressMeter - Starting traversal
23:22:28.925 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:22:28.926 INFO FilterMutectCalls - Starting pass 0 through the variants
23:22:30.126 INFO FilterMutectCalls - Finished pass 0 through the variants
23:22:30.857 INFO FilterMutectCalls - Starting pass 1 through the variants
23:22:31.996 INFO FilterMutectCalls - Finished pass 1 through the variants
23:22:32.201 INFO FilterMutectCalls - Starting pass 2 through the variants
23:22:33.292 INFO FilterMutectCalls - Finished pass 2 through the variants
23:22:33.294 INFO FilterMutectCalls - Starting pass 3 through the variants
23:22:34.267 INFO FilterMutectCalls - Finished pass 3 through the variants
23:22:34.275 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:22:34.276 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:22:34.276 INFO ProgressMeter - chr7:102248806 0.1 10316 115671.8
23:22:34.276 INFO ProgressMeter - Traversal complete. Processed 10316 total variants in 0.1 minutes.
23:22:34.288 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:22:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.10 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 FilterMutectCalls -R hg38.fa -V LS0900.mutect2.raw.vcf.gz --stats LS0900.mutect2.raw.vcf.gz.stats -O LS0900.mutect2.filtered.vcf.gz
23:22:35.699 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
23:22:35.821 INFO SelectVariants - ------------------------------------------------------------
23:22:35.824 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:22:35.824 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:22:35.824 INFO SelectVariants - Executing as ?@nf-f3c4b392c1e10e86909d6f89a74dde97-cbf32-wfcrn on Linux v6.12.88 amd64
23:22:35.824 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:22:35.824 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:22:35 PM GMT
23:22:35.824 INFO SelectVariants - ------------------------------------------------------------
23:22:35.824 INFO SelectVariants - ------------------------------------------------------------
23:22:35.825 INFO SelectVariants - HTSJDK Version: 4.1.0
23:22:35.825 INFO SelectVariants - Picard Version: 3.1.1
23:22:35.825 INFO SelectVariants - Built for Spark Version: 3.5.0
23:22:35.825 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:22:35.825 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:22:35.825 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:22:35.826 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:22:35.826 INFO SelectVariants - Deflater: IntelDeflater
23:22:35.826 INFO SelectVariants - Inflater: IntelInflater
23:22:35.826 INFO SelectVariants - GCS max retries/reopens: 20
23:22:35.826 INFO SelectVariants - Requester pays: disabled
23:22:35.826 INFO SelectVariants - Initializing engine
23:22:35.993 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.6KUqejLQ1q/LS0900.mutect2.filtered.vcf.gz
23:22:36.103 INFO SelectVariants - Done initializing engine
23:22:36.144 INFO ProgressMeter - Starting traversal
23:22:36.144 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:22:36.220 INFO ProgressMeter - chr7:6401984 0.0 2579 2119726.0
23:22:36.220 INFO ProgressMeter - Traversal complete. Processed 2579 total variants in 0.0 minutes.
23:22:36.231 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:22:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=352321536
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 LS0900.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0900.mutect2.pass.vcf.gz